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epdcx:valueString Proteomics of Streptococcus gordonii within a model developing oral microbial community
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Abstract
Background
Streptococcus gordonii is one of several species that can initiate the formation of oral biofilms that develop into the complex multispecies microbial communities referred to as dental plaque. It is in the context of dental plaque that periodontal pathogens such as Porphyromonas gingivalis cause disease. We have previously reported a whole cell quantitative proteomics investigation of P. gingivalis in a model dental plaque community of S. gordonii, P. gingivalis, and Fusobacterium nucleatum. Here we report the adaptation of S. gordonii to the same model.
Results
1122 S. gordonii proteins were detected in S. gordonii control samples, 915 in communities with F. nucleatum, 849 with P. gingivalis, and 649 with all three organisms. Quantitative comparisons showed extensive proteome changes in association with F. nucleatum or P. gingivalis individually or both P. gingivalis and F. nucleatum together. The changes were species specific, though the P. gingivalis interaction may be dominant, indicated by large differences between the proteomes with F. nucleatum or P. gingivalis but limited changes between communities with P. gingivalis or both P. gingivalis and F. nucleatum. The results were inspected manually and an ontology analysis conducted using DAVID. Extensive changes were seen in nutrition pathways with increases in energy metabolism and changes in the resulting byproducts, while the acid and sugar repressed PTS (phosphoenolpyruvate dependent phosphotransferase system) sugar transport systems showed decreases. These results were seen across all the multispecies samples, though with different profiles according to the partner species. F. nucleatum association decreased proteins for the metabolic end products acetate and ethanol but increased lactate, the primary source of acidity from streptococcal cultures. P. gingivalis containing samples had a reduction in levels of proteins for ethanol and formate but increased proteins for both acetate and lactate production. The communities also showed increases in exopolysaccharide synthesis, amino acid biosynthesis, and oxidative stress protection and decreases in adhesion and transporter proteins.
Conclusion
This study showed that S. gordonii demonstrates species specific responses during interactions with F. nucleatum or P. gingivalis. Extensive changes were seen in energy metabolism and byproduct production implicating nutrient transfer as an important community interaction.
http:purl.orgdcelements1.1creator
Hendrickson, Erik L
Wang, Tiansong
Dickinson, Brittany C
Whitmore, Sarah E
Wright, Christopher J
Lamont, Richard J
Hackett, Murray
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en
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epdcx:sesURI http:purl.orgdctermsW3CDTF 2012-09-18
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BioMed Central Ltd
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http:purl.orgeprintstatusPeerReviewed
http:purl.orgeprinttermscopyrightHolder
Erik L Hendrickson et al.; licensee BioMed Central Ltd.
http:purl.orgdctermslicense
http://creativecommons.org/licenses/by/2.0
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BMC Microbiology. 2012 Sep 18;12(1):211
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http:purl.orgdctermsURI http://dx.doi.org/10.1186/1471-2180-12-211
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PAGE 1

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 1 32.000 53.500 -0.754 7.101 0.0159 0.0586 28.3302 19.000 33.3027 19.000 15.500 15.500 22.1215 53.5000 SGO_0001 dnaA; chromosomal replication initiator protein DnaA 21.000 39.500 0.550 7.204 0.0242 0.0969 44.7319 30.000 21.8549 30.000 29.000 29.000 41.3886 39.5000 SGO_0002 dnaN; DNA polymerase III, beta subunit 137.000 190.500 -1.979 8.713 0.0019 0.0040 54.4238 36.500 142.5772 36.500 22.500 22.500 32.1119 190.5000 SGO_0004 putative lipoprotein 10.500 14.000 4.640 10.9275 14.0000 SGO_0005 hypothetical protein SGO_0005 44.000 49.000 0.462 7.817 0.0017 0.0033 68.5889 46.000 45.7912 46.000 43.500 43.500 62.0829 49.0000 SGO_0006 ABC transporter, ATP-binding protein 17.000 21.500 1.153 6.977 0.0003 0.0002 43.2408 29.000 17.6921 29.000 30.500 30.500 43.5294 21.5000 SGO_0007 trpS; tryptophanyl-tRNA synthetase 156.500 133.000 1.064 9.833 0.0005 0.0007 319.0876 214.000 162.8711 214.000 208.000 208.000 296.8562 133.0000 SGO_0008 inosine-5'-monophosphate dehydrogenase 13.000 16.500 -1.064 5.482 0.0036 0.0090 8.9464 6.000 13.5292 6.000 4.000 4.000 5.7088 16.5000 SGO_0011 proteinase, M16 family 3.500 1.807 3.5000 SGO_0012 mpp; peptidase, M16 family 15.000 12.500 -0.643 5.212 0.0434 0.1881 8.9464 6.000 15.6106 6.000 12.5000 SGO_0013 hypothetical protein SGO_0013 39.500 39.000 -2.256 6.598 0.0001 0.0000 8.2009 5.500 41.1080 5.500 6.000 6.000 8.5632 39.0000 SGO_0015 ABC transporter (ATP-binding protein) 7.500 6.000 -0.241 4.669 0.0423 0.1825 5.2187 3.500 7.8053 3.500 4.500 4.500 6.4224 6.0000 SGO_0016 cbiO; ABC transporter, ATP-binding protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 2

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 2 2.500 2.500 2.351 2.6018 2.5000 SGO_0017 ABC-type putative cobalt transport system, permease 7.000 2.807 7.0000 SGO_0019 sdhA; L-serine dehydratase, iron-sulfurdependent, alpha subunit 6.000 2.585 6.0000 SGO_0020 sdhB; L-serine dehydratase, iron-sulfurdependent, beta subunit 6.000 11.500 1.241 5.854 0.0025 0.0057 19.3838 13.000 6.2443 13.000 14.500 14.500 20.6943 11.5000 SGO_0022 trmU; tRNA (5-methylaminomethyl-2thiouridylate)-methyltransferase 14.500 17.000 0.338 6.207 0.0477 0.2100 26.0936 17.500 15.0903 17.500 11.000 11.000 15.6991 17.0000 SGO_0025 gidA; glucose inhibited division protein A 91.000 76.500 -3.976 7.514 0.0005 0.0007 3.7277 2.500 94.7046 2.500 5.500 5.500 7.8496 76.5000 SGO_0026 DHH subfamily 1 protein 30.500 37.500 0.376 7.312 0.0046 0.0126 43.2408 29.000 31.7416 29.000 32.500 32.500 46.3838 37.5000 SGO_0027 rplI; ribosomal protein L9 11.000 16.500 -0.451 5.614 0.0507 0.2268 7.4553 5.000 11.4478 5.000 9.500 9.500 13.5583 16.5000 SGO_0028 dnaC; replicative DNA helicase 19.000 24.500 0.967 7.027 0.0008 0.0011 44.7319 30.000 19.7735 30.000 29.000 29.000 41.3886 24.5000 SGO_0030 aspB; aspartate transaminase 38.000 50.000 0.024 7.492 0.1697 0.8926 45.4774 30.500 39.5470 30.500 31.500 31.500 44.9566 50.0000 SGO_0032 plsX; fatty acid/phospholipid synthesis protein PlsX 5.500 7.500 0.994 5.306 0.0039 0.0102 14.9106 10.000 5.7239 10.000 8.000 8.000 11.4175 7.5000 SGO_0033 acpP; acyl carrier protein 3.500 -0.709 2.496 1.500 1.500 2.1408 3.5000 SGO_0035 phosphoribosylformylglycinamidine synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 3

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 3 11.500 12.500 0.355 5.804 0.0083 0.0260 17.1472 11.500 11.9682 11.500 10.000 10.000 14.2719 12.5000 SGO_0042 transcription regulator, GntR family SGO_0044 PTS system, IIB component 10.500 14.000 4.640 10.9275 14.0000 SGO_0050 hypothetical protein SGO_0050 5.000 5.000 3.351 5.2035 5.0000 SGO_0051 hypothetical protein SGO_0051 40.000 48.000 0.238 7.609 0.0136 0.0480 49.9506 33.500 41.6284 33.500 39.000 39.000 55.6605 48.0000 SGO_0054 dltA; D-alanine-activating enzyme 4.000 2.058 4.1628 SGO_0055 dltB; integral membrane protein 5.000 5.500 3.420 5.2035 5.5000 SGO_0056 dltC; D-alanyl carrier protein 99.500 129.000 -2.098 8.163 0.0008 0.0012 27.5847 18.500 103.5506 18.500 18.500 18.500 26.4031 129.0000 SGO_0057 dltD protein 1257.500 653.500 1.097 12.538 0.0073 0.0222 2223.1761 1491.000 1308.6923 1491.000 1233.500 1233.500 1760.4431 653.5000 SGO_0059 pXO1; hypothetical protein SGO_0059 118.000 141.000 8.043 122.8037 141.0000 SGO_0060 hypothetical protein SGO_0060 2.500 1.380 2.6018 SGO_0062 hypothetical protein SGO_0062 86.000 91.500 -1.765 7.875 0.0002 0.0001 23.1115 15.500 89.5010 15.500 21.500 21.500 30.6847 91.5000 SGO_0063 hypothetical protein SGO_0063 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 4

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 4 214.000 208.000 -1.647 9.154 0.0003 0.0002 59.6426 40.000 222.7119 40.000 55.500 55.500 79.2092 208.0000 SGO_0064 FtsK/SpoIIIE family protein 37.500 40.000 0.339 7.484 0.0009 0.0013 51.4417 34.500 39.0266 34.500 34.000 34.000 48.5246 40.0000 SGO_0065 hypothetical protein SGO_0065 4.494 9.6919 6.500 6.500 9.000 9.000 12.8447 SGO_0066 D-3-phosphoglycerate dehydrogenase, putative 23.000 23.500 0.784 7.024 0.0059 0.0173 47.7140 32.000 23.9363 32.000 24.500 24.500 34.9662 23.5000 SGO_0067 protein with prophage function domain 30.000 28.000 -0.510 6.655 0.0016 0.0031 20.1294 13.500 31.2213 13.500 15.000 15.000 21.4079 28.0000 SGO_0068 lipoprotein, putative 19.500 22.000 -0.728 6.084 0.0007 0.0009 13.4196 9.000 20.2938 9.000 8.500 8.500 12.1311 22.0000 SGO_0069 hypothetical protein SGO_0069 19.000 24.000 0.264 6.588 0.0177 0.0667 24.6026 16.500 19.7735 16.500 19.500 19.500 27.8303 24.0000 SGO_0070 merozoite surface protein 1 2.500 1.380 2.6018 SGO_0075 hypothetical protein SGO_0075 34.000 21.500 -1.267 6.328 0.0090 0.0292 14.1651 9.500 35.3841 9.500 6.500 6.500 9.2768 21.5000 SGO_0078 hypothetical protein SGO_0078 2.500 1.380 2.6018 SGO_0079 hypothetical protein SGO_0079 51.000 58.000 -0.712 7.484 0.0011 0.0018 36.5311 24.500 53.0762 24.500 22.000 22.000 31.3983 58.0000 SGO_0080 hypothetical protein SGO_0080 3.000 6.500 1.034 4.842 0.0181 0.0685 11.9285 8.000 3.1221 8.000 5.000 5.000 7.1360 6.5000 SGO_0081 hypothetical protein SGO_0081 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 5

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 5 5.271 18.6383 12.500 12.500 14.000 14.000 19.9807 SGO_0095 mccF; microcin immunity protein MccF, putative 36.000 31.000 6.097 37.4655 31.0000 SGO_0097 hypothetical protein SGO_0097 15.500 0.979 6.324 0.0344 0.1448 28.3302 19.000 16.1310 19.000 25.000 25.000 35.6798 SGO_0098 ribonucleotide reductase-like protein 3.712 5.9643 4.000 4.000 5.000 5.000 7.1360 SGO_0099 pulA-2; pullulanase, type I 7.500 3.500 0.127 4.089 0.1827 0.9834 7.8053 4.000 4.000 5.7088 3.5000 SGO_0100 maltose operon transcription repressor 8.000 21.000 4.874 8.3257 21.0000 SGO_0101 malA; Maltodextrose utilization protein malA 234.000 247.500 -0.689 9.636 0.0001 0.0000 149.1064 100.000 243.5261 100.000 109.000 109.000 155.5641 247.5000 SGO_0104 Maltose/maltodextrin-binding protein precursor 14.000 11.500 0.873 6.200 0.0011 0.0019 24.6026 16.500 14.5699 16.500 16.000 16.000 22.8351 11.5000 SGO_0105 malQ; 4-alpha-glucanotransferase 19.000 27.000 1.969 7.831 0.0002 0.0001 91.7004 61.500 19.7735 61.500 62.500 62.500 89.1996 27.0000 SGO_0106 glgP-2; maltodextrin phosphorylase SGO_0107 LPXTG cell wall surface protein, collagen binding domain 22.500 22.000 5.505 23.4160 22.0000 SGO_0108 ruvB; Holliday junction DNA helicase RuvB 2.898 7.4553 5.000 5.000 SGO_0110 phosphotyrosine protein phosphatase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 6

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 6 8.000 9.000 4.115 8.3257 9.0000 SGO_0111 MORN motif family protein 18.000 22.500 5.366 18.7328 22.5000 SGO_0112 putative acyltransferase 3329.000 3222.500 -1.505 13.143 0.0002 0.0001 1250.2570 838.500 3464.5223 838.500 777.000 777.000 1108.9293 3222.5000 SGO_0113 acdH; alcohol-acetaldehyde dehydrogenase 9.000 3.170 9.0000 SGO_0128 hypothetical protein SGO_0128 48.500 56.500 -3.290 6.881 0.0002 0.0001 5.2187 3.500 50.4744 3.500 4.000 4.000 5.7088 56.5000 SGO_0129 atpI; v-type sodium ATP synthase, chain I 11.000 31.500 5.425 11.4478 31.5000 SGO_0131 v-type sodium ATP synthase, chain E 11.500 -1.088 4.528 0.0494 0.2205 3.7277 2.500 2.500 5.500 5.500 7.8496 11.5000 SGO_0132 ATP synthase (C/AC39) subunit 7.500 10.000 0.106 5.225 0.1182 0.5924 7.4553 5.000 7.8053 5.000 8.500 8.500 12.1311 10.0000 SGO_0134 acetyltransferase, GNAT family 77.500 79.500 -0.954 7.926 0.0003 0.0003 38.0221 25.500 80.6550 25.500 31.500 31.500 44.9566 79.5000 SGO_0135 v-type sodium ATP synthase, subunit A 106.000 127.500 -1.309 8.383 0.0007 0.0010 43.9864 29.500 110.3152 29.500 36.500 36.500 52.0926 127.5000 SGO_0136 v-type sodium ATP synthase, chain B 2.000 10.500 3.653 2.0814 10.5000 SGO_0137 V-type ATPase, D subunit 5.500 2.459 5.5000 SGO_0138 LysM domain protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 7

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 7 32.000 36.000 0.581 7.434 0.0007 0.0010 53.6783 36.000 33.3027 36.000 35.000 35.000 49.9518 36.0000 SGO_0139 thrC; threonine synthase 3.000 1.585 3.0000 SGO_0142 hypothetical protein SGO_0142 15.000 18.500 -2.511 5.213 0.0174 0.0651 2.9821 2.000 15.6106 2.000 18.5000 SGO_0144 hypothetical protein SGO_0144 61.500 60.000 -0.566 7.699 0.0007 0.0009 40.2587 27.000 64.0036 27.000 30.500 30.500 43.5294 60.0000 SGO_0145 polI; DNA polymerase I 11.000 15.500 0.659 6.116 0.0087 0.0278 23.8570 16.000 11.4478 16.000 13.000 13.000 18.5535 15.5000 SGO_0146 CoA-binding domain protein 10.500 10.000 -1.225 4.667 0.0139 0.0492 4.4732 3.000 10.9275 3.000 10.0000 SGO_0148 hypothetical protein SGO_0148 2.500 1.380 2.6018 SGO_0150 fucA1; alpha-L-fucosidase 10.500 11.500 1.009 6.079 0.0003 0.0003 21.6204 14.500 10.9275 14.500 16.500 16.500 23.5487 11.5000 SGO_0152 tgt; queuine tRNA-ribosyltransferase 309.500 251.500 0.517 10.445 0.0109 0.0367 457.7566 307.000 322.0996 307.000 254.000 254.000 362.5071 251.5000 SGO_0154 pgi; glucose-6-phosphate isomerase 179.000 139.500 -4.703 8.402 0.0009 0.0014 5.9643 4.000 186.2870 4.000 4.500 4.500 6.4224 139.5000 SGO_0155 hypothetical protein SGO_0155 90.500 80.000 -2.580 7.668 0.0004 0.0004 16.4017 11.000 94.1842 11.000 9.000 9.000 12.8447 80.0000 SGO_0156 hypothetical protein SGO_0156 6.000 4.000 3.357 6.2443 4.0000 SGO_0157 hypothetical protein SGO_0157 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 8

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 8 24.500 21.500 1.379 7.403 0.0009 0.0014 55.9149 37.500 25.4974 37.500 46.500 46.500 66.3645 21.5000 SGO_0158 2,3,4,5-tetrahydropyridine-2-carboxylate Nsuccinyltransferase, putative 4.000 -0.424 2.804 2.9821 2.000 2.000 4.0000 SGO_0159 hippurate hydrolase 32.000 41.000 0.746 7.631 0.0010 0.0016 61.1336 41.000 33.3027 41.000 44.000 44.000 62.7965 41.0000 SGO_0163 galU; UTP-glucose-1-phosphate uridylyltransferase 40.000 47.500 -0.280 7.349 0.0252 0.1009 41.7498 28.000 41.6284 28.000 22.500 22.500 32.1119 47.5000 SGO_0164 Glycerol-3-phosphate dehydrogenase [NAD (P)+] (NAD(P)H-dependent glycerol-3phosphate dehydrogenase) 9.000 10.000 4.275 9.3664 10.0000 SGO_0165 ABC transporter, permease/ATP-binding protein SP2075 35.000 39.000 -2.723 6.342 0.0082 0.0256 36.4248 4.000 4.000 5.7088 39.0000 SGO_0166 ABC transporter, permease/ATP-binding protein SP2073 5.500 10.500 4.020 5.7239 10.5000 SGO_0167 glutamine amidotransferase 8.000 9.500 4.156 8.3257 9.5000 SGO_0168 hydrolase, NUDIX family 7.500 12.500 0.502 5.611 0.0352 0.1490 17.1472 11.500 7.8053 11.500 8.000 8.000 11.4175 12.5000 SGO_0169 dut; dUTP diphosphatase 15.500 23.500 -0.402 6.118 0.0338 0.1424 12.6740 8.500 16.1310 8.500 12.000 12.000 17.1263 23.5000 SGO_0171 radA; DNA repair protein RadA 24.000 24.000 5.614 24.9770 24.0000 SGO_0172 conserved hypothetical protein TIGR00266 80.000 87.000 -3.121 7.570 0.0001 0.0000 11.1830 7.500 83.2568 7.500 6.000 6.000 8.5632 87.0000 SGO_0173 Carbonic anhydrase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 9

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 9 60.500 66.500 1.114 8.678 0.0001 0.0000 140.9055 94.500 62.9629 94.500 97.500 97.500 139.1514 66.5000 SGO_0174 gltX; glutamyl-tRNA synthetase 6.000 2.585 6.0000 SGO_0179 Membrane protein oxaA 1 precursor 24.000 42.000 -0.132 7.007 0.1414 0.7291 39.5132 26.500 24.9770 26.500 15.500 15.500 22.1215 42.0000 SGO_0180 jag; hypothetical protein SGO_0180 17.000 19.500 5.217 17.6921 19.5000 SGO_0181 lipoprotein, putative 6.500 2.700 6.5000 SGO_0182 sapR; sakacin A production response regulator 8.000 11.000 -0.745 4.646 0.0473 0.2076 8.3257 4.000 4.000 5.7088 11.0000 SGO_0188 hydrolase, TatD family 3.000 1.585 3.0000 SGO_0189 primase-related protein 12.500 22.000 -1.685 5.563 0.0110 0.0370 2.9821 2.000 13.0089 2.000 6.500 6.500 9.2768 22.0000 SGO_0190 hypothetical protein SGO_0190 10.000 10.000 -1.774 4.548 0.0060 0.0179 2.9821 2.000 10.4071 2.000 10.0000 SGO_0191 hypothetical protein SGO_0191 3.000 11.000 0.844 5.139 0.0514 0.2304 9.6919 6.500 3.1221 6.500 8.000 8.000 11.4175 11.0000 SGO_0193 ksgA; dimethyladenosine transferase 3.541 5.2187 3.500 3.500 4.500 4.500 6.4224 SGO_0197 predicted ribosome small subunit-dependent GTPase A 27.500 22.000 0.896 7.170 0.0011 0.0017 47.7140 32.000 28.6195 32.000 32.000 32.000 45.6702 22.0000 SGO_0198 rpe; ribulose-phosphate 3-epimerase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 10

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 10 74.500 83.000 -1.166 7.858 0.0002 0.0001 36.5311 24.500 77.5329 24.500 24.500 24.500 34.9662 83.0000 SGO_0200 competence-induced protein Ccs50 47.000 41.000 -0.173 7.404 0.0277 0.1122 38.7677 26.000 48.9134 26.000 28.500 28.500 40.6750 41.0000 SGO_0201 cmp-binding-factor 1 14.000 10.000 -0.101 5.559 0.1063 0.5282 10.4374 7.000 14.5699 7.000 8.500 8.500 12.1311 10.0000 SGO_0202 pur operon repressor 6.500 2.700 6.5000 SGO_0203 hypothetical protein SGO_0203 63.500 73.500 0.094 8.177 0.0899 0.4380 84.2451 56.500 66.0851 56.500 46.000 46.000 65.6509 73.5000 SGO_0204 rpsL; ribosomal protein S12 113.000 146.000 0.726 9.456 0.0085 0.0269 184.8919 124.000 117.6002 124.000 178.000 178.000 254.0404 146.0000 SGO_0205 rpsG; ribosomal protein S7 972.500 1007.500 0.873 12.482 0.0002 0.0001 1904.0885 1277.000 1012.0901 1277.000 1258.000 1258.000 1795.4093 1007.5000 SGO_0206 fusA; translation elongation factor G 748.500 1043.000 1.071 12.454 0.0007 0.0010 1889.1778 1267.000 778.9711 1267.000 1330.000 1330.000 1898.1672 1043.0000 SGO_0207 gap; glyceraldehyde-3-phosphate dehydrogenase, type I 10.000 21.500 4.996 10.4071 21.5000 SGO_0208 LPXTG cell wall surface protein, glycosyl hydrolase family 845.500 814.500 2.191 13.204 0.0002 0.0001 3694.1105 2477.500 879.9200 2477.500 2836.000 2836.000 4047.5205 814.5000 SGO_0209 pgk; phosphoglycerate kinase 98.500 143.500 -5.424 7.976 0.0012 0.0020 2.2366 1.500 102.5099 1.500 2.500 2.500 3.5680 143.5000 SGO_0210 sspA; streptococcal surface protein A 254.000 314.500 9.177 264.3402 314.5000 SGO_0211 sspB; streptococcal surface protein B .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 11

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 11 2.500 1.322 2.5000 SGO_0214 transcription regulator, MerR family 95.500 104.000 -0.087 8.628 0.0722 0.3407 104.3745 70.000 99.3878 70.000 61.500 61.500 87.7724 104.0000 SGO_0215 glnA; glutamine synthetase, type I 74.500 67.000 0.237 8.297 0.0080 0.0251 84.9906 57.000 77.5329 57.000 59.500 59.500 84.9180 67.0000 SGO_0219 metallo-beta-lactamase superfamily protein 1 4.294 8.2009 5.500 5.500 8.000 8.000 11.4175 SGO_0220 Protein of unknown function (DUF1447) superfamily 4.500 4.000 1.487 4.380 0.0087 0.0279 4.6832 8.500 8.500 12.1311 4.0000 SGO_0223 glycoproteinase family protein 9.000 13.000 0.665 5.843 0.0050 0.0141 18.6383 12.500 9.3664 12.500 11.500 11.500 16.4127 13.0000 SGO_0230 Protein of unknown function, DUF536 family 3.500 5.000 3.111 3.6425 5.0000 SGO_0231 glycerophosphoryl diester phosphodiesterase family protein 3.500 1.663 4.738 0.0558 0.2527 8.2009 5.500 5.500 10.500 10.500 14.9855 3.5000 SGO_0232 conserved hypothetical protein TIGR00103 35.000 26.500 5.976 36.4248 26.5000 SGO_0233 lipoprotein, putative 53.000 54.000 -0.219 7.669 0.0216 0.0849 52.1872 35.000 55.1576 35.000 29.500 29.500 42.1022 54.0000 SGO_0234 pepX; X-Pro dipeptidyl-peptidase 62.500 42.000 -1.563 7.157 0.0048 0.0133 15.6562 10.500 65.0444 10.500 14.000 14.000 19.9807 42.0000 SGO_0235 glycerol uptake facilitator protein-like protein 6.500 16.000 4.509 6.7646 16.0000 SGO_0236 hypothetical protein SGO_0236 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 12

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 12 5.000 11.500 1.319 5.790 0.0038 0.0097 18.6383 12.500 5.2035 12.500 14.000 14.000 19.9807 11.5000 SGO_0237 ccpA; CcpA protein (proteinase) 3.500 3.500 2.836 3.6425 3.5000 SGO_0240 mvaD; diphosphomevalonate decarboxylase 2.000 1.058 2.0814 SGO_0242 FMN-dependent dehydrogenase family protein 3.791 6.7098 4.500 4.500 5.000 5.000 7.1360 SGO_0243 hydroxymethylglutaryl-CoA reductase, degradative 3.500 4.000 2.252 5.461 0.0003 0.0002 17.1472 11.500 3.6425 11.500 13.500 13.500 19.2671 4.0000 SGO_0244 hydroxymethylglutaryl-CoA synthase 709.000 659.000 -1.086 11.004 0.0005 0.0006 318.3421 213.500 737.8631 213.500 237.500 237.500 338.9584 659.0000 SGO_0247 pfl; formate acetyltransferase 6.500 7.500 -0.542 4.617 0.0297 0.1218 6.7098 4.500 6.7646 4.500 2.500 2.500 3.5680 7.5000 SGO_0252 possible TetR-type transcriptional regulator 22.000 27.500 5.655 22.8956 27.5000 SGO_0253 hypothetical protein SGO_0253 5.000 11.000 -0.810 4.643 0.0299 0.1228 5.2187 3.500 5.2035 3.500 2.500 2.500 3.5680 11.0000 SGO_0254 helicase, RecD/TraA family 84.500 62.000 -1.618 7.630 0.0027 0.0065 23.8570 16.000 87.9400 16.000 17.000 17.000 24.2623 62.0000 SGO_0255 Signal peptidase I 6.500 11.500 4.191 6.7646 11.5000 SGO_0256 rnhC; ribonuclease HIII 3.000 1.585 3.0000 SGO_0258 hypothetical protein SGO_0258 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 13

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 13 33.500 38.000 -0.106 7.135 0.0376 0.1609 32.0579 21.500 34.8638 21.500 25.000 25.000 35.6798 38.0000 SGO_0260 DNA mismatch binding protein MutS2 3.000 1.585 3.0000 SGO_0261 acetyltransferase, GNAT family 24.500 23.000 0.829 7.073 0.0008 0.0012 45.4774 30.500 25.4974 30.500 28.500 28.500 40.6750 23.0000 SGO_0262 dipeptidase 34.000 39.000 0.527 7.504 0.0012 0.0020 51.4417 34.500 35.3841 34.500 39.000 39.000 55.6605 39.0000 SGO_0263 trx-1; thioredoxin 18.000 14.500 -1.945 5.229 0.0268 0.1082 18.7328 3.000 3.000 4.2816 14.5000 SGO_0268 mechanosensitive transport protein 7.500 10.500 4.194 7.8053 10.5000 SGO_0269 hypothetical protein SGO_0269 22.500 22.500 -0.248 6.402 0.0007 0.0009 19.3838 13.000 23.4160 13.000 13.500 13.500 19.2671 22.5000 SGO_0272 hypothetical protein SGO_0272 132.500 122.000 0.383 9.225 0.0017 0.0034 169.9813 114.000 137.8940 114.000 118.000 118.000 168.4088 122.0000 SGO_0276 gdhA; glutamate dehydrogenase (NADP) 11.500 17.000 -0.412 5.671 0.0422 0.1820 13.4196 9.000 11.9682 9.000 6.000 6.000 8.5632 17.0000 SGO_0277 pyrA; Dihydroorotate dehydrogenase 2.000 1.000 2.0000 SGO_0278 msrA; Peptide methionine sulfoxide reductase msrA/msrB 11.000 3.500 3.902 11.4478 3.5000 SGO_0279 lipoprotein, putative 24.000 23.000 -0.591 6.340 0.0170 0.0629 20.8749 14.000 24.9770 14.000 8.500 8.500 12.1311 23.0000 SGO_0280 trzA; ethylammeline chlorohydrolase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 14

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 14 17.500 22.500 5.347 18.2124 22.5000 SGO_0282 cell wall polysaccharide biosynthesis protein 2.000 1.058 2.0814 SGO_0284 transcriptional regulator 20.500 23.500 5.487 21.3345 23.5000 SGO_0286 DNA mismatch repair protein MutS, putative 3.007 4.4732 3.000 3.000 2.500 2.500 3.5680 SGO_0288 GDSL-like lipase/acylhydrolase 13.500 28.500 -1.343 5.871 0.0144 0.0519 6.7098 4.500 14.0496 4.500 6.500 6.500 9.2768 28.5000 SGO_0290 copper -translocating P-type ATPase 78.500 69.000 -1.402 7.697 0.0008 0.0011 27.5847 18.500 81.6957 18.500 20.500 20.500 29.2575 69.0000 SGO_0291 copper-translocating P-type ATPase 100.000 99.500 0.881 9.177 0.0004 0.0005 178.9277 120.000 104.0710 120.000 137.500 137.500 196.2391 99.5000 SGO_0292 spxB; pyruvate oxidase 7.500 11.500 4.271 7.8053 11.5000 SGO_0294 ABC transporter, putative 5.500 2.459 5.5000 SGO_0297 6-phospho-beta-glucosidase 1.500 0.585 1.5000 SGO_0299 putative histidine kinase SGO_0301 ABC transporter ATP-binding protein-like protein 7.000 7.500 3.886 7.2850 7.5000 SGO_0306 ABC transporter ATP-binding protein-like protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 15

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 15 2.000 4.500 2.718 2.0814 4.5000 SGO_0307 pabB; chorismate binding enzyme 2.500 2.000 1.387 3.401 0.0144 0.0522 5.9643 4.000 2.6018 4.000 2.0000 SGO_0310 metE; 5methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase 387.000 398.000 0.735 11.059 0.0001 0.0000 658.3047 441.500 402.7546 441.500 472.500 472.500 674.3489 398.0000 SGO_0312 xfp; D-xylulose 5-phosphate/D-fructose 6phosphate phosphoketolase 177.500 214.000 8.639 184.7260 214.0000 SGO_0317 LPXTG cell wall surface protein, serine protease, subtilase family 11.500 22.000 0.887 6.560 0.0098 0.0322 26.8391 18.000 11.9682 18.000 23.500 23.500 33.5390 22.0000 SGO_0321 polypeptide deformylase 2.000 0.576 2.317 2.9821 2.000 2.000 2.0000 SGO_0323 pseudouridine synthase rRNA-specific 27.500 20.500 5.618 28.6195 20.5000 SGO_0324 hypothetical protein SGO_0324 8.000 3.058 8.3257 SGO_0325 probable membrane protein, putative 51.500 49.000 -3.296 6.752 0.0097 0.0317 5.2187 3.500 53.5965 3.500 49.0000 SGO_0326 probable membrane protein, putative 3.500 4.500 -0.856 3.376 0.0346 0.1462 2.2366 1.500 3.6425 1.500 4.5000 SGO_0327 Lipopolysaccharide Nacetylglucosaminyltransferase 9.000 11.500 4.383 9.3664 11.5000 SGO_0328 transmembrane protein, putative 61.000 51.000 -4.732 6.866 0.0187 0.0718 63.4833 1.500 1.500 2.1408 51.0000 SGO_0329 hypothetical protein SGO_0329 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 16

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 16 17.000 15.000 5.031 17.6921 15.0000 SGO_0330 hypothetical protein SGO_0330 21.500 21.500 5.455 22.3753 21.5000 SGO_0331 hypothetical protein SGO_0331 19.000 33.000 5.722 19.7735 33.0000 SGO_0332 hypothetical protein SGO_0332 77.500 96.000 -0.089 8.419 0.0644 0.2989 82.0085 55.000 80.6550 55.000 58.500 58.500 83.4908 96.0000 SGO_0333 rpsO; ribosomal protein S15 2.000 2.161 3.452 8.9464 6.000 6.000 2.0000 SGO_0337 trx-2; thioredoxin 3.000 -0.424 2.389 2.2366 1.500 1.500 3.0000 SGO_0339 hypothetical protein SGO_0339 47.500 52.000 0.572 7.982 0.0036 0.0093 68.5889 46.000 49.4337 46.000 58.000 58.000 82.7772 52.0000 SGO_0342 pepF-2; oligoendopeptidase 128.500 140.500 -0.124 9.039 0.0049 0.0139 127.4860 85.500 133.7312 85.500 87.000 87.000 124.1658 140.5000 SGO_0344 pnpA; polyribonucleotide nucleotidyltransferase 4.000 8.500 3.663 4.1628 8.5000 SGO_0345 cysE; serine O-acetyltransferase 13.000 -1.348 4.537 0.0036 0.0090 5.2187 3.500 3.500 3.500 3.500 4.9952 13.0000 SGO_0348 reductase 22.000 26.000 0.002 6.611 0.1832 0.9875 24.6026 16.500 22.8956 16.500 17.000 17.000 24.2623 26.0000 SGO_0349 cysS; cysteinyl-tRNA synthetase 66.000 74.000 -0.745 7.834 0.0012 0.0022 46.9685 31.500 68.6868 31.500 27.000 27.000 38.5342 74.0000 SGO_0352 ABC transporter, ATP-binding protein SP1580 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 17

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 17 3.500 2.500 0.905 4.160 0.0171 0.0639 7.4553 5.000 3.6425 5.000 3.000 3.000 4.2816 2.5000 SGO_0353 transport protein 7.500 10.000 0.966 5.720 0.0046 0.0127 14.9106 10.000 7.8053 10.000 14.000 14.000 19.9807 10.0000 SGO_0355 RNA methyltransferase, TrmH family, group 3 2.500 1.380 2.6018 SGO_0356 hypothetical protein SGO_0356 17.500 31.000 1.449 7.485 0.0013 0.0025 68.5889 46.000 18.2124 46.000 43.000 43.000 61.3693 31.0000 SGO_0357 degV; DegV family fatty acid binding protein 133.000 180.000 0.122 9.371 0.0784 0.3765 175.2000 117.500 138.4144 117.500 118.000 118.000 168.4088 180.0000 SGO_0358 rplM; ribosomal protein L13 76.000 107.000 -0.466 8.319 0.0137 0.0485 64.1157 43.000 79.0939 43.000 48.500 48.500 69.2189 107.0000 SGO_0359 rpsI; ribosomal protein S9 8.000 5.500 -0.553 4.546 0.0329 0.1384 5.9643 4.000 8.3257 4.000 2.500 2.500 3.5680 5.5000 SGO_0361 immunity repressor protein 2.000 3.000 2.345 2.0814 3.0000 SGO_0368 merA; mercury(II) reductase 4.000 2.000 4.0000 SGO_0371 putative transcriptional regulator 13.000 7.500 1.166 6.049 0.0026 0.0062 22.3660 15.000 13.5292 15.000 16.000 16.000 22.8351 7.5000 SGO_0372 malate oxidoreductase 22.500 20.000 -0.169 6.358 0.0363 0.1547 17.8928 12.000 23.4160 12.000 14.500 14.500 20.6943 20.0000 SGO_0374 Response regulator of the LytR/AlgR family 10.000 3.322 10.0000 SGO_0376 ABC transporter ATP-binding protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 18

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 18 SGO_0378 hypothetical protein SGO_0378 3.500 20.500 4.594 3.6425 20.5000 SGO_0379 Protein of unknown function (DUF421) family 11.000 3.459 11.0000 SGO_0380 hypothetical protein SGO_0380 10.500 20.500 -0.385 5.773 0.0578 0.2637 9.6919 6.500 10.9275 6.500 9.500 9.500 13.5583 20.5000 SGO_0384 putative carboxylate-amine/thiol ligase 39.500 40.500 6.351 41.1080 40.5000 SGO_0385 exo-beta-D-fructosidase 7.500 10.500 4.194 7.8053 10.5000 SGO_0387 hypothetical protein SGO_0387 29.000 46.000 6.251 30.1806 46.0000 SGO_0388 LPXTG cell wall surface protein, zinc carboxypeptidase family 2.000 1.000 2.0000 SGO_0389 possible phosphoserine phosphatase 30.000 34.500 1.564 8.027 0.0010 0.0015 107.3566 72.000 31.2213 72.000 61.500 61.500 87.7724 34.5000 SGO_0390 glycerol-3-phosphate dehydrogenase (NAD (P)+) 3.000 2.875 5.566 0.0232 0.0922 19.3838 13.000 13.000 17.500 17.500 24.9759 3.0000 SGO_0392 phosphoglycerate mutase 10.000 24.000 5.105 10.4071 24.0000 SGO_0393 D-alanyl-D-alanine carboxypeptidase 5.000 2.322 5.0000 SGO_0396 Transcriptional regulator, PadR family .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 19

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 19 58.500 44.000 -2.695 6.928 0.0017 0.0033 11.1830 7.500 60.8815 7.500 4.000 4.000 5.7088 44.0000 SGO_0398 ABC transporter ATP-binding protein 5.500 5.000 3.423 5.7239 5.0000 SGO_0400 hrcA; heat-inducible transcription repressor HrcA 14.000 37.000 0.166 6.709 0.1742 0.9248 21.6204 14.500 14.5699 14.500 22.000 22.000 31.3983 37.0000 SGO_0401 grpE; co-chaperone GrpE 434.500 499.000 0.461 11.142 0.0013 0.0022 632.9566 424.500 452.1883 424.500 473.000 473.000 675.0625 499.0000 SGO_0402 dnaK; DnaK chaperone protein 71.000 129.500 -2.045 7.970 0.0057 0.0167 23.8570 16.000 73.8904 16.000 16.500 16.500 23.5487 129.5000 SGO_0404 dnaJ; DnaJ chaparone protein 3.500 -0.231 2.696 2.9821 2.000 2.000 3.5000 SGO_0407 truA; tRNA pseudouridine synthase A 232.000 233.000 8.890 241.4446 233.0000 SGO_0408 zmpB; zinc metalloproteinase B 1.500 1.598 3.467 0.0233 0.0929 5.2187 3.500 1.5611 3.500 3.000 3.000 4.2816 SGO_0409 pyridoxine kinase 4.454 11.9285 8.000 8.000 7.000 7.000 9.9904 SGO_0411 conserved hypothetical protein TIGR01440 353.500 428.500 0.831 11.109 0.0005 0.0006 690.3625 463.000 367.8908 463.000 506.000 506.000 722.1599 428.5000 SGO_0412 tig; trigger factor 15.500 9.500 2.022 7.008 0.0040 0.0107 40.2587 27.000 16.1310 27.000 44.000 44.000 62.7965 9.5000 SGO_0413 DNA-directed RNA polymerase delta chain 569.500 529.500 -1.044 10.702 0.0005 0.0006 274.3557 184.000 592.6841 184.000 188.500 188.500 269.0260 529.5000 SGO_0415 secA; preprotein translocase, SecA subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 20

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 20 24.000 30.500 0.754 7.228 0.0087 0.0280 55.1694 37.000 24.9770 37.000 27.500 27.500 39.2478 30.5000 SGO_0416 phospho-2-dehydro-3-deoxyheptonate aldolase 3.870 8.2009 5.500 5.500 4.500 4.500 6.4224 SGO_0418 alr; alanine racemase 2.000 1.326 2.868 5.2187 3.500 2.0814 3.500 SGO_0425 ansB; asparaginase 9.500 15.000 -0.316 5.480 0.0492 0.2190 11.1830 7.500 9.8867 7.500 6.000 6.000 8.5632 15.0000 SGO_0426 Cof family protein 9.500 9.500 1.411 6.151 0.0006 0.0008 23.8570 16.000 9.8867 16.000 19.500 19.500 27.8303 9.5000 SGO_0427 universal stress protein family 162.000 152.500 -0.208 9.238 0.0673 0.3144 167.7447 112.500 168.5950 112.500 80.500 80.500 114.8891 152.5000 SGO_0429 aspartate transaminase 314.000 340.500 9.382 326.7828 340.5000 SGO_0430 LPXTG cell wall surface protein 6.500 12.500 0.147 5.310 0.1464 0.7587 9.6919 6.500 6.7646 6.500 7.500 7.500 10.7040 12.5000 SGO_0431 GTP-sensing transcriptional pleiotropic repressor codY 32.500 26.000 0.535 7.190 0.0066 0.0198 46.2230 31.000 33.8231 31.000 28.000 28.000 39.9614 26.0000 SGO_0432 entB; isochorismatase family protein 49.000 63.500 -0.559 7.587 0.0084 0.0265 34.2945 23.000 50.9948 23.000 30.500 30.500 43.5294 63.5000 SGO_0434 aspS-2; aspartyl-tRNA synthetase 17.500 22.000 -0.003 6.327 0.1779 0.9549 18.6383 12.500 18.2124 12.500 15.000 15.000 21.4079 22.0000 SGO_0435 gatC; glutamyl-tRNA(Gln) amidotransferase, C subunit 179.500 161.500 -0.300 9.301 0.0091 0.0294 148.3608 99.500 186.8074 99.500 94.000 94.000 134.1562 161.5000 SGO_0436 gatA; glutamyl-tRNA(Gln) amidotransferase, A subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 21

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 21 100.000 103.000 0.549 8.996 0.0018 0.0038 141.6511 95.000 104.0710 95.000 113.500 113.500 161.9865 103.0000 SGO_0437 gatB; glutamyl-tRNA(Gln) amidotransferase, B subunit 3.000 3.500 1.808 4.908 0.0017 0.0035 13.4196 9.000 3.1221 9.000 7.000 7.000 9.9904 3.5000 SGO_0440 L-iditol 2-dehydrogenase BH3949 8.500 3.087 8.5000 SGO_0444 HAD superfamily (subfamily IIIA) phosphatase, TIGR01668 21.000 26.000 0.374 6.781 0.0137 0.0486 34.2945 23.000 21.8549 23.000 19.500 19.500 27.8303 26.0000 SGO_0445 GTP-binding protein 12.000 3.585 12.0000 SGO_0446 conserved hypothetical protein TIGR00253 10.000 11.500 -0.822 5.135 0.0144 0.0518 8.9464 6.000 10.4071 6.000 3.000 3.000 4.2816 11.5000 SGO_0447 nadD; nicotinate (nicotinamide) nucleotide adenylyltransferase 10.500 6.000 0.170 5.137 0.1330 0.6801 9.6919 6.500 10.9275 6.500 6.000 6.000 8.5632 6.0000 SGO_0448 conserved hypothetical protein TIGR00488 3.000 1.585 3.0000 SGO_0449 isochorismatase family protein 4.500 1.018 4.508 0.0199 0.0773 9.6919 6.500 6.500 6.000 6.000 8.5632 4.5000 SGO_0450 iojap-related protein 3.791 6.7098 4.500 4.500 5.000 5.000 7.1360 SGO_0451 methyltransferase 105.000 144.000 7.985 109.2745 144.0000 SGO_0453 lipoprotein, putative 54.000 42.500 0.236 7.740 0.0327 0.1365 55.9149 37.500 56.1983 37.500 41.500 41.500 59.2285 42.5000 SGO_0454 conserved hypothetical protein TIGR01033 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 22

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 22 155.500 136.000 -2.675 8.428 0.0004 0.0005 21.6204 14.500 161.8303 14.500 17.500 17.500 24.9759 136.0000 SGO_0455 lipoprotein, putative 7.000 6.000 3.732 7.2850 6.0000 SGO_0456 ILL5; amino acid aminohydrolase 245.000 274.500 -1.812 9.410 0.0002 0.0001 72.3166 48.500 254.9739 48.500 55.000 55.000 78.4956 274.5000 SGO_0457 ABC transporter, substrate-binding protein SP0148 801.500 708.500 -1.995 10.913 0.0005 0.0005 190.8562 128.000 834.1288 128.000 136.500 136.500 194.8119 708.5000 SGO_0458 hlpA; lipoprotein 10.000 20.500 -1.190 5.463 0.0169 0.0627 8.2009 5.500 10.4071 5.500 3.500 3.500 4.9952 20.5000 SGO_0459 succinyl-diaminopimelate desuccinylase 91.000 75.500 -2.214 7.691 0.0008 0.0013 19.3838 13.000 94.7046 13.000 12.000 12.000 17.1263 75.5000 SGO_0460 ABC transporter, ATP-binding protein SP0151 2.500 4.000 2.723 2.6018 4.0000 SGO_0463 cydD; putative ABC transporter (ATPbinding protein) 12.000 28.500 -0.141 6.233 0.1049 0.5199 16.4017 11.000 12.4885 11.000 12.500 12.500 17.8399 28.5000 SGO_0468 hypothetical protein SGO_0468 10.500 9.500 4.352 10.9275 9.5000 SGO_0469 integral membrane protein 12.000 11.000 1.201 6.277 0.0008 0.0012 29.0757 19.500 12.4885 19.500 17.500 17.500 24.9759 11.0000 SGO_0476 rhodanese family protein 4.500 2.150 5.482 0.0231 0.0917 22.3660 15.000 15.000 12.500 12.500 17.8399 4.5000 SGO_0480 hypothetical protein SGO_0480 17.000 12.000 0.911 6.419 0.0108 0.0362 22.3660 15.000 17.6921 15.000 23.500 23.500 33.5390 12.0000 SGO_0483 hypothetical protein SGO_0483 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 23

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 23 9.000 13.500 4.515 9.3664 13.5000 SGO_0484 sensor histidine kinase 39.500 37.500 -2.054 6.608 0.0002 0.0001 8.9464 6.000 41.1080 6.000 7.000 7.000 9.9904 37.5000 SGO_0488 ABC transporter, ATP-binding protein SP0483 3.343 3.7277 2.500 2.500 4.500 4.500 6.4224 SGO_0491 gidB; methyltransferase GidB 9.500 13.000 1.064 6.136 0.0009 0.0013 24.6026 16.500 9.8867 16.500 16.000 16.000 22.8351 13.0000 SGO_0494 lemA; LemA-like protein 8.000 14.000 -0.397 4.932 0.0987 0.4863 8.2009 5.500 8.3257 5.500 14.0000 SGO_0495 htpx; heat shock protein SGO_0497 gtfG; glucosyltransferase G 4.000 2.058 4.1628 SGO_0500 rggD; putative transcriptional regulator RggD 22.500 22.500 0.653 6.885 0.0004 0.0004 37.2766 25.000 23.4160 25.000 24.500 24.500 34.9662 22.5000 SGO_0501 Uncharacterized ACR, COG1399 291.000 280.000 -0.710 9.878 0.0016 0.0032 198.3115 133.000 302.8465 133.000 112.000 112.000 159.8457 280.0000 SGO_0502 floL; flotillin-like protein 350.000 340.000 0.873 10.962 0.0003 0.0002 626.2468 420.000 364.2484 420.000 465.000 465.000 663.6449 340.0000 SGO_0503 gnd; 6-phosphogluconate dehydrogenase, decarboxylating 911.000 902.500 -3.384 10.986 0.0001 0.0000 79.7719 53.500 948.0865 53.500 69.000 69.000 98.4763 902.5000 SGO_0505 PTS system, IIBC component 8.000 -1.165 3.532 2.500 2.500 3.5680 8.0000 SGO_0506 rgfB; RgfB .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 24

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 24 24.500 24.500 -0.519 6.409 0.0010 0.0016 16.4017 11.000 25.4974 11.000 13.000 13.000 18.5535 24.5000 SGO_0508 nrdR; transcriptional regulator, NrdR family 5.500 12.500 -1.245 4.446 0.0735 0.3492 5.7239 2.500 2.500 3.5680 12.5000 SGO_0509 Replication initiation and membrane attachment protein (DnaB) superfamily 6.500 9.500 1.688 6.091 0.0010 0.0015 28.3302 19.000 6.7646 19.000 16.500 16.500 23.5487 9.5000 SGO_0510 dnaI; primosomal protein DnaI 4.500 12.500 0.194 5.117 0.1773 0.9470 8.9464 6.000 4.6832 6.000 6.000 6.000 8.5632 12.5000 SGO_0511 NADPH-flavin oxidoreductase -like protein 61.000 43.000 0.530 8.008 0.0100 0.0333 74.5532 50.000 63.4833 50.000 53.500 53.500 76.3548 43.0000 SGO_0512 GTP-binding protein engA 4.500 2.170 4.5000 SGO_0513 Snf2 family protein 3.791 6.7098 4.500 4.500 5.000 5.000 7.1360 SGO_0514 hypothetical protein SGO_0514 85.500 82.000 0.105 8.471 0.0142 0.0507 91.7004 61.500 88.9807 61.500 64.500 64.500 92.0540 82.0000 SGO_0515 murC; UDP-N-acetylmuramate--alanine ligase 170.000 167.000 -1.438 8.879 0.0001 0.0001 65.6068 44.000 176.9206 44.000 43.000 43.000 61.3693 167.0000 SGO_0518 aminodeoxychorismate lyase-like protein 31.000 37.500 0.526 7.415 0.0087 0.0280 56.6604 38.000 32.2620 38.000 31.000 31.000 44.2430 37.5000 SGO_0519 greA; transcription elongation factor greA 18.000 27.500 -1.082 6.092 0.0080 0.0248 13.4196 9.000 18.7328 9.000 6.000 6.000 8.5632 27.5000 SGO_0521 Membrane protein oxaA 2 precursor 10.500 0.164 5.107 0.1254 0.6344 9.6919 6.500 6.500 10.000 10.000 14.2719 10.5000 SGO_0523 spoU rRNA Methylase family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 25

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 25 8.500 17.000 0.991 6.225 0.0078 0.0239 26.8391 18.000 8.8460 18.000 15.500 15.500 22.1215 17.0000 SGO_0526 ilvB; acetolactate synthase, large subunit, biosynthetic type 12.500 14.000 -0.395 5.587 0.0288 0.1179 8.2009 5.500 13.0089 5.500 9.000 9.000 12.8447 14.0000 SGO_0527 ilvN; acetolactate synthase, small subunit 68.000 77.000 0.581 8.528 0.0018 0.0039 117.7940 79.000 70.7683 79.000 72.500 72.500 103.4715 77.0000 SGO_0528 ilvC; ketol-acid reductoisomerase 2.000 5.500 1.401 4.686 0.0093 0.0302 7.4553 5.000 2.0814 5.000 7.500 7.500 10.7040 5.5000 SGO_0529 ilvA; threonine dehydratase 10.000 12.000 -1.277 5.023 0.0059 0.0174 2.9821 2.000 10.4071 2.000 5.000 5.000 7.1360 12.0000 SGO_0530 Cof family protein 1.500 0.871 2.143 1.5611 2.000 2.000 2.8544 SGO_0533 conserved hypothetical protein TIGR00150 42.500 54.500 -2.237 6.905 0.0008 0.0011 8.9464 6.000 44.2302 6.000 8.500 8.500 12.1311 54.5000 SGO_0535 putative transcriptional regulator LytR 30.500 36.000 -0.177 6.995 0.0193 0.0745 31.3123 21.000 31.7416 21.000 20.000 20.000 28.5439 36.0000 SGO_0536 hypothetical protein SGO_0536 11.500 16.500 1.124 6.487 0.0008 0.0011 30.5668 20.500 11.9682 20.500 21.500 21.500 30.6847 16.5000 SGO_0537 HIT family protein 41.000 32.500 -2.541 6.463 0.0012 0.0020 5.2187 3.500 42.6691 3.500 5.500 5.500 7.8496 32.5000 SGO_0538 ABC transporter, ATP-binding protein SP0522 10.000 15.000 4.667 10.4071 15.0000 SGO_0539 ABC transporter, permease protein 35.500 33.500 0.148 7.214 0.0131 0.0456 38.0221 25.500 36.9452 25.500 28.000 28.000 39.9614 33.5000 SGO_0540 hypothetical protein SGO_0540 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 26

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 26 14.000 18.500 -1.602 5.480 0.0030 0.0073 3.7277 2.500 14.5699 2.500 5.500 5.500 7.8496 18.5000 SGO_0541 methyltransferase, putative 6.500 -0.865 3.332 2.500 2.500 3.5680 6.5000 SGO_0542 hypothetical protein SGO_0542 87.500 95.000 -0.585 8.276 0.0002 0.0001 62.6247 42.000 91.0621 42.000 43.000 43.000 61.3693 95.0000 SGO_0543 nusA; transcription termination factor NusA 4.000 2.000 4.0000 SGO_0544 Protein of unknown function (DUF448) superfamily 3.500 1.807 3.5000 SGO_0545 ribosomal protein L7A family 132.500 103.500 -0.138 8.842 0.0729 0.3461 115.5574 77.500 137.8940 77.500 71.500 71.500 102.0443 103.5000 SGO_0546 infB; Translation initiation factor IF-2 1.098 1.500 1.500 2.1408 SGO_0547 rbfA; ribosome-binding factor A 105.000 91.500 -2.975 7.822 0.0004 0.0004 11.9285 8.000 109.2745 8.000 9.500 9.500 13.5583 91.5000 SGO_0548 Na/Pi-cotransporter family protein 3.500 3.756 5.724 49.2051 33.000 3.6425 33.000 SGO_0549 nagA; N-acetylglucosamine-6-phosphate deacetylase 3.500 9.000 2.595 6.355 0.0004 0.0004 33.5489 22.500 3.6425 22.500 25.000 25.000 35.6798 9.0000 SGO_0552 oxidoreductase, aldo/keto reductase family 18.000 45.500 -0.957 6.566 0.0297 0.1216 12.6740 8.500 18.7328 8.500 12.500 12.500 17.8399 45.5000 SGO_0554 hsdR; type I site-specific deoxyribonuclease 5.000 4.500 3.279 5.2035 4.5000 SGO_0556 DNA helicase-like protein, putative .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 27

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 27 3.500 1.807 3.5000 SGO_0557 HsdS specificity protein of type I restrictionmodification system 5.000 0.356 4.186 0.1015 0.5010 8.2009 5.500 5.500 3.500 3.500 4.9952 5.0000 SGO_0558 hypothetical protein SGO_0558 10.000 11.000 0.516 5.703 0.0024 0.0054 16.4017 11.000 10.4071 11.000 10.000 10.000 14.2719 11.0000 SGO_0560 hsdM; type I restriction-modification system, M subunit 56.500 65.500 0.214 8.069 0.0140 0.0500 67.8434 45.500 58.8001 45.500 53.500 53.500 76.3548 65.5000 SGO_0565 adhA; alcohol dehydrogenase 53.000 79.500 7.073 55.1576 79.5000 SGO_0566 sgc; serine protease challisin 34.500 38.000 0.047 7.232 0.0949 0.4663 35.7855 24.000 35.9045 24.000 28.500 28.500 40.6750 38.0000 SGO_0568 glyQ; glycyl-tRNA synthetase, alpha subunit 70.000 73.000 0.474 8.445 0.0001 0.0001 99.9013 67.000 72.8497 67.000 72.000 72.000 102.7579 73.0000 SGO_0569 glyS; glycyl-tRNA synthetase, beta subunit 9.000 -0.455 4.468 0.0111 0.0375 6.7098 4.500 4.500 4.500 4.500 6.4224 9.0000 SGO_0570 hypothetical protein SGO_0570 2.500 1.322 2.5000 SGO_0571 hypothetical protein SGO_0571 20.500 31.000 -0.163 6.619 0.0727 0.3439 23.8570 16.000 21.3345 16.000 15.500 15.500 22.1215 31.0000 SGO_0573 mraW; S-adenosyl-methyltransferase MraW 55.000 62.500 -3.188 7.054 0.0001 0.0001 6.7098 4.500 57.2390 4.500 4.500 4.500 6.4224 62.5000 SGO_0575 pbp2X; penicillin-binding protein 2X 8.500 3.087 8.5000 SGO_0576 mraY; phospho-N-acetylmuramoylpentapeptide-transferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 28

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 28 23.500 37.000 0.720 7.329 0.0064 0.0189 52.9328 35.500 24.4567 35.500 32.500 32.500 46.3838 37.0000 SGO_0577 ATP-dependent RNA helicase 44.500 43.500 6.489 46.3116 43.5000 SGO_0578 amino acid ABC transporter permease protein 55.500 54.500 -2.330 7.076 0.0002 0.0001 13.4196 9.000 57.7594 9.000 6.500 6.500 9.2768 54.5000 SGO_0579 amino acid ABC transporter ATP binding protein 11.000 15.000 0.719 6.131 0.0084 0.0264 18.6383 12.500 11.4478 12.500 17.500 17.500 24.9759 15.0000 SGO_0581 trxB; thioredoxin-disulfide reductase 18.000 27.000 1.890 7.748 0.0025 0.0058 70.0800 47.000 18.7328 47.000 69.500 69.500 99.1899 27.0000 SGO_0582 nicotinate phosphoribosyltransferase, putative 5.500 12.500 1.345 5.936 0.0033 0.0083 20.8749 14.000 5.7239 14.000 15.500 15.500 22.1215 12.5000 SGO_0583 nadE; NAD+ synthetase 19.500 29.500 0.921 7.164 0.0065 0.0193 53.6783 36.000 20.2938 36.000 28.000 28.000 39.9614 29.5000 SGO_0585 pepC; aminopeptidase C 154.500 171.500 -1.402 8.842 0.0003 0.0003 70.0800 47.000 160.7896 47.000 39.500 39.500 56.3741 171.5000 SGO_0586 pbp1a; penicillin-binding protein 1A 24.000 29.000 1.105 7.429 0.0068 0.0204 46.9685 31.500 24.9770 31.500 50.000 50.000 71.3597 29.0000 SGO_0589 methylase 13.500 20.500 -0.529 5.876 0.0308 0.1271 14.9106 10.000 14.0496 10.000 6.500 6.500 9.2768 20.5000 SGO_0590 Methyltransferase 208.000 211.000 -2.495 8.975 0.0000 0.0000 38.0221 25.500 216.4676 25.500 26.500 26.500 37.8206 211.0000 SGO_0591 hypothetical protein SGO_0591 8.000 9.500 1.171 5.856 0.0003 0.0002 19.3838 13.000 8.3257 13.000 14.500 14.500 20.6943 9.5000 SGO_0592 luxS; autoinducer-2 production protein LuxS .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 29

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 29 196.000 220.500 -2.047 9.043 0.0002 0.0001 55.9149 37.500 203.9791 37.500 33.000 33.000 47.0974 220.5000 SGO_0593 HD/KH domain protein 21.500 17.500 -0.071 6.280 0.1194 0.6001 17.1472 11.500 22.3753 11.500 14.500 14.500 20.6943 17.5000 SGO_0594 gmk; Guanylate kinase (GMP kinase) 40.500 43.500 -0.368 7.248 0.0003 0.0002 32.8034 22.000 42.1487 22.000 23.500 23.500 33.5390 43.5000 SGO_0595 DNA-directed RNA polymerase, omega subunit 3.000 1.643 3.1221 SGO_0596 priA; primosomal protein N'' 5.000 10.500 1.413 5.785 0.0025 0.0057 20.8749 14.000 5.2035 14.000 13.000 13.000 18.5535 10.5000 SGO_0597 fmt; methionyl-tRNA formyltransferase 6.000 6.000 0.767 5.065 0.0098 0.0324 12.6740 8.500 6.2443 8.500 6.000 6.000 8.5632 6.0000 SGO_0598 sun; sun protein 39.000 38.000 -0.624 7.019 0.0012 0.0022 27.5847 18.500 40.5877 18.500 16.500 16.500 23.5487 38.0000 SGO_0599 phosphoprotein phosphatase 105.000 115.000 -2.409 8.059 0.0001 0.0000 23.1115 15.500 109.2745 15.500 13.500 13.500 19.2671 115.0000 SGO_0600 serine/threonine protein kinase 8.000 9.000 4.115 8.3257 9.0000 SGO_0602 histidine kinase 9.500 11.500 -0.916 5.074 0.0148 0.0537 3.7277 2.500 9.8867 2.500 6.000 6.000 8.5632 11.5000 SGO_0603 response regulator 47.500 62.500 0.579 8.119 0.0028 0.0068 80.5174 54.000 49.4337 54.000 60.000 60.000 85.6316 62.5000 SGO_0604 hydrolase, haloacid dehalogenase family/peptidyl-prolyl cis-trans isomerase, cyclophilin type 162.000 181.000 -0.319 9.299 0.0034 0.0086 132.7047 89.000 168.5950 89.000 103.500 103.500 147.7145 181.0000 SGO_0606 cysK; cysteine synthase A .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 30

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 30 7.000 9.500 4.069 7.2850 9.5000 SGO_0608 comFA; competence ComFA-like protein 75.000 66.000 0.727 8.578 0.0016 0.0031 125.9949 84.500 78.0532 84.500 78.500 78.500 112.0347 66.0000 SGO_0610 ribosomal subunit interface protein 20.000 21.500 -1.293 5.901 0.0004 0.0005 7.4553 5.000 20.8142 5.000 7.000 7.000 9.9904 21.5000 SGO_0626 recX; Regulatory protein recX 2.500 1.322 2.5000 SGO_0628 ymdC; 3''-aminoglycoside phosphotransferase-like protein (kanamycin kinase) 3.500 6.500 -0.706 3.714 0.0791 0.3819 2.9821 2.000 3.6425 2.000 6.5000 SGO_0629 rumA-1; 23S rRNA (uracil-5-)methyltransferase RumA 3.000 3.710 6.407 0.0052 0.0151 41.7498 28.000 3.1221 28.000 28.000 28.000 39.9614 SGO_0631 alpha-glycerophosphate oxidase 5.243 17.8928 12.000 12.000 14.000 14.000 19.9807 SGO_0632 glpK; glycerol kinase 4.000 2.000 4.0000 SGO_0635 hypothetical protein SGO_0635 3.000 4.500 2.930 3.1221 4.5000 SGO_0636 hypothetical protein SGO_0636 65.500 63.000 0.402 8.251 0.0020 0.0044 82.7540 55.500 68.1665 55.500 63.500 63.500 90.6268 63.0000 SGO_0639 valS; valyl-tRNA synthetase 6.000 3.500 -0.116 4.207 0.1194 0.5995 3.7277 2.500 6.2443 2.500 3.500 3.500 4.9952 3.5000 SGO_0640 modification methylase 32.500 27.000 0.103 6.975 0.0807 0.3916 33.5489 22.500 33.8231 22.500 22.000 22.000 31.3983 27.0000 SGO_0641 ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 31

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 31 39.500 53.500 -1.357 7.044 0.0027 0.0063 22.3660 15.000 41.1080 15.000 10.500 10.500 14.9855 53.5000 SGO_0642 hypothetical protein SGO_0642 6.000 8.500 -0.367 4.720 0.0490 0.2176 4.4732 3.000 6.2443 3.000 5.000 5.000 7.1360 8.5000 SGO_0643 cytosine-specific methyltransferase 16.000 15.500 1.368 6.862 0.0033 0.0081 49.2051 33.000 16.6514 33.000 24.500 24.500 34.9662 15.5000 SGO_0644 hypothetical protein SGO_0644 5.000 2.322 5.0000 SGO_0649 hypothetical protein SGO_0649 71.000 69.500 -3.768 7.285 0.0002 0.0001 9.6919 6.500 73.8904 6.500 2.000 2.000 2.8544 69.5000 SGO_0652 hypothetical protein SGO_0652 10.000 -0.400 4.660 0.0528 0.2379 6.7098 4.500 4.500 6.000 6.000 8.5632 10.0000 SGO_0653 conserved hypothetical protein of unknown function (DUF1027) 74.000 97.500 -0.815 8.095 0.0039 0.0102 44.7319 30.000 77.0125 30.000 38.000 38.000 54.2333 97.5000 SGO_0654 radical SAM enzyme, Cfr family 17.000 17.500 -0.846 5.780 0.0012 0.0020 11.1830 7.500 17.6921 7.500 6.000 6.000 8.5632 17.5000 SGO_0656 trpB-2; tryptophan synthase, beta subunit 2.500 1.322 2.5000 SGO_0657 trpE; anthranilate synthase component I 3.000 1.585 3.0000 SGO_0662 trpB-1; tryptophan synthase, beta subunit 2.000 1.000 2.0000 SGO_0663 trpA-2; tryptophan synthase, alpha subunit 405.500 298.500 -0.422 10.290 0.0218 0.0858 246.0255 165.000 422.0077 165.000 200.000 200.000 285.4387 298.5000 SGO_0665 non-heme iron-containing ferritin .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 32

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 32 12.000 15.500 -1.961 5.142 0.0011 0.0019 4.4732 3.000 12.4885 3.000 2.000 2.000 2.8544 15.5000 SGO_0667 rhodanese family protein 49.000 55.500 0.694 8.122 0.0002 0.0001 85.7362 57.500 50.9948 57.500 60.500 60.500 86.3452 55.5000 SGO_0669 typA; GTP-binding protein TypA 30.500 29.500 0.437 7.176 0.0084 0.0267 46.2230 31.000 31.7416 31.000 26.000 26.000 37.1070 29.5000 SGO_0671 murD; UDP-N-acetylmuramoylalanine--Dglutamate ligase 42.500 31.500 -1.494 6.719 0.0073 0.0224 8.2009 5.500 44.2302 5.500 15.000 15.000 21.4079 31.5000 SGO_0672 murG; undecaprenyl-PP-MurNAcpentapeptide-UDPGlcNAc GlcNAc transferase 33.500 45.500 -2.932 6.419 0.0241 0.0961 5.2187 3.500 34.8638 3.500 45.5000 SGO_0673 DivIB; cell division protein DivIB 114.000 122.500 0.359 9.105 0.0012 0.0021 160.2894 107.500 118.6409 107.500 104.500 104.500 149.1417 122.5000 SGO_0674 ftsA; cell division protein FtsA 145.500 213.500 0.507 9.775 0.0084 0.0266 255.7174 171.500 151.4232 171.500 179.000 179.000 255.4676 213.5000 SGO_0675 ftsZ; cell division protein FtsZ 13.500 19.000 0.129 6.116 0.1080 0.5380 14.9106 10.000 14.0496 10.000 15.000 15.000 21.4079 19.0000 SGO_0676 conserved hypothetical protein TIGR00044 111.000 88.500 -0.679 8.372 0.0077 0.0236 55.9149 37.500 115.5188 37.500 50.000 50.000 71.3597 88.5000 SGO_0677 ylmF protein 93.500 93.000 0.819 9.042 0.0017 0.0035 153.5796 103.000 97.3063 103.000 128.500 128.500 183.3944 93.0000 SGO_0680 cell division protein DivIVA 74.500 101.000 0.809 8.932 0.0014 0.0026 158.0528 106.000 77.5329 106.000 106.500 106.500 151.9961 101.0000 SGO_0681 ileS; isoleucyl-tRNA synthetase 97.000 102.000 -1.462 8.112 0.0000 0.0000 37.2766 25.000 100.9488 25.000 25.500 25.500 36.3934 102.0000 SGO_0684 hypothetical protein SGO_0684 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 33

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 33 4.500 2.170 4.5000 SGO_0685 MutT/nudix family protein 73.500 72.500 -0.104 8.168 0.0159 0.0586 71.5711 48.000 76.4922 48.000 47.000 47.000 67.0781 72.5000 SGO_0688 ATP dependent Clp protease, ATP-binding subunit, ClpE 9.000 3.170 9.0000 SGO_0689 hypothetical protein SGO_0689 2.000 7.500 0.338 3.866 0.1779 0.9520 2.0814 3.500 3.500 4.9952 7.5000 SGO_0690 folD; methenyltetrahydrofolate cyclohydrolase 20.000 16.000 -2.268 5.513 0.0024 0.0053 6.7098 4.500 20.8142 4.500 1.500 1.500 2.1408 16.0000 SGO_0693 xseA; exodeoxyribonuclease VII, large subunit 9.500 0.972 4.814 18.6383 12.500 12.500 9.5000 SGO_0694 xseB; exodeoxyribonuclease VII, small subunit 3.321 7.000 7.000 9.9904 SGO_0695 geranyltranstransferase 4.000 4.000 3.029 4.1628 4.0000 SGO_0696 hemolysin-like protein 1.500 3.500 0.936 3.253 0.0636 0.2947 4.4732 3.000 1.5611 3.000 3.5000 SGO_0697 transcription regulator 8.000 16.000 0.402 5.779 0.0587 0.2686 14.1651 9.500 8.3257 9.500 11.500 11.500 16.4127 16.0000 SGO_0698 recN; DNA repair protein RecN 5.000 7.000 0.342 4.783 0.0207 0.0805 8.2009 5.500 5.2035 5.500 5.000 5.000 7.1360 7.0000 SGO_0699 Serine/threonine protein phosphatase 18.500 13.500 0.522 6.310 0.0140 0.0498 20.8749 14.000 19.2531 14.000 18.000 18.000 25.6895 13.5000 SGO_0700 DegV family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 34 1072.000 974.000 1.056 12.649 0.0002 0.0001 2199.3191 1475.000 1115.6407 1475.000 1496.500 1496.500 2135.7949 974.0000 SGO_0701 hup; DNA-binding histone-like protein HU 193.000 306.500 1.791 11.120 0.0004 0.0004 834.2502 559.500 200.8570 559.500 619.500 619.500 884.1463 306.5000 SGO_0704 gpmA; 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 3.500 1.807 3.5000 SGO_0705 Protein of unknown function (DUF1250) superfamily 3.000 6.000 1.431 5.021 0.0017 0.0035 11.9285 8.000 3.1221 8.000 8.000 8.000 11.4175 6.0000 SGO_0706 phoH-like protein 206.000 211.000 -5.103 8.777 0.0000 0.0000 8.9464 6.000 214.3862 6.000 3.000 3.000 4.2816 211.0000 SGO_0707 LPXTG cell wall surface protein 137.000 154.500 0.702 9.607 0.0002 0.0001 241.5523 162.000 142.5772 162.000 169.000 169.000 241.1957 154.5000 SGO_0708 ald; alanine dehydrogenase 8.500 3.145 8.8460 SGO_0711 conserved hypothetical protein TIGR00043 29.500 27.000 0.586 7.177 0.0059 0.0173 48.4596 32.500 30.7009 32.500 27.000 27.000 38.5342 27.0000 SGO_0713 sgg; GTP-binding protein Era 5.000 -0.001 3.321 3.500 3.500 4.9952 5.0000 SGO_0715 mutM; formamidopyrimidine-DNA glycosylase 17.000 22.000 -2.061 5.620 0.0009 0.0013 5.2187 3.500 17.6921 3.500 3.000 3.000 4.2816 22.0000 SGO_0719 rnr; ribonuclease R 8.500 10.500 0.112 5.337 0.0947 0.4647 8.9464 6.000 8.8460 6.000 8.500 8.500 12.1311 10.5000 SGO_0721 abpB-like dipeptidase lipoprotein 7.500 22.500 0.624 6.153 0.0651 0.3027 20.8749 14.000 7.8053 14.000 14.000 14.000 19.9807 22.5000 SGO_0722 tehB; tellurite resistance protein TehB .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 35

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 35 32.500 39.000 -2.408 6.437 0.0004 0.0003 5.9643 4.000 33.8231 4.000 5.500 5.500 7.8496 39.0000 SGO_0724 dipeptidase 4.000 2.000 4.0000 SGO_0728 ABC transporter, ATP-binding protein SP1653 3.000 5.000 3.022 3.1221 5.0000 SGO_0729 ABC transporter permease protein 9.500 7.500 4.120 9.8867 7.5000 SGO_0731 RRF2 family protein 16.000 14.000 -1.037 5.520 0.0033 0.0081 5.9643 4.000 16.6514 4.000 6.500 6.500 9.2768 14.0000 SGO_0736 hprK; HPr(Ser) kinase/phosphatase 9.000 11.000 4.348 9.3664 11.0000 SGO_0737 lgt; prolipoprotein diacylglyceryl transferase 65.000 55.000 -3.482 7.062 0.0005 0.0006 5.9643 4.000 67.6461 4.000 3.500 3.500 4.9952 55.0000 SGO_0738 Bacterial protein of unknown function (DUF948) family 11.000 9.500 0.984 5.964 0.0021 0.0046 18.6383 12.500 11.4478 12.500 16.000 16.000 22.8351 9.5000 SGO_0739 hypothetical protein SGO_0739 15.000 18.000 0.310 6.232 0.0039 0.0104 20.8749 14.000 15.6106 14.000 14.500 14.500 20.6943 18.0000 SGO_0742 peptidase, U32 family 80.000 88.000 -1.241 7.933 0.0005 0.0007 41.7498 28.000 83.2568 28.000 22.000 22.000 31.3983 88.0000 SGO_0743 peptidase, U32 family 8.000 13.500 2.842 7.443 0.0002 0.0001 72.3166 48.500 8.3257 48.500 56.000 56.000 79.9228 13.5000 SGO_0745 hypothetical protein SGO_0745 13.000 21.000 1.249 6.844 0.0018 0.0038 43.2408 29.000 13.5292 29.000 26.000 26.000 37.1070 21.0000 SGO_0749 glutathione reductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 36

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 36 708.000 584.500 -1.521 10.797 0.0013 0.0023 238.5702 160.000 736.8224 160.000 153.500 153.500 219.0742 584.5000 SGO_0750 efflux transporter, RND family, MFP subunit subfamily 82.500 77.000 0.115 8.412 0.0791 0.3822 100.6468 67.500 85.8585 67.500 54.000 54.000 77.0684 77.0000 SGO_0751 ABC transporter, ATP-binding protein SP0786 60.000 80.500 -1.394 7.621 0.0017 0.0034 26.8391 18.000 62.4426 18.000 19.000 19.000 27.1167 80.5000 SGO_0752 ABC transporter, ATP-binding protein 144.000 130.500 0.038 9.150 0.1267 0.6427 151.3430 101.500 149.8622 101.500 95.500 95.500 136.2970 130.5000 SGO_0753 lysS; lysyl-tRNA synthetase 1.835 2.500 2.500 3.5680 SGO_0754 phosphoglycerate mutase family protein 8.000 10.000 0.647 5.566 0.0123 0.0424 11.9285 8.000 8.3257 8.000 12.000 12.000 17.1263 10.0000 SGO_0755 regulatory protein 66.000 54.500 6.945 68.6868 54.5000 SGO_0757 peptidase, U32 family 117.000 122.000 0.615 9.269 0.0000 0.0000 187.1285 125.500 121.7630 125.500 130.500 130.500 186.2487 122.0000 SGO_0760 ppc; phosphoenolpyruvate carboxylase 2223.000 2341.000 0.462 13.435 0.0010 0.0017 3349.6748 2246.500 2313.4975 2246.500 2149.500 2149.500 3067.7522 2341.0000 SGO_0761 tuf; translation elongation factor Tu 384.500 417.000 0.868 11.183 0.0047 0.0131 866.3081 581.000 400.1528 581.000 449.500 449.500 641.5234 417.0000 SGO_0762 tpiA; triosephosphate isomerase 87.500 103.000 -1.037 8.173 0.0008 0.0011 43.9864 29.500 91.0621 29.500 35.500 35.500 50.6654 103.0000 SGO_0763 murA-1; UDP-N-acetylglucosamine 1carboxyvinyltransferase 15.000 15.500 4.959 15.6106 15.5000 SGO_0765 endA; DNA-entry nuclease .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 37

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 37 11.000 10.500 -0.180 5.377 0.0674 0.3152 8.2009 5.500 11.4478 5.500 8.000 8.000 11.4175 10.5000 SGO_0767 transport protein 56.000 36.000 1.279 8.306 0.0013 0.0023 108.8477 73.000 58.2797 73.000 79.500 79.500 113.4619 36.0000 SGO_0771 pepq; proline dipeptidase 508.000 476.500 -2.406 10.223 0.0002 0.0001 102.1379 68.500 528.6805 68.500 61.500 61.500 87.7724 476.5000 SGO_0773 ccpA; catabolite control protein A 56.500 46.500 -1.574 7.142 0.0017 0.0036 21.6204 14.500 58.8001 14.500 10.000 10.000 14.2719 46.5000 SGO_0774 glycosyl transferase, group 1 family protein 28.500 24.000 -0.719 6.433 0.0052 0.0149 14.1651 9.500 29.6602 9.500 13.000 13.000 18.5535 24.0000 SGO_0775 glycosyl transferase, group 1 148.000 161.500 -0.132 9.237 0.0068 0.0204 140.1600 94.000 154.0250 94.000 103.500 103.500 147.7145 161.5000 SGO_0778 thrS; threonyl-tRNA synthetase 19.500 31.000 0.258 6.808 0.0709 0.3336 35.0400 23.500 20.2938 23.500 18.000 18.000 25.6895 31.0000 SGO_0779 response regulator 22.500 17.000 -2.189 5.620 0.0017 0.0034 4.4732 3.000 23.4160 3.000 3.000 3.000 4.2816 17.0000 SGO_0780 histidine kinase 14.500 19.000 5.091 15.0903 19.0000 SGO_0781 vicX; Zn-dependent hydrolase (betalactamase superfamily) 4.500 8.000 3.665 4.6832 8.0000 SGO_0782 Protein of unknown function (DUF454) family 105.500 138.500 -1.759 8.327 0.0011 0.0018 35.7855 24.000 109.7949 24.000 26.000 26.000 37.1070 138.5000 SGO_0784 smc; chromosome segregation protein SMC 11.500 10.000 -0.875 4.804 0.0299 0.1232 5.9643 4.000 11.9682 4.000 10.0000 SGO_0785 Cof family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 38

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 38 10.500 13.500 0.800 6.061 0.0010 0.0015 21.6204 14.500 10.9275 14.500 14.500 14.500 20.6943 13.5000 SGO_0786 Cof family protein 56.000 48.000 -0.273 7.598 0.0142 0.0509 43.9864 29.500 58.2797 29.500 30.500 30.500 43.5294 48.0000 SGO_0787 ftsY; cell division protein FtsY 27.000 23.500 1.244 7.437 0.0003 0.0002 59.6426 40.000 28.0992 40.000 43.500 43.500 62.0829 23.5000 SGO_0788 zwf; glucose-6-phosphate 1-dehydrogenase 38.000 51.500 -0.585 7.246 0.0105 0.0350 34.2945 23.000 39.5470 23.000 18.500 18.500 26.4031 51.5000 SGO_0792 hypothetical protein SGO_0792 50.000 60.500 -0.049 7.789 0.1049 0.5188 52.1872 35.000 52.0355 35.000 39.500 39.500 56.3741 60.5000 SGO_0794 metallo-beta-lactamase family protein 5.500 5.000 1.371 5.264 0.0002 0.0001 13.4196 9.000 5.7239 9.000 10.000 10.000 14.2719 5.0000 SGO_0795 tributyrin esterase 10.000 3.322 10.0000 SGO_0797 RocB protein, putative 80.000 70.500 -1.256 7.768 0.0009 0.0013 33.5489 22.500 83.2568 22.500 21.500 21.500 30.6847 70.5000 SGO_0798 ABC transporter, ATP-binding protein SP1381 21.000 43.000 -1.446 6.450 0.0120 0.0409 10.4374 7.000 21.8549 7.000 8.500 8.500 12.1311 43.0000 SGO_0800 polysaccharide deacetylase family protein 80.500 71.500 1.139 8.955 0.0003 0.0002 166.2536 111.500 83.7771 111.500 122.500 122.500 174.8312 71.5000 SGO_0801 hom; homoserine dehydrogenase 18.500 21.500 0.767 6.782 0.0003 0.0002 34.2945 23.000 19.2531 23.000 24.500 24.500 34.9662 21.5000 SGO_0802 thrB; homoserine kinase 86.000 96.500 -1.866 7.889 0.0002 0.0001 24.6026 16.500 89.5010 16.500 18.500 18.500 26.4031 96.5000 SGO_0803 hypothetical protein SGO_0803 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 39

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 39 4.000 14.000 -0.227 4.969 0.0921 0.4499 7.4553 5.000 4.1628 5.000 4.000 4.000 5.7088 14.0000 SGO_0804 murB; UDP-Nacetylenolpyruvoylglucosamine reductase 42.000 37.500 -2.598 6.570 0.0004 0.0005 5.2187 3.500 43.7098 3.500 6.000 6.000 8.5632 37.5000 SGO_0805 potA; spermidine/putrescine ABC transporter, ATP-binding subunit 7.500 11.500 4.271 7.8053 11.5000 SGO_0806 potB; spermidine/putrescine ABC transporter, permease protein 33.500 69.500 -3.301 6.773 0.0501 0.2239 34.8638 3.500 3.500 4.9952 69.5000 SGO_0808 potD; spermidine/putrescine ABC transporter 8.500 7.500 -0.235 4.916 0.0150 0.0547 6.7098 4.500 8.8460 4.500 5.000 5.000 7.1360 7.5000 SGO_0812 hypothetical protein SGO_0812 3.500 1.807 3.5000 SGO_0813 fructose-bisphosphatase 4.500 0.665 3.541 5.000 5.000 7.1360 4.5000 SGO_0814 aminotransferase, class-V 46.000 55.000 -0.231 7.574 0.0182 0.0693 46.9685 31.500 47.8726 31.500 28.500 28.500 40.6750 55.0000 SGO_0815 thiI; thiamine biosynthesis protein ThiI 6.500 5.000 3.556 6.7646 5.0000 SGO_0817 hypothetical protein SGO_0817 87.000 63.500 2.010 9.582 0.0005 0.0006 284.0477 190.500 90.5417 190.500 230.000 230.000 328.2545 63.5000 SGO_0818 rplU; ribosomal protein L21 72.500 41.000 0.025 7.846 0.1704 0.8971 52.1872 35.000 75.4514 35.000 43.000 43.000 61.3693 41.0000 SGO_0820 rpmA; ribosomal protein L27 7.500 4.500 3.621 7.8053 4.5000 SGO_0822 lipoprotein, putative .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 40

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 40 4.000 -0.165 2.920 2.500 2.500 3.5680 4.0000 SGO_0823 Cof family protein 25.000 40.000 1.254 7.781 0.0010 0.0017 76.7898 51.500 26.0177 51.500 54.000 54.000 77.0684 40.0000 SGO_0824 lepA; GTP-binding protein LepA 27.000 38.500 -1.794 6.419 0.0019 0.0042 9.6919 6.500 28.0992 6.500 6.500 6.500 9.2768 38.5000 SGO_0825 lipoprotein, putative 1.500 2.000 0.755 2.710 0.0282 0.1150 2.9821 2.000 1.5611 2.000 2.0000 SGO_0830 uvrC; excinuclease ABC, C subunit 44.500 36.500 -2.252 6.649 0.0010 0.0016 10.4374 7.000 46.3116 7.000 5.000 5.000 7.1360 36.5000 SGO_0832 hypothetical protein SGO_0832 3.120 2.9821 2.000 2.000 4.000 4.000 5.7088 SGO_0833 phosphoesterase-related gene 7.000 13.500 4.377 7.2850 13.5000 SGO_0834 hypothetical protein SGO_0834 32.500 45.000 1.275 8.064 0.0004 0.0004 94.6826 63.500 33.8231 63.500 66.000 66.000 94.1948 45.0000 SGO_0835 nitroreductase 99.000 118.000 0.793 9.237 0.0004 0.0004 193.8383 130.000 103.0303 130.000 132.000 132.000 188.3895 118.0000 SGO_0836 pepV; dipeptidase PepV 3.500 1.807 3.5000 SGO_0841 oxidoreductase 3.500 9.500 0.073 4.710 0.1825 0.9811 4.4732 3.000 3.6425 3.000 6.000 6.000 8.5632 9.5000 SGO_0842 rhodanese family protein 48.500 50.000 1.269 8.420 0.0000 0.0000 122.2672 82.000 50.4744 82.000 84.000 84.000 119.8842 50.0000 SGO_0848 rpmE; ribosomal protein L31 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 41

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 41 13.000 18.000 0.055 6.011 0.1464 0.7609 19.3838 13.000 13.5292 13.000 9.500 9.500 13.5583 18.0000 SGO_0849 DHH subfamily 1 protein 22.500 22.500 1.562 7.506 0.0004 0.0004 72.3166 48.500 23.4160 48.500 44.500 44.500 63.5101 22.5000 SGO_0850 flavodoxin 10.000 4.500 0.281 4.984 0.1267 0.6444 7.4553 5.000 10.4071 5.000 6.500 6.500 9.2768 4.5000 SGO_0851 putative permease 8.000 9.500 -0.862 4.813 0.0092 0.0300 6.7098 4.500 8.3257 4.500 2.500 2.500 3.5680 9.5000 SGO_0852 TPR domain protein 13.000 6.000 -0.638 4.965 0.0412 0.1775 6.7098 4.500 13.5292 4.500 3.500 3.500 4.9952 6.0000 SGO_0853 budA; alpha-acetolactate decarboxylase 336.500 369.500 -5.332 9.527 0.0001 0.0000 7.4553 5.000 350.1988 5.000 7.500 7.500 10.7040 369.5000 SGO_0854 cshA; surface-associated protein CshA 13.000 16.500 -0.453 5.699 0.0089 0.0287 11.9285 8.000 13.5292 8.000 7.000 7.000 9.9904 16.5000 SGO_0855 fbpA; fibronectin-binding protein A 124.500 138.500 -1.459 8.517 0.0003 0.0003 43.2408 29.000 129.5683 29.000 38.500 38.500 54.9469 138.5000 SGO_0856 ABC transporter, substrate binding protein 6.000 7.000 3.727 6.2443 7.0000 SGO_0858 ABC transporter, ATP-binding protein 54.500 42.500 -0.216 7.523 0.0440 0.1920 44.7319 30.000 56.7187 30.000 28.000 28.000 39.9614 42.5000 SGO_0859 pheS; phenylalanyl-tRNA synthetase, alpha subunit 99.000 87.000 0.743 8.986 0.0008 0.0012 154.3251 103.500 103.0303 103.500 114.000 114.000 162.7000 87.0000 SGO_0861 pheT; phenylalanyl-tRNA synthetase, beta subunit 3.000 8.000 3.475 3.1221 8.0000 SGO_0862 hypothetical protein SGO_0862 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 42

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 42 2.000 1.058 2.0814 SGO_0868 hypothetical protein SGO_0868 3.000 1.585 3.0000 SGO_0877 permease domain protein 10.000 15.000 -0.639 5.374 0.0115 0.0390 8.2009 5.500 10.4071 5.500 5.500 5.500 7.8496 15.0000 SGO_0885 cobyric acid synthase 5.000 13.500 -0.777 4.851 0.0434 0.1880 3.7277 2.500 5.2035 2.500 4.500 4.500 6.4224 13.5000 SGO_0886 Mur ligase family protein 84.000 70.500 7.303 87.4196 70.5000 SGO_0887 conserved hypothetical protein TIGR00159 20.500 15.500 -1.894 5.554 0.0025 0.0055 3.7277 2.500 21.3345 2.500 4.500 4.500 6.4224 15.5000 SGO_0888 hypothetical protein SGO_0888 36.000 35.500 0.013 7.195 0.1403 0.7211 35.7855 24.000 37.4655 24.000 26.500 26.500 37.8206 35.5000 SGO_0889 glmM; phosphoglucosamine mutase 126.000 135.500 8.059 131.1294 135.5000 SGO_0890 LPXTG cell wall surface protein, collagen binding domain 44.000 38.500 0.666 7.769 0.0040 0.0106 60.3881 40.500 45.7912 40.500 51.500 51.500 73.5005 38.5000 SGO_0893 GTP-binding protein 2.000 8.000 3.334 2.0814 8.0000 SGO_0899 putative hydrolase or acyltransferase 17.000 17.500 0.470 6.395 0.0052 0.0150 26.8391 18.000 17.6921 18.000 15.500 15.500 22.1215 17.5000 SGO_0901 DNA-directed DNA polymerase III 2.000 1.058 2.0814 SGO_0904 purR; galactose operon repressor GalR .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 43

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 43 12.000 16.500 4.857 12.4885 16.5000 SGO_0905 lipoprotein, putative 10.500 14.500 1.999 6.978 0.0001 0.0000 50.6962 34.000 10.9275 34.000 35.000 35.000 49.9518 14.5000 SGO_0906 leuA; 2-isopropylmalate synthase 2.500 4.500 0.546 3.597 0.0772 0.3701 2.6018 3.500 3.500 4.9952 4.5000 SGO_0907 leuB; 3-isopropylmalate dehydrogenase 2.683 4.500 4.500 6.4224 SGO_0909 leuC; 3-isopropylmalate dehydratase, large subunit 29.000 32.500 1.860 8.180 0.0001 0.0000 111.8298 75.000 30.1806 75.000 81.000 81.000 115.6027 32.5000 SGO_0911 hypothetical protein SGO_0911 13.500 16.000 -1.047 5.481 0.0012 0.0021 8.2009 5.500 14.0496 5.500 4.500 4.500 6.4224 16.0000 SGO_0915 proV; ABC-type proline/glycine betaine transporter 17.000 20.500 5.255 17.6921 20.5000 SGO_0916 proWX; ABC transporter membranespanning permease 4.500 2.500 2.845 4.6832 2.5000 SGO_0932 galK; galactokinase 5.500 2.459 5.5000 SGO_0934 galE-2; UDP-glucose 4-epimerase 2.500 1.500 2.036 2.6018 1.5000 SGO_0936 phosphoenolpyruvate synthase, putative SGO_0938 Phosphatidylserine decarboxylase proenzyme 2 9.000 5.500 3.894 9.3664 5.5000 SGO_0940 ppsA; phosphoenolpyruvate synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 44

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 44 2.500 1.322 2.5000 SGO_0941 hypothetical protein SGO_0941 19.500 16.500 5.201 20.2938 16.5000 SGO_0942 zmpC; zinc metalloproteinase C 6.500 25.500 5.012 6.7646 25.5000 SGO_0944 ABC transporter, ATP-binding protein 30.000 28.000 -0.217 6.786 0.0285 0.1162 28.3302 19.000 31.2213 19.000 16.000 16.000 22.8351 28.0000 SGO_0946 Deblocking aminopeptidase 19.000 15.500 5.141 19.7735 15.5000 SGO_0948 pgdA; peptidoglycan N-acetylglucosamine deacetylase A 12.500 9.500 -0.476 5.268 0.0151 0.0552 7.4553 5.000 13.0089 5.000 6.000 6.000 8.5632 9.5000 SGO_0949 deaD; DEAD RNA helicase 9.000 -0.275 4.609 0.1251 0.6319 9.6919 6.500 6.500 4.000 4.000 5.7088 9.0000 SGO_0950 oxidoreductase 13.000 18.000 -0.138 5.905 0.0714 0.3362 13.4196 9.000 13.5292 9.000 10.500 10.500 14.9855 18.0000 SGO_0951 udk; uridine kinase 5.155 15.6562 10.500 10.500 14.000 14.000 19.9807 SGO_0953 endoribonuclease L-PSP, putative 18.000 17.500 0.095 6.263 0.1169 0.5847 14.1651 9.500 18.7328 9.500 18.500 18.500 26.4031 17.5000 SGO_0954 ATP-binding protein 5.500 8.500 0.411 4.555 0.0759 0.3630 5.7239 6.500 6.500 9.2768 8.5000 SGO_0955 transporter 20.500 24.500 5.518 21.3345 24.5000 SGO_0957 hypothetical protein SGO_0957 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 45

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 45 8.000 4.000 0.527 4.866 0.0492 0.2185 9.6919 6.500 8.3257 6.500 5.000 5.000 7.1360 4.0000 SGO_0959 copper homeostasis protein CutC 5.000 8.500 3.776 5.2035 8.5000 SGO_0961 ABC transporter, permease/ATP-binding protein 2.000 1.500 1.841 2.0814 1.5000 SGO_0962 ABC transporter, permease/ATP-binding protein 31.000 36.000 6.093 32.2620 36.0000 SGO_0966 hsa; streptococcal hemagglutinin 3.500 4.000 2.934 3.6425 4.0000 SGO_0969 nss; nucleotide sugar synthetase-like protein 2.500 3.500 2.609 2.6018 3.5000 SGO_0971 asp1; accessory secretory protein 3.000 1.585 3.0000 SGO_0972 asp2; accessory sescretory protein 4.000 5.500 3.272 4.1628 5.5000 SGO_0975 gtaA; glycosyl transferase, group 1 SP1758 5.000 4.500 3.279 5.2035 4.5000 SGO_0979 degV family protein 1.500 0.643 1.5611 SGO_0980 transcriptional regulator, TetR family domain protein 5.500 10.500 -0.793 4.371 0.0772 0.3697 4.4732 3.000 5.7239 3.000 10.5000 SGO_0981 comE operon protein 2 family 121.500 144.000 -2.052 8.392 0.0004 0.0003 29.0757 19.500 126.4462 19.500 25.500 25.500 36.3934 144.0000 SGO_0982 amino acid ABC transporter, amino acidbinding protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 46

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 46 25.500 29.000 -3.281 5.868 0.0096 0.0314 26.5381 2.000 2.000 2.8544 29.0000 SGO_0983 amino acid ABC transporter, ATP-binding protein SP0709 10.000 5.500 3.992 10.4071 5.5000 SGO_0986 hypothetical protein SGO_0986 48.000 44.500 0.274 7.714 0.0366 0.1563 48.4596 32.500 49.9541 32.500 47.000 47.000 67.0781 44.5000 SGO_0987 metK; S-adenosylmethionine synthetase 112.000 1.525 8.820 116.5595 235.000 235.000 335.3905 SGO_0991 hypothetical protein SGO_0991 2.098 3.000 3.000 4.2816 SGO_0993 GTP-binding protein HflX 2.000 4.500 0.996 4.243 0.0136 0.0479 5.2187 3.500 2.0814 3.500 5.000 5.000 7.1360 4.5000 SGO_0994 hypothetical protein SGO_0994 5.500 13.500 0.171 5.395 0.1330 0.6801 17.1472 11.500 5.7239 11.500 4.000 4.000 5.7088 13.5000 SGO_0995 metallo-beta-lactamase superfamily protein 5.000 5.000 3.351 5.2035 5.0000 SGO_0996 oxidoreductase, short-chain dehydrogenase/reductase family 12.000 15.000 -1.025 5.451 0.0317 0.1312 12.6740 8.500 12.4885 8.500 2.500 2.500 3.5680 15.0000 SGO_0997 hypothetical protein SGO_0997 2.500 1.958 4.529 0.0329 0.1379 11.9285 8.000 2.6018 8.000 6.000 6.000 8.5632 SGO_1000 recJ; single-stranded-DNA-specific exonuclease RecJ 42.500 31.000 1.111 7.883 0.0025 0.0058 72.3166 48.500 44.2302 48.500 62.000 62.000 88.4860 31.0000 SGO_1001 apt; adenine phosphoribosyltransferase 2.000 1.000 2.0000 SGO_1002 metA; homoserine O-succinyltransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 47

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 47 11.500 9.500 0.078 5.464 0.1208 0.6096 12.6740 8.500 11.9682 8.500 7.000 7.000 9.9904 9.5000 SGO_1003 DNA replication protein DnaD 4.000 1.083 4.433 0.0635 0.2929 11.1830 7.500 7.500 4.500 4.500 6.4224 4.0000 SGO_1004 glutathione S-transferase family protein 5.500 7.500 0.994 5.306 0.0039 0.0102 14.9106 10.000 5.7239 10.000 8.000 8.000 11.4175 7.5000 SGO_1005 Bcl-2 family protein 2.500 0.787 3.497 0.0576 0.2617 5.2187 3.500 3.500 2.500 2.500 3.5680 2.5000 SGO_1006 conserved hypothetical protein TIGR00486 2.854 2.2366 1.500 1.500 3.500 3.500 4.9952 SGO_1007 oxidoreductase, DadA family protein SP1608 57.000 68.500 1.501 8.934 0.0003 0.0002 188.6196 126.500 59.3204 126.500 121.000 121.000 172.6904 68.5000 SGO_1009 rfbA-1; glucose-1-phosphate thymidylyltransferase 28.000 29.500 0.919 7.414 0.0033 0.0084 63.3702 42.500 29.1399 42.500 34.000 34.000 48.5246 29.5000 SGO_1010 rmlC; dTDP-4-keto-6-deoxyglucose-3,5epimerase 35.000 58.000 1.150 8.223 0.0022 0.0049 108.8477 73.000 36.4248 73.000 67.000 67.000 95.6220 58.0000 SGO_1011 rfbB-1; dTDP-glucose 4,6-dehydratase 72.000 72.000 0.993 8.779 0.0001 0.0000 146.8698 98.500 74.9311 98.500 102.000 102.000 145.5737 72.0000 SGO_1012 galE-1; UDP-glucose 4-epimerase 34.500 28.500 -2.901 6.102 0.0214 0.0839 35.9045 3.000 3.000 4.2816 28.5000 SGO_1013 Glycosyltransferase involved in cell wall biogenesis 17.000 26.000 -1.298 5.936 0.0047 0.0130 9.6919 6.500 17.6921 6.500 5.500 5.500 7.8496 26.0000 SGO_1016 putative glycosyltransferase 5.500 7.000 3.669 5.7239 7.0000 SGO_1018 hypothetical protein SGO_1018 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 48

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 48 39.500 40.000 -2.504 6.579 0.0001 0.0000 5.9643 4.000 41.1080 4.000 6.000 6.000 8.5632 40.0000 SGO_1019 glycosyl transferase 37.500 37.500 0.660 7.639 0.0101 0.0334 50.6962 34.000 39.0266 34.000 50.500 50.500 72.0733 37.5000 SGO_1020 rfbD; dTDP-4-dehydrorhamnose reductase 21.000 27.500 5.625 21.8549 27.5000 SGO_1021 rgpA; rhamnosyltransferase, putative 18.500 29.000 5.593 19.2531 29.0000 SGO_1022 rhamnosyltransferase 31.500 50.000 -0.897 6.994 0.0133 0.0467 27.5847 18.500 32.7824 18.500 12.000 12.000 17.1263 50.0000 SGO_1024 putative polysaccharide ABC transporter 21.500 30.000 -0.018 6.700 0.1714 0.9072 22.3660 15.000 22.3753 15.000 20.500 20.500 29.2575 30.0000 SGO_1025 rgp; glycosyltransferase 77.000 134.500 -2.178 8.025 0.0046 0.0126 22.3660 15.000 80.1346 15.000 16.500 16.500 23.5487 134.5000 SGO_1026 rhamnosyltransferase 22.500 30.000 5.739 23.4160 30.0000 SGO_1027 hypothetical protein SGO_1027 6.500 10.500 4.110 6.7646 10.5000 SGO_1028 hypothetical protein SGO_1028 17.500 4.129 17.5000 SGO_1030 hypothetical protein SGO_1030 13.500 13.000 -0.051 5.735 0.1206 0.6069 11.9285 8.000 14.0496 8.000 10.000 10.000 14.2719 13.0000 SGO_1031 cmk; cytidylate kinase 12.000 13.500 -0.408 5.564 0.0853 0.4151 14.9106 10.000 12.4885 10.000 4.500 4.500 6.4224 13.5000 SGO_1032 infC; translation initiation factor IF-3 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 49

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 49 36.000 78.500 6.858 37.4655 78.5000 SGO_1033 rpmI; ribosomal protein L35 158.000 165.500 1.019 9.964 0.0000 0.0000 331.0162 222.000 164.4321 222.000 236.500 236.500 337.5312 165.5000 SGO_1034 rplT; ribosomal protein L20 7.000 13.000 0.688 5.690 0.0127 0.0439 15.6562 10.500 7.2850 10.500 11.000 11.000 15.6991 13.0000 SGO_1035 gloA; lactoylglutathione lyase 34.500 50.000 -1.212 6.966 0.0083 0.0259 12.6740 8.500 35.9045 8.500 18.500 18.500 26.4031 50.0000 SGO_1036 amino acid ABC transporter, ATP-binding protein SP1242 23.500 25.000 -0.955 6.229 0.0002 0.0001 13.4196 9.000 24.4567 9.000 8.500 8.500 12.1311 25.0000 SGO_1037 glutamine ABC transporter permease and substrate binding protein 4.000 8.500 0.889 5.145 0.0229 0.0908 14.1651 9.500 4.1628 9.500 6.000 6.000 8.5632 8.5000 SGO_1038 uvrB; excinuclease ABC, B subunit 4.000 5.500 3.272 4.1628 5.5000 SGO_1039 hypothetical protein SGO_1039 5.500 0.719 4.572 0.0490 0.2172 10.4374 7.000 7.000 5.500 5.500 7.8496 5.5000 SGO_1041 hypothetical protein SGO_1041 1.500 2.045 3.796 0.0095 0.0310 5.9643 4.000 4.000 4.500 4.500 6.4224 1.5000 SGO_1044 MutT/nudix family protein 14.500 22.500 0.514 6.503 0.0197 0.0765 23.1115 15.500 15.0903 15.500 21.000 21.000 29.9711 22.5000 SGO_1047 hypothetical protein SGO_1047 1.500 6.500 2.154 5.188 0.0027 0.0065 13.4196 9.000 1.5611 9.000 10.500 10.500 14.9855 6.5000 SGO_1049 tRNA pseudouridine synthase B 2.500 1.530 4.146 0.0605 0.2783 5.2187 3.500 3.500 7.000 7.000 9.9904 2.5000 SGO_1050 ribF; riboflavin biosynthesis protein RibF .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 50

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 50 3.576 11.9285 8.000 8.000 SGO_1051 negative regulator of proteolysis 4.500 3.500 0.144 3.662 0.1254 0.6353 4.4732 3.000 4.6832 3.000 3.5000 SGO_1054 NOL1/NOP2/sun family protein 41.000 51.500 -1.995 6.887 0.0009 0.0014 14.9106 10.000 42.6691 10.000 6.500 6.500 9.2768 51.5000 SGO_1055 phosphate ABC transporter, phosphatebinding protein 6.000 2.585 6.0000 SGO_1057 pstA; phosphate ABC transporter, permease protein PstA 31.500 36.000 -1.604 6.514 0.0002 0.0001 11.1830 7.500 32.7824 7.500 8.000 8.000 11.4175 36.0000 SGO_1058 pstB; Phosphate import ATP-binding protein pstB 2 (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) 23.000 23.500 0.545 6.866 0.0004 0.0004 33.5489 22.500 23.9363 22.500 25.000 25.000 35.6798 23.5000 SGO_1059 pstB; Phosphate import ATP-binding protein pstB 1 (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) 52.000 65.500 -0.234 7.789 0.0257 0.1035 54.4238 36.500 54.1169 36.500 33.000 33.000 47.0974 65.5000 SGO_1060 phosphate transport system regulatory protein 29.000 28.500 -0.937 6.481 0.0002 0.0001 15.6562 10.500 30.1806 10.500 10.500 10.500 14.9855 28.5000 SGO_1065 hypothetical protein SGO_1065 22.500 31.500 -1.426 6.237 0.0027 0.0065 11.9285 8.000 23.4160 8.000 6.000 6.000 8.5632 31.5000 SGO_1066 hypothetical protein SGO_1066 3.500 1.807 3.5000 SGO_1067 hypothetical protein SGO_1067 84.000 74.000 0.674 8.712 0.0038 0.0100 141.6511 95.000 87.4196 95.000 81.500 81.500 116.3163 74.0000 SGO_1069 membrane alanyl aminopeptidase 2.500 1.254 3.081 5.9643 4.000 4.000 2.5000 SGO_1072 ciaR; Transcriptional regulatory protein CiaR .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 51

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 51 15.000 17.500 -2.149 5.203 0.0133 0.0468 3.7277 2.500 15.6106 2.500 17.5000 SGO_1073 Sensor protein CiaH 4.000 0.098 3.050 3.000 3.000 4.2816 4.0000 SGO_1075 alpha-amylase precursor 11.500 13.500 -0.543 5.427 0.0040 0.0106 9.6919 6.500 11.9682 6.500 5.500 5.500 7.8496 13.5000 SGO_1077 coaA; pantothenate kinase 4.180 6.7098 4.500 4.500 8.000 8.000 11.4175 SGO_1078 methyltransferase domain protein 27.500 42.500 -0.010 7.139 0.1705 0.8989 30.5668 20.500 28.6195 20.500 27.500 27.500 39.2478 42.5000 SGO_1079 pdp; pyrimidine-nucleoside phosphorylase 80.500 73.000 0.227 8.409 0.0119 0.0406 95.4281 64.000 83.7771 64.000 61.500 61.500 87.7724 73.0000 SGO_1080 deoC; deoxyribose-phosphate aldolase 3.500 9.000 -0.569 4.373 0.0588 0.2694 5.2187 3.500 3.6425 3.500 2.000 2.000 2.8544 9.0000 SGO_1081 cdd; cytidine deaminase 2606.500 2801.500 -0.805 13.082 0.0002 0.0001 1529.8314 1026.000 2712.6096 1026.000 1141.000 1141.000 1628.4277 2801.5000 SGO_1082 lipoprotein 8.625 222.9140 149.500 149.500 120.500 120.500 171.9768 SGO_1083 sugar ABC transporter, ATP-binding protein SP0846 2.000 4.500 0.884 4.195 0.0275 0.1112 7.4553 5.000 2.0814 5.000 3.000 3.000 4.2816 4.5000 SGO_1088 transcription regulator, LysR family 10.500 16.000 -0.245 5.633 0.0727 0.3447 13.4196 9.000 10.9275 9.000 6.500 6.500 9.2768 16.0000 SGO_1090 pseudouridine synthase, RluA family 1.500 2.500 2.022 1.5611 2.5000 SGO_1091 hypothetical protein SGO_1091 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 52

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 52 49.500 58.500 3.057 10.001 0.0001 0.0000 439.8638 295.000 51.5151 295.000 332.500 332.500 474.5418 58.5000 SGO_1096 butA; acetoin dehydrogenase 2.000 1.000 2.0000 SGO_1097 proB; glutamate 5-kinase 3.500 2.384 5.365 0.0434 0.1888 14.1651 9.500 9.500 16.500 16.500 23.5487 3.5000 SGO_1098 proA; gamma-glutamyl phosphate reductase 2.500 1.322 2.5000 SGO_1099 proC; pyrroline-5-carboxylate reductase 14.000 3.807 14.0000 SGO_1100 phnA; alkylphosphonate utilization operon protein PhnA 9.500 5.500 3.944 9.8867 5.5000 SGO_1103 carA; carbamoyl-phosphate synthase, small subunit 9.500 9.500 4.277 9.8867 9.5000 SGO_1104 carB; carbamoyl-phosphate synthase, large subunit 16.500 10.500 -0.775 5.151 0.0690 0.3237 17.1717 5.500 5.500 7.8496 10.5000 SGO_1107 PyrR bifunctional protein 66.500 81.500 -0.059 8.205 0.0928 0.4547 70.0800 47.000 69.2072 47.000 52.000 52.000 74.2141 81.5000 SGO_1109 pyrB; aspartate carbamoyltransferase 33.000 36.500 6.147 34.3434 36.5000 SGO_1110 surface antigen SCP-like domain 45.500 61.000 -2.353 7.016 0.0010 0.0016 9.6919 6.500 47.3523 6.500 8.000 8.000 11.4175 61.0000 SGO_1111 fruR; phosphotransferase system repressor 58.000 62.500 -1.735 7.327 0.0004 0.0004 14.9106 10.000 60.3612 10.000 16.000 16.000 22.8351 62.5000 SGO_1112 fruB; 1-phosphofructokinase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 53

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 53 1053.000 1124.000 -3.955 11.208 0.0000 0.0000 86.4817 58.000 1095.8672 58.000 41.500 41.500 59.2285 1124.0000 SGO_1113 fruA; PTS system, fructose specific IIABC components 46.500 44.500 -1.137 7.080 0.0005 0.0005 23.1115 15.500 48.3930 15.500 13.500 13.500 19.2671 44.5000 SGO_1114 Protein of unknown function (DUF1149) superfamily 3.500 1.302 4.389 0.0357 0.1516 7.4553 5.000 5.000 7.000 7.000 9.9904 3.5000 SGO_1115 DegV family protein 6.500 8.500 2.860 6.972 0.0002 0.0001 58.1515 39.000 6.7646 39.000 36.500 36.500 52.0926 8.5000 SGO_1116 dapB; dihydrodipicolinate reductase 3.130 4.4732 3.000 3.000 3.000 3.000 4.2816 SGO_1117 pcnA; polynucleotide adenylyltransferase 5.000 -0.081 3.858 0.1344 0.6881 5.2187 3.500 3.500 3.000 3.000 4.2816 5.0000 SGO_1118 ABC transporter, ATP-binding protein SP1553 2.500 1.500 2.036 2.6018 1.5000 SGO_1119 Abi-alpha protein, putative 48.000 62.000 1.050 8.420 0.0004 0.0005 116.3030 78.000 49.9541 78.000 80.000 80.000 114.1755 62.0000 SGO_1120 guaA; GMP synthase 7.000 -0.972 3.402 2.500 2.500 3.5680 7.0000 SGO_1121 transcription regulator, GntR family 35.000 38.000 1.244 7.970 0.0002 0.0001 84.9906 57.000 36.4248 57.000 64.000 64.000 91.3404 38.0000 SGO_1123 ffh; signal recognition particle protein 3.500 4.500 3.025 3.6425 4.5000 SGO_1124 cell surface hydrolase 4.000 2.000 4.0000 SGO_1128 bacteriocin-associated integral membrane protein subfamily .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 54

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 54 28.000 26.500 -0.806 6.457 0.0025 0.0058 18.6383 12.500 29.1399 12.500 9.500 9.500 13.5583 26.5000 SGO_1129 lplA; lipoate protein ligase A 109.000 110.000 -0.666 8.509 0.0002 0.0001 72.3166 48.500 113.4373 48.500 48.000 48.000 68.5053 110.0000 SGO_1130 dihydrolipoamide dehydrogenase 32.000 34.000 -0.208 6.974 0.0108 0.0364 31.3123 21.000 33.3027 21.000 19.000 19.000 27.1167 34.0000 SGO_1131 sucB; dihydrolipoamide S-acetyltransferase 15.000 25.000 -0.631 6.047 0.0181 0.0688 12.6740 8.500 15.6106 8.500 9.000 9.000 12.8447 25.0000 SGO_1132 acetoin dehydrogenase 35.000 28.000 -0.813 6.658 0.0048 0.0135 20.1294 13.500 36.4248 13.500 11.500 11.500 16.4127 28.0000 SGO_1133 acoA; acetoin dehydrogenase 4.500 6.500 -0.566 3.898 0.0626 0.2887 3.7277 2.500 4.6832 2.500 6.5000 SGO_1134 hypothetical protein SGO_1134 15.000 21.500 1.267 6.969 0.0006 0.0007 43.2408 29.000 15.6106 29.000 31.500 31.500 44.9566 21.5000 SGO_1139 GTP-binding protein 85.500 76.000 0.482 8.625 0.0017 0.0033 115.5574 77.500 88.9807 77.500 80.000 80.000 114.1755 76.0000 SGO_1140 clpX; ATP-dependent Clp protease, ATPbinding subunit ClpX 4.500 7.000 0.710 4.941 0.0144 0.0518 11.1830 7.500 4.6832 7.500 5.500 5.500 7.8496 7.0000 SGO_1141 folA; dihydrofolate reductase 5.500 10.000 1.268 5.705 0.0018 0.0037 17.8928 12.000 5.7239 12.000 13.000 13.000 18.5535 10.0000 SGO_1143 thyA; thymidylate synthase 66.500 76.500 1.912 9.437 0.0000 0.0000 274.3557 184.000 69.2072 184.000 191.500 191.500 273.3075 76.5000 SGO_1144 glcK; glucokinase 6.000 7.500 3.781 6.2443 7.5000 SGO_1145 cell surface hydrolase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 55

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 55 164.000 147.500 8.314 170.6764 147.5000 SGO_1148 cshB; surface-associated protein CshB 5.500 8.500 3.830 5.7239 8.5000 SGO_1149 Pneumococcal vaccine antigen A-like protein 7.000 1.321 5.394 0.0177 0.0671 18.6383 12.500 12.500 11.500 11.500 16.4127 7.0000 SGO_1150 hypothetical protein SGO_1150 68.500 77.500 1.725 9.323 0.0000 0.0000 246.7711 165.500 71.2886 165.500 171.500 171.500 244.7637 77.5000 SGO_1151 glyA; serine hydroxymethyltransferase 47.500 32.500 0.348 7.523 0.0322 0.1340 49.9506 33.500 49.4337 33.500 36.500 36.500 52.0926 32.5000 SGO_1154 prfA; peptide chain release factor 1 9.500 21.000 0.258 6.054 0.1207 0.6079 13.4196 9.000 9.8867 9.000 15.500 15.500 22.1215 21.0000 SGO_1155 tdk; thymidine kinase 2.000 1.630 3.910 0.0590 0.2706 4.4732 3.000 3.000 6.000 6.000 8.5632 2.0000 SGO_1159 guaC; guanosine monophosphate reductase SGO_1163 Iron permease FTR1 family 4.000 5.500 3.272 4.1628 5.5000 SGO_1166 voltage-gated chloride channel family protein 54.000 62.500 0.927 8.426 0.0002 0.0001 113.3208 76.000 56.1983 76.000 78.500 78.500 112.0347 62.5000 SGO_1167 nox; NADH oxidase 37.500 34.500 0.631 7.557 0.0079 0.0244 65.6068 44.000 39.0266 44.000 34.500 34.500 49.2382 34.5000 SGO_1169 NADPH-dependent FMN reductase 125.500 129.000 -0.581 8.759 0.0002 0.0001 89.4638 60.000 130.6091 60.000 59.000 59.000 84.2044 129.0000 SGO_1170 NADPH-dependent FMN reductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 56

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 56 89.000 87.000 -4.040 7.574 0.0001 0.0000 5.2187 3.500 92.6232 3.500 4.000 4.000 5.7088 87.0000 SGO_1171 thioredoxin family protein 4.500 6.000 3.417 4.6832 6.0000 SGO_1174 histidine kinase 1.500 0.585 1.5000 SGO_1176 peptide methionine sulfoxide reductase-like protein 2.000 1.058 2.0814 SGO_1182 LPXTG cell wall surface protein 3.500 7.000 3.412 3.6425 7.0000 SGO_1184 GdmH 7.000 5.000 1.029 5.215 0.0048 0.0134 14.1651 9.500 7.2850 9.500 7.500 7.500 10.7040 5.0000 SGO_1185 acetyltransferase, GNAT family 27.500 24.000 5.718 28.6195 24.0000 SGO_1186 ABC transporter, permease/ATP-binding protein 33.500 44.000 6.301 34.8638 44.0000 SGO_1187 ABC transporter, permease/ATP-binding protein 292.500 260.500 -3.706 9.249 0.0003 0.0003 18.6383 12.500 304.4076 12.500 17.500 17.500 24.9759 260.5000 SGO_1189 lipoprotein, putative 789.500 718.000 0.125 11.651 0.0327 0.1371 865.5625 580.500 821.6402 580.500 568.000 568.000 810.6459 718.0000 SGO_1191 rplL; ribosomal protein L7/L12 144.500 163.500 0.701 9.702 0.0111 0.0375 210.2400 141.000 150.3825 141.000 216.500 216.500 308.9874 163.5000 SGO_1192 BL5; 50S ribosomal protein L10 13.500 15.000 0.996 6.452 0.0037 0.0096 33.5489 22.500 14.0496 22.500 17.500 17.500 24.9759 15.0000 SGO_1193 gid; Glucose inhibited division protein A .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 57

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 57 4.500 2.227 4.6832 SGO_1196 satD; SatD-like protein 79.500 103.500 -1.218 8.057 0.0018 0.0038 35.7855 24.000 82.7364 24.000 31.000 31.000 44.2430 103.5000 SGO_1197 topA; DNA topoisomerase I 134.000 118.000 -0.387 8.825 0.0055 0.0161 99.1557 66.500 139.4551 66.500 68.000 68.000 97.0492 118.0000 SGO_1198 DNA processing Smf protein 3.500 4.000 -0.356 3.409 0.0322 0.1336 2.9821 2.000 3.6425 2.000 4.0000 SGO_1199 acetyltransferase, CysE/LacA/LpxA/NodL family 9.000 10.000 0.592 5.619 0.0154 0.0563 11.9285 8.000 9.3664 8.000 12.500 12.500 17.8399 10.0000 SGO_1202 GTP-binding protein 15.500 20.500 0.746 6.612 0.0027 0.0066 28.3302 19.000 16.1310 19.000 23.000 23.000 32.8254 20.5000 SGO_1203 anaerobic ribonucleotide reductase 7.000 3.500 0.892 4.892 0.0147 0.0533 8.2009 5.500 7.2850 5.500 7.500 7.500 10.7040 3.5000 SGO_1205 dapA; dihydrodipicolinate synthase 42.500 50.000 -0.353 7.392 0.0040 0.0107 38.0221 25.500 44.2302 25.500 25.000 25.000 35.6798 50.0000 SGO_1206 asd; aspartate-semialdehyde dehydrogenase 4.000 8.000 3.604 4.1628 8.0000 SGO_1208 Hypothetical FAD-dependent oxidoreductase, putative 11.500 11.000 0.250 5.689 0.0723 0.3419 18.6383 12.500 11.9682 12.500 7.000 7.000 9.9904 11.0000 SGO_1210 fhs-1; formate--tetrahydrofolate ligase 16.000 29.000 -2.296 5.647 0.0472 0.2066 4.4732 3.000 16.6514 3.000 29.0000 SGO_1213 coaC; phosphopantothenoylcysteine decarboxylase 190.000 215.000 0.815 10.153 0.0002 0.0001 362.3285 243.000 197.7348 243.000 254.500 254.500 363.2207 215.0000 SGO_1215 manB; phosphomannomutase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 58

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 58 18.500 14.500 1.790 7.228 0.0010 0.0016 64.1157 43.000 19.2531 43.000 36.500 36.500 52.0926 14.5000 SGO_1216 bta; Possible bacteriocin transport accessory protein 44.000 54.000 0.089 7.683 0.0652 0.3035 53.6783 36.000 45.7912 36.000 36.500 36.500 52.0926 54.0000 SGO_1219 pta; phosphate acetyltransferase 62.000 77.000 7.145 64.5240 77.0000 SGO_1221 ppnK; Probable inorganic polyphosphate/ATP-NAD kinase 7.000 7.000 -0.323 4.321 0.0170 0.0631 7.2850 4.000 4.000 5.7088 7.0000 SGO_1222 GTP pyrophosphokinase-like protein 89.500 89.000 0.647 8.869 0.0008 0.0012 149.8519 100.500 93.1435 100.500 95.000 95.000 135.5834 89.0000 SGO_1224 Ribose-phosphate pyrophosphokinase 2 7.500 8.500 0.546 5.333 0.0081 0.0252 10.4374 7.000 7.8053 7.000 9.500 9.500 13.5583 8.5000 SGO_1225 pyridoxal-phosphate dependent aminotransferase 13.500 24.500 0.436 6.473 0.0366 0.1558 23.8570 16.000 14.0496 16.000 18.500 18.500 26.4031 24.5000 SGO_1226 hypothetical protein SGO_1226 6.500 4.500 0.534 4.773 0.0171 0.0636 8.9464 6.000 6.7646 6.000 5.000 5.000 7.1360 4.5000 SGO_1228 DNA-binding protein BH0551 33.500 30.500 -2.690 6.240 0.0003 0.0003 5.9643 4.000 34.8638 4.000 3.000 3.000 4.2816 30.5000 SGO_1230 srtA; sortase A 90.000 112.000 -1.323 8.182 0.0024 0.0054 31.3123 21.000 93.6639 21.000 37.500 37.500 53.5198 112.0000 SGO_1231 gyrA; DNA gyrase, A subunit 65.000 85.500 2.941 10.367 0.0001 0.0000 594.1889 398.500 67.6461 398.500 402.000 402.000 573.7318 85.5000 SGO_1232 L-lactate dehydrogenase 359.500 444.000 0.414 10.895 0.0030 0.0073 549.4570 368.500 374.1351 368.500 376.000 376.000 536.6247 444.0000 SGO_1234 rpsA; 30S ribosomal protein S1 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 59

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 59 17.000 15.000 0.373 6.228 0.0055 0.0159 20.1294 13.500 17.6921 13.500 15.500 15.500 22.1215 15.0000 SGO_1237 hypothetical protein SGO_1237 35.000 32.000 0.021 7.106 0.1464 0.7601 35.0400 23.500 36.4248 23.500 24.000 24.000 34.2526 32.0000 SGO_1238 ilvE; branched-chain amino acid aminotransferase 35.500 40.500 -1.117 6.822 0.0003 0.0003 17.1472 11.500 36.9452 11.500 13.000 13.000 18.5535 40.5000 SGO_1239 parC; DNA topoisomerase IV, A subunit 5.000 2.500 2.946 5.2035 2.5000 SGO_1241 aminoglycoside adenylyltransferase 72.500 63.000 -2.894 7.207 0.0175 0.0659 75.4514 6.500 6.500 9.2768 63.0000 SGO_1242 lipoprotein, putative 12.000 4.000 0.288 5.085 0.1646 0.8635 7.4553 5.000 12.4885 5.000 7.000 7.000 9.9904 4.0000 SGO_1244 hypothetical protein SGO_1244 17.000 23.000 -1.278 5.846 0.0026 0.0059 9.6919 6.500 17.6921 6.500 5.000 5.000 7.1360 23.0000 SGO_1245 parE; DNA topoisomerase IV, B subunit 8.500 6.500 3.940 8.8460 6.5000 SGO_1246 hypothetical protein SGO_1246 267.500 287.500 9.144 278.3898 287.5000 SGO_1247 5'-nucleotidase family protein 17.500 11.500 0.664 6.259 0.0221 0.0871 28.3302 19.000 18.2124 19.000 13.000 13.000 18.5535 11.5000 SGO_1248 pyrC; dihydroorotase 7.000 14.000 4.412 7.2850 14.0000 SGO_1250 ung; uracil-DNA glycosylase 2.000 1.500 1.841 2.0814 1.5000 SGO_1251 hypothetical protein SGO_1251 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 60

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 60 2.500 1.322 2.5000 SGO_1252 integral membrane protein, putative 17.500 25.000 0.695 6.813 0.0038 0.0099 32.8034 22.000 18.2124 22.000 25.500 25.500 36.3934 25.0000 SGO_1253 pyrE; orotate phosphoribosyltransferase 11.500 14.000 -1.011 5.018 0.0244 0.0978 11.9682 4.500 4.500 6.4224 14.0000 SGO_1254 pyrF; orotidine 5'-phosphate decarboxylase 2.000 5.000 -0.177 3.313 0.1403 0.7201 2.0814 2.000 2.000 2.8544 5.0000 SGO_1255 pyrd; dihydroorotate dehydrogenase B 6.000 9.500 0.296 5.116 0.0467 0.2042 8.9464 6.000 6.2443 6.000 7.000 7.000 9.9904 9.5000 SGO_1257 probable transcriptional regulator (LysR family) 4.000 9.000 3.718 4.1628 9.0000 SGO_1258 NAD-dependent deacetylase (Regulatory protein SIR2-like protein) 69.000 70.000 0.150 8.225 0.0058 0.0171 76.0443 51.000 71.8090 51.000 57.000 57.000 81.3500 70.0000 SGO_1260 deoD; purine nucleoside phosphorylase 3.500 1.807 3.5000 SGO_1261 glutamine amidotransferase, class I 106.500 95.500 0.330 8.861 0.0049 0.0137 125.2494 84.000 110.8356 84.000 93.500 93.500 133.4426 95.5000 SGO_1263 purine nucleoside phosphorylase I, inosine and guanosine-specific 220.000 282.000 0.019 10.003 0.1710 0.9034 264.6638 177.500 228.9561 177.500 175.500 175.500 250.4724 282.0000 SGO_1264 deoB; phosphopentomutase 26.000 54.000 0.958 7.844 0.0077 0.0238 71.5711 48.000 27.0585 48.000 54.000 54.000 77.0684 54.0000 SGO_1265 rpiA; ribose 5-phosphate isomerase 12.500 13.000 0.882 6.214 0.0025 0.0058 26.8391 18.000 13.0089 18.000 15.000 15.000 21.4079 13.0000 SGO_1266 trmE; tRNA modification GTPase TrmE .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 61

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 61 22.000 19.500 -1.825 5.596 0.0185 0.0707 5.9643 4.000 22.8956 4.000 19.5000 SGO_1267 thioredoxin family protein 40.000 33.500 1.903 8.469 0.0001 0.0000 138.6689 93.000 41.6284 93.000 98.500 98.500 140.5786 33.5000 SGO_1273 rpoD; RNA polymerase sigma factor 2.500 6.000 0.563 4.342 0.0490 0.2164 5.9643 4.000 2.6018 4.000 4.000 4.000 5.7088 6.0000 SGO_1274 dnaG; DNA primase 49.500 54.000 0.281 7.872 0.0142 0.0507 58.1515 39.000 51.5151 39.000 49.500 49.500 70.6461 54.0000 SGO_1276 rpsU; ribosomal protein S21 5.000 6.500 3.549 5.2035 6.5000 SGO_1280 putative membrane-associated Zndependent protease 5.500 7.500 0.982 5.300 0.0047 0.0128 11.1830 7.500 5.7239 7.500 10.500 10.500 14.9855 7.5000 SGO_1281 penicillinase repressor, putative 68.500 64.500 0.742 8.503 0.0003 0.0003 115.5574 77.500 71.2886 77.500 78.000 78.000 111.3211 64.5000 SGO_1283 oxidoreductase 15.500 14.000 0.132 6.048 0.1080 0.5381 25.3481 17.000 16.1310 17.000 7.500 7.500 10.7040 14.0000 SGO_1284 thioredoxin-disulfide reductase 9.000 13.000 4.483 9.3664 13.0000 SGO_1290 ABC transporter, permease/ATP-binding protein 4.000 4.500 3.115 4.1628 4.5000 SGO_1291 ABC transporter, permease/ATP-binding protein SP1358 44.500 50.000 0.430 7.822 0.0034 0.0085 69.3345 46.500 46.3116 46.500 42.500 42.500 60.6557 50.0000 SGO_1293 asnS; asparaginyl-tRNA synthetase 12.000 13.500 0.992 6.280 0.0004 0.0005 24.6026 16.500 12.4885 16.500 19.000 19.000 27.1167 13.5000 SGO_1297 aspC; aspartate aminotransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 62

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 62 6.000 4.500 3.425 6.2443 4.5000 SGO_1298 hypothetical protein SGO_1298 21.500 23.500 -0.420 6.325 0.0004 0.0004 17.1472 11.500 22.3753 11.500 12.000 12.000 17.1263 23.5000 SGO_1305 substrate-binding protein MsmE 7.000 6.000 3.727 7.558 0.0001 0.0000 89.4638 60.000 7.2850 60.000 60.000 60.000 85.6316 6.0000 SGO_1312 pepT; peptidase T 3.500 1.807 3.5000 SGO_1314 metal binding lipoprotein 3.500 0.030 3.428 0.1661 0.8725 2.9821 2.000 2.000 3.000 3.000 4.2816 3.5000 SGO_1315 trmD; tRNA (guanine-N1)-methyltransferase 7.000 5.000 0.266 4.747 0.0494 0.2206 6.7098 4.500 7.2850 4.500 5.500 5.500 7.8496 5.0000 SGO_1316 16S rRNA processing protein RimM 42.500 35.000 0.691 7.691 0.0033 0.0082 58.8970 39.500 44.2302 39.500 48.000 48.000 68.5053 35.0000 SGO_1323 rpsP; ribosomal protein S16 20.500 27.000 5.595 21.3345 27.0000 SGO_1324 hypothetical protein SGO_1324 13.000 21.500 0.123 6.174 0.1330 0.6792 17.8928 12.000 13.5292 12.000 13.500 13.500 19.2671 21.5000 SGO_1327 HAD-superfamily subfamily IIA hydrolase, TIGR01457 3.000 1.585 3.0000 SGO_1328 hypothetical protein SGO_1328 4.000 9.500 3.772 4.1628 9.5000 SGO_1330 transporter 3.500 1.807 3.5000 SGO_1331 HlyB/MsbA family ABC transporter .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 63

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 63 17.000 17.500 0.050 6.164 0.0802 0.3879 19.3838 13.000 17.6921 13.000 12.000 12.000 17.1263 17.5000 SGO_1336 pcrA; ATP-dependent DNA helicase PcrA 3.000 1.585 3.0000 SGO_1337 cation efflux family protein 19.500 27.000 -3.036 5.648 0.0253 0.1018 20.2938 2.000 2.000 2.8544 27.0000 SGO_1338 Signal peptidase I 551.000 600.000 1.066 11.826 0.0001 0.0001 1198.0698 803.500 573.4310 803.500 882.500 882.500 1259.4982 600.0000 SGO_1339 pyk; pyruvate kinase 213.500 213.500 0.758 10.195 0.0001 0.0000 366.8017 246.000 222.1915 246.000 259.000 259.000 369.6431 213.5000 SGO_1340 Phosphofructokinase 9.500 9.000 -1.076 4.546 0.0154 0.0566 4.4732 3.000 9.8867 3.000 9.0000 SGO_1341 dnaE; DNA-directed DNA polymerase III alpha chain 423.500 429.000 -1.281 10.262 0.0001 0.0001 190.8562 128.000 440.7405 128.000 117.500 117.500 167.6952 429.0000 SGO_1342 ABC transporter, ATP-binding protein SP1715 19.000 21.000 -1.773 5.547 0.0085 0.0271 5.9643 4.000 19.7735 4.000 21.0000 SGO_1343 ABC transporter, ATP-binding protein SP1715 39.500 30.000 6.152 41.1080 30.0000 SGO_1347 membrane associated lipoprotein 4.500 6.500 3.483 4.6832 6.5000 SGO_1355 lipoprotein, putative 3.000 4.000 2.832 3.1221 4.0000 SGO_1360 ABC transporter domain protein 6.500 2.700 6.5000 SGO_1361 ADP-ribosylhydrolase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 64

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 64 22.500 32.500 -0.053 6.770 0.1267 0.6436 26.0936 17.500 23.4160 17.500 19.000 19.000 27.1167 32.5000 SGO_1364 rumA-2; 23S rRNA (uracil-5-)methyltransferase RumA 33.500 34.500 -3.071 6.289 0.0001 0.0001 5.9643 4.000 34.8638 4.000 2.000 2.000 2.8544 34.5000 SGO_1365 transcription regulator yrfE 3.719 7.4553 5.000 5.000 4.000 4.000 5.7088 SGO_1366 pheA; prephenate dehydratase 6.000 7.500 -0.645 4.492 0.0027 0.0065 4.4732 3.000 6.2443 3.000 3.000 3.000 4.2816 7.5000 SGO_1367 aroK; shikimate kinase 1.500 7.000 1.405 4.704 0.0175 0.0655 8.9464 6.000 1.5611 6.000 6.000 6.000 8.5632 7.0000 SGO_1368 aroA; 3-phosphoshikimate 1carboxyvinyltransferase 14.000 15.500 -0.018 5.905 0.1710 0.9038 13.4196 9.000 14.5699 9.000 11.500 11.500 16.4127 15.5000 SGO_1369 L-2-hydroxyisocaproate dehydrogenase 15.500 15.500 1.245 6.740 0.0010 0.0015 41.0043 27.500 16.1310 27.500 24.000 24.000 34.2526 15.5000 SGO_1370 Protein of unknown function (DUF964) superfamily 5.500 7.000 1.553 5.640 0.0003 0.0002 17.8928 12.000 5.7239 12.000 13.500 13.500 19.2671 7.0000 SGO_1372 aroC; chorismate synthase 5.500 10.000 0.379 5.146 0.0473 0.2080 9.6919 6.500 5.7239 6.500 7.000 7.000 9.9904 10.0000 SGO_1373 aroB; 3-dehydroquinate synthase 4.000 5.000 0.232 4.333 0.0655 0.3054 6.7098 4.500 4.1628 4.500 3.000 3.000 4.2816 5.0000 SGO_1374 aroE; shikimate 5-dehydrogenase 11.000 15.000 0.563 6.044 0.0214 0.0838 23.8570 16.000 11.4478 16.000 11.000 11.000 15.6991 15.0000 SGO_1375 aroD; 3-dehydroquinate dehydratase, type I 7.500 8.000 3.982 7.8053 8.0000 SGO_1376 Methyltransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 65

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 65 105.000 123.000 -2.205 8.142 0.0003 0.0002 24.6026 16.500 109.2745 16.500 18.000 18.000 25.6895 123.0000 SGO_1377 sulfatase 24.000 27.500 -0.506 6.495 0.0150 0.0546 14.9106 10.000 24.9770 10.000 16.000 16.000 22.8351 27.5000 SGO_1381 csn1; CRISPR-associated protein, Csn1 family 91.500 106.500 0.692 9.044 0.0016 0.0032 152.0885 102.000 95.2249 102.000 122.000 122.000 174.1176 106.5000 SGO_1383 rplS; ribosomal protein L19 3.000 1.156 4.082 0.0635 0.2939 8.9464 6.000 6.000 3.500 3.500 4.9952 3.0000 SGO_1386 chorismate mutase 9.500 18.500 4.827 9.8867 18.5000 SGO_1388 pulA-1; pullulanase, type I 18.000 24.000 5.417 18.7328 24.0000 SGO_1389 conserved hypothetical protein TIGR00147 20.000 19.500 -0.884 5.960 0.0007 0.0009 11.9285 8.000 20.8142 8.000 7.000 7.000 9.9904 19.5000 SGO_1390 ligA; DNA ligase, NAD-dependent 4.059 5.9643 4.000 4.000 7.500 7.500 10.7040 SGO_1394 hypothetical protein SGO_1394 20.000 33.000 0.382 6.937 0.0390 0.1674 38.0221 25.500 20.8142 25.500 21.500 21.500 30.6847 33.0000 SGO_1397 map; methionine aminopeptidase, type I 15.000 19.500 -1.419 5.593 0.0015 0.0030 7.4553 5.000 15.6106 5.000 4.000 4.000 5.7088 19.5000 SGO_1398 hypothetical protein SGO_1398 18.500 21.500 -0.556 6.098 0.0023 0.0052 14.9106 10.000 19.2531 10.000 9.000 9.000 12.8447 21.5000 SGO_1400 murA-2; UDP-N-acetylglucosamine 1carboxyvinyltransferase 1.835 2.500 2.500 3.5680 SGO_1405 hisA; phosphoribosylformimino-5aminoimidazole carboxamide ribotide isomerase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 66

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 66 7.000 15.500 -0.695 5.167 0.0323 0.1348 6.7098 4.500 7.2850 4.500 4.500 4.500 6.4224 15.5000 SGO_1413 first chain of major exonuclease RexA 5.500 9.500 -0.773 4.582 0.0176 0.0664 3.7277 2.500 5.7239 2.500 3.500 3.500 4.9952 9.5000 SGO_1414 rexB; putative exonuclease RexB 2.000 3.500 2.481 2.0814 3.5000 SGO_1415 LPXTG cell wall surface protein, X-prolyl dipeptidylaminopeptidase, putative 3.000 1.585 3.0000 SGO_1416 putative histidine kinase 2.973 5.500 5.500 7.8496 SGO_1417 response regulator protein 28.500 30.500 -0.278 6.778 0.0007 0.0009 25.3481 17.000 29.6602 17.000 17.000 17.000 24.2623 30.5000 SGO_1422 hypothetical protein SGO_1422 2771.500 2470.500 1.751 14.510 0.0001 0.0000 8798.0219 5900.500 2884.3267 5900.500 6433.500 6433.500 9181.8488 2470.5000 SGO_1426 eno; enolase 570.000 383.500 -1.476 10.366 0.0048 0.0136 175.2000 117.500 593.2045 117.500 117.500 117.500 167.6952 383.5000 SGO_1431 EzrA; Septation ring formation regulator ezrA 33.500 53.500 0.327 7.630 0.0534 0.2414 46.2230 31.000 34.8638 31.000 44.500 44.500 63.5101 53.5000 SGO_1432 gyrB; DNA gyrase, B subunit 2.500 1.419 4.025 0.0515 0.2317 5.2187 3.500 3.500 6.000 6.000 8.5632 2.5000 SGO_1434 thiJ; 4-methyl-5(beta-hydroxyethyl)thiazole monophosphate synthesis protein 5.500 7.000 3.669 5.7239 7.0000 SGO_1437 DnaQ family exonuclease/DinG family helicase, putative 55.500 55.500 -1.888 7.169 0.0001 0.0000 16.4017 11.000 57.7594 11.000 10.000 10.000 14.2719 55.5000 SGO_1439 ftsX; cell division protein FtsX .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 67 104.500 103.000 -1.350 8.204 0.0001 0.0000 40.2587 27.000 108.7542 27.000 30.000 30.000 42.8158 103.0000 SGO_1440 cell-division ATP-binding protein FtsE 14.500 13.000 0.860 6.328 0.0120 0.0413 20.1294 13.500 15.0903 13.500 22.500 22.500 32.1119 13.0000 SGO_1441 prfB; peptide chain release factor 2 15.000 26.000 0.547 6.652 0.0188 0.0726 27.5847 18.500 15.6106 18.500 22.000 22.000 31.3983 26.0000 SGO_1446 murF; UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase 23.500 25.000 0.694 7.021 0.0026 0.0059 43.9864 29.500 24.4567 29.500 25.500 25.500 36.3934 25.0000 SGO_1447 ddlA; D-Ala-D-Ala ligase 69.500 59.500 -2.494 7.277 0.0006 0.0007 11.1830 7.500 72.3293 7.500 8.500 8.500 12.1311 59.5000 SGO_1449 pbp2b; penicillin-binding protein 2B 5.000 19.500 0.312 5.654 0.1740 0.9221 15.6562 10.500 5.2035 10.500 7.000 7.000 9.9904 19.5000 SGO_1450 hypothetical protein SGO_1450 33.500 27.000 0.844 7.426 0.0011 0.0018 55.1694 37.000 34.8638 37.000 38.500 38.500 54.9469 27.0000 SGO_1451 frr; ribosome recycling factor 30.500 24.000 1.012 7.403 0.0077 0.0237 67.8434 45.500 31.7416 45.500 32.000 32.000 45.6702 24.0000 SGO_1452 pyrH; uridylate kinase 4.100 17.1472 11.500 11.500 SGO_1453 glycosyl transferase, family 8 SP1766 18.500 12.500 4.989 19.2531 12.5000 SGO_1454 amino acid permease family protein 129.500 117.000 1.547 9.960 0.0027 0.0064 310.1413 208.000 134.7719 208.000 304.000 304.000 433.8668 117.0000 SGO_1455 rplA; ribosomal protein L1 46.500 51.000 0.563 7.956 0.0124 0.0428 61.8791 41.500 48.3930 41.500 61.000 61.000 87.0588 51.0000 SGO_1456 rplK; ribosomal protein L11 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 68

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 68 71.500 47.000 -3.777 7.025 0.0025 0.0057 5.2187 3.500 74.4107 3.500 2.500 2.500 3.5680 47.0000 SGO_1458 aha1; cation-transporting ATPase yfgQ 1.161 2.2366 1.500 1.500 SGO_1459 glyoxylase family protein 57.500 45.000 -1.693 7.097 0.0017 0.0034 16.4017 11.000 59.8408 11.000 11.000 11.000 15.6991 45.0000 SGO_1460 DNA translocase ftsK 59.500 66.500 -1.582 7.422 0.0003 0.0002 23.8570 16.000 61.9222 16.000 13.500 13.500 19.2671 66.5000 SGO_1463 peptidyl-prolyl cis-trans isomerase 55.000 73.500 -1.171 7.558 0.0021 0.0045 29.8213 20.000 57.2390 20.000 19.500 19.500 27.8303 73.5000 SGO_1464 uncharacterized probable metal-binding protein 32.000 45.000 0.016 7.297 0.1771 0.9448 44.7319 30.000 33.3027 30.000 24.000 24.000 34.2526 45.0000 SGO_1465 ABC transporter, ATP-binding protein SP0770 18.500 13.500 -0.616 5.754 0.0142 0.0510 11.9285 8.000 19.2531 8.000 6.500 6.500 9.2768 13.5000 SGO_1466 MTA/SAH nucleosidase 3.000 1.585 3.0000 SGO_1468 MutT/nudix family protein 48.500 52.500 0.365 7.880 0.0011 0.0018 64.1157 43.000 50.4744 43.000 48.000 48.000 68.5053 52.5000 SGO_1469 glmU; UDP-N-acetylglucosamine pyrophosphorylase 4.000 0.998 4.385 0.0738 0.3513 11.1830 7.500 7.500 4.000 4.000 5.7088 4.0000 SGO_1472 acetyltransferase, GNAT family 8.000 14.500 4.513 8.3257 14.5000 SGO_1475 lipoprotein, putative 3.000 1.643 3.1221 SGO_1483 ABC transporter, permease protein, probable SP0913 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 69

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 69 3.135 5.2187 3.500 3.500 2.500 2.500 3.5680 SGO_1484 ABC transporter, ATP-binding protein 2.500 1.322 2.5000 SGO_1486 beta-galactosidase 41.000 52.500 -3.730 6.626 0.0185 0.0708 42.6691 2.500 2.500 3.5680 52.5000 SGO_1487 LPXTG cell wall surface protein, Cna protein B-type domain 47.000 59.000 -2.649 6.864 0.0185 0.0704 48.9134 6.000 6.000 8.5632 59.0000 SGO_1493 hypothetical protein SGO_1493 12.000 10.500 4.523 12.4885 10.5000 SGO_1495 putative transcriptional regulator 3.000 1.643 3.1221 SGO_1498 ABC transporter, permease protein, probable SP0913 7.000 6.500 3.785 7.2850 6.5000 SGO_1504 histidine kinase 20.500 19.000 5.334 21.3345 19.0000 SGO_1507 hypothetical protein SGO_1507 3.000 0.741 3.060 5.2187 3.500 3.1221 3.500 SGO_1512 lacG; 6-phospho-beta-galactosidase 3.500 1.807 3.5000 SGO_1513 lacE; PTS system, lactose-specific IIBC component 9.500 12.000 1.216 6.199 0.0050 0.0144 20.8749 14.000 9.8867 14.000 21.500 21.500 30.6847 12.0000 SGO_1516 lacD-2; tagatose 1,6-diphosphate aldolase 4.500 6.000 0.892 4.926 0.0015 0.0030 10.4374 7.000 4.6832 7.000 6.500 6.500 9.2768 6.0000 SGO_1518 lacB-2; galactose-6-phosphate isomerase, LacB subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 70

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 70 8.000 3.058 8.3257 SGO_1520 PTS system, IIC component 4.500 2.170 4.5000 SGO_1521 PTS system IIB component (galactitol/fructose specific) SGO_1523 lacD-1; tagatose 1,6-diphosphate aldolase 3.500 1.865 3.6425 SGO_1527 Lactose phosphotransferase system repressor 21.000 24.000 -1.199 6.053 0.0017 0.0037 12.6740 8.500 21.8549 8.500 5.500 5.500 7.8496 24.0000 SGO_1529 hypothetical protein SGO_1529 95.500 79.000 0.080 8.516 0.1062 0.5268 98.4102 66.000 99.3878 66.000 62.500 62.500 89.1996 79.0000 SGO_1530 methionine-tRNA ligase 13.000 14.000 0.988 6.363 0.0013 0.0023 29.8213 20.000 13.5292 20.000 17.500 17.500 24.9759 14.0000 SGO_1531 xth; exodeoxyribonuclease III 3.500 15.000 1.089 5.713 0.0490 0.2161 23.1115 15.500 3.6425 15.500 7.500 7.500 10.7040 15.0000 SGO_1534 ArsC family 18.000 25.500 -0.019 6.475 0.1779 0.9526 28.3302 19.000 18.7328 19.000 11.500 11.500 16.4127 25.5000 SGO_1536 conserved hypothetical protein TIGR00096 3.000 6.500 3.266 3.1221 6.5000 SGO_1538 DNA-directed DNA polymerase III, delta'' chain 16.000 17.000 0.530 6.365 0.0031 0.0075 22.3660 15.000 16.6514 15.000 18.500 18.500 26.4031 17.0000 SGO_1539 tmk; thymidylate kinase 16.000 15.000 -2.147 5.138 0.0124 0.0428 16.6514 2.500 2.500 3.5680 15.0000 SGO_1540 YitT family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 71

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 71 60.500 81.000 -1.636 7.569 0.0014 0.0025 23.1115 15.500 62.9629 15.500 16.000 16.000 22.8351 81.0000 SGO_1541 atpC; ATP synthase F1, epsilon subunit 410.500 403.500 -1.008 10.281 0.0002 0.0001 199.8025 134.000 427.2113 134.000 149.500 149.500 213.3654 403.5000 SGO_1542 atpD; ATP synthase F1, beta subunit 60.500 58.500 -1.291 7.418 0.0002 0.0001 25.3481 17.000 62.9629 17.000 17.000 17.000 24.2623 58.5000 SGO_1543 atpG; ATP synthase F1, gamma subunit 330.000 352.000 -0.726 10.124 0.0001 0.0001 205.0213 137.500 343.4342 137.500 151.000 151.000 215.5062 352.0000 SGO_1544 atpA; ATP synthase F1, alpha subunit 80.000 72.500 -1.669 7.677 0.0004 0.0004 24.6026 16.500 83.2568 16.500 17.000 17.000 24.2623 72.5000 SGO_1545 atpH; ATP synthase F1, delta subunit 86.500 101.500 -1.026 8.163 0.0016 0.0031 55.1694 37.000 90.0214 37.000 28.000 28.000 39.9614 101.5000 SGO_1546 atpF; ATP synthase F0, B subunit 45.000 62.500 0.394 7.975 0.0120 0.0408 73.8077 49.500 46.8319 49.500 48.000 48.000 68.5053 62.5000 SGO_1550 glgP-1; glycogen phosphorylase 5.000 21.000 0.606 5.888 0.1122 0.5606 20.8749 14.000 5.2035 14.000 8.500 8.500 12.1311 21.0000 SGO_1551 glgA; Glycogen synthase 32.500 21.500 0.946 7.357 0.0188 0.0722 70.0800 47.000 33.8231 47.000 27.000 27.000 38.5342 21.5000 SGO_1552 glgD; glucose-1-phosphate adenylyltransferase, GlgD subunit 18.500 28.000 1.515 7.492 0.0004 0.0005 67.0979 45.000 19.2531 45.000 46.000 46.000 65.6509 28.0000 SGO_1553 glgC; glucose-1-phosphate adenylyltransferase 19.000 34.000 1.332 7.526 0.0014 0.0027 66.3523 44.500 19.7735 44.500 45.000 45.000 64.2237 34.0000 SGO_1554 glgB; 1,4-alpha-glucan branching enzyme 575.500 528.500 0.101 11.189 0.0357 0.1513 611.3362 410.000 598.9284 410.000 417.500 417.500 595.8533 528.5000 SGO_1555 ptsI; phosphoenolpyruvate-protein phosphotransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 72

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 72 646.000 635.500 0.249 11.490 0.0302 0.1244 679.1796 455.500 672.2984 455.500 622.500 622.500 888.4279 635.5000 SGO_1556 phosphocarrier protein HPr 8.000 8.000 4.029 8.3257 8.0000 SGO_1557 NrdH-redoxin 83.000 99.500 0.059 8.566 0.0833 0.4048 96.1736 64.500 86.3789 64.500 68.000 68.000 97.0492 99.5000 SGO_1558 nrdE; ribonucleoside-diphosphate reductase large chain 45.500 56.000 0.935 8.231 0.0007 0.0009 102.8834 69.000 47.3523 69.000 66.000 66.000 94.1948 56.0000 SGO_1559 ribonucleoside-diphosphate reductase, beta subunit 6.500 6.000 3.674 6.7646 6.0000 SGO_1561 putative zinc metallopeptidase 9.500 13.000 4.516 9.8867 13.0000 SGO_1562 hypothetical protein SGO_1562 46.000 23.000 -0.168 7.022 0.0959 0.4718 29.8213 20.000 47.8726 20.000 20.500 20.500 29.2575 23.0000 SGO_1564 transcription regulator, probable -related protein 146.500 192.500 0.166 9.513 0.0562 0.2548 208.0034 139.500 152.4640 139.500 124.500 124.500 177.6856 192.5000 SGO_1570 alaS; alanyl-tRNA synthetase 15.000 14.000 4.888 15.6106 14.0000 SGO_1571 Protein of unknown function (DUF567) superfamily 377.500 400.500 9.632 392.8679 400.5000 SGO_1572 proteinase maturation protein, putative 4.500 0.121 3.873 0.1440 0.7432 3.7277 2.500 2.500 4.500 4.500 6.4224 4.5000 SGO_1573 O-methyltransferase family protein 81.000 88.000 1.082 9.069 0.0001 0.0000 184.1464 123.500 84.2975 123.500 126.500 126.500 180.5400 88.0000 SGO_1574 pepF-1; oligoendopeptidase F .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 73

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 73 3.000 4.000 2.832 3.1221 4.0000 SGO_1576 ptcC; PTS system, IIC component 4.634 13.4196 9.000 9.000 8.000 8.000 11.4175 SGO_1580 PTS system, Lactose/Cellobiose specific IIB subunit 38.500 25.000 -2.854 6.245 0.0039 0.0104 2.2366 1.500 40.0673 1.500 6.000 6.000 8.5632 25.0000 SGO_1585 D-Alanyl-D-Alanine carboxypeptidase 10.000 20.500 0.437 6.170 0.0692 0.3251 26.0936 17.500 10.4071 17.500 10.500 10.500 14.9855 20.5000 SGO_1587 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase 8.000 6.500 3.890 8.3257 6.5000 SGO_1588 arcR; arginine repressor 4.500 7.000 3.546 4.6832 7.0000 SGO_1589 arcT; putative transaminase/peptidase 55.500 64.500 6.934 57.7594 64.5000 SGO_1590 arcD; arginine-ornithine antiporter 31.500 47.500 -1.436 6.786 0.0047 0.0131 18.6383 12.500 32.7824 12.500 8.000 8.000 11.4175 47.5000 SGO_1591 arcC; carbamate kinase 174.500 183.000 -0.713 9.197 0.0000 0.0000 111.0843 74.500 181.6038 74.500 78.000 78.000 111.3211 183.0000 SGO_1592 arcB; ornithine carbamoyltransferase 148.500 176.000 -0.870 8.998 0.0009 0.0015 86.4817 58.000 154.5454 58.000 66.000 66.000 94.1948 176.0000 SGO_1593 arcA; arginine deiminase 5.000 6.000 3.486 5.2035 6.0000 SGO_1594 Crp/Fnr family protein 3.500 3.500 2.836 3.6425 3.5000 SGO_1598 hypothetical protein SGO_1598 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 74

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 74 135.500 156.000 0.417 9.437 0.0020 0.0044 190.1106 127.500 141.0162 127.500 144.500 144.500 206.2294 156.0000 SGO_1599 sodA; manganese-dependent superoxide dismutase 5.500 10.000 3.975 5.7239 10.0000 SGO_1600 DNA polymerase III, delta chain 2.000 4.000 2.604 2.0814 4.0000 SGO_1601 celB; DNA internalization-related competence protein celB 38.000 47.500 -2.382 6.699 0.0006 0.0007 9.6919 6.500 39.5470 6.500 5.000 5.000 7.1360 47.5000 SGO_1604 acyltransferase family protein 31.000 39.000 -1.656 6.552 0.0008 0.0012 10.4374 7.000 32.2620 7.000 8.500 8.500 12.1311 39.0000 SGO_1605 P-type ATPase, metal cation transport 9.000 10.000 -0.708 4.993 0.0157 0.0575 8.2009 5.500 9.3664 5.500 3.000 3.000 4.2816 10.0000 SGO_1606 DNA methyltransferase signature protein 88.500 96.500 -0.739 8.236 0.0002 0.0001 55.1694 37.000 92.1028 37.000 40.500 40.500 57.8013 96.5000 SGO_1609 ATP-dependent RNA helicase, DEAD/DEAH box family 9.500 9.000 4.239 9.8867 9.0000 SGO_1614 magnesium and cobalt transporter CorA family 12.000 23.500 0.372 6.364 0.0788 0.3791 16.4017 11.000 12.4885 11.000 21.000 21.000 29.9711 23.5000 SGO_1617 prfC; peptide chain release factor 3 357.500 283.000 -1.786 9.723 0.0017 0.0033 108.8477 73.000 372.0537 73.000 57.000 57.000 81.3500 283.0000 SGO_1619 cation-transporting ATPase, E1-E2 family 14.500 17.500 -0.354 5.860 0.0078 0.0242 11.9285 8.000 15.0903 8.000 9.500 9.500 13.5583 17.5000 SGO_1621 HD domain protein 14.000 9.500 -0.155 5.499 0.0807 0.3914 10.4374 7.000 14.5699 7.000 7.500 7.500 10.7040 9.5000 SGO_1622 Cof family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 75

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 75 33.500 38.000 -0.997 6.773 0.0003 0.0003 18.6383 12.500 34.8638 12.500 12.500 12.500 17.8399 38.0000 SGO_1623 murM; MurM 19.500 12.500 -0.926 5.632 0.0115 0.0389 8.9464 6.000 20.2938 6.000 5.500 5.500 7.8496 12.5000 SGO_1624 murN; MurN protein 95.000 97.000 -1.236 8.124 0.0001 0.0000 43.2408 29.000 98.8674 29.000 28.000 28.000 39.9614 97.0000 SGO_1625 acetoin utilization putative/CBS domain protein 37.000 49.000 -0.735 7.128 0.0047 0.0132 23.8570 16.000 38.5063 16.000 20.000 20.000 28.5439 49.0000 SGO_1626 branched-chain amino acid ABC transporter, ATP-binding protein 64.500 48.500 -1.163 7.382 0.0038 0.0099 27.5847 18.500 67.1258 18.500 16.500 16.500 23.5487 48.5000 SGO_1627 branched-chain amino acid ABC transporter, ATP-binding protein 509.000 547.500 -1.166 10.605 0.0001 0.0000 241.5523 162.000 529.7212 162.000 167.000 167.000 238.3413 547.5000 SGO_1630 branched-chain amino acid ABC transporter, amino acid-binding protein 6.500 4.000 3.428 6.7646 4.0000 SGO_1631 hypothetical protein SGO_1631 37.500 42.500 -0.250 7.229 0.0036 0.0092 33.5489 22.500 39.0266 22.500 24.500 24.500 34.9662 42.5000 SGO_1632 clpP; ATP-dependent Clp protease, proteolytic subunit ClpP 45.000 49.500 0.909 8.114 0.0001 0.0000 89.4638 60.000 46.8319 60.000 64.000 64.000 91.3404 49.5000 SGO_1633 upp; uracil phosphoribosyltransferase 256.500 266.500 -5.111 9.102 0.0000 0.0000 10.4374 7.000 266.9420 7.000 4.000 4.000 5.7088 266.5000 SGO_1634 magnesium-translocating P-type ATPase 5.500 3.500 1.421 5.055 0.0014 0.0027 11.1830 7.500 5.7239 7.500 9.000 9.000 12.8447 3.5000 SGO_1638 murE; UDP-N-acetylmuramoylalanyl-Dglutamate--2,6-diaminopimelate ligase 61.500 83.500 1.546 9.176 0.0020 0.0044 185.6374 124.500 64.0036 124.500 172.000 172.000 245.4773 83.5000 SGO_1648 ppx1; inorganic pyrophosphatase, manganese-dependent .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 76

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 76 26.000 22.000 -2.242 5.905 0.0010 0.0017 3.7277 2.500 27.0585 2.500 5.000 5.000 7.1360 22.0000 SGO_1649 act; pyruvate formate-lyase-activating enzyme 109.000 138.500 7.977 113.4373 138.5000 SGO_1650 LPXTG cell wall surface protein, collagen binding domain 357.000 371.000 9.536 371.5333 371.0000 SGO_1651 LPXTG cell wall surface protein, nuclease/phosphatase domain 28.500 40.500 0.184 7.218 0.0578 0.2631 39.5132 26.500 29.6602 26.500 27.500 27.500 39.2478 40.5000 SGO_1652 intracellular glycosyl hydrolase 187.500 217.000 -2.054 8.998 0.0002 0.0001 48.4596 32.500 195.1331 32.500 35.500 35.500 50.6654 217.0000 SGO_1653 trehalose PTS enzyme II 40.500 58.500 -2.739 6.857 0.0016 0.0030 5.9643 4.000 42.1487 4.000 6.500 6.500 9.2768 58.5000 SGO_1655 CBS domain protein/possible hemolysin 10.000 12.000 4.486 10.4071 12.0000 SGO_1657 membrane protein 3.500 10.500 3.822 3.6425 10.5000 SGO_1661 radical SAM protein, TIGR01212 family 6.000 2.585 6.0000 SGO_1665 rRNA methylase 33.500 49.000 -0.970 6.980 0.0056 0.0162 23.1115 15.500 34.8638 15.500 13.500 13.500 19.2671 49.0000 SGO_1666 trkA; potassium uptake protein, Trk family 38.500 59.000 -0.728 7.307 0.0126 0.0436 33.5489 22.500 40.0673 22.500 18.000 18.000 25.6895 59.0000 SGO_1669 ribosomal large subunit pseudouridine synthase B 5.000 2.379 5.2035 SGO_1670 scpB; segregation and condensation protein B .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 77

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 77 13.000 11.500 -0.643 5.361 0.0040 0.0107 8.9464 6.000 13.5292 6.000 5.000 5.000 7.1360 11.5000 SGO_1674 phosphodiesterase, MJ0936 family 17.500 29.500 -0.654 6.276 0.0214 0.0834 12.6740 8.500 18.2124 8.500 12.000 12.000 17.1263 29.5000 SGO_1675 HAM1 protein-like protein 5.500 8.000 1.692 5.845 0.0003 0.0002 21.6204 14.500 5.7239 14.500 15.500 15.500 22.1215 8.0000 SGO_1676 murI; glutamate racemase 7.500 11.000 0.029 5.328 0.1365 0.6999 15.6562 10.500 7.8053 10.500 4.000 4.000 5.7088 11.0000 SGO_1678 lysA; diaminopimelate decarboxylase 608.000 625.000 -1.278 10.798 0.0004 0.0003 295.2306 198.000 632.7514 198.000 159.500 159.500 227.6373 625.0000 SGO_1679 phosphotransferase system enzyme II 119.000 98.500 -2.691 8.003 0.0007 0.0010 16.4017 11.000 123.8444 11.000 12.500 12.500 17.8399 98.5000 SGO_1680 phosphotransferase system enzyme II 471.500 481.500 -1.826 10.284 0.0000 0.0000 138.6689 93.000 490.6946 93.000 95.000 95.000 135.5834 481.5000 SGO_1681 PTS system, mannose/fructose/sorbose family, IID component 59.500 67.000 0.563 8.319 0.0012 0.0021 99.9013 67.000 61.9222 67.000 63.500 63.500 90.6268 67.0000 SGO_1683 serS; seryl-tRNA synthetase 9.500 14.000 1.477 6.486 0.0012 0.0020 35.7855 24.000 9.8867 24.000 21.000 21.000 29.9711 14.0000 SGO_1684 acyl-CoA dehydrogenase family 14.500 21.000 2.779 8.132 0.0001 0.0000 125.2494 84.000 15.0903 84.000 83.500 83.500 119.1707 21.0000 SGO_1685 putative peroxidase / antioxidase 62.000 68.000 -0.031 8.036 0.1317 0.6708 69.3345 46.500 64.5240 46.500 42.500 42.500 60.6557 68.0000 SGO_1687 accA; acetyl-CoA carboxylase, carboxyl transferase, alpha subunit 20.500 39.000 -0.423 6.692 0.0434 0.1883 21.6204 14.500 21.3345 14.500 15.000 15.000 21.4079 39.0000 SGO_1688 accD; acetyl-CoA carboxylase, carboxyl transferase, beta subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 78

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 78 30.500 41.500 0.770 7.623 0.0018 0.0039 59.6426 40.000 31.7416 40.000 45.000 45.000 64.2237 41.5000 SGO_1689 accC; acetyl-CoA carboxylase, biotin carboxylase 5.878 23.8570 16.000 16.000 24.500 24.500 34.9662 SGO_1690 fabZ; beta-hydroxyacyl-(acyl-carrierprotein) dehydratase FabZ 55.000 31.500 1.379 8.276 0.0017 0.0036 115.5574 77.500 57.2390 77.500 74.000 74.000 105.6123 31.5000 SGO_1691 accB; acetyl-CoA carboxylase, biotin carboxyl carrier protein 101.000 113.500 1.429 9.656 0.0001 0.0000 292.2485 196.000 105.1117 196.000 207.500 207.500 296.1426 113.5000 SGO_1692 3-oxoacyl-[acyl-carrier-protein] synthase 26.500 22.500 0.871 7.143 0.0014 0.0026 48.4596 32.500 27.5788 32.500 30.000 30.000 42.8158 22.5000 SGO_1693 fabG; 3-oxoacyl-(acyl-carrier-protein) reductase 20.000 28.000 1.047 7.221 0.0027 0.0064 44.7319 30.000 20.8142 30.000 39.000 39.000 55.6605 28.0000 SGO_1694 fabD; malonyl CoA-acyl carrier protein transacylase 147.500 154.000 0.870 9.770 0.0028 0.0067 316.1055 212.000 153.5047 212.000 175.000 175.000 249.7588 154.0000 SGO_1695 enoyl-acyl carrier protein(ACP) reductase 5.000 17.500 -0.756 5.106 0.0515 0.2316 7.4553 5.000 5.2035 5.000 3.000 3.000 4.2816 17.5000 SGO_1698 3-oxoacyl-[acyl-carrier-protein] synthase III 7.500 10.000 0.913 5.685 0.0055 0.0160 19.3838 13.000 7.8053 13.000 10.000 10.000 14.2719 10.0000 SGO_1699 transcriptional regulator, MarR family 17.000 17.500 0.135 6.207 0.0097 0.0318 20.1294 13.500 17.6921 13.500 13.000 13.000 18.5535 17.5000 SGO_1700 enoyl-CoA hydratase/isomerase family protein 36.500 40.000 0.897 7.802 0.0001 0.0000 73.0621 49.000 37.9859 49.000 50.500 50.500 72.0733 40.0000 SGO_1701 aspartate kinase 424.000 254.500 -1.595 9.842 0.0073 0.0220 105.1200 70.500 441.2609 70.500 82.000 82.000 117.0299 254.5000 SGO_1708 amiF; Oligopeptide transport ATP-binding protein amiF .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 79

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 79 381.500 400.000 -1.584 10.055 0.0001 0.0000 124.5038 83.500 397.0307 83.500 99.500 99.500 142.0057 400.0000 SGO_1709 amiE; Oligopeptide transport ATP-binding protein 49.500 46.000 -2.268 6.883 0.0003 0.0002 11.9285 8.000 51.5151 8.000 6.000 6.000 8.5632 46.0000 SGO_1710 amiD; Oligopeptide transport system permease protein 121.000 160.000 -1.467 8.602 0.0014 0.0026 49.9506 33.500 125.9259 33.500 37.000 37.000 52.8062 160.0000 SGO_1711 hppB; Oligopeptide transport system permease 712.500 715.500 -1.011 11.090 0.0001 0.0000 362.3285 243.000 741.5056 243.000 252.500 252.500 360.3663 715.5000 SGO_1712 hppA; oligopeptide-binding lipoprotein 615.000 570.500 -1.386 10.708 0.0004 0.0004 238.5702 160.000 640.0364 160.000 157.000 157.000 224.0694 570.5000 SGO_1713 hppG; oligopeptide-binding lipoprotein 263.500 264.500 -1.406 9.535 0.0001 0.0000 98.4102 66.000 274.2270 66.000 73.500 73.500 104.8987 264.5000 SGO_1715 hppH; oligopeptide-binding lipoprotein 215.000 270.500 -0.939 9.553 0.0017 0.0034 134.1957 90.000 223.7526 90.000 86.000 86.000 122.7386 270.5000 SGO_1716 oligopeptide binding protein 48.500 36.000 -3.837 6.483 0.0278 0.1132 2.9821 2.000 50.4744 2.000 36.0000 SGO_1717 pbp3; penicillin-binding protein 3 31.000 47.000 0.192 7.395 0.0742 0.3537 46.9685 31.500 32.2620 31.500 29.500 29.500 42.1022 47.0000 SGO_1718 sufB-1; FeS assembly protein SufB 5.000 2.500 2.946 5.2035 2.5000 SGO_1719 SUF system FeS assembly protein, NifU family 5.500 10.000 1.646 5.980 0.0008 0.0011 23.1115 15.500 5.7239 15.500 17.000 17.000 24.2623 10.0000 SGO_1720 aminotransferase, class-V 36.500 31.000 0.589 7.430 0.0033 0.0083 48.4596 32.500 37.9859 32.500 38.500 38.500 54.9469 31.0000 SGO_1721 sufD; FeS assembly protein SufD .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 80

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 80 19.500 25.000 0.437 6.734 0.0079 0.0243 28.3302 19.000 20.2938 19.000 23.000 23.000 32.8254 25.0000 SGO_1722 sufC; FeS assembly ATPase SufC 3.000 7.000 -0.127 3.848 0.1462 0.7567 3.1221 3.000 3.000 4.2816 7.0000 SGO_1724 mecA; Adapter protein mec 10.500 5.500 4.038 10.9275 5.5000 SGO_1725 bacA; bacitracin resistance protein 10.500 15.500 4.724 10.9275 15.5000 SGO_1726 hypothetical protein SGO_1726 64.500 71.500 -0.949 7.719 0.0005 0.0007 32.8034 22.000 67.1258 22.000 27.500 27.500 39.2478 71.5000 SGO_1727 amino acid ABC transporter, amino acidbinding/permease protein 73.000 51.000 -1.549 7.411 0.0042 0.0114 25.3481 17.000 75.9718 17.000 12.500 12.500 17.8399 51.0000 SGO_1728 glnQ; glutamine ABC transporter ATPbinding protein 6.111 30.5668 20.500 20.500 27.000 27.000 38.5342 SGO_1729 hypothetical protein SGO_1729 292.500 256.500 -1.409 9.596 0.0011 0.0019 90.2094 60.500 304.4076 60.500 86.000 86.000 122.7386 256.5000 SGO_1730 SPFH domain/Band 7 family 2.000 5.000 2.963 5.857 0.0014 0.0026 21.6204 14.500 2.0814 14.500 20.500 20.500 29.2575 5.0000 SGO_1731 DNA-binding response regulator 6.000 19.500 0.137 5.243 0.1748 0.9291 6.2443 8.500 8.500 12.1311 19.5000 SGO_1732 histidine kinase 155.500 188.000 0.067 9.482 0.0791 0.3811 184.1464 123.500 161.8303 123.500 127.000 127.000 181.2536 188.0000 SGO_1735 hypothetical protein SGO_1735 12.500 10.500 0.919 6.090 0.0042 0.0115 25.3481 17.000 13.0089 17.000 13.500 13.500 19.2671 10.5000 SGO_1736 alkaline shock protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 81

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 81 21.500 36.000 5.867 22.3753 36.0000 SGO_1737 rpmB; ribosomal protein L28 11.500 8.000 4.320 11.9682 8.0000 SGO_1738 hypothetical protein SGO_1738 9.000 7.500 4.076 9.3664 7.5000 SGO_1739 LytTr DNA-binding domain family 9.500 10.500 4.350 9.8867 10.5000 SGO_1744 ABC transporter, ATP-binding protein SP0636 810.500 659.500 1.138 12.225 0.0005 0.0006 1602.8936 1075.000 843.4951 1075.000 1177.500 1177.500 1680.5202 659.5000 SGO_1745 fba; fructose-1,6-bisphosphate aldolase, class II 2.553 3.7277 2.500 2.500 1.500 1.500 2.1408 SGO_1747 hypothetical protein SGO_1747 11.500 11.000 0.671 5.923 0.0190 0.0733 14.1651 9.500 11.9682 9.500 16.500 16.500 23.5487 11.0000 SGO_1748 pyrG; CTP synthase 19.000 30.000 0.588 6.953 0.0186 0.0713 31.3123 21.000 19.7735 21.000 30.000 30.000 42.8158 30.0000 SGO_1749 manA; mannose-6-phosphate isomerase, class I 20.000 25.000 5.518 20.8142 25.0000 SGO_1750 ABC-type multidrug/protein/lipid transport system, ATPase component 31.500 28.000 -2.262 6.233 0.0014 0.0025 3.7277 2.500 32.7824 2.500 7.500 7.500 10.7040 28.0000 SGO_1751 ABC-type multidrug/protein/lipid transport system, ATPase component 6.000 2.643 6.2443 SGO_1753 hypothetical protein SGO_1753 25.500 33.000 0.917 7.427 0.0037 0.0097 63.3702 42.500 26.5381 42.500 34.500 34.500 49.2382 33.0000 SGO_1755 scrK; fructokinase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 82

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 82 4.500 2.170 4.5000 SGO_1756 hypothetical protein SGO_1756 84.500 118.000 0.303 8.837 0.0214 0.0836 122.2672 82.000 87.9400 82.000 90.500 90.500 129.1610 118.0000 SGO_1757 glmS; glucosamine--fructose-6-phosphate aminotransferase 2.098 3.000 3.000 4.2816 SGO_1760 DNA-binding response regulator 7.000 17.500 4.631 7.2850 17.5000 SGO_1761 histidine kinase 53.000 65.500 0.005 7.920 0.1768 0.9410 53.6783 36.000 55.1576 36.000 47.500 47.500 67.7917 65.5000 SGO_1763 ABC transporter, substrate-binding protein SP0092 5.000 2.500 0.808 4.468 0.0490 0.2172 3.7277 2.500 5.2035 2.500 7.500 7.500 10.7040 2.5000 SGO_1768 glycosyl hydrolase, family 38 14.500 3.858 14.5000 SGO_1772 integral membrane protein 11.000 14.000 0.032 5.695 0.1520 0.7951 15.6562 10.500 11.4478 10.500 7.500 7.500 10.7040 14.0000 SGO_1774 alcohol dehydrogenase, zinc-containing 2.500 1.322 2.5000 SGO_1780 hypothetical protein SGO_1780 57.500 73.500 0.586 8.378 0.0027 0.0063 104.3745 70.000 59.8408 70.000 66.500 66.500 94.9084 73.5000 SGO_1784 leuS; leucyl-tRNA synthetase 3.000 1.585 3.0000 SGO_1792 transcription regulator 50.500 68.500 1.049 8.530 0.0008 0.0012 120.0306 80.500 52.5558 80.500 90.000 90.000 128.4474 68.5000 SGO_1799 endopeptidase O .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 83

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 83 147.500 128.000 -2.160 8.427 0.0005 0.0007 32.8034 22.000 153.5047 22.000 21.000 21.000 29.9711 128.0000 SGO_1800 troB; manganese ABC transporter, ATPbinding protein SP1648 1088.500 958.000 -2.784 11.227 0.0004 0.0004 178.1821 119.500 1132.8124 119.500 90.000 90.000 128.4474 958.0000 SGO_1802 Metal ABC transporter substrate-binding lipoprotein precursor 13.000 14.000 1.645 6.828 0.0001 0.0000 43.9864 29.500 13.5292 29.500 29.500 29.500 42.1022 14.0000 SGO_1803 tpx; thioredoxin peroxidase 3.000 2.632 5.330 0.0096 0.0315 19.3838 13.000 13.000 12.500 12.500 17.8399 3.0000 SGO_1804 hutI; imidazolonepropionase 1.500 4.930 6.617 0.0277 0.1125 56.6604 38.000 1.5611 38.000 28.000 28.000 39.9614 SGO_1805 hutU; urocanate hydratase 5.242 17.1472 11.500 11.500 14.500 14.500 20.6943 SGO_1806 ftcD; glutamate formiminotransferase 4.350 9.6919 6.500 6.500 7.500 7.500 10.7040 SGO_1807 serine cycle enzyme, putative 3.454 5.9643 4.000 4.000 3.500 3.500 4.9952 SGO_1808 fhs-2; formate--tetrahydrofolate ligase 4.500 5.000 1.223 5.013 0.0001 0.0000 11.1830 7.500 4.6832 7.500 8.000 8.000 11.4175 5.0000 SGO_1811 hutH; histidine ammonia-lyase 4.000 2.000 4.0000 SGO_1813 hutG; formimidoylglutamase 8.500 6.500 3.940 8.8460 6.5000 SGO_1814 putative regulatory protein 9.000 10.000 0.145 4.910 0.0440 0.1916 9.3664 7.500 7.500 10.7040 10.0000 SGO_1816 scaR; ScaR Manganese-dependent regulator of scaCBA .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 84

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 84 41.000 37.000 -1.768 6.687 0.0004 0.0004 11.9285 8.000 42.6691 8.000 8.000 8.000 11.4175 37.0000 SGO_1822 relA; GTP diphosphokinase 3.722 8.2009 5.500 5.500 3.500 3.500 4.9952 SGO_1823 conserved hypothetical protein TIGR00046 9.500 14.500 0.820 6.059 0.0028 0.0069 20.8749 14.000 9.8867 14.000 15.000 15.000 21.4079 14.5000 SGO_1824 prmA; ribosomal protein L11 methyltransferase 7.000 10.000 -0.256 4.992 0.0635 0.2934 5.9643 4.000 7.2850 4.000 6.000 6.000 8.5632 10.0000 SGO_1827 hypothetical protein SGO_1827 6.500 4.000 0.056 4.482 0.1520 0.7952 3.7277 2.500 6.7646 2.500 5.500 5.500 7.8496 4.0000 SGO_1828 ATPase, AAA family 7.000 5.000 2.739 6.583 0.0043 0.0117 52.9328 35.500 7.2850 35.500 21.500 21.500 30.6847 5.0000 SGO_1834 hypothetical protein SGO_1834 3.000 0.863 3.800 0.0170 0.0631 5.2187 3.500 3.500 4.000 4.000 5.7088 3.0000 SGO_1835 hypothetical protein SGO_1835 45.500 42.500 0.981 8.067 0.0026 0.0060 99.9013 67.000 47.3523 67.000 55.000 55.000 78.4956 42.5000 SGO_1843 pepS; aminopeptidase PepS 8.000 12.000 0.775 5.772 0.0050 0.0141 18.6383 12.500 8.3257 12.500 11.000 11.000 15.6991 12.0000 SGO_1844 cbxX/cfqX family protein 14.000 17.000 0.057 6.008 0.1039 0.5132 15.6562 10.500 14.5699 10.500 12.000 12.000 17.1263 17.0000 SGO_1847 polC; DNA polymerase III, alpha subunit, Gram-positive type 82.000 71.000 -3.095 7.448 0.0004 0.0005 9.6919 6.500 85.3382 6.500 6.000 6.000 8.5632 71.0000 SGO_1848 lipoprotein, putative 87.500 100.500 7.582 91.0621 100.5000 SGO_1849 hypothetical protein SGO_1849 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 85

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 85 96.500 117.500 0.365 8.961 0.0066 0.0196 148.3608 99.500 100.4285 99.500 92.500 92.500 132.0154 117.5000 SGO_1851 proS; prolyl-tRNA synthetase 38.000 43.500 -1.841 6.734 0.0003 0.0003 13.4196 9.000 39.5470 9.000 7.000 7.000 9.9904 43.5000 SGO_1852 membrane-associated zinc metalloprotease, putative 45.500 44.000 -1.307 7.017 0.0015 0.0028 23.8570 16.000 47.3523 16.000 10.000 10.000 14.2719 44.0000 SGO_1854 uppS; undecaprenyl diphosphate synthase 86.500 109.500 -1.217 8.163 0.0022 0.0049 52.1872 35.000 90.0214 35.000 24.500 24.500 34.9662 109.5000 SGO_1855 preprotein translocase, YajC subunit 33.500 35.500 -0.896 6.760 0.0005 0.0007 20.8749 14.000 34.8638 14.000 12.000 12.000 17.1263 35.5000 SGO_1856 ATP-dependent proteinase ATP-binding chain 10.000 16.000 -2.113 4.877 0.0396 0.1700 2.9821 2.000 10.4071 2.000 16.0000 SGO_1857 PTS system, IIABC components 2.000 1.448 3.696 0.0223 0.0881 5.9643 4.000 4.000 3.500 3.500 4.9952 2.0000 SGO_1858 beta-fructofuranosidase/sucrose 6 phoshate hydrolase 204.500 163.000 -1.332 9.034 0.0020 0.0044 79.0264 53.000 212.8251 53.000 48.500 48.500 69.2189 163.0000 SGO_1860 5'-nucleotidase, lipoprotein e(P4) family 3.500 2.171 5.189 0.0108 0.0360 17.1472 11.500 3.6425 11.500 11.000 11.000 15.6991 SGO_1861 nusB; transcription antitermination factor NusB 21.000 17.500 0.941 6.840 0.0011 0.0017 39.5132 26.500 21.8549 26.500 25.000 25.000 35.6798 17.5000 SGO_1862 alkaline shock protein 72.000 84.500 0.394 8.526 0.0017 0.0034 102.8834 69.000 74.9311 69.000 74.500 74.500 106.3259 84.5000 SGO_1863 efp; Elongation factor P (EF-P) 33.500 26.000 0.586 7.241 0.0040 0.0105 44.7319 30.000 34.8638 30.000 32.000 32.000 45.6702 26.0000 SGO_1864 X-Pro aminopeptidase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 86

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 86 48.500 55.500 -1.073 7.288 0.0003 0.0003 25.3481 17.000 50.4744 17.000 17.500 17.500 24.9759 55.5000 SGO_1865 uvrA; excinuclease ABC, A subunit 2.384 5.2187 3.500 3.500 SGO_1866 corA; magnesium and cobalt transporter 85.000 76.500 -0.785 8.025 0.0012 0.0021 46.9685 31.500 88.4603 31.500 34.000 34.000 48.5246 76.5000 SGO_1867 hypothetical protein SGO_1867 27.000 40.500 6.100 28.0992 40.5000 SGO_1869 hypothetical protein SGO_1869 31.500 45.000 -2.154 6.573 0.0017 0.0036 7.4553 5.000 32.7824 5.000 7.000 7.000 9.9904 45.0000 SGO_1870 hypothetical protein SGO_1870 20.000 24.000 5.486 20.8142 24.0000 SGO_1871 lipoprotein, putative 14.500 22.500 -2.042 5.394 0.0376 0.1612 4.4732 3.000 15.0903 3.000 22.5000 SGO_1872 hypothetical protein SGO_1872 6.500 6.000 3.674 6.7646 6.0000 SGO_1878 transcriptional regulator, TetR family domain protein 28.000 72.000 0.485 7.843 0.0748 0.3573 68.5889 46.000 29.1399 46.000 42.000 42.000 59.9421 72.0000 SGO_1879 rpsR; ribosomal protein S18 49.000 63.500 1.077 8.471 0.0008 0.0011 114.0664 76.500 50.9948 76.500 88.500 88.500 126.3066 63.5000 SGO_1880 ssb-1; single-strand binding protein 146.500 166.000 0.807 9.782 0.0045 0.0123 319.0876 214.000 152.4640 214.000 170.000 170.000 242.6229 166.0000 SGO_1881 rpsF; ribosomal protein S6 6.000 10.500 1.566 6.032 0.0038 0.0099 20.1294 13.500 6.2443 13.500 20.000 20.000 28.5439 10.5000 SGO_1882 folE; GTP cyclohydrolase I .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 87

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 87 9.500 9.000 4.239 9.8867 9.0000 SGO_1884 hypothetical protein SGO_1884 198.500 200.000 0.544 9.965 0.0001 0.0000 298.2128 200.000 206.5809 200.000 206.500 206.500 294.7154 200.0000 SGO_1885 groL; 60 kDa chaperonin/groEL protein 20.000 18.000 -0.062 6.280 0.1835 0.9903 25.3481 17.000 20.8142 17.000 9.500 9.500 13.5583 18.0000 SGO_1886 groES; chaperonin, 10 kDa 14.000 13.000 4.785 14.5699 13.0000 SGO_1887 ABC transporter, ATP-binding protein 7.500 7.500 3.936 7.8053 7.5000 SGO_1888 ABC transporter, permease protein 12.000 14.500 4.754 12.4885 14.5000 SGO_1890 PTS system, fructose(mannose)-specific IID 18.500 14.500 5.077 19.2531 14.5000 SGO_1891 PTS system, IIC component 24.500 33.000 -0.655 6.579 0.0076 0.0233 16.4017 11.000 25.4974 11.000 14.500 14.500 20.6943 33.0000 SGO_1892 PTS system, fructose(mannose)-specific IIB 6.000 8.000 3.832 6.2443 8.0000 SGO_1894 sugar-binding cell envelope protein 2.500 2.000 2.202 2.6018 2.0000 SGO_1895 response regulator 5.000 8.500 3.776 5.2035 8.5000 SGO_1897 rbsB; ribose ABC transporter (ribose-binding component) CAC1453 42.000 48.500 0.820 7.993 0.0003 0.0002 79.7719 53.500 43.7098 53.500 58.000 58.000 82.7772 48.5000 SGO_1898 glutamyl aminopeptidase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 88

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 88 6.500 2.700 6.5000 SGO_1899 hypothetical protein SGO_1899 2.500 0.545 3.292 0.0127 0.0442 3.7277 2.500 2.500 2.500 2.500 3.5680 2.5000 SGO_1900 thioredoxin family protein 17.000 14.000 1.151 6.682 0.0048 0.0136 41.7498 28.000 17.6921 28.000 20.500 20.500 29.2575 14.0000 SGO_1901 tRNA binding domain 137.000 170.500 1.319 10.098 0.0015 0.0028 433.8996 291.000 142.5772 291.000 244.500 244.500 348.9488 170.5000 SGO_1902 ssb; single-stranded DNA-binding protein 64.000 72.500 -0.014 8.113 0.1490 0.7754 66.3523 44.500 66.6054 44.500 50.000 50.000 71.3597 72.5000 SGO_1903 ATP-dependent Zn protease 4.500 2.170 4.5000 SGO_1907 sensor protein 1.500 3.000 1.890 4.365 0.0007 0.0009 8.2009 5.500 1.5611 5.500 5.500 5.500 7.8496 3.0000 SGO_1912 Bifunctional folate synthesis protein 3.000 0.948 3.872 0.0322 0.1338 5.2187 3.500 3.500 4.500 4.500 6.4224 3.0000 SGO_1914 folP; dihydropteroate synthase 70.500 86.500 0.394 8.528 0.0030 0.0074 105.1200 70.500 73.3700 70.500 73.000 73.000 104.1851 86.5000 SGO_1916 ackA; acetate kinase 6.000 5.500 0.982 5.136 0.0039 0.0104 13.4196 9.000 6.2443 9.000 7.000 7.000 9.9904 5.5000 SGO_1917 hypothetical protein SGO_1917 7.000 2.865 7.2850 SGO_1923 comYB; competence protein 142.000 157.500 -2.018 8.576 0.0002 0.0001 32.0579 21.500 147.7808 21.500 31.000 31.000 44.2430 157.5000 SGO_1924 comYA; competence protein comYA .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 89

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 89 333.500 367.000 0.180 10.573 0.0033 0.0081 413.0247 277.000 347.0767 277.000 277.500 277.500 396.0462 367.0000 SGO_1926 rpoC; DNA-directed RNA polymerase, beta chain 347.000 333.000 -0.010 10.434 0.1496 0.7797 339.9625 228.000 361.1262 228.000 244.500 244.500 348.9488 333.0000 SGO_1927 rpoB; DNA-directed RNA polymerase, beta subunit 73.500 89.000 -2.965 7.544 0.0003 0.0003 10.4374 7.000 76.4922 7.000 7.500 7.500 10.7040 89.0000 SGO_1928 pbp1b; penicillin-binding protein 1B 97.000 112.000 1.093 9.384 0.0010 0.0015 245.2800 164.500 100.9488 164.500 147.000 147.000 209.7974 112.0000 SGO_1929 tyrS; tyrosyl-tRNA synthetase 2.500 5.000 1.085 4.520 0.0051 0.0145 8.2009 5.500 2.6018 5.500 5.000 5.000 7.1360 5.0000 SGO_1930 rrmA; Ribosomal RNA large subunit methyltransferase A 1.161 2.2366 1.500 1.500 SGO_1931 lipoprotein, putative 19.000 19.000 5.277 19.7735 19.0000 SGO_1934 copper-translocating P-type ATPase 3.500 2.000 2.496 3.6425 2.0000 SGO_1935 negative transcriptional regulator, CopY 193.500 211.000 -2.189 8.974 0.0001 0.0000 47.7140 32.000 201.3773 32.000 30.000 30.000 42.8158 211.0000 SGO_1936 adcA; metal-binding (Mn) permease precursor, lipoprotein 13.500 20.000 0.029 6.096 0.1771 0.9448 18.6383 12.500 14.0496 12.500 11.000 11.000 15.6991 20.0000 SGO_1938 adcC; ATP-binding protein, Mn 2.321 3.500 3.500 4.9952 SGO_1939 adcR; repressor protein adcR 9.000 18.000 -2.186 4.917 0.0534 0.2415 9.3664 2.000 2.000 2.8544 18.0000 SGO_1957 hypothetical protein SGO_1957 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 90

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 90 127.000 102.000 2.075 10.247 0.0004 0.0003 521.8723 350.000 132.1701 350.000 321.500 321.500 458.8427 102.0000 SGO_1958 rplQ; ribosomal protein L17 152.000 125.000 0.482 9.402 0.0056 0.0164 186.3830 125.000 158.1879 125.000 145.000 145.000 206.9430 125.0000 SGO_1959 rpoA; DNA-directed RNA polymerase, alpha subunit 64.500 55.500 0.545 8.234 0.0033 0.0080 84.2451 56.500 67.1258 56.500 66.000 66.000 94.1948 55.5000 SGO_1960 rpsK; ribosomal protein S11 115.500 111.000 1.499 9.790 0.0003 0.0003 345.1813 231.500 120.2020 231.500 216.500 216.500 308.9874 111.0000 SGO_1961 rpsM; ribosomal protein S13p/S18e 5.444 16.4017 11.000 11.000 19.000 19.000 27.1167 SGO_1962 rpmJ; ribosomal protein L36 106.500 106.000 0.047 8.784 0.0231 0.0918 112.5753 75.500 110.8356 75.500 78.000 78.000 111.3211 106.0000 SGO_1964 adk; Adenylate kinase (ATP-AMP transphosphorylase) 39.000 36.500 -1.375 6.740 0.0004 0.0005 13.4196 9.000 40.5877 9.000 11.500 11.500 16.4127 36.5000 SGO_1965 Preprotein translocase secY subunit 64.500 72.500 1.359 8.989 0.0068 0.0207 140.1600 94.000 67.1258 94.000 160.000 160.000 228.3509 72.5000 SGO_1966 rplO; ribosomal protein L15 42.000 45.500 1.872 8.702 0.0003 0.0002 172.9634 116.000 43.7098 116.000 108.000 108.000 154.1369 45.5000 SGO_1967 50S ribosomal protein L30 -related protein 264.500 216.000 0.640 10.290 0.0024 0.0053 392.1498 263.000 275.2677 263.000 258.000 258.000 368.2159 216.0000 SGO_1968 rpsE; ribosomal protein S5 182.000 149.000 1.259 10.158 0.0003 0.0003 403.3328 270.500 189.4092 270.500 281.000 281.000 401.0414 149.0000 SGO_1969 rplR; ribosomal protein L18 349.000 347.500 -0.442 10.269 0.0004 0.0004 266.1549 178.500 363.2077 178.500 180.000 180.000 256.8948 347.5000 SGO_1970 BL10; 50S ribosomal protein L6 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 91

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 91 326.500 305.500 0.875 10.836 0.0004 0.0005 613.5727 411.500 339.7917 411.500 398.500 398.500 568.7366 305.5000 SGO_1971 rpsH; ribosomal protein S8 40.500 5.340 40.5000 SGO_1972 rpsN; ribosomal protein S14p/S29e 202.500 234.500 0.314 9.963 0.0026 0.0060 282.5566 189.500 210.7437 189.500 189.500 189.500 270.4532 234.5000 SGO_1973 BL6; 50S ribosomal protein L5 147.000 112.500 -0.172 8.962 0.0595 0.2735 111.0843 74.500 152.9843 74.500 85.500 85.500 122.0250 112.5000 SGO_1974 rplX; ribosomal protein L24 80.500 77.500 0.740 8.750 0.0003 0.0003 137.9234 92.500 83.7771 92.500 92.000 92.000 131.3018 77.5000 SGO_1975 rplN; ribosomal protein L14 45.500 24.000 2.575 8.892 0.0008 0.0012 181.1642 121.500 47.3523 121.500 156.000 156.000 222.6422 24.0000 SGO_1976 BS16; 30S ribosomal protein 25.000 19.500 0.014 6.513 0.1779 0.9553 20.1294 13.500 26.0177 13.500 18.000 18.000 25.6895 19.5000 SGO_1977 rpmC; ribosomal protein L29 42.500 82.500 1.442 8.829 0.0015 0.0028 164.7625 110.500 44.2302 110.500 114.500 114.500 163.4136 82.5000 SGO_1978 rplP; ribosomal protein L16 429.000 414.000 -0.999 10.334 0.0003 0.0002 220.6774 148.000 446.4644 148.000 147.000 147.000 209.7974 414.0000 SGO_1979 rpsC; ribosomal protein S3 134.000 123.000 0.869 9.533 0.0003 0.0003 244.5345 164.000 139.4551 164.000 164.000 164.000 234.0597 123.0000 SGO_1980 rplV; ribosomal protein L22 159.000 200.500 -0.198 9.418 0.0320 0.1328 149.1064 100.000 165.4728 100.000 118.500 118.500 169.1224 200.5000 SGO_1981 rpsS; ribosomal protein S19 99.500 135.500 0.327 9.069 0.0196 0.0760 159.5438 107.000 103.5506 107.000 97.000 97.000 138.4378 135.5000 SGO_1982 rplB; ribosomal protein L2 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 92

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 92 130.000 128.000 -0.214 8.948 0.0580 0.2650 135.6868 91.000 135.2923 91.000 66.500 66.500 94.9084 128.0000 SGO_1983 rplW; ribosomal protein L23 153.000 124.500 0.821 9.611 0.0017 0.0035 235.5881 158.000 159.2286 158.000 184.000 184.000 262.6036 124.5000 SGO_1984 rplD; ribosomal protein L4/L1 family 80.000 96.000 2.375 10.178 0.0072 0.0217 332.5072 223.000 83.2568 223.000 453.000 453.000 646.5186 96.0000 SGO_1985 rplC; ribosomal protein L3 56.000 42.000 0.450 7.881 0.0131 0.0458 63.3702 42.500 58.2797 42.500 50.500 50.500 72.0733 42.0000 SGO_1986 rpsJ; ribosomal protein S10 7.000 16.500 4.572 7.2850 16.5000 SGO_1988 hydrolase, haloacid dehalogenase-like family 109.500 131.000 1.403 9.800 0.0003 0.0002 337.7259 226.500 113.9577 226.500 216.500 216.500 308.9874 131.0000 SGO_1989 purA; adenylosuccinate synthetase 3.000 5.500 1.608 5.146 0.0122 0.0419 8.9464 6.000 3.1221 6.000 12.500 12.500 17.8399 5.5000 SGO_1990 glutamate--cysteine ligase, putative/amino acid ligase, putative 4.000 10.500 -0.388 4.635 0.0674 0.3156 4.4732 3.000 4.1628 3.000 4.000 4.000 5.7088 10.5000 SGO_1991 hslO; 33 kDa chaperonin /Heat shock protein 33-like protein 35.000 50.500 -0.453 7.226 0.0175 0.0657 33.5489 22.500 36.4248 22.500 20.500 20.500 29.2575 50.5000 SGO_1993 possible transcriptional regulator 2.500 1.380 2.6018 SGO_1994 lipoprotein, putative 16.500 8.000 4.654 17.1717 8.0000 SGO_1995 MutT/nudix family protein 41.000 37.000 -0.061 7.292 0.1442 0.7455 32.8034 22.000 42.6691 22.000 31.000 31.000 44.2430 37.0000 SGO_1998 clpB; ATP-dependent Clp proteinase, ATPbinding chain .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 93

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 93 443.500 404.500 0.557 11.062 0.0011 0.0018 652.3404 437.500 461.5547 437.500 434.000 434.000 619.4019 404.5000 SGO_2000 tsf; translation elongation factor Ts 455.000 425.500 0.163 10.895 0.0136 0.0480 518.1447 347.500 473.5229 347.500 341.500 341.500 487.3866 425.5000 SGO_2001 rpsB; ribosomal protein S2 46.000 62.000 6.780 47.8726 62.0000 SGO_2004 LPXTG cell wall surface protein 379.000 355.000 -4.964 9.595 0.0002 0.0001 11.1830 7.500 394.4289 7.500 9.000 9.000 12.8447 355.0000 SGO_2005 LPXTG cell wall surface protein 5.000 4.500 3.279 5.2035 4.5000 SGO_2006 thioredoxin signature protein 35.500 36.000 -0.015 7.182 0.1504 0.7846 38.0221 25.500 36.9452 25.500 24.000 24.000 34.2526 36.0000 SGO_2007 nusG; transcription termination/antitermination factor NusG 26.500 31.000 5.872 27.5788 31.0000 SGO_2008 preprotein translocase secE component related protein 38.500 36.500 6.259 40.0673 36.5000 SGO_2010 pbp2a; penicillin-binding protein 2A 248.500 246.500 8.980 258.6163 246.5000 SGO_2013 putative N-acetylmuramidase/lysin 1.500 0.585 1.5000 SGO_2015 possible polysaccharide transport protein 4.500 2.170 4.5000 SGO_2016 nucleotide sugar dehydratase, putative 6.500 -0.539 3.456 4.4732 3.000 3.000 6.5000 SGO_2017 nucleotidyl transferase, putative .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 94

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 94 15.500 16.000 -0.881 5.633 0.0003 0.0002 8.2009 5.500 16.1310 5.500 6.500 6.500 9.2768 16.0000 SGO_2019 licD; licD3 protein 6.000 2.585 6.0000 SGO_2020 glycosyltransferase 15.000 23.000 5.271 15.6106 23.0000 SGO_2021 Extracellular polysaccharide glycosyltransferase 4.000 2.000 4.0000 SGO_2022 UDP-glucose 4-epimerase BH3715 27.000 29.000 5.835 28.0992 29.0000 SGO_2023 galactosyltransferase 52.500 69.500 -1.523 7.385 0.0014 0.0026 20.1294 13.500 54.6373 13.500 16.000 16.000 22.8351 69.5000 SGO_2024 Extracellular polysaccharide biosynthesis 30.000 33.000 -0.304 6.869 0.0257 0.1036 30.5668 20.500 31.2213 20.500 15.500 15.500 22.1215 33.0000 SGO_2025 wze; putative autophosphorylating protein tyrosine kinase 30.000 38.500 -0.991 6.710 0.0019 0.0042 16.4017 11.000 31.2213 11.000 13.000 13.000 18.5535 38.5000 SGO_2026 wzd; polysaccharide export protein, MPA1 family 4.500 2.170 4.5000 SGO_2027 wzh; wzh/Putative phosphotyrosine-protein phosphatase 31.000 33.500 -2.941 6.130 0.0049 0.0138 32.2620 3.000 3.000 4.2816 33.5000 SGO_2028 wzg; transcriptional regulator 69.500 67.500 -0.854 7.763 0.0003 0.0002 39.5132 26.500 72.3293 26.500 26.500 26.500 37.8206 67.5000 SGO_2033 nrdD; ribonucleoside-triphosphate reductase 16.500 25.000 -1.989 5.567 0.0362 0.1540 5.2187 3.500 17.1717 3.500 25.0000 SGO_2034 hypothetical protein SGO_2034 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 95

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 95 21.500 22.000 5.472 22.3753 22.0000 SGO_2037 cardiolipin synthase 4.500 7.000 -1.419 3.789 0.0442 0.1931 4.6832 1.500 1.500 2.1408 7.0000 SGO_2039 dihydrofolate synthase 3.000 6.000 1.335 4.956 0.0032 0.0078 11.9285 8.000 3.1221 8.000 7.000 7.000 9.9904 6.0000 SGO_2041 conserved hypothetical protein TIGR00250 40.500 31.000 2.054 8.549 0.0006 0.0008 137.9234 92.500 42.1487 92.500 114.500 114.500 163.4136 31.0000 SGO_2042 Bacterial protein of unknown function (DUF965) superfamily 20.000 23.500 -2.954 5.560 0.0127 0.0442 20.8142 2.000 2.000 2.8544 23.5000 SGO_2043 lipoprotein, putative 294.500 365.500 0.828 10.862 0.0006 0.0008 580.7693 389.500 306.4890 389.500 426.000 426.000 607.9844 365.5000 SGO_2045 recA; recA protein 8.000 14.000 0.321 5.625 0.0568 0.2580 14.1651 9.500 8.3257 9.500 9.000 9.000 12.8447 14.0000 SGO_2046 cinA; competence induced protein 2.000 1.000 2.0000 SGO_2049 tagI; DNA-3-methyladenine glycosylase I 5.000 2.000 1.259 4.533 0.0163 0.0602 5.9643 4.000 5.2035 4.000 7.000 7.000 9.9904 2.0000 SGO_2050 ruvA; Holliday junction DNA helicase RuvA 8.000 3.000 8.0000 SGO_2052 hypothetical protein SGO_2052 19.500 27.500 -1.164 6.120 0.0053 0.0152 8.2009 5.500 20.2938 5.500 9.500 9.500 13.5583 27.5000 SGO_2053 DNA mismatch repair protein hexB 18.500 29.500 -0.084 6.562 0.1403 0.7223 18.6383 12.500 19.2531 12.500 19.000 19.000 27.1167 29.5000 SGO_2056 mutS; DNA mismatch repair protein MutS .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 96

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 96 15.000 17.500 5.049 15.6106 17.5000 SGO_2057 argR; arginine repressor 185.500 204.500 0.451 9.878 0.0008 0.0011 280.3200 188.000 193.0516 188.000 184.500 184.500 263.3172 204.5000 SGO_2058 argS; arginyl-tRNA synthetase 4.000 2.058 4.1628 SGO_2059 hypothetical protein SGO_2059 37.000 55.500 0.996 8.121 0.0014 0.0027 91.7004 61.500 38.5063 61.500 65.000 65.000 92.7676 55.5000 SGO_2060 aspS-1; aspartyl-tRNA synthetase 55.000 79.000 0.686 8.464 0.0046 0.0126 115.5574 77.500 57.2390 77.500 71.000 71.000 101.3307 79.0000 SGO_2062 hisS; histidyl-tRNA synthetase 54.500 66.000 1.647 8.986 0.0005 0.0006 205.7668 138.000 56.7187 138.000 125.000 125.000 178.3992 66.0000 SGO_2064 ilvD; dihydroxy-acid dehydratase SGO_2065 rpmF; ribosomal protein L32 42.000 27.000 1.393 7.977 0.0019 0.0041 99.1557 66.500 43.7098 66.500 57.500 57.500 82.0636 27.0000 SGO_2066 rpmG; ribosomal protein L33 12.500 38.000 -0.247 6.477 0.0921 0.4498 22.3660 15.000 13.0089 15.000 11.000 11.000 15.6991 38.0000 SGO_2070 hypothetical protein SGO_2070 SGO_2073 FtsK/SpoIIIE family subfamily, putative 20.000 15.000 -0.970 5.772 0.0103 0.0343 6.7098 4.500 20.8142 4.500 8.500 8.500 12.1311 15.0000 SGO_2080 transcription activator plcR 30.000 34.000 -2.513 6.148 0.0099 0.0328 31.2213 4.000 4.000 5.7088 34.0000 SGO_2081 lipoprotein, putative .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 97

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 97 18.000 27.000 5.515 18.7328 27.0000 SGO_2082 lipoprotein, putative 9.500 8.000 -0.180 4.686 0.0926 0.4531 9.8867 5.500 5.500 7.8496 8.0000 SGO_2084 NAD(P)H dehydrogenase, quinone family 75.500 84.500 -0.211 8.247 0.0036 0.0090 71.5711 48.000 78.5736 48.000 48.500 48.500 69.2189 84.5000 SGO_2085 purB; adenylosuccinate lyase 11.500 18.500 4.929 11.9682 18.5000 SGO_2086 hypothetical protein SGO_2086 17.500 26.500 5.483 18.2124 26.5000 SGO_2094 general stress protein GSP-781 210.000 238.500 8.836 218.5490 238.5000 SGO_2096 comB; transport protein ComB 493.500 490.000 -5.519 10.002 0.0001 0.0000 11.1830 7.500 513.5902 7.500 7.500 7.500 10.7040 490.0000 SGO_2097 comA; ATP-binding Transport protein ComA 388.500 440.000 0.885 11.230 0.0001 0.0001 774.6076 519.500 404.3157 519.500 548.500 548.500 782.8156 440.0000 SGO_2098 rpsD; ribosomal protein S4 3.098 6.000 6.000 8.5632 SGO_2099 ABC transporter ATP-binding protein 32.000 30.000 2.646 8.845 0.0002 0.0001 209.4945 140.500 33.3027 140.500 131.000 131.000 186.9623 30.0000 SGO_2100 ABC transporter substrate-binding protein 5.180 13.4196 9.000 9.000 16.000 16.000 22.8351 SGO_2102 hypothetical protein SGO_2102 3.000 1.585 3.0000 SGO_2103 hydrolase, haloacid dehalogenase-like family .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 98

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 98 291.000 295.500 -1.730 9.606 0.0001 0.0000 82.0085 55.000 302.8465 55.000 69.500 69.500 99.1899 295.5000 SGO_2104 srtB; sortase B 2230.000 2777.000 -6.934 12.327 0.0003 0.0003 22.3660 15.000 2320.7824 15.000 13.500 13.500 19.2671 2777.0000 SGO_2105 abpA; amylase-binding protein AbpA 79.000 80.500 0.037 8.367 0.1120 0.5587 77.5353 52.000 82.2161 52.000 63.000 63.000 89.9132 80.5000 SGO_2106 ribose-phosphate diphosphokinase 7.000 6.500 3.785 7.2850 6.5000 SGO_2107 general stress protein GSP-781 44.000 43.000 -2.938 6.651 0.0001 0.0000 6.7098 4.500 45.7912 4.500 3.500 3.500 4.9952 43.0000 SGO_2108 mreC; cell shape-determining protein MreC 411.000 462.500 -1.361 10.272 0.0002 0.0001 172.9634 116.000 427.7317 116.000 121.500 121.500 173.4040 462.5000 SGO_2133 Cell division protein ftsH-like protein 62.500 45.000 -0.013 7.764 0.1588 0.8316 55.9149 37.500 65.0444 37.500 36.000 36.000 51.3790 45.0000 SGO_2134 hpt; hypoxanthine phosphoribosyltransferase 5.000 2.322 5.0000 SGO_2138 Septum formation initiator family 2.500 1.380 2.6018 SGO_2139 S4 RNA-binding domain protein 5.000 7.500 3.667 5.2035 7.5000 SGO_2140 transcription-repair coupling factor 2.000 1.000 2.0000 SGO_2141 pth; peptidyl-tRNA hydrolase 48.500 60.000 0.906 8.309 0.0011 0.0018 109.5932 73.500 50.4744 73.500 68.000 68.000 97.0492 60.0000 SGO_2142 GTP-binding protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 99

Hackett Laboratory UW SgPg vs Sg Streptococcus gordonii Summary Table SgFn vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs Sg Protein Log 2 Sum q -Value Log 2 Ratio SgPg vs Sg p -Value Sg SgPg Raw Normalized Description 0 2 4 6 -2 -4 -6 Sg SgPg Log 2 Ratios Page 99 208.000 201.500 -0.255 9.587 0.0085 0.0270 163.2715 109.500 216.4676 109.500 131.500 131.500 187.6759 201.5000 SGO_2145 comE; competence response regulator ComE 58.000 54.000 -1.707 7.223 0.0003 0.0003 18.6383 12.500 60.3612 12.500 11.500 11.500 16.4127 54.0000 SGO_2146 comD; histidine protein kinase ComD 108.500 104.500 -1.324 8.249 0.0002 0.0001 43.9864 29.500 112.9170 29.500 30.000 30.000 42.8158 104.5000 SGO_2150 degP; serine protease .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.



PAGE 1

Hackett Laboratory UW Page 1 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 33.3027 32.000 13.1600 5.000 6.000 53.5000 18.0048 53.500 -1.455 6.882 SGO_0001 0.0038 0.0189 dnaA; chromosomal replication initiator protein DnaA 21.8549 21.000 23.6880 9.000 10.000 39.5000 30.0081 39.500 -0.140 6.846 SGO_0002 0.0591 0.5301 dnaN; DNA polymerase III, beta subunit 142.5772 137.000 39.4800 15.000 14.000 190.5000 42.0113 190.500 -2.017 8.695 SGO_0004 0.0009 0.0028 putative lipoprotein 45.7912 44.000 59.2200 22.500 14.500 49.0000 43.5117 49.000 0.100 7.626 SGO_0006 0.0516 0.4541 ABC transporter, ATP-binding protein 17.6921 17.000 34.2160 13.000 11.000 21.5000 33.0089 21.500 0.785 6.734 SGO_0007 0.0005 0.0012 trpS; tryptophanyl-tRNA synthetase 162.8711 156.500 277.6762 105.500 98.500 133.0000 295.5796 133.000 0.961 9.763 SGO_0008 0.0004 0.0008 inosine-5'-monophosphate dehydrogenase 13.5292 13.000 11.8440 4.500 2.000 16.5000 6.0016 16.500 -0.825 5.581 SGO_0011 0.0082 0.0486 proteinase, M16 family 41.1080 39.500 2.000 39.0000 6.0016 39.000 -2.738 6.428 SGO_0015 0.0039 0.0197 ABC transporter (ATP-binding protein) 6.2443 6.000 7.8960 3.000 3.500 11.5000 10.5028 11.500 0.104 5.176 SGO_0022 0.0906 0.8591 trmU; tRNA (5-methylaminomethyl-2thiouridylate)-methyltransferase 15.0903 14.500 14.4760 5.500 9.500 17.0000 28.5077 17.000 0.343 6.230 SGO_0025 0.0332 0.2749 gidA; glucose inhibited division protein A 94.7046 91.000 5.2640 2.000 76.5000 76.500 -4.015 7.463 SGO_0026 0.0109 0.0718 DHH subfamily 1 protein 31.7416 30.500 40.7960 15.500 20.000 37.5000 60.0162 37.500 0.520 7.410 SGO_0027 0.0109 0.0722 rplI; ribosomal protein L9 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 2 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 11.4478 11.000 3.000 16.5000 9.0024 16.500 -0.610 5.208 SGO_0028 0.0357 0.2993 dnaC; replicative DNA helicase 19.7735 19.000 38.1640 14.500 11.000 24.5000 33.0089 24.500 0.689 6.851 SGO_0030 0.0018 0.0069 aspB; aspartate transaminase 39.5470 38.000 40.7960 15.500 11.500 50.0000 34.5093 50.000 -0.245 7.365 SGO_0032 0.0180 0.1364 plsX; fatty acid/phospholipid synthesis protein PlsX 5.7239 5.500 25.0040 9.500 4.000 7.5000 12.0032 7.500 1.403 5.651 SGO_0033 0.0085 0.0517 acpP; acyl carrier protein 11.9682 11.500 14.4760 5.500 12.5000 12.500 0.243 5.283 SGO_0042 0.0113 0.0752 transcription regulator, GntR family 41.6284 40.000 28.9520 11.000 9.000 48.0000 27.0073 48.000 -0.677 7.186 SGO_0054 0.0010 0.0031 dltA; D-alanine-activating enzyme 103.5506 99.500 22.3720 8.500 7.000 129.0000 21.0057 129.000 -2.415 8.108 SGO_0057 0.0005 0.0010 dltD protein 1308.6923 1257.500 3432.1300 1304.000 1313.500 653.5000 3941.5609 653.500 1.992 13.189 SGO_0059 0.0006 0.0015 pXO1; hypothetical protein SGO_0059 89.5010 86.000 28.9520 11.000 10.000 91.5000 30.0081 91.500 -1.618 7.907 SGO_0063 0.0000 0.0000 hypothetical protein SGO_0063 222.7119 214.000 39.4800 15.000 12.500 208.0000 37.5101 208.000 -2.484 8.988 SGO_0064 0.0001 0.0000 FtsK/SpoIIIE family protein 39.0266 37.500 44.7440 17.000 14.500 40.0000 43.5117 40.000 0.159 7.386 SGO_0065 0.0007 0.0020 hypothetical protein SGO_0065 23.9363 23.000 19.7400 7.500 7.500 23.5000 22.5061 23.500 -0.170 6.487 SGO_0067 0.0082 0.0489 protein with prophage function domain .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 3 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 31.2213 30.000 17.1080 6.500 5.500 28.0000 16.5044 28.000 -0.815 6.537 SGO_0068 0.0004 0.0009 lipoprotein, putative 20.2938 19.500 11.8440 4.500 3.000 22.0000 9.0024 22.000 -1.033 5.980 SGO_0069 0.0006 0.0015 hypothetical protein SGO_0069 19.7735 19.000 30.2680 11.500 8.500 24.0000 25.5069 24.000 0.351 6.637 SGO_0070 0.0080 0.0470 merozoite surface protein 1 53.0762 51.000 34.2160 13.000 11.500 58.0000 34.5093 58.000 -0.691 7.490 SGO_0080 0.0004 0.0007 hypothetical protein SGO_0080 243.5261 234.000 157.9201 60.000 61.500 247.5000 184.5497 247.500 -0.524 9.703 SGO_0104 0.0008 0.0024 Maltose/maltodextrin-binding protein precursor 14.5699 14.000 10.5280 4.000 5.000 11.5000 15.0040 11.500 -0.043 5.689 SGO_0105 0.0920 0.8746 malQ; 4-alpha-glucanotransferase 19.7735 19.000 88.1721 33.500 29.000 27.0000 87.0234 27.000 1.923 7.794 SGO_0106 0.0001 0.0001 glgP-2; maltodextrin phosphorylase 3464.5223 3329.000 1096.2286 416.500 345.500 3222.5000 1036.7791 3222.500 -1.648 13.107 SGO_0113 0.0001 0.0001 acdH; alcohol-acetaldehyde dehydrogenase 80.6550 77.500 27.6360 10.500 13.000 79.5000 39.0105 79.500 -1.286 7.825 SGO_0135 0.0004 0.0008 v-type sodium ATP synthase, subunit A 110.3152 106.000 32.9000 12.500 15.500 127.5000 46.5125 127.500 -1.600 8.309 SGO_0136 0.0005 0.0011 v-type sodium ATP synthase, chain B 33.3027 32.000 30.2680 11.500 6.500 36.0000 19.5052 36.000 -0.511 6.896 SGO_0139 0.0090 0.0555 thrC; threonine synthase 64.0036 61.500 31.5840 12.000 12.500 60.0000 37.5101 60.000 -0.848 7.593 SGO_0145 0.0004 0.0009 polI; DNA polymerase I .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 4 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 11.4478 11.000 27.6360 10.500 3.000 15.5000 9.0024 15.500 0.244 5.991 SGO_0146 0.0505 0.4436 CoA-binding domain protein 10.9275 10.500 9.2120 3.500 2.500 11.5000 7.5020 11.500 -0.431 5.291 SGO_0152 0.0027 0.0119 tgt; queuine tRNA-ribosyltransferase 322.0996 309.500 507.9763 193.000 167.000 251.5000 501.1349 251.500 0.826 10.628 SGO_0154 0.0007 0.0018 pgi; glucose-6-phosphate isomerase 94.1842 90.500 10.5280 4.000 4.000 80.0000 12.0032 80.000 -2.949 7.620 SGO_0156 0.0003 0.0003 hypothetical protein SGO_0156 25.4974 24.500 98.7001 37.500 23.500 21.5000 70.5190 21.500 1.833 7.756 SGO_0158 0.0014 0.0050 2,3,4,5-tetrahydropyridine-2-carboxylate Nsuccinyltransferase, putative 33.3027 32.000 36.8480 14.000 12.500 41.0000 37.5101 41.000 0.009 7.216 SGO_0163 0.1026 0.9909 galU; UTP-glucose-1-phosphate uridylyltransferase 41.6284 40.000 28.9520 11.000 11.000 47.5000 33.0089 47.500 -0.524 7.239 SGO_0164 0.0018 0.0071 Glycerol-3-phosphate dehydrogenase [NAD (P)+] (NAD(P)H-dependent glycerol-3phosphate dehydrogenase) 7.8053 7.500 14.4760 5.500 5.500 12.5000 16.5044 12.500 0.646 5.680 SGO_0169 0.0064 0.0364 dut; dUTP diphosphatase 16.1310 15.500 6.5800 2.500 23.5000 23.500 -1.565 5.530 SGO_0171 0.0219 0.1728 radA; DNA repair protein RadA 62.9629 60.500 97.3841 37.000 37.000 66.5000 111.0299 66.500 0.684 8.400 SGO_0174 0.0008 0.0023 gltX; glutamyl-tRNA synthetase 24.9770 24.000 9.2120 3.500 8.000 42.0000 24.0065 42.000 -1.123 6.647 SGO_0180 0.0120 0.0809 jag; hypothetical protein SGO_0180 13.0089 12.500 2.500 22.0000 7.5020 22.000 -1.173 5.410 SGO_0190 0.0326 0.2689 hypothetical protein SGO_0190 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 5 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 28.6195 27.500 28.9520 11.000 12.000 22.0000 36.0097 22.000 0.364 6.853 SGO_0198 0.0122 0.0827 rpe; ribulose-phosphate 3-epimerase 77.5329 74.500 19.7400 7.500 9.500 83.0000 28.5077 83.000 -1.758 7.706 SGO_0200 0.0003 0.0003 competence-induced protein Ccs50 48.9134 47.000 18.4240 7.000 8.000 41.0000 24.0065 41.000 -1.090 7.048 SGO_0201 0.0011 0.0034 cmp-binding-factor 1 66.0851 63.500 65.8000 25.000 22.500 73.5000 67.5182 73.500 -0.064 8.092 SGO_0204 0.0304 0.2491 rpsL; ribosomal protein S12 117.6002 113.000 197.4001 75.000 87.500 146.0000 262.5707 146.000 0.797 9.499 SGO_0205 0.0036 0.0174 rpsG; ribosomal protein S7 1012.0901 972.500 2202.9853 837.000 627.500 1007.5000 1883.0068 1007.500 1.012 12.576 SGO_0206 0.0006 0.0015 fusA; translation elongation factor G 778.9711 748.500 2184.5613 830.000 919.500 1043.0000 2759.2427 1043.000 1.446 12.724 SGO_0207 0.0010 0.0034 gap; glyceraldehyde-3-phosphate dehydrogenase, type I 879.9200 845.500 2687.2735 1021.000 948.000 814.5000 2844.7657 814.500 1.708 12.819 SGO_0209 0.0001 0.0000 pgk; phosphoglycerate kinase 99.3878 95.500 90.8041 34.500 21.000 104.0000 63.0170 104.000 -0.427 8.481 SGO_0215 0.0090 0.0555 glnA; glutamine synthetase, type I 77.5329 74.500 68.4320 26.000 20.500 67.0000 61.5166 67.000 -0.152 8.101 SGO_0219 0.0183 0.1387 metallo-beta-lactamase superfamily protein 1 9.3664 9.000 13.1600 5.000 9.000 13.0000 27.0073 13.000 0.773 5.967 SGO_0230 0.0163 0.1203 Protein of unknown function, DUF536 family 11.8440 4.500 3.000 3.5000 9.0024 3.500 1.561 4.606 SGO_0232 0.0173 0.1289 conserved hypothetical protein TIGR00103 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

PAGE 6

Hackett Laboratory UW Page 6 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 55.1576 53.000 35.5320 13.500 10.000 54.0000 30.0081 54.000 -0.741 7.449 SGO_0234 0.0004 0.0009 pepX; X-Pro dipeptidyl-peptidase 5.2035 5.000 6.5800 2.500 4.000 11.5000 12.0032 11.500 0.200 5.141 SGO_0237 0.0774 0.7214 ccpA; CcpA protein (proteinase) 3.6425 3.500 15.7920 6.000 4.0000 4.000 2.049 4.551 SGO_0244 0.0023 0.0095 hydroxymethylglutaryl-CoA synthase 737.8631 709.000 360.5842 137.000 114.500 659.0000 343.5925 659.000 -0.986 11.037 SGO_0247 0.0004 0.0007 pfl; formate acetyltransferase 6.7646 6.500 6.5800 2.500 7.5000 7.500 -0.114 4.382 SGO_0252 0.0432 0.3739 possible TetR-type transcriptional regulator 87.9400 84.500 18.4240 7.000 5.000 62.0000 15.0040 62.000 -2.151 7.519 SGO_0255 0.0013 0.0045 Signal peptidase I 3.000 3.0000 9.0024 3.000 1.585 3.585 SGO_0258 hypothetical protein SGO_0258 34.8638 33.500 11.8440 4.500 5.500 38.0000 16.5044 38.000 -1.380 6.661 SGO_0260 0.0004 0.0008 DNA mismatch binding protein MutS2 25.4974 24.500 14.4760 5.500 4.000 23.0000 12.0032 23.000 -0.877 6.228 SGO_0262 0.0006 0.0017 dipeptidase 35.3841 34.000 107.9121 41.000 23.000 39.0000 69.0186 39.000 1.216 7.973 SGO_0263 0.0040 0.0199 trx-1; thioredoxin 23.4160 22.500 27.6360 10.500 7.500 22.5000 22.5061 22.500 0.120 6.586 SGO_0272 0.0310 0.2548 hypothetical protein SGO_0272 137.8940 132.500 164.5001 62.500 64.500 122.0000 193.5521 122.000 0.460 9.271 SGO_0276 0.0031 0.0143 gdhA; glutamate dehydrogenase (NADP) .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

PAGE 7

Hackett Laboratory UW Page 7 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 21.3345 20.500 2.000 23.5000 6.0016 23.500 -1.900 5.668 SGO_0286 0.0073 0.0419 DNA mismatch repair protein MutS, putative 14.0496 13.500 7.8960 3.000 28.5000 28.500 -1.342 5.657 SGO_0290 0.0373 0.3152 copper -translocating P-type ATPase 81.6957 78.500 13.1600 5.000 6.000 69.0000 18.0048 69.000 -2.286 7.507 SGO_0291 0.0004 0.0006 copper-translocating P-type ATPase 104.0710 100.000 221.0881 84.000 66.000 99.5000 198.0533 99.500 1.040 9.282 SGO_0292 0.0003 0.0005 spxB; pyruvate oxidase 402.7546 387.000 813.2885 309.000 260.000 398.0000 780.2100 398.000 0.992 11.225 SGO_0312 0.0001 0.0000 xfp; D-xylulose 5-phosphate/D-fructose 6phosphate phosphoketolase 184.7260 177.500 2.000 214.0000 6.0016 214.000 -5.050 8.661 SGO_0317 0.0082 0.0481 LPXTG cell wall surface protein, serine protease, subtilase family 11.9682 11.500 21.0560 8.000 9.500 22.0000 28.5077 22.000 0.594 6.384 SGO_0321 0.0162 0.1194 polypeptide deformylase 80.6550 77.500 78.9600 30.000 34.500 96.0000 103.5279 96.000 0.039 8.488 SGO_0333 0.0801 0.7503 rpsO; ribosomal protein S15 49.4337 47.500 65.8000 25.000 19.500 52.0000 58.5157 52.000 0.291 7.819 SGO_0342 0.0031 0.0143 pepF-2; oligoendopeptidase 133.7312 128.500 126.3361 48.000 43.500 140.5000 130.5351 140.500 -0.094 9.053 SGO_0344 0.0059 0.0326 pnpA; polyribonucleotide nucleotidyltransferase 22.8956 22.000 30.2680 11.500 8.500 26.0000 25.5069 26.000 0.188 6.710 SGO_0349 0.0171 0.1270 cysS; cysteinyl-tRNA synthetase 68.6868 66.000 42.1120 16.000 13.500 74.0000 40.5109 74.000 -0.788 7.816 SGO_0352 0.0003 0.0003 ABC transporter, ATP-binding protein SP1580 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 8 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 18.2124 17.500 55.2720 21.000 21.000 31.0000 63.0170 31.000 1.313 7.388 SGO_0357 0.0012 0.0041 degV; DegV family fatty acid binding protein 138.4144 133.000 192.1361 73.000 69.500 180.0000 208.5561 180.000 0.343 9.490 SGO_0358 0.0083 0.0498 rplM; ribosomal protein L13 79.0939 76.000 85.5400 32.500 34.000 107.0000 102.0275 107.000 0.022 8.546 SGO_0359 0.0981 0.9422 rpsI; ribosomal protein S9 2.0814 2.000 5.2640 2.000 3.0000 3.000 1.075 3.371 SGO_0368 0.0148 0.1064 merA; mercury(II) reductase 13.5292 13.000 18.4240 7.000 5.500 7.5000 16.5044 7.500 0.792 5.806 SGO_0372 0.0059 0.0319 malate oxidoreductase 23.4160 22.500 13.1600 5.000 2.500 20.0000 7.5020 20.000 -1.123 6.002 SGO_0374 0.0022 0.0094 Response regulator of the LytR/AlgR family 5.2640 2.000 10.0000 10.000 -0.926 3.932 SGO_0376 ABC transporter ATP-binding protein 10.9275 10.500 11.8440 4.500 4.500 20.5000 13.5036 20.500 -0.243 5.827 SGO_0384 0.0418 0.3577 putative carboxylate-amine/thiol ligase 31.2213 30.000 71.0640 27.000 26.500 34.5000 79.5214 34.500 1.196 7.757 SGO_0390 0.0003 0.0005 glycerol-3-phosphate dehydrogenase (NAD (P)+) 14.4760 5.500 3.0000 3.000 2.271 4.127 SGO_0392 phosphoglycerate mutase 60.8815 58.500 6.5800 2.500 3.000 44.0000 9.0024 44.000 -2.749 6.912 SGO_0398 0.0009 0.0028 ABC transporter ATP-binding protein 14.5699 14.000 44.7440 17.000 13.500 37.0000 40.5109 37.000 0.875 7.096 SGO_0401 0.0122 0.0835 grpE; co-chaperone GrpE .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 9 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 452.1883 434.500 644.8404 245.000 229.000 499.0000 687.1850 499.000 0.487 11.157 SGO_0402 0.0007 0.0019 dnaK; DnaK chaperone protein 73.8904 71.000 13.1600 5.000 8.000 129.5000 24.0065 129.500 -2.460 7.910 SGO_0404 0.0032 0.0147 dnaJ; DnaJ chaparone protein 241.4446 232.000 2.500 233.0000 7.5020 233.000 -4.983 8.913 SGO_0408 0.0027 0.0117 zmpB; zinc metalloproteinase B 367.8908 353.500 864.6125 328.500 275.000 428.5000 825.2221 428.500 1.089 11.280 SGO_0412 0.0002 0.0002 tig; trigger factor 16.1310 15.500 32.9000 12.500 11.500 9.5000 34.5093 9.500 1.445 6.540 SGO_0413 0.0007 0.0018 DNA-directed RNA polymerase delta chain 592.6841 569.500 235.5641 89.500 86.000 529.5000 258.0695 529.500 -1.184 10.658 SGO_0415 0.0003 0.0005 secA; preprotein translocase, SecA subunit 24.9770 24.000 31.5840 12.000 6.000 30.5000 18.0048 30.500 -0.211 6.715 SGO_0416 0.0597 0.5367 phospho-2-dehydro-3-deoxyheptonate aldolase 9.8867 9.500 10.5280 4.000 15.0000 15.000 -0.210 5.146 SGO_0426 0.0650 0.5907 Cof family protein 9.8867 9.500 27.6360 10.500 8.500 9.5000 25.5069 9.500 1.454 6.180 SGO_0427 0.0001 0.0001 universal stress protein family 168.5950 162.000 114.4921 43.500 41.000 152.5000 123.0331 152.500 -0.434 9.126 SGO_0429 0.0012 0.0042 aspartate transaminase 33.8231 32.500 36.8480 14.000 11.000 26.0000 33.0089 26.000 0.234 7.019 SGO_0432 0.0184 0.1401 entB; isochorismatase family protein 50.9948 49.000 35.5320 13.500 8.000 63.5000 24.0065 63.500 -0.962 7.443 SGO_0434 0.0026 0.0113 aspS-2; aspartyl-tRNA synthetase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 10 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 18.2124 17.500 22.3720 8.500 6.500 22.0000 19.5052 22.000 0.062 6.359 SGO_0435 0.0647 0.5867 gatC; glutamyl-tRNA(Gln) amidotransferase, C subunit 186.8074 179.500 131.6001 50.000 44.500 161.5000 133.5359 161.500 -0.390 9.261 SGO_0436 0.0025 0.0108 gatA; glutamyl-tRNA(Gln) amidotransferase, A subunit 104.0710 100.000 171.0801 65.000 33.500 103.0000 100.5271 103.000 0.341 8.903 SGO_0437 0.0263 0.2113 gatB; glutamyl-tRNA(Gln) amidotransferase, B subunit 3.1221 3.000 10.5280 4.000 3.5000 3.500 1.671 4.100 SGO_0440 0.0035 0.0167 L-iditol 2-dehydrogenase BH3949 21.8549 21.000 15.7920 6.000 7.000 26.0000 21.0057 26.000 -0.388 6.403 SGO_0445 0.0100 0.0638 GTP-binding protein 10.9275 10.500 3.9480 1.500 6.0000 6.000 -1.036 4.384 SGO_0448 0.0375 0.3180 conserved hypothetical protein TIGR00488 56.1983 54.000 27.6360 10.500 20.000 42.5000 60.0162 42.500 -0.263 7.542 SGO_0454 0.0681 0.6242 conserved hypothetical protein TIGR01033 161.8303 155.500 9.2120 3.500 5.500 136.0000 16.5044 136.000 -3.589 8.338 SGO_0455 0.0003 0.0004 lipoprotein, putative 254.9739 245.000 78.9600 30.000 27.500 274.5000 82.5222 274.500 -1.713 9.432 SGO_0457 0.0001 0.0001 ABC transporter, substrate-binding protein SP0148 834.1288 801.500 196.0841 74.500 69.500 708.5000 208.5561 708.500 -1.927 10.927 SGO_0458 0.0003 0.0006 hlpA; lipoprotein 94.7046 91.000 17.1080 6.500 5.500 75.5000 16.5044 75.500 -2.331 7.671 SGO_0460 0.0005 0.0012 ABC transporter, ATP-binding protein SP0151 12.4885 12.000 19.7400 7.500 4.500 28.5000 13.5036 28.500 -0.209 6.214 SGO_0468 0.0553 0.4919 hypothetical protein SGO_0468 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 11 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 12.4885 12.000 27.6360 10.500 10.000 11.0000 30.0081 11.000 1.297 6.342 SGO_0476 0.0002 0.0002 rhodanese family protein 2.500 4.5000 7.5020 4.500 0.737 3.585 SGO_0480 hypothetical protein SGO_0480 17.6921 17.000 28.9520 11.000 9.500 12.0000 28.5077 12.000 0.979 6.445 SGO_0483 0.0011 0.0035 hypothetical protein SGO_0483 23.4160 22.500 44.7440 17.000 15.000 22.5000 45.0121 22.500 0.967 7.084 SGO_0501 0.0000 0.0000 Uncharacterized ACR, COG1399 302.8465 291.000 138.1801 52.500 48.000 280.0000 144.0388 280.000 -1.046 9.757 SGO_0502 0.0002 0.0002 floL; flotillin-like protein 364.2484 350.000 847.5045 322.000 257.500 340.0000 772.7080 340.000 1.201 11.183 SGO_0503 0.0002 0.0003 gnd; 6-phosphogluconate dehydrogenase, decarboxylating 948.0865 911.000 63.1680 24.000 24.500 902.5000 73.5198 902.500 -3.763 10.957 SGO_0505 0.0001 0.0000 PTS system, IIBC component 25.4974 24.500 22.3720 8.500 6.000 24.5000 18.0048 24.500 -0.317 6.498 SGO_0508 0.0061 0.0338 nrdR; transcriptional regulator, NrdR family 6.7646 6.500 19.7400 7.500 5.500 9.5000 16.5044 9.500 1.171 5.714 SGO_0510 0.0011 0.0038 dnaI; primosomal protein DnaI 4.6832 4.500 10.5280 4.000 2.500 12.5000 7.5020 12.500 0.216 5.138 SGO_0511 0.0919 0.8722 NADPH-flavin oxidoreductase -like protein 63.4833 61.000 100.0161 38.000 26.500 43.0000 79.5214 43.000 0.771 8.160 SGO_0512 0.0043 0.0222 GTP-binding protein engA 88.9807 85.500 106.5961 40.500 45.000 82.0000 135.0363 82.000 0.490 8.689 SGO_0515 0.0047 0.0250 murC; UDP-N-acetylmuramate--alanine ligase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 12 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 176.9206 170.000 52.6400 20.000 21.500 167.0000 64.5174 167.000 -1.560 8.849 SGO_0518 0.0002 0.0001 aminodeoxychorismate lyase-like protein 32.2620 31.000 38.1640 14.500 13.500 37.5000 40.5109 37.500 0.177 7.214 SGO_0519 0.0112 0.0744 greA; transcription elongation factor greA 8.8460 8.500 7.8960 3.000 3.500 17.0000 10.5028 17.000 -0.429 5.467 SGO_0526 0.0284 0.2290 ilvB; acetolactate synthase, large subunit, biosynthetic type 13.0089 12.500 1.500 14.0000 4.5012 14.000 -1.584 4.978 SGO_0527 0.0063 0.0350 ilvN; acetolactate synthase, small subunit 70.7683 68.000 102.6481 39.000 26.500 77.0000 79.5214 77.000 0.292 8.366 SGO_0528 0.0128 0.0887 ilvC; ketol-acid reductoisomerase 2.0814 2.000 2.500 5.5000 7.5020 5.500 1.149 3.915 SGO_0529 0.0332 0.2748 ilvA; threonine dehydratase 44.2302 42.500 7.8960 3.000 54.5000 54.500 -2.636 6.736 SGO_0535 0.0117 0.0784 putative transcriptional regulator LytR 31.7416 30.500 35.5320 13.500 11.000 36.0000 33.0089 36.000 0.019 7.090 SGO_0536 0.0847 0.7979 hypothetical protein SGO_0536 11.9682 11.500 21.0560 8.000 8.000 16.5000 24.0065 16.500 0.678 6.200 SGO_0537 0.0029 0.0130 HIT family protein 36.9452 35.500 34.2160 13.000 10.500 33.5000 31.5085 33.500 -0.100 7.089 SGO_0540 0.0204 0.1589 hypothetical protein SGO_0540 91.0621 87.500 44.7440 17.000 17.500 95.0000 52.5141 95.000 -0.940 8.146 SGO_0543 0.0003 0.0004 nusA; transcription termination factor NusA 137.8940 132.500 72.3800 27.500 34.000 103.5000 102.0275 103.500 -0.475 8.700 SGO_0546 0.0122 0.0836 infB; Translation initiation factor IF-2 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 13 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 109.2745 105.000 7.8960 3.000 2.500 91.5000 7.5020 91.500 -3.700 7.756 SGO_0548 0.0003 0.0004 Na/Pi-cotransporter family protein 3.6425 3.500 31.5840 12.000 9.500 9.0000 28.5077 9.000 2.390 6.185 SGO_0552 0.0004 0.0009 oxidoreductase, aldo/keto reductase family 18.7328 18.000 9.2120 3.500 45.5000 45.500 -1.664 6.199 SGO_0554 0.0395 0.3367 hsdR; type I site-specific deoxyribonuclease 2.000 5.0000 6.0016 5.000 0.263 3.460 SGO_0558 hypothetical protein SGO_0558 10.4071 10.000 11.8440 4.500 3.000 11.0000 9.0024 11.000 -0.051 5.401 SGO_0560 0.0810 0.7600 hsdM; type I restriction-modification system, M subunit 58.8001 56.500 60.5360 23.000 21.500 65.5000 64.5174 65.500 0.010 7.962 SGO_0565 0.0921 0.8777 adhA; alcohol dehydrogenase 35.9045 34.500 25.0040 9.500 12.000 38.0000 36.0097 38.000 -0.300 7.076 SGO_0568 0.0184 0.1403 glyQ; glycyl-tRNA synthetase, alpha subunit 72.8497 70.000 73.6960 28.000 36.500 73.0000 109.5295 73.000 0.301 8.362 SGO_0569 0.0214 0.1686 glyS; glycyl-tRNA synthetase, beta subunit 21.3345 20.500 7.8960 3.000 5.000 31.0000 15.0040 31.000 -1.240 6.233 SGO_0573 0.0046 0.0239 mraW; S-adenosyl-methyltransferase MraW 24.4567 23.500 26.3200 10.000 13.500 37.0000 40.5109 37.000 0.118 7.003 SGO_0577 0.0712 0.6568 ATP-dependent RNA helicase 11.4478 11.000 11.8440 4.500 4.000 15.0000 12.0032 15.000 -0.136 5.652 SGO_0581 0.0353 0.2946 trxB; thioredoxin-disulfide reductase 18.7328 18.000 56.5880 21.500 13.000 27.0000 39.0105 27.000 1.063 7.143 SGO_0582 0.0042 0.0212 nicotinate phosphoribosyltransferase, putative .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 14 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 5.7239 5.500 13.1600 5.000 5.000 12.5000 15.0040 12.500 0.732 5.536 SGO_0583 0.0130 0.0915 nadE; NAD+ synthetase 20.2938 19.500 39.4800 15.000 10.500 29.5000 31.5085 29.500 0.528 6.916 SGO_0585 0.0092 0.0570 pepC; aminopeptidase C 160.7896 154.500 40.7960 15.500 15.500 171.5000 46.5125 171.500 -1.931 8.713 SGO_0586 0.0001 0.0001 pbp1a; penicillin-binding protein 1A 24.9770 24.000 55.2720 21.000 14.000 29.0000 42.0113 29.000 0.840 7.241 SGO_0589 0.0028 0.0124 methylase 14.0496 13.500 7.8960 3.000 20.5000 20.500 -1.104 5.408 SGO_0590 0.0263 0.2109 Methyltransferase 216.4676 208.000 23.6880 9.000 9.500 211.0000 28.5077 211.000 -3.040 8.906 SGO_0591 0.0000 0.0000 hypothetical protein SGO_0591 8.3257 8.000 10.5280 4.000 9.5000 9.500 0.243 4.825 SGO_0592 0.0276 0.2220 luxS; autoinducer-2 production protein LuxS 203.9791 196.000 31.5840 12.000 7.500 220.5000 22.5061 220.500 -2.992 8.903 SGO_0593 0.0001 0.0001 HD/KH domain protein 22.3753 21.500 14.4760 5.500 5.500 17.5000 16.5044 17.500 -0.356 6.147 SGO_0594 0.0097 0.0616 gmk; Guanylate kinase (GMP kinase) 42.1487 40.500 27.6360 10.500 8.000 43.5000 24.0065 43.500 -0.733 7.101 SGO_0595 0.0004 0.0006 DNA-directed RNA polymerase, omega subunit 5.2035 5.000 11.8440 4.500 3.000 10.5000 9.0024 10.500 0.482 5.192 SGO_0597 0.0290 0.2349 fmt; methionyl-tRNA formyltransferase 40.5877 39.000 18.4240 7.000 9.000 38.0000 27.0073 38.000 -0.816 6.954 SGO_0599 0.0019 0.0077 phosphoprotein phosphatase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 15 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 109.2745 105.000 11.8440 4.500 115.0000 115.000 -3.243 7.883 SGO_0600 0.0037 0.0182 serine/threonine protein kinase 49.4337 47.500 72.3800 27.500 21.500 62.5000 64.5174 62.500 0.298 7.959 SGO_0604 0.0102 0.0659 hydrolase, haloacid dehalogenase family/peptidyl-prolyl cis-trans isomerase, cyclophilin type 168.5950 162.000 126.3361 48.000 44.000 181.0000 132.0355 181.000 -0.436 9.248 SGO_0606 0.0006 0.0014 cysK; cysteine synthase A 78.0532 75.000 131.6001 50.000 27.000 66.0000 81.0218 66.000 0.525 8.478 SGO_0610 0.0148 0.1065 ribosomal subunit interface protein 20.8142 20.000 6.5800 2.500 21.5000 21.500 -1.685 5.612 SGO_0626 0.0032 0.0150 recX; Regulatory protein recX 3.1221 3.000 15.7920 6.000 6.000 18.0048 2.433 5.206 SGO_0631 0.0084 0.0510 alpha-glycerophosphate oxidase 68.1665 65.500 71.0640 27.000 18.000 63.0000 54.0145 63.000 -0.081 8.001 SGO_0639 0.0655 0.5956 valS; valyl-tRNA synthetase 6.2443 6.000 6.500 3.5000 19.5052 3.500 2.061 4.870 SGO_0640 0.0095 0.0595 modification methylase 33.8231 32.500 22.3720 8.500 6.000 27.0000 18.0048 27.000 -0.590 6.661 SGO_0641 0.0043 0.0221 ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein protein 41.1080 39.500 122.3881 46.500 35.500 53.5000 106.5287 53.500 1.284 8.338 SGO_0642 0.0006 0.0014 hypothetical protein SGO_0642 6.2443 6.000 5.2640 2.000 8.5000 8.500 -0.469 4.323 SGO_0643 0.0371 0.3127 cytosine-specific methyltransferase 16.6514 16.000 23.6880 9.000 10.000 15.5000 30.0081 15.500 0.731 6.424 SGO_0644 0.0024 0.0102 hypothetical protein SGO_0644 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 16 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 73.8904 71.000 9.2120 3.500 2.000 69.5000 6.0016 69.500 -3.269 7.309 SGO_0652 0.0001 0.0000 hypothetical protein SGO_0652 77.0125 74.000 38.1640 14.500 10.000 97.5000 30.0081 97.500 -1.356 7.923 SGO_0654 0.0011 0.0036 radical SAM enzyme, Cfr family 17.6921 17.000 14.4760 5.500 2.000 17.5000 6.0016 17.500 -0.917 5.799 SGO_0656 0.0092 0.0574 trpB-2; tryptophan synthase, beta subunit 422.0077 405.500 303.9962 115.500 68.500 298.5000 205.5553 298.500 -0.506 10.265 SGO_0665 0.0144 0.1037 non-heme iron-containing ferritin 50.9948 49.000 78.9600 30.000 29.000 55.5000 87.0234 55.500 0.640 8.090 SGO_0669 0.0006 0.0015 typA; GTP-binding protein TypA 31.7416 30.500 17.1080 6.500 6.500 29.5000 19.5052 29.500 -0.744 6.613 SGO_0671 0.0005 0.0010 murD; UDP-N-acetylmuramoylalanine--Dglutamate ligase 44.2302 42.500 3.9480 1.500 31.5000 31.500 -3.241 6.316 SGO_0672 0.0161 0.1181 murG; undecaprenyl-PP-MurNAcpentapeptide-UDPGlcNAc GlcNAc transferase 34.8638 33.500 5.2640 2.000 45.5000 45.500 -2.920 6.420 SGO_0673 0.0136 0.0962 DivIB; cell division protein DivIB 118.6409 114.000 153.9721 58.500 57.000 122.5000 171.0460 122.500 0.429 9.145 SGO_0674 0.0011 0.0037 ftsA; cell division protein FtsA 151.4232 145.500 318.4722 121.000 111.500 213.5000 334.5901 213.500 0.860 9.992 SGO_0675 0.0013 0.0044 ftsZ; cell division protein FtsZ 14.0496 13.500 15.7920 6.000 5.000 19.0000 15.0040 19.000 -0.086 5.997 SGO_0676 0.0553 0.4930 conserved hypothetical protein TIGR00044 115.5188 111.000 76.3280 29.000 15.000 88.5000 45.0121 88.500 -0.787 8.346 SGO_0677 0.0071 0.0406 ylmF protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 17 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 97.3063 93.500 107.9121 41.000 46.000 93.0000 138.0372 93.000 0.360 8.769 SGO_0680 0.0084 0.0506 cell division protein DivIVA 77.5329 74.500 111.8601 42.500 34.500 101.0000 103.5279 101.000 0.282 8.622 SGO_0681 0.0122 0.0830 ileS; isoleucyl-tRNA synthetase 100.9488 97.000 61.8520 23.500 19.500 102.0000 58.5157 102.000 -0.754 8.337 SGO_0684 0.0001 0.0000 hypothetical protein SGO_0684 76.4922 73.500 50.0080 19.000 16.000 72.5000 48.0129 72.500 -0.604 7.948 SGO_0688 0.0002 0.0003 ATP dependent Clp protease, ATP-binding subunit, ClpE 20.8142 20.000 1.500 16.0000 4.5012 16.000 -2.019 5.369 SGO_0693 0.0151 0.1091 xseA; exodeoxyribonuclease VII, large subunit 19.2531 18.500 10.5280 4.000 6.500 13.5000 19.5052 13.500 -0.170 5.972 SGO_0700 0.0741 0.6885 DegV family protein 1115.6407 1072.000 2364.8534 898.500 605.000 974.0000 1815.4886 974.000 0.991 12.614 SGO_0701 0.0019 0.0078 hup; DNA-binding histone-like protein HU 200.8570 193.000 1319.9488 501.500 452.000 306.5000 1356.3651 306.500 2.431 11.636 SGO_0704 0.0001 0.0001 gpmA; 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 3.1221 3.000 3.500 6.0000 10.5028 6.000 1.279 4.295 SGO_0706 0.0196 0.1513 phoH-like protein 214.3862 206.000 10.5280 4.000 1.500 211.0000 4.5012 211.000 -4.949 8.783 SGO_0707 0.0000 0.0000 LPXTG cell wall surface protein 142.5772 137.000 219.7721 83.500 89.500 154.5000 268.5723 154.500 0.711 9.617 SGO_0708 0.0018 0.0071 ald; alanine dehydrogenase 30.7009 29.500 42.1120 16.000 11.500 27.0000 34.5093 27.000 0.405 7.070 SGO_0713 0.0056 0.0304 sgg; GTP-binding protein Era .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 18 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 8.8460 8.500 18.4240 7.000 2.500 10.5000 7.5020 10.500 0.287 5.501 SGO_0721 0.0435 0.3781 abpB-like dipeptidase lipoprotein 16.6514 16.000 3.9480 1.500 14.0000 14.000 -1.951 5.113 SGO_0736 0.0111 0.0738 hprK; HPr(Ser) kinase/phosphatase 11.4478 11.000 19.7400 7.500 6.000 9.5000 18.0048 9.500 0.854 5.875 SGO_0739 0.0006 0.0015 hypothetical protein SGO_0739 15.6106 15.000 18.4240 7.000 18.0000 18.000 0.136 5.701 SGO_0742 0.0463 0.4048 peptidase, U32 family 83.2568 80.000 27.6360 10.500 14.500 88.0000 43.5117 88.000 -1.304 7.921 SGO_0743 0.0007 0.0019 peptidase, U32 family 8.3257 8.000 71.0640 27.000 16.000 13.5000 48.0129 13.500 2.462 7.139 SGO_0745 0.0015 0.0057 hypothetical protein SGO_0745 13.5292 13.000 26.3200 10.000 8.000 21.0000 24.0065 21.000 0.577 6.407 SGO_0749 0.0069 0.0395 glutathione reductase 736.8224 708.000 138.1801 52.500 40.000 584.5000 120.0323 584.500 -2.349 10.625 SGO_0750 0.0005 0.0012 efflux transporter, RND family, MFP subunit subfamily 85.8585 82.500 98.7001 37.500 28.500 77.0000 85.5230 77.000 0.176 8.439 SGO_0751 0.0142 0.1021 ABC transporter, ATP-binding protein SP0786 62.4426 60.000 3.000 80.5000 9.0024 80.500 -2.977 7.247 SGO_0752 0.0130 0.0914 ABC transporter, ATP-binding protein 149.8622 144.000 121.0721 46.000 46.000 130.5000 138.0372 130.500 -0.113 9.075 SGO_0753 0.0303 0.2481 lysS; lysyl-tRNA synthetase 8.3257 8.000 2.500 10.0000 7.5020 10.000 -0.282 4.691 SGO_0755 0.0355 0.2972 regulatory protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 19 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 121.7630 117.000 176.3441 67.000 51.000 122.0000 153.0412 122.000 0.431 9.163 SGO_0760 0.0019 0.0079 ppc; phosphoenolpyruvate carboxylase 2313.4975 2223.000 3711.1221 1410.000 1207.500 2341.0000 3623.4753 2341.000 0.656 13.549 SGO_0761 0.0001 0.0000 tuf; translation elongation factor Tu 400.1528 384.500 1147.5527 436.000 247.000 417.0000 741.1995 417.000 1.175 11.402 SGO_0762 0.0039 0.0197 tpiA; triosephosphate isomerase 91.0621 87.500 46.0600 17.500 8.500 103.0000 25.5069 103.000 -1.499 8.053 SGO_0763 0.0010 0.0030 murA-1; UDP-N-acetylglucosamine 1carboxyvinyltransferase 58.2797 56.000 73.6960 28.000 25.000 36.0000 75.0202 36.000 0.699 7.925 SGO_0771 0.0046 0.0243 pepq; proline dipeptidase 528.6805 508.000 84.2240 32.000 31.500 476.5000 94.5254 476.500 -2.492 10.209 SGO_0773 0.0001 0.0001 ccpA; catabolite control protein A 58.8001 56.500 14.4760 5.500 46.5000 46.500 -1.853 6.904 SGO_0774 0.0142 0.1017 glycosyl transferase, group 1 family protein 29.6602 28.500 11.8440 4.500 4.000 24.0000 12.0032 24.000 -1.162 6.276 SGO_0775 0.0009 0.0028 glycosyl transferase, group 1 154.0250 148.000 118.4401 45.000 39.500 161.5000 118.5319 161.500 -0.413 9.110 SGO_0778 0.0003 0.0004 thrS; threonyl-tRNA synthetase 20.2938 19.500 17.1080 6.500 2.500 31.0000 7.5020 31.000 -1.147 6.246 SGO_0779 0.0082 0.0488 response regulator 109.7949 105.500 17.1080 6.500 5.500 138.5000 16.5044 138.500 -2.876 8.139 SGO_0784 0.0005 0.0010 smc; chromosome segregation protein SMC 10.9275 10.500 18.4240 7.000 4.500 13.5000 13.5036 13.500 0.377 5.816 SGO_0786 0.0142 0.1012 Cof family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 20 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 58.2797 56.000 23.6880 9.000 10.500 48.0000 31.5085 48.000 -0.953 7.335 SGO_0787 0.0016 0.0064 ftsY; cell division protein FtsY 28.0992 27.000 57.9040 22.000 19.000 23.5000 57.0153 23.500 1.161 7.380 SGO_0788 0.0002 0.0002 zwf; glucose-6-phosphate 1-dehydrogenase 39.5470 38.000 36.8480 14.000 11.000 51.5000 33.0089 51.500 -0.372 7.330 SGO_0792 0.0097 0.0613 hypothetical protein SGO_0792 52.0355 50.000 35.5320 13.500 13.000 60.5000 39.0105 60.500 -0.592 7.547 SGO_0794 0.0015 0.0055 metallo-beta-lactamase family protein 5.7239 5.500 7.8960 3.000 2.500 5.0000 7.5020 5.000 0.525 4.707 SGO_0795 0.0008 0.0022 tributyrin esterase 83.2568 80.000 30.2680 11.500 10.000 70.5000 30.0081 70.500 -1.346 7.742 SGO_0798 0.0005 0.0011 ABC transporter, ATP-binding protein SP1381 21.8549 21.000 9.2120 3.500 43.0000 43.000 -1.735 6.211 SGO_0800 0.0329 0.2721 polysaccharide deacetylase family protein 83.7771 80.500 153.9721 58.500 34.000 71.5000 102.0275 71.500 0.695 8.684 SGO_0801 0.0080 0.0468 hom; homoserine dehydrogenase 19.2531 18.500 14.4760 5.500 7.000 21.5000 21.0057 21.500 -0.222 6.252 SGO_0802 0.0335 0.2779 thrB; homoserine kinase 89.5010 86.000 18.4240 7.000 3.000 96.5000 9.0024 96.500 -2.851 7.738 SGO_0803 0.0002 0.0002 hypothetical protein SGO_0803 5.2640 2.000 4.5000 4.500 0.226 3.287 SGO_0814 aminotransferase, class-V 47.8726 46.000 30.2680 11.500 11.500 55.0000 34.5093 55.000 -0.667 7.389 SGO_0815 0.0012 0.0041 thiI; thiamine biosynthesis protein ThiI .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

PAGE 21

Hackett Laboratory UW Page 21 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 90.5417 87.000 310.5762 118.000 122.500 63.5000 367.5989 63.500 2.156 9.701 SGO_0818 0.0004 0.0007 rplU; ribosomal protein L21 75.4514 72.500 73.6960 28.000 15.500 41.0000 46.5125 41.000 0.074 7.887 SGO_0820 0.0933 0.8915 rpmA; ribosomal protein L27 26.0177 25.000 51.3240 19.500 18.500 40.0000 55.5149 40.000 0.727 7.433 SGO_0824 0.0035 0.0168 lepA; GTP-binding protein LepA 46.3116 44.500 2.500 36.5000 7.5020 36.500 -2.454 6.497 SGO_0832 0.0130 0.0915 hypothetical protein SGO_0832 33.8231 32.500 75.0120 28.500 34.500 45.0000 103.5279 45.000 1.176 8.008 SGO_0835 0.0025 0.0110 nitroreductase 103.0303 99.000 171.0801 65.000 45.500 118.0000 136.5367 118.000 0.471 9.046 SGO_0836 0.0053 0.0283 pepV; dipeptidase PepV 3.6425 3.500 7.8960 3.000 2.500 9.5000 7.5020 9.500 0.388 4.835 SGO_0842 0.0615 0.5534 rhodanese family protein 50.4744 48.500 136.8641 52.000 42.500 50.0000 127.5343 50.000 1.395 8.511 SGO_0848 0.0001 0.0001 rpmE; ribosomal protein L31 23.4160 22.500 180.2921 68.500 26.500 22.5000 79.5214 22.500 2.383 8.256 SGO_0850 0.0063 0.0348 flavodoxin 350.1988 336.500 7.8960 3.000 3.000 369.5000 9.0024 369.500 -5.415 9.525 SGO_0854 0.0001 0.0000 cshA; surface-associated protein CshA 129.5683 124.500 28.9520 11.000 8.500 138.5000 25.5069 138.500 -2.301 8.333 SGO_0856 0.0001 0.0000 ABC transporter, substrate binding protein 56.7187 54.500 25.0040 9.500 10.500 42.5000 31.5085 42.500 -0.807 7.283 SGO_0859 0.0037 0.0179 pheS; phenylalanyl-tRNA synthetase, alpha subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 22 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 103.0303 99.000 147.3921 56.000 55.500 87.0000 166.5448 87.000 0.727 8.977 SGO_0861 0.0010 0.0033 pheT; phenylalanyl-tRNA synthetase, beta subunit 10.4071 10.000 7.8960 3.000 3.000 15.0000 9.0024 15.000 -0.567 5.403 SGO_0885 0.0086 0.0525 cobyric acid synthase 21.3345 20.500 1.500 15.5000 4.5012 15.500 -2.014 5.369 SGO_0888 0.0175 0.1316 hypothetical protein SGO_0888 37.4655 36.000 25.0040 9.500 5.500 35.5000 16.5044 35.500 -0.844 6.839 SGO_0889 0.0020 0.0083 glmM; phosphoglucosamine mutase 45.7912 44.000 60.5360 23.000 20.000 38.5000 60.0162 38.500 0.522 7.678 SGO_0893 0.0010 0.0033 GTP-binding protein 17.6921 17.000 7.8960 3.000 4.500 17.5000 13.5036 17.500 -0.769 5.823 SGO_0901 0.0046 0.0238 DNA-directed DNA polymerase III 10.9275 10.500 38.1640 14.500 17.500 14.5000 52.5141 14.500 1.830 6.859 SGO_0906 0.0013 0.0047 leuA; 2-isopropylmalate synthase 30.1806 29.000 77.6440 29.500 33.000 32.5000 99.0267 32.500 1.485 7.903 SGO_0911 0.0009 0.0027 hypothetical protein SGO_0911 2.6018 2.500 1.500 1.5000 4.5012 1.500 1.188 3.105 SGO_0936 0.0184 0.1408 phosphoenolpyruvate synthase, putative 9.3664 9.000 5.2640 2.000 5.5000 5.500 -0.447 4.331 SGO_0940 0.0526 0.4634 ppsA; phosphoenolpyruvate synthase 31.2213 30.000 14.4760 5.500 8.500 28.0000 25.5069 28.000 -0.622 6.632 SGO_0946 0.0098 0.0625 Deblocking aminopeptidase 13.0089 12.500 6.5800 2.500 9.5000 9.500 -0.757 4.862 SGO_0949 0.0284 0.2286 deaD; DEAD RNA helicase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 23 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 5.2640 2.000 9.0000 9.000 -0.774 3.834 SGO_0950 oxidoreductase 13.5292 13.000 13.1600 5.000 5.500 18.0000 16.5044 18.000 -0.083 5.935 SGO_0951 0.0662 0.6035 udk; uridine kinase 18.7328 18.000 19.7400 7.500 11.000 17.5000 33.0089 17.500 0.496 6.475 SGO_0954 0.0164 0.1211 ATP-binding protein 126.4462 121.500 11.8440 4.500 4.000 144.0000 12.0032 144.000 -3.500 8.201 SGO_0982 0.0002 0.0002 amino acid ABC transporter, amino acidbinding protein 49.9541 48.000 63.1680 24.000 21.000 44.5000 63.0170 44.500 0.420 7.786 SGO_0987 0.0008 0.0021 metK; S-adenosylmethionine synthetase 5.7239 5.500 5.2640 2.000 13.5000 13.500 -0.740 4.614 SGO_0995 0.0526 0.4645 metallo-beta-lactamase superfamily protein 44.2302 42.500 52.6400 20.000 24.500 31.0000 73.5198 31.000 0.748 7.654 SGO_1001 0.0066 0.0376 apt; adenine phosphoribosyltransferase 5.7239 5.500 10.5280 4.000 3.500 7.5000 10.5028 7.500 0.682 5.098 SGO_1005 0.0013 0.0047 Bcl-2 family protein 59.3204 57.000 121.0721 46.000 55.000 68.5000 165.0444 68.500 1.149 8.693 SGO_1009 0.0021 0.0088 rfbA-1; glucose-1-phosphate thymidylyltransferase 29.1399 28.000 56.5880 21.500 18.000 29.5000 54.0145 29.500 0.915 7.403 SGO_1010 0.0001 0.0001 rmlC; dTDP-4-keto-6-deoxyglucose-3,5epimerase 36.4248 35.000 67.1160 25.500 25.500 58.0000 76.5206 58.000 0.641 7.895 SGO_1011 0.0064 0.0362 rfbB-1; dTDP-glucose 4,6-dehydratase 74.9311 72.000 107.9121 41.000 37.500 72.0000 112.5303 72.000 0.585 8.521 SGO_1012 0.0002 0.0002 galE-1; UDP-glucose 4-epimerase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 24 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 35.9045 34.500 14.4760 5.500 28.5000 28.500 -1.144 6.302 SGO_1013 0.0175 0.1311 Glycosyltransferase involved in cell wall biogenesis 17.6921 17.000 6.5800 2.500 26.0000 26.000 -1.705 5.652 SGO_1016 0.0215 0.1691 putative glycosyltransferase 41.1080 39.500 3.9480 1.500 40.0000 40.000 -3.361 6.410 SGO_1019 0.0023 0.0096 glycosyl transferase 39.0266 37.500 60.5360 23.000 16.500 37.5000 49.5133 37.500 0.517 7.544 SGO_1020 0.0030 0.0137 rfbD; dTDP-4-dehydrorhamnose reductase 22.3753 21.500 22.3720 8.500 4.500 30.0000 13.5036 30.000 -0.576 6.464 SGO_1025 0.0131 0.0922 rgp; glycosyltransferase 80.1346 77.000 10.5280 4.000 4.000 134.5000 12.0032 134.500 -3.207 7.890 SGO_1026 0.0021 0.0088 rhamnosyltransferase 14.0496 13.500 5.2640 2.000 3.000 13.0000 9.0024 13.000 -0.973 5.369 SGO_1031 0.0025 0.0107 cmk; cytidylate kinase 12.4885 12.000 7.8960 3.000 3.000 13.5000 9.0024 13.500 -0.623 5.422 SGO_1032 0.0007 0.0018 infC; translation initiation factor IF-3 37.4655 36.000 19.7400 7.500 15.000 78.5000 45.0121 78.500 -0.863 7.498 SGO_1033 0.0208 0.1629 rpmI; ribosomal protein L35 164.4321 158.000 284.2562 108.000 49.500 165.5000 148.5400 165.500 0.317 9.575 SGO_1034 0.0337 0.2807 rplT; ribosomal protein L20 7.2850 7.000 13.1600 5.000 5.500 13.0000 16.5044 13.000 0.599 5.642 SGO_1035 0.0130 0.0914 gloA; lactoylglutathione lyase 35.9045 34.500 7.8960 3.000 3.000 50.0000 9.0024 50.000 -2.329 6.684 SGO_1036 0.0011 0.0035 amino acid ABC transporter, ATP-binding protein SP1242 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 25 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 4.1628 4.000 9.2120 3.500 4.500 8.5000 13.5036 8.500 0.907 5.145 SGO_1038 0.0101 0.0649 uvrB; excinuclease ABC, B subunit 15.0903 14.500 14.4760 5.500 3.000 22.5000 9.0024 22.500 -0.691 5.932 SGO_1047 0.0115 0.0768 hypothetical protein SGO_1047 1.5611 1.500 6.5800 2.500 6.5000 6.500 1.047 3.872 SGO_1049 0.0552 0.4899 tRNA pseudouridine synthase B 2.000 2.5000 6.0016 2.500 1.263 3.088 SGO_1050 ribF; riboflavin biosynthesis protein RibF 32.7824 31.500 26.3200 10.000 36.0000 36.000 -0.384 6.571 SGO_1058 0.0169 0.1253 pstB; Phosphate import ATP-binding protein pstB 2 (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) 23.9363 23.000 43.4280 16.500 14.000 23.5000 42.0113 23.500 0.849 7.054 SGO_1059 0.0001 0.0000 pstB; Phosphate import ATP-binding protein pstB 1 (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) 54.1169 52.000 23.6880 9.000 8.500 65.5000 25.5069 65.500 -1.276 7.399 SGO_1060 0.0007 0.0018 phosphate transport system regulatory protein 30.1806 29.000 13.1600 5.000 5.500 28.5000 16.5044 28.500 -0.993 6.465 SGO_1065 0.0004 0.0009 hypothetical protein SGO_1065 87.4196 84.000 96.0681 36.500 35.500 74.0000 106.5287 74.000 0.331 8.508 SGO_1069 0.0047 0.0248 membrane alanyl aminopeptidase 28.6195 27.500 18.4240 7.000 7.000 42.5000 21.0057 42.500 -0.826 6.789 SGO_1079 0.0056 0.0302 pdp; pyrimidine-nucleoside phosphorylase 83.7771 80.500 69.7480 26.500 24.500 73.0000 73.5198 73.000 -0.127 8.229 SGO_1080 0.0176 0.1329 deoC; deoxyribose-phosphate aldolase 3.6425 3.500 7.8960 3.000 9.0000 9.000 0.464 4.360 SGO_1081 0.0716 0.6617 cdd; cytidine deaminase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 26 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 2712.6096 2606.500 1817.3970 690.500 340.500 2801.5000 1021.7750 2801.500 -1.016 13.028 SGO_1082 0.0024 0.0103 lipoprotein 2.0814 2.000 3.9480 1.500 4.5000 4.500 0.367 3.396 SGO_1088 0.0737 0.6830 transcription regulator, LysR family 51.5151 49.500 368.4802 140.000 88.500 58.5000 265.5715 58.500 2.511 9.539 SGO_1096 0.0010 0.0031 butA; acetoin dehydrogenase 10.5280 4.000 3.000 3.5000 9.0024 3.500 1.476 4.525 SGO_1098 0.0115 0.0771 proA; gamma-glutamyl phosphate reductase 9.8867 9.500 11.8440 4.500 9.5000 9.500 0.289 4.965 SGO_1104 0.0092 0.0571 carB; carbamoyl-phosphate synthase, large subunit 17.1717 16.500 2.000 10.5000 6.0016 10.500 -1.162 5.074 SGO_1107 0.0311 0.2563 PyrR bifunctional protein 69.2072 66.500 56.5880 21.500 16.000 81.5000 48.0129 81.500 -0.527 7.996 SGO_1109 0.0029 0.0129 pyrB; aspartate carbamoyltransferase 47.3523 45.500 5.2640 2.000 61.0000 61.000 -3.352 6.828 SGO_1111 0.0127 0.0882 fruR; phosphotransferase system repressor 60.3612 58.000 2.000 62.5000 6.0016 62.500 -3.355 7.010 SGO_1112 0.0028 0.0123 fruB; 1-phosphofructokinase 1095.8672 1053.000 68.4320 26.000 27.500 1124.0000 82.5222 1124.000 -3.884 11.211 SGO_1113 0.0000 0.0000 fruA; PTS system, fructose specific IIABC components 48.3930 46.500 9.2120 3.500 3.500 44.5000 10.5028 44.500 -2.238 6.815 SGO_1114 0.0001 0.0001 Protein of unknown function (DUF1149) superfamily 6.7646 6.500 35.5320 13.500 15.000 8.5000 45.0121 8.500 2.399 6.582 SGO_1116 0.0006 0.0013 dapB; dihydrodipicolinate reductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 27 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 49.9541 48.000 77.6440 29.500 35.000 62.0000 105.0283 62.000 0.698 8.203 SGO_1120 0.0049 0.0263 guaA; GMP synthase 36.4248 35.000 69.7480 26.500 26.500 38.0000 79.5214 38.000 1.001 7.805 SGO_1123 0.0004 0.0010 ffh; signal recognition particle protein 29.1399 28.000 18.4240 7.000 5.500 26.5000 16.5044 26.500 -0.672 6.501 SGO_1129 0.0006 0.0016 lplA; lipoate protein ligase A 113.4373 109.000 57.9040 22.000 19.000 110.0000 57.0153 110.000 -0.959 8.402 SGO_1130 0.0001 0.0000 dihydrolipoamide dehydrogenase 33.3027 32.000 15.7920 6.000 7.500 34.0000 22.5061 34.000 -0.836 6.722 SGO_1131 0.0014 0.0050 sucB; dihydrolipoamide S-acetyltransferase 15.6106 15.000 5.2640 2.000 25.0000 25.000 -1.908 5.520 SGO_1132 0.0242 0.1926 acetoin dehydrogenase 36.4248 35.000 10.5280 4.000 6.000 28.0000 18.0048 28.000 -1.214 6.539 SGO_1133 0.0027 0.0117 acoA; acetoin dehydrogenase 4.6832 4.500 2.000 6.5000 6.0016 6.500 0.121 4.103 SGO_1134 0.0782 0.7301 hypothetical protein SGO_1134 15.6106 15.000 26.3200 10.000 9.500 21.5000 28.5077 21.500 0.580 6.523 SGO_1139 0.0034 0.0164 GTP-binding protein 88.9807 85.500 77.6440 29.500 26.500 76.0000 79.5214 76.000 -0.066 8.332 SGO_1140 0.0435 0.3780 clpX; ATP-dependent Clp protease, ATPbinding subunit ClpX 4.6832 4.500 6.5800 2.500 7.0000 7.000 0.201 4.191 SGO_1141 0.0695 0.6387 folA; dihydrofolate reductase 5.7239 5.500 13.1600 5.000 10.0000 10.000 0.799 4.852 SGO_1143 0.0299 0.2442 thyA; thymidylate synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 28 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 69.2072 66.500 259.2521 98.500 72.500 76.5000 217.5586 76.500 1.707 9.282 SGO_1144 0.0004 0.0009 glcK; glucokinase 3.500 7.0000 10.5028 7.000 0.585 4.130 SGO_1150 hypothetical protein SGO_1150 71.2886 68.500 221.0881 84.000 78.000 77.5000 234.0630 77.500 1.614 9.238 SGO_1151 0.0001 0.0000 glyA; serine hydroxymethyltransferase 49.4337 47.500 53.9560 20.500 20.500 32.5000 61.5166 32.500 0.523 7.625 SGO_1154 0.0085 0.0520 prfA; peptide chain release factor 1 9.8867 9.500 5.500 21.0000 16.5044 21.000 0.196 5.567 SGO_1155 0.0922 0.8799 tdk; thymidine kinase 56.1983 54.000 36.8480 14.000 21.000 62.5000 63.0170 62.500 -0.299 7.772 SGO_1167 0.0371 0.3123 nox; NADH oxidase 39.0266 37.500 53.9560 20.500 18.000 34.5000 54.0145 34.500 0.557 7.504 SGO_1169 0.0004 0.0009 NADPH-dependent FMN reductase 130.6091 125.500 81.5920 31.000 24.500 129.0000 73.5198 129.000 -0.745 8.696 SGO_1170 0.0002 0.0002 NADPH-dependent FMN reductase 7.2850 7.000 6.5800 2.500 3.000 5.0000 9.0024 5.000 0.351 4.801 SGO_1185 0.0232 0.1848 acetyltransferase, GNAT family 304.4076 292.500 39.4800 15.000 5.500 260.5000 16.5044 260.500 -3.464 9.278 SGO_1189 0.0003 0.0004 lipoprotein, putative 821.6402 789.500 1194.9287 454.000 444.500 718.0000 1333.8590 718.000 0.717 11.990 SGO_1191 0.0008 0.0022 rplL; ribosomal protein L7/L12 150.3825 144.500 148.7081 56.500 46.000 163.5000 138.0372 163.500 -0.130 9.230 SGO_1192 0.0106 0.0690 BL5; 50S ribosomal protein L10 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 29 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 14.0496 13.500 7.8960 3.000 3.000 15.0000 9.0024 15.000 -0.784 5.522 SGO_1193 0.0004 0.0007 gid; Glucose inhibited division protein A 4.6832 4.500 4.000 12.0032 1.358 4.061 SGO_1196 satD; SatD-like protein 82.7364 79.500 26.3200 10.000 9.500 103.5000 28.5077 103.500 -1.756 7.913 SGO_1197 0.0006 0.0017 topA; DNA topoisomerase I 139.4551 134.000 126.3361 48.000 35.500 118.0000 106.5287 118.000 -0.145 8.938 SGO_1198 0.0296 0.2408 DNA processing Smf protein 16.1310 15.500 22.3720 8.500 9.000 20.5000 27.0073 20.500 0.435 6.426 SGO_1203 0.0071 0.0404 anaerobic ribonucleotide reductase 7.2850 7.000 9.2120 3.500 2.500 3.5000 7.5020 3.500 0.719 4.781 SGO_1205 0.0129 0.0899 dapA; dihydrodipicolinate synthase 44.2302 42.500 50.0080 19.000 18.500 50.0000 55.5149 50.000 0.164 7.642 SGO_1206 0.0130 0.0915 asd; aspartate-semialdehyde dehydrogenase 11.9682 11.500 6.5800 2.500 11.0000 11.000 -0.802 4.885 SGO_1210 0.0098 0.0626 fhs-1; formate--tetrahydrofolate ligase 197.7348 190.000 243.4601 92.500 81.000 215.0000 243.0654 215.000 0.239 9.813 SGO_1215 0.0014 0.0051 manB; phosphomannomutase 19.2531 18.500 38.1640 14.500 12.000 14.5000 36.0097 14.500 1.150 6.754 SGO_1216 0.0004 0.0009 bta; Possible bacteriocin transport accessory protein 45.7912 44.000 43.4280 16.500 17.500 54.0000 52.5141 54.000 -0.058 7.613 SGO_1219 0.0681 0.6240 pta; phosphate acetyltransferase 93.1435 89.500 111.8601 42.500 44.500 89.0000 133.5359 89.000 0.425 8.740 SGO_1224 0.0033 0.0157 Ribose-phosphate pyrophosphokinase 2 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 30 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 7.8053 7.500 10.5280 4.000 4.000 8.5000 12.0032 8.500 0.465 5.279 SGO_1225 0.0018 0.0070 pyridoxal-phosphate dependent aminotransferase 14.0496 13.500 21.0560 8.000 7.500 24.5000 22.5061 24.500 0.231 6.360 SGO_1226 0.0532 0.4709 hypothetical protein SGO_1226 93.6639 90.000 27.6360 10.500 9.500 112.0000 28.5077 112.000 -1.868 8.032 SGO_1231 0.0004 0.0008 gyrA; DNA gyrase, A subunit 67.6461 65.000 615.8884 234.000 207.500 85.5000 622.6676 85.500 3.026 10.443 SGO_1232 0.0000 0.0000 L-lactate dehydrogenase 374.1351 359.500 601.4123 228.500 206.000 444.0000 618.1664 444.000 0.581 10.993 SGO_1234 0.0008 0.0023 rpsA; 30S ribosomal protein S1 17.6921 17.000 19.7400 7.500 14.000 15.0000 42.0113 15.000 0.822 6.561 SGO_1237 0.0153 0.1106 hypothetical protein SGO_1237 36.4248 35.000 23.6880 9.000 10.500 32.0000 31.5085 32.000 -0.322 6.950 SGO_1238 0.0122 0.0839 ilvE; branched-chain amino acid aminotransferase 36.9452 35.500 5.2640 2.000 1.500 40.5000 4.5012 40.500 -2.990 6.446 SGO_1239 0.0001 0.0001 parC; DNA topoisomerase IV, A subunit 75.4514 72.500 11.8440 4.500 63.0000 63.000 -2.541 7.232 SGO_1242 0.0106 0.0688 lipoprotein, putative 18.2124 17.500 9.2120 3.500 3.000 11.5000 9.0024 11.500 -0.668 5.583 SGO_1248 0.0094 0.0593 pyrC; dihydroorotase 18.2124 17.500 23.6880 9.000 10.500 25.0000 31.5085 25.000 0.357 6.621 SGO_1253 0.0183 0.1387 pyrE; orotate phosphoribosyltransferase 71.8090 69.000 84.2240 32.000 24.500 70.0000 73.5198 70.000 0.150 8.227 SGO_1260 0.0123 0.0845 deoD; purine nucleoside phosphorylase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 31 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 110.8356 106.500 63.1680 24.000 30.500 95.5000 91.5246 95.500 -0.436 8.496 SGO_1263 0.0106 0.0693 purine nucleoside phosphorylase I, inosine and guanosine-specific 228.9561 220.000 198.7161 75.500 91.000 282.0000 273.0735 282.000 -0.125 9.941 SGO_1264 0.0572 0.5115 deoB; phosphopentomutase 27.0585 26.000 56.5880 21.500 22.000 54.0000 66.0178 54.000 0.677 7.670 SGO_1265 0.0125 0.0861 rpiA; ribose 5-phosphate isomerase 13.0089 12.500 22.3720 8.500 5.500 13.0000 16.5044 13.000 0.563 6.020 SGO_1266 0.0059 0.0320 trmE; tRNA modification GTPase TrmE 41.6284 40.000 180.2921 68.500 40.500 33.5000 121.5327 33.500 1.987 8.558 SGO_1273 0.0018 0.0070 rpoD; RNA polymerase sigma factor 51.5151 49.500 64.4840 24.500 28.000 54.0000 84.0226 54.000 0.481 7.989 SGO_1276 0.0059 0.0324 rpsU; ribosomal protein S21 5.7239 5.500 2.000 7.5000 6.0016 7.500 -0.127 4.265 SGO_1281 0.0675 0.6167 penicillinase repressor, putative 71.2886 68.500 85.5400 32.500 28.500 64.5000 85.5230 64.500 0.335 8.261 SGO_1283 0.0009 0.0029 oxidoreductase 16.1310 15.500 14.4760 5.500 6.000 14.0000 18.0048 14.000 0.103 5.968 SGO_1284 0.0455 0.3963 thioredoxin-disulfide reductase 46.3116 44.500 39.4800 15.000 21.500 50.0000 64.5174 50.000 0.069 7.646 SGO_1293 0.0692 0.6353 asnS; asparaginyl-tRNA synthetase 12.4885 12.000 27.6360 10.500 9.500 13.5000 28.5077 13.500 1.112 6.360 SGO_1297 0.0001 0.0000 aspC; aspartate aminotransferase 22.3753 21.500 10.5280 4.000 2.500 23.5000 7.5020 23.500 -1.367 5.998 SGO_1305 0.0004 0.0007 substrate-binding protein MsmE .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 32 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 7.2850 7.000 65.8000 25.000 17.500 6.0000 52.5141 6.000 3.152 7.040 SGO_1312 0.0004 0.0009 pepT; peptidase T 44.2302 42.500 109.2281 41.500 34.000 35.0000 102.0275 35.000 1.424 8.182 SGO_1323 0.0002 0.0003 rpsP; ribosomal protein S16 13.5292 13.000 9.2120 3.500 3.500 21.5000 10.5028 21.500 -0.794 5.775 SGO_1327 0.0079 0.0463 HAD-superfamily subfamily IIA hydrolase, TIGR01457 17.6921 17.000 9.2120 3.500 4.000 17.5000 12.0032 17.500 -0.743 5.818 SGO_1336 0.0010 0.0032 pcrA; ATP-dependent DNA helicase PcrA 573.4310 551.000 1194.9287 454.000 364.500 600.0000 1093.7944 600.000 0.963 11.757 SGO_1339 0.0003 0.0003 pyk; pyruvate kinase 222.1915 213.500 327.6842 124.500 115.500 213.5000 346.5933 213.500 0.630 10.116 SGO_1340 0.0002 0.0003 Phosphofructokinase 440.7405 423.500 186.8721 71.000 62.500 429.0000 187.5505 429.000 -1.216 10.281 SGO_1342 0.0001 0.0000 ABC transporter, ATP-binding protein SP1715 23.4160 22.500 2.000 32.5000 6.0016 32.500 -2.201 5.952 SGO_1364 0.0174 0.1299 rumA-2; 23S rRNA (uracil-5-)methyltransferase RumA 34.8638 33.500 2.000 34.5000 6.0016 34.500 -2.531 6.236 SGO_1365 0.0012 0.0040 transcription regulator yrfE 14.5699 14.000 7.8960 3.000 15.5000 15.500 -0.928 5.247 SGO_1369 0.0072 0.0414 L-2-hydroxyisocaproate dehydrogenase 16.1310 15.500 46.0600 17.500 17.500 15.5000 52.5141 15.500 1.637 7.025 SGO_1370 0.0003 0.0004 Protein of unknown function (DUF964) superfamily 5.7239 5.500 4.000 7.0000 12.0032 7.000 0.923 4.628 SGO_1372 0.0109 0.0717 aroC; chorismate synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 33 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 5.7239 5.500 7.8960 3.000 10.0000 10.000 0.062 4.562 SGO_1373 0.1026 0.9899 aroB; 3-dehydroquinate synthase 11.4478 11.000 13.1600 5.000 15.0000 15.000 0.006 5.308 SGO_1375 0.1015 0.9771 aroD; 3-dehydroquinate dehydratase, type I 109.2745 105.000 11.8440 4.500 2.000 123.0000 6.0016 123.000 -3.781 7.966 SGO_1377 0.0002 0.0001 sulfatase 24.9770 24.000 14.4760 5.500 4.500 27.5000 13.5036 27.500 -0.907 6.330 SGO_1381 0.0003 0.0006 csn1; CRISPR-associated protein, Csn1 family 95.2249 91.500 172.3961 65.500 60.500 106.5000 181.5489 106.500 0.813 9.118 SGO_1383 0.0003 0.0004 rplS; ribosomal protein L19 20.8142 20.000 14.4760 5.500 3.000 19.5000 9.0024 19.500 -0.819 5.995 SGO_1390 0.0031 0.0140 ligA; DNA ligase, NAD-dependent 20.8142 20.000 22.3720 8.500 8.500 33.0000 25.5069 33.000 -0.134 6.668 SGO_1397 0.0535 0.4738 map; methionine aminopeptidase, type I 19.2531 18.500 17.1080 6.500 2.000 21.5000 6.0016 21.500 -1.006 5.997 SGO_1400 0.0111 0.0740 murA-2; UDP-N-acetylglucosamine 1carboxyvinyltransferase 5.7239 5.500 13.1600 5.000 3.500 9.5000 10.5028 9.500 0.673 5.281 SGO_1414 0.0084 0.0507 rexB; putative exonuclease RexB 29.6602 28.500 34.2160 13.000 17.000 30.5000 51.0137 30.500 0.474 7.184 SGO_1422 0.0121 0.0817 hypothetical protein SGO_1422 2884.3267 2771.500 10828.054 2 4114.000 3729.500 2470.5000 11191.512 2 2470.500 2.044 14.741 SGO_1426 0.0001 0.0000 eno; enolase 593.2045 570.000 135.5481 51.500 45.000 383.5000 135.0363 383.500 -1.818 10.285 SGO_1431 0.0024 0.0100 EzrA; Septation ring formation regulator ezrA .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 34 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 34.8638 33.500 51.3240 19.500 9.500 53.5000 28.5077 53.500 -0.175 7.394 SGO_1432 0.0706 0.6504 gyrB; DNA gyrase, B subunit 5.2640 2.000 2.5000 2.500 1.074 2.957 SGO_1434 thiJ; 4-methyl-5(beta-hydroxyethyl)thiazole monophosphate synthesis protein 57.7594 55.500 23.6880 9.000 10.000 55.5000 30.0081 55.500 -1.087 7.383 SGO_1439 0.0003 0.0006 ftsX; cell division protein FtsX 108.7542 104.500 25.0040 9.500 8.000 103.0000 24.0065 103.000 -2.111 8.027 SGO_1440 0.0001 0.0000 cell-division ATP-binding protein FtsE 15.0903 14.500 30.2680 11.500 4.500 13.0000 13.5036 13.000 0.530 6.167 SGO_1441 0.0258 0.2063 prfB; peptide chain release factor 2 15.6106 15.000 7.8960 3.000 1.500 26.0000 4.5012 26.000 -1.757 5.755 SGO_1446 0.0038 0.0190 murF; UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase 24.4567 23.500 21.0560 8.000 7.000 25.0000 21.0057 25.000 -0.234 6.516 SGO_1447 0.0002 0.0002 ddlA; D-Ala-D-Ala ligase 5.2035 5.000 5.2640 2.000 6.000 19.5000 18.0048 19.500 -0.049 5.584 SGO_1450 0.0945 0.9050 hypothetical protein SGO_1450 34.8638 33.500 88.1721 33.500 32.500 27.0000 97.5262 27.000 1.596 7.952 SGO_1451 0.0003 0.0004 frr; ribosome recycling factor 31.7416 30.500 46.0600 17.500 16.000 24.0000 48.0129 24.000 0.769 7.227 SGO_1452 0.0011 0.0036 pyrH; uridylate kinase 134.7719 129.500 309.2602 117.500 143.500 117.0000 430.6159 117.000 1.539 9.954 SGO_1455 0.0016 0.0063 rplA; ribosomal protein L1 48.3930 46.500 119.7561 45.500 44.000 51.0000 132.0355 51.000 1.340 8.456 SGO_1456 0.0002 0.0002 rplK; ribosomal protein L11 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 35 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 74.4107 71.500 5.2640 2.000 47.0000 47.000 -3.490 6.985 SGO_1458 0.0199 0.1543 aha1; cation-transporting ATPase yfgQ 59.8408 57.500 10.5280 4.000 45.0000 45.000 -2.301 6.850 SGO_1460 0.0154 0.1116 DNA translocase ftsK 61.9222 59.500 21.0560 8.000 6.000 66.5000 18.0048 66.500 -1.721 7.388 SGO_1463 0.0001 0.0001 peptidyl-prolyl cis-trans isomerase 57.2390 55.000 18.4240 7.000 5.000 73.5000 15.0040 73.500 -1.964 7.359 SGO_1464 0.0007 0.0020 uncharacterized probable metal-binding protein 33.3027 32.000 26.3200 10.000 7.500 45.0000 22.5061 45.000 -0.670 6.990 SGO_1465 0.0048 0.0254 ABC transporter, ATP-binding protein SP0770 50.4744 48.500 59.2200 22.500 23.000 52.5000 69.0186 52.500 0.313 7.853 SGO_1469 0.0043 0.0221 glmU; UDP-N-acetylglucosamine pyrophosphorylase 1.500 4.0000 4.5012 4.000 0.170 3.088 SGO_1472 acetyltransferase, GNAT family 5.2640 2.000 2.500 2.5000 7.5020 2.500 1.330 3.932 SGO_1486 0.0225 0.1786 beta-galactosidase 9.8867 9.500 13.1600 5.000 4.500 12.0000 13.5036 12.000 0.291 5.601 SGO_1516 0.0057 0.0306 lacD-2; tagatose 1,6-diphosphate aldolase 99.3878 95.500 68.4320 26.000 24.500 79.0000 73.5198 79.000 -0.321 8.323 SGO_1530 0.0092 0.0575 methionine-tRNA ligase 13.5292 13.000 13.1600 5.000 7.000 14.0000 21.0057 14.000 0.273 5.947 SGO_1531 0.0295 0.2398 xth; exodeoxyribonuclease III 3.6425 3.500 6.000 15.0000 18.0048 15.000 1.284 5.196 SGO_1534 0.0428 0.3687 ArsC family .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 36 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 18.7328 18.000 10.5280 4.000 5.000 25.5000 15.0040 25.500 -0.798 6.124 SGO_1536 0.0053 0.0282 conserved hypothetical protein TIGR00096 16.6514 16.000 21.0560 8.000 10.500 17.0000 31.5085 17.000 0.614 6.430 SGO_1539 0.0085 0.0520 tmk; thymidylate kinase 62.9629 60.500 11.8440 4.500 6.500 81.0000 19.5052 81.000 -2.232 7.454 SGO_1541 0.0008 0.0022 atpC; ATP synthase F1, epsilon subunit 427.2113 410.500 192.1361 73.000 72.500 403.5000 217.5586 403.500 -1.022 10.277 SGO_1542 0.0002 0.0002 atpD; ATP synthase F1, beta subunit 62.9629 60.500 11.8440 4.500 3.000 58.5000 9.0024 58.500 -2.555 7.153 SGO_1543 0.0001 0.0001 atpG; ATP synthase F1, gamma subunit 343.4342 330.000 207.9281 79.000 76.000 352.0000 228.0614 352.000 -0.675 10.144 SGO_1544 0.0002 0.0003 atpA; ATP synthase F1, alpha subunit 83.2568 80.000 14.4760 5.500 4.500 72.5000 13.5036 72.500 -2.474 7.521 SGO_1545 0.0002 0.0003 atpH; ATP synthase F1, delta subunit 90.0214 86.500 43.4280 16.500 14.000 101.5000 42.0113 101.500 -1.162 8.114 SGO_1546 0.0003 0.0005 atpF; ATP synthase F0, B subunit 46.8319 45.000 43.4280 16.500 18.000 62.5000 54.0145 62.500 -0.160 7.692 SGO_1550 0.0416 0.3558 glgP-1; glycogen phosphorylase 5.2035 5.000 10.5280 4.000 5.500 21.0000 16.5044 21.000 0.335 5.734 SGO_1551 0.0978 0.9376 glgA; Glycogen synthase 33.8231 32.500 72.3800 27.500 17.000 21.5000 51.0137 21.500 1.172 7.482 SGO_1552 0.0036 0.0174 glgD; glucose-1-phosphate adenylyltransferase, GlgD subunit 19.2531 18.500 51.3240 19.500 18.500 28.0000 55.5149 28.000 1.201 7.268 SGO_1553 0.0007 0.0018 glgC; glucose-1-phosphate adenylyltransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 37 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 19.7735 19.000 60.5360 23.000 23.000 34.0000 69.0186 34.000 1.318 7.518 SGO_1554 0.0012 0.0042 glgB; 1,4-alpha-glucan branching enzyme 598.9284 575.500 430.3322 163.500 168.500 528.5000 505.6361 528.500 -0.270 11.011 SGO_1555 0.0082 0.0487 ptsI; phosphoenolpyruvate-protein phosphotransferase 672.2984 646.000 1230.4607 467.500 561.500 635.5000 1684.9535 635.500 1.139 12.044 SGO_1556 0.0021 0.0088 phosphocarrier protein HPr 86.3789 83.000 90.8041 34.500 31.000 99.5000 93.0250 99.500 -0.012 8.530 SGO_1558 0.0856 0.8069 nrdE; ribonucleoside-diphosphate reductase large chain 47.3523 45.500 107.9121 41.000 36.500 56.0000 109.5295 56.000 1.078 8.326 SGO_1559 0.0002 0.0002 ribonucleoside-diphosphate reductase, beta subunit 152.4640 146.500 131.6001 50.000 52.500 192.5000 157.5424 192.500 -0.251 9.309 SGO_1570 0.0180 0.1358 alaS; alanyl-tRNA synthetase 392.8679 377.500 2.500 400.5000 7.5020 400.500 -5.725 9.645 SGO_1572 0.0016 0.0062 proteinase maturation protein, putative 84.2975 81.000 146.0761 55.500 52.000 88.0000 156.0420 88.000 0.810 8.890 SGO_1574 0.0002 0.0002 pepF-1; oligoendopeptidase F 40.0673 38.500 2.000 25.0000 6.0016 25.000 -2.399 6.151 SGO_1585 0.0222 0.1761 D-Alanyl-D-Alanine carboxypeptidase 10.4071 10.000 13.1600 5.000 4.000 20.5000 12.0032 20.500 -0.217 5.809 SGO_1587 0.0458 0.3997 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase 32.7824 31.500 11.8440 4.500 4.000 47.5000 12.0032 47.500 -1.727 6.702 SGO_1591 0.0018 0.0070 arcC; carbamate kinase 181.6038 174.500 153.9721 58.500 41.500 183.0000 124.5335 183.000 -0.397 9.329 SGO_1592 0.0032 0.0149 arcB; ornithine carbamoyltransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 38 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 154.5454 148.500 125.0201 47.500 43.000 176.0000 129.0347 176.000 -0.377 9.191 SGO_1593 0.0021 0.0090 arcA; arginine deiminase 141.0162 135.500 192.1361 73.000 56.000 156.0000 168.0452 156.000 0.277 9.360 SGO_1599 0.0057 0.0308 sodA; manganese-dependent superoxide dismutase 39.5470 38.000 1.500 47.5000 4.5012 47.500 -3.267 6.516 SGO_1604 0.0101 0.0647 acyltransferase family protein 32.2620 31.000 1.500 39.0000 4.5012 39.000 -2.978 6.243 SGO_1605 0.0106 0.0686 P-type ATPase, metal cation transport 92.1028 88.500 53.9560 20.500 15.500 96.5000 46.5125 96.500 -0.912 8.175 SGO_1609 0.0003 0.0004 ATP-dependent RNA helicase, DEAD/DEAH box family 12.4885 12.000 17.1080 6.500 7.000 23.5000 21.0057 23.500 0.146 6.211 SGO_1617 0.0823 0.7733 prfC; peptide chain release factor 3 372.0537 357.500 100.0161 38.000 28.500 283.0000 85.5230 283.000 -1.811 9.715 SGO_1619 0.0009 0.0029 cation-transporting ATPase, E1-E2 family 15.0903 14.500 5.2640 2.000 17.5000 17.500 -1.626 5.242 SGO_1621 0.0106 0.0693 HD domain protein 14.5699 14.000 10.5280 4.000 5.500 9.5000 16.5044 9.500 0.164 5.675 SGO_1622 0.0620 0.5594 Cof family protein 34.8638 33.500 11.8440 4.500 38.0000 38.000 -1.620 6.404 SGO_1623 0.0071 0.0405 murM; MurM 20.2938 19.500 3.500 12.5000 10.5028 12.500 -0.601 5.436 SGO_1624 0.0431 0.3719 murN; MurN protein 98.8674 95.000 27.6360 10.500 6.000 97.0000 18.0048 97.000 -2.134 7.916 SGO_1625 0.0001 0.0001 acetoin utilization putative/CBS domain protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 39 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 38.5063 37.000 25.0040 9.500 9.000 49.0000 27.0073 49.000 -0.741 7.124 SGO_1626 0.0024 0.0104 branched-chain amino acid ABC transporter, ATP-binding protein 67.1258 64.500 31.5840 12.000 7.500 48.5000 22.5061 48.500 -1.098 7.407 SGO_1627 0.0031 0.0142 branched-chain amino acid ABC transporter, ATP-binding protein 529.7212 509.000 180.2921 68.500 57.500 547.5000 172.5464 547.500 -1.610 10.482 SGO_1630 0.0001 0.0000 branched-chain amino acid ABC transporter, amino acid-binding protein 39.0266 37.500 32.9000 12.500 28.000 42.5000 84.0226 42.500 0.368 7.633 SGO_1632 0.0375 0.3174 clpP; ATP-dependent Clp protease, proteolytic subunit ClpP 46.8319 45.000 101.3321 38.500 23.500 49.5000 70.5190 49.500 0.812 8.067 SGO_1633 0.0046 0.0242 upp; uracil phosphoribosyltransferase 64.0036 61.500 185.5561 70.500 57.000 83.5000 171.0460 83.500 1.285 8.978 SGO_1648 0.0004 0.0007 ppx1; inorganic pyrophosphatase, manganese-dependent 27.0585 26.000 5.2640 2.000 22.0000 22.000 -2.213 5.763 SGO_1649 0.0122 0.0831 act; pyruvate formate-lyase-activating enzyme 29.6602 28.500 34.2160 13.000 11.500 40.5000 34.5093 40.500 -0.012 7.118 SGO_1652 0.0881 0.8335 intracellular glycosyl hydrolase 195.1331 187.500 27.6360 10.500 19.500 217.0000 58.5157 217.000 -2.355 8.961 SGO_1653 0.0004 0.0007 trehalose PTS enzyme II 34.8638 33.500 9.2120 3.500 2.000 49.0000 6.0016 49.000 -2.475 6.630 SGO_1666 0.0011 0.0038 trkA; potassium uptake protein, Trk family 40.0673 38.500 28.9520 11.000 10.000 59.0000 30.0081 59.000 -0.722 7.304 SGO_1669 0.0063 0.0352 ribosomal large subunit pseudouridine synthase B 18.2124 17.500 10.5280 4.000 5.500 29.5000 16.5044 29.500 -0.814 6.224 SGO_1675 0.0104 0.0676 HAM1 protein-like protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 40 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 5.7239 5.500 11.8440 4.500 5.500 8.0000 16.5044 8.000 1.047 5.395 SGO_1676 0.0034 0.0164 murI; glutamate racemase 7.8053 7.500 6.5800 2.500 11.0000 11.000 -0.494 4.666 SGO_1678 0.0386 0.3278 lysA; diaminopimelate decarboxylase 632.7514 608.000 215.8241 82.000 82.500 625.0000 247.5666 625.000 -1.444 10.749 SGO_1679 0.0001 0.0000 phosphotransferase system enzyme II 123.8444 119.000 30.2680 11.500 98.5000 98.500 -1.867 7.981 SGO_1680 0.0139 0.0989 phosphotransferase system enzyme II 490.6946 471.500 121.0721 46.000 52.000 481.5000 156.0420 481.500 -1.822 10.287 SGO_1681 0.0001 0.0001 PTS system, mannose/fructose/sorbose family, IID component 61.9222 59.500 90.8041 34.500 25.500 67.0000 76.5206 67.000 0.372 8.211 SGO_1683 0.0043 0.0219 serS; seryl-tRNA synthetase 9.8867 9.500 28.9520 11.000 12.500 14.0000 37.5101 14.000 1.486 6.497 SGO_1684 0.0013 0.0044 acyl-CoA dehydrogenase family 15.0903 14.500 172.3961 65.500 42.000 21.0000 126.0339 21.000 3.050 8.386 SGO_1685 0.0008 0.0023 putative peroxidase / antioxidase 64.5240 62.000 73.6960 28.000 23.500 68.0000 70.5190 68.000 0.122 8.112 SGO_1687 0.0045 0.0231 accA; acetyl-CoA carboxylase, carboxyl transferase, alpha subunit 21.3345 20.500 13.1600 5.000 3.000 39.0000 9.0024 39.000 -1.406 6.366 SGO_1688 0.0063 0.0357 accD; acetyl-CoA carboxylase, carboxyl transferase, beta subunit 31.7416 30.500 59.2200 22.500 18.500 41.5000 55.5149 41.500 0.660 7.554 SGO_1689 0.0016 0.0063 accC; acetyl-CoA carboxylase, biotin carboxylase 57.2390 55.000 63.1680 24.000 27.500 31.5000 82.5222 31.500 0.766 7.873 SGO_1691 0.0089 0.0549 accB; acetyl-CoA carboxylase, biotin carboxyl carrier protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 41 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 105.1117 101.000 205.2961 78.000 73.000 113.5000 219.0590 113.500 0.957 9.329 SGO_1692 0.0002 0.0002 3-oxoacyl-[acyl-carrier-protein] synthase 27.5788 26.500 40.7960 15.500 8.000 22.5000 24.0065 22.500 0.329 6.844 SGO_1693 0.0297 0.2420 fabG; 3-oxoacyl-(acyl-carrier-protein) reductase 20.8142 20.000 36.8480 14.000 7.500 28.0000 22.5061 28.000 0.254 6.757 SGO_1694 0.0396 0.3378 fabD; malonyl CoA-acyl carrier protein transacylase 153.5047 147.500 232.9321 88.500 57.500 154.0000 172.5464 154.000 0.383 9.478 SGO_1695 0.0104 0.0673 enoyl-acyl carrier protein(ACP) reductase 7.8053 7.500 3.500 10.0000 10.5028 10.000 0.250 4.823 SGO_1699 0.0440 0.3827 transcriptional regulator, MarR family 17.6921 17.000 7.8960 3.000 17.5000 17.500 -1.156 5.429 SGO_1700 0.0016 0.0063 enoyl-CoA hydratase/isomerase family protein 37.9859 36.500 46.0600 17.500 20.500 40.0000 61.5166 40.000 0.450 7.536 SGO_1701 0.0079 0.0461 aspartate kinase 441.2609 424.000 85.5400 32.500 34.000 254.5000 102.0275 254.500 -1.843 9.787 SGO_1708 0.0037 0.0183 amiF; Oligopeptide transport ATP-binding protein amiF 397.0307 381.500 102.6481 39.000 45.500 400.0000 136.5367 400.000 -1.751 10.017 SGO_1709 0.0001 0.0001 amiE; Oligopeptide transport ATP-binding protein 51.5151 49.500 14.4760 5.500 4.500 46.0000 13.5036 46.000 -1.800 6.971 SGO_1710 0.0002 0.0002 amiD; Oligopeptide transport system permease protein 125.9259 121.000 52.6400 20.000 23.000 160.0000 69.0186 160.000 -1.236 8.671 SGO_1711 0.0013 0.0049 hppB; Oligopeptide transport system permease 741.5056 712.500 439.5443 167.000 138.500 715.5000 415.6119 715.500 -0.769 11.175 SGO_1712 0.0001 0.0001 hppA; oligopeptide-binding lipoprotein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 42 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 640.0364 615.000 267.1482 101.500 93.500 570.5000 280.5755 570.500 -1.142 10.780 SGO_1713 0.0003 0.0005 hppG; oligopeptide-binding lipoprotein 274.2270 263.500 96.0681 36.500 36.000 264.5000 108.0291 264.500 -1.403 9.537 SGO_1715 0.0001 0.0000 hppH; oligopeptide-binding lipoprotein 223.7526 215.000 185.5561 70.500 35.000 270.5000 105.0283 270.500 -0.817 9.616 SGO_1716 0.0059 0.0323 oligopeptide binding protein 32.2620 31.000 27.6360 10.500 16.000 47.0000 48.0129 47.000 -0.096 7.275 SGO_1718 0.0867 0.8195 sufB-1; FeS assembly protein SufB 5.7239 5.500 14.4760 5.500 3.000 10.0000 9.0024 10.000 0.593 5.293 SGO_1720 0.0194 0.1486 aminotransferase, class-V 37.9859 36.500 44.7440 17.000 15.500 31.0000 46.5125 31.000 0.411 7.324 SGO_1721 0.0029 0.0128 sufD; FeS assembly protein SufD 20.2938 19.500 17.1080 6.500 11.500 25.0000 34.5093 25.000 0.109 6.599 SGO_1722 0.0647 0.5864 sufC; FeS assembly ATPase SufC 67.1258 64.500 31.5840 12.000 12.000 71.5000 36.0097 71.500 -1.039 7.688 SGO_1727 0.0002 0.0003 amino acid ABC transporter, amino acidbinding/permease protein 75.9718 73.000 27.6360 10.500 9.000 51.0000 27.0073 51.000 -1.188 7.505 SGO_1728 0.0032 0.0153 glnQ; glutamine ABC transporter ATPbinding protein 304.4076 292.500 118.4401 45.000 43.000 256.5000 129.0347 256.500 -1.177 9.659 SGO_1730 0.0006 0.0016 SPFH domain/Band 7 family 2.0814 2.000 18.4240 7.000 7.000 5.0000 21.0057 5.000 2.608 5.540 SGO_1731 0.0004 0.0007 DNA-binding response regulator 161.8303 155.500 155.2881 59.000 46.500 188.0000 139.5376 188.000 -0.245 9.332 SGO_1735 0.0086 0.0525 hypothetical protein SGO_1735 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 43 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 13.0089 12.500 10.5280 4.000 10.5000 10.500 -0.151 5.089 SGO_1736 0.0568 0.5072 alkaline shock protein 22.3753 21.500 41.500 36.0000 124.5335 36.000 2.134 7.515 SGO_1737 0.0078 0.0454 rpmB; ribosomal protein L28 843.4951 810.500 1751.5970 665.500 762.000 659.5000 2286.6155 659.500 1.424 12.436 SGO_1745 0.0013 0.0044 fba; fructose-1,6-bisphosphate aldolase, class II 11.9682 11.500 15.7920 6.000 3.500 11.0000 10.5028 11.000 0.167 5.622 SGO_1748 0.0423 0.3624 pyrG; CTP synthase 19.7735 19.000 21.0560 8.000 5.500 30.0000 16.5044 30.000 -0.386 6.448 SGO_1749 0.0200 0.1552 manA; mannose-6-phosphate isomerase, class I 26.5381 25.500 34.2160 13.000 13.000 33.0000 39.0105 33.000 0.304 7.053 SGO_1755 0.0095 0.0602 scrK; fructokinase 87.9400 84.500 73.6960 28.000 29.000 118.0000 87.0234 118.000 -0.347 8.518 SGO_1757 0.0137 0.0974 glmS; glucosamine--fructose-6-phosphate aminotransferase 55.1576 53.000 65.8000 25.000 21.000 65.5000 63.0170 65.500 0.099 7.963 SGO_1763 0.0335 0.2787 ABC transporter, substrate-binding protein SP0092 11.4478 11.000 13.1600 5.000 7.000 14.0000 21.0057 14.000 0.393 5.898 SGO_1774 0.0210 0.1646 alcohol dehydrogenase, zinc-containing 59.8408 57.500 115.8081 44.000 39.000 73.5000 117.0315 73.500 0.812 8.516 SGO_1784 0.0005 0.0011 leuS; leucyl-tRNA synthetase 52.5558 50.500 115.8081 44.000 30.500 68.5000 91.5246 68.500 0.779 8.359 SGO_1799 0.0031 0.0142 endopeptidase O 153.5047 147.500 17.1080 6.500 7.500 128.0000 22.5061 128.000 -2.837 8.327 SGO_1800 0.0003 0.0005 troB; manganese ABC transporter, ATPbinding protein SP1648 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 44 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 1132.8124 1088.500 113.1761 43.000 28.000 958.0000 84.0226 958.000 -3.417 11.160 SGO_1802 0.0003 0.0003 Metal ABC transporter substrate-binding lipoprotein precursor 13.5292 13.000 32.9000 12.500 16.000 14.0000 48.0129 14.000 1.530 6.761 SGO_1803 0.0021 0.0088 tpx; thioredoxin peroxidase 1.5611 1.500 25.0040 9.500 4.000 12.0032 3.472 5.269 SGO_1805 0.0288 0.2332 hutU; urocanate hydratase 4.6832 4.500 2.000 5.0000 6.0016 5.000 0.311 3.971 SGO_1811 0.0125 0.0864 hutH; histidine ammonia-lyase 42.6691 41.000 10.5280 4.000 37.0000 37.000 -1.916 6.495 SGO_1822 0.0097 0.0614 relA; GTP diphosphokinase 9.8867 9.500 17.1080 6.500 4.500 14.5000 13.5036 14.500 0.344 5.781 SGO_1824 0.0208 0.1628 prmA; ribosomal protein L11 methyltransferase 6.7646 6.500 2.500 4.0000 7.5020 4.000 0.528 4.191 SGO_1828 0.0428 0.3679 ATPase, AAA family 7.2850 7.000 59.2200 22.500 18.000 5.0000 54.0145 5.000 3.228 6.972 SGO_1834 0.0001 0.0001 hypothetical protein SGO_1834 6.500 3.0000 19.5052 3.000 2.701 4.492 SGO_1835 hypothetical protein SGO_1835 47.3523 45.500 77.6440 29.500 31.000 42.5000 93.0250 42.500 0.922 8.025 SGO_1843 0.0010 0.0032 pepS; aminopeptidase PepS 8.3257 8.000 6.5800 2.500 3.500 12.0000 10.5028 12.000 -0.266 5.225 SGO_1844 0.0432 0.3728 cbxX/cfqX family protein 14.5699 14.000 3.000 17.0000 9.0024 17.000 -0.806 5.342 SGO_1847 0.0155 0.1128 polC; DNA polymerase III, alpha subunit, Gram-positive type .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 45 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 85.3382 82.000 6.5800 2.500 4.000 71.0000 12.0032 71.000 -3.131 7.451 SGO_1848 0.0003 0.0006 lipoprotein, putative 100.4285 96.500 146.0761 55.500 44.000 117.5000 132.0355 117.500 0.354 8.954 SGO_1851 0.0037 0.0181 proS; prolyl-tRNA synthetase 39.5470 38.000 11.8440 4.500 43.5000 43.500 -1.808 6.568 SGO_1852 0.0073 0.0423 membrane-associated zinc metalloprotease, putative 47.3523 45.500 15.7920 6.000 8.500 44.0000 25.5069 44.000 -1.185 7.051 SGO_1854 0.0011 0.0035 uppS; undecaprenyl diphosphate synthase 34.8638 33.500 22.3720 8.500 5.500 35.5000 16.5044 35.500 -0.872 6.771 SGO_1856 0.0009 0.0027 ATP-dependent proteinase ATP-binding chain 212.8251 204.500 51.3240 19.500 20.000 163.0000 60.0162 163.000 -1.747 8.928 SGO_1860 0.0009 0.0028 5'-nucleotidase, lipoprotein e(P4) family 3.6425 3.500 1.500 4.5012 0.305 3.026 SGO_1861 nusB; transcription antitermination factor NusB 21.8549 21.000 38.1640 14.500 13.500 17.5000 40.5109 17.500 1.008 6.883 SGO_1862 0.0004 0.0008 alkaline shock protein 74.9311 72.000 105.2801 40.000 33.000 84.5000 99.0267 84.500 0.360 8.507 SGO_1863 0.0017 0.0065 efp; Elongation factor P (EF-P) 34.8638 33.500 59.2200 22.500 11.000 26.0000 33.0089 26.000 0.554 7.258 SGO_1864 0.0189 0.1444 X-Pro aminopeptidase 50.4744 48.500 17.1080 6.500 5.500 55.5000 16.5044 55.500 -1.655 7.125 SGO_1865 0.0002 0.0001 uvrA; excinuclease ABC, A subunit 88.4603 85.000 71.0640 27.000 17.000 76.5000 51.0137 76.500 -0.450 8.165 SGO_1867 0.0084 0.0500 hypothetical protein SGO_1867 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 46 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 29.1399 28.000 72.3800 27.500 25.500 72.0000 76.5206 72.000 0.700 7.966 SGO_1879 0.0195 0.1505 rpsR; ribosomal protein S18 50.9948 49.000 93.4361 35.500 30.000 63.5000 90.0242 63.500 0.689 8.219 SGO_1880 0.0009 0.0027 ssb-1; single-strand binding protein 152.4640 146.500 251.3561 95.500 74.500 166.0000 223.5602 166.000 0.575 9.632 SGO_1881 0.0010 0.0031 rpsF; ribosomal protein S6 6.2443 6.000 10.5280 4.000 4.000 10.5000 12.0032 10.500 0.473 5.296 SGO_1882 0.0155 0.1125 folE; GTP cyclohydrolase I 206.5809 198.500 248.7241 94.500 87.500 200.0000 262.5707 200.000 0.330 9.842 SGO_1885 0.0005 0.0013 groL; 60 kDa chaperonin/groEL protein 20.8142 20.000 7.8960 3.000 4.500 18.0000 13.5036 18.000 -0.907 5.912 SGO_1886 0.0036 0.0171 groES; chaperonin, 10 kDa 25.4974 24.500 19.7400 7.500 4.000 33.0000 12.0032 33.000 -0.914 6.496 SGO_1892 0.0045 0.0231 PTS system, fructose(mannose)-specific IIB 43.7098 42.000 53.9560 20.500 16.000 48.5000 48.0129 48.500 0.145 7.601 SGO_1898 0.0155 0.1136 glutamyl aminopeptidase 17.6921 17.000 26.3200 10.000 9.500 14.0000 28.5077 14.000 0.799 6.435 SGO_1901 0.0009 0.0026 tRNA binding domain 142.5772 137.000 344.7922 131.000 91.500 170.5000 274.5739 170.500 0.981 9.865 SGO_1902 0.0016 0.0059 ssb; single-stranded DNA-binding protein 66.6054 64.000 63.1680 24.000 27.000 72.5000 81.0218 72.500 0.042 8.146 SGO_1903 0.0725 0.6714 ATP-dependent Zn protease 2.000 3.0000 6.0016 3.000 1.000 3.170 SGO_1914 folP; dihydropteroate synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 47 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 73.3700 70.500 100.0161 38.000 31.500 86.5000 94.5254 86.500 0.287 8.469 SGO_1916 0.0046 0.0243 ackA; acetate kinase 6.2443 6.000 11.8440 4.500 4.000 5.5000 12.0032 5.500 1.025 5.153 SGO_1917 0.0001 0.0001 hypothetical protein SGO_1917 147.7808 142.000 22.3720 8.500 11.000 157.5000 33.0089 157.500 -2.489 8.495 SGO_1924 0.0001 0.0001 comYA; competence protein comYA 347.0767 333.500 404.0122 153.500 142.500 367.0000 427.6151 367.000 0.220 10.594 SGO_1926 0.0018 0.0071 rpoC; DNA-directed RNA polymerase, beta chain 361.1262 347.000 356.6362 135.500 136.500 333.0000 409.6102 333.000 0.140 10.512 SGO_1927 0.0173 0.1287 rpoB; DNA-directed RNA polymerase, beta subunit 76.4922 73.500 7.8960 3.000 89.0000 89.000 -3.385 7.438 SGO_1928 0.0087 0.0531 pbp1b; penicillin-binding protein 1B 100.9488 97.000 132.9161 50.500 52.000 112.0000 156.0420 112.000 0.438 8.971 SGO_1929 0.0031 0.0143 tyrS; tyrosyl-tRNA synthetase 19.7735 19.000 2.000 19.0000 6.0016 19.000 -1.691 5.485 SGO_1934 0.0037 0.0184 copper-translocating P-type ATPase 201.3773 193.500 27.6360 10.500 11.500 211.0000 34.5093 211.000 -2.739 8.890 SGO_1936 0.0001 0.0000 adcA; metal-binding (Mn) permease precursor, lipoprotein 132.1701 127.000 322.4202 122.500 127.000 102.0000 381.1026 102.000 1.594 9.873 SGO_1958 0.0005 0.0012 rplQ; ribosomal protein L17 158.1879 152.000 173.7121 66.000 60.500 125.0000 181.5489 125.000 0.337 9.318 SGO_1959 0.0063 0.0352 rpoA; DNA-directed RNA polymerase, alpha subunit 67.1258 64.500 94.7521 36.000 29.500 55.5000 88.5238 55.500 0.585 8.257 SGO_1960 0.0012 0.0041 rpsK; ribosomal protein S11 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Page 48 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 120.2020 115.500 143.4441 54.500 52.500 111.0000 157.5424 111.000 0.380 9.056 SGO_1961 0.0015 0.0056 rpsM; ribosomal protein S13p/S18e 110.8356 106.500 138.1801 52.500 51.500 106.0000 154.5416 106.000 0.431 8.993 SGO_1964 0.0013 0.0045 adk; Adenylate kinase (ATP-AMP transphosphorylase) 40.5877 39.000 15.7920 6.000 5.500 36.5000 16.5044 36.500 -1.253 6.773 SGO_1965 0.0003 0.0003 Preprotein translocase secY subunit 67.1258 64.500 151.3401 57.500 63.000 72.5000 189.0509 72.500 1.278 8.907 SGO_1966 0.0009 0.0028 rplO; ribosomal protein L15 43.7098 42.000 77.6440 29.500 33.000 45.5000 99.0267 45.500 0.975 8.055 SGO_1967 0.0016 0.0058 50S ribosomal protein L30 -related protein 275.2677 264.500 290.8362 110.500 90.000 216.0000 270.0727 216.000 0.201 10.039 SGO_1968 0.0195 0.1505 rpsE; ribosomal protein S5 189.4092 182.000 411.9082 156.500 135.500 149.0000 406.6094 149.000 1.285 10.176 SGO_1969 0.0002 0.0003 rplR; ribosomal protein L18 363.2077 349.000 332.9482 126.500 82.500 347.5000 247.5666 347.500 -0.307 10.335 SGO_1970 0.0120 0.0805 BL10; 50S ribosomal protein L6 339.7917 326.500 893.5645 339.500 224.500 305.5000 673.6813 305.500 1.268 11.111 SGO_1971 0.0015 0.0056 rpsH; ribosomal protein S8 210.7437 202.500 361.9002 137.500 102.000 234.5000 306.0824 234.500 0.582 10.121 SGO_1973 0.0019 0.0079 BL6; 50S ribosomal protein L5 152.9843 147.000 188.1881 71.500 76.000 112.5000 228.0614 112.500 0.659 9.413 SGO_1974 0.0039 0.0194 rplX; ribosomal protein L24 83.7771 80.500 181.6081 69.000 71.500 77.5000 214.5577 77.500 1.293 9.123 SGO_1975 0.0005 0.0012 rplN; ribosomal protein L14 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

PAGE 49

Hackett Laboratory UW Page 49 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 47.3523 45.500 135.5481 51.500 30.000 24.0000 90.0242 24.000 1.712 8.214 SGO_1976 0.0030 0.0137 BS16; 30S ribosomal protein 26.0177 25.000 23.6880 9.000 12.000 19.5000 36.0097 19.500 0.375 6.717 SGO_1977 0.0222 0.1763 rpmC; ribosomal protein L29 44.2302 42.500 111.8601 42.500 38.500 82.5000 115.5311 82.500 0.912 8.468 SGO_1978 0.0040 0.0201 rplP; ribosomal protein L16 446.4644 429.000 217.1401 82.500 85.500 414.0000 256.5691 414.000 -0.865 10.382 SGO_1979 0.0004 0.0010 rpsC; ribosomal protein S3 139.4551 134.000 284.2562 108.000 105.000 123.0000 315.0848 123.000 1.192 9.751 SGO_1980 0.0003 0.0005 rplV; ribosomal protein L22 165.4728 159.000 163.1841 62.000 62.500 200.5000 187.5505 200.500 -0.058 9.485 SGO_1981 0.0642 0.5800 rpsS; ribosomal protein S19 103.5506 99.500 160.5521 61.000 63.500 135.5000 190.5513 135.500 0.562 9.205 SGO_1982 0.0042 0.0214 rplB; ribosomal protein L2 135.2923 130.000 100.0161 38.000 42.500 128.0000 127.5343 128.000 -0.221 8.939 SGO_1983 0.0161 0.1179 rplW; ribosomal protein L23 159.2286 153.000 357.9522 136.000 136.500 124.5000 409.6102 124.500 1.443 10.038 SGO_1984 0.0004 0.0009 rplD; ribosomal protein L4/L1 family 83.2568 80.000 365.8482 139.000 128.000 96.0000 384.1034 96.000 2.068 9.860 SGO_1985 0.0001 0.0000 rplC; ribosomal protein L3 58.2797 56.000 101.3321 38.500 32.000 42.0000 96.0258 42.000 0.996 8.217 SGO_1986 0.0008 0.0022 rpsJ; ribosomal protein S10 113.9577 109.500 309.2602 117.500 115.500 131.0000 346.5933 131.000 1.422 9.815 SGO_1989 0.0003 0.0004 purA; adenylosuccinate synthetase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

PAGE 50

Hackett Laboratory UW Page 50 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 3.1221 3.000 9.2120 3.500 5.5000 5.500 1.153 4.157 SGO_1990 0.0196 0.1515 glutamate--cysteine ligase, putative/amino acid ligase, putative 36.4248 35.000 22.3720 8.500 11.000 50.5000 33.0089 50.500 -0.658 7.153 SGO_1993 0.0087 0.0534 possible transcriptional regulator 17.1717 16.500 10.5280 4.000 8.0000 8.000 -0.155 5.158 SGO_1995 0.0782 0.7315 MutT/nudix family protein 42.6691 41.000 25.0040 9.500 6.000 37.0000 18.0048 37.000 -0.905 6.939 SGO_1998 0.0016 0.0059 clpB; ATP-dependent Clp proteinase, ATPbinding chain 461.5547 443.500 684.3204 260.000 201.000 404.5000 603.1623 404.500 0.572 11.072 SGO_2000 0.0014 0.0052 tsf; translation elongation factor Ts 473.5229 455.000 502.7123 191.000 189.500 425.5000 568.6531 425.500 0.252 10.944 SGO_2001 0.0063 0.0353 rpsB; ribosomal protein S2 394.4289 379.000 23.6880 9.000 5.500 355.0000 16.5044 355.000 -4.242 9.625 SGO_2005 0.0001 0.0001 LPXTG cell wall surface protein 36.9452 35.500 39.4800 15.000 12.000 36.0000 36.0097 36.000 0.048 7.214 SGO_2007 0.0366 0.3079 nusG; transcription termination/antitermination factor NusG 54.6373 52.500 15.7920 6.000 6.500 69.5000 19.5052 69.500 -1.812 7.317 SGO_2024 0.0008 0.0021 Extracellular polysaccharide biosynthesis 31.2213 30.000 7.8960 3.000 4.500 33.0000 13.5036 33.000 -1.636 6.420 SGO_2025 0.0005 0.0011 wze; putative autophosphorylating protein tyrosine kinase 72.3293 69.500 26.3200 10.000 10.500 67.5000 31.5085 67.500 -1.279 7.627 SGO_2033 0.0002 0.0003 nrdD; ribonucleoside-triphosphate reductase 3.1221 3.000 5.2640 2.000 6.0000 6.000 0.282 3.847 SGO_2041 0.0764 0.7107 conserved hypothetical protein TIGR00250 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

PAGE 51

Hackett Laboratory UW Page 51 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 42.1487 40.500 219.7721 83.500 58.000 31.0000 174.0468 31.000 2.436 8.867 SGO_2042 0.0006 0.0013 Bacterial protein of unknown function (DUF965) superfamily 306.4890 294.500 668.5284 254.000 197.500 365.5000 592.6595 365.500 0.911 10.917 SGO_2045 0.0007 0.0018 recA; recA protein 8.3257 8.000 7.8960 3.000 2.000 14.0000 6.0016 14.000 -0.649 5.179 SGO_2046 0.0131 0.0925 cinA; competence induced protein 20.2938 19.500 9.2120 3.500 3.500 27.5000 10.5028 27.500 -1.264 6.077 SGO_2053 0.0018 0.0070 DNA mismatch repair protein hexB 19.2531 18.500 9.2120 3.500 7.000 29.5000 21.0057 29.500 -0.777 6.303 SGO_2056 0.0176 0.1321 mutS; DNA mismatch repair protein MutS 193.0516 185.500 376.3762 143.000 110.500 204.5000 331.5892 204.500 0.830 10.111 SGO_2058 0.0006 0.0014 argS; arginyl-tRNA synthetase 38.5063 37.000 46.0600 17.500 13.500 55.5000 40.5109 55.500 -0.098 7.496 SGO_2060 0.0584 0.5233 aspS-1; aspartyl-tRNA synthetase 57.2390 55.000 134.2321 51.000 38.000 79.0000 114.0307 79.000 0.880 8.587 SGO_2062 0.0018 0.0073 hisS; histidyl-tRNA synthetase 56.7187 54.500 169.7641 64.500 51.500 66.0000 154.5416 66.000 1.405 8.804 SGO_2064 0.0002 0.0003 ilvD; dihydroxy-acid dehydratase 43.7098 42.000 82.9080 31.500 20.500 27.0000 61.5166 27.000 1.056 7.749 SGO_2066 0.0037 0.0182 rpmG; ribosomal protein L33 13.0089 12.500 14.4760 5.500 3.000 38.0000 9.0024 38.000 -0.962 6.219 SGO_2070 0.0204 0.1592 hypothetical protein SGO_2070 78.5736 75.500 75.0120 28.500 23.500 84.5000 70.5190 84.500 -0.164 8.270 SGO_2085 0.0050 0.0265 purB; adenylosuccinate lyase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.

PAGE 52

Hackett Laboratory UW Page 52 Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs Sg Protein Log 2 Sum qValue Log 2 Ratio pValue Sg SgPgFn SgPgFn Raw SgPgFn vs Sg Sg Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPgFn vs Sg 513.5902 493.500 5.2640 2.000 490.0000 490.000 -6.574 9.979 SGO_2097 0.0032 0.0151 comA; ATP-binding Transport protein ComA 404.3157 388.500 840.9245 319.500 208.500 440.0000 625.6684 440.000 0.782 11.174 SGO_2098 0.0034 0.0159 rpsD; ribosomal protein S4 33.3027 32.000 201.3481 76.500 70.000 30.0000 210.0565 30.000 2.702 8.891 SGO_2100 0.0001 0.0000 ABC transporter substrate-binding protein 302.8465 291.000 155.2881 59.000 36.500 295.5000 109.5295 295.500 -1.198 9.753 SGO_2104 0.0005 0.0011 srtB; sortase B 2320.7824 2230.000 30.2680 11.500 10.500 2777.0000 31.5085 2777.000 -6.361 12.333 SGO_2105 0.0002 0.0003 abpA; amylase-binding protein AbpA 82.2161 79.000 73.6960 28.000 25.000 80.5000 75.0202 80.500 -0.130 8.283 SGO_2106 0.0006 0.0015 ribose-phosphate diphosphokinase 427.7317 411.000 201.3481 76.500 61.500 462.5000 184.5497 462.500 -1.206 10.318 SGO_2133 0.0002 0.0002 Cell division protein ftsH-like protein 65.0444 62.500 56.5880 21.500 13.000 45.0000 39.0105 45.000 -0.203 7.684 SGO_2134 0.0476 0.4172 hpt; hypoxanthine phosphoribosyltransferase 50.4744 48.500 78.9600 30.000 32.000 60.0000 96.0258 60.000 0.662 8.157 SGO_2142 0.0025 0.0106 GTP-binding protein 216.4676 208.000 176.3441 67.000 58.000 201.5000 174.0468 201.500 -0.254 9.586 SGO_2145 0.0013 0.0045 comE; competence response regulator ComE 60.3612 58.000 3.000 54.0000 9.0024 54.000 -2.665 6.947 SGO_2146 0.0073 0.0420 comD; histidine protein kinase ComD 112.9170 108.500 21.0560 8.000 4.000 104.5000 12.0032 104.500 -2.772 7.969 SGO_2150 0.0002 0.0001 degP; serine protease .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 624 Dot Plots Dot Plots Hendrickson et al.



PAGE 1

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 1 9.500 10.500 0.148 6.069 0.0468 0.3152 19.8503 19.000 14.5072 19.000 15.500 15.500 15.5000 17.2653 SGO_0001 dnaA; chromosomal replication initiator protein DnaA 20.000 20.500 -0.090 6.961 0.0299 0.1843 31.3426 30.000 30.5414 30.000 29.000 29.000 29.0000 33.7085 SGO_0002 dnaN; DNA polymerase III, beta subunit 29.500 18.000 -0.318 7.080 0.0514 0.3501 38.1335 36.500 45.0485 36.500 22.500 22.500 22.5000 29.5977 SGO_0004 putative lipoprotein 28.000 19.500 0.304 7.378 0.0161 0.0882 48.0586 46.000 42.7579 46.000 43.500 43.500 43.5000 32.0642 SGO_0006 ABC transporter, ATP-binding protein 9.000 5.500 1.447 6.385 0.0006 0.0008 30.2978 29.000 13.7436 29.000 30.500 30.500 30.5000 9.0437 SGO_0007 trpS; tryptophanyl-tRNA synthetase 77.000 84.500 0.755 9.426 0.0009 0.0014 223.5770 214.000 117.5843 214.000 208.000 208.000 208.0000 138.9447 SGO_0008 inosine-5'-monophosphate dehydrogenase 3.500 -0.201 4.002 0.0922 0.6812 6.2685 6.000 6.000 4.000 4.000 4.0000 5.7551 SGO_0011 proteinase, M16 family 2.500 0.514 3.987 0.0097 0.0458 5.7461 5.500 5.500 6.000 6.000 6.0000 4.1108 SGO_0015 ABC transporter (ATP-binding protein) 50.000 45.000 -2.421 7.479 0.0000 0.0000 13.5818 13.000 76.3534 13.000 14.500 14.500 14.5000 73.9942 SGO_0022 trmU; tRNA (5-methylaminomethyl-2thiouridylate)-methyltransferase 3.500 6.500 0.908 5.502 0.0157 0.0846 18.2832 17.500 5.3447 17.500 11.000 11.000 11.0000 10.6881 SGO_0025 gidA; glucose inhibited division protein A 11.000 12.500 0.756 6.646 0.0011 0.0021 30.2978 29.000 16.7978 29.000 32.500 32.500 32.5000 20.5539 SGO_0027 rplI; ribosomal protein L9 2.000 2.500 0.991 4.452 0.0119 0.0590 5.2238 5.000 3.0541 5.000 9.500 9.500 9.5000 4.1108 SGO_0028 dnaC; replicative DNA helicase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 2

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 2 44.500 42.000 -1.184 7.625 0.0001 0.0000 31.3426 30.000 67.9545 30.000 29.000 29.000 29.0000 69.0613 SGO_0030 aspB; aspartate transaminase 9.500 11.000 0.968 6.584 0.0006 0.0007 31.8649 30.500 14.5072 30.500 31.500 31.500 31.5000 18.0875 SGO_0032 plsX; fatty acid/phospholipid synthesis protein PlsX 7.500 8.500 -3.076 4.751 0.0137 0.0713 11.4530 1.500 1.500 1.5000 13.9767 SGO_0035 phosphoribosylformylglycinamidine synthase 11.000 9.500 -0.563 5.766 0.0019 0.0045 12.0147 11.500 16.7978 11.500 10.000 10.000 10.0000 15.6210 SGO_0042 transcription regulator, GntR family 59.000 58.000 -1.327 8.019 0.0002 0.0001 34.9992 33.500 90.0970 33.500 39.000 39.000 39.0000 95.3703 SGO_0054 dltA; D-alanine-activating enzyme 17.500 12.000 -0.280 6.397 0.0215 0.1239 19.3279 18.500 26.7237 18.500 18.500 18.500 18.5000 19.7318 SGO_0057 dltD protein 93.500 56.500 3.589 11.564 0.0007 0.0009 1557.7259 1491.000 142.7809 1491.000 1233.500 1233.500 1233.5000 92.9039 SGO_0059 pXO1; hypothetical protein SGO_0059 9.500 11.000 0.204 6.135 0.0400 0.2615 16.1937 15.500 14.5072 15.500 21.500 21.500 21.5000 18.0875 SGO_0063 hypothetical protein SGO_0063 16.000 12.000 1.133 7.144 0.0027 0.0079 41.7901 40.000 24.4331 40.000 55.500 55.500 55.5000 19.7318 SGO_0064 FtsK/SpoIIIE family protein 17.000 19.000 0.298 6.991 0.0071 0.0294 36.0440 34.500 25.9602 34.500 34.000 34.000 34.0000 31.2420 SGO_0065 hypothetical protein SGO_0065 2.500 1.034 4.293 0.0278 0.1684 6.7909 6.500 3.8177 6.500 9.000 9.000 9.0000 SGO_0066 D-3-phosphoglycerate dehydrogenase, putative 5.000 3.500 2.110 6.156 0.0015 0.0035 33.4321 32.000 7.6353 32.000 24.500 24.500 24.5000 5.7551 SGO_0067 protein with prophage function domain .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 3

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 3 3.500 1.338 5.123 0.0075 0.0324 14.1042 13.500 13.500 15.000 15.000 15.0000 5.7551 SGO_0068 lipoprotein, putative 2.500 0.966 4.360 0.0387 0.2518 9.9251 9.500 9.500 6.500 6.500 6.5000 4.1108 SGO_0078 hypothetical protein SGO_0078 13.500 8.000 0.527 6.346 0.0125 0.0629 25.5964 24.500 20.6154 24.500 22.000 22.000 22.0000 13.1545 SGO_0080 hypothetical protein SGO_0080 4.500 4.500 -0.142 4.788 0.0913 0.6734 8.3580 8.000 6.8718 8.000 5.000 5.000 5.0000 7.3994 SGO_0081 hypothetical protein SGO_0081 21.000 16.500 -1.125 6.431 0.0009 0.0016 13.0594 12.500 32.0684 12.500 14.000 14.000 14.0000 27.1312 SGO_0095 mccF; microcin immunity protein MccF, putative 2.500 6.500 -0.483 4.566 0.0416 0.2746 4.1790 4.000 3.8177 4.000 5.000 5.000 5.0000 10.6881 SGO_0099 pulA-2; pullulanase, type I 4.000 -0.717 3.403 4.000 4.000 4.0000 6.5773 SGO_0100 maltose operon transcription repressor 108.000 78.000 -0.447 8.985 0.0077 0.0334 104.4752 100.000 164.9234 100.000 109.000 109.000 109.0000 128.2566 SGO_0104 Maltose/maltodextrin-binding protein precursor 15.000 10.000 -0.225 6.182 0.0330 0.2061 17.2384 16.500 22.9060 16.500 16.000 16.000 16.0000 16.4432 SGO_0105 malQ; 4-alpha-glucanotransferase 84.500 64.000 -0.879 8.496 0.0019 0.0044 64.2523 61.500 129.0373 61.500 62.500 62.500 62.5000 105.2362 SGO_0106 glgP-2; maltodextrin phosphorylase 2.000 0.668 3.090 5.2238 5.000 5.000 3.2886 SGO_0110 phosphotyrosine protein phosphatase 375.000 321.500 0.584 11.427 0.0014 0.0031 876.0249 838.500 572.6507 838.500 777.000 777.000 777.0000 528.6476 SGO_0113 acdH; alcohol-acetaldehyde dehydrogenase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 4

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 4 3.000 0.434 4.222 0.0641 0.4482 5.2238 5.000 5.000 8.500 8.500 8.5000 4.9329 SGO_0134 acetyltransferase, GNAT family 41.500 29.500 -0.937 7.410 0.0031 0.0095 26.6412 25.500 63.3733 25.500 31.500 31.500 31.5000 48.5073 SGO_0135 v-type sodium ATP synthase, subunit A 35.500 29.500 -0.613 7.410 0.0019 0.0047 30.8202 29.500 54.2109 29.500 36.500 36.500 36.5000 48.5073 SGO_0136 v-type sodium ATP synthase, chain B 21.500 22.000 0.074 7.146 0.0368 0.2375 37.6111 36.000 32.8320 36.000 35.000 35.000 35.0000 36.1750 SGO_0139 thrC; threonine synthase 4.500 3.000 -1.478 3.796 0.0265 0.1585 2.0895 2.000 6.8718 2.000 4.9329 SGO_0144 hypothetical protein SGO_0144 41.500 26.500 -0.841 7.372 0.0061 0.0248 28.2083 27.000 63.3733 27.000 30.500 30.500 30.5000 43.5744 SGO_0145 polI; DNA polymerase I 15.000 10.000 -0.397 6.110 0.0195 0.1112 16.7160 16.000 22.9060 16.000 13.000 13.000 13.0000 16.4432 SGO_0146 CoA-binding domain protein 10.500 4.000 0.622 5.762 0.0322 0.1998 15.1489 14.500 16.0342 14.500 16.500 16.500 16.5000 6.5773 SGO_0152 tgt; queuine tRNA-ribosyltransferase 493.000 382.500 -1.270 10.934 0.0011 0.0022 320.7390 307.000 752.8447 307.000 254.000 254.000 254.0000 628.9508 SGO_0154 pgi; glucose-6-phosphate isomerase 70.000 74.500 -1.423 8.300 0.0006 0.0007 39.1782 37.500 106.8948 37.500 46.500 46.500 46.5000 122.5015 SGO_0158 2,3,4,5-tetrahydropyridine-2-carboxylate Nsuccinyltransferase, putative 4.500 -1.718 3.164 2.0895 2.000 6.8718 2.000 SGO_0159 hippurate hydrolase 26.500 22.000 0.182 7.353 0.0069 0.0286 42.8348 41.000 40.4673 41.000 44.000 44.000 44.0000 36.1750 SGO_0163 galU; UTP-glucose-1-phosphate uridylyltransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 5 22.000 26.500 -0.577 7.010 0.0080 0.0354 29.2531 28.000 33.5955 28.000 22.500 22.500 22.5000 43.5744 SGO_0164 Glycerol-3-phosphate dehydrogenase [NAD (P)+] (NAD(P)H-dependent glycerol-3phosphate dehydrogenase) 20.500 13.500 -1.427 6.200 0.0032 0.0101 12.0147 11.500 31.3049 11.500 8.000 8.000 8.0000 22.1983 SGO_0169 dut; dUTP diphosphatase 4.500 0.587 4.795 0.0400 0.2623 8.8804 8.500 6.8718 8.500 12.000 12.000 12.0000 SGO_0171 radA; DNA repair protein RadA 15.000 17.000 -1.884 6.016 0.0008 0.0013 7.8356 7.500 22.9060 7.500 6.000 6.000 6.0000 27.9534 SGO_0173 Carbonic anhydrase 60.000 39.000 0.356 8.459 0.0157 0.0841 98.7291 94.500 91.6241 94.500 97.500 97.500 97.5000 64.1283 SGO_0174 gltX; glutamyl-tRNA synthetase 6.500 8.500 0.815 6.068 0.0151 0.0803 27.6859 26.500 9.9259 26.500 15.500 15.500 15.5000 13.9767 SGO_0180 jag; hypothetical protein SGO_0180 5.000 3.500 -0.729 4.120 0.0340 0.2137 7.6353 4.000 4.000 4.0000 5.7551 SGO_0188 hydrolase, TatD family 1.500 4.500 0.840 4.614 0.0309 0.1910 6.7909 6.500 2.2906 6.500 8.000 8.000 8.0000 7.3994 SGO_0193 ksgA; dimethyladenosine transferase 4.500 5.000 -0.890 4.539 0.0020 0.0048 3.6566 3.500 6.8718 3.500 4.500 4.500 4.5000 8.2216 SGO_0197 predicted ribosome small subunit-dependent GTPase A 67.000 67.500 -1.704 8.123 0.0002 0.0001 33.4321 32.000 102.3136 32.000 32.000 32.000 32.0000 110.9913 SGO_0198 rpe; ribulose-phosphate 3-epimerase 13.500 13.000 0.255 6.525 0.0010 0.0018 25.5964 24.500 20.6154 24.500 24.500 24.500 24.5000 21.3761 SGO_0200 competence-induced protein Ccs50 43.000 55.000 -1.470 7.726 0.0022 0.0060 27.1636 26.000 65.6639 26.000 28.500 28.500 28.5000 90.4374 SGO_0201 cmp-binding-factor 1 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 6 5.000 7.000 -0.250 5.128 0.0384 0.2496 7.3133 7.000 7.6353 7.000 8.500 8.500 8.5000 11.5102 SGO_0202 pur operon repressor 39.500 21.500 0.174 7.649 0.0829 0.6053 59.0285 56.500 60.3192 56.500 46.000 46.000 46.0000 35.3528 SGO_0204 rpsL; ribosomal protein S12 92.500 61.500 0.345 9.103 0.0281 0.1707 129.5493 124.000 141.2538 124.000 178.000 178.000 178.0000 101.1254 SGO_0205 rpsG; ribosomal protein S7 652.000 569.500 0.424 12.143 0.0008 0.0013 1334.1488 1277.000 995.6486 1277.000 1258.000 1258.000 1258.0000 936.4379 SGO_0206 fusA; translation elongation factor G 934.000 884.000 -0.118 12.434 0.0006 0.0008 1323.7013 1267.000 1426.2819 1267.000 1330.000 1330.000 1330.0000 1453.5753 SGO_0207 gap; glyceraldehyde-3-phosphate dehydrogenase, type I 1110.000 949.000 0.736 13.083 0.0007 0.0009 2588.3741 2477.500 1695.0460 2477.500 2836.000 2836.000 2836.0000 1560.4558 SGO_0209 pgk; phosphoglycerate kinase 33.500 23.000 -4.474 6.540 0.0009 0.0016 1.5671 1.500 51.1568 1.500 2.500 2.500 2.5000 37.8193 SGO_0210 sspA; streptococcal surface protein A 51.500 48.500 -0.240 8.195 0.0085 0.0389 73.1327 70.000 78.6440 70.000 61.500 61.500 61.5000 79.7493 SGO_0215 glnA; glutamine synthetase, type I 29.000 29.000 0.373 7.721 0.0007 0.0008 59.5509 57.000 44.2850 57.000 59.500 59.500 59.5000 47.6852 SGO_0219 metallo-beta-lactamase superfamily protein 1 5.000 -0.171 4.418 0.0848 0.6214 5.7461 5.500 7.6353 5.500 8.000 8.000 8.0000 SGO_0220 Protein of unknown function (DUF1447) superfamily 3.500 0.669 3.791 5.3447 8.500 8.500 8.5000 SGO_0223 glycoproteinase family protein 6.500 2.500 0.940 5.270 0.0117 0.0564 13.0594 12.500 9.9259 12.500 11.500 11.500 11.5000 4.1108 SGO_0230 Protein of unknown function, DUF536 family .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 7 30.500 26.000 -0.442 7.280 0.0043 0.0153 36.5663 35.000 46.5756 35.000 29.500 29.500 29.5000 42.7522 SGO_0234 pepX; X-Pro dipeptidyl-peptidase 4.500 8.000 0.508 5.557 0.0255 0.1510 13.0594 12.500 6.8718 12.500 14.000 14.000 14.0000 13.1545 SGO_0237 ccpA; CcpA protein (proteinase) 6.500 7.500 -1.190 4.998 0.0013 0.0029 4.7014 4.500 9.9259 4.500 5.000 5.000 5.0000 12.3324 SGO_0243 hydroxymethylglutaryl-CoA reductase, degradative 9.500 6.500 0.032 5.664 0.1189 0.9011 12.0147 11.500 14.5072 11.500 13.500 13.500 13.5000 10.6881 SGO_0244 hydroxymethylglutaryl-CoA synthase 223.500 308.500 -0.854 10.354 0.0067 0.0274 223.0546 213.500 341.2998 213.500 237.500 237.500 237.5000 507.2715 SGO_0247 pfl; formate acetyltransferase 5.500 3.500 -1.020 4.417 0.0086 0.0395 4.7014 4.500 8.3989 4.500 2.500 2.500 2.5000 5.7551 SGO_0252 possible TetR-type transcriptional regulator 10.000 7.500 0.297 5.938 0.0082 0.0371 16.7160 16.000 15.2707 16.000 17.000 17.000 17.0000 12.3324 SGO_0255 Signal peptidase I 8.500 11.500 0.597 6.310 0.0062 0.0249 22.4622 21.500 12.9801 21.500 25.000 25.000 25.0000 18.9096 SGO_0260 DNA mismatch binding protein MutS2 18.000 14.000 0.261 6.793 0.0115 0.0553 31.8649 30.500 27.4872 30.500 28.500 28.500 28.5000 23.0204 SGO_0262 dipeptidase 14.000 22.000 0.431 7.051 0.0237 0.1383 36.0440 34.500 21.3790 34.500 39.000 39.000 39.0000 36.1750 SGO_0263 trx-1; thioredoxin 13.500 9.000 -0.367 5.966 0.0163 0.0892 13.5818 13.000 20.6154 13.000 13.500 13.500 13.5000 14.7988 SGO_0272 hypothetical protein SGO_0272 108.500 82.000 -0.334 9.070 0.0083 0.0379 119.1018 114.000 165.6869 114.000 118.000 118.000 118.0000 134.8339 SGO_0276 gdhA; glutamate dehydrogenase (NADP) .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 8 6.500 10.000 -0.766 5.384 0.0153 0.0815 9.4028 9.000 9.9259 9.000 6.000 6.000 6.0000 16.4432 SGO_0277 pyrA; Dihydroorotate dehydrogenase 25.000 11.500 -1.269 6.326 0.0124 0.0620 14.6265 14.000 38.1767 14.000 8.500 8.500 8.5000 18.9096 SGO_0280 trzA; ethylammeline chlorohydrolase 4.000 -1.232 3.610 0.0111 0.0536 3.1343 3.000 3.000 2.500 2.500 2.5000 6.5773 SGO_0288 GDSL-like lipase/acylhydrolase 11.000 9.500 0.297 6.175 0.0019 0.0045 19.3279 18.500 16.7978 18.500 20.500 20.500 20.5000 15.6210 SGO_0291 copper-translocating P-type ATPase 15.500 16.000 2.395 8.289 0.0002 0.0001 125.3703 120.000 23.6696 120.000 137.500 137.500 137.5000 26.3091 SGO_0292 spxB; pyruvate oxidase 4.500 5.500 -0.916 4.329 0.0290 0.1782 4.1790 4.000 6.8718 4.000 9.0437 SGO_0310 metE; 5methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase 444.000 380.000 -0.479 11.127 0.0008 0.0013 461.2582 441.500 678.0184 441.500 472.500 472.500 472.5000 624.8401 SGO_0312 xfp; D-xylulose 5-phosphate/D-fructose 6phosphate phosphoketolase 23.500 19.500 -0.690 6.785 0.0021 0.0052 18.8055 18.000 35.8861 18.000 23.500 23.500 23.5000 32.0642 SGO_0321 polypeptide deformylase 3.000 -1.654 2.700 1.5671 1.500 1.500 4.9329 SGO_0327 Lipopolysaccharide Nacetylglucosaminyltransferase 39.500 24.500 0.234 7.759 0.0419 0.2768 57.4614 55.000 60.3192 55.000 58.500 58.500 58.5000 40.2857 SGO_0333 rpsO; ribosomal protein S15 10.500 11.500 -3.474 5.190 0.0118 0.0574 1.5671 1.500 16.0342 1.500 18.9096 SGO_0339 hypothetical protein SGO_0339 56.500 47.000 -0.629 8.075 0.0021 0.0050 48.0586 46.000 86.2794 46.000 58.000 58.000 58.0000 77.2828 SGO_0342 pepF-2; oligoendopeptidase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 9 79.000 63.000 -0.343 8.646 0.0046 0.0170 89.3263 85.500 120.6384 85.500 87.000 87.000 87.0000 103.5919 SGO_0344 pnpA; polyribonucleotide nucleotidyltransferase 4.500 -0.942 3.810 0.0043 0.0151 3.6566 3.500 6.8718 3.500 3.500 3.500 3.5000 SGO_0348 reductase 16.000 22.000 -0.796 6.568 0.0072 0.0301 17.2384 16.500 24.4331 16.500 17.000 17.000 17.0000 36.1750 SGO_0349 cysS; cysteinyl-tRNA synthetase 25.000 24.500 -0.396 7.112 0.0042 0.0144 32.9097 31.500 38.1767 31.500 27.000 27.000 27.0000 40.2857 SGO_0352 ABC transporter, ATP-binding protein SP1580 2.500 5.000 -0.501 4.341 0.0414 0.2728 5.2238 5.000 3.8177 5.000 3.000 3.000 3.0000 8.2216 SGO_0353 transport protein 6.000 7.000 0.236 5.496 0.0349 0.2222 10.4475 10.000 9.1624 10.000 14.000 14.000 14.0000 11.5102 SGO_0355 RNA methyltransferase, TrmH family, group 3 23.000 22.000 0.351 7.343 0.0025 0.0070 48.0586 46.000 35.1226 46.000 43.000 43.000 43.0000 36.1750 SGO_0357 degV; DegV family fatty acid binding protein 108.500 83.000 -0.321 9.085 0.0082 0.0369 122.7584 117.500 165.6869 117.500 118.000 118.000 118.0000 136.4782 SGO_0358 rplM; ribosomal protein L13 34.500 19.500 0.184 7.477 0.0730 0.5246 44.9244 43.000 52.6839 43.000 48.500 48.500 48.5000 32.0642 SGO_0359 rpsI; ribosomal protein S9 3.000 4.500 -0.849 4.222 0.0132 0.0679 4.1790 4.000 4.5812 4.000 2.500 2.500 2.5000 7.3994 SGO_0361 immunity repressor protein 17.000 12.500 -0.545 6.289 0.0048 0.0177 15.6713 15.000 25.9602 15.000 16.000 16.000 16.0000 20.5539 SGO_0372 malate oxidoreductase 15.000 17.000 -0.908 6.283 0.0019 0.0047 12.5370 12.000 22.9060 12.000 14.500 14.500 14.5000 27.9534 SGO_0374 Response regulator of the LytR/AlgR family .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 10 4.500 6.500 -0.094 5.081 0.0912 0.6706 6.7909 6.500 6.8718 6.500 9.500 9.500 9.5000 10.6881 SGO_0384 putative carboxylate-amine/thiol ligase 66.500 46.500 -0.374 8.298 0.0161 0.0876 75.2222 72.000 101.5501 72.000 61.500 61.500 61.5000 76.4607 SGO_0390 glycerol-3-phosphate dehydrogenase (NAD (P)+) 18.500 19.000 -0.946 6.501 0.0011 0.0021 13.5818 13.000 28.2508 13.000 17.500 17.500 17.5000 31.2420 SGO_0392 phosphoglycerate mutase 5.000 7.500 -0.794 4.991 0.0183 0.1028 7.8356 7.500 7.6353 7.500 4.000 4.000 4.0000 12.3324 SGO_0398 ABC transporter ATP-binding protein 16.500 17.500 -0.561 6.510 0.0076 0.0327 15.1489 14.500 25.1966 14.500 22.000 22.000 22.0000 28.7755 SGO_0401 grpE; co-chaperone GrpE 492.500 474.000 -0.741 11.257 0.0002 0.0001 443.4974 424.500 752.0812 424.500 473.000 473.000 473.0000 779.4058 SGO_0402 dnaK; DnaK chaperone protein 10.500 11.000 -0.036 6.073 0.0706 0.5026 16.7160 16.000 16.0342 16.000 16.500 16.500 16.5000 18.0875 SGO_0404 dnaJ; DnaJ chaparone protein 4.000 4.500 -1.686 3.963 0.0161 0.0876 2.0895 2.000 6.1083 2.000 7.3994 SGO_0407 truA; tRNA pseudouridine synthase A 115.000 139.000 -5.919 8.682 0.0007 0.0010 3.6566 3.500 175.6129 3.500 3.000 3.000 3.0000 228.5599 SGO_0409 pyridoxine kinase 61.000 140.500 -4.261 8.407 0.0072 0.0303 8.3580 8.000 93.1512 8.000 7.000 7.000 7.0000 231.0264 SGO_0411 conserved hypothetical protein TIGR01440 216.500 177.000 0.673 10.654 0.0006 0.0008 483.7204 463.000 330.6103 463.000 506.000 506.000 506.0000 291.0439 SGO_0412 tig; trigger factor 25.000 25.500 -0.184 7.251 0.0657 0.4612 28.2083 27.000 38.1767 27.000 44.000 44.000 44.0000 41.9301 SGO_0413 DNA-directed RNA polymerase delta chain .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 11 125.500 101.500 0.090 9.530 0.0349 0.2222 192.2344 184.000 191.6471 184.000 188.500 188.500 188.5000 166.8981 SGO_0415 secA; preprotein translocase, SecA subunit 35.000 32.000 -0.702 7.428 0.0028 0.0085 38.6558 37.000 53.4474 37.000 27.500 27.500 27.5000 52.6181 SGO_0416 phospho-2-dehydro-3-deoxyheptonate aldolase 8.500 8.500 -1.405 5.217 0.0004 0.0004 5.7461 5.500 12.9801 5.500 4.500 4.500 4.5000 13.9767 SGO_0418 alr; alanine racemase 4.500 -0.910 3.396 3.6566 3.500 6.8718 3.500 SGO_0425 ansB; asparaginase 9.000 11.000 -1.201 5.513 0.0025 0.0071 7.8356 7.500 13.7436 7.500 6.000 6.000 6.0000 18.0875 SGO_0426 Cof family protein 37.500 42.500 -1.809 7.352 0.0008 0.0012 16.7160 16.000 57.2651 16.000 19.500 19.500 19.5000 69.8834 SGO_0427 universal stress protein family 67.000 66.500 -0.121 8.678 0.0795 0.5757 117.5346 112.500 102.3136 112.500 80.500 80.500 80.5000 109.3470 SGO_0429 aspartate transaminase 5.000 -0.204 4.493 0.0326 0.2026 6.7909 6.500 6.500 7.500 7.500 7.5000 8.2216 SGO_0431 GTP-sensing transcriptional pleiotropic repressor codY 5.000 1.873 6.100 0.0126 0.0633 32.3873 31.000 31.000 28.000 28.000 28.0000 8.2216 SGO_0432 entB; isochorismatase family protein 13.000 20.500 0.066 6.756 0.1206 0.9195 24.0293 23.000 19.8519 23.000 30.500 30.500 30.5000 33.7085 SGO_0434 aspS-2; aspartyl-tRNA synthetase 8.500 8.500 0.055 5.782 0.0639 0.4458 13.0594 12.500 12.9801 12.500 15.000 15.000 15.0000 13.9767 SGO_0435 gatC; glutamyl-tRNA(Gln) amidotransferase, C subunit 46.000 38.500 0.568 8.373 0.0013 0.0027 103.9529 99.500 70.2451 99.500 94.000 94.000 94.0000 63.3062 SGO_0436 gatA; glutamyl-tRNA(Gln) amidotransferase, A subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 12

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 12 52.000 37.500 0.601 8.467 0.0037 0.0121 99.2515 95.000 79.4076 95.000 113.500 113.500 113.5000 61.6618 SGO_0437 gatB; glutamyl-tRNA(Gln) amidotransferase, B subunit 28.500 30.500 -2.526 6.782 0.0004 0.0003 9.4028 9.000 43.5215 9.000 7.000 7.000 7.0000 50.1516 SGO_0440 L-iditol 2-dehydrogenase BH3949 22.500 19.500 -0.617 6.781 0.0019 0.0044 24.0293 23.000 34.3590 23.000 19.500 19.500 19.5000 32.0642 SGO_0445 GTP-binding protein 11.500 7.000 -1.713 5.261 0.0044 0.0155 6.2685 6.000 17.5613 6.000 3.000 3.000 3.0000 11.5102 SGO_0447 nadD; nicotinate (nicotinamide) nucleotide adenylyltransferase 12.000 8.500 -1.326 5.495 0.0019 0.0046 6.7909 6.500 18.3248 6.500 6.000 6.000 6.0000 13.9767 SGO_0448 conserved hypothetical protein TIGR00488 6.500 5.500 -0.570 4.989 0.0013 0.0029 6.7909 6.500 9.9259 6.500 6.000 6.000 6.0000 9.0437 SGO_0450 iojap-related protein 21.000 28.000 0.070 7.311 0.1040 0.7740 39.1782 37.500 32.0684 37.500 41.500 41.500 41.5000 46.0408 SGO_0454 conserved hypothetical protein TIGR01033 1.500 2.829 5.127 0.0111 0.0532 15.1489 14.500 2.2906 14.500 17.500 17.500 17.5000 SGO_0455 lipoprotein, putative 13.500 12.500 1.359 7.198 0.0002 0.0001 50.6705 48.500 20.6154 48.500 55.000 55.000 55.0000 20.5539 SGO_0457 ABC transporter, substrate-binding protein SP0148 56.500 37.500 0.889 8.708 0.0015 0.0034 133.7283 128.000 86.2794 128.000 136.500 136.500 136.5000 61.6618 SGO_0458 hlpA; lipoprotein 6.500 7.500 -1.303 4.977 0.0023 0.0064 5.7461 5.500 9.9259 5.500 3.500 3.500 3.5000 12.3324 SGO_0459 succinyl-diaminopimelate desuccinylase 6.000 6.000 0.425 5.479 0.0025 0.0072 13.5818 13.000 9.1624 13.000 12.000 12.000 12.0000 9.8659 SGO_0460 ABC transporter, ATP-binding protein SP0151 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 13

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 13 31.000 17.000 -1.602 6.634 0.0051 0.0196 11.4923 11.000 47.3391 11.000 12.500 12.500 12.5000 27.9534 SGO_0468 hypothetical protein SGO_0468 2.000 2.521 5.363 0.0119 0.0583 20.3727 19.500 19.500 17.500 17.500 17.5000 3.2886 SGO_0476 rhodanese family protein 146.500 289.000 -4.542 9.506 0.0050 0.0191 15.6713 15.000 223.7155 15.000 12.500 12.500 12.5000 475.2073 SGO_0480 hypothetical protein SGO_0480 11.000 9.500 0.245 6.162 0.0367 0.2361 15.6713 15.000 16.7978 15.000 23.500 23.500 23.5000 15.6210 SGO_0483 hypothetical protein SGO_0483 2.000 7.000 0.160 4.799 0.1077 0.8086 6.2685 6.000 3.0541 6.000 7.000 7.000 7.0000 11.5102 SGO_0488 ABC transporter, ATP-binding protein SP0483 5.000 4.000 -1.048 4.414 0.0033 0.0108 2.6119 2.500 7.6353 2.500 4.500 4.500 4.5000 6.5773 SGO_0491 gidB; methyltransferase GidB 64.500 44.500 -2.354 7.679 0.0013 0.0025 17.2384 16.500 98.4959 16.500 16.000 16.000 16.0000 73.1721 SGO_0494 lemA; LemA-like protein 7.000 6.000 -0.838 4.717 0.0118 0.0577 5.7461 5.500 10.6895 5.500 9.8659 SGO_0495 htpx; heat shock protein 3.000 2.358 5.796 0.0062 0.0253 26.1188 25.000 25.000 24.500 24.500 24.5000 4.9329 SGO_0501 Uncharacterized ACR, COG1399 44.000 27.000 1.192 8.502 0.0023 0.0064 138.9521 133.000 67.1910 133.000 112.000 112.000 112.0000 44.3965 SGO_0502 floL; flotillin-like protein 545.500 472.000 -0.832 11.295 0.0004 0.0003 438.7960 420.000 833.0158 420.000 465.000 465.000 465.0000 776.1171 SGO_0503 gnd; 6-phosphogluconate dehydrogenase, decarboxylating 42.500 27.000 0.210 7.872 0.0512 0.3479 55.8943 53.500 64.9004 53.500 69.000 69.000 69.0000 44.3965 SGO_0505 PTS system, IIBC component .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 14

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 14 8.500 -0.087 5.228 0.0712 0.5085 11.4923 11.000 12.9801 11.000 13.000 13.000 13.0000 SGO_0508 nrdR; transcriptional regulator, NrdR family 11.500 7.000 0.348 6.032 0.0275 0.1659 19.8503 19.000 17.5613 19.000 16.500 16.500 16.5000 11.5102 SGO_0510 dnaI; primosomal protein DnaI 7.000 10.000 -1.112 5.300 0.0054 0.0209 6.2685 6.000 10.6895 6.000 6.000 6.000 6.0000 16.4432 SGO_0511 NADPH-flavin oxidoreductase -like protein 30.000 23.500 0.329 7.571 0.0043 0.0149 52.2376 50.000 45.8121 50.000 53.500 53.500 53.5000 38.6414 SGO_0512 GTP-binding protein engA 66.000 50.500 -0.507 8.288 0.0038 0.0126 64.2523 61.500 100.7865 61.500 64.500 64.500 64.5000 83.0380 SGO_0515 murC; UDP-N-acetylmuramate--alanine ligase 12.500 11.500 1.227 6.988 0.0002 0.0001 45.9691 44.000 19.0884 44.000 43.000 43.000 43.0000 18.9096 SGO_0518 aminodeoxychorismate lyase-like protein 19.500 13.000 0.476 6.929 0.0132 0.0679 39.7006 38.000 29.7778 38.000 31.000 31.000 31.0000 21.3761 SGO_0519 greA; transcription elongation factor greA 7.000 -0.509 4.706 0.0488 0.3295 9.4028 9.000 10.6895 9.000 6.000 6.000 6.0000 SGO_0521 Membrane protein oxaA 2 precursor 21.500 20.000 -1.995 6.366 0.0002 0.0001 6.7909 6.500 32.8320 6.500 10.000 10.000 10.0000 32.8863 SGO_0523 spoU rRNA Methylase family protein 7.000 11.500 0.264 5.998 0.0611 0.4254 18.8055 18.000 10.6895 18.000 15.500 15.500 15.5000 18.9096 SGO_0526 ilvB; acetolactate synthase, large subunit, biosynthetic type 6.000 6.000 -0.403 5.078 0.0196 0.1122 5.7461 5.500 9.1624 5.500 9.000 9.000 9.0000 9.8659 SGO_0527 ilvN; acetolactate synthase, small subunit 77.500 57.000 -0.445 8.520 0.0078 0.0339 82.5354 79.000 118.3478 79.000 72.500 72.500 72.5000 93.7260 SGO_0528 ilvC; ketol-acid reductoisomerase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 15

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 15 4.500 7.000 -0.507 4.959 0.0259 0.1541 5.2238 5.000 6.8718 5.000 7.500 7.500 7.5000 11.5102 SGO_0529 ilvA; threonine dehydratase 3.000 4.500 -0.849 4.253 0.0220 0.1276 2.0895 2.000 4.5812 2.000 5.000 5.000 5.0000 7.3994 SGO_0530 Cof family protein 4.000 -1.611 3.019 6.1083 2.000 2.000 2.0000 SGO_0533 conserved hypothetical protein TIGR00150 4.000 0.257 4.384 0.0652 0.4574 6.2685 6.000 6.1083 6.000 8.500 8.500 8.5000 SGO_0535 putative transcriptional regulator LytR 16.000 13.500 -0.118 6.485 0.0126 0.0637 21.4174 20.500 24.4331 20.500 21.500 21.500 21.5000 22.1983 SGO_0537 HIT family protein 7.000 11.000 -1.633 5.245 0.0054 0.0210 3.6566 3.500 10.6895 3.500 5.500 5.500 5.5000 18.0875 SGO_0538 ABC transporter, ATP-binding protein SP0522 37.000 31.500 -0.986 7.348 0.0004 0.0003 26.6412 25.500 56.5015 25.500 28.000 28.000 28.0000 51.7960 SGO_0540 hypothetical protein SGO_0540 5.500 4.500 -1.057 4.580 0.0057 0.0224 2.6119 2.500 8.3989 2.500 5.500 5.500 5.5000 7.3994 SGO_0541 methyltransferase, putative 13.500 12.000 1.107 6.991 0.0000 0.0000 43.8796 42.000 20.6154 42.000 43.000 43.000 43.0000 19.7318 SGO_0543 nusA; transcription termination factor NusA 40.500 45.000 0.170 8.171 0.0265 0.1583 80.9683 77.500 61.8463 77.500 71.500 71.500 71.5000 73.9942 SGO_0546 infB; Translation initiation factor IF-2 2.000 1.438 4.402 0.0127 0.0642 8.3580 8.000 8.000 9.500 9.500 9.5000 3.2886 SGO_0548 Na/Pi-cotransporter family protein 1.500 3.912 5.200 34.4768 33.000 2.2906 33.000 SGO_0549 nagA; N-acetylglucosamine-6-phosphate deacetylase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 16

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 16 29.500 22.500 -0.752 7.028 0.0022 0.0058 23.5069 22.500 45.0485 22.500 25.000 25.000 25.0000 36.9971 SGO_0552 oxidoreductase, aldo/keto reductase family 12.500 14.500 -1.018 6.007 0.0028 0.0083 8.8804 8.500 19.0884 8.500 12.500 12.500 12.5000 23.8426 SGO_0554 hsdR; type I site-specific deoxyribonuclease 3.000 -0.137 3.826 0.1100 0.8286 5.7461 5.500 5.500 3.500 3.500 3.5000 4.9329 SGO_0558 hypothetical protein SGO_0558 1.500 2.120 4.582 0.0118 0.0572 11.4923 11.000 11.000 10.000 10.000 10.0000 2.4665 SGO_0560 hsdM; type I restriction-modification system, M subunit 128.000 95.500 -1.797 8.825 0.0009 0.0015 47.5362 45.500 195.4648 45.500 53.500 53.500 53.5000 157.0322 SGO_0565 adhA; alcohol dehydrogenase 8.500 4.500 1.448 6.209 0.0014 0.0031 25.0741 24.000 12.9801 24.000 28.500 28.500 28.5000 7.3994 SGO_0568 glyQ; glycyl-tRNA synthetase, alpha subunit 38.000 47.000 0.084 8.115 0.0814 0.5918 69.9984 67.000 58.0286 67.000 72.000 72.000 72.0000 77.2828 SGO_0569 glyS; glycyl-tRNA synthetase, beta subunit 15.500 8.500 -0.176 6.126 0.0588 0.4067 16.7160 16.000 23.6696 16.000 15.500 15.500 15.5000 13.9767 SGO_0573 mraW; S-adenosyl-methyltransferase MraW 17.500 9.000 0.804 6.796 0.0075 0.0319 37.0887 35.500 26.7237 35.500 32.500 32.500 32.5000 14.7988 SGO_0577 ATP-dependent RNA helicase 3.000 3.000 0.718 4.668 0.0075 0.0323 9.4028 9.000 4.5812 9.000 6.500 6.500 6.5000 4.9329 SGO_0579 amino acid ABC transporter ATP binding protein 3.500 5.500 1.121 5.490 0.0046 0.0168 13.0594 12.500 5.3447 12.500 17.500 17.500 17.5000 9.0437 SGO_0581 trxB; thioredoxin-disulfide reductase 96.000 91.500 -1.346 8.699 0.0006 0.0007 49.1034 47.000 146.5986 47.000 69.500 69.500 69.5000 150.4549 SGO_0582 nicotinate phosphoribosyltransferase, putative .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 17

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 17 23.000 15.000 -0.967 6.490 0.0045 0.0163 14.6265 14.000 35.1226 14.000 15.500 15.500 15.5000 24.6647 SGO_0583 nadE; NAD+ synthetase 77.500 81.500 -1.956 8.313 0.0004 0.0004 37.6111 36.000 118.3478 36.000 28.000 28.000 28.0000 134.0117 SGO_0585 pepC; aminopeptidase C 20.500 23.500 0.341 7.309 0.0144 0.0754 49.1034 47.000 31.3049 47.000 39.500 39.500 39.5000 38.6414 SGO_0586 pbp1a; penicillin-binding protein 1A 49.000 29.500 -0.571 7.688 0.0196 0.1119 32.9097 31.500 74.8264 31.500 50.000 50.000 50.0000 48.5073 SGO_0589 methylase 11.000 8.500 -0.895 5.577 0.0044 0.0159 10.4475 10.000 16.7978 10.000 6.500 6.500 6.5000 13.9767 SGO_0590 Methyltransferase 18.500 17.000 -0.081 6.773 0.0005 0.0005 26.6412 25.500 28.2508 25.500 26.500 26.500 26.5000 27.9534 SGO_0591 hypothetical protein SGO_0591 7.500 6.000 0.401 5.626 0.0027 0.0078 13.5818 13.000 11.4530 13.000 14.500 14.500 14.5000 9.8659 SGO_0592 luxS; autoinducer-2 production protein LuxS 9.000 11.000 1.189 6.701 0.0013 0.0027 39.1782 37.500 13.7436 37.500 33.000 33.000 33.0000 18.0875 SGO_0593 HD/KH domain protein 14.500 11.500 -0.633 6.078 0.0028 0.0086 12.0147 11.500 22.1425 11.500 14.500 14.500 14.5000 18.9096 SGO_0594 gmk; Guanylate kinase (GMP kinase) 9.000 6.000 0.997 6.131 0.0011 0.0021 22.9846 22.000 13.7436 22.000 23.500 23.500 23.5000 9.8659 SGO_0595 DNA-directed RNA polymerase, omega subunit 13.000 15.000 -0.682 6.173 0.0032 0.0104 14.6265 14.000 19.8519 14.000 13.000 13.000 13.0000 24.6647 SGO_0597 fmt; methionyl-tRNA formyltransferase 4.000 0.150 4.423 0.0894 0.6563 8.8804 8.500 8.500 6.000 6.000 6.0000 6.5773 SGO_0598 sun; sun protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 18

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 18 40.500 33.500 -1.709 7.255 0.0004 0.0003 19.3279 18.500 61.8463 18.500 16.500 16.500 16.5000 55.0846 SGO_0599 phosphoprotein phosphatase 14.000 9.500 -0.306 6.059 0.0240 0.1406 16.1937 15.500 21.3790 15.500 13.500 13.500 13.5000 15.6210 SGO_0600 serine/threonine protein kinase 7.000 6.000 -1.375 4.866 0.0031 0.0096 2.6119 2.500 10.6895 2.500 6.000 6.000 6.0000 9.8659 SGO_0603 response regulator 87.000 82.500 -1.206 8.588 0.0001 0.0000 56.4166 54.000 132.8550 54.000 60.000 60.000 60.0000 135.6561 SGO_0604 hydrolase, haloacid dehalogenase family/peptidyl-prolyl cis-trans isomerase, cyclophilin type 52.000 49.500 0.287 8.481 0.0032 0.0103 92.9830 89.000 79.4076 89.000 103.500 103.500 103.5000 81.3936 SGO_0606 cysK; cysteine synthase A 84.000 60.000 -0.434 8.621 0.0095 0.0444 88.2816 84.500 128.2737 84.500 78.500 78.500 78.5000 98.6590 SGO_0610 ribosomal subunit interface protein 3.000 0.400 4.071 0.0495 0.3347 5.2238 5.000 4.5812 5.000 7.000 7.000 7.0000 SGO_0626 recX; Regulatory protein recX 2.500 2.906 5.932 0.0044 0.0161 29.2531 28.000 3.8177 28.000 28.000 28.000 28.0000 SGO_0631 alpha-glycerophosphate oxidase 29.000 32.000 0.330 7.771 0.0060 0.0237 57.9838 55.500 44.2850 55.500 63.500 63.500 63.5000 52.6181 SGO_0639 valS; valyl-tRNA synthetase 16.000 11.500 0.081 6.473 0.0774 0.5594 23.5069 22.500 24.4331 22.500 22.000 22.000 22.0000 18.9096 SGO_0641 ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein protein 4.500 8.000 0.432 5.530 0.0425 0.2821 15.6713 15.000 6.8718 15.000 10.500 10.500 10.5000 13.1545 SGO_0642 hypothetical protein SGO_0642 5.500 6.000 -1.201 4.722 0.0021 0.0051 3.1343 3.000 8.3989 3.000 5.000 5.000 5.0000 9.8659 SGO_0643 cytosine-specific methyltransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 19

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 19 8.000 5.500 1.467 6.326 0.0028 0.0083 34.4768 33.000 12.2165 33.000 24.500 24.500 24.5000 9.0437 SGO_0644 hypothetical protein SGO_0644 2.500 2.000 0.057 3.991 0.0810 0.5877 6.7909 6.500 3.8177 6.500 2.000 2.000 2.0000 3.2886 SGO_0652 hypothetical protein SGO_0652 4.000 2.498 6.237 0.0141 0.0739 31.3426 30.000 6.1083 30.000 38.000 38.000 38.0000 SGO_0654 radical SAM enzyme, Cfr family 8.000 22.500 -1.633 5.978 0.0164 0.0904 7.8356 7.500 12.2165 7.500 6.000 6.000 6.0000 36.9971 SGO_0656 trpB-2; tryptophan synthase, beta subunit 107.500 75.000 0.384 9.366 0.0119 0.0585 172.3842 165.000 164.1599 165.000 200.000 200.000 200.0000 123.3237 SGO_0665 non-heme iron-containing ferritin 38.500 43.000 -0.097 7.966 0.0429 0.2855 60.0733 57.500 58.7921 57.500 60.500 60.500 60.5000 70.7056 SGO_0669 typA; GTP-binding protein TypA 46.500 38.000 -1.199 7.584 0.0008 0.0012 32.3873 31.000 71.0087 31.000 26.000 26.000 26.0000 62.4840 SGO_0671 murD; UDP-N-acetylmuramoylalanine--Dglutamate ligase 14.000 16.500 -1.375 6.114 0.0055 0.0216 5.7461 5.500 21.3790 5.500 15.000 15.000 15.0000 27.1312 SGO_0672 murG; undecaprenyl-PP-MurNAcpentapeptide-UDPGlcNAc GlcNAc transferase 4.500 7.000 -1.282 4.462 0.0387 0.2526 3.6566 3.500 6.8718 3.500 11.5102 SGO_0673 DivIB; cell division protein DivIB 84.500 74.000 -0.210 8.869 0.0037 0.0120 112.3109 107.500 129.0373 107.500 104.500 104.500 104.5000 121.6794 SGO_0674 ftsA; cell division protein FtsA 155.500 101.000 -0.149 9.573 0.0515 0.3515 179.1750 171.500 237.4591 171.500 179.000 179.000 179.0000 166.0759 SGO_0675 ftsZ; cell division protein FtsZ 4.500 8.000 0.397 5.507 0.0465 0.3128 10.4475 10.000 6.8718 10.000 15.000 15.000 15.0000 13.1545 SGO_0676 conserved hypothetical protein TIGR00044 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 20

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 20 26.500 27.000 0.062 7.443 0.0778 0.5626 39.1782 37.500 40.4673 37.500 50.000 50.000 50.0000 44.3965 SGO_0677 ylmF protein 55.000 33.000 0.801 8.548 0.0049 0.0186 107.6095 103.000 83.9888 103.000 128.500 128.500 128.5000 54.2624 SGO_0680 cell division protein DivIVA 33.500 31.500 1.077 8.323 0.0001 0.0000 110.7438 106.000 51.1568 106.000 106.500 106.500 106.5000 51.7960 SGO_0681 ileS; isoleucyl-tRNA synthetase 49.000 52.000 -1.632 7.728 0.0004 0.0004 26.1188 25.000 74.8264 25.000 25.500 25.500 25.5000 85.5044 SGO_0684 hypothetical protein SGO_0684 31.000 48.000 -0.332 7.804 0.0336 0.2103 50.1481 48.000 47.3391 48.000 47.000 47.000 47.0000 78.9272 SGO_0688 ATP dependent Clp protease, ATP-binding subunit, ClpE 5.000 7.500 -1.471 4.553 0.0349 0.2212 7.6353 3.500 3.500 3.5000 12.3324 SGO_0690 folD; methenyltetrahydrofolate cyclohydrolase 10.000 18.500 -3.021 5.697 0.0055 0.0215 4.7014 4.500 15.2707 4.500 1.500 1.500 1.5000 30.4198 SGO_0693 xseA; exodeoxyribonuclease VII, large subunit 3.500 0.389 3.626 5.3447 7.000 7.000 7.0000 SGO_0695 geranyltranstransferase 11.000 12.000 -0.769 5.857 0.0019 0.0043 9.9251 9.500 16.7978 9.500 11.500 11.500 11.5000 19.7318 SGO_0698 recN; DNA repair protein RecN 6.000 7.000 -0.938 4.974 0.0023 0.0060 5.7461 5.500 9.1624 5.500 5.000 5.000 5.0000 11.5102 SGO_0699 Serine/threonine protein phosphatase 7.500 4.000 0.903 5.663 0.0060 0.0237 14.6265 14.000 11.4530 14.000 18.000 18.000 18.0000 6.5773 SGO_0700 DegV family protein 705.500 919.000 0.251 12.458 0.0282 0.1725 1541.0098 1475.000 1077.3468 1475.000 1496.500 1496.500 1496.5000 1511.1263 SGO_0701 hup; DNA-binding histone-like protein HU .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 21

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 21 341.500 278.500 0.300 11.092 0.0038 0.0127 584.5390 559.500 521.4939 559.500 619.500 619.500 619.5000 457.9420 SGO_0704 gpmA; 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 15.000 14.500 -1.515 5.980 0.0001 0.0000 8.3580 8.000 22.9060 8.000 8.000 8.000 8.0000 23.8426 SGO_0706 phoH-like protein 118.500 89.500 -5.234 8.398 0.0005 0.0005 6.2685 6.000 180.9576 6.000 3.000 3.000 3.0000 147.1663 SGO_0707 LPXTG cell wall surface protein 564.500 516.500 -2.339 11.001 0.0000 0.0000 169.2499 162.000 862.0301 162.000 169.000 169.000 169.0000 849.2892 SGO_0708 ald; alanine dehydrogenase 32.500 31.500 -0.744 7.343 0.0012 0.0024 33.9545 32.500 49.6297 32.500 27.000 27.000 27.0000 51.7960 SGO_0713 sgg; GTP-binding protein Era 5.500 6.500 -1.516 4.686 0.0013 0.0029 3.6566 3.500 8.3989 3.500 3.000 3.000 3.0000 10.6881 SGO_0719 rnr; ribonuclease R 6.500 6.000 -0.439 5.111 0.0072 0.0300 6.2685 6.000 9.9259 6.000 8.500 8.500 8.5000 9.8659 SGO_0721 abpB-like dipeptidase lipoprotein 5.000 5.000 0.853 5.475 0.0002 0.0001 14.6265 14.000 7.6353 14.000 14.000 14.000 14.0000 8.2216 SGO_0722 tehB; tellurite resistance protein TehB 4.500 6.000 -0.780 4.723 0.0077 0.0334 4.1790 4.000 6.8718 4.000 5.500 5.500 5.5000 9.8659 SGO_0724 dipeptidase 12.500 13.000 -1.954 5.676 0.0005 0.0005 4.1790 4.000 19.0884 4.000 6.500 6.500 6.5000 21.3761 SGO_0736 hprK; HPr(Ser) kinase/phosphatase 3.000 1.551 5.087 0.0174 0.0968 13.0594 12.500 12.500 16.000 16.000 16.0000 4.9329 SGO_0739 hypothetical protein SGO_0739 13.000 12.000 -0.443 6.102 0.0000 0.0000 14.6265 14.000 19.8519 14.000 14.500 14.500 14.5000 19.7318 SGO_0742 peptidase, U32 family .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 22

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 22 9.000 7.000 1.012 6.258 0.0031 0.0096 29.2531 28.000 13.7436 28.000 22.000 22.000 22.0000 11.5102 SGO_0743 peptidase, U32 family 12.000 1.433 6.982 0.0106 0.0504 50.6705 48.500 48.500 56.000 56.000 56.0000 19.7318 SGO_0745 hypothetical protein SGO_0745 30.500 45.000 -1.065 7.467 0.0068 0.0278 30.2978 29.000 46.5756 29.000 26.000 26.000 26.0000 73.9942 SGO_0749 glutathione reductase 6.000 7.000 3.963 8.415 0.0001 0.0000 167.1604 160.000 9.1624 160.000 153.500 153.500 153.5000 11.5102 SGO_0750 efflux transporter, RND family, MFP subunit subfamily 3.500 5.500 3.150 7.118 0.0009 0.0015 70.5208 67.500 5.3447 67.500 54.000 54.000 54.0000 9.0437 SGO_0751 ABC transporter, ATP-binding protein SP0786 50.000 27.500 0.776 8.336 0.0061 0.0244 106.0424 101.500 76.3534 101.500 95.500 95.500 95.5000 45.2187 SGO_0753 lysS; lysyl-tRNA synthetase 3.500 -1.203 3.045 2.500 2.500 2.5000 5.7551 SGO_0754 phosphoglycerate mutase family protein 4.000 5.500 0.430 5.150 0.0253 0.1495 8.3580 8.000 6.1083 8.000 12.000 12.000 12.0000 9.0437 SGO_0755 regulatory protein 75.000 80.000 0.092 8.988 0.0338 0.2120 131.1164 125.500 114.5301 125.500 130.500 130.500 130.5000 131.5453 SGO_0760 ppc; phosphoenolpyruvate carboxylase 1976.000 2103.500 -0.524 13.422 0.0022 0.0058 2347.0363 2246.500 3017.4872 2246.500 2149.500 2149.500 2149.5000 3458.8186 SGO_0761 tuf; translation elongation factor Tu 150.500 181.500 0.996 10.630 0.0038 0.0129 607.0012 581.000 229.8238 581.000 449.500 449.500 449.5000 298.4433 SGO_0762 tpiA; triosephosphate isomerase 24.500 22.000 -0.153 7.128 0.0151 0.0803 30.8202 29.500 37.4132 29.500 35.500 35.500 35.5000 36.1750 SGO_0763 murA-1; UDP-N-acetylglucosamine 1carboxyvinyltransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 23

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 23 10.500 5.500 -0.829 5.279 0.0144 0.0755 5.7461 5.500 16.0342 5.500 8.000 8.000 8.0000 9.0437 SGO_0767 transport protein 58.500 46.000 -0.078 8.325 0.0501 0.3396 76.2669 73.000 89.3335 73.000 79.500 79.500 79.5000 75.6385 SGO_0771 pepq; proline dipeptidase 42.500 46.500 -0.087 8.100 0.0601 0.4177 71.5655 68.500 64.9004 68.500 61.500 61.500 61.5000 76.4607 SGO_0773 ccpA; catabolite control protein A 6.500 6.500 0.257 5.516 0.0357 0.2284 15.1489 14.500 9.9259 14.500 10.000 10.000 10.0000 10.6881 SGO_0774 glycosyl transferase, group 1 family protein 7.000 9.500 -0.186 5.622 0.0562 0.3873 9.9251 9.500 10.6895 9.500 13.000 13.000 13.0000 15.6210 SGO_0775 glycosyl transferase, group 1 45.500 44.500 0.500 8.428 0.0005 0.0005 98.2067 94.000 69.4816 94.000 103.500 103.500 103.5000 73.1721 SGO_0778 thrS; threonyl-tRNA synthetase 40.500 33.500 -1.473 7.317 0.0007 0.0008 24.5517 23.500 61.8463 23.500 18.000 18.000 18.0000 55.0846 SGO_0779 response regulator 5.500 3.000 -1.070 4.283 0.0082 0.0369 3.1343 3.000 8.3989 3.000 3.000 3.000 3.0000 4.9329 SGO_0780 histidine kinase 14.500 21.000 -0.115 6.752 0.0695 0.4919 25.0741 24.000 22.1425 24.000 26.000 26.000 26.0000 34.5306 SGO_0784 smc; chromosome segregation protein SMC 4.000 -0.548 3.363 4.1790 4.000 6.1083 4.000 SGO_0785 Cof family protein 2.500 1.850 5.077 0.0050 0.0193 15.1489 14.500 14.500 14.500 14.500 14.5000 4.1108 SGO_0786 Cof family protein 17.500 11.500 0.448 6.741 0.0087 0.0402 30.8202 29.500 26.7237 29.500 30.500 30.500 30.5000 18.9096 SGO_0787 ftsY; cell division protein FtsY .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 24

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 24 49.000 60.500 -1.017 8.020 0.0028 0.0083 41.7901 40.000 74.8264 40.000 43.500 43.500 43.5000 99.4811 SGO_0788 zwf; glucose-6-phosphate 1-dehydrogenase 7.000 4.500 1.245 5.922 0.0025 0.0071 24.0293 23.000 10.6895 23.000 18.500 18.500 18.5000 7.3994 SGO_0792 hypothetical protein SGO_0792 28.000 33.500 -0.353 7.442 0.0119 0.0588 36.5663 35.000 42.7579 35.000 39.500 39.500 39.5000 55.0846 SGO_0794 metallo-beta-lactamase family protein 8.500 11.500 -0.692 5.681 0.0081 0.0360 9.4028 9.000 12.9801 9.000 10.000 10.000 10.0000 18.9096 SGO_0795 tributyrin esterase 16.500 16.000 -0.196 6.593 0.0045 0.0162 23.5069 22.500 25.1966 22.500 21.500 21.500 21.5000 26.3091 SGO_0798 ABC transporter, ATP-binding protein SP1381 3.500 3.000 0.619 4.705 0.0019 0.0047 7.3133 7.000 5.3447 7.000 8.500 8.500 8.5000 4.9329 SGO_0800 polysaccharide deacetylase family protein 54.500 47.500 0.567 8.645 0.0005 0.0004 116.4899 111.500 83.2252 111.500 122.500 122.500 122.5000 78.1050 SGO_0801 hom; homoserine dehydrogenase 16.000 14.500 0.008 6.597 0.0826 0.6016 24.0293 23.000 24.4331 23.000 24.500 24.500 24.5000 23.8426 SGO_0802 thrB; homoserine kinase 4.000 5.500 -0.701 4.607 0.0102 0.0483 5.2238 5.000 6.1083 5.000 4.000 4.000 4.0000 9.0437 SGO_0804 murB; UDP-Nacetylenolpyruvoylglucosamine reductase 4.500 5.500 -0.751 4.677 0.0092 0.0427 3.6566 3.500 6.8718 3.500 6.000 6.000 6.0000 9.0437 SGO_0805 potA; spermidine/putrescine ABC transporter, ATP-binding subunit 2.500 -0.125 2.871 3.8177 3.500 3.500 3.5000 SGO_0808 potD; spermidine/putrescine ABC transporter 10.000 12.000 -1.840 5.482 0.0012 0.0023 4.7014 4.500 15.2707 4.500 5.000 5.000 5.0000 19.7318 SGO_0812 hypothetical protein SGO_0812 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 25

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 25 9.000 10.500 0.991 6.530 0.0013 0.0026 32.9097 31.500 13.7436 31.500 28.500 28.500 28.5000 17.2653 SGO_0815 thiI; thiamine biosynthesis protein ThiI 17.500 3.001 8.832 0.0110 0.0524 199.0253 190.500 26.7237 190.500 230.000 230.000 230.0000 SGO_0818 rplU; ribosomal protein L21 15.000 0.685 6.704 0.0229 0.1335 36.5663 35.000 35.000 43.000 43.000 43.0000 24.6647 SGO_0820 rpmA; ribosomal protein L27 3.500 2.500 -0.907 3.580 0.0282 0.1720 5.3447 2.500 2.500 2.5000 4.1108 SGO_0823 Cof family protein 22.500 20.500 0.663 7.458 0.0000 0.0000 53.8047 51.500 34.3590 51.500 54.000 54.000 54.0000 33.7085 SGO_0824 lepA; GTP-binding protein LepA 3.000 0.536 4.160 0.0096 0.0448 6.7909 6.500 4.5812 6.500 6.500 6.500 6.5000 SGO_0825 lipoprotein, putative 2.000 -0.654 2.427 2.0895 2.000 2.000 3.2886 SGO_0830 uvrC; excinuclease ABC, C subunit 2.000 0.985 3.942 0.0356 0.2272 7.3133 7.000 3.0541 7.000 5.000 5.000 5.0000 SGO_0832 hypothetical protein SGO_0832 11.500 9.000 -2.479 5.265 0.0007 0.0009 2.0895 2.000 17.5613 2.000 4.000 4.000 4.0000 14.7988 SGO_0833 phosphoesterase-related gene 93.000 86.500 -1.103 8.702 0.0000 0.0000 66.3418 63.500 142.0174 63.500 66.000 66.000 66.0000 142.2333 SGO_0835 nitroreductase 130.500 109.000 -0.497 9.336 0.0013 0.0026 135.8178 130.000 199.2824 130.000 132.000 132.000 132.0000 179.2304 SGO_0836 pepV; dipeptidase PepV 22.500 13.500 -2.671 6.038 0.0025 0.0072 3.1343 3.000 34.3590 3.000 6.000 6.000 6.0000 22.1983 SGO_0842 rhodanese family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 26

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 26 18.000 10.000 1.996 7.739 0.0004 0.0003 85.6697 82.000 27.4872 82.000 84.000 84.000 84.0000 16.4432 SGO_0848 rpmE; ribosomal protein L31 15.000 9.000 -0.697 5.926 0.0132 0.0684 13.5818 13.000 22.9060 13.000 9.500 9.500 9.5000 14.7988 SGO_0849 DHH subfamily 1 protein 16.000 11.000 1.176 7.105 0.0011 0.0020 50.6705 48.500 24.4331 48.500 44.500 44.500 44.5000 18.0875 SGO_0850 flavodoxin 7.000 -0.875 4.486 0.0156 0.0837 5.2238 5.000 10.6895 5.000 6.500 6.500 6.5000 SGO_0851 putative permease 5.000 5.000 -1.209 4.527 0.0025 0.0071 4.7014 4.500 7.6353 4.500 2.500 2.500 2.5000 8.2216 SGO_0852 TPR domain protein 3.500 3.000 -0.340 4.208 0.0129 0.0661 4.7014 4.500 5.3447 4.500 3.500 3.500 3.5000 4.9329 SGO_0853 budA; alpha-acetolactate decarboxylase 33.500 17.000 -2.595 6.521 0.0044 0.0160 5.2238 5.000 51.1568 5.000 7.500 7.500 7.5000 27.9534 SGO_0854 cshA; surface-associated protein CshA 3.500 4.500 0.282 4.813 0.0271 0.1633 8.3580 8.000 5.3447 8.000 7.000 7.000 7.0000 7.3994 SGO_0855 fbpA; fibronectin-binding protein A 5.500 6.500 1.850 6.458 0.0011 0.0021 30.2978 29.000 8.3989 29.000 38.500 38.500 38.5000 10.6881 SGO_0856 ABC transporter, substrate binding protein 29.000 28.500 -0.621 7.234 0.0007 0.0010 31.3426 30.000 44.2850 30.000 28.000 28.000 28.0000 46.8630 SGO_0859 pheS; phenylalanyl-tRNA synthetase, alpha subunit 35.500 40.000 0.895 8.418 0.0007 0.0009 108.1319 103.500 54.2109 103.500 114.000 114.000 114.0000 65.7726 SGO_0861 pheT; phenylalanyl-tRNA synthetase, beta subunit 11.500 7.000 -1.339 5.333 0.0042 0.0146 5.7461 5.500 17.5613 5.500 5.500 5.500 5.5000 11.5102 SGO_0885 cobyric acid synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 27

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 27 7.000 6.000 -1.583 4.790 0.0009 0.0015 2.6119 2.500 10.6895 2.500 4.500 4.500 4.5000 9.8659 SGO_0886 Mur ligase family protein 11.500 10.500 0.566 6.433 0.0003 0.0003 25.0741 24.000 17.5613 24.000 26.500 26.500 26.5000 17.2653 SGO_0889 glmM; phosphoglucosamine mutase 33.000 30.500 -0.107 7.603 0.0440 0.2940 42.3125 40.500 50.3933 40.500 51.500 51.500 51.5000 50.1516 SGO_0893 GTP-binding protein 11.500 12.000 -0.125 6.162 0.0425 0.2819 18.8055 18.000 17.5613 18.000 15.500 15.500 15.5000 19.7318 SGO_0901 DNA-directed DNA polymerase III 56.500 51.000 -1.270 7.911 0.0000 0.0000 35.5216 34.000 86.2794 34.000 35.000 35.000 35.0000 83.8601 SGO_0906 leuA; 2-isopropylmalate synthase 4.500 3.000 -0.372 4.027 0.0561 0.3851 6.8718 4.500 4.500 4.5000 4.9329 SGO_0909 leuC; 3-isopropylmalate dehydratase, large subunit 45.000 39.500 0.254 8.195 0.0012 0.0024 78.3564 75.000 68.7181 75.000 81.000 81.000 81.0000 64.9505 SGO_0911 hypothetical protein SGO_0911 23.000 20.000 -0.931 6.698 0.0008 0.0011 19.8503 19.000 35.1226 19.000 16.000 16.000 16.0000 32.8863 SGO_0946 Deblocking aminopeptidase 5.000 2.500 -0.001 4.522 0.1088 0.8182 5.2238 5.000 7.6353 5.000 6.000 6.000 6.0000 4.1108 SGO_0949 deaD; DEAD RNA helicase 12.000 8.000 -1.575 5.402 0.0029 0.0089 6.7909 6.500 18.3248 6.500 4.000 4.000 4.0000 13.1545 SGO_0950 oxidoreductase 6.500 8.000 -0.202 5.426 0.0329 0.2049 9.4028 9.000 9.9259 9.000 10.500 10.500 10.5000 13.1545 SGO_0951 udk; uridine kinase 13.000 10.000 -0.415 6.016 0.0367 0.2361 9.9251 9.500 19.8519 9.500 18.500 18.500 18.5000 16.4432 SGO_0954 ATP-binding protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 28

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 28 3.000 3.000 0.451 4.001 0.0127 0.0640 4.5812 6.500 6.500 6.5000 4.9329 SGO_0955 transporter 14.000 8.000 -1.525 5.534 0.0049 0.0184 6.7909 6.500 21.3790 6.500 5.000 5.000 5.0000 13.1545 SGO_0959 copper homeostasis protein CutC 1.500 0.346 2.486 3.1343 3.000 3.000 2.4665 SGO_0981 comE operon protein 2 family 10.000 10.000 0.524 6.278 0.0049 0.0186 20.3727 19.500 15.2707 19.500 25.500 25.500 25.5000 16.4432 SGO_0982 amino acid ABC transporter, amino acidbinding protein 28.000 25.000 -0.070 7.365 0.0982 0.7269 33.9545 32.500 42.7579 32.500 47.000 47.000 47.0000 41.1079 SGO_0987 metK; S-adenosylmethionine synthetase 2.500 3.500 -0.644 3.652 0.0469 0.3163 3.8177 3.000 3.000 3.0000 5.7551 SGO_0993 GTP-binding protein HflX 9.000 12.000 -1.248 5.629 0.0117 0.0566 12.0147 11.500 13.7436 11.500 4.000 4.000 4.0000 19.7318 SGO_0995 metallo-beta-lactamase superfamily protein 5.000 6.000 -0.881 4.852 0.0342 0.2148 8.8804 8.500 7.6353 8.500 2.500 2.500 2.5000 9.8659 SGO_0997 hypothetical protein SGO_0997 9.000 9.000 -1.010 5.423 0.0013 0.0025 8.3580 8.000 13.7436 8.000 6.000 6.000 6.0000 14.7988 SGO_1000 recJ; single-stranded-DNA-specific exonuclease RecJ 33.000 48.500 -0.178 7.924 0.0588 0.4071 50.6705 48.500 50.3933 48.500 62.000 62.000 62.0000 79.7493 SGO_1001 apt; adenine phosphoribosyltransferase 2.500 2.500 0.993 4.573 0.0021 0.0054 8.8804 8.500 3.8177 8.500 7.000 7.000 7.0000 4.1108 SGO_1003 DNA replication protein DnaD 2.000 3.000 0.613 4.345 0.0244 0.1438 7.8356 7.500 3.0541 7.500 4.500 4.500 4.5000 4.9329 SGO_1004 glutathione S-transferase family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 29

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 29 5.000 3.500 0.464 4.993 0.0129 0.0658 10.4475 10.000 7.6353 10.000 8.000 8.000 8.0000 5.7551 SGO_1005 Bcl-2 family protein 2.000 -0.015 3.203 0.1268 0.9734 3.6566 3.500 3.0541 3.500 2.500 2.500 2.5000 SGO_1006 conserved hypothetical protein TIGR00486 115.000 122.500 -0.573 9.300 0.0019 0.0047 132.1612 126.500 175.6129 126.500 121.000 121.000 121.0000 201.4287 SGO_1009 rfbA-1; glucose-1-phosphate thymidylyltransferase 26.000 20.000 0.105 7.238 0.0678 0.4775 44.4020 42.500 39.7038 42.500 34.000 34.000 34.0000 32.8863 SGO_1010 rmlC; dTDP-4-keto-6-deoxyglucose-3,5epimerase 90.500 123.000 -1.226 8.918 0.0039 0.0133 76.2669 73.000 138.1997 73.000 67.000 67.000 67.0000 202.2509 SGO_1011 rfbB-1; dTDP-glucose 4,6-dehydratase 102.500 99.000 -0.640 9.034 0.0002 0.0001 102.9081 98.500 156.5245 98.500 102.000 102.000 102.0000 162.7873 SGO_1012 galE-1; UDP-glucose 4-epimerase 3.000 -0.717 2.988 3.000 3.000 3.0000 4.9329 SGO_1013 Glycosyltransferase involved in cell wall biogenesis 2.500 0.679 4.010 0.0282 0.1722 6.7909 6.500 3.8177 6.500 5.500 5.500 5.5000 SGO_1016 putative glycosyltransferase 3.000 0.022 3.918 0.1180 0.8916 4.1790 4.000 4.000 6.000 6.000 6.0000 4.9329 SGO_1019 glycosyl transferase 37.000 37.500 -0.479 7.674 0.0085 0.0391 35.5216 34.000 56.5015 34.000 50.500 50.500 50.5000 61.6618 SGO_1020 rfbD; dTDP-4-dehydrorhamnose reductase 2.000 3.500 1.861 5.327 0.0044 0.0154 19.3279 18.500 3.0541 18.500 12.000 12.000 12.0000 5.7551 SGO_1024 putative polysaccharide ABC transporter 8.500 3.500 1.052 5.779 0.0087 0.0402 15.6713 15.000 12.9801 15.000 20.500 20.500 20.5000 5.7551 SGO_1025 rgp; glycosyltransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 30

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 30 10.500 13.500 -0.231 6.138 0.0308 0.1900 15.6713 15.000 16.0342 15.000 16.500 16.500 16.5000 22.1983 SGO_1026 rhamnosyltransferase 4.000 4.500 0.443 4.994 0.0067 0.0276 8.3580 8.000 6.1083 8.000 10.000 10.000 10.0000 7.3994 SGO_1031 cmk; cytidylate kinase 79.000 68.000 1.012 9.453 0.0001 0.0000 231.9350 222.000 120.6384 222.000 236.500 236.500 236.5000 111.8135 SGO_1034 rplT; ribosomal protein L20 10.000 10.500 -0.564 5.768 0.0013 0.0027 10.9699 10.500 15.2707 10.500 11.000 11.000 11.0000 17.2653 SGO_1035 gloA; lactoylglutathione lyase 21.000 11.500 -0.942 6.292 0.0161 0.0871 8.8804 8.500 32.0684 8.500 18.500 18.500 18.5000 18.9096 SGO_1036 amino acid ABC transporter, ATP-binding protein SP1242 1.500 4.000 1.204 4.743 0.0083 0.0375 9.4028 9.000 2.2906 9.000 8.500 8.500 8.5000 6.5773 SGO_1037 glutamine ABC transporter permease and substrate binding protein 7.000 4.500 -0.205 5.088 0.0722 0.5173 9.9251 9.500 10.6895 9.500 6.000 6.000 6.0000 7.3994 SGO_1038 uvrB; excinuclease ABC, B subunit 6.500 -0.646 4.507 0.0268 0.1605 7.3133 7.000 9.9259 7.000 5.500 5.500 5.5000 SGO_1041 hypothetical protein SGO_1041 3.000 -0.186 3.767 0.0278 0.1681 4.1790 4.000 4.000 4.500 4.500 4.5000 4.9329 SGO_1044 MutT/nudix family protein 1.500 2.902 5.310 0.0170 0.0942 16.1937 15.500 15.500 21.000 21.000 21.0000 2.4665 SGO_1047 hypothetical protein SGO_1047 3.000 0.036 3.963 0.1129 0.8522 3.6566 3.500 3.500 7.000 7.000 7.0000 4.9329 SGO_1050 ribF; riboflavin biosynthesis protein RibF 4.000 3.000 2.143 5.896 0.0001 0.0001 23.5069 22.500 6.1083 22.500 25.000 25.000 25.0000 4.9329 SGO_1059 pstB; Phosphate import ATP-binding protein pstB 1 (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 31

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 31 7.500 9.500 1.407 6.618 0.0009 0.0014 38.1335 36.500 11.4530 36.500 33.000 33.000 33.0000 15.6210 SGO_1060 phosphate transport system regulatory protein 9.000 6.500 -0.175 5.520 0.0316 0.1956 10.9699 10.500 13.7436 10.500 10.500 10.500 10.5000 10.6881 SGO_1065 hypothetical protein SGO_1065 10.500 11.000 -1.266 5.599 0.0009 0.0016 8.3580 8.000 16.0342 8.000 6.000 6.000 6.0000 18.0875 SGO_1066 hypothetical protein SGO_1066 49.000 46.500 0.250 8.375 0.0127 0.0644 99.2515 95.000 74.8264 95.000 81.500 81.500 81.5000 76.4607 SGO_1069 membrane alanyl aminopeptidase 17.000 16.000 -2.645 5.819 0.0021 0.0051 4.1790 4.000 25.9602 4.000 26.3091 SGO_1072 ciaR; Transcriptional regulatory protein CiaR 4.000 -1.332 3.200 2.6119 2.500 2.500 6.5773 SGO_1073 Sensor protein CiaH 9.500 6.500 -2.053 4.817 0.0216 0.1250 14.5072 3.000 3.000 3.0000 10.6881 SGO_1075 alpha-amylase precursor 1.500 9.500 0.031 4.917 0.0724 0.5199 6.7909 6.500 2.2906 6.500 5.500 5.500 5.5000 15.6210 SGO_1077 coaA; pantothenate kinase 8.500 10.000 -1.252 5.397 0.0030 0.0090 4.7014 4.500 12.9801 4.500 8.000 8.000 8.0000 16.4432 SGO_1078 methyltransferase domain protein 20.000 39.500 -0.876 7.174 0.0185 0.1042 21.4174 20.500 30.5414 20.500 27.500 27.500 27.5000 64.9505 SGO_1079 pdp; pyrimidine-nucleoside phosphorylase 37.000 31.500 0.245 7.887 0.0045 0.0165 66.8642 64.000 56.5015 64.000 61.500 61.500 61.5000 51.7960 SGO_1080 deoC; deoxyribose-phosphate aldolase 443.000 316.500 0.898 11.735 0.0011 0.0019 1071.9160 1026.000 676.4913 1026.000 1141.000 1141.000 1141.0000 520.4260 SGO_1082 lipoprotein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 32 41.500 39.500 1.096 8.662 0.0021 0.0055 156.1905 149.500 63.3733 149.500 120.500 120.500 120.5000 64.9505 SGO_1083 sugar ABC transporter, ATP-binding protein SP0846 4.000 0.249 4.491 0.0722 0.5174 9.4028 9.000 9.000 6.500 6.500 6.5000 6.5773 SGO_1090 pseudouridine synthase, RluA family 2269.000 2308.500 -3.502 12.948 0.0001 0.0001 308.2020 295.000 3464.9183 295.000 332.500 332.500 332.5000 3795.9033 SGO_1096 butA; acetoin dehydrogenase 18.500 17.000 -1.135 6.369 0.0019 0.0043 9.9251 9.500 28.2508 9.500 16.500 16.500 16.5000 27.9534 SGO_1098 proA; gamma-glutamyl phosphate reductase 1.500 1.157 2.994 5.500 5.500 5.5000 2.4665 SGO_1107 PyrR bifunctional protein 11.500 11.000 1.503 7.095 0.0001 0.0000 49.1034 47.000 17.5613 47.000 52.000 52.000 52.0000 18.0875 SGO_1109 pyrB; aspartate carbamoyltransferase 3.000 3.000 0.633 4.603 0.0021 0.0054 6.7909 6.500 4.5812 6.500 8.000 8.000 8.0000 4.9329 SGO_1111 fruR; phosphotransferase system repressor 5.000 5.500 0.638 5.431 0.0121 0.0598 10.4475 10.000 7.6353 10.000 16.000 16.000 16.0000 9.0437 SGO_1112 fruB; 1-phosphofructokinase 30.000 12.500 0.709 7.396 0.0246 0.1456 60.5956 58.000 45.8121 58.000 41.500 41.500 41.5000 20.5539 SGO_1113 fruA; PTS system, fructose specific IIABC components 5.000 2.500 1.400 5.373 0.0022 0.0060 16.1937 15.500 7.6353 15.500 13.500 13.500 13.5000 4.1108 SGO_1114 Protein of unknown function (DUF1149) superfamily 11.500 -1.645 4.960 0.0095 0.0441 5.2238 5.000 5.000 7.000 7.000 7.0000 18.9096 SGO_1115 DegV family protein 19.500 16.500 0.440 7.068 0.0022 0.0059 40.7453 39.000 29.7778 39.000 36.500 36.500 36.5000 27.1312 SGO_1116 dapB; dihydrodipicolinate reductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 33

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 33 6.500 2.000 -0.898 4.274 0.0269 0.1619 3.1343 3.000 9.9259 3.000 3.000 3.000 3.0000 3.2886 SGO_1117 pcnA; polynucleotide adenylyltransferase 5.500 6.000 -1.459 4.639 0.0008 0.0011 3.6566 3.500 8.3989 3.500 3.000 3.000 3.0000 9.8659 SGO_1118 ABC transporter, ATP-binding protein SP1553 67.000 78.500 -0.509 8.618 0.0052 0.0203 81.4907 78.000 102.3136 78.000 80.000 80.000 80.0000 129.0788 SGO_1120 guaA; GMP synthase 35.000 29.000 0.290 7.812 0.0038 0.0129 59.5509 57.000 53.4474 57.000 64.000 64.000 64.0000 47.6852 SGO_1123 ffh; signal recognition particle protein 10.500 10.000 -0.544 5.782 0.0047 0.0173 13.0594 12.500 16.0342 12.500 9.500 9.500 9.5000 16.4432 SGO_1129 lplA; lipoate protein ligase A 5.500 6.500 2.380 6.880 0.0001 0.0000 50.6705 48.500 8.3989 48.500 48.000 48.000 48.0000 10.6881 SGO_1130 dihydrolipoamide dehydrogenase 2.500 2.419 5.484 0.0116 0.0560 21.9398 21.000 3.8177 21.000 19.000 19.000 19.0000 SGO_1131 sucB; dihydrolipoamide S-acetyltransferase 7.000 0.146 5.214 0.0706 0.5025 14.1042 13.500 13.500 11.500 11.500 11.5000 11.5102 SGO_1133 acoA; acetoin dehydrogenase 9.000 16.500 -2.886 5.443 0.0357 0.2287 2.6119 2.500 13.7436 2.500 27.1312 SGO_1134 hypothetical protein SGO_1134 11.500 10.000 0.862 6.582 0.0002 0.0001 30.2978 29.000 17.5613 29.000 31.500 31.500 31.5000 16.4432 SGO_1139 GTP-binding protein 39.000 40.500 0.354 8.166 0.0015 0.0034 80.9683 77.500 59.5557 77.500 80.000 80.000 80.0000 66.5948 SGO_1140 clpX; ATP-dependent Clp protease, ATPbinding subunit ClpX 8.500 14.500 -1.422 5.648 0.0080 0.0352 7.8356 7.500 12.9801 7.500 5.500 5.500 5.5000 23.8426 SGO_1141 folA; dihydrofolate reductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 34

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 34 3.500 5.500 0.877 5.319 0.0041 0.0140 12.5370 12.000 5.3447 12.000 13.000 13.000 13.0000 9.0437 SGO_1143 thyA; thymidylate synthase 152.500 157.500 -0.356 9.774 0.0022 0.0056 192.2344 184.000 232.8779 184.000 191.500 191.500 191.5000 258.9798 SGO_1144 glcK; glucokinase 5.500 4.000 0.721 5.305 0.0023 0.0062 13.0594 12.500 8.3989 12.500 11.500 11.500 11.5000 6.5773 SGO_1150 hypothetical protein SGO_1150 165.000 156.000 -0.562 9.736 0.0001 0.0000 172.9065 165.500 251.9663 165.500 171.500 171.500 171.5000 256.5133 SGO_1151 glyA; serine hydroxymethyltransferase 30.000 12.500 0.220 7.107 0.1010 0.7485 34.9992 33.500 45.8121 33.500 36.500 36.500 36.5000 20.5539 SGO_1154 prfA; peptide chain release factor 1 4.500 2.000 1.345 5.132 0.0082 0.0365 9.4028 9.000 6.8718 9.000 15.500 15.500 15.5000 3.2886 SGO_1155 tdk; thymidine kinase 4.500 5.000 -0.794 4.599 0.0100 0.0472 3.1343 3.000 6.8718 3.000 6.000 6.000 6.0000 8.2216 SGO_1159 guaC; guanosine monophosphate reductase 13.000 11.000 2.059 7.614 0.0000 0.0000 79.4012 76.000 19.8519 76.000 78.500 78.500 78.5000 18.0875 SGO_1167 nox; NADH oxidase 12.500 7.500 1.376 6.806 0.0027 0.0078 45.9691 44.000 19.0884 44.000 34.500 34.500 34.5000 12.3324 SGO_1169 NADPH-dependent FMN reductase 15.500 12.000 1.493 7.367 0.0002 0.0001 62.6851 60.000 23.6696 60.000 59.000 59.000 59.0000 19.7318 SGO_1170 NADPH-dependent FMN reductase 5.000 2.000 -0.390 4.216 0.0429 0.2851 3.6566 3.500 7.6353 3.500 4.000 4.000 4.0000 3.2886 SGO_1171 thioredoxin family protein 2.500 1.176 4.409 0.0260 0.1546 9.9251 9.500 3.8177 9.500 7.500 7.500 7.5000 SGO_1185 acetyltransferase, GNAT family .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 35

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 35 20.000 21.500 -1.120 6.592 0.0013 0.0026 13.0594 12.500 30.5414 12.500 17.500 17.500 17.5000 35.3528 SGO_1189 lipoprotein, putative 178.000 155.500 1.155 10.733 0.0002 0.0001 606.4788 580.500 271.8182 580.500 568.000 568.000 568.0000 255.6911 SGO_1191 rplL; ribosomal protein L7/L12 50.500 68.000 0.944 9.110 0.0071 0.0297 147.3101 141.000 77.1170 141.000 216.500 216.500 216.5000 111.8135 SGO_1192 BL5; 50S ribosomal protein L10 17.000 18.000 -0.451 6.593 0.0082 0.0371 23.5069 22.500 25.9602 22.500 17.500 17.500 17.5000 29.5977 SGO_1193 gid; Glucose inhibited division protein A 9.000 13.000 0.702 6.511 0.0076 0.0330 25.0741 24.000 13.7436 24.000 31.000 31.000 31.0000 21.3761 SGO_1197 topA; DNA topoisomerase I 6.500 9.000 -0.246 5.510 0.0543 0.3719 8.3580 8.000 9.9259 8.000 12.500 12.500 12.5000 14.7988 SGO_1202 GTP-binding protein 19.500 22.000 -0.619 6.766 0.0034 0.0112 19.8503 19.000 29.7778 19.000 23.000 23.000 23.0000 36.1750 SGO_1203 anaerobic ribonucleotide reductase 7.500 3.000 -0.195 4.889 0.0680 0.4795 5.7461 5.500 11.4530 5.500 7.500 7.500 7.5000 4.9329 SGO_1205 dapA; dihydrodipicolinate synthase 23.500 24.500 -0.559 6.998 0.0013 0.0029 26.6412 25.500 35.8861 25.500 25.000 25.000 25.0000 40.2857 SGO_1206 asd; aspartate-semialdehyde dehydrogenase 11.500 14.000 -1.072 5.922 0.0057 0.0223 13.0594 12.500 17.5613 12.500 7.000 7.000 7.0000 23.0204 SGO_1210 fhs-1; formate--tetrahydrofolate ligase 4.500 2.000 -0.601 3.733 0.0674 0.4737 3.1343 3.000 6.8718 3.000 3.2886 SGO_1213 coaC; phosphopantothenoylcysteine decarboxylase 178.000 184.500 -0.176 10.082 0.0080 0.0351 253.8748 243.000 271.8182 243.000 254.500 254.500 254.5000 303.3763 SGO_1215 manB; phosphomannomutase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 36

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 36 21.500 17.000 0.419 7.152 0.0080 0.0349 44.9244 43.000 32.8320 43.000 36.500 36.500 36.5000 27.9534 SGO_1216 bta; Possible bacteriocin transport accessory protein 31.500 60.500 -0.901 7.792 0.0163 0.0896 37.6111 36.000 48.1027 36.000 36.500 36.500 36.5000 99.4811 SGO_1219 pta; phosphate acetyltransferase 1.500 0.698 2.693 4.000 4.000 4.0000 2.4665 SGO_1222 GTP pyrophosphokinase-like protein 23.500 22.500 1.455 8.092 0.0003 0.0002 104.9976 100.500 35.8861 100.500 95.000 95.000 95.0000 36.9971 SGO_1224 Ribose-phosphate pyrophosphokinase 2 4.000 6.000 0.103 5.035 0.1024 0.7602 7.3133 7.000 6.1083 7.000 9.500 9.500 9.5000 9.8659 SGO_1225 pyridoxal-phosphate dependent aminotransferase 10.000 14.500 -0.118 6.216 0.0701 0.4969 16.7160 16.000 15.2707 16.000 18.500 18.500 18.5000 23.8426 SGO_1226 hypothetical protein SGO_1226 5.500 4.500 -0.494 4.758 0.0045 0.0167 6.2685 6.000 8.3989 6.000 5.000 5.000 5.0000 7.3994 SGO_1228 DNA-binding protein BH0551 35.500 24.000 -0.689 7.258 0.0135 0.0698 21.9398 21.000 54.2109 21.000 37.500 37.500 37.5000 39.4636 SGO_1231 gyrA; DNA gyrase, A subunit 277.000 247.500 -0.020 10.687 0.0601 0.4179 416.3338 398.500 422.9980 398.500 402.000 402.000 402.0000 406.9682 SGO_1232 L-lactate dehydrogenase 163.000 112.000 0.829 10.222 0.0014 0.0032 384.9913 368.500 248.9122 368.500 376.000 376.000 376.0000 184.1634 SGO_1234 rpsA; 30S ribosomal protein S1 46.000 26.000 -1.175 7.336 0.0066 0.0269 24.5517 23.500 70.2451 23.500 24.000 24.000 24.0000 42.7522 SGO_1238 ilvE; branched-chain amino acid aminotransferase 2.000 5.000 1.318 5.182 0.0052 0.0202 12.0147 11.500 3.0541 11.500 13.000 13.000 13.0000 8.2216 SGO_1239 parC; DNA topoisomerase IV, A subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 37

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 37 14.500 27.000 -0.965 6.635 0.0161 0.0872 19.8503 19.000 22.1425 19.000 13.000 13.000 13.0000 44.3965 SGO_1248 pyrC; dihydroorotase 10.000 5.000 1.111 6.169 0.0032 0.0103 22.9846 22.000 15.2707 22.000 25.500 25.500 25.5000 8.2216 SGO_1253 pyrE; orotate phosphoribosyltransferase 11.500 6.000 -0.991 5.347 0.0106 0.0504 6.2685 6.000 17.5613 6.000 7.000 7.000 7.0000 9.8659 SGO_1257 probable transcriptional regulator (LysR family) 18.000 15.500 1.058 7.351 0.0002 0.0002 53.2824 51.000 27.4872 51.000 57.000 57.000 57.0000 25.4869 SGO_1260 deoD; purine nucleoside phosphorylase 22.000 18.500 1.503 7.938 0.0002 0.0001 87.7592 84.000 33.5955 84.000 93.500 93.500 93.5000 30.4198 SGO_1263 purine nucleoside phosphorylase I, inosine and guanosine-specific 149.500 103.000 -0.124 9.567 0.0535 0.3653 185.4436 177.500 228.2967 177.500 175.500 175.500 175.5000 169.3645 SGO_1264 deoB; phosphopentomutase 15.500 15.500 1.083 7.260 0.0003 0.0002 50.1481 48.000 23.6696 48.000 54.000 54.000 54.0000 25.4869 SGO_1265 rpiA; ribose 5-phosphate isomerase 11.000 11.500 -0.086 6.119 0.0707 0.5041 18.8055 18.000 16.7978 18.000 15.000 15.000 15.0000 18.9096 SGO_1266 trmE; tRNA modification GTPase TrmE 27.000 15.500 1.594 8.036 0.0006 0.0008 97.1620 93.000 41.2308 93.000 98.500 98.500 98.5000 25.4869 SGO_1273 rpoD; RNA polymerase sigma factor 8.500 7.000 1.877 6.842 0.0007 0.0010 40.7453 39.000 12.9801 39.000 49.500 49.500 49.5000 11.5102 SGO_1276 rpsU; ribosomal protein S21 1.500 1.879 4.379 0.0216 0.1249 7.8356 7.500 7.500 10.500 10.500 10.5000 2.4665 SGO_1281 penicillinase repressor, putative 27.500 19.500 1.115 7.864 0.0006 0.0008 80.9683 77.500 41.9944 77.500 78.000 78.000 78.0000 32.0642 SGO_1283 oxidoreductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 38

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 38 3.500 7.500 0.508 5.424 0.0537 0.3677 17.7608 17.000 5.3447 17.000 7.500 7.500 7.5000 12.3324 SGO_1284 thioredoxin-disulfide reductase 22.500 24.000 0.303 7.365 0.0076 0.0328 48.5810 46.500 34.3590 46.500 42.500 42.500 42.5000 39.4636 SGO_1293 asnS; asparaginyl-tRNA synthetase 34.000 22.000 -1.260 6.958 0.0033 0.0109 17.2384 16.500 51.9203 16.500 19.000 19.000 19.0000 36.1750 SGO_1297 aspC; aspartate aminotransferase 40.000 36.000 0.028 7.925 0.0440 0.2936 62.6851 60.000 61.0827 60.000 60.000 60.000 60.0000 59.1954 SGO_1312 pepT; peptidase T 4.000 -1.287 3.485 0.0152 0.0809 2.0895 2.000 6.1083 2.000 3.000 3.000 3.0000 SGO_1315 trmD; tRNA (guanine-N1)-methyltransferase 2.500 2.500 0.360 4.180 0.0050 0.0190 4.7014 4.500 3.8177 4.500 5.500 5.500 5.5000 4.1108 SGO_1316 16S rRNA processing protein RimM 19.500 15.500 0.692 7.175 0.0021 0.0051 41.2677 39.500 29.7778 39.500 48.000 48.000 48.0000 25.4869 SGO_1323 rpsP; ribosomal protein S16 6.500 6.000 0.395 5.518 0.0009 0.0015 12.5370 12.000 9.9259 12.000 13.500 13.500 13.5000 9.8659 SGO_1327 HAD-superfamily subfamily IIA hydrolase, TIGR01457 8.500 12.000 -0.326 5.865 0.0282 0.1730 13.5818 13.000 12.9801 13.000 12.000 12.000 12.0000 19.7318 SGO_1336 pcrA; ATP-dependent DNA helicase PcrA 6.500 6.000 -2.307 4.446 0.0012 0.0024 9.9259 2.000 2.000 2.0000 9.8659 SGO_1338 Signal peptidase I 447.500 362.500 0.431 11.551 0.0019 0.0043 839.4586 803.500 683.3631 803.500 882.500 882.500 882.5000 596.0645 SGO_1339 pyk; pyruvate kinase 227.000 228.000 -0.483 10.273 0.0008 0.0011 257.0091 246.000 346.6445 246.000 259.000 259.000 259.0000 374.9040 SGO_1340 Phosphofructokinase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 39

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 39 4.000 7.500 -1.469 4.431 0.0448 0.3009 3.1343 3.000 6.1083 3.000 12.3324 SGO_1341 dnaE; DNA-directed DNA polymerase III alpha chain 155.000 115.000 -0.755 9.403 0.0030 0.0092 133.7283 128.000 236.6956 128.000 117.500 117.500 117.5000 189.0963 SGO_1342 ABC transporter, ATP-binding protein SP1715 7.000 8.000 0.652 5.934 0.0013 0.0028 18.2832 17.500 10.6895 17.500 19.000 19.000 19.0000 13.1545 SGO_1364 rumA-2; 23S rRNA (uracil-5-)methyltransferase RumA 11.500 13.000 -2.745 5.496 0.0007 0.0010 4.1790 4.000 17.5613 4.000 2.000 2.000 2.0000 21.3761 SGO_1365 transcription regulator yrfE 6.500 7.500 -1.851 4.827 0.0009 0.0014 3.1343 3.000 9.9259 3.000 3.000 3.000 3.0000 12.3324 SGO_1367 aroK; shikimate kinase 9.000 7.500 -1.086 5.261 0.0005 0.0005 6.2685 6.000 13.7436 6.000 6.000 6.000 6.0000 12.3324 SGO_1368 aroA; 3-phosphoshikimate 1carboxyvinyltransferase 72.500 63.000 -3.364 7.878 0.0001 0.0000 9.4028 9.000 110.7125 9.000 11.500 11.500 11.5000 103.5919 SGO_1369 L-2-hydroxyisocaproate dehydrogenase 21.000 14.500 -0.075 6.763 0.0826 0.6023 28.7307 27.500 32.0684 27.500 24.000 24.000 24.0000 23.8426 SGO_1370 Protein of unknown function (DUF964) superfamily 3.000 1.399 4.953 0.0083 0.0379 12.5370 12.000 12.000 13.500 13.500 13.5000 4.9329 SGO_1372 aroC; chorismate synthase 4.500 -0.102 4.405 0.0224 0.1302 6.7909 6.500 6.500 7.000 7.000 7.0000 7.3994 SGO_1373 aroB; 3-dehydroquinate synthase 5.500 5.500 0.638 5.497 0.0111 0.0536 16.7160 16.000 8.3989 16.000 11.000 11.000 11.0000 9.0437 SGO_1375 aroD; 3-dehydroquinate dehydratase, type I 19.000 17.000 -0.693 6.527 0.0002 0.0001 17.2384 16.500 29.0143 16.500 18.000 18.000 18.0000 27.9534 SGO_1377 sulfatase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 40 14.500 9.500 -0.525 6.005 0.0188 0.1061 10.4475 10.000 22.1425 10.000 16.000 16.000 16.0000 15.6210 SGO_1381 csn1; CRISPR-associated protein, Csn1 family 44.500 51.000 0.595 8.571 0.0030 0.0093 106.5647 102.000 67.9545 102.000 122.000 122.000 122.0000 83.8601 SGO_1383 rplS; ribosomal protein L19 15.500 20.500 -2.592 6.069 0.0018 0.0042 6.2685 6.000 23.6696 6.000 3.500 3.500 3.5000 33.7085 SGO_1386 chorismate mutase 5.000 6.500 -0.240 5.074 0.0349 0.2218 8.3580 8.000 7.6353 8.000 7.000 7.000 7.0000 10.6881 SGO_1390 ligA; DNA ligase, NAD-dependent 4.000 -0.126 4.153 0.1186 0.8978 4.1790 4.000 6.1083 4.000 7.500 7.500 7.5000 SGO_1394 hypothetical protein SGO_1394 15.000 17.500 -0.101 6.641 0.0692 0.4893 26.6412 25.500 22.9060 25.500 21.500 21.500 21.5000 28.7755 SGO_1397 map; methionine aminopeptidase, type I 2.500 3.500 -0.036 4.232 0.1077 0.8090 5.2238 5.000 3.8177 5.000 4.000 4.000 4.0000 5.7551 SGO_1398 hypothetical protein SGO_1398 10.000 7.500 -0.501 5.556 0.0058 0.0230 10.4475 10.000 15.2707 10.000 9.000 9.000 9.0000 12.3324 SGO_1400 murA-2; UDP-N-acetylglucosamine 1carboxyvinyltransferase 3.500 8.500 -0.910 4.834 0.0232 0.1353 4.7014 4.500 5.3447 4.500 4.500 4.500 4.5000 13.9767 SGO_1413 first chain of major exonuclease RexA 6.500 10.000 -2.079 5.022 0.0038 0.0129 2.6119 2.500 9.9259 2.500 3.500 3.500 3.5000 16.4432 SGO_1414 rexB; putative exonuclease RexB 29.500 43.000 -1.700 7.234 0.0037 0.0120 17.7608 17.000 45.0485 17.000 17.000 17.000 17.0000 70.7056 SGO_1422 hypothetical protein SGO_1422 2120.500 2216.500 0.874 14.250 0.0003 0.0003 6164.5617 5900.500 3238.1486 5900.500 6433.500 6433.500 6433.5000 3644.6263 SGO_1426 eno; enolase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 41 102.000 79.000 -0.244 9.039 0.0119 0.0586 122.7584 117.500 155.7610 117.500 117.500 117.500 117.5000 129.9010 SGO_1431 EzrA; Septation ring formation regulator ezrA 16.000 16.500 0.560 7.005 0.0084 0.0385 32.3873 31.000 24.4331 31.000 44.500 44.500 44.5000 27.1312 SGO_1432 gyrB; DNA gyrase, B subunit 3.500 2.500 -0.001 4.256 0.1190 0.9037 3.6566 3.500 5.3447 3.500 6.000 6.000 6.0000 4.1108 SGO_1434 thiJ; 4-methyl-5(beta-hydroxyethyl)thiazole monophosphate synthesis protein 7.000 6.000 0.062 5.394 0.0593 0.4113 11.4923 11.000 10.6895 11.000 10.000 10.000 10.0000 9.8659 SGO_1439 ftsX; cell division protein FtsX 42.500 39.500 -1.158 7.555 0.0000 0.0000 28.2083 27.000 64.9004 27.000 30.000 30.000 30.0000 64.9505 SGO_1440 cell-division ATP-binding protein FtsE 14.000 19.000 -0.537 6.479 0.0212 0.1216 14.1042 13.500 21.3790 13.500 22.500 22.500 22.5000 31.2420 SGO_1441 prfB; peptide chain release factor 2 8.500 10.000 0.497 6.145 0.0048 0.0181 19.3279 18.500 12.9801 18.500 22.000 22.000 22.0000 16.4432 SGO_1446 murF; UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase 13.000 12.000 0.502 6.584 0.0037 0.0122 30.8202 29.500 19.8519 29.500 25.500 25.500 25.5000 19.7318 SGO_1447 ddlA; D-Ala-D-Ala ligase 6.000 6.500 -0.175 5.241 0.0703 0.4995 10.9699 10.500 9.1624 10.500 7.000 7.000 7.0000 10.6881 SGO_1450 hypothetical protein SGO_1450 17.000 10.500 0.866 6.911 0.0024 0.0066 38.6558 37.000 25.9602 37.000 38.500 38.500 38.5000 17.2653 SGO_1451 frr; ribosome recycling factor 15.000 13.500 0.790 6.962 0.0074 0.0313 47.5362 45.500 22.9060 45.500 32.000 32.000 32.0000 22.1983 SGO_1452 pyrH; uridylate kinase 2.000 1.869 3.936 12.0147 11.500 11.500 3.2886 SGO_1453 glycosyl transferase, family 8 SP1766 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 42

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 42 72.500 70.000 1.187 9.545 0.0031 0.0097 217.3085 208.000 110.7125 208.000 304.000 304.000 304.0000 115.1021 SGO_1455 rplA; ribosomal protein L1 18.500 11.000 1.186 7.235 0.0044 0.0159 43.3572 41.500 28.2508 41.500 61.000 61.000 61.0000 18.0875 SGO_1456 rplK; ribosomal protein L11 13.000 8.000 -2.418 5.291 0.0023 0.0064 3.6566 3.500 19.8519 3.500 2.500 2.500 2.5000 13.1545 SGO_1458 aha1; cation-transporting ATPase yfgQ 8.000 9.000 -3.101 4.837 0.0133 0.0686 1.5671 1.500 12.2165 1.500 14.7988 SGO_1459 glyoxylase family protein 3.000 3.000 1.242 5.000 0.0001 0.0000 11.4923 11.000 4.5812 11.000 11.000 11.000 11.0000 4.9329 SGO_1460 DNA translocase ftsK 7.000 4.000 0.841 5.569 0.0059 0.0232 16.7160 16.000 10.6895 16.000 13.500 13.500 13.5000 6.5773 SGO_1463 peptidyl-prolyl cis-trans isomerase 4.500 5.000 1.867 6.138 0.0013 0.0026 31.3426 30.000 6.8718 30.000 24.000 24.000 24.0000 8.2216 SGO_1465 ABC transporter, ATP-binding protein SP0770 6.500 6.500 -0.483 5.149 0.0044 0.0157 8.3580 8.000 9.9259 8.000 6.500 6.500 6.5000 10.6881 SGO_1466 MTA/SAH nucleosidase 19.000 17.000 0.705 7.228 0.0004 0.0003 44.9244 43.000 29.0143 43.000 48.000 48.000 48.0000 27.9534 SGO_1469 glmU; UDP-N-acetylglucosamine pyrophosphorylase 8.500 3.500 -0.627 4.934 0.0371 0.2402 7.8356 7.500 12.9801 7.500 4.000 4.000 4.0000 5.7551 SGO_1472 acetyltransferase, GNAT family 17.500 12.500 -3.229 5.637 0.0167 0.0923 26.7237 2.500 2.500 2.5000 20.5539 SGO_1487 LPXTG cell wall surface protein, Cna protein B-type domain 8.000 9.000 -1.164 5.045 0.0191 0.1084 12.2165 6.000 6.000 6.0000 14.7988 SGO_1493 hypothetical protein SGO_1493 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 43

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 43 2.500 3.500 -0.358 3.726 0.0645 0.4512 3.6566 3.500 3.8177 3.500 5.7551 SGO_1512 lacG; 6-phospho-beta-galactosidase 5.500 4.000 -0.089 4.876 0.1076 0.8056 8.8804 8.500 8.3989 8.500 5.500 5.500 5.5000 6.5773 SGO_1529 hypothetical protein SGO_1529 32.500 20.000 0.700 7.741 0.0048 0.0180 68.9537 66.000 49.6297 66.000 62.500 62.500 62.5000 32.8863 SGO_1530 methionine-tRNA ligase 9.500 6.000 0.677 5.972 0.0060 0.0243 20.8950 20.000 14.5072 20.000 17.500 17.500 17.5000 9.8659 SGO_1531 xth; exodeoxyribonuclease III 8.000 7.000 -0.106 5.567 0.1294 0.9952 16.1937 15.500 12.2165 15.500 7.500 7.500 7.5000 11.5102 SGO_1534 ArsC family 6.500 4.000 0.903 5.581 0.0127 0.0647 19.8503 19.000 9.9259 19.000 11.500 11.500 11.5000 6.5773 SGO_1536 conserved hypothetical protein TIGR00096 10.500 6.500 0.379 5.928 0.0213 0.1226 15.6713 15.000 16.0342 15.000 18.500 18.500 18.5000 10.6881 SGO_1539 tmk; thymidylate kinase 18.000 33.500 -1.273 6.843 0.0107 0.0508 16.1937 15.500 27.4872 15.500 16.000 16.000 16.0000 55.0846 SGO_1541 atpC; ATP synthase F1, epsilon subunit 290.500 273.500 -1.626 10.208 0.0000 0.0000 139.9968 134.000 443.6134 134.000 149.500 149.500 149.5000 449.7204 SGO_1542 atpD; ATP synthase F1, beta subunit 41.500 29.500 -1.674 7.196 0.0013 0.0029 17.7608 17.000 63.3733 17.000 17.000 17.000 17.0000 48.5073 SGO_1543 atpG; ATP synthase F1, gamma subunit 125.500 106.000 -0.311 9.368 0.0025 0.0072 143.6535 137.500 191.6471 137.500 151.000 151.000 151.0000 174.2975 SGO_1544 atpA; ATP synthase F1, alpha subunit 33.000 36.500 -1.684 7.176 0.0007 0.0008 17.2384 16.500 50.3933 16.500 17.000 17.000 17.0000 60.0175 SGO_1545 atpH; ATP synthase F1, delta subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 44 30.000 12.000 0.130 7.047 0.1240 0.9498 38.6558 37.000 45.8121 37.000 28.000 28.000 28.0000 19.7318 SGO_1546 atpF; ATP synthase F0, B subunit 25.000 29.000 0.224 7.536 0.0179 0.1003 51.7152 49.500 38.1767 49.500 48.000 48.000 48.0000 47.6852 SGO_1550 glgP-1; glycogen phosphorylase 25.500 21.000 -1.718 6.594 0.0009 0.0014 14.6265 14.000 38.9402 14.000 8.500 8.500 8.5000 34.5306 SGO_1551 glgA; Glycogen synthase 35.500 27.500 -0.443 7.456 0.0307 0.1890 49.1034 47.000 54.2109 47.000 27.000 27.000 27.0000 45.2187 SGO_1552 glgD; glucose-1-phosphate adenylyltransferase, GlgD subunit 50.500 32.500 -0.465 7.805 0.0137 0.0711 47.0139 45.000 77.1170 45.000 46.000 46.000 46.0000 53.4403 SGO_1553 glgC; glucose-1-phosphate adenylyltransferase 75.000 59.000 -1.204 8.243 0.0008 0.0013 46.4915 44.500 114.5301 44.500 45.000 45.000 45.0000 97.0146 SGO_1554 glgB; 1,4-alpha-glucan branching enzyme 329.500 296.000 -0.227 10.842 0.0007 0.0011 428.3485 410.000 503.1690 410.000 417.500 417.500 417.5000 486.7175 SGO_1555 ptsI; phosphoenolpyruvate-protein phosphotransferase 515.500 384.500 -0.374 11.298 0.0151 0.0799 475.8847 455.500 787.2038 455.500 622.500 622.500 622.5000 632.2395 SGO_1556 phosphocarrier protein HPr 81.000 56.500 -0.663 8.459 0.0051 0.0197 67.3865 64.500 123.6925 64.500 68.000 68.000 68.0000 92.9039 SGO_1558 nrdE; ribonucleoside-diphosphate reductase large chain 24.500 24.000 0.844 7.748 0.0005 0.0005 72.0879 69.000 37.4132 69.000 66.000 66.000 66.0000 39.4636 SGO_1559 ribonucleoside-diphosphate reductase, beta subunit 65.000 43.500 0.677 8.785 0.0044 0.0160 145.7430 139.500 99.2594 139.500 124.500 124.500 124.5000 71.5277 SGO_1570 alaS; alanyl-tRNA synthetase 5.000 -1.155 3.882 0.0245 0.1448 2.6119 2.500 7.6353 2.500 4.500 4.500 4.5000 SGO_1573 O-methyltransferase family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 45 67.500 54.000 0.417 8.805 0.0019 0.0047 129.0269 123.500 103.0771 123.500 126.500 126.500 126.5000 88.7931 SGO_1574 pepF-1; oligoendopeptidase F 2.000 2.000 1.452 4.570 0.0007 0.0009 9.4028 9.000 3.0541 9.000 8.000 8.000 8.0000 3.2886 SGO_1580 PTS system, Lactose/Cellobiose specific IIB subunit 8.000 10.500 -0.068 5.865 0.1190 0.9045 18.2832 17.500 12.2165 17.500 10.500 10.500 10.5000 17.2653 SGO_1587 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase 40.000 38.500 -2.605 7.184 0.0002 0.0001 13.0594 12.500 61.0827 12.500 8.000 8.000 8.0000 63.3062 SGO_1591 arcC; carbamate kinase 379.500 455.000 -3.079 10.535 0.0008 0.0012 77.8341 74.500 579.5225 74.500 78.000 78.000 78.0000 748.1637 SGO_1592 arcB; ornithine carbamoyltransferase 270.000 229.500 -2.641 9.840 0.0002 0.0001 60.5956 58.000 412.3085 58.000 66.000 66.000 66.0000 377.3705 SGO_1593 arcA; arginine deiminase 298.500 248.500 -1.637 10.158 0.0003 0.0002 133.2059 127.500 455.8299 127.500 144.500 144.500 144.5000 408.6125 SGO_1599 sodA; manganese-dependent superoxide dismutase 6.000 5.500 -0.644 4.907 0.0028 0.0085 6.7909 6.500 9.1624 6.500 5.000 5.000 5.0000 9.0437 SGO_1604 acyltransferase family protein 1.500 1.500 1.730 4.362 0.0005 0.0005 7.3133 7.000 2.2906 7.000 8.500 8.500 8.5000 2.4665 SGO_1605 P-type ATPase, metal cation transport 10.000 8.500 1.437 6.760 0.0001 0.0000 38.6558 37.000 15.2707 37.000 40.500 40.500 40.5000 13.9767 SGO_1609 ATP-dependent RNA helicase, DEAD/DEAH box family 9.500 12.000 -0.123 6.060 0.1068 0.7985 11.4923 11.000 14.5072 11.000 21.000 21.000 21.0000 19.7318 SGO_1617 prfC; peptide chain release factor 3 19.000 18.000 1.170 7.584 0.0024 0.0068 76.2669 73.000 29.0143 73.000 57.000 57.000 57.0000 29.5977 SGO_1619 cation-transporting ATPase, E1-E2 family .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 46 6.000 6.500 -0.151 5.237 0.0278 0.1678 8.3580 8.000 9.1624 8.000 9.500 9.500 9.5000 10.6881 SGO_1621 HD domain protein 15.000 12.000 -1.521 5.844 0.0006 0.0006 7.3133 7.000 22.9060 7.000 7.500 7.500 7.5000 19.7318 SGO_1622 Cof family protein 12.500 10.500 -0.507 5.952 0.0012 0.0023 13.0594 12.500 19.0884 12.500 12.500 12.500 12.5000 17.2653 SGO_1623 murM; MurM 10.000 6.000 -1.064 5.206 0.0060 0.0240 6.2685 6.000 15.2707 6.000 5.500 5.500 5.5000 9.8659 SGO_1624 murN; MurN protein 30.000 31.000 -0.730 7.277 0.0008 0.0013 30.2978 29.000 45.8121 29.000 28.000 28.000 28.0000 50.9738 SGO_1625 acetoin utilization putative/CBS domain protein 4.500 1.305 5.463 0.0170 0.0947 16.7160 16.000 16.000 20.000 20.000 20.0000 7.3994 SGO_1626 branched-chain amino acid ABC transporter, ATP-binding protein 27.500 22.500 2.093 8.698 0.0000 0.0000 169.2499 162.000 41.9944 162.000 167.000 167.000 167.0000 36.9971 SGO_1630 branched-chain amino acid ABC transporter, amino acid-binding protein 36.500 47.000 -1.451 7.500 0.0023 0.0064 23.5069 22.500 55.7380 22.500 24.500 24.500 24.5000 77.2828 SGO_1632 clpP; ATP-dependent Clp protease, proteolytic subunit ClpP 60.000 43.000 -0.346 8.175 0.0121 0.0602 62.6851 60.000 91.6241 60.000 64.000 64.000 64.0000 70.7056 SGO_1633 upp; uracil phosphoribosyltransferase 4.000 3.500 -0.133 4.535 0.1063 0.7935 7.3133 7.000 6.1083 7.000 4.000 4.000 4.0000 5.7551 SGO_1634 magnesium-translocating P-type ATPase 6.500 8.500 -0.488 5.348 0.0125 0.0623 7.8356 7.500 9.9259 7.500 9.000 9.000 9.0000 13.9767 SGO_1638 murE; UDP-N-acetylmuramoylalanyl-Dglutamate--2,6-diaminopimelate ligase 62.000 59.500 0.636 8.950 0.0052 0.0203 130.0717 124.500 94.6782 124.500 172.000 172.000 172.0000 97.8368 SGO_1648 ppx1; inorganic pyrophosphatase, manganese-dependent .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 47 9.000 8.500 -1.939 5.143 0.0006 0.0007 2.6119 2.500 13.7436 2.500 5.000 5.000 5.0000 13.9767 SGO_1649 act; pyruvate formate-lyase-activating enzyme 10.000 7.500 1.008 6.371 0.0005 0.0005 27.6859 26.500 15.2707 26.500 27.500 27.500 27.5000 12.3324 SGO_1652 intracellular glycosyl hydrolase 20.500 23.000 0.013 7.115 0.1226 0.9373 33.9545 32.500 31.3049 32.500 35.500 35.500 35.5000 37.8193 SGO_1653 trehalose PTS enzyme II 4.500 7.500 -0.821 4.901 0.0162 0.0886 4.1790 4.000 6.8718 4.000 6.500 6.500 6.5000 12.3324 SGO_1655 CBS domain protein/possible hemolysin 33.000 30.000 -1.754 7.016 0.0001 0.0000 16.1937 15.500 50.3933 15.500 13.500 13.500 13.5000 49.3295 SGO_1666 trkA; potassium uptake protein, Trk family 15.000 9.000 0.160 6.308 0.0762 0.5497 23.5069 22.500 22.9060 22.500 18.000 18.000 18.0000 14.7988 SGO_1669 ribosomal large subunit pseudouridine synthase B 7.500 6.500 -0.983 5.062 0.0007 0.0010 6.2685 6.000 11.4530 6.000 5.000 5.000 5.0000 10.6881 SGO_1674 phosphodiesterase, MJ0936 family 11.500 13.000 -0.908 5.903 0.0027 0.0079 8.8804 8.500 17.5613 8.500 12.000 12.000 12.0000 21.3761 SGO_1675 HAM1 protein-like protein 6.500 5.500 0.694 5.633 0.0003 0.0002 15.1489 14.500 9.9259 14.500 15.500 15.500 15.5000 9.0437 SGO_1676 murI; glutamate racemase 9.000 11.000 -1.251 5.548 0.0083 0.0379 10.9699 10.500 13.7436 10.500 4.000 4.000 4.0000 18.0875 SGO_1678 lysA; diaminopimelate decarboxylase 60.000 48.000 1.095 9.069 0.0023 0.0062 206.8610 198.000 91.6241 198.000 159.500 159.500 159.5000 78.9272 SGO_1679 phosphotransferase system enzyme II 30.500 37.000 0.852 8.227 0.0011 0.0020 97.1620 93.000 46.5756 93.000 95.000 95.000 95.0000 60.8397 SGO_1681 PTS system, mannose/fructose/sorbose family, IID component .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 48

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 48 44.500 23.500 0.380 7.907 0.0346 0.2185 69.9984 67.000 67.9545 67.000 63.500 63.500 63.5000 38.6414 SGO_1683 serS; seryl-tRNA synthetase 17.500 17.000 1.647 7.820 0.0001 0.0000 87.7592 84.000 26.7237 84.000 83.500 83.500 83.5000 27.9534 SGO_1685 putative peroxidase / antioxidase 28.000 19.500 0.295 7.374 0.0188 0.1060 48.5810 46.500 42.7579 46.500 42.500 42.500 42.5000 32.0642 SGO_1687 accA; acetyl-CoA carboxylase, carboxyl transferase, alpha subunit 14.000 13.000 -0.504 6.188 0.0000 0.0000 15.1489 14.500 21.3790 14.500 15.000 15.000 15.0000 21.3761 SGO_1688 accD; acetyl-CoA carboxylase, carboxyl transferase, beta subunit 38.500 41.000 -0.538 7.735 0.0021 0.0051 41.7901 40.000 58.7921 40.000 45.000 45.000 45.0000 67.4170 SGO_1689 accC; acetyl-CoA carboxylase, biotin carboxylase 6.000 10.500 0.686 6.080 0.0188 0.1070 16.7160 16.000 9.1624 16.000 24.500 24.500 24.5000 17.2653 SGO_1690 fabZ; beta-hydroxyacyl-(acyl-carrierprotein) dehydratase FabZ 24.500 12.500 1.481 7.734 0.0013 0.0027 80.9683 77.500 37.4132 77.500 74.000 74.000 74.0000 20.5539 SGO_1691 accB; acetyl-CoA carboxylase, biotin carboxyl carrier protein 197.500 213.000 -0.657 10.055 0.0015 0.0034 204.7715 196.000 301.5960 196.000 207.500 207.500 207.5000 350.2393 SGO_1692 3-oxoacyl-[acyl-carrier-protein] synthase 25.000 24.000 -0.282 7.146 0.0033 0.0107 33.9545 32.500 38.1767 32.500 30.000 30.000 30.0000 39.4636 SGO_1693 fabG; 3-oxoacyl-(acyl-carrier-protein) reductase 12.000 16.000 0.671 6.845 0.0067 0.0276 31.3426 30.000 18.3248 30.000 39.000 39.000 39.0000 26.3091 SGO_1694 fabD; malonyl CoA-acyl carrier protein transacylase 71.000 73.500 0.782 9.289 0.0030 0.0092 221.4875 212.000 108.4219 212.000 175.000 175.000 175.0000 120.8572 SGO_1695 enoyl-acyl carrier protein(ACP) reductase 11.000 10.500 -0.547 5.849 0.0043 0.0152 13.5818 13.000 16.7978 13.000 10.000 10.000 10.0000 17.2653 SGO_1699 transcriptional regulator, MarR family .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 49

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 49 55.500 65.000 -2.813 7.773 0.0007 0.0010 14.1042 13.500 84.7523 13.500 13.000 13.000 13.0000 106.8805 SGO_1700 enoyl-CoA hydratase/isomerase family protein 30.000 33.000 0.028 7.657 0.1026 0.7627 51.1929 49.000 45.8121 49.000 50.500 50.500 50.5000 54.2624 SGO_1701 aspartate kinase 36.500 27.500 0.630 8.003 0.0022 0.0059 73.6550 70.500 55.7380 70.500 82.000 82.000 82.0000 45.2187 SGO_1708 amiF; Oligopeptide transport ATP-binding protein amiF 20.000 22.500 1.471 7.990 0.0006 0.0007 87.2368 83.500 30.5414 83.500 99.500 99.500 99.5000 36.9971 SGO_1709 amiE; Oligopeptide transport ATP-binding protein 10.500 9.000 1.224 6.684 0.0002 0.0001 34.9992 33.500 16.0342 33.500 37.000 37.000 37.0000 14.7988 SGO_1711 hppB; Oligopeptide transport system permease 111.000 65.000 0.912 9.612 0.0027 0.0079 253.8748 243.000 169.5046 243.000 252.500 252.500 252.5000 106.8805 SGO_1712 hppA; oligopeptide-binding lipoprotein 137.500 96.500 -0.172 9.436 0.0368 0.2370 167.1604 160.000 209.9719 160.000 157.000 157.000 157.0000 158.6765 SGO_1713 hppG; oligopeptide-binding lipoprotein 51.000 43.000 -0.060 8.185 0.0447 0.2998 68.9537 66.000 77.8805 66.000 73.500 73.500 73.5000 70.7056 SGO_1715 hppH; oligopeptide-binding lipoprotein 70.000 49.000 -0.045 8.522 0.0912 0.6716 94.0277 90.000 106.8948 90.000 86.000 86.000 86.0000 80.5715 SGO_1716 oligopeptide binding protein 3.500 4.000 -1.505 3.809 0.0180 0.1005 2.0895 2.000 5.3447 2.000 6.5773 SGO_1717 pbp3; penicillin-binding protein 3 11.000 16.000 0.568 6.721 0.0097 0.0454 32.9097 31.500 16.7978 31.500 29.500 29.500 29.5000 26.3091 SGO_1718 sufB-1; FeS assembly protein SufB 24.000 16.500 0.197 7.090 0.0384 0.2496 33.9545 32.500 36.6496 32.500 38.500 38.500 38.5000 27.1312 SGO_1721 sufD; FeS assembly protein SufD .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 50

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 50 18.000 15.000 -0.285 6.570 0.0075 0.0318 19.8503 19.000 27.4872 19.000 23.000 23.000 23.0000 24.6647 SGO_1722 sufC; FeS assembly ATPase SufC 3.000 -0.717 2.988 3.000 3.000 3.0000 4.9329 SGO_1724 mecA; Adapter protein mec 11.500 7.500 0.773 6.329 0.0041 0.0141 22.9846 22.000 17.5613 22.000 27.500 27.500 27.5000 12.3324 SGO_1727 amino acid ABC transporter, amino acidbinding/permease protein 14.500 14.500 -0.625 6.253 0.0044 0.0160 17.7608 17.000 22.1425 17.000 12.500 12.500 12.5000 23.8426 SGO_1728 glnQ; glutamine ABC transporter ATPbinding protein 97.000 144.000 -2.961 8.759 0.0025 0.0072 21.4174 20.500 148.1256 20.500 27.000 27.000 27.0000 236.7815 SGO_1729 hypothetical protein SGO_1729 163.500 113.000 -1.547 9.192 0.0021 0.0053 63.2075 60.500 249.6757 60.500 86.000 86.000 86.0000 185.8077 SGO_1730 SPFH domain/Band 7 family 2.000 2.500 2.314 5.420 0.0013 0.0029 15.1489 14.500 3.0541 14.500 20.500 20.500 20.5000 4.1108 SGO_1731 DNA-binding response regulator 82.500 59.000 0.211 8.904 0.0244 0.1434 129.0269 123.500 125.9831 123.500 127.000 127.000 127.0000 97.0146 SGO_1735 hypothetical protein SGO_1735 15.500 9.000 -0.273 6.124 0.0440 0.2941 17.7608 17.000 23.6696 17.000 13.500 13.500 13.5000 14.7988 SGO_1736 alkaline shock protein 422.000 351.000 0.915 11.782 0.0003 0.0002 1123.1089 1075.000 644.4229 1075.000 1177.500 1177.500 1177.5000 577.1549 SGO_1745 fba; fructose-1,6-bisphosphate aldolase, class II 4.500 -1.902 3.525 0.0129 0.0660 2.6119 2.500 2.500 1.500 1.500 1.5000 7.3994 SGO_1747 hypothetical protein SGO_1747 3.500 1.153 5.008 0.0403 0.2643 9.9251 9.500 9.500 16.500 16.500 16.5000 5.7551 SGO_1748 pyrG; CTP synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 51

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 51 19.500 13.000 0.024 6.688 0.1201 0.9143 21.9398 21.000 29.7778 21.000 30.000 30.000 30.0000 21.3761 SGO_1749 manA; mannose-6-phosphate isomerase, class I 7.000 6.500 1.873 6.648 0.0011 0.0021 44.4020 42.500 10.6895 42.500 34.500 34.500 34.5000 10.6881 SGO_1755 scrK; fructokinase 38.000 21.500 0.959 8.074 0.0028 0.0085 85.6697 82.000 58.0286 82.000 90.500 90.500 90.5000 35.3528 SGO_1757 glmS; glucosamine--fructose-6-phosphate aminotransferase 4.000 -1.133 3.260 3.000 3.000 3.0000 6.5773 SGO_1760 DNA-binding response regulator 21.000 15.000 0.588 7.148 0.0069 0.0284 37.6111 36.000 32.0684 36.000 47.500 47.500 47.5000 24.6647 SGO_1763 ABC transporter, substrate-binding protein SP0092 17.000 13.500 -2.439 5.865 0.0010 0.0018 2.6119 2.500 25.9602 2.500 7.500 7.500 7.5000 22.1983 SGO_1768 glycosyl hydrolase, family 38 18.500 16.000 -1.588 6.190 0.0005 0.0006 10.9699 10.500 28.2508 10.500 7.500 7.500 7.5000 26.3091 SGO_1774 alcohol dehydrogenase, zinc-containing 42.500 33.000 0.233 8.016 0.0129 0.0663 73.1327 70.000 64.9004 70.000 66.500 66.500 66.5000 54.2624 SGO_1784 leuS; leucyl-tRNA synthetase 117.500 108.000 -1.037 9.053 0.0001 0.0000 84.1026 80.500 179.4305 80.500 90.000 90.000 90.0000 177.5861 SGO_1799 endopeptidase O 9.000 4.500 3.394 7.883 0.0013 0.0025 124.8479 119.500 13.7436 119.500 90.000 90.000 90.0000 7.3994 SGO_1802 Metal ABC transporter substrate-binding lipoprotein precursor 15.500 12.000 0.481 6.697 0.0022 0.0059 30.8202 29.500 23.6696 29.500 29.500 29.500 29.5000 19.7318 SGO_1803 tpx; thioredoxin peroxidase 4.000 3.500 1.136 5.246 0.0003 0.0002 13.5818 13.000 6.1083 13.000 12.500 12.500 12.5000 5.7551 SGO_1804 hutI; imidazolonepropionase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 52

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 52 1.500 3.863 6.129 0.0204 0.1167 39.7006 38.000 2.2906 38.000 28.000 28.000 28.0000 SGO_1805 hutU; urocanate hydratase 6.000 -1.367 4.133 0.0081 0.0358 4.1790 4.000 4.000 3.500 3.500 3.5000 9.8659 SGO_1808 fhs-2; formate--tetrahydrofolate ligase 7.000 -0.540 4.773 0.0042 0.0146 7.8356 7.500 7.500 8.000 8.000 8.0000 11.5102 SGO_1811 hutH; histidine ammonia-lyase 9.500 6.500 -0.731 5.031 0.0357 0.2282 14.5072 7.500 7.500 7.5000 10.6881 SGO_1816 scaR; ScaR Manganese-dependent regulator of scaCBA 17.500 21.000 -1.893 6.278 0.0011 0.0022 8.3580 8.000 26.7237 8.000 8.000 8.000 8.0000 34.5306 SGO_1822 relA; GTP diphosphokinase 6.500 8.500 0.331 5.742 0.0167 0.0927 14.6265 14.000 9.9259 14.000 15.000 15.000 15.0000 13.9767 SGO_1824 prmA; ribosomal protein L11 methyltransferase 7.000 -1.094 4.383 0.0183 0.1026 4.1790 4.000 10.6895 4.000 6.000 6.000 6.0000 SGO_1827 hypothetical protein SGO_1827 6.000 3.500 -0.938 4.525 0.0147 0.0777 2.6119 2.500 9.1624 2.500 5.500 5.500 5.5000 5.7551 SGO_1828 ATPase, AAA family 116.000 80.500 -2.439 8.524 0.0013 0.0027 37.0887 35.500 177.1399 35.500 21.500 21.500 21.5000 132.3674 SGO_1834 hypothetical protein SGO_1834 9.500 -1.923 4.470 0.0032 0.0102 3.6566 3.500 14.5072 3.500 4.000 4.000 4.0000 SGO_1835 hypothetical protein SGO_1835 41.500 37.000 -0.001 7.961 0.1224 0.9344 69.9984 67.000 63.3733 67.000 55.000 55.000 55.0000 60.8397 SGO_1843 pepS; aminopeptidase PepS 6.500 5.000 0.408 5.399 0.0074 0.0314 13.0594 12.500 9.9259 12.500 11.000 11.000 11.0000 8.2216 SGO_1844 cbxX/cfqX family protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 53

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 53 7.000 12.500 -0.370 5.761 0.0377 0.2442 10.9699 10.500 10.6895 10.500 12.000 12.000 12.0000 20.5539 SGO_1847 polC; DNA polymerase III, alpha subunit, Gram-positive type 69.500 52.500 0.035 8.603 0.1049 0.7821 103.9529 99.500 106.1313 99.500 92.500 92.500 92.5000 86.3266 SGO_1851 proS; prolyl-tRNA synthetase 5.000 6.500 0.517 5.493 0.0244 0.1434 16.7160 16.000 7.6353 16.000 10.000 10.000 10.0000 10.6881 SGO_1854 uppS; undecaprenyl diphosphate synthase 132.500 65.000 -3.472 8.392 0.0042 0.0144 14.6265 14.000 202.3366 14.000 12.000 12.000 12.0000 106.8805 SGO_1856 ATP-dependent proteinase ATP-binding chain 3.500 4.000 -0.633 4.293 0.0040 0.0137 4.1790 4.000 5.3447 4.000 3.500 3.500 3.5000 6.5773 SGO_1858 beta-fructofuranosidase/sucrose 6 phoshate hydrolase 74.500 39.000 -0.721 8.138 0.0156 0.0833 55.3719 53.000 113.7666 53.000 48.500 48.500 48.5000 64.1283 SGO_1860 5'-nucleotidase, lipoprotein e(P4) family 54.500 59.500 -1.778 7.869 0.0006 0.0006 27.6859 26.500 83.2252 26.500 25.000 25.000 25.0000 97.8368 SGO_1862 alkaline shock protein 27.500 19.000 1.017 7.780 0.0009 0.0014 72.0879 69.000 41.9944 69.000 74.500 74.500 74.5000 31.2420 SGO_1863 efp; Elongation factor P (EF-P) 53.000 51.000 -1.379 7.834 0.0001 0.0000 31.3426 30.000 80.9346 30.000 32.000 32.000 32.0000 83.8601 SGO_1864 X-Pro aminopeptidase 17.500 19.000 -0.713 6.543 0.0014 0.0032 17.7608 17.000 26.7237 17.000 17.500 17.500 17.5000 31.2420 SGO_1865 uvrA; excinuclease ABC, A subunit 3.000 4.500 2.522 6.302 0.0002 0.0001 32.9097 31.500 4.5812 31.500 34.000 34.000 34.0000 7.3994 SGO_1867 hypothetical protein SGO_1867 23.500 28.500 0.132 7.433 0.0562 0.3870 48.0586 46.000 35.8861 46.000 42.000 42.000 42.0000 46.8630 SGO_1879 rpsR; ribosomal protein S18 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 54 24.000 22.500 1.192 7.919 0.0004 0.0003 79.9236 76.500 36.6496 76.500 88.500 88.500 88.5000 36.9971 SGO_1880 ssb-1; single-strand binding protein 44.500 65.500 1.188 9.153 0.0034 0.0109 223.5770 214.000 67.9545 214.000 170.000 170.000 170.0000 107.7027 SGO_1881 rpsF; ribosomal protein S6 10.000 6.500 0.395 5.908 0.0260 0.1553 14.1042 13.500 15.2707 13.500 20.000 20.000 20.0000 10.6881 SGO_1882 folE; GTP cyclohydrolase I 909.500 842.500 -2.739 11.639 0.0000 0.0000 208.9505 200.000 1388.8687 200.000 206.500 206.500 206.5000 1385.3362 SGO_1885 groL; 60 kDa chaperonin/groEL protein 17.500 38.500 -1.663 6.874 0.0125 0.0626 17.7608 17.000 26.7237 17.000 9.500 9.500 9.5000 63.3062 SGO_1886 groES; chaperonin, 10 kDa 79.000 46.500 -2.895 7.801 0.0024 0.0068 11.4923 11.000 120.6384 11.000 14.500 14.500 14.5000 76.4607 SGO_1892 PTS system, fructose(mannose)-specific IIB 111.500 124.000 -1.710 8.931 0.0007 0.0009 55.8943 53.500 170.2681 53.500 58.000 58.000 58.0000 203.8952 SGO_1898 glutamyl aminopeptidase 10.000 4.500 1.204 6.178 0.0069 0.0283 29.2531 28.000 15.2707 28.000 20.500 20.500 20.5000 7.3994 SGO_1901 tRNA binding domain 51.000 35.500 -0.484 7.863 0.0087 0.0402 46.4915 44.500 77.8805 44.500 50.000 50.000 50.0000 58.3732 SGO_1903 ATP-dependent Zn protease 5.000 -0.548 4.283 0.0072 0.0301 5.7461 5.500 5.500 5.500 5.500 5.5000 8.2216 SGO_1912 Bifunctional folate synthesis protein 4.500 4.000 -0.729 4.433 0.0011 0.0020 3.6566 3.500 6.8718 3.500 4.500 4.500 4.5000 6.5773 SGO_1914 folP; dihydropteroate synthase 37.500 36.000 0.333 8.040 0.0002 0.0001 73.6550 70.500 57.2651 70.500 73.000 73.000 73.0000 59.1954 SGO_1916 ackA; acetate kinase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 55

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 55 4.000 5.000 0.195 4.942 0.0506 0.3436 9.4028 9.000 6.1083 9.000 7.000 7.000 7.0000 8.2216 SGO_1917 hypothetical protein SGO_1917 146.500 130.500 0.371 9.973 0.0006 0.0007 289.3964 277.000 223.7155 277.000 277.500 277.500 277.5000 214.5832 SGO_1926 rpoC; DNA-directed RNA polymerase, beta chain 141.000 74.500 0.571 9.680 0.0141 0.0739 238.2036 228.000 215.3166 228.000 244.500 244.500 244.5000 122.5015 SGO_1927 rpoB; DNA-directed RNA polymerase, beta subunit 48.000 45.500 1.102 8.867 0.0008 0.0013 171.8618 164.500 73.2993 164.500 147.000 147.000 147.0000 74.8164 SGO_1929 tyrS; tyrosyl-tRNA synthetase 9.000 8.000 1.236 6.497 0.0004 0.0004 33.4321 32.000 13.7436 32.000 30.000 30.000 30.0000 13.1545 SGO_1936 adcA; metal-binding (Mn) permease precursor, lipoprotein 3.500 5.500 -1.798 4.035 0.0345 0.2178 5.3447 2.000 2.000 2.0000 9.0437 SGO_1957 hypothetical protein SGO_1957 27.500 21.000 3.171 9.577 0.0002 0.0002 365.6633 350.000 41.9944 350.000 321.500 321.500 321.5000 34.5306 SGO_1958 rplQ; ribosomal protein L17 61.000 66.000 0.453 8.899 0.0029 0.0089 130.5941 125.000 93.1512 125.000 145.000 145.000 145.0000 108.5249 SGO_1959 rpoA; DNA-directed RNA polymerase, alpha subunit 30.500 18.000 0.749 7.652 0.0050 0.0192 59.0285 56.500 46.5756 56.500 66.000 66.000 66.0000 29.5977 SGO_1960 rpsK; ribosomal protein S11 27.000 19.000 2.673 9.052 0.0002 0.0001 241.8602 231.500 41.2308 231.500 216.500 216.500 216.5000 31.2420 SGO_1961 rpsM; ribosomal protein S13p/S18e 47.500 28.000 0.441 8.106 0.0161 0.0875 78.8788 75.500 72.5358 75.500 78.000 78.000 78.0000 46.0408 SGO_1964 adk; Adenylate kinase (ATP-AMP transphosphorylase) 75.000 34.000 0.648 8.744 0.0282 0.1723 98.2067 94.000 114.5301 94.000 160.000 160.000 160.0000 55.9067 SGO_1966 rplO; ribosomal protein L15 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 56

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 56 13.000 21.500 2.111 8.152 0.0006 0.0007 121.1913 116.000 19.8519 116.000 108.000 108.000 108.0000 35.3528 SGO_1967 50S ribosomal protein L30 -related protein 84.000 58.500 1.261 9.565 0.0006 0.0007 274.7699 263.000 128.2737 263.000 258.000 258.000 258.0000 96.1925 SGO_1968 rpsE; ribosomal protein S5 71.000 41.000 1.721 9.530 0.0005 0.0005 282.6055 270.500 108.4219 270.500 281.000 281.000 281.0000 67.4170 SGO_1969 rplR; ribosomal protein L18 52.000 38.500 1.370 8.992 0.0003 0.0002 186.4883 178.500 79.4076 178.500 180.000 180.000 180.0000 63.3062 SGO_1970 BL10; 50S ribosomal protein L6 79.000 75.500 1.758 10.068 0.0002 0.0001 429.9156 411.500 120.6384 411.500 398.500 398.500 398.5000 124.1459 SGO_1971 rpsH; ribosomal protein S8 60.500 51.000 1.138 9.139 0.0002 0.0001 197.9806 189.500 92.3876 189.500 189.500 189.500 189.5000 83.8601 SGO_1973 BL6; 50S ribosomal protein L5 34.500 22.500 0.886 7.983 0.0021 0.0053 77.8341 74.500 52.6839 74.500 85.500 85.500 85.5000 36.9971 SGO_1974 rplX; ribosomal protein L24 40.500 26.000 0.875 8.196 0.0021 0.0051 96.6396 92.500 61.8463 92.500 92.000 92.000 92.0000 42.7522 SGO_1975 rplN; ribosomal protein L14 14.500 18.000 2.459 8.387 0.0007 0.0009 126.9374 121.500 22.1425 121.500 156.000 156.000 156.0000 29.5977 SGO_1976 BS16; 30S ribosomal protein 7.500 0.476 5.445 0.0390 0.2551 14.1042 13.500 11.4530 13.500 18.000 18.000 18.0000 SGO_1977 rpmC; ribosomal protein L29 25.000 20.500 1.680 8.238 0.0001 0.0000 115.4451 110.500 38.1767 110.500 114.500 114.500 114.5000 33.7085 SGO_1978 rplP; ribosomal protein L16 88.500 102.000 0.002 9.240 0.1243 0.9528 154.6234 148.000 135.1456 148.000 147.000 147.000 147.0000 167.7202 SGO_1979 rpsC; ribosomal protein S3 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 57

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 57 53.500 43.000 1.141 8.930 0.0002 0.0002 171.3394 164.000 81.6982 164.000 164.000 164.000 164.0000 70.7056 SGO_1980 rplV; ribosomal protein L22 64.000 60.500 0.174 8.715 0.0107 0.0510 104.4752 100.000 97.7324 100.000 118.500 118.500 118.5000 99.4811 SGO_1981 rpsS; ribosomal protein S19 78.500 44.500 0.153 8.650 0.0843 0.6166 111.7885 107.000 119.8749 107.000 97.000 97.000 97.0000 73.1721 SGO_1982 rplB; ribosomal protein L2 14.500 31.500 1.231 7.880 0.0079 0.0346 95.0725 91.000 22.1425 91.000 66.500 66.500 66.5000 51.7960 SGO_1983 rplW; ribosomal protein L23 81.500 77.000 0.473 9.229 0.0014 0.0030 165.0709 158.000 124.4561 158.000 184.000 184.000 184.0000 126.6123 SGO_1984 rplD; ribosomal protein L4/L1 family 123.000 85.500 0.999 9.986 0.0136 0.0706 232.9798 223.000 187.8294 223.000 453.000 453.000 453.0000 140.5890 SGO_1985 rplC; ribosomal protein L3 19.000 16.000 0.777 7.231 0.0011 0.0020 44.4020 42.500 29.0143 42.500 50.500 50.500 50.5000 26.3091 SGO_1986 rpsJ; ribosomal protein S10 89.500 75.000 0.802 9.478 0.0007 0.0008 236.6364 226.500 136.6726 226.500 216.500 216.500 216.5000 123.3237 SGO_1989 purA; adenylosuccinate synthetase 21.500 25.000 -2.053 6.535 0.0013 0.0027 6.2685 6.000 32.8320 6.000 12.500 12.500 12.5000 41.1079 SGO_1990 glutamate--cysteine ligase, putative/amino acid ligase, putative 12.500 12.000 -2.454 5.522 0.0001 0.0000 3.1343 3.000 19.0884 3.000 4.000 4.000 4.0000 19.7318 SGO_1991 hslO; 33 kDa chaperonin /Heat shock protein 33-like protein 7.500 6.000 1.046 6.030 0.0009 0.0014 23.5069 22.500 11.4530 22.500 20.500 20.500 20.5000 9.8659 SGO_1993 possible transcriptional regulator 17.000 15.500 0.053 6.720 0.0848 0.6222 22.9846 22.000 25.9602 22.000 31.000 31.000 31.0000 25.4869 SGO_1998 clpB; ATP-dependent Clp proteinase, ATPbinding chain .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 58

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 58 247.500 199.000 0.341 10.640 0.0032 0.0103 457.0792 437.500 377.9494 437.500 434.000 434.000 434.0000 327.2189 SGO_2000 tsf; translation elongation factor Ts 180.000 200.500 0.226 10.354 0.0122 0.0605 363.0515 347.500 274.8723 347.500 341.500 341.500 341.5000 329.6853 SGO_2001 rpsB; ribosomal protein S2 2.500 1.031 4.389 0.0158 0.0855 7.8356 7.500 7.500 9.000 9.000 9.0000 4.1108 SGO_2005 LPXTG cell wall surface protein 22.500 20.500 -0.429 6.891 0.0009 0.0016 26.6412 25.500 34.3590 25.500 24.000 24.000 24.0000 33.7085 SGO_2007 nusG; transcription termination/antitermination factor NusG 41.000 42.000 -1.280 7.538 0.0003 0.0003 27.6859 26.500 62.6098 26.500 26.500 26.500 26.5000 69.0613 SGO_2033 nrdD; ribonucleoside-triphosphate reductase 4.000 -0.740 3.288 3.6566 3.500 6.1083 3.500 SGO_2034 hypothetical protein SGO_2034 35.000 17.500 1.423 8.197 0.0021 0.0052 96.6396 92.500 53.4474 92.500 114.500 114.500 114.5000 28.7755 SGO_2042 Bacterial protein of unknown function (DUF965) superfamily 32.000 27.000 3.160 9.855 0.0000 0.0000 406.9311 389.500 48.8662 389.500 426.000 426.000 426.0000 44.3965 SGO_2045 recA; recA protein 7.000 6.000 -0.120 5.303 0.0188 0.1070 9.9251 9.500 10.6895 9.500 9.000 9.000 9.0000 9.8659 SGO_2046 cinA; competence induced protein 1.500 1.133 3.770 0.0411 0.2701 4.1790 4.000 4.000 7.000 7.000 7.0000 2.4665 SGO_2050 ruvA; Holliday junction DNA helicase RuvA 9.500 7.500 -0.856 5.395 0.0050 0.0190 5.7461 5.500 14.5072 5.500 9.500 9.500 9.5000 12.3324 SGO_2053 DNA mismatch repair protein hexB 19.000 23.000 -1.072 6.628 0.0033 0.0109 13.0594 12.500 29.0143 12.500 19.000 19.000 19.0000 37.8193 SGO_2056 mutS; DNA mismatch repair protein MutS .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 59

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 59 152.500 148.500 -0.325 9.745 0.0011 0.0020 196.4135 188.000 232.8779 188.000 184.500 184.500 184.5000 244.1809 SGO_2058 argS; arginyl-tRNA synthetase 29.000 33.000 0.399 7.832 0.0038 0.0130 64.2523 61.500 44.2850 61.500 65.000 65.000 65.0000 54.2624 SGO_2060 aspS-1; aspartyl-tRNA synthetase 80.500 63.500 -0.579 8.567 0.0028 0.0084 80.9683 77.500 122.9290 77.500 71.000 71.000 71.0000 104.4141 SGO_2062 hisS; histidyl-tRNA synthetase 67.000 59.000 0.430 8.872 0.0029 0.0089 144.1758 138.000 102.3136 138.000 125.000 125.000 125.0000 97.0146 SGO_2064 ilvD; dihydroxy-acid dehydratase 12.500 1.727 7.190 0.0158 0.0853 69.4760 66.500 19.0884 66.500 57.500 57.500 57.5000 SGO_2066 rpmG; ribosomal protein L33 8.500 4.000 0.507 5.531 0.0345 0.2179 15.6713 15.000 12.9801 15.000 11.000 11.000 11.0000 6.5773 SGO_2070 hypothetical protein SGO_2070 3.500 5.000 -0.269 4.253 0.0745 0.5363 5.3447 5.500 5.500 5.5000 8.2216 SGO_2084 NAD(P)H dehydrogenase, quinone family 22.500 19.500 0.571 7.367 0.0003 0.0003 50.1481 48.000 34.3590 48.000 48.500 48.500 48.5000 32.0642 SGO_2085 purB; adenylosuccinate lyase 313.000 224.500 0.377 10.921 0.0072 0.0303 542.7489 519.500 477.9724 519.500 548.500 548.500 548.5000 369.1489 SGO_2098 rpsD; ribosomal protein S4 9.000 6.500 3.516 8.239 0.0002 0.0001 146.7877 140.500 13.7436 140.500 131.000 131.000 131.0000 10.6881 SGO_2100 ABC transporter substrate-binding protein 44.500 26.000 0.230 7.893 0.0562 0.3877 57.4614 55.000 67.9545 55.000 69.500 69.500 69.5000 42.7522 SGO_2104 srtB; sortase B 303.000 291.000 -5.016 9.922 0.0000 0.0000 15.6713 15.000 462.7017 15.000 13.500 13.500 13.5000 478.4959 SGO_2105 abpA; amylase-binding protein AbpA .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.

PAGE 60

Hackett Laboratory UW SgPg vs SgFn Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn SgPgFn vs SgPg Coverage SgPg vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio p -Value SgFn SgPg SgPg Description SgFn 0 2 4 6 -2 -4 -6 SgPg vs SgFn Raw Normalized Log 2 Ratios Page 60 55.500 39.000 -0.334 8.056 0.0167 0.0923 54.3271 52.000 84.7523 52.000 63.000 63.000 63.0000 64.1283 SGO_2106 ribose-phosphate diphosphokinase 121.000 90.000 -0.447 9.169 0.0060 0.0240 121.1913 116.000 184.7753 116.000 121.500 121.500 121.5000 147.9884 SGO_2133 Cell division protein ftsH-like protein 63.500 62.000 -1.405 8.099 0.0001 0.0000 39.1782 37.500 96.9688 37.500 36.000 36.000 36.0000 101.9476 SGO_2134 hpt; hypoxanthine phosphoribosyltransferase 22.000 23.500 1.004 7.762 0.0008 0.0011 76.7893 73.500 33.5955 73.500 68.000 68.000 68.0000 38.6414 SGO_2142 GTP-binding protein 27.500 21.000 -0.325 7.102 0.0081 0.0362 30.8202 29.500 41.9944 29.500 30.000 30.000 30.0000 34.5306 SGO_2150 degP; serine protease .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 713 Dot Plots Dot Plots Hendrickson et al.



PAGE 1

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 1 9.500 10.500 -0.553 5.134 0.0078 0.0292 6.0383 19.000 9.5000 5.000 15.500 6.000 8.2613 11.3062 SGO_0001 dnaA; chromosomal replication initiator protein DnaA 20.000 20.500 -0.780 6.060 0.0016 0.0035 10.8689 30.000 20.0000 9.000 29.000 10.000 13.7688 22.0740 SGO_0002 dnaN; DNA polymerase III, beta subunit 29.500 18.000 -0.356 6.431 0.0274 0.1457 18.1149 36.500 29.5000 15.000 22.500 14.000 19.2764 19.3820 SGO_0004 putative lipoprotein 28.000 19.500 -0.058 6.587 0.1084 0.7696 27.1724 46.000 28.0000 22.500 43.500 14.500 19.9648 20.9972 SGO_0006 ABC transporter, ATP-binding protein 9.000 5.500 1.079 5.516 0.0015 0.0031 15.6996 29.000 9.0000 13.000 30.500 11.000 15.1457 5.9223 SGO_0007 trpS; tryptophanyl-tRNA synthetase 77.000 84.500 0.651 8.752 0.0013 0.0020 127.4082 214.000 77.0000 105.500 208.000 98.500 135.6229 90.9879 SGO_0008 inosine-5'-monophosphate dehydrogenase 3.500 0.038 3.580 0.1191 0.8484 5.4345 6.000 4.500 4.000 2.000 2.7538 3.7687 SGO_0011 proteinase, M16 family 2.500 0.033 2.445 5.500 6.000 2.000 2.7538 2.6919 SGO_0015 ABC transporter (ATP-binding protein) 50.000 45.000 -3.558 6.740 0.0001 0.0000 3.6230 13.000 50.0000 3.000 14.500 3.500 4.8191 48.4551 SGO_0022 trmU; tRNA (5-methylaminomethyl-2thiouridylate)-methyltransferase 3.500 6.500 0.913 4.918 0.0230 0.1173 6.6421 17.500 3.5000 5.500 11.000 9.500 13.0804 6.9991 SGO_0025 gidA; glucose inhibited division protein A 11.000 12.500 0.900 6.144 0.0071 0.0259 18.7187 29.000 11.0000 15.500 32.500 20.000 27.5376 13.4597 SGO_0027 rplI; ribosomal protein L9 2.000 2.500 0.832 3.141 0.0235 0.1219 5.000 2.0000 9.500 3.000 4.1306 2.6919 SGO_0028 dnaC; replicative DNA helicase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 2

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 2 44.500 42.000 -1.462 6.935 0.0001 0.0000 17.5111 30.000 44.5000 14.500 29.000 11.000 15.1457 45.2247 SGO_0030 aspB; aspartate transaminase 9.500 11.000 0.699 5.805 0.0031 0.0086 18.7187 30.500 9.5000 15.500 31.500 11.500 15.8341 11.8446 SGO_0032 plsX; fatty acid/phospholipid synthesis protein PlsX 11.000 9.500 -0.675 4.801 0.0136 0.0616 6.6421 11.500 11.0000 5.500 10.000 10.2294 SGO_0042 transcription regulator, GntR family 59.000 58.000 -2.242 7.201 0.0001 0.0000 13.2843 33.500 59.0000 11.000 39.000 9.000 12.3919 62.4532 SGO_0054 dltA; D-alanine-activating enzyme 17.500 12.000 -0.596 5.653 0.0078 0.0291 10.2651 18.500 17.5000 8.500 18.500 7.000 9.6382 12.9214 SGO_0057 dltD protein 93.500 56.500 4.484 11.789 0.0004 0.0002 1574.7891 1491.000 93.5000 1304.000 1233.500 1313.500 1808.5350 60.8380 SGO_0059 pXO1; hypothetical protein SGO_0059 9.500 11.000 0.350 5.597 0.0071 0.0258 13.2843 15.500 9.5000 11.000 21.500 10.000 13.7688 11.8446 SGO_0063 hypothetical protein SGO_0063 16.000 12.000 0.296 6.006 0.0101 0.0407 18.1149 40.000 16.0000 15.000 55.500 12.500 17.2110 12.9214 SGO_0064 FtsK/SpoIIIE family protein 17.000 19.000 0.118 6.285 0.0397 0.2305 20.5302 34.500 17.0000 17.000 34.000 14.500 19.9648 20.4588 SGO_0065 hypothetical protein SGO_0065 2.500 1.422 4.018 0.0352 0.2001 5.4345 6.500 2.5000 4.500 9.000 6.000 8.2613 SGO_0066 D-3-phosphoglycerate dehydrogenase, putative 5.000 3.500 1.156 4.815 0.0012 0.0019 9.0575 32.000 5.0000 7.500 24.500 7.500 10.3266 3.7687 SGO_0067 protein with prophage function domain 3.500 1.033 4.262 0.0063 0.0223 7.8498 13.500 6.500 15.000 5.500 7.5729 3.7687 SGO_0068 lipoprotein, putative .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 3

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 3 13.500 8.000 0.548 5.745 0.0105 0.0445 15.6996 24.500 13.5000 13.000 22.000 11.500 15.8341 8.6142 SGO_0080 hypothetical protein SGO_0080 2.500 6.500 -0.792 3.575 0.0732 0.4882 2.4153 4.000 2.5000 2.000 5.000 6.9991 SGO_0099 pulA-2; pullulanase, type I 108.000 78.000 -0.282 8.448 0.0219 0.1109 72.4596 100.000 108.0000 60.000 109.000 61.500 84.6783 83.9888 SGO_0104 Maltose/maltodextrin-binding protein precursor 15.000 10.000 -1.140 5.228 0.0045 0.0140 4.8306 16.500 15.0000 4.000 16.000 5.000 6.8844 10.7678 SGO_0105 malQ; 4-alpha-glucanotransferase 84.500 64.000 -0.925 7.869 0.0018 0.0039 40.4566 61.500 84.5000 33.500 62.500 29.000 39.9296 68.9139 SGO_0106 glgP-2; maltodextrin phosphorylase 375.000 321.500 0.441 10.731 0.0011 0.0015 502.9905 838.500 375.0000 416.500 777.000 345.500 475.7129 346.1846 SGO_0113 acdH; alcohol-acetaldehyde dehydrogenase 41.500 29.500 -1.269 6.698 0.0026 0.0068 12.6804 25.500 41.5000 10.500 31.500 13.000 17.8995 31.7650 SGO_0135 v-type sodium ATP synthase, subunit A 35.500 29.500 -0.904 6.696 0.0022 0.0052 15.0958 29.500 35.5000 12.500 36.500 15.500 21.3417 31.7650 SGO_0136 v-type sodium ATP synthase, chain B 21.500 22.000 -1.017 6.088 0.0023 0.0056 13.8881 36.000 21.5000 11.500 35.000 6.500 8.9497 23.6891 SGO_0139 thrC; threonine synthase 41.500 26.500 -1.124 6.669 0.0048 0.0153 14.4919 27.000 41.5000 12.000 30.500 12.500 17.2110 28.5347 SGO_0145 polI; DNA polymerase I 15.000 10.000 -0.812 5.412 0.0355 0.2024 12.6804 16.000 15.0000 10.500 13.000 3.000 4.1306 10.7678 SGO_0146 CoA-binding domain protein 10.500 4.000 -0.818 4.490 0.0268 0.1420 4.2268 14.500 10.5000 3.500 16.500 2.500 3.4422 4.3071 SGO_0152 tgt; queuine tRNA-ribosyltransferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 4 493.000 382.500 -0.961 10.418 0.0014 0.0025 233.0784 307.000 493.0000 193.000 254.000 167.000 229.9394 411.8681 SGO_0154 pgi; glucose-6-phosphate isomerase 70.000 74.500 -0.969 7.832 0.0020 0.0047 45.2873 37.500 70.0000 37.500 46.500 23.500 32.3567 80.2201 SGO_0158 2,3,4,5-tetrahydropyridine-2-carboxylate Nsuccinyltransferase, putative 26.500 22.000 -0.555 6.398 0.0013 0.0022 16.9072 41.000 26.5000 14.000 44.000 12.500 17.2110 23.6891 SGO_0163 galU; UTP-glucose-1-phosphate uridylyltransferase 22.000 26.500 -0.821 6.303 0.0038 0.0111 13.2843 28.000 22.0000 11.000 22.500 11.000 15.1457 28.5347 SGO_0164 Glycerol-3-phosphate dehydrogenase [NAD (P)+] (NAD(P)H-dependent glycerol-3phosphate dehydrogenase) 20.500 13.500 -1.283 5.622 0.0033 0.0094 6.6421 11.500 20.5000 5.500 8.000 5.500 7.5729 14.5365 SGO_0169 dut; dUTP diphosphatase 4.500 -0.576 2.911 3.0192 8.500 4.5000 2.500 12.000 SGO_0171 radA; DNA repair protein RadA 60.000 39.000 -0.073 7.627 0.0875 0.6035 44.6834 94.500 60.0000 37.000 97.500 37.000 50.9446 41.9944 SGO_0174 gltX; glutamyl-tRNA synthetase 6.500 8.500 -0.177 4.949 0.1287 0.9284 4.2268 26.500 6.5000 3.500 15.500 8.000 11.0151 9.1526 SGO_0180 jag; hypothetical protein SGO_0180 4.500 5.000 -0.253 3.809 0.0515 0.3175 3.500 4.5000 4.500 3.000 4.1306 5.3839 SGO_0197 predicted ribosome small subunit-dependent GTPase A 67.000 67.500 -2.236 7.405 0.0002 0.0001 13.2843 32.000 67.0000 11.000 32.000 12.000 16.5226 72.6826 SGO_0198 rpe; ribulose-phosphate 3-epimerase 13.500 13.000 -0.337 5.633 0.0212 0.1059 9.0575 24.500 13.5000 7.500 24.500 9.500 13.0804 13.9981 SGO_0200 competence-induced protein Ccs50 43.000 55.000 -2.387 6.927 0.0016 0.0032 8.4536 26.000 43.0000 7.000 28.500 8.000 11.0151 59.2229 SGO_0201 cmp-binding-factor 1 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 5 39.500 21.500 0.016 6.952 0.1239 0.8855 30.1915 56.500 39.5000 25.000 46.000 22.500 30.9799 23.1508 SGO_0204 rpsL; ribosomal protein S12 92.500 61.500 0.417 8.530 0.0214 0.1072 90.5745 124.000 92.5000 75.000 178.000 87.500 120.4772 66.2219 SGO_0205 rpsG; ribosomal protein S7 652.000 569.500 0.564 11.617 0.0024 0.0061 1010.8117 1277.000 652.0000 837.000 1258.000 627.500 863.9937 613.2259 SGO_0206 fusA; translation elongation factor G 934.000 884.000 0.257 12.020 0.0183 0.0872 1002.3581 1267.000 934.0000 830.000 1330.000 919.500 1266.0433 951.8731 SGO_0207 gap; glyceraldehyde-3-phosphate dehydrogenase, type I 1110.000 949.000 0.252 12.189 0.0031 0.0085 1233.0212 2477.500 1110.0000 1021.000 2836.000 948.000 1305.2845 1021.8637 SGO_0209 pgk; phosphoglycerate kinase 51.500 48.500 -0.579 7.445 0.0059 0.0205 41.6643 70.000 51.5000 34.500 61.500 21.000 28.9145 52.2238 SGO_0215 glnA; glutamine synthetase, type I 29.000 29.000 -0.016 6.905 0.1133 0.8056 31.3992 57.000 29.0000 26.000 59.500 20.500 28.2261 31.2266 SGO_0219 metallo-beta-lactamase superfamily protein 1 6.500 2.500 1.048 4.788 0.0233 0.1196 6.0383 12.500 6.5000 5.000 11.500 9.000 12.3919 2.6919 SGO_0230 Protein of unknown function, DUF536 family 30.500 26.000 -0.964 6.469 0.0008 0.0008 16.3034 35.000 30.5000 13.500 29.500 10.000 13.7688 27.9963 SGO_0234 pepX; X-Pro dipeptidyl-peptidase 4.500 8.000 -0.611 4.436 0.0348 0.1970 3.0192 12.500 4.5000 2.500 14.000 4.000 5.5075 8.6142 SGO_0237 ccpA; CcpA protein (proteinase) 6.500 7.500 -0.226 4.377 0.0612 0.3979 4.500 6.5000 5.000 4.500 6.1960 8.0758 SGO_0243 hydroxymethylglutaryl-CoA reductase, degradative 9.500 6.500 -0.170 4.570 0.0834 0.5695 7.2460 11.500 9.5000 6.000 13.500 6.9991 SGO_0244 hydroxymethylglutaryl-CoA synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 6 223.500 308.500 -0.755 9.779 0.0088 0.0343 165.4495 213.500 223.5000 137.000 237.500 114.500 157.6530 332.1865 SGO_0247 pfl; formate acetyltransferase 5.500 3.500 -0.593 3.619 0.0510 0.3132 3.0192 4.500 5.5000 2.500 2.500 3.7687 SGO_0252 possible TetR-type transcriptional regulator 10.000 7.500 -0.236 5.062 0.0282 0.1521 8.4536 16.000 10.0000 7.000 17.000 5.000 6.8844 8.0758 SGO_0255 Signal peptidase I 3.000 0.355 2.880 3.000 4.1306 3.2303 SGO_0258 hypothetical protein SGO_0258 8.500 11.500 -0.677 5.083 0.0123 0.0543 5.4345 21.500 8.5000 4.500 25.000 5.500 7.5729 12.3830 SGO_0260 DNA mismatch binding protein MutS2 18.000 14.000 -1.445 5.499 0.0010 0.0014 6.6421 30.500 18.0000 5.500 28.500 4.000 5.5075 15.0749 SGO_0262 dipeptidase 14.000 22.000 1.121 6.893 0.0087 0.0340 49.5141 34.500 14.0000 41.000 39.000 23.000 31.6683 23.6891 SGO_0263 trx-1; thioredoxin 13.500 9.000 0.001 5.530 0.1304 0.9477 12.6804 13.000 13.5000 10.500 13.500 7.500 10.3266 9.6910 SGO_0272 hypothetical protein SGO_0272 108.500 82.000 -0.258 8.496 0.0206 0.1025 75.4788 114.000 108.5000 62.500 118.000 64.500 88.8089 88.2959 SGO_0276 gdhA; glutamate dehydrogenase (NADP) 3.500 -0.453 2.705 2.000 2.7538 3.7687 SGO_0286 DNA mismatch repair protein MutS, putative 11.000 9.500 -0.587 5.151 0.0046 0.0146 6.0383 18.500 11.0000 5.000 20.500 6.000 8.2613 10.2294 SGO_0291 copper-translocating P-type ATPase 15.500 16.000 2.555 7.814 0.0003 0.0001 101.4435 120.000 15.5000 84.000 137.500 66.000 90.8742 17.2285 SGO_0292 spxB; pyruvate oxidase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 7 444.000 380.000 -0.222 10.630 0.0039 0.0115 373.1670 441.500 444.0000 309.000 472.500 260.000 357.9894 409.1762 SGO_0312 xfp; D-xylulose 5-phosphate/D-fructose 6phosphate phosphoketolase 23.500 19.500 -0.983 6.071 0.0015 0.0030 9.6613 18.000 23.5000 8.000 23.500 9.500 13.0804 20.9972 SGO_0321 polypeptide deformylase 39.500 24.500 0.362 7.225 0.0310 0.1718 36.2298 55.000 39.5000 30.000 58.500 34.500 47.5024 26.3811 SGO_0333 rpsO; ribosomal protein S15 56.500 47.000 -0.909 7.359 0.0009 0.0010 30.1915 46.000 56.5000 25.000 58.000 19.500 26.8492 50.6086 SGO_0342 pepF-2; oligoendopeptidase 79.000 63.000 -0.313 8.048 0.0061 0.0214 57.9677 85.500 79.0000 48.000 87.000 43.500 59.8944 67.8371 SGO_0344 pnpA; polyribonucleotide nucleotidyltransferase 16.000 22.000 -0.611 6.029 0.0125 0.0552 13.8881 16.500 16.0000 11.500 17.000 8.500 11.7035 23.6891 SGO_0349 cysS; cysteinyl-tRNA synthetase 25.000 24.500 -0.438 6.480 0.0007 0.0007 19.3226 31.500 25.0000 16.000 27.000 13.500 18.5879 26.3811 SGO_0352 ABC transporter, ATP-binding protein SP1580 23.000 22.000 0.214 6.658 0.0091 0.0360 25.3609 46.000 23.0000 21.000 43.000 21.000 28.9145 23.6891 SGO_0357 degV; DegV family fatty acid binding protein 108.500 83.000 -0.100 8.576 0.0520 0.3226 88.1592 117.500 108.5000 73.000 118.000 69.500 95.6933 89.3727 SGO_0358 rplM; ribosomal protein L13 34.500 19.500 0.671 7.145 0.0101 0.0418 39.2490 43.000 34.5000 32.500 48.500 34.000 46.8140 20.9972 SGO_0359 rpsI; ribosomal protein S9 3.000 4.500 -0.659 3.359 0.0554 0.3497 2.4153 3.0000 2.000 4.8455 SGO_0368 merA; mercury(II) reductase 17.000 12.500 -0.919 5.539 0.0025 0.0064 8.4536 15.000 17.0000 7.000 16.000 5.500 7.5729 13.4597 SGO_0372 malate oxidoreductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 8 15.000 17.000 -1.862 5.419 0.0013 0.0022 6.0383 12.000 15.0000 5.000 14.500 2.500 3.4422 18.3053 SGO_0374 Response regulator of the LytR/AlgR family 4.500 6.500 0.048 4.532 0.1293 0.9361 5.4345 6.500 4.5000 4.500 9.500 4.500 6.1960 6.9991 SGO_0384 putative carboxylate-amine/thiol ligase 66.500 46.500 -0.742 7.537 0.0050 0.0165 32.6068 72.000 66.5000 27.000 61.500 26.500 36.4874 50.0702 SGO_0390 glycerol-3-phosphate dehydrogenase (NAD (P)+) 18.500 19.000 -1.550 5.511 0.0113 0.0485 6.6421 13.000 18.5000 5.500 17.500 20.4588 SGO_0392 phosphoglycerate mutase 5.000 7.500 -0.848 4.338 0.0119 0.0517 3.0192 7.500 5.0000 2.500 4.000 3.000 4.1306 8.0758 SGO_0398 ABC transporter ATP-binding protein 16.500 17.500 0.148 6.218 0.0233 0.1210 20.5302 14.500 16.5000 17.000 22.000 13.500 18.5879 18.8436 SGO_0401 grpE; co-chaperone GrpE 492.500 474.000 -0.715 10.656 0.0003 0.0001 295.8768 424.500 492.5000 245.000 473.000 229.000 315.3061 510.3935 SGO_0402 dnaK; DnaK chaperone protein 10.500 11.000 -0.451 5.300 0.0313 0.1735 6.0383 16.000 10.5000 5.000 16.500 8.000 11.0151 11.8446 SGO_0404 dnaJ; DnaJ chaparone protein 61.000 140.500 -4.144 7.766 0.0451 0.2683 5.4345 8.000 61.0000 4.500 7.000 151.2875 SGO_0411 conserved hypothetical protein TIGR01440 216.500 177.000 0.932 10.208 0.0004 0.0003 396.7164 463.000 216.5000 328.500 506.000 275.000 378.6426 190.5900 SGO_0412 tig; trigger factor 25.000 25.500 -0.761 6.382 0.0007 0.0007 15.0958 27.000 25.0000 12.500 44.000 11.500 15.8341 27.4579 SGO_0413 DNA-directed RNA polymerase delta chain 125.500 101.500 -0.050 8.850 0.0760 0.5089 108.0856 184.000 125.5000 89.500 188.500 86.000 118.4119 109.2931 SGO_0415 secA; preprotein translocase, SecA subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 9 35.000 32.000 -1.666 6.527 0.0009 0.0010 14.4919 37.000 35.0000 12.000 27.500 6.000 8.2613 34.4569 SGO_0416 phospho-2-dehydro-3-deoxyheptonate aldolase 9.000 11.000 -1.096 4.682 0.0291 0.1586 4.8306 7.500 9.0000 4.000 6.000 11.8446 SGO_0426 Cof family protein 37.500 42.500 -1.766 6.750 0.0009 0.0012 12.6804 16.000 37.5000 10.500 19.500 8.500 11.7035 45.7631 SGO_0427 universal stress protein family 67.000 66.500 -0.347 7.952 0.0016 0.0034 52.5332 112.500 67.0000 43.500 80.500 41.000 56.4522 71.6058 SGO_0429 aspartate transaminase 5.000 1.572 5.226 0.0121 0.0526 16.9072 31.000 14.000 28.000 11.000 15.1457 5.3839 SGO_0432 entB; isochorismatase family protein 13.000 20.500 -0.338 5.963 0.0483 0.2909 16.3034 23.000 13.0000 13.500 30.500 8.000 11.0151 22.0740 SGO_0434 aspS-2; aspartyl-tRNA synthetase 8.500 8.500 0.120 5.204 0.0298 0.1626 10.2651 12.500 8.5000 8.500 15.000 6.500 8.9497 9.1526 SGO_0435 gatC; glutamyl-tRNA(Gln) amidotransferase, C subunit 46.000 38.500 0.478 7.708 0.0009 0.0010 60.3830 99.500 46.0000 50.000 94.000 44.500 61.2713 41.4560 SGO_0436 gatA; glutamyl-tRNA(Gln) amidotransferase, A subunit 52.000 37.500 0.393 7.762 0.0355 0.2029 78.4979 95.000 52.0000 65.000 113.500 33.500 46.1256 40.3792 SGO_0437 gatB; glutamyl-tRNA(Gln) amidotransferase, B subunit 28.500 30.500 -2.663 6.048 0.0122 0.0534 4.8306 9.000 28.5000 4.000 7.000 32.8418 SGO_0440 L-iditol 2-dehydrogenase BH3949 22.500 19.500 -1.379 5.916 0.0006 0.0005 7.2460 23.000 22.5000 6.000 19.500 7.000 9.6382 20.9972 SGO_0445 GTP-binding protein 12.000 8.500 -2.532 4.521 0.0206 0.1025 1.8115 6.500 12.0000 1.500 6.000 9.1526 SGO_0448 conserved hypothetical protein TIGR00488 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 10

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 10 21.000 28.000 -0.429 6.514 0.0563 0.3573 12.6804 37.500 21.0000 10.500 41.500 20.000 27.5376 30.1498 SGO_0454 conserved hypothetical protein TIGR01033 1.500 1.915 3.733 0.0398 0.2313 4.2268 14.500 1.5000 3.500 17.500 5.500 7.5729 SGO_0455 lipoprotein, putative 13.500 12.500 1.458 6.659 0.0001 0.0000 36.2298 48.500 13.5000 30.000 55.000 27.500 37.8643 13.4597 SGO_0457 ABC transporter, substrate-binding protein SP0148 56.500 37.500 0.958 8.142 0.0015 0.0029 89.9707 128.000 56.5000 74.500 136.500 69.500 95.6933 40.3792 SGO_0458 hlpA; lipoprotein 6.000 6.000 0.308 4.801 0.0014 0.0024 7.8498 13.000 6.0000 6.500 12.000 5.500 7.5729 6.4607 SGO_0460 ABC transporter, ATP-binding protein SP0151 31.000 17.000 -1.669 6.013 0.0058 0.0201 9.0575 11.000 31.0000 7.500 12.500 4.500 6.1960 18.3053 SGO_0468 hypothetical protein SGO_0468 2.000 2.617 4.838 0.0082 0.0313 12.6804 19.500 10.500 17.500 10.000 13.7688 2.1536 SGO_0476 rhodanese family protein 146.500 289.000 -5.955 8.849 0.0388 0.2230 15.000 146.5000 12.500 2.500 3.4422 311.1893 SGO_0480 hypothetical protein SGO_0480 11.000 9.500 0.313 5.573 0.0011 0.0015 13.2843 15.000 11.0000 11.000 23.500 9.500 13.0804 10.2294 SGO_0483 hypothetical protein SGO_0483 138.500 126.500 -6.245 8.111 0.0022 0.0054 1.8115 138.5000 1.500 136.2126 SGO_0497 gtfG; glucosyltransferase G 3.000 2.672 5.473 0.0013 0.0023 20.5302 25.000 17.000 24.500 15.000 20.6532 3.2303 SGO_0501 Uncharacterized ACR, COG1399 44.000 27.000 0.856 7.662 0.0028 0.0076 63.4022 133.000 44.0000 52.500 112.000 48.000 66.0904 29.0730 SGO_0502 floL; flotillin-like protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 11

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 11 545.500 472.000 -0.504 10.811 0.0012 0.0018 388.8666 420.000 545.5000 322.000 465.000 257.500 354.5472 508.2399 SGO_0503 gnd; 6-phosphogluconate dehydrogenase, decarboxylating 42.500 27.000 -0.169 7.069 0.0565 0.3604 28.9838 53.500 42.5000 24.000 69.000 24.500 33.7336 29.0730 SGO_0505 PTS system, IIBC component 8.500 0.116 4.756 0.0856 0.5856 10.2651 11.000 8.5000 8.500 13.000 6.000 8.2613 SGO_0508 nrdR; transcriptional regulator, NrdR family 11.500 7.000 -0.169 5.157 0.0612 0.3971 9.0575 19.000 11.5000 7.500 16.500 5.500 7.5729 7.5375 SGO_0510 dnaI; primosomal protein DnaI 7.000 10.000 -1.090 4.703 0.0072 0.0263 4.8306 6.000 7.0000 4.000 6.000 2.500 3.4422 10.7678 SGO_0511 NADPH-flavin oxidoreductase -like protein 30.000 23.500 0.571 7.105 0.0060 0.0210 45.8911 50.000 30.0000 38.000 53.500 26.500 36.4874 25.3043 SGO_0512 GTP-binding protein engA 66.000 50.500 -0.122 7.853 0.0635 0.4155 48.9102 61.500 66.0000 40.500 64.500 45.000 61.9597 54.3774 SGO_0515 murC; UDP-N-acetylmuramate--alanine ligase 12.500 11.500 1.104 6.297 0.0015 0.0027 24.1532 44.000 12.5000 20.000 43.000 21.500 29.6030 12.3830 SGO_0518 aminodeoxychorismate lyase-like protein 19.500 13.000 0.127 6.121 0.0722 0.4804 17.5111 38.000 19.5000 14.500 31.000 13.500 18.5879 13.9981 SGO_0519 greA; transcription elongation factor greA 7.000 11.500 -1.156 4.798 0.0101 0.0413 3.6230 18.000 7.0000 3.000 15.500 3.500 4.8191 12.3830 SGO_0526 ilvB; acetolactate synthase, large subunit, biosynthetic type 6.000 6.000 -1.592 3.861 0.0089 0.0352 5.500 6.0000 9.000 1.500 2.0653 6.4607 SGO_0527 ilvN; acetolactate synthase, small subunit 77.500 57.000 -0.734 7.797 0.0048 0.0157 47.0988 79.000 77.5000 39.000 72.500 26.500 36.4874 61.3764 SGO_0528 ilvC; ketol-acid reductoisomerase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 12

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 12 4.500 7.000 -0.759 3.952 0.0542 0.3391 5.000 4.5000 7.500 2.500 3.4422 7.5375 SGO_0529 ilvA; threonine dehydratase 4.000 -0.143 2.930 3.6230 6.000 4.0000 3.000 8.500 SGO_0535 putative transcriptional regulator LytR 16.000 13.500 -0.564 5.678 0.0016 0.0033 9.6613 20.500 16.0000 8.000 21.500 8.000 11.0151 14.5365 SGO_0537 HIT family protein 37.000 31.500 -1.234 6.659 0.0004 0.0002 15.6996 25.500 37.0000 13.000 28.000 10.500 14.4573 33.9186 SGO_0540 hypothetical protein SGO_0540 13.500 12.000 0.752 6.151 0.0016 0.0032 20.5302 42.000 13.5000 17.000 43.000 17.500 24.0954 12.9214 SGO_0543 nusA; transcription termination factor NusA 40.500 45.000 -0.168 7.401 0.0612 0.3987 33.2107 77.500 40.5000 27.500 71.500 34.000 46.8140 48.4551 SGO_0546 infB; Translation initiation factor IF-2 2.000 0.714 3.205 0.0101 0.0417 3.6230 8.000 3.000 9.500 2.500 3.4422 2.1536 SGO_0548 Na/Pi-cotransporter family protein 29.500 22.500 -0.957 6.345 0.0017 0.0037 14.4919 22.500 29.5000 12.000 25.000 9.500 13.0804 24.2275 SGO_0552 oxidoreductase, aldo/keto reductase family 12.500 14.500 -1.725 5.015 0.0204 0.1000 4.2268 8.500 12.5000 3.500 12.500 15.6133 SGO_0554 hsdR; type I site-specific deoxyribonuclease 3.000 -0.230 2.581 5.500 3.500 2.000 2.7538 3.2303 SGO_0558 hypothetical protein SGO_0558 1.500 1.553 3.483 0.0247 0.1292 5.4345 11.000 4.500 10.000 3.000 4.1306 1.6152 SGO_0560 hsdM; type I restriction-modification system, M subunit 128.000 95.500 -2.000 8.171 0.0010 0.0013 27.7762 45.500 128.0000 23.000 53.500 21.500 29.6030 102.8324 SGO_0565 adhA; alcohol dehydrogenase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 13

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 13 8.500 4.500 1.101 5.369 0.0073 0.0268 11.4728 24.000 8.5000 9.500 28.500 12.000 16.5226 4.8455 SGO_0568 glyQ; glycyl-tRNA synthetase, alpha subunit 38.000 47.000 -0.089 7.432 0.1037 0.7297 33.8145 67.000 38.0000 28.000 72.000 36.500 50.2562 50.6086 SGO_0569 glyS; glycyl-tRNA synthetase, beta subunit 15.500 8.500 -1.254 5.136 0.0101 0.0414 3.6230 16.000 15.5000 3.000 15.500 5.000 6.8844 9.1526 SGO_0573 mraW; S-adenosyl-methyltransferase MraW 17.500 9.000 0.202 5.854 0.0868 0.5957 12.0766 35.500 17.5000 10.000 32.500 13.500 18.5879 9.6910 SGO_0577 ATP-dependent RNA helicase 3.500 5.500 0.265 4.348 0.0563 0.3569 5.4345 12.500 3.5000 4.500 17.500 4.000 5.5075 5.9223 SGO_0581 trxB; thioredoxin-disulfide reductase 96.000 91.500 -2.174 7.897 0.0002 0.0001 25.9647 47.000 96.0000 21.500 69.500 13.000 17.8995 98.5253 SGO_0582 nicotinate phosphoribosyltransferase, putative 23.000 15.000 -1.580 5.703 0.0027 0.0071 6.0383 14.000 23.0000 5.000 15.500 5.000 6.8844 16.1517 SGO_0583 nadE; NAD+ synthetase 77.500 81.500 -2.349 7.628 0.0004 0.0002 18.1149 36.000 77.5000 15.000 28.000 10.500 14.4573 87.7575 SGO_0585 pepC; aminopeptidase C 20.500 23.500 -0.188 6.424 0.0303 0.1667 18.7187 47.000 20.5000 15.500 39.500 15.500 21.3417 25.3043 SGO_0586 pbp1a; penicillin-binding protein 1A 49.000 29.500 -0.835 6.970 0.0101 0.0417 25.3609 31.500 49.0000 21.000 50.000 14.000 19.2764 31.7650 SGO_0589 methylase 11.000 8.500 -1.470 4.571 0.0188 0.0905 3.6230 10.000 11.0000 3.000 6.500 9.1526 SGO_0590 Methyltransferase 18.500 17.000 -0.626 5.925 0.0013 0.0021 10.8689 25.500 18.5000 9.000 26.500 9.500 13.0804 18.3053 SGO_0591 hypothetical protein SGO_0591 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 14

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 14 7.500 6.000 -0.527 4.232 0.0281 0.1510 4.8306 13.000 7.5000 4.000 14.500 6.4607 SGO_0592 luxS; autoinducer-2 production protein LuxS 9.000 11.000 0.245 5.513 0.0449 0.2657 14.4919 37.500 9.0000 12.000 33.000 7.500 10.3266 11.8446 SGO_0593 HD/KH domain protein 14.500 11.500 -0.918 5.361 0.0014 0.0025 6.6421 11.500 14.5000 5.500 14.500 5.500 7.5729 12.3830 SGO_0594 gmk; Guanylate kinase (GMP kinase) 9.000 6.000 0.632 5.291 0.0054 0.0183 12.6804 22.000 9.0000 10.500 23.500 8.000 11.0151 6.4607 SGO_0595 DNA-directed RNA polymerase, omega subunit 13.000 15.000 -1.613 5.275 0.0013 0.0022 5.4345 14.000 13.0000 4.500 13.000 3.000 4.1306 16.1517 SGO_0597 fmt; methionyl-tRNA formyltransferase 40.500 33.500 -1.901 6.606 0.0006 0.0005 8.4536 18.500 40.5000 7.000 16.500 9.000 12.3919 36.0721 SGO_0599 phosphoprotein phosphatase 14.000 9.500 -1.139 4.891 0.0315 0.1751 5.4345 15.500 14.0000 4.500 13.500 10.2294 SGO_0600 serine/threonine protein kinase 87.000 82.500 -1.487 7.899 0.0001 0.0000 33.2107 54.000 87.0000 27.500 60.000 21.500 29.6030 88.8343 SGO_0604 hydrolase, haloacid dehalogenase family/peptidyl-prolyl cis-trans isomerase, cyclophilin type 52.000 49.500 0.171 7.806 0.0019 0.0043 57.9677 89.000 52.0000 48.000 103.500 44.000 60.5828 53.3006 SGO_0606 cysK; cysteine synthase A 84.000 60.000 -0.637 7.943 0.0136 0.0613 60.3830 84.500 84.0000 50.000 78.500 27.000 37.1758 64.6068 SGO_0610 ribosomal subunit interface protein 3.000 0.009 2.590 3.0192 5.000 3.0000 2.500 7.000 SGO_0626 recX; Regulatory protein recX 2.500 1.630 4.171 0.0136 0.0613 7.2460 28.000 2.5000 6.000 28.000 6.000 8.2613 SGO_0631 alpha-glycerophosphate oxidase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 15

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 15 29.000 32.000 -0.153 6.917 0.0555 0.3511 32.6068 55.500 29.0000 27.000 63.500 18.000 24.7839 34.4569 SGO_0639 valS; valyl-tRNA synthetase 16.000 11.500 -0.612 5.552 0.0071 0.0258 10.2651 22.500 16.0000 8.500 22.000 6.000 8.2613 12.3830 SGO_0641 ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein protein 4.500 8.000 3.073 6.884 0.0005 0.0003 56.1562 15.000 4.5000 46.500 10.500 35.500 48.8793 8.6142 SGO_0642 hypothetical protein SGO_0642 5.500 6.000 -1.303 3.846 0.0181 0.0853 2.4153 3.000 5.5000 2.000 5.000 6.4607 SGO_0643 cytosine-specific methyltransferase 8.000 5.500 0.830 5.269 0.0045 0.0138 10.8689 33.000 8.0000 9.000 24.500 10.000 13.7688 5.9223 SGO_0644 hypothetical protein SGO_0644 2.500 2.000 0.556 3.540 0.0164 0.0761 4.2268 6.500 2.5000 3.500 2.000 2.000 2.7538 2.1536 SGO_0652 hypothetical protein SGO_0652 4.000 1.957 5.141 0.0205 0.1015 17.5111 30.000 4.0000 14.500 38.000 10.000 13.7688 SGO_0654 radical SAM enzyme, Cfr family 8.000 22.500 -1.703 5.379 0.0202 0.0985 6.6421 7.500 8.0000 5.500 6.000 2.000 2.7538 24.2275 SGO_0656 trpB-2; tryptophan synthase, beta subunit 107.500 75.000 0.300 8.721 0.0397 0.2299 139.4848 165.000 107.5000 115.500 200.000 68.500 94.3164 80.7585 SGO_0665 non-heme iron-containing ferritin 38.500 43.000 -0.151 7.331 0.0325 0.1814 36.2298 57.500 38.5000 30.000 60.500 29.000 39.9296 46.3015 SGO_0669 typA; GTP-binding protein TypA 46.500 38.000 -2.380 6.703 0.0004 0.0002 7.8498 31.000 46.5000 6.500 26.000 6.500 8.9497 40.9176 SGO_0671 murD; UDP-N-acetylmuramoylalanine--Dglutamate ligase 14.000 16.500 -3.122 5.069 0.0180 0.0847 1.8115 5.500 14.0000 1.500 15.000 17.7669 SGO_0672 murG; undecaprenyl-PP-MurNAcpentapeptide-UDPGlcNAc GlcNAc transferase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 16

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 16 4.500 7.000 -1.270 3.853 0.0431 0.2539 2.4153 3.500 4.5000 2.000 7.5375 SGO_0673 DivIB; cell division protein DivIB 84.500 74.000 -0.140 8.291 0.0145 0.0659 70.6481 107.500 84.5000 58.500 104.500 57.000 78.4823 79.6817 SGO_0674 ftsA; cell division protein FtsA 155.500 101.000 0.204 9.139 0.0478 0.2859 146.1269 171.500 155.5000 121.000 179.000 111.500 153.5224 108.7547 SGO_0675 ftsZ; cell division protein FtsZ 4.500 8.000 0.182 4.768 0.0997 0.6987 7.2460 10.000 4.5000 6.000 15.000 5.000 6.8844 8.6142 SGO_0676 conserved hypothetical protein TIGR00044 26.500 27.000 -0.046 6.798 0.1359 0.9911 35.0221 37.500 26.5000 29.000 50.000 15.000 20.6532 29.0730 SGO_0677 ylmF protein 55.000 33.000 0.341 7.668 0.0356 0.2039 49.5141 103.000 55.0000 41.000 128.500 46.000 63.3366 35.5337 SGO_0680 cell division protein DivIVA 33.500 31.500 0.551 7.377 0.0007 0.0008 51.3256 106.000 33.5000 42.500 106.500 34.500 47.5024 33.9186 SGO_0681 ileS; isoleucyl-tRNA synthetase 49.000 52.000 -0.924 7.324 0.0010 0.0012 28.3800 25.000 49.0000 23.500 25.500 19.500 26.8492 55.9925 SGO_0684 hypothetical protein SGO_0684 31.000 48.000 -0.832 6.996 0.0118 0.0511 22.9455 48.000 31.0000 19.000 47.000 16.000 22.0301 51.6854 SGO_0688 ATP dependent Clp protease, ATP-binding subunit, ClpE 10.000 18.500 -2.773 4.999 0.0401 0.2338 4.500 10.0000 1.500 1.500 2.0653 19.9204 SGO_0693 xseA; exodeoxyribonuclease VII, large subunit 7.500 4.000 0.210 4.677 0.0820 0.5588 4.8306 14.000 7.5000 4.000 18.000 6.500 8.9497 4.3071 SGO_0700 DegV family protein 705.500 919.000 0.186 11.819 0.0600 0.3839 1085.0828 1475.000 705.5000 898.500 1496.500 605.000 833.0138 989.5603 SGO_0701 hup; DNA-binding histone-like protein HU .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 17

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 17 341.500 278.500 0.940 10.868 0.0004 0.0002 605.6417 559.500 341.5000 501.500 619.500 452.000 622.3508 299.8831 SGO_0704 gpmA; 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 15.000 14.500 -1.667 5.147 0.0054 0.0186 8.000 15.0000 8.000 3.500 4.8191 15.6133 SGO_0706 phoH-like protein 118.500 89.500 -5.080 7.793 0.0006 0.0005 4.8306 6.000 118.5000 4.000 3.000 1.500 2.0653 96.3718 SGO_0707 LPXTG cell wall surface protein 564.500 516.500 -2.330 10.393 0.0001 0.0000 100.8396 162.000 564.5000 83.500 169.000 89.500 123.2310 556.1566 SGO_0708 ald; alanine dehydrogenase 32.500 31.500 -0.925 6.666 0.0007 0.0007 19.3226 32.500 32.5000 16.000 27.000 11.500 15.8341 33.9186 SGO_0713 sgg; GTP-binding protein Era 6.500 6.000 -0.265 4.636 0.1044 0.7373 8.4536 6.000 6.5000 7.000 8.500 2.500 3.4422 6.4607 SGO_0721 abpB-like dipeptidase lipoprotein 12.500 13.000 -2.868 4.823 0.0101 0.0416 1.8115 4.000 12.5000 1.500 6.500 13.9981 SGO_0736 hprK; HPr(Ser) kinase/phosphatase 3.000 1.421 4.361 0.0109 0.0466 9.0575 12.500 7.500 16.000 6.000 8.2613 3.2303 SGO_0739 hypothetical protein SGO_0739 13.000 12.000 -0.616 5.103 0.0023 0.0056 8.4536 14.000 13.0000 7.000 14.500 12.9214 SGO_0742 peptidase, U32 family 9.000 7.000 0.950 5.620 0.0085 0.0330 12.6804 28.000 9.0000 10.500 22.000 14.500 19.9648 7.5375 SGO_0743 peptidase, U32 family 12.000 1.053 6.078 0.0389 0.2241 32.6068 48.500 27.000 56.000 16.000 22.0301 12.9214 SGO_0745 hypothetical protein SGO_0745 30.500 45.000 -1.737 6.673 0.0041 0.0126 12.0766 29.000 30.5000 10.000 26.000 8.000 11.0151 48.4551 SGO_0749 glutathione reductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 18

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 18 6.000 7.000 3.135 7.045 0.0004 0.0002 63.4022 160.000 6.0000 52.500 153.500 40.000 55.0753 7.5375 SGO_0750 efflux transporter, RND family, MFP subunit subfamily 3.500 5.500 3.211 6.554 0.0004 0.0003 45.2873 67.500 3.5000 37.500 54.000 28.500 39.2411 5.9223 SGO_0751 ABC transporter, ATP-binding protein SP0786 50.000 27.500 0.624 7.633 0.0121 0.0526 55.5524 101.500 50.0000 46.000 95.500 46.000 63.3366 29.6114 SGO_0753 lysS; lysyl-tRNA synthetase 4.000 5.500 -0.500 3.740 0.0565 0.3592 8.000 4.0000 12.000 2.500 3.4422 5.9223 SGO_0755 regulatory protein 75.000 80.000 -0.093 8.287 0.0546 0.3434 80.9132 125.500 75.0000 67.000 130.500 51.000 70.2210 86.1424 SGO_0760 ppc; phosphoenolpyruvate carboxylase 1976.000 2103.500 -0.330 12.893 0.0045 0.0138 1702.8011 2246.500 1976.0000 1410.000 2149.500 1207.500 1662.5854 2265.0056 SGO_0761 tuf; translation elongation factor Tu 150.500 181.500 1.303 10.244 0.0054 0.0182 526.5399 581.000 150.5000 436.000 449.500 247.000 340.0899 195.4355 SGO_0762 tpiA; triosephosphate isomerase 24.500 22.000 -0.615 6.340 0.0148 0.0673 21.1341 29.500 24.5000 17.500 35.500 8.500 11.7035 23.6891 SGO_0763 murA-1; UDP-N-acetylglucosamine 1carboxyvinyltransferase 58.500 46.000 -0.658 7.462 0.0020 0.0046 33.8145 73.000 58.5000 28.000 79.500 25.000 34.4221 49.5319 SGO_0771 pepq; proline dipeptidase 42.500 46.500 -0.172 7.448 0.0253 0.1330 38.6451 68.500 42.5000 32.000 61.500 31.500 43.3718 50.0702 SGO_0773 ccpA; catabolite control protein A 6.500 6.500 -0.022 4.332 0.1048 0.7413 6.6421 14.500 6.5000 5.500 10.000 6.9991 SGO_0774 glycosyl transferase, group 1 family protein 7.000 9.500 -0.629 4.816 0.0103 0.0434 5.4345 9.500 7.0000 4.500 13.000 4.000 5.5075 10.2294 SGO_0775 glycosyl transferase, group 1 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 19

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 19 45.500 44.500 0.220 7.659 0.0011 0.0016 54.3447 94.000 45.5000 45.000 103.500 39.500 54.3869 47.9167 SGO_0778 thrS; threonyl-tRNA synthetase 40.500 33.500 -2.878 6.457 0.0005 0.0004 7.8498 23.500 40.5000 6.500 18.000 2.500 3.4422 36.0721 SGO_0779 response regulator 14.500 21.000 -1.232 5.715 0.0055 0.0190 7.8498 24.000 14.5000 6.500 26.000 5.500 7.5729 22.6124 SGO_0784 smc; chromosome segregation protein SMC 2.500 1.427 4.116 0.0282 0.1522 8.4536 14.500 7.000 14.500 4.500 6.1960 2.6919 SGO_0786 Cof family protein 17.500 11.500 -0.232 5.787 0.0490 0.2959 10.8689 29.500 17.5000 9.000 30.500 10.500 14.4573 12.3830 SGO_0787 ftsY; cell division protein FtsY 49.000 60.500 -1.100 7.383 0.0027 0.0071 26.5685 40.000 49.0000 22.000 43.500 19.000 26.1608 65.1452 SGO_0788 zwf; glucose-6-phosphate 1-dehydrogenase 7.000 4.500 1.458 5.456 0.0009 0.0011 16.9072 23.000 7.0000 14.000 18.500 11.000 15.1457 4.8455 SGO_0792 hypothetical protein SGO_0792 28.000 33.500 -0.896 6.619 0.0029 0.0081 16.3034 35.000 28.0000 13.500 39.500 13.000 17.8995 36.0721 SGO_0794 metallo-beta-lactamase family protein 8.500 11.500 -1.539 4.805 0.0031 0.0086 3.6230 9.000 8.5000 3.000 10.000 2.500 3.4422 12.3830 SGO_0795 tributyrin esterase 16.500 16.000 -0.286 5.940 0.0007 0.0007 13.8881 22.500 16.5000 11.500 21.500 10.000 13.7688 17.2285 SGO_0798 ABC transporter, ATP-binding protein SP1381 3.500 3.000 0.330 3.454 0.0202 0.0988 4.2268 7.000 3.5000 3.500 8.500 3.2303 SGO_0800 polysaccharide deacetylase family protein 54.500 47.500 0.123 7.802 0.0693 0.4577 70.6481 111.500 54.5000 58.500 122.500 34.000 46.8140 51.1470 SGO_0801 hom; homoserine dehydrogenase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 20

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 20 16.000 14.500 -0.982 5.582 0.0015 0.0031 6.6421 23.000 16.0000 5.500 24.500 7.000 9.6382 15.6133 SGO_0802 thrB; homoserine kinase 9.000 10.500 0.556 5.645 0.0041 0.0124 13.8881 31.500 9.0000 11.500 28.500 11.500 15.8341 11.3062 SGO_0815 thiI; thiamine biosynthesis protein ThiI 17.500 3.147 8.361 0.0134 0.0601 142.5039 190.500 17.5000 118.000 230.000 122.500 168.6681 SGO_0818 rplU; ribosomal protein L21 15.000 0.734 6.156 0.0515 0.3181 33.8145 35.000 28.000 43.000 15.500 21.3417 16.1517 SGO_0820 rpmA; ribosomal protein L27 22.500 20.500 0.136 6.548 0.0078 0.0297 23.5494 51.500 22.5000 19.500 54.000 18.500 25.4723 22.0740 SGO_0824 lepA; GTP-binding protein LepA 2.000 0.783 2.444 7.000 2.0000 5.000 2.500 3.4422 SGO_0832 hypothetical protein SGO_0832 93.000 86.500 -1.203 8.066 0.0008 0.0008 34.4183 63.500 93.0000 28.500 66.000 34.500 47.5024 93.1414 SGO_0835 nitroreductase 130.500 109.000 -0.820 8.604 0.0015 0.0029 78.4979 130.000 130.5000 65.000 132.000 45.500 62.6481 117.3690 SGO_0836 pepV; dipeptidase PepV 22.500 13.500 -2.356 5.463 0.0027 0.0073 3.6230 3.000 22.5000 3.000 6.000 2.500 3.4422 14.5365 SGO_0842 rhodanese family protein 18.000 10.000 2.122 7.230 0.0005 0.0003 62.7983 82.000 18.0000 52.000 84.000 42.500 58.5175 10.7678 SGO_0848 rpmE; ribosomal protein L31 16.000 11.000 1.997 7.200 0.0101 0.0422 82.7247 48.500 16.0000 68.500 44.500 26.500 36.4874 11.8446 SGO_0850 flavodoxin 33.500 17.000 -2.678 5.896 0.0048 0.0152 3.6230 5.000 33.5000 3.000 7.500 3.000 4.1306 18.3053 SGO_0854 cshA; surface-associated protein CshA .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 21

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 21 5.500 6.500 1.007 5.228 0.0013 0.0022 13.2843 29.000 5.5000 11.000 38.500 8.500 11.7035 6.9991 SGO_0856 ABC transporter, substrate binding protein 29.000 28.500 -1.212 6.420 0.0006 0.0004 11.4728 30.000 29.0000 9.500 28.000 10.500 14.4573 30.6882 SGO_0859 pheS; phenylalanyl-tRNA synthetase, alpha subunit 35.500 40.000 0.878 7.798 0.0013 0.0023 67.6290 103.500 35.5000 56.000 114.000 55.500 76.4170 43.0712 SGO_0861 pheT; phenylalanyl-tRNA synthetase, beta subunit 11.500 7.000 -1.267 4.744 0.0049 0.0163 3.6230 5.500 11.5000 3.000 5.500 3.000 4.1306 7.5375 SGO_0885 cobyric acid synthase 11.500 10.500 -0.291 5.387 0.0344 0.1939 11.4728 24.000 11.5000 9.500 26.500 5.500 7.5729 11.3062 SGO_0889 glmM; phosphoglucosamine mutase 33.000 30.500 -0.251 6.921 0.0001 0.0000 27.7762 40.500 33.0000 23.000 51.500 20.000 27.5376 32.8418 SGO_0893 GTP-binding protein 11.500 12.000 -1.363 5.098 0.0016 0.0033 3.6230 18.000 11.5000 3.000 15.500 4.500 6.1960 12.9214 SGO_0901 DNA-directed DNA polymerase III 56.500 51.000 -1.439 7.258 0.0005 0.0004 17.5111 34.000 56.5000 14.500 35.000 17.500 24.0954 54.9158 SGO_0906 leuA; 2-isopropylmalate synthase 45.000 39.500 -0.121 7.397 0.0554 0.3488 35.6260 75.000 45.0000 29.500 81.000 33.000 45.4371 42.5328 SGO_0911 hypothetical protein SGO_0911 23.000 20.000 -1.336 5.975 0.0016 0.0033 6.6421 19.000 23.0000 5.500 16.000 8.500 11.7035 21.5356 SGO_0946 Deblocking aminopeptidase 5.000 2.500 -0.281 3.421 0.0875 0.6042 3.0192 5.000 5.0000 2.500 6.000 2.6919 SGO_0949 deaD; DEAD RNA helicase 12.000 8.000 -2.074 4.525 0.0255 0.1345 2.4153 6.500 12.0000 2.000 4.000 8.6142 SGO_0950 oxidoreductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 22

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 22 6.500 8.000 -0.146 4.844 0.0608 0.3924 6.0383 9.000 6.5000 5.000 10.500 5.500 7.5729 8.6142 SGO_0951 udk; uridine kinase 13.000 10.000 -0.015 5.584 0.1274 0.9148 9.0575 9.500 13.0000 7.500 18.500 11.000 15.1457 10.7678 SGO_0954 ATP-binding protein 10.000 10.000 -0.924 4.987 0.0004 0.0002 5.4345 19.500 10.0000 4.500 25.500 4.000 5.5075 10.7678 SGO_0982 amino acid ABC transporter, amino acidbinding protein 28.000 25.000 0.076 6.818 0.0052 0.0176 28.9838 32.500 28.0000 24.000 47.000 21.000 28.9145 26.9195 SGO_0987 metK; S-adenosylmethionine synthetase 2.500 3.500 -0.346 3.118 0.0694 0.4602 2.4153 2.5000 2.000 3.000 3.7687 SGO_0993 GTP-binding protein HflX 9.000 12.000 -2.159 4.605 0.0271 0.1436 2.4153 11.500 9.0000 2.000 4.000 12.9214 SGO_0995 metallo-beta-lactamase superfamily protein 33.000 48.500 -0.540 7.161 0.0225 0.1147 24.1532 48.500 33.0000 20.000 62.000 24.500 33.7336 52.2238 SGO_1001 apt; adenine phosphoribosyltransferase 5.000 3.500 0.152 4.203 0.0501 0.3034 4.8306 10.000 5.0000 4.000 8.000 3.500 4.8191 3.7687 SGO_1005 Bcl-2 family protein 115.000 122.500 -0.925 8.563 0.0020 0.0047 55.5524 126.500 115.0000 46.000 121.000 55.000 75.7285 131.9055 SGO_1009 rfbA-1; glucose-1-phosphate thymidylyltransferase 26.000 20.000 0.100 6.619 0.0511 0.3146 25.9647 42.500 26.0000 21.500 34.000 18.000 24.7839 21.5356 SGO_1010 rmlC; dTDP-4-keto-6-deoxyglucose-3,5epimerase 90.500 123.000 -1.735 8.174 0.0028 0.0076 30.7953 73.000 90.5000 25.500 67.000 25.500 35.1105 132.4439 SGO_1011 rfbB-1; dTDP-glucose 4,6-dehydratase 102.500 99.000 -1.048 8.277 0.0001 0.0000 49.5141 98.500 102.5000 41.000 102.000 37.500 51.6331 106.6012 SGO_1012 galE-1; UDP-glucose 4-epimerase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 23

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 23 3.000 1.040 3.303 6.6421 5.500 3.000 3.2303 SGO_1013 Glycosyltransferase involved in cell wall biogenesis 2.500 0.272 2.464 3.0192 6.500 2.5000 2.500 5.500 SGO_1016 putative glycosyltransferase 3.000 -0.835 2.334 1.8115 4.000 1.500 6.000 3.2303 SGO_1019 glycosyl transferase 37.000 37.500 -0.622 6.999 0.0020 0.0046 27.7762 34.000 37.0000 23.000 50.500 16.500 22.7186 40.3792 SGO_1020 rfbD; dTDP-4-dehydrorhamnose reductase 8.500 3.500 0.495 4.844 0.0527 0.3287 10.2651 15.000 8.5000 8.500 20.500 4.500 6.1960 3.7687 SGO_1025 rgp; glycosyltransferase 10.500 13.500 -1.260 5.145 0.0030 0.0084 4.8306 15.000 10.5000 4.000 16.500 4.000 5.5075 14.5365 SGO_1026 rhamnosyltransferase 4.000 4.500 -0.479 3.944 0.0246 0.1287 2.4153 8.000 4.0000 2.000 10.000 3.000 4.1306 4.8455 SGO_1031 cmk; cytidylate kinase 17.500 14.500 -0.273 5.973 0.0937 0.6504 9.0575 17.5000 7.500 15.000 20.6532 15.6133 SGO_1033 rpmI; ribosomal protein L35 79.000 68.000 0.310 8.455 0.0481 0.2893 130.4273 222.000 79.0000 108.000 236.500 49.500 68.1557 73.2210 SGO_1034 rplT; ribosomal protein L20 10.000 10.500 -0.653 5.126 0.0027 0.0070 6.0383 10.500 10.0000 5.000 11.000 5.500 7.5729 11.3062 SGO_1035 gloA; lactoylglutathione lyase 21.000 11.500 -2.060 5.362 0.0045 0.0142 3.6230 8.500 21.0000 3.000 18.500 3.000 4.1306 12.3830 SGO_1036 amino acid ABC transporter, ATP-binding protein SP1242 7.000 4.500 -0.187 4.477 0.0694 0.4605 4.2268 9.500 7.0000 3.500 6.000 4.500 6.1960 4.8455 SGO_1038 uvrB; excinuclease ABC, B subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 24

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 24 1.500 1.697 3.631 0.0356 0.2046 6.6421 15.500 5.500 21.000 3.000 4.1306 1.6152 SGO_1047 hypothetical protein SGO_1047 3.000 -0.230 2.581 3.500 7.000 2.000 2.7538 3.2303 SGO_1050 ribF; riboflavin biosynthesis protein RibF 4.000 3.000 2.447 5.537 0.0001 0.0000 19.9264 22.500 4.0000 16.500 25.000 14.000 19.2764 3.2303 SGO_1059 pstB; Phosphate import ATP-binding protein pstB 1 (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) 7.500 9.500 0.365 5.333 0.0135 0.0606 10.8689 36.500 7.5000 9.000 33.000 8.500 11.7035 10.2294 SGO_1060 phosphate transport system regulatory protein 9.000 6.500 -0.231 4.888 0.0351 0.1995 6.0383 10.500 9.0000 5.000 10.500 5.500 7.5729 6.9991 SGO_1065 hypothetical protein SGO_1065 49.000 46.500 -0.094 7.585 0.0233 0.1204 44.0796 95.000 49.0000 36.500 81.500 35.500 48.8793 50.0702 SGO_1069 membrane alanyl aminopeptidase 20.000 39.500 -1.692 6.333 0.0101 0.0421 8.4536 20.500 20.0000 7.000 27.500 7.000 9.6382 42.5328 SGO_1079 pdp; pyrimidine-nucleoside phosphorylase 37.000 31.500 -0.109 7.094 0.0180 0.0847 32.0030 64.000 37.0000 26.500 61.500 24.500 33.7336 33.9186 SGO_1080 deoC; deoxyribose-phosphate aldolase 443.000 316.500 0.686 11.027 0.0202 0.0984 833.8895 1026.000 443.0000 690.500 1141.000 340.500 468.8284 340.8007 SGO_1082 lipoprotein 41.500 39.500 0.463 7.643 0.0001 0.0000 57.9677 149.500 41.5000 48.000 120.500 42.000 57.8291 42.5328 SGO_1083 sugar ABC transporter, ATP-binding protein SP0846 2269.000 2308.500 -4.048 12.301 0.0002 0.0001 169.0724 295.000 2269.0000 140.000 332.500 88.500 121.8541 2485.7454 SGO_1096 butA; acetoin dehydrogenase 18.500 17.000 -2.043 5.516 0.0001 0.0000 4.8306 9.500 18.5000 4.000 16.500 3.000 4.1306 18.3053 SGO_1098 proA; gamma-glutamyl phosphate reductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 25

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 25 3.000 0.750 3.115 5.4345 4.500 3.2303 SGO_1104 carB; carbamoyl-phosphate synthase, large subunit 1.500 0.770 2.127 5.500 2.000 2.7538 1.6152 SGO_1107 PyrR bifunctional protein 11.500 11.000 1.035 6.157 0.0011 0.0017 25.9647 47.000 11.5000 21.500 52.000 16.000 22.0301 11.8446 SGO_1109 pyrB; aspartate carbamoyltransferase 3.000 3.000 -0.366 3.112 0.0209 0.1038 2.4153 6.500 3.0000 2.000 8.000 3.2303 SGO_1111 fruR; phosphotransferase system repressor 5.000 5.500 -0.983 3.774 0.0214 0.1074 10.000 5.0000 16.000 2.000 2.7538 5.9223 SGO_1112 fruB; 1-phosphofructokinase 30.000 12.500 0.779 6.817 0.0182 0.0864 31.3992 58.000 30.0000 26.000 41.500 27.500 37.8643 13.4597 SGO_1113 fruA; PTS system, fructose specific IIABC components 5.000 2.500 0.299 4.065 0.0612 0.3976 4.2268 15.500 5.0000 3.500 13.500 3.500 4.8191 2.6919 SGO_1114 Protein of unknown function (DUF1149) superfamily 19.500 16.500 -0.021 6.214 0.1274 0.9159 16.3034 39.000 19.5000 13.500 36.500 15.000 20.6532 17.7669 SGO_1116 dapB; dihydrodipicolinate reductase 67.000 78.500 -0.861 7.879 0.0041 0.0122 35.6260 78.000 67.0000 29.500 80.000 35.000 48.1909 84.5272 SGO_1120 guaA; GMP synthase 35.000 29.000 0.048 7.074 0.0814 0.5514 32.0030 57.000 35.0000 26.500 64.000 26.500 36.4874 31.2266 SGO_1123 ffh; signal recognition particle protein 10.500 10.000 -0.410 5.221 0.0013 0.0022 8.4536 12.500 10.5000 7.000 9.500 5.500 7.5729 10.7678 SGO_1129 lplA; lipoate protein ligase A 5.500 6.500 2.087 6.027 0.0001 0.0000 26.5685 48.500 5.5000 22.000 48.000 19.000 26.1608 6.9991 SGO_1130 dihydrolipoamide dehydrogenase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 26

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 26 2.500 1.791 4.327 0.0283 0.1530 7.2460 21.000 2.5000 6.000 19.000 7.500 10.3266 SGO_1131 sucB; dihydrolipoamide S-acetyltransferase 7.000 -0.255 4.367 0.0958 0.6663 4.8306 13.500 4.000 11.500 6.000 8.2613 7.5375 SGO_1133 acoA; acetoin dehydrogenase 9.000 16.500 -2.199 4.884 0.0423 0.2490 2.500 9.0000 2.000 2.7538 17.7669 SGO_1134 hypothetical protein SGO_1134 11.500 10.000 0.176 5.568 0.0074 0.0275 12.0766 29.000 11.5000 10.000 31.500 9.500 13.0804 10.7678 SGO_1139 GTP-binding protein 39.000 40.500 -0.194 7.274 0.0080 0.0304 35.6260 77.500 39.0000 29.500 80.000 26.500 36.4874 43.6096 SGO_1140 clpX; ATP-dependent Clp protease, ATPbinding subunit ClpX 8.500 14.500 -1.932 4.762 0.0407 0.2387 3.0192 7.500 8.5000 2.500 5.500 15.6133 SGO_1141 folA; dihydrofolate reductase 3.500 5.500 0.407 3.951 0.0709 0.4709 6.0383 12.000 3.5000 5.000 13.000 5.9223 SGO_1143 thyA; thymidylate synthase 152.500 157.500 -0.562 9.079 0.0024 0.0060 118.9545 184.000 152.5000 98.500 191.500 72.500 99.8240 169.5928 SGO_1144 glcK; glucokinase 5.500 4.000 -0.014 3.870 0.1271 0.9104 12.500 5.5000 11.500 3.500 4.8191 4.3071 SGO_1150 hypothetical protein SGO_1150 165.000 156.000 -0.674 9.082 0.0002 0.0001 101.4435 165.500 165.0000 84.000 171.500 78.000 107.3968 167.9776 SGO_1151 glyA; serine hydroxymethyltransferase 30.000 12.500 0.396 6.592 0.0614 0.4010 24.7570 33.500 30.0000 20.500 36.500 20.500 28.2261 13.4597 SGO_1154 prfA; peptide chain release factor 1 4.500 2.000 1.283 3.830 0.0310 0.1716 9.000 4.5000 15.500 5.500 7.5729 2.1536 SGO_1155 tdk; thymidine kinase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 27

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 27 13.000 11.000 0.833 6.143 0.0129 0.0571 16.9072 76.000 13.0000 14.000 78.500 21.000 28.9145 11.8446 SGO_1167 nox; NADH oxidase 12.500 7.500 1.302 6.132 0.0011 0.0015 24.7570 44.000 12.5000 20.500 34.500 18.000 24.7839 8.0758 SGO_1169 NADPH-dependent FMN reductase 15.500 12.000 1.328 6.638 0.0006 0.0005 37.4375 60.000 15.5000 31.000 59.000 24.500 33.7336 12.9214 SGO_1170 NADPH-dependent FMN reductase 2.500 0.498 3.270 0.0501 0.3038 3.0192 9.500 2.5000 2.500 7.500 3.000 4.1306 SGO_1185 acetyltransferase, GNAT family 20.000 21.500 -0.877 6.105 0.0154 0.0708 18.1149 12.500 20.0000 15.000 17.500 5.500 7.5729 23.1508 SGO_1189 lipoprotein, putative 178.000 155.500 1.746 10.556 0.0004 0.0002 548.2778 580.500 178.0000 454.000 568.000 444.500 612.0242 167.4392 SGO_1191 rplL; ribosomal protein L7/L12 50.500 68.000 0.112 7.996 0.0872 0.5997 68.2328 141.000 50.5000 56.500 216.500 46.000 63.3366 73.2210 SGO_1192 BL5; 50S ribosomal protein L10 17.000 18.000 -2.230 5.464 0.0004 0.0003 3.6230 22.500 17.0000 3.000 17.500 3.000 4.1306 19.3820 SGO_1193 gid; Glucose inhibited division protein A 9.000 13.000 0.163 5.590 0.0770 0.5164 12.0766 24.000 9.0000 10.000 31.000 9.500 13.0804 13.9981 SGO_1197 topA; DNA topoisomerase I 19.500 22.000 -0.930 6.041 0.0020 0.0048 10.2651 19.000 19.5000 8.500 23.000 9.000 12.3919 23.6891 SGO_1203 anaerobic ribonucleotide reductase 7.500 3.000 -0.368 4.202 0.0507 0.3092 4.2268 5.500 7.5000 3.500 7.500 2.500 3.4422 3.2303 SGO_1205 dapA; dihydrodipicolinate synthase 23.500 24.500 -0.043 6.619 0.0817 0.5556 22.9455 25.500 23.5000 19.000 25.000 18.500 25.4723 26.3811 SGO_1206 asd; aspartate-semialdehyde dehydrogenase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 28

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 28 11.500 14.000 -2.125 4.887 0.0218 0.1097 3.0192 12.500 11.5000 2.500 7.000 15.0749 SGO_1210 fhs-1; formate--tetrahydrofolate ligase 178.000 184.500 -0.753 9.229 0.0009 0.0010 111.7086 243.000 178.0000 92.500 254.500 81.000 111.5275 198.6658 SGO_1215 manB; phosphomannomutase 21.500 17.000 -0.222 6.206 0.0131 0.0582 17.5111 43.000 21.5000 14.500 36.500 12.000 16.5226 18.3053 SGO_1216 bta; Possible bacteriocin transport accessory protein 31.500 60.500 -1.048 7.136 0.0161 0.0745 19.9264 36.000 31.5000 16.500 36.500 17.500 24.0954 65.1452 SGO_1219 pta; phosphate acetyltransferase 23.500 22.500 1.233 7.325 0.0011 0.0015 51.3256 100.500 23.5000 42.500 95.000 44.500 61.2713 24.2275 SGO_1224 Ribose-phosphate pyrophosphokinase 2 4.000 6.000 0.021 4.378 0.1295 0.9390 4.8306 7.000 4.0000 4.000 9.500 4.000 5.5075 6.4607 SGO_1225 pyridoxal-phosphate dependent aminotransferase 10.000 14.500 -0.323 5.511 0.0327 0.1832 9.6613 16.000 10.0000 8.000 18.500 7.500 10.3266 15.6133 SGO_1226 hypothetical protein SGO_1226 35.500 24.000 -1.234 6.445 0.0028 0.0078 12.6804 21.000 35.5000 10.500 37.500 9.500 13.0804 25.8427 SGO_1231 gyrA; DNA gyrase, A subunit 277.000 247.500 0.065 10.119 0.0078 0.0295 282.5925 398.500 277.0000 234.000 402.000 207.500 285.7031 266.5029 SGO_1232 L-lactate dehydrogenase 163.000 112.000 0.997 9.720 0.0011 0.0016 275.9504 368.500 163.0000 228.500 376.000 206.000 283.6378 120.5993 SGO_1234 rpsA; 30S ribosomal protein S1 46.000 26.000 -1.517 6.634 0.0056 0.0194 10.8689 23.500 46.0000 9.000 24.000 10.500 14.4573 27.9963 SGO_1238 ilvE; branched-chain amino acid aminotransferase 2.000 5.000 -0.555 3.569 0.0403 0.2359 2.4153 11.500 2.0000 2.000 13.000 1.500 2.0653 5.3839 SGO_1239 parC; DNA topoisomerase IV, A subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 29

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 29 14.500 27.000 -2.297 5.699 0.0069 0.0249 4.2268 19.000 14.5000 3.500 13.000 3.000 4.1306 29.0730 SGO_1248 pyrC; dihydroorotase 10.000 5.000 0.773 5.347 0.0134 0.0603 10.8689 22.000 10.0000 9.000 25.500 10.500 14.4573 5.3839 SGO_1253 pyrE; orotate phosphoribosyltransferase 18.000 15.500 1.059 6.742 0.0009 0.0010 38.6451 51.000 18.0000 32.000 57.000 24.500 33.7336 16.6901 SGO_1260 deoD; purine nucleoside phosphorylase 22.000 18.500 0.737 6.819 0.0083 0.0316 28.9838 84.000 22.0000 24.000 93.500 30.500 41.9949 19.9204 SGO_1263 purine nucleoside phosphorylase I, inosine and guanosine-specific 149.500 103.000 -0.269 8.897 0.0403 0.2361 91.1784 177.500 149.5000 75.500 175.500 91.000 125.2963 110.9083 SGO_1264 deoB; phosphopentomutase 15.500 15.500 0.802 6.467 0.0014 0.0026 25.9647 48.000 15.5000 21.500 54.000 22.000 30.2914 16.6901 SGO_1265 rpiA; ribose 5-phosphate isomerase 11.000 11.500 -0.405 5.365 0.0117 0.0504 10.2651 18.000 11.0000 8.500 15.000 5.500 7.5729 12.3830 SGO_1266 trmE; tRNA modification GTPase TrmE 27.000 15.500 1.678 7.509 0.0037 0.0108 82.7247 93.000 27.0000 68.500 98.500 40.500 55.7637 16.6901 SGO_1273 rpoD; RNA polymerase sigma factor 8.500 7.000 2.077 6.395 0.0013 0.0021 29.5877 39.000 8.5000 24.500 49.500 28.000 38.5527 7.5375 SGO_1276 rpsU; ribosomal protein S21 1.500 0.770 2.127 7.500 10.500 2.000 2.7538 1.6152 SGO_1281 penicillinase repressor, putative 27.500 19.500 0.708 6.989 0.0018 0.0041 39.2490 77.500 27.5000 32.500 78.000 28.500 39.2411 20.9972 SGO_1283 oxidoreductase 3.500 7.500 0.479 4.727 0.0518 0.3205 6.6421 17.000 3.5000 5.500 7.500 6.000 8.2613 8.0758 SGO_1284 thioredoxin-disulfide reductase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 30

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 30 22.500 24.000 -0.058 6.586 0.1292 0.9336 18.1149 46.500 22.5000 15.000 42.500 21.500 29.6030 25.8427 SGO_1293 asnS; asparaginyl-tRNA synthetase 34.000 22.000 -1.140 6.383 0.0042 0.0127 12.6804 16.500 34.0000 10.500 19.000 9.500 13.0804 23.6891 SGO_1297 aspC; aspartate aminotransferase 40.000 36.000 -0.546 7.056 0.0025 0.0065 30.1915 60.000 40.0000 25.000 60.000 17.500 24.0954 38.7641 SGO_1312 pepT; peptidase T 19.500 15.500 1.425 7.057 0.0003 0.0002 50.1179 39.500 19.5000 41.500 48.000 34.000 46.8140 16.6901 SGO_1323 rpsP; ribosomal protein S16 6.500 6.000 -0.522 4.460 0.0011 0.0014 4.2268 12.000 6.5000 3.500 13.500 3.500 4.8191 6.4607 SGO_1327 HAD-superfamily subfamily IIA hydrolase, TIGR01457 8.500 12.000 -1.119 4.961 0.0062 0.0218 4.2268 13.000 8.5000 3.500 12.000 4.000 5.5075 12.9214 SGO_1336 pcrA; ATP-dependent DNA helicase PcrA 447.500 362.500 0.328 10.883 0.0048 0.0154 548.2778 803.500 447.5000 454.000 882.500 364.500 501.8736 390.3326 SGO_1339 pyk; pyruvate kinase 227.000 228.000 -0.610 9.611 0.0008 0.0008 150.3537 246.000 227.0000 124.500 259.000 115.500 159.0299 245.5057 SGO_1340 Phosphofructokinase 155.000 115.000 -0.690 8.816 0.0033 0.0095 85.7439 128.000 155.0000 71.000 117.500 62.500 86.0551 123.8296 SGO_1342 ABC transporter, ATP-binding protein SP1715 7.000 8.000 -1.496 4.199 0.0205 0.1008 17.500 7.0000 19.000 2.000 2.7538 8.6142 SGO_1364 rumA-2; 23S rRNA (uracil-5-)methyltransferase RumA 11.500 13.000 -2.204 4.820 0.0169 0.0791 4.000 11.5000 2.000 2.000 2.7538 13.9981 SGO_1365 transcription regulator yrfE 72.500 63.000 -4.275 7.170 0.0063 0.0223 3.6230 9.000 72.5000 3.000 11.500 67.8371 SGO_1369 L-2-hydroxyisocaproate dehydrogenase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 31

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 31 21.000 14.500 0.318 6.355 0.0193 0.0935 21.1341 27.500 21.0000 17.500 24.000 17.500 24.0954 15.6133 SGO_1370 Protein of unknown function (DUF964) superfamily 3.000 0.770 3.127 12.000 13.500 4.000 5.5075 3.2303 SGO_1372 aroC; chorismate synthase 4.500 -0.419 3.082 3.6230 6.500 3.000 7.000 4.8455 SGO_1373 aroB; 3-dehydroquinate synthase 5.500 5.500 0.081 4.126 0.0571 0.3649 6.0383 16.000 5.5000 5.000 11.000 5.9223 SGO_1375 aroD; 3-dehydroquinate dehydratase, type I 19.000 17.000 -2.269 5.508 0.0005 0.0004 5.4345 16.500 19.0000 4.500 18.000 2.000 2.7538 18.3053 SGO_1377 sulfatase 14.500 9.500 -0.925 5.231 0.0052 0.0172 6.6421 10.000 14.5000 5.500 16.000 4.500 6.1960 10.2294 SGO_1381 csn1; CRISPR-associated protein, Csn1 family 44.500 51.000 0.716 8.032 0.0013 0.0023 79.1018 102.000 44.5000 65.500 122.000 60.500 83.3014 54.9158 SGO_1383 rplS; ribosomal protein L19 5.000 6.500 -0.176 4.509 0.0817 0.5555 6.6421 8.000 5.0000 5.500 7.000 3.000 4.1306 6.9991 SGO_1390 ligA; DNA ligase, NAD-dependent 15.000 17.500 -0.617 5.803 0.0048 0.0153 10.2651 25.500 15.0000 8.500 21.500 8.500 11.7035 18.8436 SGO_1397 map; methionine aminopeptidase, type I 10.000 7.500 -0.951 4.842 0.0202 0.0980 7.8498 10.000 10.0000 6.500 9.000 2.000 2.7538 8.0758 SGO_1400 murA-2; UDP-N-acetylglucosamine 1carboxyvinyltransferase 6.500 10.000 -0.633 4.814 0.0183 0.0876 6.0383 2.500 6.5000 5.000 3.500 3.500 4.8191 10.7678 SGO_1414 rexB; putative exonuclease RexB 29.500 43.000 -0.947 6.844 0.0101 0.0413 15.6996 17.000 29.5000 13.000 17.000 17.000 23.4070 46.3015 SGO_1422 hypothetical protein SGO_1422 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 32

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 32 2120.500 2216.500 1.167 13.835 0.0002 0.0001 4968.3146 5900.500 2120.5000 4114.000 6433.500 3729.500 5135.0827 2386.6817 SGO_1426 eno; enolase 102.000 79.000 -0.585 8.282 0.0028 0.0076 62.1945 117.500 102.0000 51.500 117.500 45.000 61.9597 85.0656 SGO_1431 EzrA; Septation ring formation regulator ezrA 16.000 16.500 0.058 6.137 0.0965 0.6723 23.5494 31.000 16.0000 19.500 44.500 9.500 13.0804 17.7669 SGO_1432 gyrB; DNA gyrase, B subunit 3.500 2.500 -0.346 3.106 0.0544 0.3410 2.4153 3.500 3.5000 2.000 6.000 2.6919 SGO_1434 thiJ; 4-methyl-5(beta-hydroxyethyl)thiazole monophosphate synthesis protein 7.000 6.000 0.863 5.252 0.0027 0.0072 10.8689 11.000 7.0000 9.000 10.000 10.000 13.7688 6.4607 SGO_1439 ftsX; cell division protein FtsX 42.500 39.500 -1.919 6.748 0.0000 0.0000 11.4728 27.000 42.5000 9.500 30.000 8.000 11.0151 42.5328 SGO_1440 cell-division ATP-binding protein FtsE 14.000 19.000 -0.867 5.769 0.0186 0.0894 13.8881 13.500 14.0000 11.500 22.500 4.500 6.1960 20.4588 SGO_1441 prfB; peptide chain release factor 2 8.500 10.000 -1.806 4.641 0.0016 0.0034 3.6230 18.500 8.5000 3.000 22.000 1.500 2.0653 10.7678 SGO_1446 murF; UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase 13.000 12.000 -0.426 5.499 0.0000 0.0000 9.6613 29.500 13.0000 8.000 25.500 7.000 9.6382 12.9214 SGO_1447 ddlA; D-Ala-D-Ala ligase 6.000 6.500 -0.537 4.565 0.0809 0.5462 2.4153 10.500 6.0000 2.000 7.000 6.000 8.2613 6.9991 SGO_1450 hypothetical protein SGO_1450 17.000 10.500 1.618 6.827 0.0008 0.0008 40.4566 37.000 17.0000 33.500 38.500 32.500 44.7487 11.3062 SGO_1451 frr; ribosome recycling factor 15.000 13.500 0.547 6.184 0.0004 0.0002 21.1341 45.500 15.0000 17.500 32.000 16.000 22.0301 14.5365 SGO_1452 pyrH; uridylate kinase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 33

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 33 2.000 2.151 4.446 0.0325 0.1818 12.0766 11.500 10.000 5.500 7.5729 2.1536 SGO_1453 glycosyl transferase, family 8 SP1766 72.500 70.000 1.180 8.929 0.0033 0.0095 141.9001 208.000 72.5000 117.500 304.000 143.500 197.5826 75.3746 SGO_1455 rplA; ribosomal protein L1 18.500 11.000 1.963 7.189 0.0006 0.0004 54.9485 41.500 18.5000 45.500 61.000 44.000 60.5828 11.8446 SGO_1456 rplK; ribosomal protein L11 13.000 8.000 -2.131 4.587 0.0298 0.1627 2.4153 3.500 13.0000 2.000 2.500 8.6142 SGO_1458 aha1; cation-transporting ATPase yfgQ 3.000 3.000 0.634 3.467 0.0102 0.0427 4.8306 11.000 3.0000 4.000 11.000 3.2303 SGO_1460 DNA translocase ftsK 7.000 4.000 0.702 4.869 0.0085 0.0325 9.6613 16.000 7.0000 8.000 13.500 6.000 8.2613 4.3071 SGO_1463 peptidyl-prolyl cis-trans isomerase 4.500 5.000 1.182 5.013 0.0011 0.0016 12.0766 30.000 4.5000 10.000 24.000 7.500 10.3266 5.3839 SGO_1465 ABC transporter, ATP-binding protein SP0770 19.000 17.000 0.653 6.587 0.0017 0.0038 27.1724 43.000 19.0000 22.500 48.000 23.000 31.6683 18.3053 SGO_1469 glmU; UDP-N-acetylglucosamine pyrophosphorylase 8.500 3.500 -1.454 3.841 0.0537 0.3353 7.500 8.5000 4.000 1.500 2.0653 3.7687 SGO_1472 acetyltransferase, GNAT family 5.000 -0.794 3.441 0.0286 0.1547 2.4153 5.0000 2.000 2.500 3.4422 SGO_1486 beta-galactosidase 32.500 20.000 0.299 6.897 0.0330 0.1849 31.3992 66.000 32.5000 26.000 62.500 24.500 33.7336 21.5356 SGO_1530 methionine-tRNA ligase 9.500 6.000 -0.038 4.984 0.1282 0.9234 6.0383 20.000 9.5000 5.000 17.500 7.000 9.6382 6.4607 SGO_1531 xth; exodeoxyribonuclease III .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 34 8.000 7.000 0.089 4.573 0.0468 0.2795 15.500 8.0000 7.500 6.000 8.2613 7.5375 SGO_1534 ArsC family 6.500 4.000 0.124 4.493 0.0921 0.6369 4.8306 19.000 6.5000 4.000 11.500 5.000 6.8844 4.3071 SGO_1536 conserved hypothetical protein TIGR00096 10.500 6.500 0.463 5.379 0.0278 0.1490 9.6613 15.000 10.5000 8.000 18.500 10.500 14.4573 6.9991 SGO_1539 tmk; thymidylate kinase 18.000 33.500 -1.869 6.097 0.0086 0.0335 5.4345 15.500 18.0000 4.500 16.000 6.500 8.9497 36.0721 SGO_1541 atpC; ATP synthase F1, epsilon subunit 290.500 273.500 -1.641 9.594 0.0001 0.0000 88.1592 134.000 290.5000 73.000 149.500 72.500 99.8240 294.4992 SGO_1542 atpD; ATP synthase F1, beta subunit 41.500 29.500 -2.938 6.372 0.0011 0.0015 5.4345 17.000 41.5000 4.500 17.000 3.000 4.1306 31.7650 SGO_1543 atpG; ATP synthase F1, gamma subunit 125.500 106.000 -0.260 8.780 0.0054 0.0184 95.4052 137.500 125.5000 79.000 151.000 76.000 104.6431 114.1386 SGO_1544 atpA; ATP synthase F1, alpha subunit 33.000 36.500 -2.489 6.412 0.0006 0.0005 6.6421 16.500 33.0000 5.500 17.000 4.500 6.1960 39.3025 SGO_1545 atpH; ATP synthase F1, delta subunit 30.000 12.000 -0.007 6.360 0.1038 0.7314 19.9264 37.000 30.0000 16.500 28.000 14.000 19.2764 12.9214 SGO_1546 atpF; ATP synthase F0, B subunit 25.000 29.000 -0.330 6.657 0.0181 0.0857 19.9264 49.500 25.0000 16.500 48.000 18.000 24.7839 31.2266 SGO_1550 glgP-1; glycogen phosphorylase 25.500 21.000 -1.989 5.919 0.0006 0.0006 4.8306 14.000 25.5000 4.000 8.500 5.500 7.5729 22.6124 SGO_1551 glgA; Glycogen synthase 35.500 27.500 -0.218 6.928 0.0481 0.2886 33.2107 47.000 35.5000 27.500 27.000 17.000 23.4070 29.6114 SGO_1552 glgD; glucose-1-phosphate adenylyltransferase, GlgD subunit .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 35 50.500 32.500 -0.779 7.072 0.0074 0.0272 23.5494 45.000 50.5000 19.500 46.000 18.500 25.4723 34.9953 SGO_1553 glgC; glucose-1-phosphate adenylyltransferase 75.000 59.000 -1.219 7.629 0.0011 0.0015 27.7762 44.500 75.0000 23.000 45.000 23.000 31.6683 63.5300 SGO_1554 glgB; 1,4-alpha-glucan branching enzyme 329.500 296.000 -0.598 10.074 0.0012 0.0019 197.4525 410.000 329.5000 163.500 417.500 168.500 232.0047 318.7267 SGO_1555 ptsI; phosphoenolpyruvate-protein phosphotransferase 515.500 384.500 0.516 11.147 0.0126 0.0555 564.5812 455.500 515.5000 467.500 622.500 561.500 773.1194 414.0217 SGO_1556 phosphocarrier protein HPr 81.000 56.500 -0.735 7.821 0.0049 0.0160 41.6643 64.500 81.0000 34.500 68.000 31.000 42.6834 60.8380 SGO_1558 nrdE; ribonucleoside-diphosphate reductase large chain 24.500 24.000 0.987 7.230 0.0001 0.0000 49.5141 69.000 24.5000 41.000 66.000 36.500 50.2562 25.8427 SGO_1559 ribonucleoside-diphosphate reductase, beta subunit 65.000 43.500 0.260 7.934 0.0345 0.1952 60.3830 139.500 65.0000 50.000 124.500 52.500 72.2863 46.8399 SGO_1570 alaS; alanyl-tRNA synthetase 11.500 5.500 -1.262 4.383 0.0507 0.3099 11.5000 2.500 3.4422 5.9223 SGO_1572 proteinase maturation protein, putative 67.500 54.000 0.145 8.046 0.0233 0.1197 67.0251 123.500 67.5000 55.500 126.500 52.000 71.5979 58.1461 SGO_1574 pepF-1; oligoendopeptidase F 2.000 2.000 1.302 3.866 0.0039 0.0118 4.2268 9.000 2.0000 3.500 8.000 4.500 6.1960 2.1536 SGO_1580 PTS system, Lactose/Cellobiose specific IIB subunit 8.000 10.500 -0.722 4.947 0.0075 0.0278 6.0383 17.500 8.0000 5.000 10.500 4.000 5.5075 11.3062 SGO_1587 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase 40.000 38.500 -2.896 6.530 0.0001 0.0000 5.4345 12.500 40.0000 4.500 8.000 4.000 5.5075 41.4560 SGO_1591 arcC; carbamate kinase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 36 379.500 455.000 -2.763 9.962 0.0010 0.0014 70.6481 74.500 379.5000 58.500 78.000 41.500 57.1406 489.9347 SGO_1592 arcB; ornithine carbamoyltransferase 270.000 229.500 -2.148 9.308 0.0002 0.0001 57.3639 58.000 270.0000 47.500 66.000 43.000 59.2059 247.1209 SGO_1593 arcA; arginine deiminase 298.500 248.500 -1.777 9.514 0.0004 0.0002 88.1592 127.500 298.5000 73.000 144.500 56.000 77.1054 267.5797 SGO_1599 sodA; manganese-dependent superoxide dismutase 6.000 5.500 -1.529 3.806 0.0025 0.0063 6.500 6.0000 5.000 1.500 2.0653 5.9223 SGO_1604 acyltransferase family protein 1.500 1.500 0.408 2.373 0.0156 0.0719 7.000 1.5000 8.500 1.500 2.0653 1.6152 SGO_1605 P-type ATPase, metal cation transport 10.000 8.500 1.265 6.028 0.0008 0.0009 24.7570 37.000 10.0000 20.500 40.500 15.500 21.3417 9.1526 SGO_1609 ATP-dependent RNA helicase, DEAD/DEAH box family 9.500 12.000 -0.349 5.319 0.0224 0.1137 7.8498 11.000 9.5000 6.500 21.000 7.000 9.6382 12.9214 SGO_1617 prfC; peptide chain release factor 3 19.000 18.000 1.145 6.949 0.0009 0.0012 45.8911 73.000 19.0000 38.000 57.000 28.500 39.2411 19.3820 SGO_1619 cation-transporting ATPase, E1-E2 family 6.000 6.500 -1.424 3.946 0.0167 0.0775 2.4153 8.000 6.0000 2.000 9.500 6.9991 SGO_1621 HD domain protein 15.000 12.000 -1.203 5.334 0.0019 0.0044 4.8306 7.000 15.0000 4.000 7.500 5.500 7.5729 12.9214 SGO_1622 Cof family protein 12.500 10.500 -1.129 4.870 0.0131 0.0586 5.4345 12.500 12.5000 4.500 12.500 11.3062 SGO_1623 murM; MurM 10.000 6.000 -0.738 4.411 0.0501 0.3047 6.000 10.0000 5.500 3.500 4.8191 6.4607 SGO_1624 murN; MurN protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 37 30.000 31.000 -1.628 6.398 0.0008 0.0009 12.6804 29.000 30.0000 10.500 28.000 6.000 8.2613 33.3802 SGO_1625 acetoin utilization putative/CBS domain protein 4.500 1.299 4.843 0.0101 0.0412 11.4728 16.000 9.500 20.000 9.000 12.3919 4.8455 SGO_1626 branched-chain amino acid ABC transporter, ATP-binding protein 27.500 22.500 1.649 7.739 0.0001 0.0000 82.7247 162.000 27.5000 68.500 167.000 57.500 79.1707 24.2275 SGO_1630 branched-chain amino acid ABC transporter, amino acid-binding protein 36.500 47.000 -0.833 7.137 0.0239 0.1245 15.0958 22.500 36.5000 12.500 24.500 28.000 38.5527 50.6086 SGO_1632 clpP; ATP-dependent Clp protease, proteolytic subunit ClpP 60.000 43.000 -0.442 7.533 0.0195 0.0946 46.4949 60.000 60.0000 38.500 64.000 23.500 32.3567 46.3015 SGO_1633 upp; uracil phosphoribosyltransferase 62.000 59.500 0.375 8.178 0.0014 0.0026 85.1401 124.500 62.0000 70.500 172.000 57.000 78.4823 64.0684 SGO_1648 ppx1; inorganic pyrophosphatase, manganese-dependent 9.000 8.500 -1.910 4.362 0.0027 0.0073 2.4153 2.500 9.0000 2.000 5.000 9.1526 SGO_1649 act; pyruvate formate-lyase-activating enzyme 10.000 7.500 0.811 5.633 0.0010 0.0012 15.6996 26.500 10.0000 13.000 27.500 11.500 15.8341 8.0758 SGO_1652 intracellular glycosyl hydrolase 20.500 23.000 -0.288 6.406 0.0813 0.5500 12.6804 32.500 20.5000 10.500 35.500 19.500 26.8492 24.7659 SGO_1653 trehalose PTS enzyme II 33.000 30.000 -3.259 6.176 0.0001 0.0000 4.2268 15.500 33.0000 3.500 13.500 2.000 2.7538 32.3034 SGO_1666 trkA; potassium uptake protein, Trk family 15.000 9.000 0.166 5.693 0.0746 0.4987 13.2843 22.500 15.0000 11.000 18.000 10.000 13.7688 9.6910 SGO_1669 ribosomal large subunit pseudouridine synthase B 11.500 13.000 -1.069 5.244 0.0031 0.0088 4.8306 8.500 11.5000 4.000 12.000 5.500 7.5729 13.9981 SGO_1675 HAM1 protein-like protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 38 6.500 5.500 0.048 4.668 0.0972 0.6784 5.4345 14.500 6.5000 4.500 15.500 5.500 7.5729 5.9223 SGO_1676 murI; glutamate racemase 9.000 11.000 -1.774 4.577 0.0233 0.1208 3.0192 10.500 9.0000 2.500 4.000 11.8446 SGO_1678 lysA; diaminopimelate decarboxylase 60.000 48.000 0.929 8.341 0.0012 0.0019 99.0281 198.000 60.0000 82.000 159.500 82.500 113.5928 51.6854 SGO_1679 phosphotransferase system enzyme II 30.500 37.000 0.855 7.626 0.0043 0.0131 55.5524 93.000 30.5000 46.000 95.000 52.000 71.5979 39.8408 SGO_1681 PTS system, mannose/fructose/sorbose family, IID component 44.500 23.500 0.189 7.196 0.0866 0.5936 41.6643 67.000 44.5000 34.500 63.500 25.500 35.1105 25.3043 SGO_1683 serS; seryl-tRNA synthetase 17.500 17.000 1.918 7.432 0.0017 0.0038 79.1018 84.000 17.5000 65.500 83.500 42.000 57.8291 18.3053 SGO_1685 putative peroxidase / antioxidase 28.000 19.500 0.448 6.848 0.0070 0.0253 33.8145 46.500 28.0000 28.000 42.500 23.500 32.3567 20.9972 SGO_1687 accA; acetyl-CoA carboxylase, carboxyl transferase, alpha subunit 14.000 13.000 -1.487 5.254 0.0006 0.0005 6.0383 14.500 14.0000 5.000 15.000 3.000 4.1306 13.9981 SGO_1688 accD; acetyl-CoA carboxylase, carboxyl transferase, beta subunit 38.500 41.000 -0.648 7.080 0.0015 0.0031 27.1724 40.000 38.5000 22.500 45.000 18.500 25.4723 44.1480 SGO_1689 accC; acetyl-CoA carboxylase, biotin carboxylase 6.000 10.500 -0.770 4.468 0.0601 0.3863 4.8306 16.000 6.0000 4.000 24.500 11.3062 SGO_1690 fabZ; beta-hydroxyacyl-(acyl-carrierprotein) dehydratase FabZ 24.500 12.500 0.867 6.712 0.0097 0.0386 28.9838 77.500 24.5000 24.000 74.000 27.500 37.8643 13.4597 SGO_1691 accB; acetyl-CoA carboxylase, biotin carboxyl carrier protein 197.500 213.000 -1.129 9.280 0.0009 0.0011 94.1975 196.000 197.5000 78.000 207.500 73.000 100.5124 229.3540 SGO_1692 3-oxoacyl-[acyl-carrier-protein] synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 39 25.000 24.000 -0.824 6.332 0.0053 0.0180 18.7187 32.500 25.0000 15.500 30.000 8.000 11.0151 25.8427 SGO_1693 fabG; 3-oxoacyl-(acyl-carrier-protein) reductase 12.000 16.000 -0.122 5.819 0.1009 0.7086 16.9072 30.000 12.0000 14.000 39.000 7.500 10.3266 17.2285 SGO_1694 fabD; malonyl CoA-acyl carrier protein transacylase 71.000 73.500 0.295 8.393 0.0233 0.1203 106.8779 212.000 71.0000 88.500 175.000 57.500 79.1707 79.1433 SGO_1695 enoyl-acyl carrier protein(ACP) reductase 11.000 10.500 -1.210 4.762 0.0048 0.0154 13.000 11.0000 10.000 3.500 4.8191 11.3062 SGO_1699 transcriptional regulator, MarR family 55.500 65.000 -4.105 7.012 0.0167 0.0776 3.6230 13.500 55.5000 3.000 13.000 69.9907 SGO_1700 enoyl-CoA hydratase/isomerase family protein 30.000 33.000 -0.419 6.844 0.0121 0.0527 21.1341 49.000 30.0000 17.500 50.500 20.500 28.2261 35.5337 SGO_1701 aspartate kinase 36.500 27.500 0.383 7.250 0.0103 0.0432 39.2490 70.500 36.5000 32.500 82.000 34.000 46.8140 29.6114 SGO_1708 amiF; Oligopeptide transport ATP-binding protein amiF 20.000 22.500 1.303 7.267 0.0024 0.0059 47.0988 83.500 20.0000 39.000 99.500 45.500 62.6481 24.2275 SGO_1709 amiE; Oligopeptide transport ATP-binding protein 10.500 9.000 1.455 6.248 0.0017 0.0038 24.1532 33.500 10.5000 20.000 37.000 23.000 31.6683 9.6910 SGO_1711 hppB; Oligopeptide transport system permease 111.000 65.000 1.154 9.163 0.0016 0.0033 201.6793 243.000 111.0000 167.000 252.500 138.500 190.6982 69.9907 SGO_1712 hppA; oligopeptide-binding lipoprotein 137.500 96.500 0.072 8.945 0.0937 0.6499 122.5775 160.000 137.5000 101.500 157.000 93.500 128.7385 103.9092 SGO_1713 hppG; oligopeptide-binding lipoprotein 51.000 43.000 -0.056 7.577 0.0676 0.4455 44.0796 66.000 51.0000 36.500 73.500 36.000 49.5678 46.3015 SGO_1715 hppH; oligopeptide-binding lipoprotein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 40

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 40 70.000 49.000 0.076 8.001 0.0978 0.6839 85.1401 90.000 70.0000 70.500 86.000 35.000 48.1909 52.7622 SGO_1716 oligopeptide binding protein 11.000 16.000 0.280 5.976 0.0608 0.3913 12.6804 31.500 11.0000 10.500 29.500 16.000 22.0301 17.2285 SGO_1718 sufB-1; FeS assembly protein SufB 24.000 16.500 0.020 6.386 0.1345 0.9787 20.5302 32.500 24.0000 17.000 38.500 15.500 21.3417 17.7669 SGO_1721 sufD; FeS assembly protein SufD 18.000 15.000 -0.613 5.854 0.0224 0.1139 7.8498 19.000 18.0000 6.500 23.000 11.500 15.8341 16.1517 SGO_1722 sufC; FeS assembly ATPase SufC 11.500 7.500 0.683 5.661 0.0048 0.0156 14.4919 22.000 11.5000 12.000 27.500 12.000 16.5226 8.0758 SGO_1727 amino acid ABC transporter, amino acidbinding/permease protein 14.500 14.500 -0.263 5.786 0.0020 0.0047 12.6804 17.000 14.5000 10.500 12.500 9.000 12.3919 15.6133 SGO_1728 glnQ; glutamine ABC transporter ATPbinding protein 97.000 144.000 -3.517 8.099 0.0025 0.0064 13.8881 20.500 97.0000 11.500 27.000 6.000 8.2613 155.0562 SGO_1729 hypothetical protein SGO_1729 163.500 113.000 -1.314 8.639 0.0024 0.0058 54.3447 60.500 163.5000 45.000 86.000 43.000 59.2059 121.6761 SGO_1730 SPFH domain/Band 7 family 2.000 2.500 1.960 4.510 0.0006 0.0004 8.4536 14.500 2.0000 7.000 20.500 7.000 9.6382 2.6919 SGO_1731 DNA-binding response regulator 82.500 59.000 -0.100 8.136 0.0649 0.4266 71.2520 123.500 82.5000 59.000 127.000 46.500 64.0250 63.5300 SGO_1735 hypothetical protein SGO_1735 15.500 9.000 -1.343 4.908 0.0394 0.2279 4.8306 17.000 15.5000 4.000 13.500 9.6910 SGO_1736 alkaline shock protein 422.000 351.000 1.201 11.373 0.0022 0.0053 803.6980 1075.000 422.0000 665.500 1177.500 762.000 1049.1843 377.9496 SGO_1745 fba; fructose-1,6-bisphosphate aldolase, class II .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 41 4.500 -0.419 3.082 3.6230 2.500 3.000 1.500 4.8455 SGO_1747 hypothetical protein SGO_1747 3.500 0.649 3.985 0.0510 0.3132 7.2460 9.500 6.000 16.500 3.500 4.8191 3.7687 SGO_1748 pyrG; CTP synthase 19.500 13.000 -0.950 5.665 0.0052 0.0173 9.6613 21.000 19.5000 8.000 30.000 5.500 7.5729 13.9981 SGO_1749 manA; mannose-6-phosphate isomerase, class I 7.000 6.500 1.260 5.573 0.0006 0.0006 15.6996 42.500 7.0000 13.000 34.500 13.000 17.8995 6.9991 SGO_1755 scrK; fructokinase 38.000 21.500 0.309 7.076 0.0451 0.2675 33.8145 82.000 38.0000 28.000 90.500 29.000 39.9296 23.1508 SGO_1757 glmS; glucosamine--fructose-6-phosphate aminotransferase 21.000 15.000 0.682 6.589 0.0020 0.0048 30.1915 36.000 21.0000 25.000 47.500 21.000 28.9145 16.1517 SGO_1763 ABC transporter, substrate-binding protein SP0092 18.500 16.000 -1.227 5.684 0.0015 0.0028 6.0383 10.500 18.5000 5.000 7.500 7.000 9.6382 17.2285 SGO_1774 alcohol dehydrogenase, zinc-containing 42.500 33.000 0.459 7.530 0.0023 0.0057 53.1371 70.000 42.5000 44.000 66.500 39.000 53.6984 35.5337 SGO_1784 leuS; leucyl-tRNA synthetase 117.500 108.000 -1.307 8.362 0.0004 0.0002 53.1371 80.500 117.5000 44.000 90.000 30.500 41.9949 116.2922 SGO_1799 endopeptidase O 9.000 4.500 2.760 6.705 0.0014 0.0025 51.9294 119.500 9.0000 43.000 90.000 28.000 38.5527 4.8455 SGO_1802 Metal ABC transporter substrate-binding lipoprotein precursor 15.500 12.000 0.366 6.034 0.0255 0.1343 15.0958 29.500 15.5000 12.500 29.500 16.000 22.0301 12.9214 SGO_1803 tpx; thioredoxin peroxidase 1.500 2.406 4.208 0.0435 0.2567 11.4728 38.000 1.5000 9.500 28.000 4.000 5.5075 SGO_1805 hutU; urocanate hydratase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 42 6.000 0.110 4.382 0.1057 0.7490 5.4345 4.000 4.500 3.500 6.500 8.9497 6.4607 SGO_1808 fhs-2; formate--tetrahydrofolate ligase 7.000 -1.453 3.363 7.500 8.000 2.000 2.7538 7.5375 SGO_1811 hutH; histidine ammonia-lyase 17.500 21.000 -2.042 5.490 0.0212 0.1059 4.8306 8.000 17.5000 4.000 8.000 22.6124 SGO_1822 relA; GTP diphosphokinase 6.500 8.500 -0.145 4.892 0.0667 0.4389 7.8498 14.000 6.5000 6.500 15.000 4.500 6.1960 9.1526 SGO_1824 prmA; ribosomal protein L11 methyltransferase 6.000 3.500 -0.466 3.724 0.0639 0.4192 2.500 6.0000 5.500 2.500 3.4422 3.7687 SGO_1828 ATPase, AAA family 116.000 80.500 -1.950 7.992 0.0015 0.0030 27.1724 35.500 116.0000 22.500 21.500 18.000 24.7839 86.6807 SGO_1834 hypothetical protein SGO_1834 9.500 -0.086 4.206 3.500 9.5000 4.000 6.500 8.9497 SGO_1835 hypothetical protein SGO_1835 41.500 37.000 -0.060 7.319 0.0775 0.5213 35.6260 67.000 41.5000 29.500 55.000 31.000 42.6834 39.8408 SGO_1843 pepS; aminopeptidase PepS 6.500 5.000 -0.633 4.302 0.0107 0.0454 3.0192 12.500 6.5000 2.500 11.000 3.500 4.8191 5.3839 SGO_1844 cbxX/cfqX family protein 7.000 12.500 -1.233 4.620 0.0507 0.3100 10.500 7.0000 12.000 3.000 4.1306 13.4597 SGO_1847 polC; DNA polymerase III, alpha subunit, Gram-positive type 69.500 52.500 0.024 7.987 0.1208 0.8624 67.0251 99.500 69.5000 55.500 92.500 44.000 60.5828 56.5309 SGO_1851 proS; prolyl-tRNA synthetase 5.000 6.500 0.638 4.952 0.0188 0.0905 7.2460 16.000 5.0000 6.000 10.000 8.500 11.7035 6.9991 SGO_1854 uppS; undecaprenyl diphosphate synthase .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 43 132.500 65.000 -3.449 7.784 0.0046 0.0145 10.2651 14.000 132.5000 8.500 12.000 5.500 7.5729 69.9907 SGO_1856 ATP-dependent proteinase ATP-binding chain 74.500 39.000 -1.135 7.389 0.0101 0.0407 23.5494 53.000 74.5000 19.500 48.500 20.000 27.5376 41.9944 SGO_1860 5'-nucleotidase, lipoprotein e(P4) family 54.500 59.500 -1.712 7.273 0.0007 0.0007 17.5111 26.500 54.5000 14.500 25.000 13.500 18.5879 64.0684 SGO_1862 alkaline shock protein 27.500 19.000 0.982 7.147 0.0012 0.0019 48.3064 69.000 27.5000 40.000 74.500 33.000 45.4371 20.4588 SGO_1863 efp; Elongation factor P (EF-P) 53.000 51.000 -1.411 7.231 0.0014 0.0026 27.1724 30.000 53.0000 22.500 32.000 11.000 15.1457 54.9158 SGO_1864 X-Pro aminopeptidase 17.500 19.000 -1.295 5.738 0.0008 0.0010 7.8498 17.000 17.5000 6.500 17.500 5.500 7.5729 20.4588 SGO_1865 uvrA; excinuclease ABC, A subunit 3.000 4.500 2.857 5.997 0.0015 0.0030 32.6068 31.500 3.0000 27.000 34.000 17.000 23.4070 4.8455 SGO_1867 hypothetical protein SGO_1867 23.500 28.500 0.347 6.937 0.0108 0.0460 33.2107 46.000 23.5000 27.500 42.000 25.500 35.1105 30.6882 SGO_1879 rpsR; ribosomal protein S18 24.000 22.500 0.803 7.049 0.0001 0.0000 42.8719 76.500 24.0000 35.500 88.500 30.000 41.3065 24.2275 SGO_1880 ssb-1; single-strand binding protein 44.500 65.500 0.957 8.379 0.0031 0.0087 115.3316 214.000 44.5000 95.500 170.000 74.500 102.5777 70.5291 SGO_1881 rpsF; ribosomal protein S6 10.000 6.500 -0.698 4.773 0.0085 0.0331 4.8306 13.500 10.0000 4.000 20.000 4.000 5.5075 6.9991 SGO_1882 folE; GTP cyclohydrolase I 909.500 842.500 -2.954 11.002 0.0000 0.0000 114.1239 200.000 909.5000 94.500 206.500 87.500 120.4772 907.1867 SGO_1885 groL; 60 kDa chaperonin/groEL protein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 44 17.500 38.500 -2.507 6.104 0.0097 0.0386 3.6230 17.000 17.5000 3.000 9.500 4.500 6.1960 41.4560 SGO_1886 groES; chaperonin, 10 kDa 79.000 46.500 -3.155 7.166 0.0025 0.0065 9.0575 11.000 79.0000 7.500 14.500 4.000 5.5075 50.0702 SGO_1892 PTS system, fructose(mannose)-specific IIB 111.500 124.000 -2.385 8.189 0.0006 0.0006 24.7570 53.500 111.5000 20.500 58.000 16.000 22.0301 133.5207 SGO_1898 glutamyl aminopeptidase 10.000 4.500 0.852 5.322 0.0102 0.0424 12.0766 28.000 10.0000 10.000 20.500 9.500 13.0804 4.8455 SGO_1901 tRNA binding domain 51.000 35.500 -0.428 7.280 0.0167 0.0781 28.9838 44.500 51.0000 24.000 50.000 27.000 37.1758 38.2257 SGO_1903 ATP-dependent Zn protease 4.500 4.000 -0.677 3.531 0.0094 0.0372 3.500 4.5000 4.500 2.000 2.7538 4.3071 SGO_1914 folP; dihydropteroate synthase 37.500 36.000 0.227 7.371 0.0018 0.0041 45.8911 70.500 37.5000 38.000 73.000 31.500 43.3718 38.7641 SGO_1916 ackA; acetate kinase 4.000 5.000 0.237 4.345 0.0275 0.1467 5.4345 9.000 4.0000 4.500 7.000 4.000 5.5075 5.3839 SGO_1917 hypothetical protein SGO_1917 146.500 130.500 0.411 9.385 0.0008 0.0009 185.3759 277.000 146.5000 153.500 277.500 142.500 196.2057 140.5197 SGO_1926 rpoC; DNA-directed RNA polymerase, beta chain 141.000 74.500 0.722 9.162 0.0101 0.0410 163.6380 228.000 141.0000 135.500 244.500 136.500 187.9444 80.2201 SGO_1927 rpoB; DNA-directed RNA polymerase, beta subunit 48.000 45.500 0.446 7.843 0.0035 0.0103 60.9868 164.500 48.0000 50.500 147.000 52.000 71.5979 48.9935 SGO_1929 tyrS; tyrosyl-tRNA synthetase 9.000 8.000 0.686 5.528 0.0033 0.0095 12.6804 32.000 9.0000 10.500 30.000 11.500 15.8341 8.6142 SGO_1936 adcA; metal-binding (Mn) permease precursor, lipoprotein .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 45 27.500 21.000 2.689 8.543 0.0006 0.0004 147.9384 350.000 27.5000 122.500 321.500 127.000 174.8641 22.6124 SGO_1958 rplQ; ribosomal protein L17 61.000 66.000 0.308 8.205 0.0048 0.0153 79.7056 125.000 61.0000 66.000 145.000 60.500 83.3014 71.0674 SGO_1959 rpoA; DNA-directed RNA polymerase, alpha subunit 30.500 18.000 0.789 7.066 0.0045 0.0141 43.4758 56.500 30.5000 36.000 66.000 29.500 40.6180 19.3820 SGO_1960 rpsK; ribosomal protein S11 27.000 19.000 1.553 7.536 0.0006 0.0004 65.8175 231.500 27.0000 54.500 216.500 52.500 72.2863 20.4588 SGO_1961 rpsM; ribosomal protein S13p/S18e 47.500 28.000 0.825 7.728 0.0045 0.0139 63.4022 75.500 47.5000 52.500 78.000 51.500 70.9094 30.1498 SGO_1964 adk; Adenylate kinase (ATP-AMP transphosphorylase) 75.000 34.000 0.567 8.065 0.0299 0.1641 69.4405 94.000 75.0000 57.500 160.000 63.000 86.7436 36.6105 SGO_1966 rplO; ribosomal protein L15 13.000 21.500 1.214 6.873 0.0039 0.0118 35.6260 116.000 13.0000 29.500 108.000 33.000 45.4371 23.1508 SGO_1967 50S ribosomal protein L30 -related protein 84.000 58.500 0.822 8.659 0.0017 0.0037 133.4465 263.000 84.0000 110.500 258.000 90.000 123.9194 62.9916 SGO_1968 rpsE; ribosomal protein S5 71.000 41.000 1.746 8.939 0.0006 0.0005 188.9988 270.500 71.0000 156.500 281.000 135.500 186.5676 44.1480 SGO_1969 rplR; ribosomal protein L18 52.000 38.500 1.504 8.491 0.0022 0.0051 152.7690 178.500 52.0000 126.500 180.000 82.500 113.5928 41.4560 SGO_1970 BL10; 50S ribosomal protein L6 79.000 75.500 2.151 9.780 0.0014 0.0024 410.0007 411.500 79.0000 339.500 398.500 224.500 309.1101 81.2969 SGO_1971 rpsH; ribosomal protein S8 60.500 51.000 1.406 8.721 0.0009 0.0011 166.0533 189.500 60.5000 137.500 189.500 102.000 140.4420 54.9158 SGO_1973 BL6; 50S ribosomal protein L5 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 46

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 46 34.500 22.500 1.717 7.964 0.0011 0.0016 86.3477 74.500 34.5000 71.500 85.500 76.000 104.6431 24.2275 SGO_1974 rplX; ribosomal protein L24 40.500 26.000 1.428 7.967 0.0013 0.0021 83.3286 92.500 40.5000 69.000 92.000 71.500 98.4471 27.9963 SGO_1975 rplN; ribosomal protein L14 14.500 18.000 1.596 7.102 0.0038 0.0111 62.1945 121.500 14.5000 51.500 156.000 30.000 41.3065 19.3820 SGO_1976 BS16; 30S ribosomal protein 7.500 0.837 5.125 0.0457 0.2725 10.8689 13.500 7.5000 9.000 18.000 12.000 16.5226 SGO_1977 rpmC; ribosomal protein L29 25.000 20.500 1.151 7.242 0.0002 0.0001 51.3256 110.500 25.0000 42.500 114.500 38.500 53.0100 22.0740 SGO_1978 rplP; ribosomal protein L16 88.500 102.000 0.136 8.699 0.0521 0.3237 99.6320 148.000 88.5000 82.500 147.000 85.500 117.7234 109.8315 SGO_1979 rpsC; ribosomal protein S3 53.500 43.000 1.464 8.550 0.0005 0.0003 130.4273 164.000 53.5000 108.000 164.000 105.000 144.5726 46.3015 SGO_1980 rplV; ribosomal protein L22 64.000 60.500 0.314 8.180 0.0049 0.0163 74.8749 100.000 64.0000 62.000 118.500 62.500 86.0551 65.1452 SGO_1981 rpsS; ribosomal protein S19 78.500 44.500 0.388 8.167 0.0310 0.1712 73.6673 107.000 78.5000 61.000 97.000 63.500 87.4320 47.9167 SGO_1982 rplB; ribosomal protein L2 14.500 31.500 1.224 7.256 0.0069 0.0248 45.8911 91.000 14.5000 38.000 66.500 42.500 58.5175 33.9186 SGO_1983 rplW; ribosomal protein L23 81.500 77.000 1.096 9.013 0.0008 0.0008 164.2418 158.000 81.5000 136.000 184.000 136.500 187.9444 82.9120 SGO_1984 rplD; ribosomal protein L4/L1 family 123.000 85.500 0.693 9.127 0.0024 0.0061 167.8648 223.000 123.0000 139.000 453.000 128.000 176.2409 92.0646 SGO_1985 rplC; ribosomal protein L3 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 47

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 47 19.000 16.000 1.323 6.986 0.0002 0.0001 46.4949 42.500 19.0000 38.500 50.500 32.000 44.0602 17.2285 SGO_1986 rpsJ; ribosomal protein S10 89.500 75.000 0.821 8.880 0.0010 0.0013 141.9001 226.500 89.5000 117.500 216.500 115.500 159.0299 80.7585 SGO_1989 purA; adenylosuccinate synthetase 21.500 25.000 -2.509 5.718 0.0181 0.0858 4.2268 6.000 21.5000 3.500 12.500 26.9195 SGO_1990 glutamate--cysteine ligase, putative/amino acid ligase, putative 7.500 6.000 0.841 5.299 0.0076 0.0285 10.2651 22.500 7.5000 8.500 20.500 11.000 15.1457 6.4607 SGO_1993 possible transcriptional regulator 6.000 10.500 -0.770 4.468 0.0601 0.3863 4.8306 6.0000 4.000 11.3062 SGO_1995 MutT/nudix family protein 17.000 15.500 -0.791 5.739 0.0021 0.0049 11.4728 22.000 17.0000 9.500 31.000 6.000 8.2613 16.6901 SGO_1998 clpB; ATP-dependent Clp proteinase, ATPbinding chain 247.500 199.000 0.356 10.040 0.0060 0.0208 313.9917 437.500 247.5000 260.000 434.000 201.000 276.7534 214.2791 SGO_2000 tsf; translation elongation factor Ts 180.000 200.500 0.316 9.794 0.0097 0.0386 230.6631 347.500 180.0000 191.000 341.500 189.500 260.9192 215.8943 SGO_2001 rpsB; ribosomal protein S2 2.500 1.753 4.401 0.0290 0.1574 10.8689 7.500 9.000 9.000 5.500 7.5729 2.6919 SGO_2005 LPXTG cell wall surface protein 22.500 20.500 -0.365 6.308 0.0012 0.0019 18.1149 25.500 22.5000 15.000 24.000 12.000 16.5226 22.0740 SGO_2007 nusG; transcription termination/antitermination factor NusG 41.000 42.000 -1.704 6.817 0.0004 0.0002 12.0766 26.500 41.0000 10.000 26.500 10.500 14.4573 45.2247 SGO_2033 nrdD; ribonucleoside-triphosphate reductase 35.000 17.500 1.805 7.874 0.0017 0.0037 100.8396 92.500 35.0000 83.500 114.500 58.000 79.8592 18.8436 SGO_2042 Bacterial protein of unknown function (DUF965) superfamily .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 48

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 48 32.000 27.000 3.243 9.321 0.0003 0.0001 306.7457 389.500 32.0000 254.000 426.000 197.500 271.9343 29.0730 SGO_2045 recA; recA protein 7.000 6.000 -1.090 4.310 0.0010 0.0012 3.6230 9.500 7.0000 3.000 9.000 2.000 2.7538 6.4607 SGO_2046 cinA; competence induced protein 9.500 7.500 -0.957 4.735 0.0014 0.0024 4.2268 5.500 9.5000 3.500 9.500 3.500 4.8191 8.0758 SGO_2053 DNA mismatch repair protein hexB 19.000 23.000 -1.765 5.849 0.0027 0.0072 4.2268 12.500 19.0000 3.500 19.000 7.000 9.6382 24.7659 SGO_2056 mutS; DNA mismatch repair protein MutS 152.500 148.500 0.054 9.316 0.0612 0.3967 172.6954 188.000 152.5000 143.000 184.500 110.500 152.1455 159.9018 SGO_2058 argS; arginyl-tRNA synthetase 29.000 33.000 -0.696 6.704 0.0031 0.0087 21.1341 61.500 29.0000 17.500 65.000 13.500 18.5879 35.5337 SGO_2060 aspS-1; aspartyl-tRNA synthetase 80.500 63.500 -0.386 8.038 0.0077 0.0286 61.5907 77.500 80.5000 51.000 71.000 38.000 52.3215 68.3755 SGO_2062 hisS; histidyl-tRNA synthetase 67.000 59.000 0.188 8.126 0.0073 0.0270 77.8941 138.000 67.0000 64.500 125.000 51.500 70.9094 63.5300 SGO_2064 ilvD; dihydroxy-acid dehydratase 12.500 1.390 6.300 0.0278 0.1487 38.0413 66.500 12.5000 31.500 57.500 20.500 28.2261 SGO_2066 rpmG; ribosomal protein L33 8.500 4.000 -0.208 4.559 0.0776 0.5231 6.6421 15.000 8.5000 5.500 11.000 3.000 4.1306 4.3071 SGO_2070 hypothetical protein SGO_2070 22.500 19.500 0.619 6.785 0.0006 0.0006 34.4183 48.000 22.5000 28.500 48.500 23.500 32.3567 20.9972 SGO_2085 purB; adenylosuccinate lyase 313.000 224.500 0.275 10.262 0.0340 0.1914 385.8475 519.500 313.0000 319.500 548.500 208.500 287.0800 241.7370 SGO_2098 rpsD; ribosomal protein S4 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.

PAGE 49

Hackett Laboratory UW Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgPg Coverage SgPgFn vs SgFn Protein Log 2 Sum q -Value Log 2 Ratio SgPgFn vs SgFn p -Value SgFn SgPgFn Raw SgPgFn Normalized Description 0 2 4 6 -2 -4 -6 SgFn Log 2 Ratios SgPgFn vs SgFn Streptococcus gordonii Page 49 9.000 6.500 3.572 7.678 0.0001 0.0000 92.3860 140.500 9.0000 76.500 131.000 70.000 96.3818 6.9991 SGO_2100 ABC transporter substrate-binding protein 44.500 26.000 0.762 7.600 0.0117 0.0501 71.2520 55.000 44.5000 59.000 69.500 36.500 50.2562 27.9963 SGO_2104 srtB; sortase B 303.000 291.000 -4.443 9.332 0.0000 0.0000 13.8881 15.000 303.0000 11.500 13.500 10.500 14.4573 313.3428 SGO_2105 abpA; amylase-binding protein AbpA 55.500 39.000 -0.501 7.373 0.0085 0.0332 33.8145 52.000 55.5000 28.000 63.000 25.000 34.4221 41.9944 SGO_2106 ribose-phosphate diphosphokinase 121.000 90.000 -0.292 8.626 0.0149 0.0680 92.3860 116.000 121.0000 76.500 121.500 61.500 84.6783 96.9102 SGO_2133 Cell division protein ftsH-like protein 63.500 62.000 -1.595 7.444 0.0006 0.0004 25.9647 37.500 63.5000 21.500 36.000 13.000 17.8995 66.7603 SGO_2134 hpt; hypoxanthine phosphoribosyltransferase 22.000 23.500 0.760 6.995 0.0026 0.0067 36.2298 73.500 22.0000 30.000 68.000 32.000 44.0602 25.3043 SGO_2142 GTP-binding protein 27.500 21.000 -1.773 6.029 0.0014 0.0025 9.6613 29.500 27.5000 8.000 30.000 4.000 5.5075 22.6124 SGO_2150 degP; serine protease .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 584 Dot Plots Dot Plots Hendrickson et al.



PAGE 1

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 1 -0.702 5.838 19.8503 19.000 0.0183 0.0240 9.2209 5.000 15.500 6.000 15.5000 12.6156 dnaA; chromosomal replication initiator protein DnaA SGO_0001 -0.691 6.614 31.3426 30.000 0.0067 0.0043 16.5976 9.000 29.000 10.000 29.0000 21.0259 dnaN; DNA polymerase III, beta subunit SGO_0002 -0.038 6.879 38.1335 36.500 0.2009 0.7232 27.6627 15.000 22.500 14.000 22.5000 29.4363 putative lipoprotein SGO_0004 -0.362 7.354 48.0586 46.000 0.0348 0.0653 41.4940 22.500 43.500 14.500 43.5000 30.4876 ABC transporter, ATP-binding protein SGO_0006 -0.368 6.754 30.2978 29.000 0.0012 0.0001 23.9743 13.000 30.500 11.000 30.5000 23.1285 trpS; tryptophanyl-tRNA synthetase SGO_0007 -0.103 9.703 223.5770 214.000 0.0397 0.0811 194.5610 105.500 208.000 98.500 208.0000 207.1055 inosine-5'-monophosphate dehydrogenase SGO_0008 0.238 4.509 6.2685 6.000 0.1464 0.4687 8.2988 4.500 4.000 2.000 4.0000 4.2052 proteinase, M16 family SGO_0011 -0.482 3.996 5.7461 5.500 0.0283 0.0484 6.000 2.000 6.0000 4.2052 ABC transporter (ATP-binding protein) SGO_0015 -1.137 5.357 13.5818 13.000 0.0037 0.0010 5.5325 3.000 14.500 3.500 14.5000 7.3591 trmU; tRNA (5-methylaminomethyl-2thiouridylate)-methyltransferase SGO_0022 0.005 5.892 18.2832 17.500 0.2382 0.9134 10.1430 5.500 11.000 9.500 11.0000 19.9746 gidA; glucose inhibited division protein A SGO_0025 -0.039 3.561 2.6119 2.500 0.2247 0.8413 3.6884 2.000 5.500 5.5000 DHH subfamily 1 protein SGO_0026 0.144 7.060 30.2978 29.000 0.1271 0.3931 28.5848 15.500 32.500 20.000 32.5000 42.0519 rplI; ribosomal protein L9 SGO_0027 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 2

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 2 -0.159 4.394 5.2238 5.000 0.1982 0.7084 9.500 3.000 9.5000 6.3078 dnaC; replicative DNA helicase SGO_0028 -0.278 6.784 31.3426 30.000 0.0184 0.0244 26.7406 14.500 29.000 11.000 29.0000 23.1285 aspB; aspartate transaminase SGO_0030 -0.269 6.860 31.8649 30.500 0.0188 0.0254 28.5848 15.500 31.500 11.500 31.5000 24.1798 plsX; fatty acid/phospholipid synthesis protein PlsX SGO_0032 0.409 5.472 10.4475 10.000 0.0935 0.2631 17.5197 9.500 8.000 4.000 8.0000 8.4104 acpP; acyl carrier protein SGO_0033 -0.112 5.007 12.0147 11.500 0.1627 0.5485 10.1430 5.500 10.000 10.0000 transcription regulator, GntR family SGO_0042 -0.915 6.823 34.9992 33.500 0.0031 0.0007 20.2860 11.000 39.000 9.000 39.0000 18.9233 dltA; D-alanine-activating enzyme SGO_0054 -0.316 6.092 19.3279 18.500 0.0050 0.0020 15.6755 8.500 18.500 7.000 18.5000 14.7182 dltD protein SGO_0057 0.895 12.958 1557.7259 1491.000 0.0058 0.0034 2404.8107 1304.000 1233.500 1313.500 1233.5000 2761.7566 pXO1; hypothetical protein SGO_0059 SGO_0059 0.146 6.304 16.1937 15.500 0.1104 0.3266 20.2860 11.000 21.500 10.000 21.5000 21.0259 hypothetical protein SGO_0063 SGO_0063 -0.837 7.241 41.7901 40.000 0.0120 0.0121 27.6627 15.000 55.500 12.500 55.5000 26.2824 FtsK/SpoIIIE family protein SGO_0064 -0.179 7.043 36.0440 34.500 0.0094 0.0077 31.3511 17.000 34.000 14.500 34.0000 30.4876 hypothetical protein SGO_0065 SGO_0065 0.388 5.198 6.7909 6.500 0.0661 0.1647 8.2988 4.500 9.000 6.000 9.0000 12.6156 D-3-phosphoglycerate dehydrogenase, putative SGO_0066 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 3

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 3 -0.954 6.452 33.4321 32.000 0.0122 0.0126 13.8313 7.500 24.500 7.500 24.5000 15.7695 protein with prophage function domain SGO_0067 -0.305 5.719 14.1042 13.500 0.0051 0.0023 11.9872 6.500 15.000 5.500 15.0000 11.5643 lipoprotein, putative SGO_0068 -0.305 5.023 9.4028 9.000 0.0396 0.0796 8.2988 4.500 8.500 3.000 8.5000 6.3078 hypothetical protein SGO_0069 SGO_0069 0.087 6.244 17.2384 16.500 0.1261 0.3884 21.2081 11.500 19.500 8.500 19.5000 17.8720 merozoite surface protein 1 SGO_0070 0.021 6.581 25.5964 24.500 0.2181 0.8060 23.9743 13.000 22.000 11.500 22.0000 24.1798 hypothetical protein SGO_0080 SGO_0080 -0.310 3.686 4.1790 4.000 0.0956 0.2721 3.6884 2.000 5.000 5.0000 pulA-2; pullulanase, type I SGO_0099 0.165 8.825 104.4752 100.000 0.0450 0.0968 110.6508 60.000 109.000 61.500 109.0000 129.3095 Maltose/maltodextrin-binding protein precursor SGO_0104 -0.915 5.676 17.2384 16.500 0.0067 0.0043 7.3767 4.000 16.000 5.000 16.0000 10.5130 malQ; 4-alpha-glucanotransferase SGO_0105 -0.046 7.963 64.2523 61.500 0.0238 0.0370 61.7800 33.500 62.500 29.000 62.5000 60.9752 glgP-2; maltodextrin phosphorylase SGO_0106 -0.143 11.620 876.0249 838.500 0.0405 0.0836 768.1010 416.500 777.000 345.500 777.0000 726.4461 acdH; alcohol-acetaldehyde dehydrogenase SGO_0113 -0.332 6.712 26.6412 25.500 0.0532 0.1238 19.3639 10.500 31.500 13.000 31.5000 27.3337 v-type sodium ATP synthase, subunit A SGO_0135 -0.291 6.942 30.8202 29.500 0.0664 0.1660 23.0522 12.500 36.500 15.500 36.5000 32.5902 v-type sodium ATP synthase, chain B SGO_0136 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 4

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 4 -1.092 6.748 37.6111 36.000 0.0063 0.0038 21.2081 11.500 35.000 6.500 35.0000 13.6669 thrC; threonine synthase SGO_0139 -0.282 6.743 28.2083 27.000 0.0224 0.0329 22.1302 12.000 30.500 12.500 30.5000 26.2824 polI; DNA polymerase I SGO_0145 -0.416 5.791 16.7160 16.000 0.1828 0.6415 19.3639 10.500 13.000 3.000 13.0000 6.3078 CoA-binding domain protein SGO_0146 -1.441 5.438 15.1489 14.500 0.0019 0.0003 6.4546 3.500 16.500 2.500 16.5000 5.2565 tgt; queuine tRNA-ribosyltransferase SGO_0152 0.309 10.324 320.7390 307.000 0.0256 0.0417 355.9267 193.000 254.000 167.000 254.0000 351.1331 pgi; glucose-6-phosphate isomerase SGO_0154 -0.369 5.181 11.4923 11.000 0.0319 0.0567 7.3767 4.000 9.000 4.000 9.0000 8.4104 hypothetical protein SGO_0156 SGO_0156 0.454 7.674 39.1782 37.500 0.0376 0.0735 69.1567 37.500 46.500 23.500 46.5000 49.4109 2,3,4,5-tetrahydropyridine-2-carboxylate Nsuccinyltransferase, putative SGO_0158 -0.737 7.118 42.8348 41.000 0.0007 0.0000 25.8185 14.000 44.000 12.500 44.0000 26.2824 galU; UTP-glucose-1-phosphate uridylyltransferase SGO_0163 -0.244 6.572 29.2531 28.000 0.0594 0.1433 20.2860 11.000 22.500 11.000 22.5000 23.1285 Glycerol-3-phosphate dehydrogenase [NAD (P)+] (NAD(P)H-dependent glycerol-3phosphate dehydrogenase) SGO_0164 0.144 5.383 12.0147 11.500 0.1609 0.5407 10.1430 5.500 8.000 5.500 8.0000 11.5643 dut; dUTP diphosphatase SGO_0169 -1.163 4.672 8.8804 8.500 0.0664 0.1664 4.6104 2.500 12.000 12.0000 radA; DNA repair protein RadA SGO_0171 -0.429 8.419 98.7291 94.500 0.0055 0.0029 68.2347 37.000 97.500 37.000 97.5000 77.7960 gltX; glutamyl-tRNA synthetase SGO_0174 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 5 -0.991 6.054 27.6859 26.500 0.0521 0.1201 6.4546 3.500 15.500 8.000 15.5000 16.8207 jag; hypothetical protein SGO_0180 SGO_0180 0.512 3.791 2.0895 2.000 0.2040 0.7382 6.500 2.500 6.5000 5.2565 hypothetical protein SGO_0190 SGO_0190 0.637 3.854 3.6566 3.500 0.0520 0.1190 4.500 3.000 4.5000 6.3078 predicted ribosome small subunit-dependent GTPase A SGO_0197 -0.532 6.794 33.4321 32.000 0.0089 0.0068 20.2860 11.000 32.000 12.000 32.0000 25.2311 rpe; ribulose-phosphate 3-epimerase SGO_0198 -0.591 6.391 25.5964 24.500 0.0165 0.0202 13.8313 7.500 24.500 9.500 24.5000 19.9746 competence-induced protein Ccs50 SGO_0200 -0.917 6.416 27.1636 26.000 0.0048 0.0017 12.9093 7.000 28.500 8.000 28.5000 16.8207 cmp-binding-factor 1 SGO_0201 -0.158 7.633 59.0285 56.500 0.0830 0.2217 46.1045 25.000 46.000 22.500 46.0000 47.3084 rpsL; ribosomal protein S12 SGO_0204 0.071 9.299 129.5493 124.000 0.2016 0.7269 138.3135 75.000 178.000 87.500 178.0000 183.9769 rpsG; ribosomal protein S7 SGO_0205 0.140 12.413 1334.1488 1277.000 0.0590 0.1419 1543.5786 837.000 1258.000 627.500 1258.0000 1319.3775 fusA; translation elongation factor G SGO_0206 0.375 12.579 1323.7013 1267.000 0.0248 0.0399 1530.6694 830.000 1330.000 919.500 1330.0000 1933.3348 gap; glyceraldehyde-3-phosphate dehydrogenase, type I SGO_0207 -0.484 13.183 2588.3741 2477.500 0.0050 0.0022 1882.9077 1021.000 2836.000 948.000 2836.0000 1993.2587 pgk; phosphoglycerate kinase SGO_0209 -0.339 7.921 73.1327 70.000 0.0562 0.1327 63.6242 34.500 61.500 21.000 61.5000 44.1545 glnA; glutamine synthetase, type I SGO_0215 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 6 -0.389 7.715 59.5509 57.000 0.0050 0.0021 47.9487 26.000 59.500 20.500 59.5000 43.1032 metallo-beta-lactamase superfamily protein 1 SGO_0219 0.108 5.720 13.0594 12.500 0.1672 0.5724 9.2209 5.000 11.500 9.000 11.5000 18.9233 Protein of unknown function, DUF536 family SGO_0230 -0.102 4.947 5.7461 5.500 0.1775 0.6200 8.2988 4.500 10.500 3.000 10.5000 6.3078 conserved hypothetical protein TIGR00103 SGO_0232 -0.522 6.807 36.5663 35.000 0.0178 0.0227 24.8964 13.500 29.500 10.000 29.5000 21.0259 pepX; X-Pro dipeptidyl-peptidase SGO_0234 -1.119 5.325 13.0594 12.500 0.0099 0.0084 4.6104 2.500 14.000 4.000 14.0000 8.4104 ccpA; CcpA protein (proteinase) SGO_0237 0.965 4.260 4.7014 4.500 0.0166 0.0206 5.000 4.500 5.0000 9.4617 hydroxymethylglutaryl-CoA reductase, degradative SGO_0243 -0.203 5.193 12.0147 11.500 0.0935 0.2633 11.0651 6.000 13.500 13.5000 hydroxymethylglutaryl-CoA synthase SGO_0244 0.100 9.898 223.0546 213.500 0.0316 0.0559 252.6527 137.000 237.500 114.500 237.5000 240.7470 pfl; formate acetyltransferase SGO_0247 0.427 3.562 4.7014 4.500 0.1586 0.5274 4.6104 2.500 2.500 2.5000 possible TetR-type transcriptional regulator SGO_0252 -0.533 5.836 16.7160 16.000 0.0073 0.0051 12.9093 7.000 17.000 5.000 17.0000 10.5130 Signal peptidase I SGO_0255 -1.274 6.073 22.4622 21.500 0.0045 0.0014 8.2988 4.500 25.000 5.500 25.0000 11.5643 DNA mismatch binding protein MutS2 SGO_0260 -1.706 6.302 31.8649 30.500 0.0019 0.0003 10.1430 5.500 28.500 4.000 28.5000 8.4104 dipeptidase SGO_0262 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 7 0.690 7.637 36.0440 34.500 0.0306 0.0536 75.6114 41.000 39.000 23.000 39.0000 48.3597 trx-1; thioredoxin SGO_0263 0.368 5.959 13.5818 13.000 0.0212 0.0303 19.3639 10.500 13.500 7.500 13.5000 15.7695 hypothetical protein SGO_0272 SGO_0272 0.077 8.931 119.1018 114.000 0.1104 0.3263 115.2612 62.500 118.000 64.500 118.0000 135.6173 gdhA; glutamate dehydrogenase (NADP) SGO_0276 0.001 4.065 4.7014 4.500 0.2458 0.9518 5.5325 3.000 6.500 6.5000 copper -translocating P-type ATPase SGO_0290 -0.884 5.946 19.3279 18.500 0.0057 0.0032 9.2209 5.000 20.500 6.000 20.5000 12.6156 copper-translocating P-type ATPase SGO_0291 0.159 9.120 125.3703 120.000 0.0391 0.0774 154.9111 84.000 137.500 66.000 137.5000 138.7712 spxB; pyruvate oxidase SGO_0292 0.258 11.002 461.2582 441.500 0.0042 0.0012 569.8516 309.000 472.500 260.000 472.5000 546.6743 xfp; D-xylulose 5-phosphate/D-fructose 6phosphate phosphoketolase SGO_0312 -0.292 6.267 18.8055 18.000 0.0650 0.1584 14.7534 8.000 23.500 9.500 23.5000 19.9746 polypeptide deformylase SGO_0321 0.128 7.930 57.4614 55.000 0.1089 0.3178 55.3254 30.000 58.500 34.500 58.5000 72.5395 rpsO; ribosomal protein S15 SGO_0333 -0.280 7.594 48.0586 46.000 0.0330 0.0606 46.1045 25.000 58.000 19.500 58.0000 41.0006 pepF-2; oligoendopeptidase SGO_0342 0.030 8.477 89.3263 85.500 0.0735 0.1898 88.5206 48.000 87.000 43.500 87.0000 91.4628 pnpA; polyribonucleotide nucleotidyltransferase SGO_0344 0.186 6.196 17.2384 16.500 0.0419 0.0871 21.2081 11.500 17.000 8.500 17.0000 17.8720 cysS; cysteinyl-tRNA synthetase SGO_0349 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 8 -0.043 6.880 32.9097 31.500 0.1733 0.6020 29.5069 16.000 27.000 13.500 27.0000 28.3850 ABC transporter, ATP-binding protein SP1580 SGO_0352 -0.137 7.442 48.0586 46.000 0.0627 0.1523 38.7278 21.000 43.000 21.000 43.0000 44.1545 degV; DegV family fatty acid binding protein SGO_0357 0.221 9.027 122.7584 117.500 0.0116 0.0115 134.6251 73.000 118.000 69.500 118.0000 146.1303 rplM; ribosomal protein L13 SGO_0358 0.488 7.813 44.9244 43.000 0.0120 0.0122 59.9358 32.500 48.500 34.000 48.5000 71.4882 rpsI; ribosomal protein S9 SGO_0359 -0.374 5.811 15.6713 15.000 0.0055 0.0029 12.9093 7.000 16.000 5.500 16.0000 11.5643 malate oxidoreductase SGO_0372 -0.954 5.376 12.5370 12.000 0.0145 0.0161 9.2209 5.000 14.500 2.500 14.5000 5.2565 Response regulator of the LytR/AlgR family SGO_0374 0.142 5.090 6.7909 6.500 0.1416 0.4514 8.2988 4.500 9.500 4.500 9.5000 9.4617 putative carboxylate-amine/thiol ligase SGO_0384 -0.369 7.920 75.2222 72.000 0.0236 0.0363 49.7929 27.000 61.500 26.500 61.5000 55.7187 glycerol-3-phosphate dehydrogenase (NAD (P)+) SGO_0390 -0.604 5.365 13.5818 13.000 0.0830 0.2216 10.1430 5.500 17.500 17.5000 phosphoglycerate mutase SGO_0392 -0.054 4.508 7.8356 7.500 0.2021 0.7300 4.6104 2.500 4.000 3.000 4.0000 6.3078 ABC transporter ATP-binding protein SGO_0398 0.708 6.598 15.1489 14.500 0.0127 0.0135 31.3511 17.000 22.000 13.500 22.0000 28.3850 grpE; co-chaperone GrpE SGO_0401 0.026 10.853 443.4974 424.500 0.1603 0.5363 451.8241 245.000 473.000 229.000 473.0000 481.4939 dnaK; DnaK chaperone protein SGO_0402 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 9 -0.415 5.889 16.7160 16.000 0.0769 0.2007 9.2209 5.000 16.500 8.000 16.5000 16.8207 dnaJ; DnaJ chaparone protein SGO_0404 0.118 4.564 8.3580 8.000 0.1587 0.5290 8.2988 4.500 7.000 7.0000 conserved hypothetical protein TIGR01440 SGO_0411 0.259 11.086 483.7204 463.000 0.0051 0.0025 605.8131 328.500 506.000 275.000 506.0000 578.2132 tig; trigger factor SGO_0412 -0.577 6.900 28.2083 27.000 0.0368 0.0718 23.0522 12.500 44.000 11.500 44.0000 24.1798 DNA-directed RNA polymerase delta chain SGO_0413 -0.140 9.505 192.2344 184.000 0.0226 0.0337 165.0541 89.500 188.500 86.000 188.5000 180.8230 secA; preprotein translocase, SecA subunit SGO_0415 -0.964 6.657 38.6558 37.000 0.0227 0.0340 22.1302 12.000 27.500 6.000 27.5000 12.6156 phospho-2-dehydro-3-deoxyheptonate aldolase SGO_0416 0.105 4.407 7.8356 7.500 0.1979 0.7048 7.3767 4.000 6.000 6.0000 Cof family protein SGO_0426 0.043 6.199 16.7160 16.000 0.1767 0.6150 19.3639 10.500 19.500 8.500 19.5000 17.8720 universal stress protein family SGO_0427 -0.226 8.510 117.5346 112.500 0.0878 0.2406 80.2218 43.500 80.500 41.000 80.5000 86.2063 aspartate transaminase SGO_0429 -0.301 6.773 32.3873 31.000 0.0214 0.0309 25.8185 14.000 28.000 11.000 28.0000 23.1285 entB; isochorismatase family protein SGO_0432 -0.404 6.589 24.0293 23.000 0.0524 0.1213 24.8964 13.500 30.500 8.000 30.5000 16.8207 aspS-2; aspartyl-tRNA synthetase SGO_0434 0.065 5.843 13.0594 12.500 0.1504 0.4844 15.6755 8.500 15.000 6.500 15.0000 13.6669 gatC; glutamyl-tRNA(Gln) amidotransferase, C subunit SGO_0435 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 10 -0.090 8.584 103.9529 99.500 0.0541 0.1266 92.2090 50.000 94.000 44.500 94.0000 93.5654 gatA; glutamyl-tRNA(Gln) amidotransferase, A subunit SGO_0436 -0.208 8.655 99.2515 95.000 0.1558 0.5048 119.8717 65.000 113.500 33.500 113.5000 70.4369 gatB; glutamyl-tRNA(Gln) amidotransferase, B subunit SGO_0437 -0.137 4.572 9.4028 9.000 0.1770 0.6170 7.3767 4.000 7.000 7.0000 L-iditol 2-dehydrogenase BH3949 SGO_0440 -0.762 6.115 24.0293 23.000 0.0125 0.0132 11.0651 6.000 19.500 7.000 19.5000 14.7182 GTP-binding protein SGO_0445 -1.206 3.960 6.7909 6.500 0.0358 0.0691 2.7663 1.500 6.000 6.0000 conserved hypothetical protein TIGR00488 SGO_0448 -0.499 7.151 39.1782 37.500 0.0878 0.2397 19.3639 10.500 41.500 20.000 41.5000 42.0519 conserved hypothetical protein TIGR01033 SGO_0454 -0.914 5.663 15.1489 14.500 0.0166 0.0204 6.4546 3.500 17.500 5.500 17.5000 11.5643 lipoprotein, putative SGO_0455 0.099 7.774 50.6705 48.500 0.0397 0.0810 55.3254 30.000 55.000 27.500 55.0000 57.8213 ABC transporter, substrate-binding protein SP0148 SGO_0457 0.069 9.113 133.7283 128.000 0.0419 0.0868 137.3914 74.500 136.500 69.500 136.5000 146.1303 hlpA; lipoprotein SGO_0458 -0.117 5.619 13.5818 13.000 0.0524 0.1210 11.9872 6.500 12.000 5.500 12.0000 11.5643 ABC transporter, ATP-binding protein SP0151 SGO_0460 -0.067 5.563 11.4923 11.000 0.2181 0.8046 13.8313 7.500 12.500 4.500 12.5000 9.4617 hypothetical protein SGO_0468 SGO_0468 0.096 6.290 20.3727 19.500 0.0979 0.2804 19.3639 10.500 17.500 10.000 17.5000 21.0259 rhodanese family protein SGO_0476 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 11 -1.413 5.063 15.6713 15.000 0.0499 0.1131 12.500 2.500 12.5000 5.2565 hypothetical protein SGO_0480 SGO_0480 0.069 6.312 15.6713 15.000 0.2214 0.8252 20.2860 11.000 23.500 9.500 23.5000 19.9746 hypothetical protein SGO_0483 SGO_0483 0.314 6.827 26.1188 25.000 0.0037 0.0010 31.3511 17.000 24.500 15.000 24.5000 31.5389 Uncharacterized ACR, COG1399 SGO_0501 -0.336 8.810 138.9521 133.000 0.0263 0.0431 96.8194 52.500 112.000 48.000 112.0000 100.9245 floL; flotillin-like protein SGO_0502 0.328 10.994 438.7960 420.000 0.0086 0.0064 593.8260 322.000 465.000 257.500 465.0000 541.4178 gnd; 6-phosphogluconate dehydrogenase, decarboxylating SGO_0503 -0.379 7.786 55.8943 53.500 0.0264 0.0435 44.2603 24.000 69.000 24.500 69.0000 51.5135 PTS system, IIBC component SGO_0505 0.202 5.722 11.4923 11.000 0.0616 0.1493 15.6755 8.500 13.000 6.000 13.0000 12.6156 nrdR; transcriptional regulator, NrdR family SGO_0508 -0.517 5.948 19.8503 19.000 0.0158 0.0183 13.8313 7.500 16.500 5.500 16.5000 11.5643 dnaI; primosomal protein DnaI SGO_0510 0.022 4.638 6.2685 6.000 0.2139 0.7868 7.3767 4.000 6.000 2.500 6.0000 5.2565 NADPH-flavin oxidoreductase -like protein SGO_0511 0.241 7.855 52.2376 50.000 0.0443 0.0950 70.0788 38.000 53.500 26.500 53.5000 55.7187 GTP-binding protein engA SGO_0512 0.385 8.219 64.2523 61.500 0.0246 0.0388 74.6893 40.500 64.500 45.000 64.5000 94.6167 murC; UDP-N-acetylmuramate--alanine ligase SGO_0515 -0.123 7.418 45.9691 44.000 0.0956 0.2702 36.8836 20.000 43.000 21.500 43.0000 45.2058 aminodeoxychorismate lyase-like protein SGO_0518 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 12 -0.349 6.975 39.7006 38.000 0.0315 0.0556 26.7406 14.500 31.000 13.500 31.0000 28.3850 greA; transcription elongation factor greA SGO_0519 -1.420 5.561 18.8055 18.000 0.0050 0.0022 5.5325 3.000 15.500 3.500 15.5000 7.3591 ilvB; acetolactate synthase, large subunit, biosynthetic type SGO_0526 -1.189 4.162 5.7461 5.500 0.0867 0.2343 9.000 1.500 9.0000 3.1539 ilvN; acetolactate synthase, small subunit SGO_0527 -0.289 8.143 82.5354 79.000 0.0423 0.0885 71.9230 39.000 72.500 26.500 72.5000 55.7187 ilvC; ketol-acid reductoisomerase SGO_0528 -0.252 4.168 5.2238 5.000 0.1566 0.5093 7.500 2.500 7.5000 5.2565 ilvA; threonine dehydratase SGO_0529 -0.400 4.343 6.2685 6.000 0.1153 0.3452 5.5325 3.000 8.500 8.5000 putative transcriptional regulator LytR SGO_0535 0.196 6.491 21.9398 21.000 0.0198 0.0277 24.8964 13.500 20.000 11.000 20.0000 23.1285 hypothetical protein SGO_0536 SGO_0536 -0.446 6.219 21.4174 20.500 0.0051 0.0025 14.7534 8.000 21.500 8.000 21.5000 16.8207 HIT family protein SGO_0537 -0.248 6.654 26.6412 25.500 0.0094 0.0078 23.9743 13.000 28.000 10.500 28.0000 22.0772 hypothetical protein SGO_0540 SGO_0540 -0.355 7.276 43.8796 42.000 0.0105 0.0098 31.3511 17.000 43.000 17.500 43.0000 36.7954 nusA; transcription termination factor NusA SGO_0543 -0.338 8.102 80.9683 77.500 0.0476 0.1054 50.7149 27.500 71.500 34.000 71.5000 71.4882 infB; Translation initiation factor IF-2 SGO_0546 -0.725 4.840 8.3580 8.000 0.0050 0.0019 5.5325 3.000 9.500 2.500 9.5000 5.2565 Na/Pi-cotransporter family protein SGO_0548 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 13 -0.205 6.502 23.5069 22.500 0.0184 0.0242 22.1302 12.000 25.000 9.500 25.0000 19.9746 oxidoreductase, aldo/keto reductase family SGO_0552 -0.707 4.799 8.8804 8.500 0.0921 0.2571 6.4546 3.500 12.500 12.5000 hsdR; type I site-specific deoxyribonuclease SGO_0554 -0.093 3.750 5.7461 5.500 0.2118 0.7732 3.500 2.000 3.5000 4.2052 hypothetical protein SGO_0558 SGO_0558 -0.567 5.174 11.4923 11.000 0.0151 0.0173 8.2988 4.500 10.000 3.000 10.0000 6.3078 hsdM; type I restriction-modification system, M subunit SGO_0560 -0.204 7.560 47.5362 45.500 0.0246 0.0387 42.4161 23.000 53.500 21.500 53.5000 45.2058 adhA; alcohol dehydrogenase SGO_0565 -0.346 6.590 25.0741 24.000 0.0499 0.1129 17.5197 9.500 28.500 12.000 28.5000 25.2311 glyQ; glycyl-tRNA synthetase, alpha subunit SGO_0568 -0.173 8.079 69.9984 67.000 0.1338 0.4182 51.6370 28.000 72.000 36.500 72.0000 76.7447 glyS; glycyl-tRNA synthetase, beta subunit SGO_0569 -1.078 5.593 16.7160 16.000 0.0120 0.0121 5.5325 3.000 15.500 5.000 15.5000 10.5130 mraW; S-adenosyl-methyltransferase MraW SGO_0573 -0.602 6.863 37.0887 35.500 0.0238 0.0368 18.4418 10.000 32.500 13.500 32.5000 28.3850 ATP-dependent RNA helicase SGO_0577 -0.856 5.563 13.0594 12.500 0.0121 0.0124 8.2988 4.500 17.500 4.000 17.5000 8.4104 trxB; thioredoxin-disulfide reductase SGO_0581 -0.827 7.536 49.1034 47.000 0.0224 0.0331 39.6499 21.500 69.500 13.000 69.5000 27.3337 nicotinate phosphoribosyltransferase, putative SGO_0582 -0.613 5.640 14.6265 14.000 0.0045 0.0014 9.2209 5.000 15.500 5.000 15.5000 10.5130 nadE; NAD+ synthetase SGO_0583 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 14

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 14 -0.393 6.850 37.6111 36.000 0.0426 0.0898 27.6627 15.000 28.000 10.500 28.0000 22.0772 pepC; aminopeptidase C SGO_0585 -0.529 7.227 49.1034 47.000 0.0163 0.0197 28.5848 15.500 39.500 15.500 39.5000 32.5902 pbp1a; penicillin-binding protein 1A SGO_0586 -0.265 7.239 32.9097 31.500 0.0979 0.2806 38.7278 21.000 50.000 14.000 50.0000 29.4363 methylase SGO_0589 -0.575 4.491 10.4475 10.000 0.1229 0.3763 5.5325 3.000 6.500 6.5000 Methyltransferase SGO_0590 -0.545 6.487 26.6412 25.500 0.0058 0.0034 16.5976 9.000 26.500 9.500 26.5000 19.9746 hypothetical protein SGO_0591 SGO_0591 -0.928 5.148 13.5818 13.000 0.0264 0.0438 7.3767 4.000 14.500 14.5000 luxS; autoinducer-2 production protein LuxS SGO_0592 -0.945 6.782 39.1782 37.500 0.0089 0.0068 22.1302 12.000 33.000 7.500 33.0000 15.7695 HD/KH domain protein SGO_0593 -0.285 5.592 12.0147 11.500 0.0336 0.0621 10.1430 5.500 14.500 5.500 14.5000 11.5643 gmk; Guanylate kinase (GMP kinase) SGO_0594 -0.365 6.369 22.9846 22.000 0.0086 0.0063 19.3639 10.500 23.500 8.000 23.5000 16.8207 DNA-directed RNA polymerase, omega subunit SGO_0595 -0.930 5.400 14.6265 14.000 0.0057 0.0031 8.2988 4.500 13.000 3.000 13.0000 6.3078 fmt; methionyl-tRNA formyltransferase SGO_0597 -0.192 6.080 19.3279 18.500 0.1225 0.3743 12.9093 7.000 16.500 9.000 16.5000 18.9233 phosphoprotein phosphatase SGO_0599 -0.833 5.248 16.1937 15.500 0.0549 0.1291 8.2988 4.500 13.500 13.5000 serine/threonine protein kinase SGO_0600 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 15

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 15 -0.281 7.730 56.4166 54.000 0.0121 0.0124 50.7149 27.500 60.000 21.500 60.0000 45.2058 hydrolase, haloacid dehalogenase family/peptidyl-prolyl cis-trans isomerase, cyclophilin type SGO_0604 -0.116 8.560 92.9830 89.000 0.0452 0.0978 88.5206 48.000 103.500 44.000 103.5000 92.5141 cysK; cysteine synthase A SGO_0606 -0.202 8.303 88.2816 84.500 0.1450 0.4632 92.2090 50.000 78.500 27.000 78.5000 56.7700 ribosomal subunit interface protein SGO_0610 -0.391 4.073 5.2238 5.000 0.1141 0.3401 4.6104 2.500 7.000 7.0000 recX; Regulatory protein recX SGO_0626 -1.276 6.339 29.2531 28.000 0.0012 0.0001 11.0651 6.000 28.000 6.000 28.0000 12.6156 alpha-glycerophosphate oxidase SGO_0631 -0.428 5.532 12.5370 12.000 0.0101 0.0091 9.2209 5.000 14.000 5.000 14.0000 10.5130 glpK; glycerol kinase SGO_0632 -0.483 7.708 57.9838 55.500 0.0168 0.0211 49.7929 27.000 63.500 18.000 63.5000 37.8467 valS; valyl-tRNA synthetase SGO_0639 2.176 4.306 2.6119 2.500 0.0195 0.0266 3.500 6.500 3.5000 13.6669 modification methylase SGO_0640 -0.693 6.206 23.5069 22.500 0.0057 0.0032 15.6755 8.500 22.000 6.000 22.0000 12.6156 ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain protein protein SGO_0641 2.641 7.544 15.6713 15.000 0.0019 0.0003 85.7544 46.500 10.500 35.500 10.5000 74.6421 hypothetical protein SGO_0642 SGO_0642 -0.102 3.563 3.1343 3.000 0.2074 0.7545 3.6884 2.000 5.000 5.0000 cytosine-specific methyltransferase SGO_0643 -0.638 6.594 34.4768 33.000 0.0262 0.0428 16.5976 9.000 24.500 10.000 24.5000 21.0259 hypothetical protein SGO_0644 SGO_0644 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 16

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 16 0.499 4.282 6.7909 6.500 0.1697 0.5840 6.4546 3.500 2.000 2.000 2.0000 4.2052 hypothetical protein SGO_0652 SGO_0652 -0.541 6.872 31.3426 30.000 0.0183 0.0237 26.7406 14.500 38.000 10.000 38.0000 21.0259 radical SAM enzyme, Cfr family SGO_0654 -0.070 4.817 7.8356 7.500 0.2354 0.8955 10.1430 5.500 6.000 2.000 6.0000 4.2052 trpB-2; tryptophan synthase, beta subunit SGO_0656 -0.084 9.511 172.3842 165.000 0.2049 0.7441 213.0028 115.500 200.000 68.500 200.0000 144.0277 non-heme iron-containing ferritin SGO_0665 -0.054 7.888 60.0733 57.500 0.0984 0.2826 55.3254 30.000 60.500 29.000 60.5000 60.9752 typA; GTP-binding protein TypA SGO_0669 -1.181 6.393 32.3873 31.000 0.0058 0.0033 11.9872 6.500 26.000 6.500 26.0000 13.6669 murD; UDP-N-acetylmuramoylalanine--Dglutamate ligase SGO_0671 -1.747 4.555 5.7461 5.500 0.1156 0.3479 2.7663 1.500 15.000 15.0000 murG; undecaprenyl-PP-MurNAcpentapeptide-UDPGlcNAc GlcNAc transferase SGO_0672 0.012 2.877 3.6566 3.500 3.6884 2.000 DivIB; cell division protein DivIB SGO_0673 0.070 8.796 112.3109 107.500 0.0972 0.2773 107.8845 58.500 104.500 57.000 104.5000 119.8478 ftsA; cell division protein FtsA SGO_0674 0.353 9.672 179.1750 171.500 0.0028 0.0006 223.1458 121.000 179.000 111.500 179.0000 234.4392 ftsZ; cell division protein FtsZ SGO_0675 -0.215 5.555 10.4475 10.000 0.0878 0.2400 11.0651 6.000 15.000 5.000 15.0000 10.5130 conserved hypothetical protein TIGR00044 SGO_0676 -0.108 7.445 39.1782 37.500 0.2139 0.7877 53.4812 29.000 50.000 15.000 50.0000 31.5389 ylmF protein SGO_0677 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 17

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 17 -0.460 8.674 107.6095 103.000 0.0226 0.0338 75.6114 41.000 128.500 46.000 128.5000 96.7193 cell division protein DivIVA SGO_0680 -0.526 8.524 110.7438 106.000 0.0026 0.0005 78.3776 42.500 106.500 34.500 106.5000 72.5395 ileS; isoleucyl-tRNA synthetase SGO_0681 0.708 7.087 26.1188 25.000 0.0016 0.0002 43.3382 23.500 25.500 19.500 25.5000 41.0006 hypothetical protein SGO_0684 SGO_0684 -0.500 7.374 50.1481 48.000 0.0031 0.0007 35.0394 19.000 47.000 16.000 47.0000 33.6415 ATP dependent Clp protease, ATP-binding subunit, ClpE SGO_0688 0.248 3.226 4.7014 4.500 0.2508 0.9789 1.500 1.500 1.5000 3.1539 xseA; exodeoxyribonuclease VII, large subunit SGO_0693 -0.692 5.746 14.6265 14.000 0.0354 0.0673 7.3767 4.000 18.000 6.500 18.0000 13.6669 DegV family protein SGO_0700 -0.065 12.543 1541.0098 1475.000 0.1866 0.6611 1656.9957 898.500 1496.500 605.000 1496.5000 1272.0691 hup; DNA-binding histone-like protein HU SGO_0701 0.640 11.588 584.5390 559.500 0.0012 0.0001 924.8563 501.500 619.500 452.000 619.5000 950.3723 gpmA; 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase SGO_0704 -0.152 4.568 8.3580 8.000 0.0575 0.1368 8.000 3.500 8.0000 7.3591 phoH-like protein SGO_0706 0.154 4.307 6.2685 6.000 0.1982 0.7097 7.3767 4.000 3.000 1.500 3.0000 3.1539 LPXTG cell wall surface protein SGO_0707 0.009 9.410 169.2499 162.000 0.2272 0.8553 153.9890 83.500 169.000 89.500 169.0000 188.1821 ald; alanine dehydrogenase SGO_0708 -0.181 6.841 33.9545 32.500 0.0893 0.2463 29.5069 16.000 27.000 11.500 27.0000 24.1798 sgg; GTP-binding protein Era SGO_0713 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 18

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 18 0.174 5.042 6.2685 6.000 0.1577 0.5139 12.9093 7.000 8.500 2.500 8.5000 5.2565 abpB-like dipeptidase lipoprotein SGO_0721 -0.914 3.749 4.1790 4.000 0.0956 0.2697 2.7663 1.500 6.500 6.5000 hprK; HPr(Ser) kinase/phosphatase SGO_0736 -0.130 5.795 13.0594 12.500 0.0902 0.2502 13.8313 7.500 16.000 6.000 16.0000 12.6156 hypothetical protein SGO_0739 SGO_0739 -0.174 5.394 14.6265 14.000 0.0184 0.0243 12.9093 7.000 14.500 14.5000 peptidase, U32 family SGO_0742 -0.062 6.660 29.2531 28.000 0.2296 0.8666 19.3639 10.500 22.000 14.500 22.0000 30.4876 peptidase, U32 family SGO_0743 -0.380 7.571 50.6705 48.500 0.0455 0.0988 49.7929 27.000 56.000 16.000 56.0000 33.6415 hypothetical protein SGO_0745 SGO_0745 -0.672 6.517 30.2978 29.000 0.0067 0.0042 18.4418 10.000 26.000 8.000 26.0000 16.8207 glutathione reductase SGO_0749 -0.828 8.970 167.1604 160.000 0.0037 0.0010 96.8194 52.500 153.500 40.000 153.5000 84.1037 efflux transporter, RND family, MFP subunit subfamily SGO_0750 0.061 7.986 70.5208 67.500 0.1979 0.7045 69.1567 37.500 54.000 28.500 54.0000 59.9239 ABC transporter, ATP-binding protein SP0786 SGO_0751 -1.583 5.463 18.8055 18.000 0.0073 0.0049 19.000 3.000 19.0000 6.3078 ABC transporter, ATP-binding protein SGO_0752 -0.152 8.582 106.0424 101.500 0.0514 0.1174 84.8323 46.000 95.500 46.000 95.5000 96.7193 lysS; lysyl-tRNA synthetase SGO_0753 -0.930 4.679 8.3580 8.000 0.0843 0.2256 12.000 2.500 12.0000 5.2565 regulatory protein SGO_0755 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 19

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 19 -0.184 8.944 131.1164 125.500 0.0275 0.0469 123.5601 67.000 130.500 51.000 130.5000 107.2323 ppc; phosphoenolpyruvate carboxylase SGO_0760 0.194 13.234 2347.0363 2246.500 0.0122 0.0126 2600.2938 1410.000 2149.500 1207.500 2149.5000 2538.8817 tuf; translation elongation factor Tu SGO_0761 0.307 11.217 607.0012 581.000 0.0902 0.2505 804.0625 436.000 449.500 247.000 449.5000 519.3406 tpiA; triosephosphate isomerase SGO_0762 -0.462 6.864 30.8202 29.500 0.0656 0.1614 32.2731 17.500 35.500 8.500 35.5000 17.8720 murA-1; UDP-N-acetylglucosamine 1carboxyvinyltransferase SGO_0763 -0.580 8.022 76.2669 73.000 0.0012 0.0001 51.6370 28.000 79.500 25.000 79.5000 52.5648 pepq; proline dipeptidase SGO_0771 -0.086 8.013 71.5655 68.500 0.1168 0.3541 59.0138 32.000 61.500 31.500 61.5000 66.2317 ccpA; catabolite control protein A SGO_0773 -0.279 5.141 15.1489 14.500 0.1579 0.5182 10.1430 5.500 10.000 10.0000 glycosyl transferase, group 1 family protein SGO_0774 -0.443 5.309 9.9251 9.500 0.0248 0.0395 8.2988 4.500 13.000 4.000 13.0000 8.4104 glycosyl transferase, group 1 SGO_0775 -0.280 8.523 98.2067 94.000 0.0045 0.0014 82.9881 45.000 103.500 39.500 103.5000 83.0524 thrS; threonyl-tRNA synthetase SGO_0778 -1.405 5.902 24.5517 23.500 0.0158 0.0186 11.9872 6.500 18.000 2.500 18.0000 5.2565 response regulator SGO_0779 -1.117 6.222 25.0741 24.000 0.0007 0.0000 11.9872 6.500 26.000 5.500 26.0000 11.5643 smc; chromosome segregation protein SMC SGO_0784 -0.423 5.701 15.1489 14.500 0.0238 0.0369 12.9093 7.000 14.500 4.500 14.5000 9.4617 Cof family protein SGO_0786 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 20

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 20 -0.680 6.644 30.8202 29.500 0.0078 0.0056 16.5976 9.000 30.500 10.500 30.5000 22.0772 ftsY; cell division protein FtsY SGO_0787 -0.083 7.373 41.7901 40.000 0.0165 0.0200 40.5720 22.000 43.500 19.000 43.5000 39.9493 zwf; glucose-6-phosphate 1-dehydrogenase SGO_0788 0.213 6.515 24.0293 23.000 0.0667 0.1684 25.8185 14.000 18.500 11.000 18.5000 23.1285 hypothetical protein SGO_0792 SGO_0792 -0.543 7.003 36.5663 35.000 0.0048 0.0017 24.8964 13.500 39.500 13.000 39.5000 27.3337 metallo-beta-lactamase family protein SGO_0794 -0.846 4.916 9.4028 9.000 0.0016 0.0002 5.5325 3.000 10.000 2.500 10.0000 5.2565 tributyrin esterase SGO_0795 -0.090 6.447 23.5069 22.500 0.0451 0.0973 21.2081 11.500 21.500 10.000 21.5000 21.0259 ABC transporter, ATP-binding protein SP1381 SGO_0798 -0.289 4.477 7.3133 7.000 0.0893 0.2470 6.4546 3.500 8.500 8.5000 polysaccharide deacetylase family protein SGO_0800 -0.444 8.709 116.4899 111.500 0.0357 0.0679 107.8845 58.500 122.500 34.000 122.5000 71.4882 hom; homoserine dehydrogenase SGO_0801 -0.990 6.198 24.0293 23.000 0.0056 0.0030 10.1430 5.500 24.500 7.000 24.5000 14.7182 thrB; homoserine kinase SGO_0802 -0.985 5.780 17.2384 16.500 0.0183 0.0238 12.9093 7.000 18.500 3.000 18.5000 6.3078 hypothetical protein SGO_0803 SGO_0803 -0.439 3.119 3.6884 2.000 5.000 5.0000 aminotransferase, class-V SGO_0814 -0.436 6.739 32.9097 31.500 0.0128 0.0137 21.2081 11.500 28.500 11.500 28.5000 24.1798 thiI; thiamine biosynthesis protein ThiI SGO_0815 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 21

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 21 0.146 9.821 199.0253 190.500 0.0805 0.2119 217.6132 118.000 230.000 122.500 230.0000 257.5677 rplU; ribosomal protein L21 SGO_0818 0.049 7.356 36.5663 35.000 0.1989 0.7149 51.6370 28.000 43.000 15.500 43.0000 32.5902 rpmA; ribosomal protein L27 SGO_0820 -0.527 7.513 53.8047 51.500 0.0019 0.0003 35.9615 19.500 54.000 18.500 54.0000 38.8980 lepA; GTP-binding protein LepA SGO_0824 -0.202 4.135 7.3133 7.000 0.1685 0.5790 5.000 2.500 5.0000 5.2565 hypothetical protein SGO_0832 SGO_0832 -0.100 8.008 66.3418 63.500 0.1676 0.5747 52.5591 28.500 66.000 34.500 66.0000 72.5395 nitroreductase SGO_0835 -0.322 8.917 135.8178 130.000 0.0227 0.0344 119.8717 65.000 132.000 45.500 132.0000 95.6680 pepV; dipeptidase PepV SGO_0836 0.314 4.316 3.1343 3.000 0.1271 0.3929 5.5325 3.000 6.000 2.500 6.0000 5.2565 rhodanese family protein SGO_0842 0.126 8.471 85.6697 82.000 0.0199 0.0280 95.8974 52.000 84.000 42.500 84.0000 89.3602 rpmE; ribosomal protein L31 SGO_0848 0.821 8.115 50.6705 48.500 0.0532 0.1238 126.3263 68.500 44.500 26.500 44.5000 55.7187 flavodoxin SGO_0850 -0.083 4.618 5.2238 5.000 0.1668 0.5698 5.5325 3.000 7.500 3.000 7.5000 6.3078 cshA; surface-associated protein CshA SGO_0854 -0.843 6.741 30.2978 29.000 0.0099 0.0084 20.2860 11.000 38.500 8.500 38.5000 17.8720 ABC transporter, substrate binding protein SGO_0856 -0.591 6.628 31.3426 30.000 0.0101 0.0091 17.5197 9.500 28.000 10.500 28.0000 22.0772 pheS; phenylalanyl-tRNA synthetase, alpha subunit SGO_0859 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 22 -0.016 8.788 108.1319 103.500 0.2193 0.8146 103.2741 56.000 114.000 55.500 114.0000 116.6939 pheT; phenylalanyl-tRNA synthetase, beta subunit SGO_0861 0.072 4.529 5.7461 5.500 0.1023 0.2951 5.5325 3.000 5.500 3.000 5.5000 6.3078 cobyric acid synthase SGO_0885 -0.120 3.360 2.6119 2.500 0.2049 0.7437 4.500 1.500 4.5000 3.1539 hypothetical protein SGO_0888 SGO_0888 -0.857 6.334 25.0741 24.000 0.0094 0.0079 17.5197 9.500 26.500 5.500 26.5000 11.5643 glmM; phosphoglucosamine mutase SGO_0889 -0.144 7.478 42.3125 40.500 0.0694 0.1766 42.4161 23.000 51.500 20.000 51.5000 42.0519 GTP-binding protein SGO_0893 -1.239 5.624 18.8055 18.000 0.0092 0.0073 5.5325 3.000 15.500 4.500 15.5000 9.4617 DNA-directed DNA polymerase III SGO_0901 -0.169 7.067 35.5216 34.000 0.1085 0.3157 26.7406 14.500 35.000 17.500 35.0000 36.7954 leuA; 2-isopropylmalate synthase SGO_0906 -0.375 8.145 78.3564 75.000 0.0196 0.0271 54.4033 29.500 81.000 33.000 81.0000 69.3856 hypothetical protein SGO_0911 SGO_0911 -0.405 5.997 19.8503 19.000 0.0811 0.2141 10.1430 5.500 16.000 8.500 16.0000 17.8720 Deblocking aminopeptidase SGO_0946 -0.280 3.985 5.2238 5.000 0.0869 0.2354 4.6104 2.500 6.000 6.0000 deaD; DEAD RNA helicase SGO_0949 -0.499 3.856 6.7909 6.500 0.1382 0.4363 3.6884 2.000 4.000 4.0000 oxidoreductase SGO_0950 0.056 5.347 9.4028 9.000 0.1726 0.5963 9.2209 5.000 10.500 5.500 10.5000 11.5643 udk; uridine kinase SGO_0951 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 23 0.400 6.031 9.9251 9.500 0.1104 0.3269 13.8313 7.500 18.500 11.000 18.5000 23.1285 ATP-binding protein SGO_0954 -1.448 5.968 20.3727 19.500 0.0050 0.0022 8.2988 4.500 25.500 4.000 25.5000 8.4104 amino acid ABC transporter, amino acidbinding protein SGO_0982 0.146 7.404 33.9545 32.500 0.1271 0.3950 44.2603 24.000 47.000 21.000 47.0000 44.1545 metK; S-adenosylmethionine synthetase SGO_0987 0.298 2.742 3.6884 2.000 3.000 3.0000 GTP-binding protein HflX SGO_0993 -0.910 4.300 12.0147 11.500 0.1485 0.4762 3.6884 2.000 4.000 4.0000 metallo-beta-lactamase superfamily protein SGO_0995 -0.363 7.652 50.6705 48.500 0.0482 0.1077 36.8836 20.000 62.000 24.500 62.0000 51.5135 apt; adenine phosphoribosyltransferase SGO_1001 -0.311 5.052 10.4475 10.000 0.0394 0.0786 7.3767 4.000 8.000 3.500 8.0000 7.3591 Bcl-2 family protein SGO_1005 -0.352 8.825 132.1612 126.500 0.0358 0.0687 84.8323 46.000 121.000 55.000 121.0000 115.6426 rfbA-1; glucose-1-phosphate thymidylyltransferase SGO_1009 -0.004 7.284 44.4020 42.500 0.2348 0.8913 39.6499 21.500 34.000 18.000 34.0000 37.8467 rmlC; dTDP-4-keto-6-deoxyglucose-3,5epimerase SGO_1010 -0.510 7.930 76.2669 73.000 0.0092 0.0074 47.0266 25.500 67.000 25.500 67.0000 53.6161 rfbB-1; dTDP-glucose 4,6-dehydratase SGO_1011 -0.408 8.489 102.9081 98.500 0.0012 0.0001 75.6114 41.000 102.000 37.500 102.0000 78.8473 galE-1; UDP-glucose 4-epimerase SGO_1012 1.757 3.716 10.1430 5.500 3.000 3.0000 Glycosyltransferase involved in cell wall biogenesis SGO_1013 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 24

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 24 -0.407 4.079 6.7909 6.500 0.0910 0.2534 4.6104 2.500 5.500 5.5000 putative glycosyltransferase SGO_1016 -0.856 3.694 4.1790 4.000 0.0874 0.2378 2.7663 1.500 6.000 6.0000 glycosyl transferase SGO_1019 -0.143 7.350 35.5216 34.000 0.1361 0.4272 42.4161 23.000 50.500 16.500 50.5000 34.6928 rfbD; dTDP-4-dehydrorhamnose reductase SGO_1020 -0.558 5.938 15.6713 15.000 0.0438 0.0934 15.6755 8.500 20.500 4.500 20.5000 9.4617 rgp; glycosyltransferase SGO_1025 -1.030 5.584 15.6713 15.000 0.0017 0.0002 7.3767 4.000 16.500 4.000 16.5000 8.4104 rhamnosyltransferase SGO_1026 -0.922 4.825 8.3580 8.000 0.0158 0.0184 3.6884 2.000 10.000 3.000 10.0000 6.3078 cmk; cytidylate kinase SGO_1031 -0.215 4.744 10.4475 10.000 0.1382 0.4357 5.5325 3.000 4.500 3.000 4.5000 6.3078 infC; translation initiation factor IF-3 SGO_1032 -0.702 9.592 231.9350 222.000 0.0321 0.0574 199.1714 108.000 236.500 49.500 236.5000 104.0784 rplT; ribosomal protein L20 SGO_1034 -0.089 5.418 10.9699 10.500 0.1403 0.4457 9.2209 5.000 11.000 5.500 11.0000 11.5643 gloA; lactoylglutathione lyase SGO_1035 -1.118 5.294 8.8804 8.500 0.0358 0.0685 5.5325 3.000 18.500 3.000 18.5000 6.3078 amino acid ABC transporter, ATP-binding protein SP1242 SGO_1036 0.018 4.993 9.9251 9.500 0.2552 0.9977 6.4546 3.500 6.000 4.500 6.0000 9.4617 uvrB; excinuclease ABC, B subunit SGO_1038 -1.205 5.745 16.1937 15.500 0.0107 0.0100 10.1430 5.500 21.000 3.000 21.0000 6.3078 hypothetical protein SGO_1047 SGO_1047 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 25

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 25 -1.108 4.615 9.4028 9.000 0.0348 0.0652 4.6104 2.500 10.500 10.5000 tRNA pseudouridine synthase B SGO_1049 -0.267 3.894 3.6566 3.500 0.1782 0.6234 7.000 2.000 7.0000 4.2052 ribF; riboflavin biosynthesis protein RibF SGO_1050 -1.595 3.476 8.3580 8.000 2.7663 1.500 negative regulator of proteolysis SGO_1051 1.220 5.099 7.8356 7.500 0.0073 0.0050 18.4418 10.000 8.000 8.0000 pstB; Phosphate import ATP-binding protein pstB 2 (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) SGO_1058 0.304 6.760 23.5069 22.500 0.0048 0.0016 30.4290 16.500 25.000 14.000 25.0000 29.4363 pstB; Phosphate import ATP-binding protein pstB 1 (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) SGO_1059 -1.042 6.723 38.1335 36.500 0.0043 0.0012 16.5976 9.000 33.000 8.500 33.0000 17.8720 phosphate transport system regulatory protein SGO_1060 -0.056 5.401 10.9699 10.500 0.1849 0.6538 9.2209 5.000 10.500 5.500 10.5000 11.5643 hypothetical protein SGO_1065 SGO_1065 -0.344 8.334 99.2515 95.000 0.0248 0.0395 67.3126 36.500 81.500 35.500 81.5000 74.6421 membrane alanyl aminopeptidase SGO_1069 -0.816 6.258 21.4174 20.500 0.0107 0.0101 12.9093 7.000 27.500 7.000 27.5000 14.7182 pdp; pyrimidine-nucleoside phosphorylase SGO_1079 -0.354 7.838 66.8642 64.000 0.0064 0.0039 48.8708 26.500 61.500 24.500 61.5000 51.5135 deoC; deoxyribose-phosphate aldolase SGO_1080 1.033 3.484 3.6566 3.500 0.0735 0.1892 5.5325 3.000 2.000 2.0000 cdd; cytidine deaminase SGO_1081 -0.212 12.037 1071.9160 1026.000 0.1609 0.5401 1273.4063 690.500 1141.000 340.500 1141.0000 715.9331 lipoprotein SGO_1082 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 26

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 26 -0.634 8.825 156.1905 149.500 0.0148 0.0168 88.5206 48.000 120.500 42.000 120.5000 88.3089 sugar ABC transporter, ATP-binding protein SP0846 SGO_1083 -0.517 3.458 5.2238 5.000 0.1390 0.4396 2.7663 1.500 3.000 3.0000 transcription regulator, LysR family SGO_1088 -0.546 10.083 308.2020 295.000 0.0167 0.0208 258.1852 140.000 332.500 88.500 332.5000 186.0795 butA; acetoin dehydrogenase SGO_1096 -0.908 5.326 9.9251 9.500 0.0271 0.0453 7.3767 4.000 16.500 3.000 16.5000 6.3078 proA; gamma-glutamyl phosphate reductase SGO_1098 -0.387 3.279 5.500 2.000 5.5000 4.2052 PyrR bifunctional protein SGO_1107 -0.468 7.446 49.1034 47.000 0.0077 0.0055 39.6499 21.500 52.000 16.000 52.0000 33.6415 pyrB; aspartate carbamoyltransferase SGO_1109 -0.999 4.208 6.7909 6.500 0.0466 0.1029 3.6884 2.000 8.000 8.0000 fruR; phosphotransferase system repressor SGO_1111 -1.620 4.938 10.4475 10.000 0.0735 0.1901 16.000 2.000 16.0000 4.2052 fruB; 1-phosphofructokinase SGO_1112 0.070 7.700 60.5956 58.000 0.2139 0.7865 47.9487 26.000 41.500 27.500 41.5000 57.8213 fruA; PTS system, fructose specific IIABC components SGO_1113 -1.101 5.443 16.1937 15.500 0.0051 0.0023 6.4546 3.500 13.500 3.500 13.5000 7.3591 Protein of unknown function (DUF1149) superfamily SGO_1114 -0.461 7.063 40.7453 39.000 0.0163 0.0196 24.8964 13.500 36.500 15.000 36.5000 31.5389 dapB; dihydrodipicolinate reductase SGO_1116 -0.352 8.177 81.4907 78.000 0.0319 0.0570 54.4033 29.500 80.000 35.000 80.0000 73.5908 guaA; GMP synthase SGO_1120 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 27

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 27 -0.243 7.834 59.5509 57.000 0.0198 0.0276 48.8708 26.500 64.000 26.500 64.0000 55.7187 ffh; signal recognition particle protein SGO_1123 0.133 5.556 13.0594 12.500 0.1407 0.4477 12.9093 7.000 9.500 5.500 9.5000 11.5643 lplA; lipoate protein ligase A SGO_1129 -0.293 7.485 50.6705 48.500 0.0045 0.0014 40.5720 22.000 48.000 19.000 48.0000 39.9493 dihydrolipoamide dehydrogenase SGO_1130 -0.628 6.083 21.9398 21.000 0.0172 0.0217 11.0651 6.000 19.000 7.500 19.0000 15.7695 sucB; dihydrolipoamide S-acetyltransferase SGO_1131 -1.277 4.431 8.8804 8.500 0.0092 0.0072 3.6884 2.000 9.000 9.0000 acetoin dehydrogenase SGO_1132 -0.401 5.511 14.1042 13.500 0.0753 0.1952 7.3767 4.000 11.500 6.000 11.5000 12.6156 acoA; acetoin dehydrogenase SGO_1133 0.687 2.769 2.6119 2.500 2.000 4.2052 hypothetical protein SGO_1134 SGO_1134 -0.687 6.647 30.2978 29.000 0.0017 0.0002 18.4418 10.000 31.500 9.500 31.5000 19.9746 GTP-binding protein SGO_1139 -0.548 8.083 80.9683 77.500 0.0007 0.0000 54.4033 29.500 80.000 26.500 80.0000 55.7187 clpX; ATP-dependent Clp protease, ATPbinding subunit ClpX SGO_1140 -0.510 4.166 7.8356 7.500 0.1108 0.3287 4.6104 2.500 5.500 5.5000 folA; dihydrofolate reductase SGO_1141 -0.469 5.119 12.5370 12.000 0.0256 0.0415 9.2209 5.000 13.000 13.0000 thyA; thymidylate synthase SGO_1143 -0.205 9.487 192.2344 184.000 0.0330 0.0604 181.6517 98.500 191.500 72.500 191.5000 152.4380 glcK; glucokinase SGO_1144 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 28

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 28 -0.736 4.996 13.0594 12.500 0.0458 0.1000 11.500 3.500 11.5000 7.3591 hypothetical protein SGO_1150 SGO_1150 -0.112 9.374 172.9065 165.500 0.0151 0.0172 154.9111 84.000 171.500 78.000 171.5000 164.0023 glyA; serine hydroxymethyltransferase SGO_1151 0.176 7.252 34.9992 33.500 0.0328 0.0595 37.8057 20.500 36.500 20.500 36.5000 43.1032 prfA; peptide chain release factor 1 SGO_1154 -0.062 5.189 9.4028 9.000 0.2203 0.8197 15.500 5.500 15.5000 11.5643 tdk; thymidine kinase SGO_1155 -1.225 7.832 79.4012 76.000 0.0061 0.0037 25.8185 14.000 78.500 21.000 78.5000 44.1545 nox; NADH oxidase SGO_1167 -0.074 7.287 45.9691 44.000 0.1579 0.5196 37.8057 20.500 34.500 18.000 34.5000 37.8467 NADPH-dependent FMN reductase SGO_1169 -0.164 7.848 62.6851 60.000 0.0268 0.0445 57.1696 31.000 59.000 24.500 59.0000 51.5135 NADPH-dependent FMN reductase SGO_1170 -0.678 4.825 9.9251 9.500 0.0219 0.0318 4.6104 2.500 7.500 3.000 7.5000 6.3078 acetyltransferase, GNAT family SGO_1185 0.243 6.125 13.0594 12.500 0.1382 0.4349 27.6627 15.000 17.500 5.500 17.5000 11.5643 lipoprotein, putative SGO_1189 0.592 11.525 606.4788 580.500 0.0050 0.0022 837.2577 454.000 568.000 444.500 568.0000 934.6028 rplL; ribosomal protein L7/L12 SGO_1191 -0.831 9.141 147.3101 141.000 0.0196 0.0270 104.1962 56.500 216.500 46.000 216.5000 96.7193 BL5; 50S ribosomal protein L10 SGO_1192 -1.780 5.724 23.5069 22.500 0.0061 0.0036 5.5325 3.000 17.500 3.000 17.5000 6.3078 gid; Glucose inhibited division protein A SGO_1193 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 29

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 29 -0.539 6.562 25.0741 24.000 0.0140 0.0154 18.4418 10.000 31.000 9.500 31.0000 19.9746 topA; DNA topoisomerase I SGO_1197 0.242 8.232 69.4760 66.500 0.0289 0.0498 88.5206 48.000 68.000 35.500 68.0000 74.6421 DNA processing Smf protein SGO_1198 -0.311 6.275 19.8503 19.000 0.0295 0.0509 15.6755 8.500 23.000 9.000 23.0000 18.9233 anaerobic ribonucleotide reductase SGO_1203 -0.173 4.641 5.7461 5.500 0.1033 0.2994 6.4546 3.500 7.500 2.500 7.5000 5.2565 dapA; dihydrodipicolinate synthase SGO_1205 0.517 6.972 26.6412 25.500 0.0053 0.0027 35.0394 19.000 25.000 18.500 25.0000 38.8980 asd; aspartate-semialdehyde dehydrogenase SGO_1206 -1.052 4.625 13.0594 12.500 0.1103 0.3245 4.6104 2.500 7.000 7.0000 fhs-1; formate--tetrahydrofolate ligase SGO_1210 -0.577 9.730 253.8748 243.000 0.0000 0.0000 170.5866 92.500 254.500 81.000 254.5000 170.3101 manB; phosphomannomutase SGO_1215 -0.641 7.060 44.9244 43.000 0.0103 0.0094 26.7406 14.500 36.500 12.000 36.5000 25.2311 bta; Possible bacteriocin transport accessory protein SGO_1216 -0.147 7.143 37.6111 36.000 0.0656 0.1621 30.4290 16.500 36.500 17.500 36.5000 36.7954 pta; phosphate acetyltransferase SGO_1219 -0.222 8.539 104.9976 100.500 0.0384 0.0755 78.3776 42.500 95.000 44.500 95.0000 93.5654 Ribose-phosphate pyrophosphokinase 2 SGO_1224 -0.082 5.027 7.3133 7.000 0.1579 0.5157 7.3767 4.000 9.500 4.000 9.5000 8.4104 pyridoxal-phosphate dependent aminotransferase SGO_1225 -0.205 6.039 16.7160 16.000 0.0203 0.0288 14.7534 8.000 18.500 7.500 18.5000 15.7695 hypothetical protein SGO_1226 SGO_1226 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 30

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 30 -0.544 6.626 21.9398 21.000 0.0495 0.1114 19.3639 10.500 37.500 9.500 37.5000 19.9746 gyrA; DNA gyrase, A subunit SGO_1231 0.085 10.720 416.3338 398.500 0.0113 0.0108 431.5381 234.000 402.000 207.500 402.0000 436.2882 L-lactate dehydrogenase SGO_1232 0.167 10.658 384.9913 368.500 0.0048 0.0016 421.3951 228.500 376.000 206.000 376.0000 433.1343 rpsA; 30S ribosomal protein S1 SGO_1234 0.449 6.187 14.1042 13.500 0.0848 0.2281 13.8313 7.500 15.500 14.000 15.5000 29.4363 hypothetical protein SGO_1237 SGO_1237 -0.343 6.447 24.5517 23.500 0.0305 0.0530 16.5976 9.000 24.000 10.500 24.0000 22.0772 ilvE; branched-chain amino acid aminotransferase SGO_1238 -1.874 4.994 12.0147 11.500 0.0012 0.0001 3.6884 2.000 13.000 1.500 13.0000 3.1539 parC; DNA topoisomerase IV, A subunit SGO_1239 0.352 3.887 8.2988 4.500 6.500 6.5000 lipoprotein, putative SGO_1242 -1.332 5.511 19.8503 19.000 0.0136 0.0148 6.4546 3.500 13.000 3.000 13.0000 6.3078 pyrC; dihydroorotase SGO_1248 -0.339 6.446 22.9846 22.000 0.0353 0.0668 16.5976 9.000 25.500 10.500 25.5000 22.0772 pyrE; orotate phosphoribosyltransferase SGO_1253 0.001 7.787 53.2824 51.000 0.2478 0.9628 59.0138 32.000 57.000 24.500 57.0000 51.5135 deoD; purine nucleoside phosphorylase SGO_1260 -0.766 8.178 87.7592 84.000 0.0100 0.0088 44.2603 24.000 93.500 30.500 93.5000 64.1291 purine nucleoside phosphorylase I, inosine and guanosine-specific SGO_1263 -0.144 9.434 185.4436 177.500 0.1271 0.3944 139.2356 75.500 175.500 91.000 175.5000 191.3360 deoB; phosphopentomutase SGO_1264 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 31 -0.281 7.570 50.1481 48.000 0.0190 0.0257 39.6499 21.500 54.000 22.000 54.0000 46.2571 rpiA; ribose 5-phosphate isomerase SGO_1265 -0.319 5.932 18.8055 18.000 0.0570 0.1353 15.6755 8.500 15.000 5.500 15.0000 11.5643 trmE; tRNA modification GTPase TrmE SGO_1266 0.084 8.669 97.1620 93.000 0.1635 0.5535 126.3263 68.500 98.500 40.500 98.5000 85.1550 rpoD; RNA polymerase sigma factor SGO_1273 0.200 7.602 40.7453 39.000 0.0874 0.2374 45.1824 24.500 49.500 28.000 49.5000 58.8726 rpsU; ribosomal protein S21 SGO_1276 -1.109 4.494 7.8356 7.500 0.0665 0.1670 10.500 2.000 10.5000 4.2052 penicillinase repressor, putative SGO_1281 -0.407 8.123 80.9683 77.500 0.0016 0.0002 59.9358 32.500 78.000 28.500 78.0000 59.9239 oxidoreductase SGO_1283 -0.029 5.586 17.7608 17.000 0.1982 0.7089 10.1430 5.500 7.500 6.000 7.5000 12.6156 thioredoxin-disulfide reductase SGO_1284 -0.362 7.357 48.5810 46.500 0.0731 0.1879 27.6627 15.000 42.500 21.500 42.5000 45.2058 asnS; asparaginyl-tRNA synthetase SGO_1293 0.120 6.240 17.2384 16.500 0.0340 0.0635 19.3639 10.500 19.000 9.500 19.0000 19.9746 aspC; aspartate aminotransferase SGO_1297 -0.947 5.196 12.0147 11.500 0.0053 0.0026 7.3767 4.000 12.000 2.500 12.0000 5.2565 substrate-binding protein MsmE SGO_1305 -0.574 7.684 62.6851 60.000 0.0079 0.0057 46.1045 25.000 60.000 17.500 60.0000 36.7954 pepT; peptidase T SGO_1312 0.733 7.891 41.2677 39.500 0.0043 0.0012 76.5335 41.500 48.000 34.000 48.0000 71.4882 rpsP; ribosomal protein S16 SGO_1323 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 32

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 32 -0.917 5.317 12.5370 12.000 0.0026 0.0005 6.4546 3.500 13.500 3.500 13.5000 7.3591 HAD-superfamily subfamily IIA hydrolase, TIGR01457 SGO_1327 -0.793 5.338 13.5818 13.000 0.0073 0.0051 6.4546 3.500 12.000 4.000 12.0000 8.4104 pcrA; ATP-dependent DNA helicase PcrA SGO_1336 -0.104 11.699 839.4586 803.500 0.0426 0.0899 837.2577 454.000 882.500 364.500 882.5000 766.3954 pyk; pyruvate kinase SGO_1339 -0.128 9.949 257.0091 246.000 0.0114 0.0111 229.6004 124.500 259.000 115.500 259.0000 242.8496 Phosphofructokinase SGO_1340 0.066 9.004 133.7283 128.000 0.1095 0.3209 130.9368 71.000 117.500 62.500 117.5000 131.4121 ABC transporter, ATP-binding protein SP1715 SGO_1342 -2.148 5.375 18.2832 17.500 0.0143 0.0158 19.000 2.000 19.0000 4.2052 rumA-2; 23S rRNA (uracil-5-)methyltransferase RumA SGO_1364 0.541 3.376 4.1790 4.000 0.1526 0.4924 2.000 2.000 2.0000 4.2052 transcription regulator yrfE SGO_1365 -0.910 4.724 9.4028 9.000 0.0565 0.1337 5.5325 3.000 11.500 11.5000 L-2-hydroxyisocaproate dehydrogenase SGO_1369 0.392 6.928 28.7307 27.500 0.0178 0.0228 32.2731 17.500 24.000 17.500 24.0000 36.7954 Protein of unknown function (DUF964) superfamily SGO_1370 -0.629 5.106 12.5370 12.000 0.0352 0.0663 13.500 4.000 13.5000 8.4104 aroC; chorismate synthase SGO_1372 -0.318 4.272 6.7909 6.500 0.0284 0.0487 5.5325 3.000 7.000 7.0000 aroB; 3-dehydroquinate synthase SGO_1373 -0.556 5.207 16.7160 16.000 0.1164 0.3516 9.2209 5.000 11.000 11.0000 aroD; 3-dehydroquinate dehydratase, type I SGO_1375 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 33

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 33 -1.576 5.577 17.2384 16.500 0.0051 0.0025 8.2988 4.500 18.000 2.000 18.0000 4.2052 sulfatase SGO_1377 -0.400 5.525 10.4475 10.000 0.0533 0.1243 10.1430 5.500 16.000 4.500 16.0000 9.4617 csn1; CRISPR-associated protein, Csn1 family SGO_1381 0.121 8.897 106.5647 102.000 0.0576 0.1374 120.7938 65.500 122.000 60.500 122.0000 127.2069 rplS; ribosomal protein L19 SGO_1383 0.065 4.991 8.3580 8.000 0.1897 0.6735 10.1430 5.500 7.000 3.000 7.0000 6.3078 ligA; DNA ligase, NAD-dependent SGO_1390 -0.516 6.352 26.6412 25.500 0.0165 0.0202 15.6755 8.500 21.500 8.500 21.5000 17.8720 map; methionine aminopeptidase, type I SGO_1397 -0.450 5.155 10.4475 10.000 0.1586 0.5277 11.9872 6.500 9.000 2.000 9.0000 4.2052 murA-2; UDP-N-acetylglucosamine 1carboxyvinyltransferase SGO_1400 1.446 4.504 2.6119 2.500 0.0057 0.0031 9.2209 5.000 3.500 3.500 3.5000 7.3591 rexB; putative exonuclease RexB SGO_1414 0.752 6.562 17.7608 17.000 0.0229 0.0351 23.9743 13.000 17.000 17.000 17.0000 35.7441 hypothetical protein SGO_1422 SGO_1422 0.293 14.775 6164.5617 5900.500 0.0037 0.0009 7586.9564 4114.000 6433.500 3729.500 6433.5000 7841.6227 eno; enolase SGO_1426 -0.341 8.748 122.7584 117.500 0.0026 0.0005 94.9753 51.500 117.500 45.000 117.5000 94.6167 EzrA; Septation ring formation regulator ezrA SGO_1431 -0.502 7.053 32.3873 31.000 0.0667 0.1681 35.9615 19.500 44.500 9.500 44.5000 19.9746 gyrB; DNA gyrase, B subunit SGO_1432 -0.345 3.738 3.6566 3.500 0.1566 0.5087 3.6884 2.000 6.000 6.0000 thiJ; 4-methyl-5(beta-hydroxyethyl)thiazole monophosphate synthesis protein SGO_1434 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 34

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 34 0.801 5.885 11.4923 11.000 0.0103 0.0094 16.5976 9.000 10.000 10.000 10.0000 21.0259 ftsX; cell division protein FtsX SGO_1439 -0.761 6.532 28.2083 27.000 0.0017 0.0002 17.5197 9.500 30.000 8.000 30.0000 16.8207 cell-division ATP-binding protein FtsE SGO_1440 -0.331 6.072 14.1042 13.500 0.1586 0.5279 21.2081 11.500 22.500 4.500 22.5000 9.4617 prfB; peptide chain release factor 2 SGO_1441 -2.303 5.644 19.3279 18.500 0.0026 0.0006 5.5325 3.000 22.000 1.500 22.0000 3.1539 murF; UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase SGO_1446 -0.928 6.423 30.8202 29.500 0.0057 0.0032 14.7534 8.000 25.500 7.000 25.5000 14.7182 ddlA; D-Ala-D-Ala ligase SGO_1447 -0.361 5.099 10.9699 10.500 0.2139 0.7870 3.6884 2.000 7.000 6.000 7.0000 12.6156 hypothetical protein SGO_1450 SGO_1450 0.752 7.695 38.6558 37.000 0.0032 0.0008 61.7800 33.500 38.500 32.500 38.5000 68.3343 frr; ribosome recycling factor SGO_1451 -0.243 7.184 47.5362 45.500 0.0848 0.2275 32.2731 17.500 32.000 16.000 32.0000 33.6415 pyrH; uridylate kinase SGO_1452 0.282 5.393 12.0147 11.500 0.1618 0.5445 18.4418 10.000 5.500 11.5643 glycosyl transferase, family 8 SP1766 SGO_1453 -0.007 10.022 217.3085 208.000 0.2492 0.9697 216.6911 117.500 304.000 143.500 304.0000 301.7222 rplA; ribosomal protein L1 SGO_1455 0.777 8.133 43.3572 41.500 0.0094 0.0079 83.9102 45.500 61.000 44.000 61.0000 92.5141 rplK; ribosomal protein L11 SGO_1456 0.287 3.299 3.6566 3.500 0.1503 0.4830 3.6884 2.000 2.500 2.5000 aha1; cation-transporting ATPase yfgQ SGO_1458 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 35

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 35 -0.608 4.901 11.4923 11.000 0.0251 0.0404 7.3767 4.000 11.000 11.0000 DNA translocase ftsK SGO_1460 -0.139 5.848 16.7160 16.000 0.1013 0.2915 14.7534 8.000 13.500 6.000 13.5000 12.6156 peptidyl-prolyl cis-trans isomerase SGO_1463 -0.793 5.996 20.8950 20.000 0.0050 0.0018 12.9093 7.000 19.500 5.000 19.5000 10.5130 uncharacterized probable metal-binding protein SGO_1464 -0.686 6.485 31.3426 30.000 0.0158 0.0184 18.4418 10.000 24.000 7.500 24.0000 15.7695 ABC transporter, ATP-binding protein SP0770 SGO_1465 -0.052 7.514 44.9244 43.000 0.1588 0.5306 41.4940 22.500 48.000 23.000 48.0000 48.3597 glmU; UDP-N-acetylglucosamine pyrophosphorylase SGO_1469 -0.828 3.906 7.8356 7.500 0.1256 0.3862 4.000 1.500 4.0000 3.1539 acetyltransferase, GNAT family SGO_1472 -0.925 5.776 14.6265 14.000 0.0172 0.0219 9.2209 5.000 21.500 4.500 21.5000 9.4617 lacD-2; tagatose 1,6-diphosphate aldolase SGO_1516 -0.402 7.851 68.9537 66.000 0.0073 0.0049 47.9487 26.000 62.500 24.500 62.5000 51.5135 methionine-tRNA ligase SGO_1530 -0.715 5.962 20.8950 20.000 0.0212 0.0304 9.2209 5.000 17.500 7.000 17.5000 14.7182 xth; exodeoxyribonuclease III SGO_1531 0.195 5.182 16.1937 15.500 0.2345 0.8886 7.500 6.000 7.5000 12.6156 ArsC family SGO_1534 -0.779 5.622 19.8503 19.000 0.0396 0.0794 7.3767 4.000 11.500 5.000 11.5000 10.5130 conserved hypothetical protein TIGR00096 SGO_1536 0.084 6.150 15.6713 15.000 0.1727 0.5986 14.7534 8.000 18.500 10.500 18.5000 22.0772 tmk; thymidylate kinase SGO_1539 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 36 -0.596 5.759 16.1937 15.500 0.0271 0.0458 8.2988 4.500 16.000 6.500 16.0000 13.6669 atpC; ATP synthase F1, epsilon subunit SGO_1541 -0.014 9.171 139.9968 134.000 0.2260 0.8480 134.6251 73.000 149.500 72.500 149.5000 152.4380 atpD; ATP synthase F1, beta subunit SGO_1542 -1.264 5.625 17.7608 17.000 0.0026 0.0005 8.2988 4.500 17.000 3.000 17.0000 6.3078 atpG; ATP synthase F1, gamma subunit SGO_1543 0.051 9.229 143.6535 137.500 0.1101 0.3231 145.6902 79.000 151.000 76.000 151.0000 159.7971 atpA; ATP synthase F1, alpha subunit SGO_1544 -0.805 5.751 17.2384 16.500 0.0010 0.0001 10.1430 5.500 17.000 4.500 17.0000 9.4617 atpH; ATP synthase F1, delta subunit SGO_1545 -0.137 6.983 38.6558 37.000 0.1164 0.3521 30.4290 16.500 28.000 14.000 28.0000 29.4363 atpF; ATP synthase F0, B subunit SGO_1546 -0.554 7.392 51.7152 49.500 0.0092 0.0072 30.4290 16.500 48.000 18.000 48.0000 37.8467 glgP-1; glycogen phosphorylase SGO_1550 -0.272 5.395 14.6265 14.000 0.1285 0.4007 7.3767 4.000 8.500 5.500 8.5000 11.5643 glgA; Glycogen synthase SGO_1551 0.226 7.345 49.1034 47.000 0.1627 0.5498 50.7149 27.500 27.000 17.000 27.0000 35.7441 glgD; glucose-1-phosphate adenylyltransferase, GlgD subunit SGO_1552 -0.314 7.391 47.0139 45.000 0.0050 0.0021 35.9615 19.500 46.000 18.500 46.0000 38.8980 glgC; glucose-1-phosphate adenylyltransferase SGO_1553 -0.014 7.510 46.4915 44.500 0.2269 0.8526 42.4161 23.000 45.000 23.000 45.0000 48.3597 glgB; 1,4-alpha-glucan branching enzyme SGO_1554 -0.372 10.552 428.3485 410.000 0.0100 0.0088 301.5234 163.500 417.500 168.500 417.5000 354.2870 ptsI; phosphoenolpyruvate-protein phosphotransferase SGO_1555 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 37 0.890 11.617 475.8847 455.500 0.0158 0.0186 862.1541 467.500 622.500 561.500 622.5000 1180.6063 phosphocarrier protein HPr SGO_1556 -0.072 8.045 67.3865 64.500 0.0087 0.0065 63.6242 34.500 68.000 31.000 68.0000 65.1804 nrdE; ribonucleoside-diphosphate reductase large chain SGO_1558 0.143 8.182 72.0879 69.000 0.0200 0.0282 75.6114 41.000 66.000 36.500 66.0000 76.7447 ribonucleoside-diphosphate reductase, beta subunit SGO_1559 -0.417 8.885 145.7430 139.500 0.0185 0.0248 92.2090 50.000 124.500 52.500 124.5000 110.3862 alaS; alanyl-tRNA synthetase SGO_1570 -0.272 8.868 129.0269 123.500 0.0050 0.0020 102.3520 55.500 126.500 52.000 126.5000 109.3349 pepF-1; oligoendopeptidase F SGO_1574 -0.150 5.058 9.4028 9.000 0.1529 0.4943 6.4546 3.500 8.000 4.500 8.0000 9.4617 PTS system, Lactose/Cellobiose specific IIB subunit SGO_1580 0.456 3.557 1.5671 1.500 0.2327 0.8803 6.000 2.000 6.0000 4.2052 D-Alanyl-D-Alanine carboxypeptidase SGO_1585 -0.654 5.537 18.2832 17.500 0.0426 0.0902 9.2209 5.000 10.500 4.000 10.5000 8.4104 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase SGO_1587 -0.291 5.239 13.0594 12.500 0.0865 0.2333 8.2988 4.500 8.000 4.000 8.0000 8.4104 arcC; carbamate kinase SGO_1591 0.316 8.455 77.8341 74.500 0.0271 0.0457 107.8845 58.500 78.000 41.500 78.0000 87.2576 arcB; ornithine carbamoyltransferase SGO_1592 0.493 8.251 60.5956 58.000 0.0030 0.0007 87.5985 47.500 66.000 43.000 66.0000 90.4115 arcA; arginine deiminase SGO_1593 -0.140 9.050 133.2059 127.500 0.0520 0.1195 134.6251 73.000 144.500 56.000 144.5000 117.7452 sodA; manganese-dependent superoxide dismutase SGO_1599 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 38 -0.886 3.902 6.7909 6.500 0.0769 0.2010 5.000 1.500 5.0000 3.1539 acyltransferase family protein SGO_1604 -1.322 4.245 7.3133 7.000 0.0396 0.0791 8.500 1.500 8.5000 3.1539 P-type ATPase, metal cation transport SGO_1605 -0.173 7.225 38.6558 37.000 0.0366 0.0712 37.8057 20.500 40.500 15.500 40.5000 32.5902 ATP-dependent RNA helicase, DEAD/DEAH box family SGO_1609 -0.226 5.887 11.4923 11.000 0.1256 0.3856 11.9872 6.500 21.000 7.000 21.0000 14.7182 prfC; peptide chain release factor 3 SGO_1617 -0.025 8.040 76.2669 73.000 0.2193 0.8120 70.0788 38.000 57.000 28.500 57.0000 59.9239 cation-transporting ATPase, E1-E2 family SGO_1619 -1.273 4.429 8.3580 8.000 0.0358 0.0691 3.6884 2.000 9.500 9.5000 HD domain protein SGO_1621 0.319 5.077 7.3133 7.000 0.0728 0.1866 7.3767 4.000 7.500 5.500 7.5000 11.5643 Cof family protein SGO_1622 -0.623 5.081 13.0594 12.500 0.0248 0.0397 8.2988 4.500 12.500 12.5000 murM; MurM SGO_1623 0.326 4.258 6.2685 6.000 0.0656 0.1623 5.500 3.500 5.5000 7.3591 murN; MurN protein SGO_1624 -0.898 6.496 30.2978 29.000 0.0094 0.0077 19.3639 10.500 28.000 6.000 28.0000 12.6156 acetoin utilization putative/CBS domain protein SGO_1625 -0.006 6.193 16.7160 16.000 0.2367 0.9031 17.5197 9.500 20.000 9.000 20.0000 18.9233 branched-chain amino acid ABC transporter, ATP-binding protein SGO_1626 0.065 6.204 19.3279 18.500 0.1828 0.6418 22.1302 12.000 16.500 7.500 16.5000 15.7695 branched-chain amino acid ABC transporter, ATP-binding protein SGO_1627 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 39 -0.444 9.189 169.2499 162.000 0.0012 0.0001 126.3263 68.500 167.000 57.500 167.0000 120.8991 branched-chain amino acid ABC transporter, amino acid-binding protein SGO_1630 0.618 7.022 23.5069 22.500 0.0768 0.1997 23.0522 12.500 24.500 28.000 24.5000 58.8726 clpP; ATP-dependent Clp protease, proteolytic subunit ClpP SGO_1632 -0.097 7.949 62.6851 60.000 0.1841 0.6500 71.0009 38.500 64.000 23.500 64.0000 49.4109 upp; uracil phosphoribosyltransferase SGO_1633 -0.261 9.108 130.0717 124.500 0.0541 0.1270 130.0147 70.500 172.000 57.000 172.0000 119.8478 ppx1; inorganic pyrophosphatase, manganese-dependent SGO_1648 0.029 3.498 2.6119 2.500 0.2429 0.9375 3.6884 2.000 5.000 5.0000 act; pyruvate formate-lyase-activating enzyme SGO_1649 -0.197 6.691 27.6859 26.500 0.0007 0.0000 23.9743 13.000 27.500 11.500 27.5000 24.1798 intracellular glycosyl hydrolase SGO_1652 -0.301 7.020 33.9545 32.500 0.1579 0.5204 19.3639 10.500 35.500 19.500 35.5000 41.0006 trehalose PTS enzyme II SGO_1653 -1.505 5.335 16.1937 15.500 0.0052 0.0026 6.4546 3.500 13.500 2.000 13.5000 4.2052 trkA; potassium uptake protein, Trk family SGO_1666 0.006 6.372 23.5069 22.500 0.2463 0.9553 20.2860 11.000 18.000 10.000 18.0000 21.0259 ribosomal large subunit pseudouridine synthase B SGO_1669 -0.161 5.315 8.8804 8.500 0.1661 0.5658 7.3767 4.000 12.000 5.500 12.0000 11.5643 HAM1 protein-like protein SGO_1675 -0.645 5.659 15.1489 14.500 0.0113 0.0108 8.2988 4.500 15.500 5.500 15.5000 11.5643 murI; glutamate racemase SGO_1676 -0.523 4.291 10.9699 10.500 0.1651 0.5609 4.6104 2.500 4.000 4.0000 lysA; diaminopimelate decarboxylase SGO_1678 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 40

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 40 -0.165 9.433 206.8610 198.000 0.0933 0.2616 151.2228 82.000 159.500 82.500 159.5000 173.4640 phosphotransferase system enzyme II SGO_1679 0.823 5.498 11.4923 11.000 0.0228 0.0348 21.2081 11.500 12.500 12.5000 phosphotransferase system enzyme II SGO_1680 0.003 8.594 97.1620 93.000 0.2354 0.8967 84.8323 46.000 95.000 52.000 95.0000 109.3349 PTS system, mannose/fructose/sorbose family, IID component SGO_1681 -0.191 7.970 69.9984 67.000 0.0457 0.0994 63.6242 34.500 63.500 25.500 63.5000 53.6161 serS; seryl-tRNA synthetase SGO_1683 0.009 6.534 25.0741 24.000 0.2382 0.9134 20.2860 11.000 21.000 12.500 21.0000 26.2824 acyl-CoA dehydrogenase family SGO_1684 0.271 8.571 87.7592 84.000 0.0582 0.1392 120.7938 65.500 83.500 42.000 83.5000 88.3089 putative peroxidase / antioxidase SGO_1685 0.153 7.586 48.5810 46.500 0.0385 0.0760 51.6370 28.000 42.500 23.500 42.5000 49.4109 accA; acetyl-CoA carboxylase, carboxyl transferase, alpha subunit SGO_1687 -0.983 5.513 15.1489 14.500 0.0057 0.0032 9.2209 5.000 15.000 3.000 15.0000 6.3078 accD; acetyl-CoA carboxylase, carboxyl transferase, beta subunit SGO_1688 -0.110 7.385 41.7901 40.000 0.0381 0.0748 41.4940 22.500 45.000 18.500 45.0000 38.8980 accC; acetyl-CoA carboxylase, biotin carboxylase SGO_1689 -1.456 5.603 16.7160 16.000 0.0713 0.1821 7.3767 4.000 24.500 24.5000 fabZ; beta-hydroxyacyl-(acyl-carrierprotein) dehydratase FabZ SGO_1690 -0.614 8.006 80.9683 77.500 0.0102 0.0092 44.2603 24.000 74.000 27.500 74.0000 57.8213 accB; acetyl-CoA carboxylase, biotin carboxyl carrier protein SGO_1691 -0.472 9.471 204.7715 196.000 0.0019 0.0003 143.8460 78.000 207.500 73.000 207.5000 153.4893 3-oxoacyl-[acyl-carrier-protein] synthase SGO_1692 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 41

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 41 -0.542 6.773 33.9545 32.500 0.0397 0.0812 28.5848 15.500 30.000 8.000 30.0000 16.8207 fabG; 3-oxoacyl-(acyl-carrier-protein) reductase SGO_1693 -0.793 6.806 31.3426 30.000 0.0204 0.0291 25.8185 14.000 39.000 7.500 39.0000 15.7695 fabD; malonyl CoA-acyl carrier protein transacylase SGO_1694 -0.487 9.411 221.4875 212.000 0.0306 0.0534 163.2099 88.500 175.000 57.500 175.0000 120.8991 enoyl-acyl carrier protein(ACP) reductase SGO_1695 -0.663 4.951 13.5818 13.000 0.0888 0.2445 10.000 3.500 10.0000 7.3591 transcriptional regulator, MarR family SGO_1699 -1.291 5.028 14.1042 13.500 0.0264 0.0438 5.5325 3.000 13.000 13.0000 enoyl-CoA hydratase/isomerase family protein SGO_1700 -0.447 7.468 51.1929 49.000 0.0184 0.0246 32.2731 17.500 50.500 20.500 50.5000 43.1032 aspartate kinase SGO_1701 -0.248 8.165 73.6550 70.500 0.0330 0.0603 59.9358 32.500 82.000 34.000 82.0000 71.4882 amiF; Oligopeptide transport ATP-binding protein amiF SGO_1708 -0.168 8.469 87.2368 83.500 0.1043 0.3029 71.9230 39.000 99.500 45.500 99.5000 95.6680 amiE; Oligopeptide transport ATP-binding protein SGO_1709 0.468 5.086 8.3580 8.000 0.0227 0.0342 10.1430 5.500 6.000 4.500 6.0000 9.4617 amiD; Oligopeptide transport system permease protein SGO_1710 0.231 7.297 34.9992 33.500 0.0594 0.1436 36.8836 20.000 37.000 23.000 37.0000 48.3597 hppB; Oligopeptide transport system permease SGO_1711 0.242 10.111 253.8748 243.000 0.0051 0.0024 307.9781 167.000 252.500 138.500 252.5000 291.2092 hppA; oligopeptide-binding lipoprotein SGO_1712 0.244 9.467 167.1604 160.000 0.0073 0.0050 187.1843 101.500 157.000 93.500 157.0000 196.5925 hppG; oligopeptide-binding lipoprotein SGO_1713 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 42 0.004 8.157 68.9537 66.000 0.2404 0.9264 67.3126 36.500 73.500 36.000 73.5000 75.6934 hppH; oligopeptide-binding lipoprotein SGO_1715 0.121 8.584 94.0277 90.000 0.1586 0.5254 130.0147 70.500 86.000 35.000 86.0000 73.5908 oligopeptide binding protein SGO_1716 -0.288 6.851 32.9097 31.500 0.1156 0.3481 19.3639 10.500 29.500 16.000 29.5000 33.6415 sufB-1; FeS assembly protein SufB SGO_1718 -1.053 5.634 16.1937 15.500 0.0073 0.0051 10.1430 5.500 17.000 3.000 17.0000 6.3078 aminotransferase, class-V SGO_1720 -0.178 7.092 33.9545 32.500 0.0300 0.0521 31.3511 17.000 38.500 15.500 38.5000 32.5902 sufD; FeS assembly protein SufD SGO_1721 -0.328 6.304 19.8503 19.000 0.1360 0.4258 11.9872 6.500 23.000 11.500 23.0000 24.1798 sufC; FeS assembly ATPase SufC SGO_1722 -0.089 6.612 22.9846 22.000 0.1273 0.3962 22.1302 12.000 27.500 12.000 27.5000 25.2311 amino acid ABC transporter, amino acidbinding/permease protein SGO_1727 0.361 6.099 17.7608 17.000 0.0393 0.0781 19.3639 10.500 12.500 9.000 12.5000 18.9233 glnQ; glutamine ABC transporter ATPbinding protein SGO_1728 -0.556 6.362 21.4174 20.500 0.0426 0.0903 21.2081 11.500 27.000 6.000 27.0000 12.6156 hypothetical protein SGO_1729 SGO_1729 0.232 8.334 63.2075 60.500 0.0701 0.1788 82.9881 45.000 86.000 43.000 86.0000 90.4115 SPFH domain/Band 7 family SGO_1730 -0.354 5.984 15.1489 14.500 0.0428 0.0909 12.9093 7.000 20.500 7.000 20.5000 14.7182 DNA-binding response regulator SGO_1731 -0.312 8.854 129.0269 123.500 0.0071 0.0047 108.8066 59.000 127.000 46.500 127.0000 97.7706 hypothetical protein SGO_1735 SGO_1735 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 43 -1.070 5.272 17.7608 17.000 0.0656 0.1608 7.3767 4.000 13.500 13.5000 alkaline shock protein SGO_1736 0.286 12.325 1123.1089 1075.000 0.0441 0.0943 1227.3018 665.500 1177.500 762.000 1177.5000 1602.1763 fba; fructose-1,6-bisphosphate aldolase, class II SGO_1745 1.483 3.270 2.6119 2.500 0.0461 0.1009 5.5325 3.000 1.500 1.5000 hypothetical protein SGO_1747 SGO_1747 -0.504 5.487 9.9251 9.500 0.0660 0.1637 11.0651 6.000 16.500 3.500 16.5000 7.3591 pyrG; CTP synthase SGO_1748 -0.974 6.290 21.9398 21.000 0.0133 0.0144 14.7534 8.000 30.000 5.500 30.0000 11.5643 manA; mannose-6-phosphate isomerase, class I SGO_1749 -0.613 7.025 44.4020 42.500 0.0163 0.0196 23.9743 13.000 34.500 13.000 34.5000 27.3337 scrK; fructokinase SGO_1755 -0.650 8.174 85.6697 82.000 0.0050 0.0019 51.6370 28.000 90.500 29.000 90.5000 60.9752 glmS; glucosamine--fructose-6-phosphate aminotransferase SGO_1757 0.094 7.454 37.6111 36.000 0.1393 0.4415 46.1045 25.000 47.500 21.000 47.5000 44.1545 ABC transporter, substrate-binding protein SP0092 SGO_1763 0.361 5.406 10.9699 10.500 0.0878 0.2411 9.2209 5.000 7.500 7.000 7.5000 14.7182 alcohol dehydrogenase, zinc-containing SGO_1774 0.226 8.242 73.1327 70.000 0.0100 0.0089 81.1439 44.000 66.500 39.000 66.5000 82.0011 leuS; leucyl-tRNA synthetase SGO_1784 -0.270 8.319 84.1026 80.500 0.0358 0.0694 81.1439 44.000 90.000 30.500 90.0000 64.1291 endopeptidase O SGO_1799 -0.676 6.165 22.9846 22.000 0.0092 0.0071 11.9872 6.500 21.000 7.500 21.0000 15.7695 troB; manganese ABC transporter, ATPbinding protein SP1648 SGO_1800 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 44 -0.634 8.464 124.8479 119.500 0.0272 0.0462 79.2997 43.000 90.000 28.000 90.0000 58.8726 Metal ABC transporter substrate-binding lipoprotein precursor SGO_1802 -0.115 6.871 30.8202 29.500 0.1727 0.5975 23.0522 12.500 29.500 16.000 29.5000 33.6415 tpx; thioredoxin peroxidase SGO_1803 -1.458 6.549 39.7006 38.000 0.0146 0.0165 17.5197 9.500 28.000 4.000 28.0000 8.4104 hutU; urocanate hydratase SGO_1805 -0.584 5.473 12.0147 11.500 0.0226 0.0335 7.3767 4.000 14.500 5.000 14.5000 10.5130 ftcD; glutamate formiminotransferase SGO_1806 1.477 4.890 4.1790 4.000 0.0163 0.0196 8.2988 4.500 3.500 6.500 3.5000 13.6669 fhs-2; formate--tetrahydrofolate ligase SGO_1808 -0.913 4.325 7.8356 7.500 0.0131 0.0141 8.000 2.000 8.0000 4.2052 hutH; histidine ammonia-lyase SGO_1811 -0.149 4.569 8.3580 8.000 0.0583 0.1398 7.3767 4.000 8.000 8.0000 relA; GTP diphosphokinase SGO_1822 -0.476 5.675 14.6265 14.000 0.0116 0.0115 11.9872 6.500 15.000 4.500 15.0000 9.4617 prmA; ribosomal protein L11 methyltransferase SGO_1824 0.472 3.741 2.6119 2.500 0.1647 0.5585 5.500 2.500 5.5000 5.2565 ATPase, AAA family SGO_1828 0.489 7.108 37.0887 35.500 0.0493 0.1104 41.4940 22.500 21.500 18.000 21.5000 37.8467 hypothetical protein SGO_1834 SGO_1834 1.837 4.414 3.6566 3.500 0.0114 0.0111 4.000 6.500 4.0000 13.6669 hypothetical protein SGO_1835 SGO_1835 -0.059 7.934 69.9984 67.000 0.1835 0.6466 54.4033 29.500 55.000 31.000 55.0000 65.1804 pepS; aminopeptidase PepS SGO_1843 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 45

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 45 -1.041 5.171 13.0594 12.500 0.0100 0.0089 4.6104 2.500 11.000 3.500 11.0000 7.3591 cbxX/cfqX family protein SGO_1844 -0.863 4.872 10.9699 10.500 0.0339 0.0631 12.000 3.000 12.0000 6.3078 polC; DNA polymerase III, alpha subunit, Gram-positive type SGO_1847 -0.036 4.690 6.7909 6.500 0.2404 0.9247 4.6104 2.500 6.000 4.000 6.0000 8.4104 lipoprotein, putative SGO_1848 -0.011 8.612 103.9529 99.500 0.2296 0.8672 102.3520 55.500 92.500 44.000 92.5000 92.5141 proS; prolyl-tRNA synthetase SGO_1851 0.033 4.627 9.4028 9.000 0.2454 0.9485 8.2988 4.500 7.000 7.0000 membrane-associated zinc metalloprotease, putative SGO_1852 0.121 5.798 16.7160 16.000 0.1989 0.7144 11.0651 6.000 10.000 8.500 10.0000 17.8720 uppS; undecaprenyl diphosphate synthase SGO_1854 0.023 5.751 14.6265 14.000 0.2247 0.8416 15.6755 8.500 12.000 5.500 12.0000 11.5643 ATP-dependent proteinase ATP-binding chain SGO_1856 -0.414 7.507 55.3719 53.000 0.0146 0.0165 35.9615 19.500 48.500 20.000 48.5000 42.0519 5'-nucleotidase, lipoprotein e(P4) family SGO_1860 -1.866 4.710 12.0147 11.500 0.0246 0.0386 11.000 1.500 11.0000 3.1539 nusB; transcription antitermination factor NusB SGO_1861 0.067 6.752 27.6859 26.500 0.0956 0.2722 26.7406 14.500 25.000 13.500 25.0000 28.3850 alkaline shock protein SGO_1862 -0.035 8.179 72.0879 69.000 0.1094 0.3198 73.7672 40.000 74.500 33.000 74.5000 69.3856 efp; Elongation factor P (EF-P) SGO_1863 -0.032 7.000 31.3426 30.000 0.2382 0.9116 41.4940 22.500 32.000 11.000 32.0000 23.1285 X-Pro aminopeptidase SGO_1864 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 46

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 46 -0.582 5.878 17.7608 17.000 0.0007 0.0000 11.9872 6.500 17.500 5.500 17.5000 11.5643 uvrA; excinuclease ABC, A subunit SGO_1865 1.334 3.687 3.6566 3.500 9.2209 5.000 corA; magnesium and cobalt transporter SGO_1866 0.335 7.252 32.9097 31.500 0.0477 0.1060 49.7929 27.000 34.000 17.000 34.0000 35.7441 hypothetical protein SGO_1867 SGO_1867 0.215 7.603 48.0586 46.000 0.0228 0.0348 50.7149 27.500 42.000 25.500 42.0000 53.6161 rpsR; ribosomal protein S18 SGO_1879 -0.388 8.214 79.9236 76.500 0.0069 0.0045 65.4684 35.500 88.500 30.000 88.5000 63.0778 ssb-1; single-strand binding protein SGO_1880 -0.231 9.505 223.5770 214.000 0.0656 0.1618 176.1192 95.500 170.000 74.500 170.0000 156.6432 rpsF; ribosomal protein S6 SGO_1881 -1.092 5.641 14.1042 13.500 0.0125 0.0131 7.3767 4.000 20.000 4.000 20.0000 8.4104 folE; GTP cyclohydrolase I SGO_1882 -0.214 9.596 208.9505 200.000 0.0050 0.0022 174.2750 94.500 206.500 87.500 206.5000 183.9769 groL; 60 kDa chaperonin/groEL protein SGO_1885 -0.844 5.401 17.7608 17.000 0.0466 0.1028 5.5325 3.000 9.500 4.500 9.5000 9.4617 groES; chaperonin, 10 kDa SGO_1886 -0.259 5.592 11.4923 11.000 0.1219 0.3717 13.8313 7.500 14.500 4.000 14.5000 8.4104 PTS system, fructose(mannose)-specific IIB SGO_1892 -0.675 7.534 55.8943 53.500 0.0026 0.0006 37.8057 20.500 58.000 16.000 58.0000 33.6415 glutamyl aminopeptidase SGO_1898 -0.352 6.462 29.2531 28.000 0.0503 0.1141 18.4418 10.000 20.500 9.500 20.5000 19.9746 tRNA binding domain SGO_1901 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 47

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 47 -0.339 9.940 304.0230 291.000 0.0402 0.0826 241.5876 131.000 244.500 91.500 244.5000 192.3873 ssb; single-stranded DNA-binding protein SGO_1902 0.056 7.626 46.4915 44.500 0.1705 0.5878 44.2603 24.000 50.000 27.000 50.0000 56.7700 ATP-dependent Zn protease SGO_1903 0.052 3.628 3.6566 3.500 0.2193 0.8139 4.500 2.000 4.5000 4.2052 folP; dihydropteroate synthase SGO_1914 -0.106 8.144 73.6550 70.500 0.0163 0.0194 70.0788 38.000 73.000 31.500 73.0000 66.2317 ackA; acetate kinase SGO_1916 0.042 5.049 9.4028 9.000 0.2247 0.8395 8.2988 4.500 7.000 4.000 7.0000 8.4104 hypothetical protein SGO_1917 SGO_1917 -0.471 6.528 22.4622 21.500 0.0494 0.1109 15.6755 8.500 31.000 11.000 31.0000 23.1285 comYA; competence protein comYA SGO_1924 0.039 10.167 289.3964 277.000 0.0956 0.2716 283.0816 153.500 277.500 142.500 277.5000 299.6196 rpoC; DNA-directed RNA polymerase, beta chain SGO_1926 0.150 9.994 238.2036 228.000 0.0423 0.0883 249.8864 135.500 244.500 136.500 244.5000 287.0040 rpoB; DNA-directed RNA polymerase, beta subunit SGO_1927 -0.421 4.347 7.3133 7.000 0.0219 0.0317 5.5325 3.000 7.500 7.5000 pbp1b; penicillin-binding protein 1B SGO_1928 -0.655 9.026 171.8618 164.500 0.0087 0.0065 93.1311 50.500 147.000 52.000 147.0000 109.3349 tyrS; tyrosyl-tRNA synthetase SGO_1929 -0.550 6.741 33.4321 32.000 0.0107 0.0101 19.3639 10.500 30.000 11.500 30.0000 24.1798 adcA; metal-binding (Mn) permease precursor, lipoprotein SGO_1936 -0.481 10.205 365.6633 350.000 0.0116 0.0114 225.9120 122.500 321.500 127.000 321.5000 267.0294 rplQ; ribosomal protein L17 SGO_1958 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 48

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 48 -0.145 9.035 130.5941 125.000 0.0322 0.0578 121.7159 66.000 145.000 60.500 145.0000 127.2069 rpoA; DNA-directed RNA polymerase, alpha subunit SGO_1959 0.040 7.986 59.0285 56.500 0.1586 0.5270 66.3905 36.000 66.000 29.500 66.0000 62.0265 rpsK; ribosomal protein S11 SGO_1960 -1.119 9.386 241.8602 231.500 0.0026 0.0006 100.5078 54.500 216.500 52.500 216.5000 110.3862 rpsM; ribosomal protein S13p/S18e SGO_1961 0.805 5.815 11.4923 11.000 0.0818 0.2172 25.8185 14.000 19.000 19.0000 rpmJ; ribosomal protein L36 SGO_1962 0.384 8.500 78.8788 75.500 0.0076 0.0054 96.8194 52.500 78.000 51.500 78.0000 108.2836 adk; Adenylate kinase (ATP-AMP transphosphorylase) SGO_1964 0.121 5.444 9.4028 9.000 0.0928 0.2595 11.0651 6.000 11.500 5.500 11.5000 11.5643 Preprotein translocase secY subunit SGO_1965 -0.081 8.956 98.2067 94.000 0.1835 0.6466 106.0403 57.500 160.000 63.000 160.0000 132.4634 rplO; ribosomal protein L15 SGO_1966 -0.897 8.463 121.1913 116.000 0.0054 0.0028 54.4033 29.500 108.000 33.000 108.0000 69.3856 50S ribosomal protein L30 -related protein SGO_1967 -0.439 9.855 274.7699 263.000 0.0048 0.0017 203.7819 110.500 258.000 90.000 258.0000 189.2334 rpsE; ribosomal protein S5 SGO_1968 0.025 10.151 282.6055 270.500 0.0183 0.0240 288.6142 156.500 281.000 135.500 281.0000 284.9014 rplR; ribosomal protein L18 SGO_1969 0.135 9.595 186.4883 178.500 0.1111 0.3304 233.2888 126.500 180.000 82.500 180.0000 173.4640 BL10; 50S ribosomal protein L6 SGO_1970 0.393 10.912 429.9156 411.500 0.0327 0.0590 626.0991 339.500 398.500 224.500 398.5000 472.0323 rpsH; ribosomal protein S8 SGO_1971 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 49

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 49 0.268 9.741 197.9806 189.500 0.0248 0.0399 253.5747 137.500 189.500 102.000 189.5000 214.4645 BL6; 50S ribosomal protein L5 SGO_1973 0.831 8.830 77.8341 74.500 0.0071 0.0046 131.8589 71.500 85.500 76.000 85.5000 159.7971 rplX; ribosomal protein L24 SGO_1974 0.553 8.865 96.6396 92.500 0.0092 0.0073 127.2484 69.000 92.000 71.500 92.0000 150.3354 rplN; ribosomal protein L14 SGO_1975 -0.862 8.785 126.9374 121.500 0.0140 0.0153 94.9753 51.500 156.000 30.000 156.0000 63.0778 BS16; 30S ribosomal protein SGO_1976 0.361 6.208 14.1042 13.500 0.0684 0.1734 16.5976 9.000 18.000 12.000 18.0000 25.2311 rpmC; ribosomal protein L29 SGO_1977 -0.529 8.605 115.4451 110.500 0.0007 0.0000 78.3776 42.500 114.500 38.500 114.5000 80.9499 rplP; ribosomal protein L16 SGO_1978 0.134 9.307 154.6234 148.000 0.0661 0.1645 152.1448 82.500 147.000 85.500 147.0000 179.7717 rpsC; ribosomal protein S3 SGO_1979 0.323 9.561 171.3394 164.000 0.0094 0.0076 199.1714 108.000 164.000 105.000 164.0000 220.7723 rplV; ribosomal protein L22 SGO_1980 0.140 8.873 104.4752 100.000 0.0680 0.1722 114.3392 62.000 118.500 62.500 118.5000 131.4121 rpsS; ribosomal protein S19 SGO_1981 0.235 8.829 111.7885 107.000 0.0419 0.0871 112.4950 61.000 97.000 63.500 97.0000 133.5147 rplB; ribosomal protein L2 SGO_1982 -0.007 8.326 95.0725 91.000 0.2399 0.9214 70.0788 38.000 66.500 42.500 66.5000 89.3602 rplW; ribosomal protein L23 SGO_1983 0.622 9.793 165.0709 158.000 0.0066 0.0041 250.8085 136.000 184.000 136.500 184.0000 287.0040 rplD; ribosomal protein L4/L1 family SGO_1984 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 50

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 50 -0.307 10.243 232.9798 223.000 0.1025 0.2963 256.3410 139.000 453.000 128.000 453.0000 269.1320 rplC; ribosomal protein L3 SGO_1985 0.546 7.865 44.4020 42.500 0.0050 0.0018 71.0009 38.500 50.500 32.000 50.5000 67.2830 rpsJ; ribosomal protein S10 SGO_1986 0.019 9.834 236.6364 226.500 0.2083 0.7590 216.6911 117.500 216.500 115.500 216.5000 242.8496 purA; adenylosuccinate synthetase SGO_1989 -0.456 4.657 6.2685 6.000 0.1579 0.5196 6.4546 3.500 12.500 12.5000 glutamate--cysteine ligase, putative/amino acid ligase, putative SGO_1990 -0.205 6.372 23.5069 22.500 0.1151 0.3438 15.6755 8.500 20.500 11.000 20.5000 23.1285 possible transcriptional regulator SGO_1993 -0.844 6.394 22.9846 22.000 0.0172 0.0218 17.5197 9.500 31.000 6.000 31.0000 12.6156 clpB; ATP-dependent Clp proteinase, ATPbinding chain SGO_1998 0.015 10.808 457.0792 437.500 0.2122 0.7760 479.4868 260.000 434.000 201.000 434.0000 422.6213 tsf; translation elongation factor Ts SGO_2000 0.089 10.507 363.0515 347.500 0.0813 0.2151 352.2384 191.000 341.500 189.500 341.5000 398.4415 rpsB; ribosomal protein S2 SGO_2001 0.722 5.492 7.8356 7.500 0.0219 0.0321 16.5976 9.000 9.000 5.500 9.0000 11.5643 LPXTG cell wall surface protein SGO_2005 0.063 6.694 26.6412 25.500 0.1174 0.3566 27.6627 15.000 24.000 12.000 24.0000 25.2311 nusG; transcription termination/antitermination factor NusG SGO_2007 -0.289 5.777 14.1042 13.500 0.0339 0.0630 11.0651 6.000 16.000 6.500 16.0000 13.6669 Extracellular polysaccharide biosynthesis SGO_2024 -1.332 5.698 21.4174 20.500 0.0123 0.0128 5.5325 3.000 15.500 4.500 15.5000 9.4617 wze; putative autophosphorylating protein tyrosine kinase SGO_2025 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 51

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 51 -0.425 6.565 27.6859 26.500 0.0099 0.0085 18.4418 10.000 26.500 10.500 26.5000 22.0772 nrdD; ribonucleoside-triphosphate reductase SGO_2033 -1.052 4.251 8.3580 8.000 0.0482 0.1073 3.6884 2.000 7.000 7.0000 conserved hypothetical protein TIGR00250 SGO_2041 0.382 8.928 96.6396 92.500 0.0313 0.0550 153.9890 83.500 114.500 58.000 114.5000 121.9504 Bacterial protein of unknown function (DUF965) superfamily SGO_2042 0.083 10.745 406.9311 389.500 0.0818 0.2174 468.4217 254.000 426.000 197.500 426.0000 415.2622 recA; recA protein SGO_2045 -0.970 4.841 9.9251 9.500 0.0050 0.0022 5.5325 3.000 9.000 2.000 9.0000 4.2052 cinA; competence induced protein SGO_2046 -0.100 4.861 5.7461 5.500 0.1661 0.5663 6.4546 3.500 9.500 3.500 9.5000 7.3591 DNA mismatch repair protein hexB SGO_2053 -0.693 5.734 13.0594 12.500 0.0656 0.1610 6.4546 3.500 19.000 7.000 19.0000 14.7182 mutS; DNA mismatch repair protein MutS SGO_2056 0.379 9.776 196.4135 188.000 0.0103 0.0095 263.7177 143.000 184.500 110.500 184.5000 232.3366 argS; arginyl-tRNA synthetase SGO_2058 -1.094 7.569 64.2523 61.500 0.0012 0.0001 32.2731 17.500 65.000 13.500 65.0000 28.3850 aspS-1; aspartyl-tRNA synthetase SGO_2060 0.193 8.348 80.9683 77.500 0.0506 0.1152 94.0532 51.000 71.000 38.000 71.0000 79.8986 hisS; histidyl-tRNA synthetase SGO_2062 -0.242 8.955 144.1758 138.000 0.0271 0.0454 118.9496 64.500 125.000 51.500 125.0000 108.2836 ilvD; dihydroxy-acid dehydratase SGO_2064 -0.337 7.834 69.4760 66.500 0.0466 0.1024 58.0917 31.500 57.500 20.500 57.5000 43.1032 rpmG; ribosomal protein L33 SGO_2066 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 52

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 52 -0.715 5.430 15.6713 15.000 0.0332 0.0611 10.1430 5.500 11.000 3.000 11.0000 6.3078 hypothetical protein SGO_2070 SGO_2070 0.047 7.648 50.1481 48.000 0.0778 0.2038 52.5591 28.500 48.500 23.500 48.5000 49.4109 purB; adenylosuccinate lyase SGO_2085 -1.055 4.250 7.8356 7.500 0.0195 0.0268 3.6884 2.000 7.500 7.5000 comA; ATP-binding Transport protein ComA SGO_2097 -0.102 11.049 542.7489 519.500 0.1579 0.5181 589.2155 319.500 548.500 208.500 548.5000 438.3908 rpsD; ribosomal protein S4 SGO_2098 0.055 9.145 146.7877 140.500 0.1191 0.3624 141.0798 76.500 131.000 70.000 131.0000 147.1815 ABC transporter substrate-binding protein SGO_2100 -1.959 4.836 9.4028 9.000 0.0805 0.2118 16.000 1.500 16.0000 3.1539 hypothetical protein SGO_2102 SGO_2102 0.532 8.288 57.4614 55.000 0.0328 0.0594 108.8066 59.000 69.500 36.500 69.5000 76.7447 srtB; sortase B SGO_2104 0.573 6.179 15.6713 15.000 0.0050 0.0019 21.2081 11.500 13.500 10.500 13.5000 22.0772 abpA; amylase-binding protein AbpA SGO_2105 -0.167 7.791 54.3271 52.000 0.0396 0.0799 51.6370 28.000 63.000 25.000 63.0000 52.5648 ribose-phosphate diphosphokinase SGO_2106 0.155 9.003 121.1913 116.000 0.0195 0.0267 141.0798 76.500 121.500 61.500 121.5000 129.3095 Cell division protein ftsH-like protein SGO_2133 -0.190 7.151 39.1782 37.500 0.1153 0.3458 39.6499 21.500 36.000 13.000 36.0000 27.3337 hpt; hypoxanthine phosphoribosyltransferase SGO_2134 -0.244 8.063 76.7893 73.500 0.0397 0.0812 55.3254 30.000 68.000 32.000 68.0000 67.2830 GTP-binding protein SGO_2142 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.

PAGE 53

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn Coverage SgPgFn vs SgPg Protein Log 2 Sum q -Value Log 2 Ratio p -Value Raw SgPgFn vs SgPg SgPg SgPgFn SgPgFn Normalized Description Log 2 Ratios 0 2 4 6 -2 -4 -6 SgPg SgPgFn vs SgPg Page 53 0.001 8.941 114.4004 109.500 0.2492 0.9711 123.5601 67.000 131.500 58.000 131.5000 121.9504 comE; competence response regulator ComE SGO_2145 -0.958 4.948 13.0594 12.500 0.0402 0.0827 11.500 3.000 11.5000 6.3078 comD; histidine protein kinase ComD SGO_2146 -1.449 6.392 30.8202 29.500 0.0050 0.0020 14.7534 8.000 30.000 4.000 30.0000 8.4104 degP; serine protease SGO_2150 .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 627 Dot Plots Dot Plots Hendrickson et al.



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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 1 15.6% 4 16 48.2% 9 33.3% 26.4% 7 24 57.3% 9 32.9% SGO_0001 dnaA; chromosomal replication initiator protein DnaA 7 26.0% 10 34.2% 11.9% 4 9 27.5% 11 35.4% 11.9% 4 10 30.7% 11 33.3% SGO_0002 dnaN; DNA polymerase III, beta subunit 7 24.9% 7 27.8% 43.6% 8 15 62.2% 11 52.3% 41.3% 9 14 59.3% 12 52.9% SGO_0004 putative lipoprotein 11 51.7% 9 35.5% 8 10.9% 11 16.0% SGO_0005 hypothetical protein SGO_0005 26.7% 10 17 41.5% 21 52.2% 26.7% 9 20 44.8% 18 45.7% SGO_0006 ABC transporter, ATP-binding protein 17 44.8% 15 43.5% 28.2% 7 8 34.7% 9 34.4% 20.6% 5 9 35.0% 8 34.7% SGO_0007 trpS; tryptophanyl-tRNA synthetase 7 28.8% 7 29.7% 52.3% 20 23 54.8% 30 77.7% 57.0% 20 26 58.2% 28 70.4% SGO_0008 inosine-5'-monophosphate dehydrogenase 22 62.9% 26 64.5% 25.1% 8 7 22.7% 3 11.3% 13.7% 4 10 27.2% 4 11.6% SGO_0011 proteinase, M16 family 5 17.6% 3 8.4% SGO_0012 mpp; peptidase, M16 family 3 13.7% 4 17.2% 4 18.1% 4 18.1% 5 21.0% SGO_0013 hypothetical protein SGO_0013 8 41.6% 5 24.8% 15.7% 3 9 42.3% 6 33.6% SGO_0015 ABC transporter (ATP-binding protein) 3 15.0% 4 24.7% 4 24.0% 4 17.9% 4 16.8% SGO_0016 cbiO; ABC transporter, ATP-binding protein Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 2 4 12.5% 4 13.3% SGO_0017 ABC-type putative cobalt transport system, permease 6 24.1% SGO_0019 sdhA; L-serine dehydratase, iron-sulfur-dependent, alpha subunit 3 19.7% SGO_0020 sdhB; L-serine dehydratase, iron-sulfur-dependent, beta subunit 3 26.9% 3 24.2% 20.6% 5 6 20.4% 8 28.4% 15.0% 3 8 29.5% 11 31.1% SGO_0022 trmU; tRNA (5-methylaminomethyl-2-thiouridylate)methyltransferase 15 55.2% 15 56.3% 8.1% 4 10 23.8% 11 23.9% 14.9% 7 10 22.8% 10 22.1% SGO_0025 gidA; glucose inhibited division protein A 4 9.5% 6 13.8% 6.8% 4 20 32.3% 4 9.1% 21 33.1% 5 7.3% SGO_0026 DHH subfamily 1 protein 58.7% 7 7 54.7% 8 63.3% 52.7% 8 11 72.0% 8 55.3% SGO_0027 rplI; ribosomal protein L9 7 46.7% 9 64.0% 9 30.6% 5 17.7% 9.5% 3 13 41.9% 7 27.5% SGO_0028 dnaC; replicative DNA helicase 4 11.8% 4 13.7% 40.8% 11 12 47.3% 15 57.7% 42.8% 11 13 46.1% 14 49.9% SGO_0030 aspB; aspartate transaminase 18 54.2% 19 59.7% 18.0% 5 11 36.9% 12 44.1% 11.1% 4 16 42.6% 11 39.3% SGO_0032 plsX; fatty acid/phospholipid synthesis protein PlsX 7 30.0% 7 27.9% 40.5% 3 4 41.8% 3 40.5% 51.9% 4 6 57.0% 4 51.9% SGO_0033 acpP; acyl carrier protein 3 3.6% 3 4.2% SGO_0035 phosphoribosylformylglycinamidine synthase 4 5.5% 5 6.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 3 17.6% 3 3 15.1% 5 33.2% 5 26.5% 5 29.8% SGO_0042 transcription regulator, GntR family 6 43.3% 5 35.3% SGO_0044 PTS system, IIB component 7 33.5% 10 40.4% SGO_0050 hypothetical protein SGO_0050 3 16.1% 4 28.6% SGO_0051 hypothetical protein SGO_0051 20.9% 6 16 40.8% 13 31.8% 20.3% 7 16 38.5% 16 38.9% SGO_0054 dltA; D-alanine-activating enzyme 13 36.3% 13 37.7% 3 9.9% SGO_0055 dltB; integral membrane protein 3 39.2% 4 36.7% SGO_0056 dltC; D-alanyl carrier protein 3 31.6% 25.4% 7 20 58.3% 13 43.8% 19.9% 6 26 64.0% 12 40.0% SGO_0057 dltD protein 14 48.8% 9 32.9% 45.3% 4 4 45.3% 4 45.3% 45.3% 5 4 45.3% 5 45.3% SGO_0059 pXO1; hypothetical protein SGO_0059 4 45.3% 4 45.3% 36 45.3% 45 49.0% SGO_0060 hypothetical protein SGO_0060 3 5.0% 3 51.2% SGO_0062 hypothetical protein SGO_0062 14.4% 5 14 32.1% 7 22.3% 17.5% 7 17 42.9% 9 27.3% SGO_0063 hypothetical protein SGO_0063 4 10.8% 7 18.9% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 4 13.6% 14 50 43.8% 29 28.5% 16.4% 17 52 42.8% 30 30.6% SGO_0064 FtsK/SpoIIIE family protein 9 8.5% 11 11.8% 35.9% 10 16 49.9% 13 48.2% 37.0% 12 18 50.4% 15 56.2% SGO_0065 hypothetical protein SGO_0065 9 33.7% 11 38.1% 36.6% 3 4 36.6% 36.6% 3 5 58.4% SGO_0066 D-3-phosphoglycerate dehydrogenase, putative 3 36.6% 28.1% 8 8 25.7% 13 37.3% 20.0% 6 9 29.7% 14 42.6% SGO_0067 protein with prophage function domain 4 14.6% 5 17.1% 24.3% 3 7 40.7% 7 40.7% 23.2% 3 7 40.7% 6 40.1% SGO_0068 lipoprotein, putative 4 28.2% 25.5% 3 5 38.6% 5 38.6% 31.0% 4 7 45.7% 4 31.0% SGO_0069 hypothetical protein SGO_0069 38.8% 4 4 33.6% 4 34.3% 39.6% 4 5 39.6% 4 34.3% SGO_0070 merozoite surface protein 1 4 23.6% SGO_0075 hypothetical protein SGO_0075 7 38.2% 5 25.0% 7 38.6% 4 25.0% SGO_0078 hypothetical protein SGO_0078 3 20.9% 3 27.6% SGO_0079 hypothetical protein SGO_0079 24.4% 10 17 38.7% 14 31.8% 23.3% 10 22 49.8% 12 29.7% SGO_0080 hypothetical protein SGO_0080 9 20.8% 7 18.0% 3 11.5% 3 11.5% 3 11.5% 6 29.8% SGO_0081 hypothetical protein SGO_0081 5 21.6% 4 13.3% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 5 8 38.8% 6 34.4% SGO_0095 mccF; microcin immunity protein MccF, putative 8 39.1% 9 47.3% 3 12.4% 5 22.5% SGO_0097 hypothetical protein SGO_0097 3 21.7% 3 21.7% 3 21.7% SGO_0098 ribonucleotide reductase-like protein 5.6% 3 7 16.6% 6 16.6% SGO_0099 pulA-2; pullulanase, type I 4 11.3% 7 15.8% 6 27.4% 4 20.7% 3 11.9% SGO_0100 maltose operon transcription repressor 4 21.6% 5 25.8% 10 37.5% SGO_0101 malA; Maltodextrose utilization protein malA 57.7% 20 23 59.6% 23 61.8% 50.1% 17 26 65.1% 23 61.8% SGO_0104 Maltose/maltodextrin-binding protein precursor 19 56.8% 18 56.8% 9.1% 4 8 19.6% 9 21.5% 6.6% 3 9 19.8% 9 21.7% SGO_0105 malQ; 4-alpha-glucanotransferase 8 24.6% 8 22.3% 31.9% 17 12 20.5% 23 42.0% 29.3% 15 15 22.7% 28 51.1% SGO_0106 glgP-2; maltodextrin phosphorylase 27 49.1% 24 47.5% 5.6% 4 SGO_0107 LPXTG cell wall surface protein, collagen binding domain 8 30.7% 9 30.7% SGO_0108 ruvB; Holliday junction DNA helicase RuvB 4 15.4% 3 13.9% 3 40.7% SGO_0110 phosphotyrosine protein phosphatase 4 46.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 6 4 27.0% 6 36.5% SGO_0111 MORN motif family protein 10 22.0% 9 22.2% SGO_0112 putative acyltransferase 59.1% 45 53 63.8% 47 60.5% 60.2% 45 57 66.0% 48 60.9% SGO_0113 acdH; alcohol-acetaldehyde dehydrogenase 53 66.8% 51 76.3% 5 60.7% SGO_0128 hypothetical protein SGO_0128 13 29.2% 4 11.1% 16 31.6% 4 8.8% SGO_0129 atpI; v-type sodium ATP synthase, chain I 6 34.7% 6 35.2% SGO_0131 v-type sodium ATP synthase, chain E 3 27.6% 4 29.1% 3 12.8% 3 13.1% 4 15.4% SGO_0132 ATP synthase (C/AC39) subunit 6 27.3% 6 26.4% 8 39.0% 7 35.1% SGO_0134 acetyltransferase, GNAT family 4 17.7% 16.1% 8 22 49.0% 13 28.4% 20.0% 9 24 49.5% 18 48.5% SGO_0135 v-type sodium ATP synthase, subunit A 16 34.9% 10 23.3% 36.2% 10 22 54.7% 12 43.5% 36.2% 10 22 54.5% 13 45.9% SGO_0136 v-type sodium ATP synthase, chain B 16 48.9% 14 44.6% 3 16.4% 4 15.5% SGO_0137 V-type ATPase, D subunit 4 17.7% SGO_0138 LysM domain protein 5 22.0% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 7 30.0% 10 11 37.0% 12 43.5% 19.8% 6 12 38.3% 13 42.9% SGO_0139 thrC; threonine synthase 14 44.9% 11 35.8% 3 15.5% SGO_0142 hypothetical protein SGO_0142 14 15.6% 3 1.9% 18 18.1% SGO_0144 hypothetical protein SGO_0144 4 4.2% 3 3.1% 19.9% 11 31 45.3% 21 34.8% 22.0% 11 25 37.6% 22 38.1% SGO_0145 polI; DNA polymerase I 25 41.1% 21 34.7% 41.4% 5 5 41.4% 7 58.6% 23.4% 3 6 46.2% 5 46.2% SGO_0146 CoA-binding domain protein 7 58.6% 7 66.9% 5 33.3% 3 21.1% 7 38.2% SGO_0148 hypothetical protein SGO_0148 3 10.0% SGO_0150 fucA1; alpha-L-fucosidase 17.9% 3 4 21.1% 5 27.4% 19.7% 4 4 21.1% 7 36.3% SGO_0152 tgt; queuine tRNA-ribosyltransferase 6 31.3% 4 17.4% 53.9% 18 16 47.9% 26 63.3% 54.8% 20 21 48.6% 23 61.0% SGO_0154 pgi; glucose-6-phosphate isomerase 32 71.3% 33 74.6% 15 52.6% 3 16.6% 15 57.0% 5 16.6% SGO_0155 hypothetical protein SGO_0155 16.4% 3 9 41.0% 3 16.4% 17.2% 3 11 42.5% 3 16.4% SGO_0156 hypothetical protein SGO_0156 4 16.8% 5 20.6% SGO_0157 hypothetical protein SGO_0157 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 8 37.9% 6 8 42.2% 7 41.4% 45.3% 8 8 42.2% 8 41.4% SGO_0158 2,3,4,5-tetrahydropyridine-2-carboxylate Nsuccinyltransferase, putative 7 38.8% 6 34.9% 3 10.6% 5 19.9% SGO_0159 hippurate hydrolase 3 10.6% 29.1% 6 7 36.4% 10 45.4% 40.7% 8 8 40.1% 9 41.7% SGO_0163 galU; UTP-glucose-1-phosphate uridylyltransferase 11 48.3% 10 48.7% 38.2% 8 12 55.9% 11 56.2% 41.1% 9 13 61.5% 11 58.6% SGO_0164 Glycerol-3-phosphate dehydrogenase [NAD(P)+] (NAD(P)H-dependent glycerol-3-phosphate dehydrogenase) 14 69.2% 12 60.7% 9 22.3% 8 17.8% SGO_0165 ABC transporter, permease/ATP-binding protein SP2075 11 26.5% 10 25.1% 3 3.7% SGO_0166 ABC transporter, permease/ATP-binding protein SP2073 5 27.1% 5 32.3% SGO_0167 glutamine amidotransferase 4 30.2% 5 39.6% SGO_0168 hydrolase, NUDIX family 3 22.8% 42.9% 5 5 41.5% 4 42.9% 37.4% 4 5 52.4% 4 44.2% SGO_0169 dut; dUTP diphosphatase 5 42.9% 4 28.6% 11.4% 3 7 21.7% 9 31.8% 12 40.1% 10 35.0% SGO_0171 radA; DNA repair protein RadA 5 20.2% 7 44.1% 7 44.5% SGO_0172 conserved hypothetical protein TIGR00266 3 25.4% 7 56.7% 4 36.0% 7 56.7% 4 37.2% SGO_0173 Carbonic anhydrase 3 34.1% 5 50.0% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 9 44.9% 17 22 52.2% 27 57.9% 47.4% 18 22 53.2% 23 56.9% SGO_0174 gltX; glutamyl-tRNA synthetase 19 45.4% 23 54.8% 3 7.0% SGO_0179 Membrane protein oxaA 1 precursor 10.3% 3 11 34.1% 8 30.9% 28.1% 8 13 38.4% 7 25.3% SGO_0180 jag; hypothetical protein SGO_0180 7 30.9% 4 19.7% 12 40.4% 15 55.1% SGO_0181 lipoprotein, putative 3 21.0% SGO_0182 sapR; sakacin A production response regulator 3 20.5% 4 32.4% 5 20.7% 6 27.0% 3 14.5% SGO_0188 hydrolase, TatD family 6 35.9% 3 17.6% 3 20.4% SGO_0189 primase-related protein 9 34.2% 3 15.8% 15.5% 3 16 51.8% 4 20.1% SGO_0190 hypothetical protein SGO_0190 7 17.8% 4 14.9% 9 27.0% SGO_0191 hypothetical protein SGO_0191 3 14.1% 7 32.8% 5 20.7% 6 24.5% SGO_0193 ksgA; dimethyladenosine transferase 3 12.8% 4 17.9% 3 20.2% 17.8% 3 5 37.3% SGO_0197 predicted ribosome small subunit-dependent GTPase A 4 25.7% 6 39.7% 35.6% 7 8 51.1% 10 65.3% 29.7% 5 7 37.9% 9 58.9% SGO_0198 rpe; ribulose-phosphate 3-epimerase 10 71.2% 10 74.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 10 20.3% 5 15 42.6% 12 45.0% 30.9% 7 21 51.9% 11 45.2% SGO_0200 competence-induced protein Ccs50 10 38.8% 9 38.3% 26.2% 6 10 46.3% 11 47.9% 26.8% 7 12 51.1% 13 52.1% SGO_0201 cmp-binding-factor 1 12 48.2% 13 49.2% 3 20.3% 4 25.5% 4 25.8% 5 33.2% SGO_0202 pur operon repressor 5 33.6% 5 32.1% 4 27.9% SGO_0203 hypothetical protein SGO_0203 45.3% 8 7 25.5% 7 39.4% 45.3% 8 7 25.5% 7 39.4% SGO_0204 rpsL; ribosomal protein S12 8 45.3% 6 43.8% 60.3% 9 12 67.3% 11 59.6% 53.8% 10 14 74.4% 10 59.0% SGO_0205 rpsG; ribosomal protein S7 11 62.8% 13 80.1% 77.5% 38 41 83.5% 42 83.5% 79.8% 38 46 86.0% 45 83.8% SGO_0206 fusA; translation elongation factor G 38 79.2% 44 97.4% 58.6% 16 14 47.9% 19 62.2% 58.9% 18 15 50.6% 18 59.5% SGO_0207 gap; glyceraldehyde-3-phosphate dehydrogenase, type I 25 69.3% 27 91.1% 12 9.7% 16 14.3% SGO_0208 LPXTG cell wall surface protein, glycosyl hydrolase family 13 11.3% 12 9.9% 80.5% 26 26 72.2% 27 81.5% 72.2% 24 29 72.9% 28 82.5% SGO_0209 pgk; phosphoglycerate kinase 29 76.7% 29 87.2% 17 14.3% 3 2.1% 28 20.6% 4 4.3% SGO_0210 sspA; streptococcal surface protein A 20 21.1% 15 18.4% 20 13.4% 18 13.2% SGO_0211 sspB; streptococcal surface protein B 4 3.0% 5 4.5% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 11 4 30.6% SGO_0214 transcription regulator, MerR family 49.6% 15 16 47.1% 18 54.5% 34.4% 12 20 52.7% 16 52.5% SGO_0215 glnA; glutamine synthetase, type I 17 48.7% 19 56.3% 23.2% 10 17 44.3% 20 51.3% 27.0% 11 17 44.5% 23 58.9% SGO_0219 metallo-beta-lactamase superfamily protein 1 18 45.0% 15 38.8% 4 59.2% 5 68.4% SGO_0220 Protein of unknown function (DUF1447) superfamily 3 53.9% 3 11.3% 3 11.3% 3 12.2% SGO_0223 glycoproteinase family protein 3 11.6% 27.2% 4 4 25.6% 6 37.8% 44.4% 7 8 43.3% 5 31.1% SGO_0230 Protein of unknown function, DUF536 family 6 40.0% 5 31.1% 4 11.1% 6 17.1% SGO_0231 glycerophosphoryl diester phosphodiesterase family protein 26.9% 3 3 26.9% 26.9% 3 4 33.6% 3 26.9% SGO_0232 conserved hypothetical protein TIGR00103 7 31.9% 10 48.9% SGO_0233 lipoprotein, putative 3 26.7% 6 45.2% 23.7% 13 20 35.3% 19 34.8% 10.0% 5 21 36.2% 18 30.8% SGO_0234 pepX; X-Pro dipeptidyl-peptidase 18 35.6% 19 38.5% 3 11.3% 4 21.9% 4 14.1% 3 18.7% SGO_0235 glycerol uptake facilitator protein-like protein 6 12.0% 6 11.7% SGO_0236 hypothetical protein SGO_0236 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 12 17.1% 3 3 18.0% 7 38.0% 18.0% 3 8 42.4% 8 45.7% SGO_0237 ccpA; CcpA protein (proteinase) 4 26.1% 6 36.7% 5 23.8% 4 21.3% SGO_0240 mvaD; diphosphomevalonate decarboxylase 3 10.8% SGO_0242 FMN-dependent dehydrogenase family protein 3 14.7% 3 12.3% 14.2% 5 4 15.8% SGO_0243 hydroxymethylglutaryl-CoA reductase, degradative 3 6.6% 4 9.4% 19.9% 6 3 8.7% 8 31.6% 5 18.1% 8 28.1% SGO_0244 hydroxymethylglutaryl-CoA synthase 7 20.9% 7 28.3% 51.1% 33 45 67.2% 39 66.7% 51.9% 30 47 68.1% 38 62.6% SGO_0247 pfl; formate acetyltransferase 43 66.4% 43 69.3% 9.4% 3 7 32.1% 6 26.9% 6 26.9% 3 14.6% SGO_0252 possible TetR-type transcriptional regulator 4 16.0% 3 14.6% 10 42.7% 12 36.9% SGO_0253 hypothetical protein SGO_0253 6 13.1% 6 12.1% 11 21.3% 4 9.5% SGO_0254 helicase, RecD/TraA family 19.0% 5 11 48.5% 4 29.0% 26.5% 5 13 48.5% 6 39.5% SGO_0255 Signal peptidase I 7 46.5% 5 33.0% 4 17.9% 6 22.3% SGO_0256 rnhC; ribonuclease HIII 3 16.9% 27.7% 3 3 23.8% SGO_0258 hypothetical protein SGO_0258 3 56.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 13

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 13 8.4% 6 16 29.7% 13 24.3% 10.8% 7 23 40.2% 15 28.7% SGO_0260 DNA mismatch binding protein MutS2 8 17.5% 11 22.4% 3 16.4% SGO_0261 acetyltransferase, GNAT family 19.9% 7 11 34.1% 12 32.8% 15.9% 5 9 30.5% 12 30.3% SGO_0262 dipeptidase 9 29.7% 9 32.4% 42.3% 4 4 42.3% 4 42.3% 41.3% 3 4 42.3% 4 42.3% SGO_0263 trx-1; thioredoxin 4 42.3% 6 67.3% 10 45.5% 8 38.7% 4 17.2% SGO_0268 mechanosensitive transport protein 3 22.5% 4 31.9% SGO_0269 hypothetical protein SGO_0269 39.3% 4 6 55.7% 5 42.6% 39.3% 4 5 48.4% 5 42.6% SGO_0272 hypothetical protein SGO_0272 7 54.9% 6 49.2% 42.4% 16 19 44.9% 23 59.2% 55.6% 20 24 48.2% 25 65.4% SGO_0276 gdhA; glutamate dehydrogenase (NADP) 24 63.2% 22 62.9% 5 31.7% 5 35.3% 5 31.7% 4 27.9% SGO_0277 pyrA; Dihydroorotate dehydrogenase 4 28.8% 5 35.6% 3 14.8% SGO_0278 msrA; Peptide methionine sulfoxide reductase msrA/msrB 3 15.8% 6 29.4% 4 23.7% SGO_0279 lipoprotein, putative 6 20.4% 7 20.9% 7 23.4% 6 20.6% SGO_0280 trzA; ethylammeline chlorohydrolase 10 41.0% 6 23.6% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 14

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 14 9 27.1% 11 37.6% SGO_0282 cell wall polysaccharide biosynthesis protein 3 9.3% SGO_0284 transcriptional regulator 7 16.0% 8.3% 3 10 24.5% SGO_0286 DNA mismatch repair protein MutS, putative 3 7.7% 3 21.1% 4 30.9% SGO_0288 GDSL-like lipase/acylhydrolase 3 21.6% 28.5% 3 3 28.5% 3 28.5% 3 28.5% 3 28.5% SGO_0290 copper -translocating P-type ATPase 16.6% 7 16 31.1% 9 20.7% 13.9% 6 16 33.5% 9 20.8% SGO_0291 copper-translocating P-type ATPase 8 19.3% 6 13.4% 55.5% 23 19 45.9% 28 64.1% 60.2% 24 24 51.1% 29 64.1% SGO_0292 spxB; pyruvate oxidase 14 34.7% 11 35.4% 4 8.6% 5 10.1% SGO_0294 ABC transporter, putative 4 11.5% SGO_0297 6-phospho-beta-glucosidase 6 15.9% 9 27.6% 3 11.0% SGO_0299 putative histidine kinase 14.2% 3 SGO_0301 ABC transporter ATP-binding protein-like protein 4 17.9% 6 21.9% SGO_0306 ABC transporter ATP-binding protein-like protein Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 15

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 15 4 8.8% 6 12.5% SGO_0307 pabB; chorismate binding enzyme 3 5.5% 4 6.8% 3 4.9% SGO_0310 metE; 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase 4 8.7% 5 8.3% 53.5% 34 33 46.3% 40 56.9% 55.5% 38 34 48.5% 41 57.2% SGO_0312 xfp; D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase 45 58.4% 55 71.2% 43 46.8% 2.6% 3 52 50.1% SGO_0317 LPXTG cell wall surface protein, serine protease, subtilase family 42.2% 5 8 57.8% 7 51.5% 42.2% 6 10 71.1% 8 56.4% SGO_0321 polypeptide deformylase 8 61.3% 8 57.4% 3 18.6% 3 14.9% SGO_0323 pseudouridine synthase rRNA-specific 10 22.6% 10 22.3% SGO_0324 hypothetical protein SGO_0324 7 25.4% SGO_0325 probable membrane protein, putative 19 38.9% 3 8.5% 23 46.5% SGO_0326 probable membrane protein, putative 5 17.2% 3 11.4% 4 13.7% SGO_0327 Lipopolysaccharide N-acetylglucosaminyltransferase 4 12.4% 5 9.8% 5 9.8% SGO_0328 transmembrane protein, putative 20 47.0% 21 49.4% 3 8.6% SGO_0329 hypothetical protein SGO_0329 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 16

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 16 8 40.1% 8 38.5% SGO_0330 hypothetical protein SGO_0330 4 19.7% 6 23.3% SGO_0331 hypothetical protein SGO_0331 12 40.6% 14 40.8% SGO_0332 hypothetical protein SGO_0332 38.2% 10 8 34.8% 11 68.5% 66.3% 10 11 68.5% 11 68.5% SGO_0333 rpsO; ribosomal protein S15 9 68.5% 8 66.3% 3 33.7% 3 34.6% SGO_0337 trx-2; thioredoxin 3 11.8% 4 16.3% SGO_0339 hypothetical protein SGO_0339 7 27.0% 7 31.9% 26.9% 12 15 34.6% 17 39.1% 19.2% 10 15 33.4% 18 43.0% SGO_0342 pepF-2; oligoendopeptidase 19 44.5% 21 45.0% 38.6% 22 27 48.1% 28 48.4% 26.0% 16 31 48.5% 26 50.4% SGO_0344 pnpA; polyribonucleotide nucleotidyltransferase 29 47.3% 27 44.1% 3 16.1% 6 23.4% SGO_0345 cysE; serine O-acetyltransferase 3 31.8% 4 36.4% 3 31.8% SGO_0348 reductase 5 48.0% 25.7% 10 11 32.2% 12 36.5% 18.3% 7 11 31.8% 11 32.7% SGO_0349 cysS; cysteinyl-tRNA synthetase 10 28.6% 11 31.1% 26.1% 7 14 42.3% 13 48.4% 21.5% 6 16 47.6% 12 39.6% SGO_0352 ABC transporter, ATP-binding protein SP1580 12 40.7% 12 37.8% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 17

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 17 3 6.0% 5 7.8% 3 5.2% 3 6.0% SGO_0353 transport protein 4 7.6% 3 6.3% 5 27.6% 6 35.0% 7 28.0% 5 30.9% SGO_0355 RNA methyltransferase, TrmH family, group 3 4 20.6% 4 23.5% 3 16.4% SGO_0356 hypothetical protein SGO_0356 57.1% 8 8 44.3% 11 59.6% 47.7% 9 9 47.4% 12 63.8% SGO_0357 degV; DegV family fatty acid binding protein 10 59.6% 6 39.0% 70.3% 8 11 78.4% 9 65.5% 75.7% 10 11 79.1% 11 79.1% SGO_0358 rplM; ribosomal protein L13 10 73.0% 12 77.7% 21.5% 5 5 27.7% 5 21.5% 21.5% 5 6 28.5% 5 21.5% SGO_0359 rpsI; ribosomal protein S9 6 28.5% 4 20.8% 6 33.1% 5 40.7% 5 33.1% 3 28.5% SGO_0361 immunity repressor protein 4 35.5% 5 35.5% 9.4% 3 3 9.8% 4 10.9% SGO_0368 merA; mercury(II) reductase 5 11.9% 5 13.2% 4 39.7% SGO_0371 putative transcriptional regulator 25.1% 7 6 18.9% 8 30.1% 17.4% 6 8 22.2% 7 23.1% SGO_0372 malate oxidoreductase 12 25.7% 10 24.0% 23.4% 5 7 29.5% 8 40.6% 14.3% 4 8 34.4% 9 41.8% SGO_0374 Response regulator of the LytR/AlgR family 9 40.6% 9 46.3% 24.3% 4 5 23.9% SGO_0376 ABC transporter ATP-binding protein Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 18

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 18 SGO_0378 hypothetical protein SGO_0378 3 29.9% 6 31.6% 7 34.9% SGO_0379 Protein of unknown function (DUF421) family 3 23.3% SGO_0380 hypothetical protein SGO_0380 25.3% 4 3 15.7% 3 15.7% 29.2% 5 5 22.8% 6 34.3% SGO_0384 putative carboxylate-amine/thiol ligase 4 23.1% 6 29.2% 19 19.9% 24 27.5% SGO_0385 exo-beta-D-fructosidase 21 21.7% 18 19.0% 4 22.1% 6 31.7% SGO_0387 hypothetical protein SGO_0387 19 25.3% 27 36.4% SGO_0388 LPXTG cell wall surface protein, zinc carboxypeptidase family 16 26.6% 13 18.7% 3 28.4% SGO_0389 possible phosphoserine phosphatase 3 37.5% 3 45.5% 34.4% 11 14 43.4% 23 56.4% 37.1% 13 18 50.3% 18 49.7% SGO_0390 glycerol-3-phosphate dehydrogenase (NAD(P)+) 19 51.2% 16 48.8% 14.5% 3 6 32.5% 4 25.4% 6 32.5% SGO_0392 phosphoglycerate mutase 7 36.4% 5 28.9% 8 53.7% 10 63.8% SGO_0393 D-alanyl-D-alanine carboxypeptidase 3 16.3% 3 25.2% SGO_0396 Transcriptional regulator, PadR family Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 19

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 19 17.5% 4 12 49.5% 5 20.4% 17.9% 4 10 35.1% 3 14.0% SGO_0398 ABC transporter ATP-binding protein 4 16.1% 5 20.7% 4 12.8% 4 12.5% SGO_0400 hrcA; heat-inducible transcription repressor HrcA 8 27.6% 4 16.6% 33.9% 6 8 41.8% 7 33.9% 33.9% 7 10 53.7% 8 41.8% SGO_0401 grpE; co-chaperone GrpE 9 46.9% 9 53.7% 61.6% 29 29 56.8% 32 64.3% 64.6% 33 36 63.8% 33 64.4% SGO_0402 dnaK; DnaK chaperone protein 40 71.3% 42 74.6% 19.7% 6 15 42.0% 8 28.9% 27.8% 8 21 50.1% 13 35.7% SGO_0404 dnaJ; DnaJ chaparone protein 6 23.6% 9 26.2% 3 19.7% 3 16.9% SGO_0407 truA; tRNA pseudouridine synthase A 3 17.3% 3 17.3% 65 42.9% 3.6% 4 68 42.0% SGO_0408 zmpB; zinc metalloproteinase B 3 17.0% 3 28.5% 4 26.9% SGO_0409 pyridoxine kinase 14 67.2% 13 70.8% 12.8% 3 3 12.8% 3 12.8% SGO_0411 conserved hypothetical protein TIGR01440 12 80.7% 11 84.5% 73.1% 27 28 73.8% 32 81.0% 73.1% 27 35 85.9% 32 81.0% SGO_0412 tig; trigger factor 33 83.8% 30 84.3% 32.3% 4 5 45.1% 5 33.3% 33.3% 5 3 22.6% 5 33.3% SGO_0413 DNA-directed RNA polymerase delta chain 6 46.2% 7 35.9% 46.2% 29 41 59.2% 39 59.8% 55.5% 33 45 61.2% 34 54.9% SGO_0415 secA; preprotein translocase, SecA subunit 34 53.6% 30 50.6% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 20

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 20 42.3% 11 12 44.9% 15 59.5% 27.4% 6 14 53.6% 12 46.4% SGO_0416 phospho-2-dehydro-3-deoxyheptonate aldolase 15 51.0% 14 50.7% 4 18.5% 4 12.5% SGO_0418 alr; alanine racemase 7 26.4% 6 22.8% 3 16.9% 3 16.9% SGO_0425 ansB; asparaginase 4 22.5% 14.3% 5 10 24.6% 7 14.9% 13 31.3% 6 13.2% SGO_0426 Cof family protein 6 16.6% 11 32.2% 30.7% 4 5 38.7% 6 57.3% 51.3% 6 7 44.7% 6 57.3% SGO_0427 universal stress protein family 8 62.7% 8 76.7% 51.7% 15 18 56.7% 20 61.6% 51.5% 16 18 59.2% 19 59.9% SGO_0429 aspartate transaminase 18 57.2% 17 56.7% 29 48.6% 38 57.1% SGO_0430 LPXTG cell wall surface protein 17 29.0% 14 25.3% 8 32.1% 6 28.6% 6 23.7% 5 20.6% SGO_0431 GTP-sensing transcriptional pleiotropic repressor codY 4 16.4% 29.2% 3 4 36.2% 3 29.2% 29.2% 3 5 40.0% 3 29.2% SGO_0432 entB; isochorismatase family protein 4 36.2% 26.6% 11 19 47.6% 14 40.1% 22.5% 8 22 49.7% 13 36.3% SGO_0434 aspS-2; aspartyl-tRNA synthetase 12 33.2% 17 42.0% 41.0% 4 5 59.0% 5 79.0% 49.0% 4 5 51.0% 5 78.0% SGO_0435 gatC; glutamyl-tRNA(Gln) amidotransferase, C subunit 5 80.0% 5 89.0% 43.6% 16 22 55.9% 21 52.7% 52.7% 19 25 54.9% 19 50.6% SGO_0436 gatA; glutamyl-tRNA(Gln) amidotransferase, A subunit 16 42.2% 18 43.9% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 21

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 21 43.8% 17 20 47.0% 22 57.2% 30.2% 13 21 48.8% 21 56.6% SGO_0437 gatB; glutamyl-tRNA(Gln) amidotransferase, B subunit 19 55.6% 19 52.0% 29.0% 4 4 21.6% 7 37.1% 5 26.1% 4 25.3% SGO_0440 L-iditol 2-dehydrogenase BH3949 11 49.7% 13 62.4% 3 19.5% SGO_0444 HAD superfamily (subfamily IIIA) phosphatase, TIGR01668 22.0% 6 11 42.1% 14 54.6% 21.2% 6 13 48.1% 14 45.9% SGO_0445 GTP-binding protein 12 42.9% 10 38.6% 3 53.4% SGO_0446 conserved hypothetical protein TIGR00253 4 34.3% 4 38.1% 4 24.8% 3 30.0% SGO_0447 nadD; nicotinate (nicotinamide) nucleotide adenylyltransferase 6 43.8% 5 48.6% 22.1% 3 5 32.7% 5 35.2% 4 28.1% 7 49.2% SGO_0448 conserved hypothetical protein TIGR00488 9 50.8% 6 40.7% 3 18.6% SGO_0449 isochorismatase family protein 4 32.2% 4 38.0% 3 32.2% SGO_0450 iojap-related protein 3 24.0% 4 30.6% 4 20.9% 4 20.9% SGO_0451 methyltransferase 18 56.2% 26 64.5% SGO_0453 lipoprotein, putative 20.2% 3 6 31.9% 6 32.8% 20.2% 3 8 40.3% 4 26.9% SGO_0454 conserved hypothetical protein TIGR01033 4 25.6% 4 25.6% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 22

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 22 24.4% 6 21 61.0% 10 40.9% 27.6% 7 21 59.9% 9 35.5% SGO_0455 lipoprotein, putative 3 8.7% 4 13.8% 5 17.0% SGO_0456 ILL5; amino acid aminohydrolase 5 26.8% 9 42.2% 33.0% 9 17 48.8% 11 36.8% 20.4% 6 23 57.5% 12 40.0% SGO_0457 ABC transporter, substrate-binding protein SP0148 6 27.7% 7 34.0% 59.2% 15 24 71.4% 17 61.3% 60.6% 16 27 70.7% 16 61.0% SGO_0458 hlpA; lipoprotein 17 67.9% 11 55.1% 8 30.9% 8 24.7% 10 35.2% 4 14.2% SGO_0459 succinyl-diaminopimelate desuccinylase 6 21.2% 7 25.2% 14.7% 6 12 34.2% 10 31.4% 18.1% 6 12 33.6% 8 23.7% SGO_0460 ABC transporter, ATP-binding protein SP0151 5 13.8% 6 17.8% 3 6.5% 5 10.9% SGO_0463 cydD; putative ABC transporter (ATP-binding protein) 28.5% 6 7 26.3% 7 29.2% 24.9% 5 8 31.0% 11 42.3% SGO_0468 hypothetical protein SGO_0468 7 26.3% 7 26.3% 3 10.2% 3 10.2% SGO_0469 integral membrane protein 38.1% 9 7 31.7% 12 46.6% 30.5% 7 6 25.0% 11 48.2% SGO_0476 rhodanese family protein 3 15.5% 3 30.7% 30.7% 3 3 32.8% 3 30.7% SGO_0480 hypothetical protein SGO_0480 8 62.8% 6 58.4% 26.2% 5 11 45.7% 7 33.1% 32.1% 7 10 40.1% 12 55.3% SGO_0483 hypothetical protein SGO_0483 7 37.1% 5 33.8% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 23

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 23 5 18.0% 6 18.5% SGO_0484 sensor histidine kinase 4 12.9% 19 39.8% 8 21.9% 18 35.7% 6 19.1% SGO_0488 ABC transporter, ATP-binding protein SP0483 4 10.9% 7 21.9% 4 21.1% 4 26.6% SGO_0491 gidB; methyltransferase GidB 5 31.6% 4 22.4% 5 27.5% 8 51.3% 8 50.8% 9 53.4% SGO_0494 lemA; LemA-like protein 15 72.0% 11 68.3% 4 21.2% 3 19.2% 6 28.6% SGO_0495 htpx; heat shock protein 4 23.2% 5 32.3% 2.5% 3 SGO_0497 gtfG; glucosyltransferase G 44 38.3% 45 39.5% 3 12.1% SGO_0500 rggD; putative transcriptional regulator RggD 34.1% 6 7 43.2% 8 43.2% 34.1% 6 8 50.0% 7 43.2% SGO_0501 Uncharacterized ACR, COG1399 3 22.7% 51.1% 22 29 58.4% 25 56.2% 51.9% 21 34 61.9% 27 57.6% SGO_0502 floL; flotillin-like protein 20 47.5% 15 37.1% 69.2% 25 23 62.2% 28 74.3% 66.9% 27 27 65.2% 31 78.7% SGO_0503 gnd; 6-phosphogluconate dehydrogenase, decarboxylating 33 77.6% 32 81.9% 21.6% 10 21 35.2% 16 31.0% 23.6% 11 22 37.5% 20 36.2% SGO_0505 PTS system, IIBC component 16 34.2% 14 31.8% 3 15.5% 3 14.8% SGO_0506 rgfB; RgfB Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 24

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 24 19.7% 3 3 19.7% 3 19.7% 22.3% 4 3 19.7% 3 19.7% SGO_0508 nrdR; transcriptional regulator, NrdR family 4 22.3% 5 16.9% 10 23.7% 4 11.5% SGO_0509 Replication initiation and membrane attachment protein (DnaB) superfamily 34.4% 8 7 30.1% 13 60.2% 15.1% 6 7 26.1% 10 37.8% SGO_0510 dnaI; primosomal protein DnaI 8 31.1% 7 34.4% 17.2% 3 3 16.4% 5 29.4% 17.2% 3 8 36.6% 7 34.9% SGO_0511 NADPH-flavin oxidoreductase -like protein 6 38.2% 7 42.9% 33.5% 10 13 35.1% 11 34.2% 32.8% 10 17 42.0% 11 36.9% SGO_0512 GTP-binding protein engA 11 31.0% 8 27.8% 4 5.3% SGO_0513 Snf2 family protein 6 10.2% 3 4.6% 4 14.4% 4 24.6% SGO_0514 hypothetical protein SGO_0514 26.0% 8 12 35.4% 15 50.3% 31.8% 9 14 41.5% 15 50.3% SGO_0515 murC; UDP-N-acetylmuramate--alanine ligase 16 47.4% 15 51.5% 26.3% 10 21 48.4% 15 42.7% 26.9% 9 26 51.4% 17 45.9% SGO_0518 aminodeoxychorismate lyase-like protein 9 21.0% 8 23.2% 51.3% 5 8 51.3% 10 71.3% 53.1% 6 10 58.1% 9 58.8% SGO_0519 greA; transcription elongation factor greA 6 61.9% 4 39.4% 5 18.7% 3 8.4% 7 22.6% 3 11.0% SGO_0521 Membrane protein oxaA 2 precursor 3 8.4% 6 34.6% 6 33.7% 4 26.4% SGO_0523 spoU rRNA Methylase family protein 7 52.4% 9 59.3% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 25

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 25 5.4% 3 11 29.4% 12 31.5% 9.6% 4 13 29.6% 13 28.9% SGO_0526 ilvB; acetolactate synthase, large subunit, biosynthetic type 6 14.2% 9 19.4% 4 25.3% 3 19.0% 20.9% 3 5 32.3% 3 20.3% SGO_0527 ilvN; acetolactate synthase, small subunit 3 25.9% 3 12.7% 38.5% 10 12 40.9% 16 50.6% 33.2% 10 13 43.2% 17 50.9% SGO_0528 ilvC; ketol-acid reductoisomerase 14 42.9% 14 42.4% 3 11.5% 6 28.1% 12.5% 3 7 19.2% 7 27.6% SGO_0529 ilvA; threonine dehydratase 5 16.8% 7 26.9% 6 33.3% 4 27.8% 7 37.8% 6 33.3% SGO_0530 Cof family protein 5 29.6% 7 40.0% 3 18.8% 3 18.8% SGO_0533 conserved hypothetical protein TIGR00150 3 21.3% 12.4% 3 10 33.3% 4 16.9% 13 40.2% 5 18.9% SGO_0535 putative transcriptional regulator LytR 4 16.4% 79.0% 7 6 60.0% 7 73.0% 57.0% 4 6 60.0% 6 60.0% SGO_0536 hypothetical protein SGO_0536 42.8% 4 4 38.7% 4 38.7% 44.5% 5 6 43.4% 4 38.7% SGO_0537 HIT family protein 3 32.9% 4 50.9% 8 39.9% 4 20.2% 7 39.9% 4 22.2% SGO_0538 ABC transporter, ATP-binding protein SP0522 6 28.0% 8 31.7% 6 13.1% 7 16.5% SGO_0539 ABC transporter, permease protein 47.3% 10 11 55.7% 14 73.5% 46.2% 10 11 53.0% 12 59.5% SGO_0540 hypothetical protein SGO_0540 12 58.0% 13 59.1% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 26

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 26 6 36.3% 4 20.3% 9 49.5% 7 49.1% SGO_0541 methyltransferase, putative 5 32.1% 5 39.2% 3 14.2% 4 24.7% SGO_0542 hypothetical protein SGO_0542 27.6% 10 17 40.0% 15 37.0% 30.5% 11 18 41.9% 16 44.1% SGO_0543 nusA; transcription termination factor NusA 9 26.9% 8 25.4% 3 24.5% SGO_0544 Protein of unknown function (DUF448) superfamily 3 39.4% SGO_0545 ribosomal protein L7A family 22.1% 15 25 33.4% 26 31.5% 19.7% 15 32 39.0% 27 32.8% SGO_0546 infB; Translation initiation factor IF-2 22 29.9% 21 35.0% 3 36.5% SGO_0547 rbfA; ribosome-binding factor A 9.0% 4 12 27.4% 7 14.7% 6.6% 4 14 26.3% 6 14.5% SGO_0548 Na/Pi-cotransporter family protein 3 9.2% 3 9.1% 3 11.0% SGO_0549 nagA; N-acetylglucosamine-6-phosphate deacetylase 3 14.4% 33.8% 6 4 20.6% 10 53.0% 37.4% 7 7 34.5% 8 42.3% SGO_0552 oxidoreductase, aldo/keto reductase family 15 67.3% 14 60.1% 5.8% 4 19 26.5% 8 12.2% 24 32.5% 13 21.0% SGO_0554 hsdR; type I site-specific deoxyribonuclease 10 15.4% 13 20.9% 6 7.0% 5 8.5% SGO_0556 DNA helicase-like protein, putative Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 27

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 27 4 13.9% SGO_0557 HsdS specificity protein of type I restrictionmodification system 4 26.0% 18.5% 3 5 32.7% 3 20.9% SGO_0558 hypothetical protein SGO_0558 3 20.5% 17.8% 5 6 20.7% 5 18.1% 15.3% 4 7 18.1% 4 15.7% SGO_0560 hsdM; type I restriction-modification system, M subunit 3 12.1% 46.8% 11 14 70.0% 14 60.3% 52.4% 11 18 74.7% 12 60.3% SGO_0565 adhA; alcohol dehydrogenase 19 73.2% 18 72.6% 34 28.4% 43 32.7% SGO_0566 sgc; serine protease challisin 23 21.9% 23 23.1% 28.9% 7 9 41.6% 11 42.3% 35.1% 9 8 36.1% 12 51.1% SGO_0568 glyQ; glycyl-tRNA synthetase, alpha subunit 6 25.6% 5 19.0% 33.3% 19 21 35.3% 27 49.5% 40.8% 22 23 35.9% 27 47.4% SGO_0569 glyS; glycyl-tRNA synthetase, beta subunit 19 34.8% 16 30.0% 3 29.4% 4 37.6% 3 29.4% SGO_0570 hypothetical protein SGO_0570 3 7.8% SGO_0571 hypothetical protein SGO_0571 18.4% 3 7 36.4% 6 32.3% 19.0% 4 10 50.6% 6 33.5% SGO_0573 mraW; S-adenosyl-methyltransferase MraW 5 23.7% 5 28.5% 25 47.8% 3 5.6% 23 46.7% 3 6.5% SGO_0575 pbp2X; penicillin-binding protein 2X 3 11.0% SGO_0576 mraY; phospho-N-acetylmuramoyl-pentapeptidetransferase Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 28

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 28 26.8% 8 14 42.1% 16 46.3% 21.3% 6 17 45.2% 17 52.3% SGO_0577 ATP-dependent RNA helicase 12 35.6% 10 27.5% 5 24.5% 6 29.7% SGO_0578 amino acid ABC transporter permease protein 8 54.3% 9 51.8% 12 63.2% 4 28.7% SGO_0579 amino acid ABC transporter ATP binding protein 3 24.7% 3 21.9% 25.0% 6 7 25.7% 6 29.9% 16.1% 4 8 29.9% 9 38.5% SGO_0581 trxB; thioredoxin-disulfide reductase 5 24.3% 5 17.8% 23.5% 8 14 28.2% 17 45.9% 34.4% 12 16 35.2% 19 47.3% SGO_0582 nicotinate phosphoribosyltransferase, putative 22 48.8% 18 39.9% 19.3% 4 6 29.9% 9 42.3% 25.5% 5 5 23.4% 6 29.2% SGO_0583 nadE; NAD+ synthetase 7 29.6% 7 32.1% 21.8% 6 6 21.2% 11 37.6% 20.9% 5 13 30.2% 13 39.6% SGO_0585 pepC; aminopeptidase C 22 53.2% 16 44.6% 21.8% 9 26 50.0% 19 41.6% 25.7% 12 26 48.5% 17 35.0% SGO_0586 pbp1a; penicillin-binding protein 1A 13 20.8% 12 23.3% 61.2% 5 6 61.2% 6 61.2% 61.2% 6 6 61.2% 6 61.2% SGO_0589 methylase 4 52.6% 4 45.7% 12.6% 4 7 23.2% 7 18.8% 10 25.0% 7 20.9% SGO_0590 Methyltransferase 9 22.9% 10 26.0% 23.7% 7 24 60.3% 14 40.8% 19.9% 8 26 60.7% 15 44.7% SGO_0591 hypothetical protein SGO_0591 11 39.7% 9 26.9% 33.8% 5 5 30.6% 7 56.9% 4 25.6% 7 55.6% SGO_0592 luxS; autoinducer-2 production protein LuxS 3 18.1% 4 34.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 29

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 29 27.5% 11 25 45.2% 21 43.9% 16.3% 8 30 47.3% 20 39.3% SGO_0593 HD/KH domain protein 8 21.3% 10 23.4% 20.2% 5 8 40.4% 8 48.6% 30.3% 5 8 40.4% 8 55.8% SGO_0594 gmk; Guanylate kinase (GMP kinase) 8 48.1% 7 41.3% 58.3% 6 5 43.7% 6 59.2% 59.2% 6 6 59.2% 7 59.2% SGO_0595 DNA-directed RNA polymerase, omega subunit 4 43.7% 4 43.7% 5 8.8% SGO_0596 priA; primosomal protein N'' 6 14.0% 5 8.7% 14.8% 3 6 32.5% 11 46.9% 16.7% 3 6 27.7% 8 39.5% SGO_0597 fmt; methionyl-tRNA formyltransferase 10 37.6% 9 39.9% 7 20.4% 10 30.2% 6 17.8% 6 17.4% SGO_0598 sun; sun protein 6 20.4% 20.3% 5 11 48.0% 9 39.8% 30.9% 6 11 43.9% 7 35.4% SGO_0599 phosphoprotein phosphatase 15 64.6% 13 52.4% 13.6% 5 22 48.8% 12 28.5% 24 52.5% 12 32.4% SGO_0600 serine/threonine protein kinase 9 19.8% 7 16.9% 7 24.0% 7 27.4% SGO_0602 histidine kinase 4 21.5% 5 25.7% 5 25.7% 4 20.1% SGO_0603 response regulator 7 35.0% 6 30.8% 19.3% 8 14 46.9% 18 59.3% 35.8% 12 18 54.8% 20 63.6% SGO_0604 hydrolase, haloacid dehalogenase family/peptidylprolyl cis-trans isomerase, cyclophilin type 20 62.1% 21 69.0% 82.5% 16 17 70.2% 15 75.1% 81.9% 15 15 69.6% 16 81.2% SGO_0606 cysK; cysteine synthase A 14 77.7% 13 76.7% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 30

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 30 4 13.4% 4 14.1% SGO_0608 comFA; competence ComFA-like protein 51.7% 8 8 48.9% 9 52.8% 37.8% 6 9 53.9% 9 52.8% SGO_0610 ribosomal subunit interface protein 11 55.6% 9 54.4% 15.5% 3 7 42.2% 4 18.6% 4 23.6% 5 22.9% SGO_0626 recX; Regulatory protein recX 3 13.6% 3 21.1% SGO_0628 ymdC; 3''-aminoglycoside phosphotransferase-like protein (kanamycin kinase) 4 15.9% 3 10.6% 6 23.1% SGO_0629 rumA-1; 23S rRNA (uracil-5-)-methyltransferase RumA 14.6% 6 4 10.0% 18 36.2% 10.0% 5 17 36.7% SGO_0631 alpha-glycerophosphate oxidase 4 9.4% 19.9% 5 6 17.9% 13.9% 4 6 18.9% SGO_0632 glpK; glycerol kinase 5 21.4% SGO_0635 hypothetical protein SGO_0635 4 17.4% 3 41.4% 3 39.1% SGO_0636 hypothetical protein SGO_0636 31.3% 19 23 35.6% 30 46.0% 28.9% 17 23 38.5% 29 44.4% SGO_0639 valS; valyl-tRNA synthetase 16 27.8% 19 37.8% 4 17.7% 4 12.6% 14.3% 4 4 16.2% 3 13.4% SGO_0640 modification methylase 16.9% 9 17 30.0% 21 40.1% 11.0% 6 15 27.8% 18 37.7% SGO_0641 ATPase, histidine kinase-, DNA gyrase B-, and HSP90like domain protein protein 17 34.6% 13 24.5% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 31

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 31 21.2% 7 15 35.5% 10 23.4% 15.9% 6 19 37.2% 10 24.4% SGO_0642 hypothetical protein SGO_0642 5 14.7% 4 11.8% 8.9% 3 8 24.6% 5 15.0% 7 24.6% 7 25.9% SGO_0643 cytosine-specific methyltransferase 3 12.1% 3 9.9% 30.6% 9 9 28.1% 16 42.5% 34.0% 11 11 34.3% 14 39.1% SGO_0644 hypothetical protein SGO_0644 7 20.5% 8 23.7% 3 19.1% SGO_0649 hypothetical protein SGO_0649 13.8% 4 16 39.5% 7 21.6% 11.0% 4 19 48.7% 4 15.3% SGO_0652 hypothetical protein SGO_0652 3 11.8% 4 14.7% 4 24.2% 5 28.1% 3 19.1% SGO_0653 conserved hypothetical protein of unknown function (DUF1027) 21.3% 6 13 48.1% 10 35.4% 18.2% 5 20 53.9% 10 35.4% SGO_0654 radical SAM enzyme, Cfr family 4 17.7% 18.6% 5 7 23.9% 5 20.4% 17.6% 4 8 28.8% 6 22.4% SGO_0656 trpB-2; tryptophan synthase, beta subunit 8 29.0% 10 30.5% 4 10.0% SGO_0657 trpE; anthranilate synthase component I 3 9.8% SGO_0662 trpB-1; tryptophan synthase, beta subunit 5 19.9% 3 10.3% 3 13.1% SGO_0663 trpA-2; tryptophan synthase, alpha subunit 53.8% 6 9 71.3% 8 66.7% 53.8% 6 8 66.7% 8 64.3% SGO_0665 non-heme iron-containing ferritin 8 66.7% 10 74.3% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 32

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 32 4 38.3% 4 38.3% 5 39.1% 3 29.7% SGO_0667 rhodanese family protein 30.1% 14 15 33.3% 18 35.1% 26.7% 12 16 35.8% 16 34.8% SGO_0669 typA; GTP-binding protein TypA 12 27.6% 17 38.2% 13.6% 3 11 31.6% 18 54.0% 17.3% 5 15 39.1% 17 51.3% SGO_0671 murD; UDP-N-acetylmuramoylalanine--D-glutamate ligase 19 58.4% 14 46.7% 9.6% 3 18 61.5% 7 28.4% 16 54.2% 10 39.3% SGO_0672 murG; undecaprenyl-PP-MurNAc-pentapeptideUDPGlcNAc GlcNAc transferase 8 32.6% 10 37.6% 10.1% 3 12 29.2% 4 15.1% 18 32.2% SGO_0673 DivIB; cell division protein DivIB 5 17.4% 5 16.4% 47.9% 15 19 52.4% 18 54.3% 46.6% 15 23 59.2% 19 55.4% SGO_0674 ftsA; cell division protein FtsA 19 53.0% 17 52.1% 43.9% 15 17 49.2% 17 48.9% 46.1% 15 19 49.4% 17 50.8% SGO_0675 ftsZ; cell division protein FtsZ 20 52.3% 18 50.6% 31.4% 4 5 32.7% 4 24.7% 17.9% 3 7 39.0% 6 38.1% SGO_0676 conserved hypothetical protein TIGR00044 5 27.4% 5 32.3% 31.7% 3 8 50.3% 4 37.0% 31.7% 3 9 63.5% 7 56.6% SGO_0677 ylmF protein 7 55.6% 6 53.4% 52.4% 13 13 57.3% 15 57.3% 54.5% 12 13 57.3% 15 57.3% SGO_0680 cell division protein DivIVA 12 56.5% 9 43.9% 33.2% 21 23 32.5% 30 40.6% 30.8% 19 28 36.1% 29 41.0% SGO_0681 ileS; isoleucyl-tRNA synthetase 22 33.9% 21 39.6% 41.4% 4 4 41.4% 5 41.4% 41.4% 4 5 42.4% 4 41.4% SGO_0684 hypothetical protein SGO_0684 5 41.4% 6 42.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 33

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 33 3 32.7% SGO_0685 MutT/nudix family protein 3 34.0% 27.6% 14 27 48.1% 24 41.7% 23.4% 13 35 50.2% 26 48.2% SGO_0688 ATP dependent Clp protease, ATP-binding subunit, ClpE 15 24.7% 16 31.6% 4 31.6% SGO_0689 hypothetical protein SGO_0689 3 17.3% 4 20.8% 3 17.3% SGO_0690 folD; methenyltetrahydrofolate cyclohydrolase 3 17.3% 5 25.0% 12 33.6% 3 10.8% 8.5% 3 14 33.2% 3 10.8% SGO_0693 xseA; exodeoxyribonuclease VII, large subunit 8 24.7% 15 39.2% 3 45.7% 3 61.4% SGO_0694 xseB; exodeoxyribonuclease VII, small subunit 3 16.5% SGO_0695 geranyltranstransferase 3 9.6% 3 10.3% 4 18.1% SGO_0696 hemolysin-like protein 3 34.3% 3 32.9% 4 34.3% SGO_0697 transcription regulator 8 24.6% 6 17.8% 14 38.2% 12 33.3% SGO_0698 recN; DNA repair protein RecN 10 27.0% 7 18.3% 3 26.4% 3 31.4% 3 25.2% 4 35.1% SGO_0699 Serine/threonine protein phosphatase 5 41.7% 6 35.1% 11.6% 3 7 39.4% 8 42.2% 18.1% 4 7 33.6% 9 45.1% SGO_0700 DegV family protein 6 31.4% 4 16.2% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 34

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 34 62.6% 7 7 59.3% 6 49.5% 64.8% 9 10 73.6% 7 62.6% SGO_0701 hup; DNA-binding histone-like protein HU 8 73.6% 8 70.3% 81.3% 18 15 70.9% 21 80.4% 77.4% 18 20 72.6% 22 82.6% SGO_0704 gpmA; 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 17 79.1% 18 83.9% 3 45.5% SGO_0705 Protein of unknown function (DUF1250) superfamily 3 12.0% 7 32.8% 17.8% 5 6 24.7% 7 32.8% SGO_0706 phoH-like protein 11 47.3% 10 42.8% 4.9% 6 36 28.7% 10 11.6% 2.3% 3 46 33.0% 4 3.2% SGO_0707 LPXTG cell wall surface protein 32 25.8% 30 25.5% 71.9% 16 18 65.1% 19 77.6% 68.9% 17 20 76.8% 22 88.6% SGO_0708 ald; alanine dehydrogenase 23 92.7% 28 98.4% 3 12.7% SGO_0711 conserved hypothetical protein TIGR00043 4 20.6% 29.1% 7 14 51.8% 14 54.8% 36.8% 9 10 41.5% 12 45.5% SGO_0713 sgg; GTP-binding protein Era 15 61.9% 16 59.5% 3 18.2% 3 19.0% SGO_0715 mutM; formamidopyrimidine-DNA glycosylase 14 22.9% 4 8.6% 15 25.3% 5 10.9% SGO_0719 rnr; ribonuclease R 6 11.3% 6 11.4% 11.1% 6 7 13.7% 4 7.5% 5.4% 3 10 19.8% 3 6.3% SGO_0721 abpB-like dipeptidase lipoprotein 4 8.0% 4 6.6% 4 19.2% 5 19.6% 9 37.1% 5 19.9% SGO_0722 tehB; tellurite resistance protein TehB 5 22.0% 5 22.0% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 35

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 35 12 32.5% 5 16.1% 14 36.0% 6 18.1% SGO_0724 dipeptidase 6 20.5% 5 14.4% 4 27.0% SGO_0728 ABC transporter, ATP-binding protein SP1653 4 5.2% 7 9.7% SGO_0729 ABC transporter permease protein 4 41.6% 4 41.6% SGO_0731 RRF2 family protein 11.9% 3 9 43.1% 5 22.8% 8 37.9% 5 21.5% SGO_0736 hprK; HPr(Ser) kinase/phosphatase 10 46.3% 9 42.8% 3 14.5% 3 14.5% SGO_0737 lgt; prolipoprotein diacylglyceryl transferase 5 57.5% 4 51.2% 5 57.5% 3 28.3% SGO_0738 Bacterial protein of unknown function (DUF948) family 43.5% 4 7 43.5% 8 63.9% 55.8% 6 7 46.9% 7 63.9% SGO_0739 hypothetical protein SGO_0739 4 28.6% 16.8% 4 4 17.2% 4 18.8% 5 20.7% 5 25.9% SGO_0742 peptidase, U32 family 7 29.8% 6 29.4% 21.5% 7 13 38.1% 10 30.1% 24.5% 7 16 48.8% 10 28.7% SGO_0743 peptidase, U32 family 9 27.3% 6 17.8% 44.3% 4 3 44.3% 4 44.3% 44.3% 4 3 44.3% 4 44.3% SGO_0745 hypothetical protein SGO_0745 3 38.6% 20.3% 7 5 19.2% 11 45.9% 21.4% 6 9 29.0% 9 38.8% SGO_0749 glutathione reductase 12 48.6% 12 45.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 36

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 36 49.0% 12 21 64.0% 16 53.8% 41.4% 12 20 61.9% 18 60.9% SGO_0750 efflux transporter, RND family, MFP subunit subfamily 5 16.8% 4 18.8% 44.6% 7 9 45.0% 13 74.5% 40.3% 7 11 56.3% 11 68.4% SGO_0751 ABC transporter, ATP-binding protein SP0786 3 20.8% 5 34.2% 10 28.5% 5 17.5% 13.0% 5 14 36.6% 6 16.7% SGO_0752 ABC transporter, ATP-binding protein 32.5% 16 22 45.8% 24 48.0% 33.3% 16 26 45.4% 22 45.8% SGO_0753 lysS; lysyl-tRNA synthetase 20 38.1% 19 40.3% 3 27.7% SGO_0754 phosphoglycerate mutase family protein 4 42.3% 6 57.0% 4 43.7% 41.8% 4 6 55.1% 6 55.1% SGO_0755 regulatory protein 4 39.2% 5 44.9% 10 49.2% 9 52.4% SGO_0757 peptidase, U32 family 24.1% 18 37 44.2% 40 50.7% 23.8% 18 41 44.4% 38 45.9% SGO_0760 ppc; phosphoenolpyruvate carboxylase 34 42.7% 29 40.4% 79.4% 36 31 78.1% 37 79.9% 81.2% 36 32 78.1% 36 79.9% SGO_0761 tuf; translation elongation factor Tu 42 82.2% 52 98.0% 54.0% 12 12 54.0% 14 55.2% 54.0% 12 12 54.0% 13 55.2% SGO_0762 tpiA; triosephosphate isomerase 13 55.2% 13 54.0% 26.3% 9 19 59.9% 14 45.5% 24.4% 8 17 58.2% 15 54.2% SGO_0763 murA-1; UDP-N-acetylglucosamine 1carboxyvinyltransferase 11 41.1% 12 40.4% 4 21.9% 8 49.1% SGO_0765 endA; DNA-entry nuclease Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 37

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 37 9 40.5% 6 33.2% 10 46.4% 8 42.2% SGO_0767 transport protein 11 50.5% 6 33.2% 48.1% 12 12 45.0% 12 58.9% 41.4% 10 13 52.8% 15 65.3% SGO_0771 pepq; proline dipeptidase 16 64.7% 14 60.3% 60.5% 13 25 82.3% 18 74.6% 61.7% 12 26 82.6% 17 74.3% SGO_0773 ccpA; catabolite control protein A 14 65.3% 14 65.3% 17.1% 4 12 38.0% 5 20.6% 17 47.0% 7 31.5% SGO_0774 glycosyl transferase, group 1 family protein 5 15.9% 6 20.9% 12.4% 4 13 32.3% 9 23.8% 19.7% 7 12 29.3% 8 23.6% SGO_0775 glycosyl transferase, group 1 11 30.9% 10 30.2% 33.2% 18 23 46.7% 25 53.8% 39.7% 19 25 43.7% 28 56.1% SGO_0778 thrS; threonyl-tRNA synthetase 24 56.0% 21 50.4% 30.0% 5 7 45.5% 13 65.2% 14.2% 3 12 54.1% 13 61.4% SGO_0779 response regulator 16 70.0% 15 65.2% 14 37.7% 3 5.3% 12 36.9% 4 13.2% SGO_0780 histidine kinase 7 19.4% 4 14.8% 11 43.8% 13 51.3% SGO_0781 vicX; Zn-dependent hydrolase (beta-lactamase superfamily) 3 23.2% 3 16.9% 3 16.9% SGO_0782 Protein of unknown function (DUF454) family 10.0% 9 53 48.3% 24 24.9% 10.0% 8 57 50.8% 27 30.6% SGO_0784 smc; chromosome segregation protein SMC 18 21.9% 18 21.6% 4 20.4% 3 20.0% 6 33.6% SGO_0785 Cof family protein 3 15.8% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 38

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 38 33.8% 5 6 39.4% 6 39.4% 33.8% 5 5 33.8% 7 46.1% SGO_0786 Cof family protein 4 25.7% 15.3% 6 20 47.1% 12 31.4% 17.4% 7 24 54.6% 14 33.5% SGO_0787 ftsY; cell division protein FtsY 14 38.9% 9 23.8% 19.8% 7 7 18.5% 15 40.7% 20.6% 9 12 30.5% 13 38.5% SGO_0788 zwf; glucose-6-phosphate 1-dehydrogenase 19 47.5% 18 47.5% 18.5% 11 21 34.6% 21 35.4% 18.0% 9 20 34.9% 15 23.5% SGO_0792 hypothetical protein SGO_0792 7 13.5% 6 12.7% 20.4% 9 16 38.9% 20 35.6% 25.9% 10 19 41.6% 19 39.4% SGO_0794 metallo-beta-lactamase family protein 19 43.4% 15 39.2% 26.6% 4 4 24.0% 5 32.3% 21.7% 3 5 31.2% 6 41.8% SGO_0795 tributyrin esterase 6 31.2% 9 44.9% 6 12.8% SGO_0797 RocB protein, putative 4 12.3% 29.6% 5 11 64.8% 11 63.2% 35.2% 6 10 55.1% 11 60.3% SGO_0798 ABC transporter, ATP-binding protein SP1381 8 49.0% 8 48.2% 15.7% 3 11 48.2% 6 29.7% 11 48.2% 5 23.3% SGO_0800 polysaccharide deacetylase family protein 4 23.0% 4 16.3% 50.5% 16 15 48.4% 18 60.0% 42.5% 12 16 53.5% 17 54.2% SGO_0801 hom; homoserine dehydrogenase 16 54.9% 17 55.4% 28.1% 5 10 54.9% 10 55.6% 41.0% 8 12 60.1% 10 60.1% SGO_0802 thrB; homoserine kinase 8 43.1% 13 63.5% 15.3% 3 7 20.8% 7 21.8% 15.3% 4 8 23.8% 8 23.8% SGO_0803 hypothetical protein SGO_0803 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 39

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 39 5 17.2% 4 11.9% 6 25.2% 4 22.2% SGO_0804 murB; UDP-N-acetylenolpyruvoylglucosamine reductase 4 20.5% 4 20.5% 12 30.9% 3 13.8% 12 28.1% 5 11.7% SGO_0805 potA; spermidine/putrescine ABC transporter, ATPbinding subunit 4 21.0% 4 21.8% 4 15.7% 4 15.7% SGO_0806 potB; spermidine/putrescine ABC transporter, permease protein 13 57.0% 16 57.3% 6 29.2% SGO_0808 potD; spermidine/putrescine ABC transporter 3 12.4% 7 35.6% 5 25.6% 8 39.6% 5 30.0% SGO_0812 hypothetical protein SGO_0812 5 31.5% 7 38.9% 3 4.4% SGO_0813 fructose-bisphosphatase 3 3.8% 3 7.7% 7.4% 3 5 27.4% 3 13.9% SGO_0814 aminotransferase, class-V 22.0% 6 15 51.2% 14 47.3% 26.5% 7 18 59.2% 13 41.6% SGO_0815 thiI; thiamine biosynthesis protein ThiI 8 31.4% 9 33.4% 5 22.3% 3 18.8% SGO_0817 hypothetical protein SGO_0817 49.0% 3 3 49.0% 4 57.7% 49.0% 3 4 54.8% 3 49.0% SGO_0818 rplU; ribosomal protein L21 3 49.0% 37.1% 3 3 37.1% 5 49.5% 37.1% 3 3 37.1% 5 49.5% SGO_0820 rpmA; ribosomal protein L27 3 37.1% 3 30.3% 5 36.0% SGO_0822 lipoprotein, putative Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 40

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 40 4 23.7% 4 25.9% SGO_0823 Cof family protein 4 21.5% 3 13.7% 29.8% 11 11 31.3% 15 38.9% 27.8% 10 19 46.5% 12 34.3% SGO_0824 lepA; GTP-binding protein LepA 10 26.5% 13 32.1% 9 54.0% 4 27.5% 7 35.1% 3 20.4% SGO_0825 lipoprotein, putative 3 20.4% 3 7.0% 3 8.5% 3 7.4% SGO_0830 uvrC; excinuclease ABC, C subunit 3 10.8% 7 73.7% 3 39.5% 40.4% 3 8 78.9% 3 47.4% SGO_0832 hypothetical protein SGO_0832 3 43.0% 3 19.2% 5 28.1% SGO_0833 phosphoesterase-related gene 7 40.2% 7 31.3% 4 8.1% 5 9.2% SGO_0834 hypothetical protein SGO_0834 3 7.4% 57.2% 10 8 39.8% 12 58.7% 61.2% 10 11 63.7% 11 58.7% SGO_0835 nitroreductase 12 62.7% 11 62.7% 54.4% 15 17 52.2% 21 65.5% 48.4% 13 16 46.5% 22 66.0% SGO_0836 pepV; dipeptidase PepV 21 60.0% 22 69.2% 4 13.9% SGO_0841 oxidoreductase 14 51.8% 15 56.1% 34.7% 3 4 51.0% 3 40.8% 34.7% 3 4 51.0% 5 58.2% SGO_0842 rhodanese family protein 8 62.2% 5 58.2% 60.6% 5 3 59.6% 5 60.6% 60.6% 4 3 59.6% 6 61.7% SGO_0848 rpmE; ribosomal protein L31 5 60.6% 3 59.6% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 41

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 41 9 31.2% 10 43.3% 12 43.0% 8 34.7% SGO_0849 DHH subfamily 1 protein 10 41.1% 7 32.5% 51.7% 4 4 51.7% 4 51.7% 51.7% 4 3 38.1% 4 51.7% SGO_0850 flavodoxin 5 55.8% 4 51.7% 6 18.8% 3 15.2% 3 11.1% 3 15.7% SGO_0851 putative permease 3 15.5% 8 29.9% 4 14.8% 7 24.2% 3 12.3% SGO_0852 TPR domain protein 4 15.8% 5 17.8% 6 37.2% 3 19.7% 4 25.1% 3 22.2% SGO_0853 budA; alpha-acetolactate decarboxylase 3 21.8% 4 24.7% 3.1% 4 65 33.6% 7 5.9% 2.6% 4 71 35.1% 10 9.1% SGO_0854 cshA; surface-associated protein CshA 23 18.9% 18 15.7% 10 24.2% 9 24.5% 12 28.9% 8 18.4% SGO_0855 fbpA; fibronectin-binding protein A 6 14.0% 6 18.2% 27.8% 6 14 68.3% 12 60.8% 27.2% 6 19 73.1% 12 56.3% SGO_0856 ABC transporter, substrate binding protein 6 32.3% 5 24.6% 4 16.7% 7 33.7% SGO_0858 ABC transporter, ATP-binding protein 20.6% 6 13 44.4% 11 39.0% 31.2% 9 13 42.1% 11 39.3% SGO_0859 pheS; phenylalanyl-tRNA synthetase, alpha subunit 10 34.7% 11 36.1% 30.3% 16 25 42.9% 26 50.2% 29.8% 16 27 40.2% 26 44.9% SGO_0861 pheT; phenylalanyl-tRNA synthetase, beta subunit 15 29.0% 15 33.6% 3 14.3% 4 24.5% SGO_0862 hypothetical protein SGO_0862 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 42

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 42 3 59.7% SGO_0868 hypothetical protein SGO_0868 3 13.9% SGO_0877 permease domain protein 20.3% 3 7 44.4% 4 24.9% 17.6% 3 8 47.9% 4 24.9% SGO_0885 cobyric acid synthase 6 40.6% 6 39.1% 4 13.4% 4 12.8% 8 21.5% 5 17.7% SGO_0886 Mur ligase family protein 6 18.1% 5 13.6% 7 24.6% 10 28.5% SGO_0887 conserved hypothetical protein TIGR00159 6 41.5% 3 25.8% 25.8% 3 8 48.0% 3 25.8% SGO_0888 hypothetical protein SGO_0888 24.2% 9 14 42.0% 14 40.9% 12.9% 4 15 49.1% 14 47.1% SGO_0889 glmM; phosphoglucosamine mutase 6 19.3% 9 28.9% 7 11.0% 9 12.5% SGO_0890 LPXTG cell wall surface protein, collagen binding domain 9 17.3% 8 15.7% 39.0% 10 16 53.2% 15 54.4% 42.0% 11 18 56.9% 18 58.3% SGO_0893 GTP-binding protein 15 56.7% 14 53.9% 4 15.0% 7 24.6% SGO_0899 putative hydrolase or acyltransferase 10.3% 3 10 28.1% 10 26.8% 18.3% 6 8 21.0% 11 32.9% SGO_0901 DNA-directed DNA polymerase III 10 29.9% 8 23.4% 3 10.5% SGO_0904 purR; galactose operon repressor GalR Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 43

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 43 5 40.8% 6 45.9% SGO_0905 lipoprotein, putative 29.3% 10 9 25.7% 16 36.0% 38.1% 13 9 24.1% 14 35.1% SGO_0906 leuA; 2-isopropylmalate synthase 15 33.3% 15 35.1% 3 11.6% 3 12.8% 3 11.6% SGO_0907 leuB; 3-isopropylmalate dehydrogenase 4 10.4% SGO_0909 leuC; 3-isopropylmalate dehydratase, large subunit 4 18.7% 3 16.1% 54.4% 9 6 36.3% 14 69.1% 48.3% 9 12 57.9% 10 57.1% SGO_0911 hypothetical protein SGO_0911 12 65.3% 11 58.7% 6 43.4% 3 21.9% 8 47.5% 3 25.2% SGO_0915 proV; ABC-type proline/glycine betaine transporter 12 32.4% 13 36.4% SGO_0916 proWX; ABC transporter membrane-spanning permease 6 15.3% 5 17.1% SGO_0932 galK; galactokinase 5 22.2% SGO_0934 galE-2; UDP-glucose 4-epimerase 3 15.9% 3 15.9% 4 6.4% 5.5% 3 3 4.9% SGO_0936 phosphoenolpyruvate synthase, putative 15.2% 3 SGO_0938 Phosphatidylserine decarboxylase proenzyme 2 7.6% 3 8 16.1% 5 8.6% SGO_0940 ppsA; phosphoenolpyruvate synthase Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 44

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 44 4 18.2% SGO_0941 hypothetical protein SGO_0941 17 8.7% 17 10.7% SGO_0942 zmpC; zinc metalloproteinase C 3 20.4% 4 27.4% SGO_0944 ABC transporter, ATP-binding protein 15.4% 4 6 21.2% 7 24.6% 18.3% 5 7 26.1% 4 15.1% SGO_0946 Deblocking aminopeptidase 7 25.8% 8 32.5% 9 28.0% 8 20.6% SGO_0948 pgdA; peptidoglycan N-acetylglucosamine deacetylase A 7 16.1% 10 29.2% 10.0% 3 8 27.0% 5 17.0% 8 24.0% 5 18.6% SGO_0949 deaD; DEAD RNA helicase 5 24.0% 4 15.9% 22.4% 3 3 16.9% 6 28.8% 3 16.9% SGO_0950 oxidoreductase 7 31.9% 5 23.3% 27.6% 4 7 43.8% 7 44.3% 22.9% 3 8 48.1% 7 54.8% SGO_0951 udk; uridine kinase 6 44.8% 6 44.8% 3 42.1% 3 42.1% SGO_0953 endoribonuclease L-PSP, putative 11.8% 3 8 32.1% 6 28.7% 18.6% 4 7 30.4% 9 37.5% SGO_0954 ATP-binding protein 7 26.0% 6 26.4% 5 22.8% 6 26.5% 6 27.2% SGO_0955 transporter 5 21.3% 4 17.3% 6 46.6% 6 46.6% SGO_0957 hypothetical protein SGO_0957 3 24.5% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 45

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 45 5 36.2% 5 36.2% 3 24.8% 5 36.2% SGO_0959 copper homeostasis protein CutC 6 45.7% 6 37.6% 5 15.4% 7 15.9% SGO_0961 ABC transporter, permease/ATP-binding protein 3 7.6% 3 8.3% SGO_0962 ABC transporter, permease/ATP-binding protein 9 5.6% 10 6.3% SGO_0966 hsa; streptococcal hemagglutinin 5 4.2% 5 3.8% 4 17.1% 3 17.1% SGO_0969 nss; nucleotide sugar synthetase-like protein 3 13.8% 4 9.1% 4 9.9% SGO_0971 asp1; accessory secretory protein 5 12.0% SGO_0972 asp2; accessory sescretory protein 6 16.6% 4 10.3% SGO_0975 gtaA; glycosyl transferase, group 1 SP1758 4 15.7% 4 16.7% SGO_0979 degV family protein 3 18.0% SGO_0980 transcriptional regulator, TetR family domain protein 6 40.6% 4 31.6% 5 41.9% SGO_0981 comE operon protein 2 family 3 20.6% 24.3% 4 19 68.0% 11 47.9% 25.4% 4 23 70.8% 10 49.6% SGO_0982 amino acid ABC transporter, amino acid-binding protein 4 25.4% 3 17.6% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 46

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 46 5 36.9% 5 36.9% 3 21.0% SGO_0983 amino acid ABC transporter, ATP-binding protein SP0709 5 26.5% 5 26.5% SGO_0986 hypothetical protein SGO_0986 35.9% 11 12 30.6% 16 40.4% 28.0% 10 13 34.1% 10 30.3% SGO_0987 metK; S-adenosylmethionine synthetase 16 38.4% 14 39.4% 3 53.6% 3 53.6% SGO_0991 hypothetical protein SGO_0991 12.9% 4 5 13.8% SGO_0993 GTP-binding protein HflX 3 8.5% 4 10.2% 3 21.7% 3 24.6% 5 39.1% 3 24.6% SGO_0994 hypothetical protein SGO_0994 20.4% 4 7 23.0% 13 56.0% 7 31.4% 6 27.5% SGO_0995 metallo-beta-lactamase superfamily protein 4 22.7% 6 28.5% 5 25.5% 6 38.6% SGO_0996 oxidoreductase, short-chain dehydrogenase/reductase family 7 34.6% 4 23.1% 7 34.6% 3 17.5% SGO_0997 hypothetical protein SGO_0997 3 17.5% 3 17.5% 4 8.1% 9 17.9% 7 14.1% SGO_1000 recJ; single-stranded-DNA-specific exonuclease RecJ 9 19.2% 11 22.9% 72.9% 12 11 67.1% 11 78.2% 75.9% 10 11 77.6% 13 82.9% SGO_1001 apt; adenine phosphoribosyltransferase 9 67.6% 8 68.8% 4 15.3% SGO_1002 metA; homoserine O-succinyltransferase Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 47

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 47 7 38.5% 5 29.6% 5 29.6% 6 32.3% SGO_1003 DNA replication protein DnaD 3 16.4% 4 23.9% 4 17.2% 3 14.1% 3 13.4% SGO_1004 glutathione S-transferase family protein 3 14.1% 5 25.2% 27.5% 4 3 21.0% 5 27.1% 23.1% 3 5 30.1% 6 39.3% SGO_1005 Bcl-2 family protein 5 34.5% 5 27.1% 4 22.6% 3 14.3% 3 15.8% SGO_1006 conserved hypothetical protein TIGR00486 3 15.8% 3 11.5% 3 11.5% SGO_1007 oxidoreductase, DadA family protein SP1608 77.5% 15 13 63.3% 17 77.2% 70.6% 15 16 65.4% 19 85.1% SGO_1009 rfbA-1; glucose-1-phosphate thymidylyltransferase 23 87.9% 21 92.0% 42.6% 7 7 42.6% 7 42.6% 38.1% 6 9 47.2% 7 42.6% SGO_1010 rmlC; dTDP-4-keto-6-deoxyglucose-3,5-epimerase 8 47.2% 7 48.2% 47.7% 14 10 38.2% 16 51.7% 49.1% 13 16 53.2% 17 51.7% SGO_1011 rfbB-1; dTDP-glucose 4,6-dehydratase 20 64.4% 17 57.5% 43.4% 11 14 50.1% 14 47.5% 55.8% 14 12 48.1% 14 57.8% SGO_1012 galE-1; UDP-glucose 4-epimerase 17 56.9% 18 62.8% 17.8% 3 6 37.3% 7 41.5% 3 23.7% SGO_1013 Glycosyltransferase involved in cell wall biogenesis 3 16.9% 15.8% 3 8 41.5% 5 26.9% 9 46.9% 5 27.3% SGO_1016 putative glycosyltransferase 3 12.3% 4 9.1% 3 8.1% SGO_1018 hypothetical protein SGO_1018 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 48

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 48 13.6% 3 7 29.2% 4 19.2% 8 29.2% 4 19.5% SGO_1019 glycosyl transferase 4 24.0% 32.9% 8 13 55.1% 12 57.2% 29.0% 7 14 60.1% 15 67.1% SGO_1020 rfbD; dTDP-4-dehydrorhamnose reductase 15 62.5% 15 67.8% 9 38.2% 14 47.6% SGO_1021 rgpA; rhamnosyltransferase, putative 8 35.8% 7 31.3% SGO_1022 rhamnosyltransferase 15 37.8% 9 26.5% 17 40.3% 7 17.7% SGO_1024 putative polysaccharide ABC transporter 4 15.5% 5 17.4% 24.7% 9 12 39.6% 9 28.1% 19.8% 6 15 45.4% 10 31.6% SGO_1025 rgp; glycosyltransferase 8 30.7% 5 22.7% 5.8% 3 22 34.7% 8 19.2% 5.8% 3 29 40.4% 12 26.5% SGO_1026 rhamnosyltransferase 9 16.0% 10 17.7% 11 20.2% 13 23.5% SGO_1027 hypothetical protein SGO_1027 3 28.4% 4 28.4% SGO_1028 hypothetical protein SGO_1028 3 28.9% SGO_1030 hypothetical protein SGO_1030 23.1% 3 6 39.1% 7 48.0% 23.6% 3 7 45.3% 7 51.1% SGO_1031 cmk; cytidylate kinase 6 43.1% 5 34.2% 24.4% 4 4 29.0% 4 30.7% 20.5% 3 4 29.0% 4 30.7% SGO_1032 infC; translation initiation factor IF-3 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 49

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 49 18.2% 3 3 18.2% 18.2% 4 5 30.3% SGO_1033 rpmI; ribosomal protein L35 5 33.3% 4 18.2% 47.1% 5 7 52.1% 7 52.1% 51.3% 5 7 52.1% 7 52.1% SGO_1034 rplT; ribosomal protein L20 6 54.6% 8 73.9% 28.6% 3 4 34.1% 3 28.6% 28.6% 3 4 34.1% 3 28.6% SGO_1035 gloA; lactoylglutathione lyase 5 36.5% 5 38.1% 17.5% 3 10 54.9% 7 45.5% 20.3% 3 9 52.0% 10 64.6% SGO_1036 amino acid ABC transporter, ATP-binding protein SP1242 13 69.1% 6 35.8% 9 26.6% 5 9.5% 13 37.1% 8 21.6% SGO_1037 glutamine ABC transporter permease and substrate binding protein 3 8.0% 4 14.2% 10.1% 6 6 10.6% 7 14.8% 13.1% 7 8 15.6% 8 16.0% SGO_1038 uvrB; excinuclease ABC, B subunit 9 19.2% 9 19.9% 4 18.2% 3 10.5% SGO_1039 hypothetical protein SGO_1039 3 27.1% 3 24.3% 4 40.3% SGO_1041 hypothetical protein SGO_1041 3 32.0% 3 26.5% 3 22.6% 4 32.9% SGO_1044 MutT/nudix family protein 3 23.9% 14.6% 5 10 29.2% 8 22.2% 9.4% 3 14 35.4% 9 27.1% SGO_1047 hypothetical protein SGO_1047 3 9.7% 20.5% 3 3 18.8% 4 21.6% 6 29.8% 4 22.6% SGO_1049 tRNA pseudouridine synthase B 4 15.4% 16.4% 4 3 9.8% 3 12.1% SGO_1050 ribF; riboflavin biosynthesis protein RibF 3 10.5% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 50

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 50 21.8% 3 5 43.6% SGO_1051 negative regulator of proteolysis 4 13.8% 3 14.5% 5 18.2% SGO_1054 NOL1/NOP2/sun family protein 12 67.2% 4 21.2% 13 71.3% 5 25.9% SGO_1055 phosphate ABC transporter, phosphate-binding protein 4 10.2% SGO_1057 pstA; phosphate ABC transporter, permease protein PstA 13.1% 4 12 40.8% 5 17.6% 14 46.1% 4 15.4% SGO_1058 pstB; Phosphate import ATP-binding protein pstB 2 (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) 44.8% 7 9 46.4% 7 48.4% 38.5% 6 9 46.4% 8 48.8% SGO_1059 pstB; Phosphate import ATP-binding protein pstB 1 (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) 3 17.9% 3 17.9% 37.8% 6 11 55.8% 9 54.4% 37.8% 6 11 55.8% 12 57.6% SGO_1060 phosphate transport system regulatory protein 7 39.2% 7 41.0% 32.1% 4 8 41.7% 4 32.1% 27.8% 3 8 43.3% 4 32.1% SGO_1065 hypothetical protein SGO_1065 7 42.8% 4 32.1% 12 37.3% 5 12.0% 14 37.0% 4 11.1% SGO_1066 hypothetical protein SGO_1066 8 23.9% 10 25.0% 3 57.1% SGO_1067 hypothetical protein SGO_1067 3 64.3% 37.5% 21 32 45.6% 36 53.5% 35.1% 20 27 40.0% 31 51.0% SGO_1069 membrane alanyl aminopeptidase 27 44.3% 35 54.9% 4 21.4% 3 14.7% SGO_1072 ciaR; Transcriptional regulatory protein CiaR 5 31.3% 7 34.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 51

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 51 6 17.6% 4 9.9% 6 17.6% SGO_1073 Sensor protein CiaH 5 15.2% 4 12.2% 3 11.2% SGO_1075 alpha-amylase precursor 7 22.8% 5 15.3% 5 19.6% 4 14.4% 6 25.2% 5 14.4% SGO_1077 coaA; pantothenate kinase 3 13.7% 5 18.6% 3 35.0% 3 35.0% SGO_1078 methyltransferase domain protein 3 35.0% 4 42.6% 20.0% 5 10 31.3% 12 39.8% 25.6% 7 11 28.9% 10 35.5% SGO_1079 pdp; pyrimidine-nucleoside phosphorylase 9 29.2% 11 36.5% 72.3% 13 11 68.6% 12 70.9% 70.9% 12 12 70.9% 13 72.3% SGO_1080 deoC; deoxyribose-phosphate aldolase 12 70.9% 10 61.4% 44.2% 3 3 38.8% 4 58.1% 5 55.0% 3 44.2% SGO_1081 cdd; cytidine deaminase 65.9% 20 22 66.5% 19 65.9% 63.4% 18 31 75.0% 20 63.4% SGO_1082 lipoprotein 22 65.9% 20 62.2% 43.4% 19 28 61.1% 47.6% 18 24 58.1% SGO_1083 sugar ABC transporter, ATP-binding protein SP0846 19 53.8% 20 49.1% 23.2% 3 3 17.9% 7 28.5% 5 24.8% 4 20.9% SGO_1088 transcription regulator, LysR family 7 31.1% 9 33.1% 8 33.1% 8 33.4% SGO_1090 pseudouridine synthase, RluA family 4 20.9% 3 20.5% 4 29.0% SGO_1091 hypothetical protein SGO_1091 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 52

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 52 61.4% 12 10 53.1% 12 61.4% 61.4% 11 10 58.3% 12 61.4% SGO_1096 butA; acetoin dehydrogenase 15 64.6% 20 82.7% 3 8.7% SGO_1097 proB; glutamate 5-kinase 3 9.8% 13.8% 3 6 22.9% 14.3% 3 4 11.9% 7 26.4% SGO_1098 proA; gamma-glutamyl phosphate reductase 8 31.4% 6 21.4% 3 19.0% SGO_1099 proC; pyrroline-5-carboxylate reductase 4 18.7% 5 23.9% 4 34.8% SGO_1100 phnA; alkylphosphonate utilization operon protein PhnA 3 13.4% 3 14.8% SGO_1103 carA; carbamoyl-phosphate synthase, small subunit 4.2% 4 14 20.8% 9 11.2% SGO_1104 carB; carbamoyl-phosphate synthase, large subunit 4 5.9% 7 49.1% 26.6% 3 7 49.1% 4 33.5% SGO_1107 PyrR bifunctional protein 3 28.3% 45.1% 10 14 50.3% 14 48.0% 37.3% 8 15 52.9% 16 57.8% SGO_1109 pyrB; aspartate carbamoyltransferase 9 38.6% 10 38.9% 15 26.4% 21 35.4% SGO_1110 surface antigen SCP-like domain 4 7.9% 21.9% 4 13 59.1% 7 40.1% 14 60.3% 4 22.7% SGO_1111 fruR; phosphotransferase system repressor 4 21.5% 3 18.2% 11 51.8% 8 37.3% 14.9% 3 14 60.4% 11 59.4% SGO_1112 fruB; 1-phosphofructokinase 5 32.7% 4 22.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 53

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 53 18.7% 8 21 34.8% 13 27.6% 24.2% 11 26 41.3% 14 27.4% SGO_1113 fruA; PTS system, fructose specific IIABC components 9 16.8% 5 10.7% 31.5% 4 7 42.7% 7 51.6% 25.0% 3 6 36.3% 5 31.5% SGO_1114 Protein of unknown function (DUF1149) superfamily 5 42.7% 3 29.8% 3 13.4% 3 12.0% 3 12.0% SGO_1115 DegV family protein 3 13.4% 43.1% 6 6 43.1% 7 43.5% 43.1% 6 6 43.5% 7 43.5% SGO_1116 dapB; dihydrodipicolinate reductase 7 39.6% 6 37.6% 4 9.8% 4 15.8% SGO_1117 pcnA; polynucleotide adenylyltransferase 7 30.8% 4 17.3% 4 8.9% 6 12.7% 5 9.7% SGO_1118 ABC transporter, ATP-binding protein SP1553 5 12.4% 8 14.8% 4 9.4% 3 5.8% SGO_1119 Abi-alpha protein, putative 46.3% 15 21 50.4% 21 54.4% 45.8% 17 25 57.3% 24 54.1% SGO_1120 guaA; GMP synthase 20 49.0% 25 64.3% 5 16.8% 3 22.4% SGO_1121 transcription regulator, GntR family 41.2% 13 11 28.4% 20 54.4% 44.7% 14 14 38.7% 21 54.4% SGO_1123 ffh; signal recognition particle protein 16 47.1% 14 43.3% 3 18.0% 4 22.5% SGO_1124 cell surface hydrolase 6 10.3% SGO_1128 bacteriocin-associated integral membrane protein subfamily Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 54

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 54 26.4% 7 9 33.1% 8 35.3% 26.4% 6 11 35.6% 8 33.7% SGO_1129 lplA; lipoate protein ligase A 6 14.9% 4 14.9% 30.0% 13 21 39.7% 14 28.6% 24.2% 11 20 42.0% 17 35.4% SGO_1130 dihydrolipoamide dehydrogenase 4 8.1% 5 14.8% 19.3% 4 10 34.9% 8 32.3% 23.9% 5 16 40.3% 9 35.4% SGO_1131 sucB; dihydrolipoamide S-acetyltransferase 4 18.4% 17.6% 3 5 22.4% 6 26.1% 7 28.5% 5 26.1% SGO_1132 acetoin dehydrogenase 29.2% 6 7 30.1% 6 26.7% 20.5% 4 8 33.2% 7 30.7% SGO_1133 acoA; acetoin dehydrogenase 5 15.8% 6 16.5% 4 14.4% 12.4% 4 6 22.9% SGO_1134 hypothetical protein SGO_1134 7 20.9% 12 37.6% 49.2% 7 9 58.9% 13 73.1% 43.7% 8 12 64.5% 14 78.7% SGO_1139 GTP-binding protein 10 55.8% 8 49.7% 35.9% 12 15 43.8% 20 67.5% 45.7% 14 20 49.1% 20 67.2% SGO_1140 clpX; ATP-dependent Clp protease, ATP-binding subunit ClpX 15 46.9% 16 46.0% 23.5% 3 5 40.6% 4 36.5% 4 25.9% 4 36.5% SGO_1141 folA; dihydrofolate reductase 4 36.5% 7 53.5% 16.5% 3 3 16.5% 4 21.1% 4 21.1% 4 19.7% SGO_1143 thyA; thymidylate synthase 3 17.2% 4 23.7% 58.6% 13 14 45.5% 19 72.1% 64.3% 13 19 63.9% 18 69.0% SGO_1144 glcK; glucokinase 19 79.6% 19 77.1% 4 21.7% 4 17.8% SGO_1145 cell surface hydrolase Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 55

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 55 46 28.8% 48 29.5% SGO_1148 cshB; surface-associated protein CshB 11 9.0% 11 8.8% 5 36.0% 6 42.0% SGO_1149 Pneumococcal vaccine antigen A-like protein 8 37.0% 12.7% 3 9 37.3% 9 38.0% SGO_1150 hypothetical protein SGO_1150 8 32.1% 5 22.8% 49.8% 16 15 45.0% 19 55.0% 44.0% 14 16 46.0% 22 58.3% SGO_1151 glyA; serine hydroxymethyltransferase 25 68.6% 22 67.4% 38.2% 11 10 36.2% 11 37.6% 38.4% 10 12 44.3% 13 46.5% SGO_1154 prfA; peptide chain release factor 1 10 46.2% 8 33.1% 7 41.9% 5 24.1% 16.2% 4 8 46.1% 5 26.2% SGO_1155 tdk; thymidine kinase 4 29.8% 4 28.8% 4 21.1% 3 18.3% 5 30.9% SGO_1159 guaC; guanosine monophosphate reductase 3 12.2% 3 12.2% 7.8% 3 SGO_1163 Iron permease FTR1 family 3 9.1% 3 9.9% SGO_1166 voltage-gated chloride channel family protein 42.4% 15 13 31.7% 17 48.9% 39.7% 14 18 39.7% 16 43.2% SGO_1167 nox; NADH oxidase 8 27.9% 7 21.6% 35.3% 6 12 53.7% 12 53.2% 40.8% 7 11 48.8% 11 46.8% SGO_1169 NADPH-dependent FMN reductase 4 29.9% 4 29.9% 30.4% 8 13 42.8% 15 45.4% 35.5% 10 15 43.5% 13 42.8% SGO_1170 NADPH-dependent FMN reductase 6 21.5% 8 31.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 56

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 56 12 76.9% 5 46.3% 14 76.9% 4 35.0% SGO_1171 thioredoxin family protein 4 36.3% 4 39.4% 3 7.1% 6 12.0% SGO_1174 histidine kinase 3 11.0% SGO_1176 peptide methionine sulfoxide reductase-like protein 3 8.9% SGO_1182 LPXTG cell wall surface protein 4 23.2% 4 19.4% SGO_1184 GdmH 15.8% 3 4 21.7% 5 27.7% 16.3% 3 4 21.7% 4 21.7% SGO_1185 acetyltransferase, GNAT family 3 26.1% 12 30.5% 14 34.6% SGO_1186 ABC transporter, permease/ATP-binding protein 13 27.2% 16 34.4% SGO_1187 ABC transporter, permease/ATP-binding protein 22.2% 3 8 45.8% 4 28.8% 22.2% 3 12 60.8% 5 30.1% SGO_1189 lipoprotein, putative 6 50.3% 3 20.3% 86.9% 13 12 93.4% 15 89.3% 82.8% 12 11 82.8% 13 89.3% SGO_1191 rplL; ribosomal protein L7/L12 13 82.8% 10 82.8% 68.7% 10 9 53.6% 12 75.9% 63.3% 10 11 64.5% 13 72.9% SGO_1192 BL5; 50S ribosomal protein L10 5 47.0% 8 60.8% 16.9% 4 9 31.1% 12 48.2% 15.8% 4 10 38.1% 14 62.2% SGO_1193 gid; Glucose inhibited division protein A 12 51.4% 14 62.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 57

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 57 3 23.3% 17.2% 3 SGO_1196 satD; SatD-like protein 21.1% 10 29 49.9% 14 30.0% 19.5% 10 33 52.2% 18 35.7% SGO_1197 topA; DNA topoisomerase I 9 21.2% 9 23.4% 46.1% 12 14 50.4% 13 51.8% 45.7% 10 16 57.5% 10 44.3% SGO_1198 DNA processing Smf protein 3 26.0% 3 26.0% 5 34.4% SGO_1199 acetyltransferase, CysE/LacA/LpxA/NodL family 6 26.9% 8 37.1% 9 34.6% 10 44.5% SGO_1202 GTP-binding protein 7 33.9% 5 19.8% 51.8% 4 4 36.6% 6 63.4% 51.8% 4 6 67.0% 8 78.6% SGO_1203 anaerobic ribonucleotide reductase 7 77.7% 9 79.5% 15.8% 4 4 17.0% 6 24.8% 19.6% 4 5 20.3% 6 26.7% SGO_1205 dapA; dihydrodipicolinate synthase 7 24.4% 3 13.8% 36.9% 8 9 41.3% 11 48.6% 29.3% 7 12 49.4% 10 41.3% SGO_1206 asd; aspartate-semialdehyde dehydrogenase 9 36.6% 10 46.4% 3 25.8% 5 36.8% SGO_1208 Hypothetical FAD-dependent oxidoreductase, putative 9.2% 3 6 13.3% 6 13.3% 6 14.4% 4 8.8% SGO_1210 fhs-1; formate--tetrahydrofolate ligase 11 25.7% 9 25.4% 7 55.2% 4 37.7% 9 62.8% SGO_1213 coaC; phosphopantothenoylcysteine decarboxylase 5 49.7% 3 25.7% 69.8% 26 30 71.9% 31 78.0% 66.1% 26 32 75.0% 35 79.5% SGO_1215 manB; phosphomannomutase 28 74.3% 32 78.3% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 58

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 58 68.7% 7 6 62.6% 7 60.9% 60.9% 7 5 53.0% 8 78.3% SGO_1216 bta; Possible bacteriocin transport accessory protein 7 73.9% 5 53.0% 33.8% 8 9 42.5% 10 45.5% 30.8% 7 11 45.8% 11 52.9% SGO_1219 pta; phosphate acetyltransferase 11 52.9% 11 50.8% 12 57.3% 17 70.4% SGO_1221 ppnK; Probable inorganic polyphosphate/ATP-NAD kinase 3 14.6% 9 42.3% 4 21.3% 6 33.5% 4 26.2% SGO_1222 GTP pyrophosphokinase-like protein 3 18.6% 39.8% 11 17 58.4% 16 54.0% 51.6% 14 17 59.6% 14 52.2% SGO_1224 Ribose-phosphate pyrophosphokinase 2 13 51.6% 10 41.3% 20.0% 4 6 24.3% 7 34.1% 33.9% 7 6 24.5% 8 36.8% SGO_1225 pyridoxal-phosphate dependent aminotransferase 6 27.2% 5 21.1% 45.2% 4 6 50.4% 5 45.2% 40.9% 4 5 45.2% 5 45.2% SGO_1226 hypothetical protein SGO_1226 5 45.2% 4 40.9% 6 34.4% 6 27.9% 7 36.3% 6 35.3% SGO_1228 DNA-binding protein BH0551 5 21.4% 5 30.7% 9 46.6% 4 23.9% 9 34.7% 3 22.7% SGO_1230 srtA; sortase A 14.0% 11 28 40.0% 17 26.9% 14.9% 10 34 44.3% 23 34.0% SGO_1231 gyrA; DNA gyrase, A subunit 20 37.0% 12 19.6% 55.2% 14 12 51.5% 20 58.5% 55.2% 15 12 49.7% 18 57.6% SGO_1232 L-lactate dehydrogenase 18 59.8% 15 51.5% 63.6% 26 23 56.6% 28 67.3% 62.6% 27 28 57.9% 26 58.1% SGO_1234 rpsA; 30S ribosomal protein S1 31 69.3% 24 60.3% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 59

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 59 44.7% 4 5 82.9% 6 82.9% 82.9% 5 6 82.9% 6 82.9% SGO_1237 hypothetical protein SGO_1237 30.0% 7 7 30.3% 9 37.6% 32.9% 8 8 35.3% 11 47.1% SGO_1238 ilvE; branched-chain amino acid aminotransferase 11 47.4% 10 40.9% 4.5% 3 18 26.6% 11 19.7% 5.6% 3 19 29.4% 9 14.3% SGO_1239 parC; DNA topoisomerase IV, A subunit 3 6.4% 7 12.7% 4 18.4% 3 15.9% SGO_1241 aminoglycoside adenylyltransferase 36.2% 3 6 42.2% 8 49.1% 3 36.2% SGO_1242 lipoprotein, putative 9 22.3% 5 18.9% 5 15.5% 5 17.0% SGO_1244 hypothetical protein SGO_1244 12 22.7% 6 12.3% 12 23.1% 6 12.8% SGO_1245 parE; DNA topoisomerase IV, B subunit 3 13.6% 3 13.6% SGO_1246 hypothetical protein SGO_1246 36 55.2% 41 61.8% SGO_1247 5'-nucleotidase family protein 25 40.7% 21 49.6% 12.6% 4 5 13.5% 7 16.6% 13.7% 4 7 18.0% 7 18.2% SGO_1248 pyrC; dihydroorotase 9 32.2% 8 24.6% 5 38.7% 5 35.9% SGO_1250 ung; uracil-DNA glycosylase 3 21.7% 4 33.2% 3 16.4% 3 16.4% SGO_1251 hypothetical protein SGO_1251 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 60

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 60 3 7.0% SGO_1252 integral membrane protein, putative 38.8% 4 5 42.1% 9 72.2% 37.8% 4 7 43.5% 7 62.2% SGO_1253 pyrE; orotate phosphoribosyltransferase 8 55.0% 5 43.5% 6 42.2% 7 49.1% 4 33.9% SGO_1254 pyrF; orotidine 5'-phosphate decarboxylase 4 31.1% 4 26.6% 4 30.8% SGO_1255 pyrd; dihydroorotate dehydrogenase B 4 15.2% 6 27.8% 7 22.5% 8 30.1% SGO_1257 probable transcriptional regulator (LysR family) 8 31.1% 6 28.8% 3 16.5% 5 25.5% SGO_1258 NAD-dependent deacetylase (Regulatory protein SIR2-like protein) 4 22.2% 4 27.2% 40.1% 7 10 53.2% 10 61.6% 40.1% 7 10 51.9% 9 57.8% SGO_1260 deoD; purine nucleoside phosphorylase 8 52.3% 9 58.2% 5 27.5% SGO_1261 glutamine amidotransferase, class I 43.5% 7 9 45.7% 6 40.5% 48.7% 10 7 43.5% 6 40.5% SGO_1263 purine nucleoside phosphorylase I, inosine and guanosine-specific 6 40.1% 8 49.8% 65.0% 21 22 65.0% 23 66.7% 66.5% 22 22 65.3% 23 66.7% SGO_1264 deoB; phosphopentomutase 22 64.5% 18 66.7% 28.0% 5 9 59.1% 6 41.8% 28.0% 5 9 59.1% 9 59.1% SGO_1265 rpiA; ribose 5-phosphate isomerase 6 30.2% 4 23.6% 12.0% 6 12 33.0% 8 19.7% 10.3% 6 10 26.7% 11 27.1% SGO_1266 trmE; tRNA modification GTPase TrmE 9 31.9% 9 23.6% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 61

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 61 6 48.5% 3 28.1% 7 54.5% SGO_1267 thioredoxin family protein 56.5% 17 15 51.1% 17 56.8% 49.2% 13 15 51.9% 17 57.6% SGO_1273 rpoD; RNA polymerase sigma factor 13 47.6% 8 34.9% 4 8.6% 5 12.6% 7 12.6% 7 17.2% SGO_1274 dnaG; DNA primase 36.2% 4 4 36.2% 5 36.2% 36.2% 4 5 37.9% 5 37.9% SGO_1276 rpsU; ribosomal protein S21 3 34.5% 4 37.9% 4 20.4% 4 17.9% SGO_1280 putative membrane-associated Zn-dependent protease 4 44.8% 5 59.2% 36.8% 3 4 44.8% 5 59.2% SGO_1281 penicillinase repressor, putative 3 36.8% 39.5% 11 13 45.2% 18 59.6% 35.8% 10 14 44.1% 16 52.1% SGO_1283 oxidoreductase 8 27.4% 8 32.2% 17.4% 4 7 33.2% 9 45.0% 28.9% 6 9 45.3% 7 34.8% SGO_1284 thioredoxin-disulfide reductase 6 33.9% 10 43.5% 6 17.1% 7 21.6% SGO_1290 ABC transporter, permease/ATP-binding protein 6 13.8% 3 5.0% SGO_1291 ABC transporter, permease/ATP-binding protein SP1358 20.4% 8 13 31.4% 16 37.8% 25.6% 9 15 38.1% 14 34.4% SGO_1293 asnS; asparaginyl-tRNA synthetase 11 30.3% 13 36.1% 30.9% 8 9 28.8% 9 44.6% 30.4% 8 8 27.0% 10 42.1% SGO_1297 aspC; aspartate aminotransferase 10 42.3% 10 42.3% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 62

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 62 5 28.4% 4 25.9% SGO_1298 hypothetical protein SGO_1298 22.7% 6 15 42.7% 12 38.2% 14.5% 4 18 45.2% 12 35.0% SGO_1305 substrate-binding protein MsmE 46.6% 13 6 19.1% 17 60.5% 40.4% 12 8 26.2% 16 56.6% SGO_1312 pepT; peptidase T 14 49.5% 15 56.6% 5 21.9% SGO_1314 metal binding lipoprotein 3 20.2% 4 26.7% 4 23.5% SGO_1315 trmD; tRNA (guanine-N1)-methyltransferase 5 36.6% 6 37.2% 5 34.9% 6 38.4% 4 33.1% SGO_1316 16S rRNA processing protein RimM 3 26.2% 3 18.6% 43.3% 3 3 43.3% 3 43.3% 43.3% 3 3 43.3% 3 43.3% SGO_1323 rpsP; ribosomal protein S16 4 50.0% 3 43.3% 5 30.6% 6 30.6% SGO_1324 hypothetical protein SGO_1324 15.6% 3 7 35.5% 8 38.7% 21.1% 5 10 43.4% 8 38.7% SGO_1327 HAD-superfamily subfamily IIA hydrolase, TIGR01457 6 24.2% 4 18.0% 3 11.8% SGO_1328 hypothetical protein SGO_1328 3 9.1% 7 16.5% SGO_1330 transporter 5 13.1% SGO_1331 HlyB/MsbA family ABC transporter Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 63

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 63 7.1% 5 12 23.9% 16 33.5% 9.7% 6 15 28.0% 14 27.8% SGO_1336 pcrA; ATP-dependent DNA helicase PcrA 7 14.0% 8 16.3% 3 9.1% SGO_1337 cation efflux family protein 8 42.2% 11 60.5% 3 15.7% SGO_1338 Signal peptidase I 4 30.8% 4 30.8% 69.1% 27 25 56.1% 29 72.5% 74.7% 28 32 69.5% 34 78.6% SGO_1339 pyk; pyruvate kinase 35 79.2% 36 81.0% 42.9% 15 14 43.8% 20 61.3% 42.9% 15 20 60.4% 20 60.1% SGO_1340 Phosphofructokinase 20 52.7% 19 50.3% 10 14.4% 4 5.7% 8 12.2% SGO_1341 dnaE; DNA-directed DNA polymerase III alpha chain 4 5.8% 7 10.0% 65.0% 16 18 68.4% 18 65.4% 65.0% 16 18 68.4% 17 65.4% SGO_1342 ABC transporter, ATP-binding protein SP1715 18 67.5% 19 74.8% 5 15.4% 3 10.5% 5 15.4% SGO_1343 ABC transporter, ATP-binding protein SP1715 10 37.4% 13 45.6% SGO_1347 membrane associated lipoprotein 3 13.5% 4 27.9% 4 22.1% SGO_1355 lipoprotein, putative 3 16.2% 3 9.0% 6 14.6% SGO_1360 ABC transporter domain protein 3 21.1% SGO_1361 ADP-ribosylhydrolase 3 23.2% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 64

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 64 13 33.3% 13 42.1% 12.3% 4 17 44.5% 13 43.6% SGO_1364 rumA-2; 23S rRNA (uracil-5-)-methyltransferase RumA 4 16.4% 7 27.0% 14 40.2% 5 19.4% 13.5% 3 18 45.6% 3 8.4% SGO_1365 transcription regulator yrfE 5 13.8% 6 14.0% 6 34.5% 4 21.5% SGO_1366 pheA; prephenate dehydratase 5 42.2% 3 21.1% 6 40.4% 3 18.0% SGO_1367 aroK; shikimate kinase 6 39.1% 6 42.2% 3 8.7% 5 20.4% 6 20.4% 5 24.1% SGO_1368 aroA; 3-phosphoshikimate 1-carboxyvinyltransferase 8 30.9% 8 32.1% 15.5% 3 6 28.3% 5 25.3% 8 32.2% 6 35.9% SGO_1369 L-2-hydroxyisocaproate dehydrogenase 9 40.8% 9 43.4% 33.9% 3 6 73.2% 6 73.2% 51.8% 4 6 73.2% 4 51.8% SGO_1370 Protein of unknown function (DUF964) superfamily 6 73.2% 5 56.3% 3 10.1% 6 30.4% 12.6% 3 8 33.8% 11 41.8% SGO_1372 aroC; chorismate synthase 3 15.2% 17.2% 3 3 15.8% 5 26.8% 6 25.9% 5 26.8% SGO_1373 aroB; 3-dehydroquinate synthase 3 16.9% 3 13.0% 6 28.4% 4 16.8% 3 16.8% SGO_1374 aroE; shikimate 5-dehydrogenase 23.1% 4 7 41.3% 6 37.8% 8 50.7% 6 38.2% SGO_1375 aroD; 3-dehydroquinate dehydratase, type I 4 26.2% 3 17.8% 5 17.6% 5 18.3% SGO_1376 Methyltransferase Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 65

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 65 6.7% 4 22 43.8% 11 23.6% 8.8% 4 27 49.0% 13 26.2% SGO_1377 sulfatase 11 24.7% 14 31.8% 3.1% 3 18 20.0% 9 11.6% 4.4% 4 28 27.6% 12 14.8% SGO_1381 csn1; CRISPR-associated protein, Csn1 family 12 13.9% 13 13.4% 40.0% 6 9 53.0% 6 46.1% 53.0% 9 10 60.9% 6 40.0% SGO_1383 rplS; ribosomal protein L19 8 47.0% 10 57.4% 5 62.5% 3 30.7% 3 48.9% SGO_1386 chorismate mutase 8 72.7% 7 68.2% 9 16.9% 14 27.1% SGO_1388 pulA-1; pullulanase, type I 3 6.4% 6 13.1% 6 21.4% 6 20.1% SGO_1389 conserved hypothetical protein TIGR00147 3 11.9% 4 14.2% 12.7% 6 13 26.8% 7 15.5% 12.7% 6 13 29.9% 7 15.3% SGO_1390 ligA; DNA ligase, NAD-dependent 8 16.0% 10 23.6% 3 14.5% 3 16.2% SGO_1394 hypothetical protein SGO_1394 6 46.8% 30.2% 6 8 42.8% 8 45.6% 26.3% 5 9 48.1% 8 44.2% SGO_1397 map; methionine aminopeptidase, type I 9 41.8% 8 39.6% 15 47.8% 5 14.1% 14 38.4% 4 10.8% SGO_1398 hypothetical protein SGO_1398 3 8.9% 3 8.5% 22.6% 6 6 22.9% 9 29.0% 14.8% 3 11 37.6% 7 23.8% SGO_1400 murA-2; UDP-N-acetylglucosamine 1carboxyvinyltransferase 7 20.7% 6 24.8% 3 13.8% SGO_1405 hisA; phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 66

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 66 8 8.7% 8 8.6% 16 18.0% 7 7.7% SGO_1413 first chain of major exonuclease RexA 6 7.4% 12 15.9% 4.8% 3 8 11.5% 4 5.6% 5.9% 4 10 14.7% 6 9.0% SGO_1414 rexB; putative exonuclease RexB 6 8.3% 8 12.2% 4 5.7% 5 6.3% SGO_1415 LPXTG cell wall surface protein, X-prolyl dipeptidylaminopeptidase, putative 5 14.8% SGO_1416 putative histidine kinase 4 27.1% SGO_1417 response regulator protein 20.8% 6 9 28.9% 9 34.2% 20.8% 6 10 29.8% 8 25.9% SGO_1422 hypothetical protein SGO_1422 10 39.0% 10 31.3% 75.1% 27 31 75.1% 32 77.2% 77.2% 31 31 77.0% 30 77.2% SGO_1426 eno; enolase 32 77.9% 33 85.7% 39.0% 18 31 53.5% 25 47.7% 40.1% 20 28 50.3% 27 49.0% SGO_1431 EzrA; Septation ring formation regulator ezrA 21 43.6% 20 41.3% 10.9% 6 18 33.4% 16 33.3% 9.4% 6 20 38.7% 19 37.9% SGO_1432 gyrB; DNA gyrase, B subunit 12 26.5% 14 34.1% 22.0% 3 4 40.1% 4 32.4% 3 25.8% SGO_1434 thiJ; 4-methyl-5(beta-hydroxyethyl)-thiazole monophosphate synthesis protein 4 29.1% 3 28.0% 6 9.2% 7 11.0% SGO_1437 DnaQ family exonuclease/DinG family helicase, putative 17.2% 3 8 23.4% 5 17.5% 17.2% 3 10 25.6% 4 17.2% SGO_1439 ftsX; cell division protein FtsX 5 19.5% 5 21.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 67

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 67 43.5% 7 14 69.6% 10 59.1% 45.7% 6 18 74.3% 10 55.2% SGO_1440 cell-division ATP-binding protein FtsE 15 69.1% 13 67.4% 20.3% 5 8 29.9% 9 30.2% 11.8% 3 6 22.8% 11 35.2% SGO_1441 prfB; peptide chain release factor 2 8 30.2% 7 27.5% 11.2% 4 12 36.0% 12 37.3% 11.4% 3 14 39.7% 12 34.2% SGO_1446 murF; UDP-N-acetylmuramoyl-tripeptide--D-alanyl-Dalanine ligase 9 27.6% 8 25.2% 26.1% 6 13 45.1% 14 52.0% 23.3% 5 15 53.2% 14 50.6% SGO_1447 ddlA; D-Ala-D-Ala ligase 8 32.2% 8 28.7% 24 47.7% 9 21.9% 26 50.6% 11 26.3% SGO_1449 pbp2b; penicillin-binding protein 2B 14.8% 3 6 27.1% 6 28.2% 28.2% 6 7 30.6% 5 22.2% SGO_1450 hypothetical protein SGO_1450 4 19.0% 5 23.6% 40.0% 6 6 43.8% 6 42.7% 39.5% 6 7 44.3% 7 43.8% SGO_1451 frr; ribosome recycling factor 4 33.5% 4 33.5% 54.4% 9 10 46.9% 7 45.6% 34.0% 6 9 45.2% 7 45.6% SGO_1452 pyrH; uridylate kinase 6 38.6% 4 27.4% 6.4% 3 4 11.7% 8.3% 3 SGO_1453 glycosyl transferase, family 8 SP1766 3 8.7% 3 6.6% 3 6.6% SGO_1454 amino acid permease family protein 49.3% 9 8 39.3% 9 45.0% 45.0% 9 12 50.7% 9 49.3% SGO_1455 rplA; ribosomal protein L1 10 59.4% 10 55.9% 44.7% 6 4 30.5% 4 30.5% 42.6% 6 5 37.6% 4 30.5% SGO_1456 rplK; ribosomal protein L11 4 35.5% 5 51.8% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 68

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 68 7.7% 4 19 33.8% 5 8.2% 21 38.2% 4 9.0% SGO_1458 aha1; cation-transporting ATPase yfgQ 11 20.8% 8 15.1% 3 35.2% SGO_1459 glyoxylase family protein 6 67.2% 5 65.6% 6.4% 4 17 32.5% 11 23.0% 19 34.3% 7 12.3% SGO_1460 DNA translocase ftsK 4 8.7% 4 8.5% 27.0% 5 14 61.4% 11 52.1% 28.5% 6 15 61.4% 7 40.1% SGO_1463 peptidyl-prolyl cis-trans isomerase 5 27.0% 4 17.6% 84.6% 5 10 94.9% 8 85.9% 50.0% 4 11 100.0% 7 85.9% SGO_1464 uncharacterized probable metal-binding protein 26.7% 8 17 43.9% 13 34.3% 21.4% 6 20 50.5% 10 31.4% SGO_1465 ABC transporter, ATP-binding protein SP0770 8 25.5% 6 19.1% 7 40.0% 7 42.2% 4 19.6% 6 37.0% SGO_1466 MTA/SAH nucleosidase 6 33.0% 6 27.0% 3 20.2% SGO_1468 MutT/nudix family protein 44.0% 13 12 35.9% 13 48.4% 38.6% 13 13 43.1% 14 45.8% SGO_1469 glmU; UDP-N-acetylglucosamine pyrophosphorylase 10 31.2% 7 23.7% 5 32.0% 24.7% 3 3 20.6% 5 30.4% SGO_1472 acetyltransferase, GNAT family 5 24.7% 3 15.0% 7 22.1% 9 32.7% SGO_1475 lipoprotein, putative 4 9.8% SGO_1483 ABC transporter, permease protein, probable SP0913 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 69

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 69 3 20.8% 3 20.8% SGO_1484 ABC transporter, ATP-binding protein 3.2% 4 3.9% 5 5 3.1% SGO_1486 beta-galactosidase 8 5.9% 12 9.4% 18 12.8% 4 4.0% SGO_1487 LPXTG cell wall surface protein, Cna protein B-type domain 11 10.5% 7 5.0% 10 25.3% 14 38.9% 4 16.1% SGO_1493 hypothetical protein SGO_1493 4 12.7% 6 19.9% 3 34.6% 6 53.4% SGO_1495 putative transcriptional regulator 3 5.7% SGO_1498 ABC transporter, permease protein, probable SP0913 3 13.8% 5 20.9% SGO_1504 histidine kinase 7 23.6% 11 30.5% SGO_1507 hypothetical protein SGO_1507 3 9.2% 5 13.7% SGO_1512 lacG; 6-phospho-beta-galactosidase 4 18.2% 5 18.4% 3 5.5% SGO_1513 lacE; PTS system, lactose-specific IIBC component 22.4% 4 8 37.1% 9 44.2% 31.3% 6 9 31.3% 13 53.4% SGO_1516 lacD-2; tagatose 1,6-diphosphate aldolase 4 28.1% 6 46.2% 6 33.9% 6 46.2% SGO_1518 lacB-2; galactose-6-phosphate isomerase, LacB subunit Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 70

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 70 4 10.4% SGO_1520 PTS system, IIC component 4 47.5% SGO_1521 PTS system IIB component (galactitol/fructose specific) SGO_1523 lacD-1; tagatose 1,6-diphosphate aldolase 3 17.9% SGO_1527 Lactose phosphotransferase system repressor 6 32.3% 5 27.7% 10 46.7% 3 18.2% SGO_1529 hypothetical protein SGO_1529 6 27.4% 6 34.7% 36.6% 17 23 46.4% 26 52.9% 35.0% 15 27 53.5% 24 50.2% SGO_1530 methionine-tRNA ligase 22 47.0% 16 33.3% 34.9% 6 11 54.9% 10 60.0% 33.1% 5 11 59.6% 8 49.5% SGO_1531 xth; exodeoxyribonuclease III 6 29.1% 5 26.5% 5 35.9% 8 68.4% 34.2% 4 6 49.6% 6 62.4% SGO_1534 ArsC family 4 46.2% 5 57.3% 17.3% 4 10 40.5% 9 43.0% 18.7% 4 11 45.8% 10 42.3% SGO_1536 conserved hypothetical protein TIGR00096 4 19.4% 5 26.1% 4 20.4% 3 16.7% SGO_1538 DNA-directed DNA polymerase III, delta'' chain 22.2% 4 7 42.0% 8 48.1% 42.0% 6 7 41.5% 9 48.6% SGO_1539 tmk; thymidylate kinase 7 36.3% 5 29.7% 3 12.2% 6 19.2% 4 23.0% SGO_1540 YitT family protein Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 71

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 71 27.5% 3 4 33.3% 5 32.6% 39.9% 6 5 33.3% 4 32.6% SGO_1541 atpC; ATP synthase F1, epsilon subunit 8 40.6% 6 31.2% 58.5% 19 25 73.3% 24 64.1% 58.8% 20 30 75.4% 22 62.2% SGO_1542 atpD; ATP synthase F1, beta subunit 30 75.9% 29 72.6% 21.2% 4 15 55.6% 10 36.9% 19.8% 4 16 50.2% 11 47.1% SGO_1543 atpG; ATP synthase F1, gamma subunit 12 55.6% 10 44.4% 26.1% 9 17 41.9% 17 45.1% 22.8% 9 16 41.9% 17 45.1% SGO_1544 atpA; ATP synthase F1, alpha subunit 15 43.7% 17 48.3% 33.7% 4 5 42.1% 4 28.7% 33.7% 4 6 46.6% 4 33.7% SGO_1545 atpH; ATP synthase F1, delta subunit 6 39.9% 8 58.4% 47.0% 10 14 56.1% 10 49.4% 48.8% 9 15 61.6% 11 49.4% SGO_1546 atpF; ATP synthase F0, B subunit 15 61.6% 8 39.0% 22.4% 13 22 38.1% 25 45.0% 32.7% 20 27 44.4% 27 44.2% SGO_1550 glgP-1; glycogen phosphorylase 19 30.2% 26 42.7% 9.0% 3 5 17.4% 9 25.0% 14.7% 5 14 36.8% 6 16.8% SGO_1551 glgA; Glycogen synthase 14 38.0% 15 42.6% 26.6% 8 8 28.6% 12 41.7% 33.4% 8 9 26.9% 12 43.7% SGO_1552 glgD; glucose-1-phosphate adenylyltransferase, GlgD subunit 13 47.7% 11 42.0% 27.6% 7 7 23.9% 14 45.5% 27.1% 7 10 33.9% 15 50.5% SGO_1553 glgC; glucose-1-phosphate adenylyltransferase 14 46.1% 18 53.4% 28.9% 12 13 30.8% 16 33.6% 21.5% 8 15 34.6% 20 38.5% SGO_1554 glgB; 1,4-alpha-glucan branching enzyme 24 47.4% 22 48.0% 55.3% 24 25 62.2% 28 66.6% 54.4% 21 31 69.8% 26 65.3% SGO_1555 ptsI; phosphoenolpyruvate-protein phosphotransferase 28 68.3% 31 74.5% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 72

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 72 39.1% 3 3 39.1% 3 39.1% 39.1% 3 5 41.4% 3 39.1% SGO_1556 phosphocarrier protein HPr 5 41.4% 4 39.1% 3 68.1% 3 68.1% SGO_1557 NrdH-redoxin 38.8% 19 27 48.0% 25 47.3% 30.7% 16 32 49.4% 30 52.0% SGO_1558 nrdE; ribonucleoside-diphosphate reductase large chain 31 53.8% 23 40.3% 33.9% 9 12 40.4% 13 46.4% 28.2% 9 13 41.1% 13 46.4% SGO_1559 ribonucleoside-diphosphate reductase, beta subunit 11 46.4% 10 38.9% 3 13.6% 3 13.6% SGO_1561 putative zinc metallopeptidase 4 10.6% 3 10.6% SGO_1562 hypothetical protein SGO_1562 3 53.7% 3 53.7% 3 53.7% 3 53.7% SGO_1564 transcription regulator, probable -related protein 35.4% 23 33 43.5% 37 47.0% 37.4% 29 41 50.2% 34 42.4% SGO_1570 alaS; alanyl-tRNA synthetase 29 42.4% 24 38.6% 6 43.5% 7 44.7% SGO_1571 Protein of unknown function (DUF567) superfamily 26 69.3% 17.8% 4 26 70.9% SGO_1572 proteinase maturation protein, putative 8 32.0% 5 20.7% 3 29.4% 4 17.5% 5 39.5% SGO_1573 O-methyltransferase family protein 3 23.2% 29.8% 15 17 35.5% 21 49.8% 30.8% 15 18 37.0% 24 52.7% SGO_1574 pepF-1; oligoendopeptidase F 22 44.2% 21 44.7% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 73 3 8.9% 3 8.2% SGO_1576 ptcC; PTS system, IIC component 49.0% 4 4 49.0% 49.0% 3 4 49.0% SGO_1580 PTS system, Lactose/Cellobiose specific IIB subunit 3 45.2% 3 49.0% 14 40.4% 3 13.3% 6.7% 3 13 37.8% 5 19.6% SGO_1585 D-Alanyl-D-Alanine carboxypeptidase 24.3% 4 5 26.9% 4 24.3% 19.0% 3 9 42.1% 4 24.3% SGO_1587 queA; S-adenosylmethionine:tRNA ribosyltransferaseisomerase 4 23.4% 8 33.0% 4 48.1% 5 48.1% SGO_1588 arcR; arginine repressor 5 13.5% 7 19.8% SGO_1589 arcT; putative transaminase/peptidase 11 29.3% 10 30.0% 5 9.9% 6 11.7% SGO_1590 arcD; arginine-ornithine antiporter 4 9.1% 3 9.1% 27.6% 5 10 43.5% 9 39.0% 32.4% 6 13 54.3% 7 27.6% SGO_1591 arcC; carbamate kinase 17 70.8% 17 65.4% 42.3% 10 15 53.8% 12 49.4% 45.3% 11 15 52.7% 12 46.7% SGO_1592 arcB; ornithine carbamoyltransferase 25 64.8% 26 73.1% 60.4% 18 28 72.6% 20 62.3% 53.3% 17 30 76.5% 24 66.7% SGO_1593 arcA; arginine deiminase 42 88.3% 38 84.8% 5 22.8% 6 26.3% SGO_1594 Crp/Fnr family protein 3 11.8% 5 17.4% SGO_1598 hypothetical protein SGO_1598 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 74

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 74 56.2% 10 10 56.2% 10 52.2% 56.2% 11 9 52.2% 10 52.2% SGO_1599 sodA; manganese-dependent superoxide dismutase 15 57.2% 13 57.2% 6 25.8% 7 27.8% SGO_1600 DNA polymerase III, delta chain 3 4.0% 4 5.6% SGO_1601 celB; DNA internalization-related competence protein celB 12 48.3% 6 28.4% 18.6% 3 15 55.9% 5 23.7% SGO_1604 acyltransferase family protein 6 30.5% 5 32.6% 16 29.3% 5 11.0% 6.1% 3 20 31.3% 5 11.9% SGO_1605 P-type ATPase, metal cation transport 3 6.5% 3 8.0% 4 25.0% 4 25.0% 4 25.0% 3 19.2% SGO_1606 DNA methyltransferase signature protein 35.2% 12 18 45.9% 14 38.4% 35.0% 13 22 51.2% 15 42.8% SGO_1609 ATP-dependent RNA helicase, DEAD/DEAH box family 7 17.2% 6 17.0% 9 32.5% 8 25.2% SGO_1614 magnesium and cobalt transporter CorA family 24.1% 9 12 37.0% 10 23.9% 25.9% 9 19 48.2% 16 38.1% SGO_1617 prfC; peptide chain release factor 3 8 20.6% 10 20.4% 19.7% 12 26 34.0% 21 32.7% 18.3% 11 26 34.0% 20 35.2% SGO_1619 cation-transporting ATPase, E1-E2 family 10 17.4% 15 26.8% 10.4% 3 8 25.2% 5 16.9% 9 26.3% 7 25.2% SGO_1621 HD domain protein 6 21.7% 9 31.2% 29.0% 6 9 40.5% 6 29.0% 20.1% 4 10 43.1% 6 29.7% SGO_1622 Cof family protein 6 30.5% 4 21.2% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 75

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 75 20.5% 5 10 31.5% 11 37.2% 15 48.7% 11 39.1% SGO_1623 murM; MurM 8 23.2% 8 24.9% 8 25.1% 5 15.6% 14.8% 5 10 25.1% 5 13.1% SGO_1624 murN; MurN protein 7 17.8% 7 24.1% 57.8% 9 15 77.1% 13 64.2% 39.4% 6 16 77.5% 12 59.6% SGO_1625 acetoin utilization putative/CBS domain protein 11 61.9% 10 55.5% 23.7% 4 9 50.8% 8 45.3% 35.2% 6 9 46.6% 8 42.8% SGO_1626 branched-chain amino acid ABC transporter, ATPbinding protein 5 32.2% 33.1% 5 7 41.7% 6 37.0% 33.1% 5 10 46.9% 5 27.6% SGO_1627 branched-chain amino acid ABC transporter, ATPbinding protein 52.3% 17 25 62.9% 20 61.1% 47.9% 16 30 70.4% 20 59.3% SGO_1630 branched-chain amino acid ABC transporter, amino acid-binding protein 15 50.0% 14 45.6% 3 28.1% 3 29.2% SGO_1631 hypothetical protein SGO_1631 36.7% 6 4 15.8% 5 37.8% 15.8% 4 5 21.4% 5 37.8% SGO_1632 clpP; ATP-dependent Clp protease, proteolytic subunit ClpP 5 39.8% 5 39.8% 66.5% 12 9 58.9% 14 67.5% 54.1% 10 12 59.8% 13 67.5% SGO_1633 upp; uracil phosphoribosyltransferase 14 67.5% 14 72.2% 34 42.7% 8 13.9% 35 44.0% 6 8.7% SGO_1634 magnesium-translocating P-type ATPase 5 9.5% 5 6.5% 6 15.4% 8 25.6% 6 15.6% 6 16.8% SGO_1638 murE; UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase 9 22.2% 10 31.4% 43.1% 10 10 43.4% 12 58.8% 36.0% 8 12 46.6% 12 58.8% SGO_1648 ppx1; inorganic pyrophosphatase, manganesedependent 12 59.5% 11 53.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 76 14.1% 3 9 45.7% 3 14.1% 12 58.0% 5 23.4% SGO_1649 act; pyruvate formate-lyase-activating enzyme 6 33.1% 10 48.0% 14 22.5% 16 24.8% SGO_1650 LPXTG cell wall surface protein, collagen binding domain 28 45.6% 31 46.6% SGO_1651 LPXTG cell wall surface protein, nuclease/phosphatase domain 20 32.7% 18 34.1% 18.3% 7 13 31.2% 12 31.1% 19.2% 7 12 28.7% 10 29.4% SGO_1652 intracellular glycosyl hydrolase 5 13.9% 4 10.9% 10.9% 5 20 32.4% 12 25.9% 14.1% 7 25 35.0% 12 24.5% SGO_1653 trehalose PTS enzyme II 9 18.5% 5 9.6% 10 27.1% 4 12.1% 15 33.0% 4 13.0% SGO_1655 CBS domain protein/possible hemolysin 5 16.1% 6 20.2% 4 5.3% 6 8.0% SGO_1657 membrane protein 3 11.2% 6 31.7% SGO_1661 radical SAM protein, TIGR01212 family 6 26.9% 4 35.7% SGO_1665 rRNA methylase 19.6% 6 16 39.5% 13 35.8% 14.3% 4 20 47.0% 13 36.9% SGO_1666 trkA; potassium uptake protein, Trk family 14 34.8% 14 38.3% 47.1% 10 12 45.0% 11 40.5% 33.9% 8 17 57.4% 13 45.9% SGO_1669 ribosomal large subunit pseudouridine synthase B 11 55.8% 8 36.4% 4 30.9% SGO_1670 scpB; segregation and condensation protein B Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 77

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 77 5 32.4% 5 27.7% 5 32.4% 3 22.5% SGO_1674 phosphodiesterase, MJ0936 family 4 29.5% 5 37.0% 12.6% 3 7 26.2% 9 40.3% 16.9% 4 11 37.5% 7 35.4% SGO_1675 HAM1 protein-like protein 6 20.9% 8 31.7% 23.1% 4 4 22.3% 9 45.5% 29.9% 6 4 25.4% 11 59.8% SGO_1676 murI; glutamate racemase 4 23.5% 4 21.6% 13.0% 3 4 13.9% 6 23.8% 5 19.2% 3 13.0% SGO_1678 lysA; diaminopimelate decarboxylase 6 24.0% 6 22.4% 61.4% 16 19 60.8% 17 60.8% 59.6% 15 23 68.1% 16 59.9% SGO_1679 phosphotransferase system enzyme II 15 64.7% 19 68.4% 18.7% 4 4 18.7% 4 18.7% 4 18.7% 4 18.7% SGO_1680 phosphotransferase system enzyme II 38.6% 9 13 44.2% 10 41.9% 38.6% 9 15 44.2% 10 41.9% SGO_1681 PTS system, mannose/fructose/sorbose family, IID component 10 41.9% 7 35.6% 40.0% 11 19 55.1% 18 61.9% 43.5% 13 19 56.5% 19 63.3% SGO_1683 serS; seryl-tRNA synthetase 17 60.2% 13 50.6% 28.0% 7 7 26.3% 12 46.6% 36.7% 9 6 24.3% 12 43.8% SGO_1684 acyl-CoA dehydrogenase family 26.4% 4 4 33.0% 5 37.4% 25.3% 3 4 26.9% 5 37.4% SGO_1685 putative peroxidase / antioxidase 5 34.1% 4 33.0% 35.9% 7 10 48.0% 10 48.0% 39.1% 9 8 36.3% 10 44.5% SGO_1687 accA; acetyl-CoA carboxylase, carboxyl transferase, alpha subunit 11 48.4% 8 35.2% 22.3% 5 7 25.4% 10 43.6% 17.1% 4 13 41.1% 11 45.3% SGO_1688 accD; acetyl-CoA carboxylase, carboxyl transferase, beta subunit 8 36.2% 9 35.2% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 78

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 78 29.0% 9 14 48.1% 13 44.9% 32.2% 9 14 45.8% 15 51.0% SGO_1689 accC; acetyl-CoA carboxylase, biotin carboxylase 13 48.4% 14 52.3% 34.3% 4 6 40.0% 7 46.4% SGO_1690 fabZ; beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ 3 27.1% 5 40.7% 27.8% 6 4 25.3% 7 39.5% 39.5% 6 5 28.4% 8 46.3% SGO_1691 accB; acetyl-CoA carboxylase, biotin carboxyl carrier protein 8 42.0% 9 47.5% 63.7% 17 15 65.4% 22 78.8% 61.2% 16 17 62.0% 21 71.2% SGO_1692 3-oxoacyl-[acyl-carrier-protein] synthase 25 74.1% 27 77.3% 50.0% 9 7 39.3% 15 73.0% 20.9% 4 11 47.5% 13 63.5% SGO_1693 fabG; 3-oxoacyl-(acyl-carrier-protein) reductase 11 55.7% 12 59.4% 43.8% 10 10 45.4% 11 58.5% 38.2% 8 13 55.9% 13 60.8% SGO_1694 fabD; malonyl CoA-acyl carrier protein transacylase 9 43.5% 9 42.2% 54.9% 13 12 52.2% 17 60.8% 45.4% 10 13 52.8% 13 50.0% SGO_1695 enoyl-acyl carrier protein(ACP) reductase 15 57.1% 12 52.2% 4 22.8% 6 27.2% 7 32.1% 4 22.5% SGO_1698 3-oxoacyl-[acyl-carrier-protein] synthase III 4 48.3% 4 47.5% 40.8% 3 5 48.3% 4 48.3% SGO_1699 transcriptional regulator, MarR family 3 40.8% 4 50.8% 18.6% 4 7 33.8% 7 30.4% 6 25.5% 6 30.4% SGO_1700 enoyl-CoA hydratase/isomerase family protein 9 45.6% 9 47.9% 31.6% 11 11 28.7% 17 52.4% 27.4% 10 14 37.3% 19 55.9% SGO_1701 aspartate kinase 12 40.8% 16 45.6% 43.6% 9 16 62.9% 14 65.5% 49.5% 9 20 74.6% 13 65.1% SGO_1708 amiF; Oligopeptide transport ATP-binding protein amiF 11 42.7% 10 51.1% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 79

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 79 42.5% 12 16 49.6% 11 40.0% 44.5% 12 17 51.8% 11 40.0% SGO_1709 amiE; Oligopeptide transport ATP-binding protein 9 34.1% 10 33.2% 13.0% 4 6 16.2% 5 15.6% 17.9% 4 9 24.7% 4 15.3% SGO_1710 amiD; Oligopeptide transport system permease protein 20.1% 10 19 31.1% 11 23.1% 25.5% 12 22 38.0% 14 30.1% SGO_1711 hppB; Oligopeptide transport system permease 7 14.9% 7 15.1% 53.5% 31 36 53.2% 31 51.3% 49.2% 27 42 57.0% 31 50.1% SGO_1712 hppA; oligopeptide-binding lipoprotein 27 45.9% 21 45.6% 54.4% 28 35 57.1% 33 58.0% 43.6% 20 38 58.5% 30 52.6% SGO_1713 hppG; oligopeptide-binding lipoprotein 29 54.2% 22 47.6% 42.9% 21 32 61.7% 31 62.4% 47.9% 23 35 64.1% 29 57.5% SGO_1715 hppH; oligopeptide-binding lipoprotein 23 49.5% 23 48.5% 46.1% 21 40 68.0% 26 50.7% 37.8% 17 38 66.9% 29 58.3% SGO_1716 oligopeptide binding protein 24 47.2% 18 38.6% 16 58.5% 4 13.3% 16 59.5% SGO_1717 pbp3; penicillin-binding protein 3 4 16.3% 4 13.6% 23.6% 9 16 36.4% 16 51.5% 26.4% 11 20 50.9% 13 39.1% SGO_1718 sufB-1; FeS assembly protein SufB 10 30.2% 14 36.8% 4 33.8% 3 33.8% SGO_1719 SUF system FeS assembly protein, NifU family 19.3% 4 4 15.1% 8 34.4% 16.1% 3 9 38.5% 6 25.6% SGO_1720 aminotransferase, class-V 31.2% 10 9 28.8% 10 31.2% 23.3% 6 8 26.0% 11 34.3% SGO_1721 sufD; FeS assembly protein SufD 8 28.6% 8 28.6% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 80

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 80 25.8% 7 9 34.8% 14 56.3% 19.5% 5 9 39.1% 10 48.4% SGO_1722 sufC; FeS assembly ATPase SufC 11 50.0% 5 25.4% 3 13.6% 6 32.6% 4 24.8% SGO_1724 mecA; Adapter protein mec 3 23.6% 3 12.4% 3 12.4% SGO_1725 bacA; bacitracin resistance protein 8 16.7% 10 18.3% SGO_1726 hypothetical protein SGO_1726 16.9% 4 16 44.3% 8 28.4% 16.7% 4 16 43.6% 10 33.2% SGO_1727 amino acid ABC transporter, amino acidbinding/permease protein 7 24.8% 7 23.8% 33.3% 7 8 44.7% 7 44.3% 38.6% 6 9 47.6% 6 40.7% SGO_1728 glnQ; glutamine ABC transporter ATP-binding protein 6 45.1% 6 40.7% 50.0% 3 4 61.1% 61.1% 4 4 61.1% SGO_1729 hypothetical protein SGO_1729 5 68.1% 4 61.1% 51.9% 13 26 75.6% 19 61.7% 54.9% 19 32 78.3% 21 63.4% SGO_1730 SPFH domain/Band 7 family 25 71.5% 25 70.5% 26.1% 4 3 23.6% 6 38.2% 37.2% 6 3 18.6% 8 49.7% SGO_1731 DNA-binding response regulator 4 22.1% 3 24.1% 6 19.1% 7 23.0% 3 9.6% SGO_1732 histidine kinase 50.7% 18 22 61.0% 21 56.0% 47.3% 16 23 64.6% 21 56.0% SGO_1735 hypothetical protein SGO_1735 21 58.5% 25 60.6% 28.9% 3 4 33.1% 4 33.1% 4 33.1% 4 33.1% SGO_1736 alkaline shock protein 4 33.1% 4 33.1% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 81

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 81 3 38.7% 40.3% 4 4 40.3% SGO_1737 rpmB; ribosomal protein L28 4 21.2% 4 21.2% SGO_1738 hypothetical protein SGO_1738 3 14.0% 6 36.5% 7 36.5% SGO_1739 LytTr DNA-binding domain family 3 27.7% 9 34.8% 8 34.2% SGO_1744 ABC transporter, ATP-binding protein SP0636 7 25.8% 54.9% 16 15 51.9% 14 51.2% 54.9% 16 17 56.7% 15 51.2% SGO_1745 fba; fructose-1,6-bisphosphate aldolase, class II 18 54.9% 22 63.8% 27.2% 3 3 25.0% 3 33.1% SGO_1747 hypothetical protein SGO_1747 3 27.2% 21.0% 6 9 25.0% 7 23.8% 17.9% 6 11 24.2% 12 36.5% SGO_1748 pyrG; CTP synthase 3 11.4% 11.5% 3 7 36.6% 8 43.6% 28.0% 6 9 42.7% 7 36.6% SGO_1749 manA; mannose-6-phosphate isomerase, class I 6 28.0% 10 47.1% 11 21.4% 13 25.1% SGO_1750 ABC-type multidrug/protein/lipid transport system, ATPase component 13 27.0% 3 6.1% 13 28.2% 6 11.4% SGO_1751 ABC-type multidrug/protein/lipid transport system, ATPase component 3 22.8% SGO_1753 hypothetical protein SGO_1753 67.6% 11 8 47.2% 11 67.6% 57.5% 9 8 43.5% 12 67.6% SGO_1755 scrK; fructokinase 6 39.5% 7 47.2% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 82

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 82 6 49.4% SGO_1756 hypothetical protein SGO_1756 39.3% 14 19 44.4% 24 54.6% 47.6% 17 24 48.4% 25 61.0% SGO_1757 glmS; glucosamine--fructose-6-phosphate aminotransferase 13 34.3% 12 35.0% 4 14.3% SGO_1760 DNA-binding response regulator 3 9.6% 6 13.8% 10 18.9% SGO_1761 histidine kinase 53.9% 15 18 48.4% 17 54.5% 40.7% 12 20 56.6% 19 56.4% SGO_1763 ABC transporter, substrate-binding protein SP0092 17 46.1% 11 39.3% 6 13.8% 3 7.9% 5 10.5% 8 15.5% SGO_1768 glycosyl hydrolase, family 38 12 23.7% 13 26.6% 3 11.8% SGO_1772 integral membrane protein 21.2% 4 5 27.5% 6 30.4% 23.8% 4 8 40.6% 6 29.0% SGO_1774 alcohol dehydrogenase, zinc-containing 8 36.5% 8 39.4% 3 16.7% SGO_1780 hypothetical protein SGO_1780 3 14.3% 20.9% 12 14 20.6% 16 25.1% 27.7% 16 18 25.1% 16 26.9% SGO_1784 leuS; leucyl-tRNA synthetase 20 28.6% 12 21.4% 3 13.7% SGO_1792 transcription regulator 3 12.8% 59.8% 23 19 42.5% 26 63.3% 41.7% 16 25 51.6% 28 64.3% SGO_1799 endopeptidase O 32 72.1% 27 65.1% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 83

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 83 34.3% 6 18 76.2% 10 56.1% 30.1% 6 19 75.7% 10 53.1% SGO_1800 troB; manganese ABC transporter, ATP-binding protein SP1648 71.6% 16 26 75.2% 21 70.6% 72.6% 16 32 85.8% 18 66.8% SGO_1802 Metal ABC transporter substrate-binding lipoprotein precursor 7 38.4% 4 27.4% 29.4% 4 4 37.4% 5 51.5% 28.8% 3 5 38.0% 7 52.1% SGO_1803 tpx; thioredoxin peroxidase 5 51.5% 5 51.5% 10 40.1% 4 18.1% 10 37.1% SGO_1804 hutI; imidazolonepropionase 6 23.0% 4 17.8% 16.3% 8 3 7.0% 16 29.4% 5.6% 3 20 39.1% SGO_1805 hutU; urocanate hydratase 3 7.1% 20.7% 5 9 38.5% 16.4% 4 9 29.4% SGO_1806 ftcD; glutamate formiminotransferase 3 23.6% 3 23.6% SGO_1807 serine cycle enzyme, putative 7.9% 3 6 18.7% 13.5% 5 6 18.3% SGO_1808 fhs-2; formate--tetrahydrofolate ligase 4 9.5% 4 12.3% 5 15.4% 12.3% 4 5 15.4% 7 22.2% SGO_1811 hutH; histidine ammonia-lyase 3 10.7% 3 11.6% SGO_1813 hutG; formimidoylglutamase 3 12.8% 6 7.9% 5 6.5% SGO_1814 putative regulatory protein 6 7.7% 5 8.8% 3 15.8% 4 23.7% 5 27.9% SGO_1816 scaR; ScaR Manganese-dependent regulator of scaCBA 6 33.0% 5 24.7% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 84

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 84 7.0% 4 22 33.7% 10 19.5% 25 39.8% 5 11.0% SGO_1822 relA; GTP diphosphokinase 9 15.3% 10 15.6% 4 28.3% 3 19.0% SGO_1823 conserved hypothetical protein TIGR00046 30.8% 5 6 34.6% 4 25.5% 29.6% 5 8 40.6% 6 36.2% SGO_1824 prmA; ribosomal protein L11 methyltransferase 4 25.5% 5 27.7% 5 35.3% 3 27.6% 4 27.6% 3 27.6% SGO_1827 hypothetical protein SGO_1827 3 27.6% 6 19.7% 3 12.6% 11.4% 3 3 12.8% 4 15.6% SGO_1828 ATPase, AAA family 5 15.4% 3 10.4% 54.1% 8 5 27.6% 6 43.4% 55.6% 8 5 28.1% 7 52.6% SGO_1834 hypothetical protein SGO_1834 11 69.9% 11 73.5% 3 29.9% 47.8% 3 3 29.9% 3 29.9% SGO_1835 hypothetical protein SGO_1835 3 29.9% 31.2% 10 11 33.4% 13 38.0% 29.5% 10 12 40.0% 13 38.0% SGO_1843 pepS; aminopeptidase PepS 14 49.4% 11 43.8% 6.5% 3 5 7.9% 10 18.9% 10.0% 5 12 20.0% 12 18.6% SGO_1844 cbxX/cfqX family protein 6 10.5% 9 16.1% 13 12.5% 10 9.4% 4.8% 6 15 14.6% 14 13.9% SGO_1847 polC; DNA polymerase III, alpha subunit, Grampositive type 10 8.7% 11 12.0% 22.2% 5 9 47.8% 4 23.9% 17.8% 4 10 48.3% 4 23.9% SGO_1848 lipoprotein, putative 8 68.4% 7 63.2% SGO_1849 hypothetical protein SGO_1849 Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 85

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 85 37.2% 19 25 54.5% 25 54.7% 45.0% 20 28 55.8% 28 60.2% SGO_1851 proS; prolyl-tRNA synthetase 21 45.9% 23 53.7% 16.8% 4 9 27.6% 5 17.7% 10 29.7% 5 18.5% SGO_1852 membrane-associated zinc metalloprotease, putative 32.1% 6 12 57.0% 6 32.1% 28.5% 6 12 50.6% 7 39.4% SGO_1854 uppS; undecaprenyl diphosphate synthase 6 34.5% 6 32.1% 4 47.3% 3 47.3% 4 47.3% 3 47.3% SGO_1855 preprotein translocase, YajC subunit 18.2% 8 17 35.8% 12 22.9% 9.8% 4 19 34.7% 12 26.7% SGO_1856 ATP-dependent proteinase ATP-binding chain 37 69.2% 26 54.8% 4 11.3% 3 8.5% 7 15.3% SGO_1857 PTS system, IIABC components 5 17.6% 3 9.3% 5 19.6% SGO_1858 beta-fructofuranosidase/sucrose 6 phoshate hydrolase 4 17.8% 5 16.7% 41.4% 7 10 47.4% 11 48.1% 29.5% 5 14 55.8% 9 47.0% SGO_1860 5'-nucleotidase, lipoprotein e(P4) family 17 61.8% 13 55.8% 3 23.4% 4 40.1% 23.4% 3 4 40.1% SGO_1861 nusB; transcription antitermination factor NusB 40.3% 3 3 40.3% 3 38.8% 47.3% 4 3 40.3% 3 38.8% SGO_1862 alkaline shock protein 4 46.5% 5 63.6% 41.4% 6 8 58.1% 7 50.5% 41.4% 6 8 58.1% 8 66.1% SGO_1863 efp; Elongation factor P (EF-P) 7 61.3% 5 46.2% 25.2% 6 10 46.2% 10 43.1% 25.2% 6 13 51.6% 10 52.7% SGO_1864 X-Pro aminopeptidase 13 58.4% 13 63.7% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 86

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 86 16.5% 8 26 35.1% 17 29.2% 16.3% 8 30 43.4% 20 35.9% SGO_1865 uvrA; excinuclease ABC, A subunit 15 28.7% 14 28.2% 8.3% 3 3 11.1% SGO_1866 corA; magnesium and cobalt transporter 20.1% 3 5 23.2% 4 22.8% 22.8% 4 5 23.2% 4 22.8% SGO_1867 hypothetical protein SGO_1867 3 15.6% 4 22.8% 9 29.8% 13 46.3% SGO_1869 hypothetical protein SGO_1869 14 28.8% 4 8.9% 16 34.4% 3 6.3% SGO_1870 hypothetical protein SGO_1870 11 34.0% 11 34.3% SGO_1871 lipoprotein, putative 6 25.1% 5 21.0% 11 40.2% SGO_1872 hypothetical protein SGO_1872 3 20.6% 3 17.2% SGO_1878 transcriptional regulator, TetR family domain protein 4 29.9% 31.6% 3 7 44.3% 5 41.8% 44.3% 5 7 44.3% 6 41.8% SGO_1879 rpsR; ribosomal protein S18 4 43.0% 7 59.5% 79.8% 8 8 79.8% 8 79.8% 73.0% 7 8 79.8% 8 79.8% SGO_1880 ssb-1; single-strand binding protein 7 69.3% 6 57.1% 78.1% 8 7 74.0% 8 74.0% 74.0% 8 8 82.3% 7 72.9% SGO_1881 rpsF; ribosomal protein S6 8 76.0% 9 78.1% 19.8% 3 3 19.8% 4 20.3% 25.1% 4 5 46.0% 4 20.3% SGO_1882 folE; GTP cyclohydrolase I 4 20.3% 5 40.1% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 87

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 87 6 30.6% 8 43.3% SGO_1884 hypothetical protein SGO_1884 56.7% 25 30 60.7% 29 63.5% 61.1% 24 36 65.2% 34 70.6% SGO_1885 groL; 60 kDa chaperonin/groEL protein 40 73.5% 35 75.4% 41.9% 3 4 54.8% 4 54.8% 41.9% 3 4 54.8% 3 41.9% SGO_1886 groES; chaperonin, 10 kDa 4 54.8% 4 51.6% 3 13.9% 7 29.6% SGO_1887 ABC transporter, ATP-binding protein 5 11.6% 7 12.8% SGO_1888 ABC transporter, permease protein 3 11.2% 3 11.2% SGO_1890 PTS system, fructose(mannose)-specific IID 3 13.8% 4 24.7% SGO_1891 PTS system, IIC component 52.4% 5 5 52.4% 5 52.4% 42.7% 4 6 56.1% 5 52.4% SGO_1892 PTS system, fructose(mannose)-specific IIB 7 56.1% 6 59.8% 3 12.4% 7 27.4% SGO_1894 sugar-binding cell envelope protein 3 15.0% 3 14.5% SGO_1895 response regulator 3 12.9% 6 22.7% SGO_1897 rbsB; ribose ABC transporter (ribose-binding component) CAC1453 49.9% 11 9 40.6% 13 63.4% 40.6% 9 10 49.3% 13 63.4% SGO_1898 glutamyl aminopeptidase 15 71.3% 17 70.1% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 88

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 88 3 30.5% SGO_1899 hypothetical protein SGO_1899 3 36.2% 4 48.6% 3 43.8% SGO_1900 thioredoxin family protein 31.7% 5 6 36.1% 7 44.7% 30.3% 5 5 31.7% 7 36.1% SGO_1901 tRNA binding domain 4 22.6% 5 26.4% 59.5% 6 5 57.3% 6 59.5% 59.5% 6 6 64.1% 6 59.5% SGO_1902 ssb; single-stranded DNA-binding protein 44.2% 15 17 39.1% 20 46.4% 39.5% 13 19 39.3% 23 52.8% SGO_1903 ATP-dependent Zn protease 25 50.0% 20 49.0% 3 15.7% SGO_1907 sensor protein 3 20.4% 5 29.3% 4 27.4% 3 20.7% SGO_1912 Bifunctional folate synthesis protein 4 25.6% 3 14.6% 11.8% 3 4 15.6% 4 18.1% SGO_1914 folP; dihydropteroate synthase 4 15.0% 5 21.2% 48.0% 14 19 61.4% 19 61.4% 46.7% 12 19 60.6% 21 68.7% SGO_1916 ackA; acetate kinase 13 41.4% 13 47.7% 29.3% 5 3 17.7% 6 37.5% 18.9% 3 4 20.5% 6 37.5% SGO_1917 hypothetical protein SGO_1917 3 18.6% 6 34.4% 5 17.2% SGO_1923 comYB; competence protein 23.5% 7 17 54.9% 11 41.1% 15.4% 5 16 54.9% 9 34.5% SGO_1924 comYA; competence protein comYA Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 89

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 89 48.3% 55 55 49.6% 69 57.5% 50.3% 55 69 57.0% 73 62.6% SGO_1926 rpoC; DNA-directed RNA polymerase, beta chain 51 52.1% 56 57.9% 52.1% 44 50 53.6% 61 63.4% 51.9% 43 53 54.5% 57 63.7% SGO_1927 rpoB; DNA-directed RNA polymerase, beta subunit 44 55.0% 37 49.8% 10.4% 5 27 36.4% 9 17.0% 30 42.4% 12 24.0% SGO_1928 pbp1b; penicillin-binding protein 1B 41.6% 13 11 37.6% 19 56.0% 46.7% 13 16 40.2% 21 60.3% SGO_1929 tyrS; tyrosyl-tRNA synthetase 17 56.2% 16 57.4% 4 15.2% 3 12.1% 6 24.5% 3 12.1% SGO_1930 rrmA; Ribosomal RNA large subunit methyltransferase A 3 30.9% SGO_1931 lipoprotein, putative 11 26.9% 5.4% 3 14 32.5% SGO_1934 copper-translocating P-type ATPase 5 49.0% 3 27.3% SGO_1935 negative transcriptional regulator, CopY 16.2% 5 25 58.2% 18 50.8% 18.2% 6 35 65.6% 15 41.2% SGO_1936 adcA; metal-binding (Mn) permease precursor, lipoprotein 8 24.2% 8 24.8% 6 43.2% 3 22.9% 8 48.3% 3 22.9% SGO_1938 adcC; ATP-binding protein, Mn 4 30.6% SGO_1939 adcR; repressor protein adcR 8 30.8% 12 41.3% 3 13.4% SGO_1957 hypothetical protein SGO_1957 4 12.0% 6 19.5% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 90

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 90 54.7% 6 5 47.7% 6 48.4% 47.7% 5 7 54.7% 6 48.4% SGO_1958 rplQ; ribosomal protein L17 5 47.7% 5 51.6% 54.8% 15 17 50.3% 20 68.3% 63.5% 18 19 55.8% 19 62.2% SGO_1959 rpoA; DNA-directed RNA polymerase, alpha subunit 20 59.0% 15 56.7% 33.9% 4 3 22.8% 5 50.4% 22.8% 3 4 33.1% 4 33.9% SGO_1960 rpsK; ribosomal protein S11 4 33.9% 5 47.2% 59.5% 13 16 69.4% 17 69.4% 69.4% 14 16 69.4% 14 69.4% SGO_1961 rpsM; ribosomal protein S13p/S18e 11 62.8% 8 47.9% 60.5% 3 3 60.5% 3 60.5% SGO_1962 rpmJ; ribosomal protein L36 67.9% 12 10 64.6% 13 68.9% 58.0% 9 11 64.6% 14 79.2% SGO_1964 adk; Adenylate kinase (ATP-AMP transphosphorylase) 13 62.7% 11 62.3% 8.5% 3 8 20.2% 6 15.4% 8.5% 3 9 20.6% 5 13.8% SGO_1965 Preprotein translocase secY subunit 56.2% 12 6 49.3% 7 50.7% 50.7% 9 5 28.8% 8 50.7% SGO_1966 rplO; ribosomal protein L15 7 50.7% 5 47.3% 54.1% 5 4 54.1% 4 54.1% 54.1% 4 4 54.1% 4 54.1% SGO_1967 50S ribosomal protein L30 -related protein 3 54.1% 3 35.1% 72.0% 12 11 65.9% 10 71.3% 72.0% 11 12 67.1% 11 71.3% SGO_1968 rpsE; ribosomal protein S5 8 60.4% 9 76.2% 47.5% 5 4 39.8% 4 39.8% 39.8% 4 5 50.0% 4 39.8% SGO_1969 rplR; ribosomal protein L18 4 39.8% 4 39.8% 59.6% 9 9 59.6% 9 59.6% 59.6% 8 10 65.7% 11 66.3% SGO_1970 BL10; 50S ribosomal protein L6 12 71.9% 6 49.4% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 91

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 91 58.3% 12 12 59.8% 12 58.3% 58.3% 11 12 59.8% 13 59.8% SGO_1971 rpsH; ribosomal protein S8 13 59.8% 10 50.0% 3 49.2% SGO_1972 rpsN; ribosomal protein S14p/S29e 77.2% 14 18 83.9% 16 80.6% 75.0% 15 17 81.7% 17 78.3% SGO_1973 BL6; 50S ribosomal protein L5 15 70.6% 15 88.3% 47.5% 8 8 47.5% 9 52.5% 47.5% 8 9 63.4% 9 52.5% SGO_1974 rplX; ribosomal protein L24 9 63.4% 6 54.5% 32.0% 5 4 27.0% 5 34.4% 32.0% 5 6 36.1% 4 27.0% SGO_1975 rplN; ribosomal protein L14 4 22.1% 4 22.1% 38.4% 5 4 25.6% 5 38.4% 38.4% 5 4 25.6% 6 58.1% SGO_1976 BS16; 30S ribosomal protein 3 25.6% 6 53.5% 57.4% 4 4 42.6% 5 45.6% 50.0% 3 8 73.5% 5 58.8% SGO_1977 rpmC; ribosomal protein L29 4 50.0% 33.6% 4 4 33.6% 6 44.5% 37.2% 4 8 52.6% 6 44.5% SGO_1978 rplP; ribosomal protein L16 6 42.3% 4 40.1% 49.8% 10 12 55.8% 11 53.9% 53.9% 9 14 59.4% 10 53.5% SGO_1979 rpsC; ribosomal protein S3 14 58.1% 13 69.6% 54.4% 6 8 58.8% 7 57.0% 60.5% 7 9 69.3% 8 61.4% SGO_1980 rplV; ribosomal protein L22 6 50.9% 5 49.1% 55.9% 6 8 57.0% 8 57.0% 57.0% 8 9 58.1% 9 57.0% SGO_1981 rpsS; ribosomal protein S19 8 48.4% 10 64.5% 50.2% 10 10 47.3% 11 56.0% 56.0% 12 12 52.7% 11 45.5% SGO_1982 rplB; ribosomal protein L2 10 52.0% 11 54.2% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 92

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 92 69.4% 7 7 69.4% 8 69.4% 76.5% 8 9 84.7% 7 69.4% SGO_1983 rplW; ribosomal protein L23 6 59.2% 6 68.4% 51.7% 7 7 37.7% 8 51.7% 51.7% 7 8 41.5% 8 51.7% SGO_1984 rplD; ribosomal protein L4/L1 family 9 47.8% 9 49.8% 59.6% 10 8 45.2% 9 53.8% 59.6% 10 10 48.1% 10 56.7% SGO_1985 rplC; ribosomal protein L3 11 63.9% 10 64.9% 45.1% 6 5 38.2% 5 38.2% 45.1% 6 5 38.2% 5 38.2% SGO_1986 rpsJ; ribosomal protein S10 5 38.2% 5 45.1% 6 26.6% 6 25.7% SGO_1988 hydrolase, haloacid dehalogenase-like family 5 20.6% 67.0% 26 25 67.0% 31 69.5% 66.7% 26 26 67.2% 29 65.8% SGO_1989 purA; adenylosuccinate synthetase 24 61.9% 25 63.3% 8.7% 4 3 6.4% 7 15.3% 7 10.9% 8 19.8% SGO_1990 glutamate--cysteine ligase, putative/amino acid ligase, putative 10 23.7% 12 26.4% 3 12.8% 3 16.2% 8 32.4% 4 19.7% SGO_1991 hslO; 33 kDa chaperonin /Heat shock protein 33-like protein 6 23.1% 5 19.7% 22.4% 3 10 49.8% 9 49.8% 29.7% 5 14 70.3% 8 49.8% SGO_1993 possible transcriptional regulator 6 35.6% 6 45.1% 3 25.9% SGO_1994 lipoprotein, putative 13.4% 3 4 16.0% 4 16.0% SGO_1995 MutT/nudix family protein 3 11.8% 4 22.1% 17.2% 10 19 30.2% 21 32.3% 13.6% 8 24 32.6% 23 34.7% SGO_1998 clpB; ATP-dependent Clp proteinase, ATP-binding chain 13 20.6% 15 24.2% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 93

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 93 66.9% 16 16 67.4% 20 79.8% 61.7% 15 16 67.4% 18 78.1% SGO_2000 tsf; translation elongation factor Ts 17 68.6% 19 78.4% 66.9% 19 17 63.8% 19 65.8% 69.2% 20 19 68.5% 18 63.1% SGO_2001 rpsB; ribosomal protein S2 23 69.2% 23 80.8% 20 41.9% 25 41.3% SGO_2004 LPXTG cell wall surface protein 5 13.1% 6 14.3% 3.6% 9 46 19.3% 5 1.8% 1.9% 5 54 21.0% 5 2.3% SGO_2005 LPXTG cell wall surface protein 4 1.9% 3 27.3% 3 28.9% SGO_2006 thioredoxin signature protein 36.5% 5 7 47.8% 6 43.3% 47.8% 7 8 53.4% 7 55.6% SGO_2007 nusG; transcription termination/antitermination factor NusG 8 56.7% 7 48.9% 3 31.0% 3 31.0% SGO_2008 preprotein translocase secE component -related protein 17 33.1% 17 33.2% SGO_2010 pbp2a; penicillin-binding protein 2A 6 17.3% 4 8.4% 35 48.2% 40 53.4% SGO_2013 putative N-acetylmuramidase/lysin 5 6.0% 5 6.6% 3 6.4% SGO_2015 possible polysaccharide transport protein 4 10.5% SGO_2016 nucleotide sugar dehydratase, putative 3 29.6% 5 41.3% SGO_2017 nucleotidyl transferase, putative Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 94

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 94 8 34.7% 6 22.6% 9 38.2% 4 18.8% SGO_2019 licD; licD3 protein 4 16.0% SGO_2020 glycosyltransferase 7 34.9% 11 45.5% SGO_2021 Extracellular polysaccharide glycosyltransferase 4 17.7% SGO_2022 UDP-glucose 4-epimerase BH3715 7 33.3% 6 33.3% SGO_2023 galactosyltransferase 6.5% 3 19 32.3% 10 18.9% 10.0% 4 24 38.8% 8 14.9% SGO_2024 Extracellular polysaccharide biosynthesis 16.9% 3 13 60.2% 10 43.7% 28.6% 5 12 54.5% 9 44.2% SGO_2025 wze; putative autophosphorylating protein tyrosine kinase 5 31.6% 6 37.7% 6 31.6% 5 31.6% SGO_2026 wzd; polysaccharide export protein, MPA1 family 5 12.3% SGO_2027 wzh; wzh/Putative phosphotyrosine-protein phosphatase 12 29.8% 13 31.5% 3 8.6% SGO_2028 wzg; transcriptional regulator 17.7% 7 22 40.2% 14 33.4% 21.1% 9 31 48.2% 14 31.9% SGO_2033 nrdD; ribonucleoside-triphosphate reductase 23 39.0% 16 30.4% 8 14.0% 4 7.6% 11 19.3% SGO_2034 hypothetical protein SGO_2034 3 7.1% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 95

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 95 8 21.0% 9 22.4% SGO_2037 cardiolipin synthase 5 11.4% 6 14.0% 5 16.7% 6 18.7% 3 8.7% SGO_2039 dihydrofolate synthase 23.0% 3 4 33.8% 6 43.9% 5 38.1% 4 33.8% SGO_2041 conserved hypothetical protein TIGR00250 63.6% 4 5 67.0% 3 53.4% 63.6% 4 4 63.6% 3 53.4% SGO_2042 Bacterial protein of unknown function (DUF965) superfamily 5 68.2% 4 63.6% 8 58.9% 7 44.7% 3 21.6% SGO_2043 lipoprotein, putative 51.4% 17 18 52.2% 18 53.3% 54.3% 17 22 54.8% 19 55.6% SGO_2045 recA; recA protein 16 49.3% 13 41.0% 8.6% 4 7 19.9% 4 10.0% 9.8% 4 5 12.2% 4 9.6% SGO_2046 cinA; competence induced protein 5 14.4% 5 10.0% 3 29.3% SGO_2049 tagI; DNA-3-methyladenine glycosylase I 5 37.2% 3 25.5% 3 17.3% 4 26.0% SGO_2050 ruvA; Holliday junction DNA helicase RuvA 3 23.5% 4 25.4% SGO_2052 hypothetical protein SGO_2052 13.3% 5 9 20.2% 5 13.8% 17.3% 7 12 28.4% 10 27.5% SGO_2053 DNA mismatch repair protein hexB 9 23.5% 6 14.4% 8.0% 5 15 20.2% 11 21.4% 22.6% 10 17 28.1% 14 28.6% SGO_2056 mutS; DNA mismatch repair protein MutS 13 21.3% 18 31.5% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 96

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 96 7 59.3% 6 49.0% SGO_2057 argR; arginine repressor 56.6% 25 31 59.8% 37 66.2% 52.0% 24 37 65.7% 36 64.1% SGO_2058 argS; arginyl-tRNA synthetase 39 69.4% 36 70.5% 5 19.0% SGO_2059 hypothetical protein SGO_2059 16.6% 8 15 31.5% 21 43.0% 19.7% 8 22 42.0% 19 39.4% SGO_2060 aspS-1; aspartyl-tRNA synthetase 12 28.1% 15 37.0% 37.1% 14 16 45.8% 21 66.0% 40.4% 14 17 48.6% 20 62.4% SGO_2062 hisS; histidyl-tRNA synthetase 19 63.1% 18 55.2% 41.9% 15 16 40.0% 22 54.0% 40.3% 14 18 40.3% 24 60.4% SGO_2064 ilvD; dihydroxy-acid dehydratase 19 48.8% 18 47.7% SGO_2065 rpmF; ribosomal protein L32 34.7% 3 3 34.7% 4 44.9% 44.9% 4 4 53.1% 3 34.7% SGO_2066 rpmG; ribosomal protein L33 5 65.3% 34.8% 7 7 31.4% 9 48.8% 12.4% 3 9 40.1% 8 42.8% SGO_2070 hypothetical protein SGO_2070 7 37.1% 3 15.7% 13.0% 3 SGO_2073 FtsK/SpoIIIE family subfamily, putative 7 29.7% 4 20.6% 6 29.7% 5 22.9% SGO_2080 transcription activator plcR 10 47.4% 15 60.9% 3 24.3% SGO_2081 lipoprotein, putative Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 97

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 97 9 43.0% 12 50.6% SGO_2082 lipoprotein, putative 3 17.7% 4 27.7% 5 27.7% 5 42.0% SGO_2084 NAD(P)H dehydrogenase, quinone family 3 13.3% 4 25.5% 46.4% 13 21 58.7% 16 50.6% 32.7% 9 23 56.8% 17 53.4% SGO_2085 purB; adenylosuccinate lyase 12 37.4% 13 43.6% 6 15.6% 8 18.9% SGO_2086 hypothetical protein SGO_2086 8 26.0% 11 37.7% SGO_2094 general stress protein GSP-781 16 51.8% 21 60.6% SGO_2096 comB; transport protein ComB 2.9% 3 30 47.3% 10 16.0% 32 49.7% 8 17.6% SGO_2097 comA; ATP-binding Transport protein ComA 75.4% 21 17 65.0% 20 61.6% 76.4% 22 21 65.5% 21 66.5% SGO_2098 rpsD; ribosomal protein S4 16 69.0% 16 58.6% 4 22.9% SGO_2099 ABC transporter ATP-binding protein 49.7% 18 14 45.8% 25 60.5% 54.2% 18 12 42.5% 22 59.3% SGO_2100 ABC transporter substrate-binding protein 7 27.1% 5 22.3% 5 60.4% 45.8% 3 5 60.4% SGO_2102 hypothetical protein SGO_2102 4 21.0% SGO_2103 hydrolase, haloacid dehalogenase-like family 3 21.5% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 98

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 98 34.7% 9 15 48.4% 13 54.4% 35.4% 9 18 57.9% 13 57.2% SGO_2104 srtB; sortase B 13 53.7% 13 51.9% 48.2% 6 9 55.9% 5 39.0% 44.6% 6 12 69.7% 7 48.2% SGO_2105 abpA; amylase-binding protein AbpA 11 55.9% 12 69.7% 45.5% 14 13 44.2% 14 43.0% 34.3% 10 16 48.0% 14 40.8% SGO_2106 ribose-phosphate diphosphokinase 14 40.8% 15 44.9% 4 22.7% 4 23.5% SGO_2107 general stress protein GSP-781 10 55.1% 5 32.4% 11 57.8% 3 20.6% SGO_2108 mreC; cell shape-determining protein MreC 37.6% 19 32 50.5% 25 47.4% 37.9% 18 40 57.6% 22 40.9% SGO_2133 Cell division protein ftsH-like protein 33 53.6% 26 47.3% 38.3% 8 6 26.7% 11 46.7% 37.2% 6 7 33.3% 10 46.7% SGO_2134 hpt; hypoxanthine phosphoribosyltransferase 12 52.8% 12 52.8% 5 42.6% SGO_2138 Septum formation initiator family 3 43.2% SGO_2139 S4 RNA-binding domain protein 6 6.6% 8 9.5% SGO_2140 transcription-repair coupling factor 3 18.5% SGO_2141 pth; peptidyl-tRNA hydrolase 44.7% 13 15 56.9% 16 61.2% 56.9% 15 17 62.0% 18 61.2% SGO_2142 GTP-binding protein 14 53.4% 16 58.5% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.

PAGE 99

Hackett Laboratory UW Streptococcus gordonii Summary Table SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg vs SgFn SgPgFn vs SgFn SgPgFn vs SgPg Coverage n Sg Coverage n SgPg Coverage n SgPgFn Coverage Description Sg SgPg Rep I Rep II Rep I Rep II Rep I Rep II n SgFn Coverage SgFn Rep I Rep II SgPgFn Protein Coverage Page 99 56.9% 15 17 56.5% 15 56.1% 56.9% 16 20 61.6% 17 56.1% SGO_2145 comE; competence response regulator ComE 11 29.4% 7 23.2% 6.0% 3 11 32.0% 6 19.9% SGO_2146 comD; histidine protein kinase ComD 34.8% 7 11 44.8% 8 39.3% 24.4% 5 14 52.1% 9 39.5% SGO_2150 degP; serine protease 9 34.5% 9 32.7% Proteins found: ABC Transporter Filter by category: Show detected proteins only Show all proteins 1179 Dot Plots Dot Plots Hendrickson et al.



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0.005 q-Value < SgFn vs Sg SgPg vs Sg SgPg vs SgFn SgPgFn vs SgPg SgPgFn vs SgFn Consensus* vs Sg SgPgFn vs Sg Sg / SgPgFn SgPgFn / Sg 1 ! ! ! !! !! !!! !!!!! ! !! !!!! ! !! !!!!!!! ! !!!!!!!! 51 !!! !! ! ! !! !! ! !! !!!!!!!!! !!!!!!!!!! !!!!!!!!!! 101 !!! ! !!!! !! !!!!!!! !!!!!!!!!! !!!! !! !! ! !!!! ! !!!! 151 ! ! ! ! !! !! ! !!!! ! !! !!!!! !!!!!!!!! !!!!!!! ! 201 !! !!! ! !!!! !!! ! !!!!!!!!! ! ! !! !!! !!! !! !!! 251 ! !! !! ! ! ! !!!!!!! ! !!! !!!! !!!!! !!! ! !!!!!!!! 301 !!!!!!!!!! ! !!!! !!! !!!!!!!!! !! !!!!!!! ! ! !!!! ! 351 ! !!!! !! !!!!!!! !! ! ! ! !!!! !!! !!!!! ! !!!!! !! 401 ! ! !!! !! !! ! !!!! !!!!! ! ! ! ! ! ! !! !!!! !! !! 451 !!! ! !! ! !!!!!!! !! !!!!! !!! !! !!!!!!! !!!!!!!!!! 501 ! ! !! ! ! !! !! ! !!!!! !!!! !!!! !! !! !! !! ! !! 551 ! ! !!! ! !!!! !! !! !! !!! !!! ! ! ! !! ! ! ! ! ! !! 601 !!! ! !!! !!!!!!!!!! !!!!! !!!! !!!!!!! !! ! ! !!!!!! 651 ! ! ! !!!! !!!! !!! ! !! !! !! !! ! !! !!! !! !! !!!!!! 701 !! ! ! !! !! !!!!!!! !!!!!!!!! !!!!! !! ! ! ! !!! ! 751 !!! ! !!!! !! !!!!!!! ! ! !! ! !!! ! ! !! ! ! !! ! 801 !! !!!!!!! !!! ! !! ! !!! !!!!!! ! !! ! !!!! ! !!!!! ! 851 !!! ! !! ! !!!!!!!!! !!!!!!!!!! !!!! !! ! !! !!!!!!! 901 !!!! !!!! !!!!!!!!! !!!!!!!!!! !!!!! !!! !!!!! !! ! 951 !! !!!!!! !!!!!!!!!! !!!!!!!!!! ! !!!! !!! !!!! !!!!! 1001 !!! !!! !! ! !! !! ! !!!! ! !!!! !! !!! ! !! !!!!!! ! ! 1051 !!!!!!! ! !!!! !!! ! !!!!!!!! !! ! !!!!! !! !!!!! ! !! 1101 !!! !! ! ! !!! ! !!! !! !!!!! !! ! ! !!!! ! ! ! !!!!! 1151 !! !! !!!!! !!!!!! ! ! !!!!!!!!!! !!!! !!! ! ! !! ! !! 1201 !! ! !! !!! !!!! !! !! ! !!! !! !!!! ! ! !! !! ! ! !!!!! !! 1251 !! !!!!!! !! !!!! !!!! !! !! !!!! ! ! !!!!!! !! !!! !!! 1301 !!!! !!!!! ! !!!!!!!! !! !!! !!! !!!!! !! !! ! !!!!!!!! 1351 !!!!!!!!!! !!! ! !!! ! !! ! ! !!! ! !!!!!! !!!!!! !! 1401 !!!!!!!!!! !!! !!!!!! ! !!! !!!! ! ! !!!! !! !!!! !! !! 1451 !! !! !! ! ! !! !!! !!! ! ! !!!!!!!! !!!!! !!!! !!!!!!!!!! 1501 !!!!!!!!!! !!!!! !!!! !!!!!!!!! ! !! ! !! ! !!!!!! !!! 1551 !!! ! ! ! !!!!!!!!! ! ! !!!!!! !!!! ! !!! !!! !!!!! ! 1601 !!! !! !!! ! !!!!!! ! ! !!!! !!! !! ! ! !!!!!!! !!!!!!! ! 1651 ! !!!!!!! !!!!! !! ! !!!! ! ! ! ! !!! ! ! ! !!! !!! ! 1701 !!!!!! !!! !!! ! ! ! ! !!!! !! ! !!! !!! !!! !!!! !! !! 1751 !!!! ! !!! !! !!!!!!! !!! !!!!!! !!! !!!!!! !!!!!!!! ! 1801 ! ! !!!!! !!!!!!!!! ! ! !!! !! !!! !! !!!!! !! ! !! ! !! 1851 ! ! ! !!! !!! ! ! !!! !!!!!!!! ! ! !! ! !!!! ! !!!!! !! 1901 !! !!!!!!! !!! ! !! !!! !!! ! !! ! !!! ! !!!! !!!!!!!!!! 1951 !!!!!!! ! ! !! ! !! ! ! !!!! ! ! ! !!! !! ! !! ! !! ! 2001 !!! ! !!! !!!!!!!!!! !!! !! !!!!! !! !!!!!!! ! !! ! !!!! 2051 !! !! ! ! ! ! ! !!! !!!!!!!!!! !!!! !!!!! !!!!!! ! ! 2101 !!! !!! !!!! !!!!!!!!!! !!!!!!!!!! !! ! !!!!!! ! !! ! !!! Hendrickson et al. a consensus view of those proteins that trend the same in SgPg/Sg and SgPgFn/Sg



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Proteomicsof Streptococcusgordonii withina modeldevelopingoralmicrobialcommunityHendrickson etal. Hendrickson etal.BMCMicrobiology 2012, 12 :211 http://www.biomedcentral.com/1471-2180/12/211

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RESEARCHARTICLEOpenAccessProteomicsof Streptococcusgordonii withina modeldevelopingoralmicrobialcommunityErikLHendrickson1,TiansongWang1,2,BrittanyCDickinson3,SarahEWhitmore4,ChristopherJWright4, RichardJLamont4andMurrayHackett1*AbstractBackground: Streptococcusgordonii isoneofseveralspeciesthatcaninitiatetheformationoforalbiofilmsthat developintothecomplexmultispeciesmicrobialcommunitiesreferredtoasdentalplaque.Itisinthecontextof dentalplaquethatperiodontalpathogenssuchas Porphyromonasgingivalis causedisease.Wehavepreviously reportedawholecellquantitativeproteomicsinvestigationof P.gingivalis inamodeldentalplaquecommunityof S.gordonii P.gingivalis ,and Fusobacteriumnucleatum .Herewereporttheadaptationof S.gordonii tothesame model. Results: 1122 S.gordonii proteinsweredetectedin S.gordonii controlsamples,915incommunitieswith F. nucleatum ,849with P.gingivalis ,and649withallthreeorganisms.Quantitativecomparisonsshowedextensive proteomechangesinassociationwith F.nucleatum or P.gingivalis individuallyorboth P.gingivalis and F.nucleatum together.Thechangeswerespeciesspecific,thoughthe P.gingivalis interactionmaybedominant,indicatedby largedifferencesbetweentheproteomeswith F.nucleatum or P.gingivalis butlimitedchangesbetween communitieswith P.gingivalis orboth P.gingivalis and F.nucleatum .Theresultswereinspectedmanuallyandan ontologyanalysisconductedusingDAVID.Extensivechangeswereseeninnutritionpathwayswithincreasesin energymetabolismandchangesintheresultingbyproducts,whiletheacidandsugarrepressedPTS (phosphoenolpyruvatedependentphosphotransferasesystem)sugartransportsystemsshoweddecreases.These resultswereseenacrossallthemultispeciessamples,thoughwithdifferentprofilesaccordingtothepartner species. F.nucleatum associationdecreasedproteinsforthemetabolicendproductsacetateandethanolbut increasedlactate,theprimarysourceofacidityfromstreptococcalcultures. P.gingivalis containingsampleshada reductioninlevelsofproteinsforethanolandformatebutincreasedproteinsforbothacetateandlactate production.Thecommunitiesalsoshowedincreasesinexopolysaccharidesynthesis,aminoacidbiosynthesis,and oxidativestressprotectionanddecreasesinadhesionandtransporterproteins. Conclusion: Thisstudyshowedthat S.gordonii demonstratesspeciesspecificresponsesduringinteractionswith F. nucleatum or P.gingivalis .Extensivechangeswereseeninenergymetabolismandbyproductproduction implicatingnutrienttransferasanimportantcommunityinteraction. Keywords: Streptococcusgordonii ,Oralbiofilm,Proteomics,Modelcommunity, Porphyromonasgingivalis Fusobacteriumnucleatum *Correspondence: mhackett@u.washington.edu1DepartmentofChemicalEngineering,UniversityofWashington,Box 355014,Seattle,WA98195,USA Fulllistofauthorinformationisavailableattheendofthearticle 2012Hendricksonetal.;licenseeBioMedCentralLtd.ThisisanOpenAccessarticledistributedunderthetermsofthe CreativeCommonsAttributionLicense(http://creativecommons.org/licenses/by/2.0),whichpermitsunrestricteduse, distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited.Hendrickson etal.BMCMicrobiology 2012, 12 :211 http://www.biomedcentral.com/1471-2180/12/211

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BackgroundOralinfections,suchascariesandperiodontaldisease, areamongthemostcommoninstancesofbacterial pathogenesisinhumans.Currentmodelsoforaldisease developmentcenteraroundthemicrobialcommunities foundindentalplaquebiofilms.Developmentofthe dentalplaquebiofilminvolvescompetitionandcooperationamonghundredsofdifferentorganisms.Earlycolonizingorganisms,dominatedbystreptococcisuchas S. gordonii [1],bindtoavarietyofhostderivedmolecules coatingoralsurfacesknownastheacquiredpellicle.Secondarycolonizingspeciesthenadheretothoseboundto thepellicle. Fusobacteriumnucleatum canbindthese earlycolonizingorganismsandlateradditionstothe biofilm[2].Inaddition, F.nucleatum isaerotolerantand metabolicactivitycanreducetheconcentrationofoxygentolevelsthatcanbetoleratedbymorepathogenic organismssuchas P.gingivalis [3]. P.gingivalis canbind toboth F.nucleatum and S.gordonii [4,5],andthese organismsaremetabolicallycompatiblewhenassociated [3,6].Whiledestructionofperiodontaltissueisgenerally associatedwithlatercolonizerslike P.gingivalis ,pathogenicityisexpressedwithinthecontextofthemicrobial community. Ithasrecentlybeenshownthatnutrienttransfer withinacommunitycanplayanimportantrolein pathogenicity[7].Co-culturewith S.gordonii resultedin increasedvirulenceoftheperiodontalpathogen Aggregatibacteractinomycetemcomitans .Theincreasewas dependentontheabilityof A.actinomycetemcomitans to utilizeL-lactate,abyproductof S.gordonii energymetabolism,asanenergysource.Furthermore,amutant strainunabletoutilizeL-lactateshowedsignificantly decreasedvirulenceintheco-culturehighlightingthe importanceofmetabolitecross-feeding. Oralmicrobialcommunitiesarealsoknownforalteringtheirlocalenvironment.Themoststrikingexample occursindentalcarieswherespeciessuchas Streptococcusmutans significantlyreducethepHtoapointwhere enamelisdemineralized[8].Thisshiftinecologyalso effectsthedevelopmentofthedentalplaque,selecting formoreaciduricorganismssuchaslactobacilli.While S.gordonii doesnotproduceacidatthesamelevelsor atlowerpHasdoes S.mutans S.gordonii hasbeen foundtoproduceaciddowntopH5.5[9]andmayalso changethelocalecologyduringformationofdental plaque. Thelargenumberofspeciesinvolved,theheterogeneitybetweenhostsaswellaswithintheoralcavity,and thesmallsamplesizesthatcanbeharvestedfromthe oralcavitycomparedtolaboratorygrownsamples,all presentsignificantexperimentalchallengesinexamining microbialinteractionsindentalplaquedevelopment.In ordertoinvestigatetheseinteractionsinamore experimentallytractablesystem[10],wehavedeveloped amodelofnascentcommunityinteractions[11]using threerepresentativespeciesoforalbacteria, S.gordonii F.nucleatum ,and P.gingivalis. Wehavepreviously reportedourresultsfor P.gingivalis proteinexpression, whichshowedextensivechangesin18hourpelletswith S.gordonii and F.nucleatum ,especiallyinthecellenvelopeproteomeandinvitaminsynthesispathways[11]. Herewereportchangesin S.gordonii proteinlevelsin modelnascentcommunitieswith F.nucleatum P.gingi-valis ,andallthreespeciescombined.ResultsanddiscussionBacteriaintheoralcavityassembleintocomplexheterotypiccommunitiesthatengageinmultilevelsignaling andresponseinteractions[12,13].Bacteriacancommunicatethroughdirectcontact;solublesecretedfactors suchasautoinducers;anddetectionandutilizationof metabolicproductsofpartnerspecies[14,15].Proteomic investigationofsuchcommunitiesinvitropresentsnumerouschallengesincludingsamplesizeandrelevance totheinvivosituation.Wehavedevelopedamodelthat includeselementsfromthreemajorspeciesofdental biofilmsthatrepresentearly( S.gordonii )mid( F.nucleatum )andlate( P.gingivalis )colonizers,organismsthat formcloseassociationswithoneanother,asillustrated usingscanningconfocalmicroscopy(Figure1).Bygeneratingpelletsoftheseorganisms,wehaveprovided conditionsunderwhichtheyareinclosecontact,thus allowingsignalingthroughcontactdependentmechanismsandshortrangechemicalmediators.Thismodel alsoallowsseparationoftheinteractionstageof Figure1 Multispeciescommunityof S.gordonii P.gingivalis and F.nucleatum Confocallaserscanninganalysisofheterotypic communitiesof S.gordonii (red), F.nucleatum (green)and P. gingivalis (yellow).Bacterialaccumulationswereanalysedonan OlympusFV500laserscanningconfocalmicroscope.Aseriesof 1 mfluorescentsliceswerere-constructedusingVolocitysoftware. Theareashownmeasuresapproximately4050 m. Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page2of23 http://www.biomedcentral.com/1471-2180/12/211

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communitydevelopment(ourmajorinterest)fromcommunitydevelopmentthroughbacterialgrowthanddivision.Byavoidinggrowthcyclesinfluencedbynutrient diffusion,thereislessopportunityforresultstobeconfoundedbydifferentialproteinexpressionduetodifferentphysiologicalmicroniches.ProteindetectionThewholecellproteomeof S.gordonii wasmeasuredeitheraloneinasinglespeciesassembled18hourbiofilm orincommunitieswith F.nucleatum (SgFn), P.gingivalis (SgPg),orboth P.gingivalis and F.nucleatum (SgPgFn).Table1showsthenumberof S.gordonii proteinsidentifiedbythreeormoreuniquepeptidesacross twobiologicalreplicatesofeachsample.Thenumberof identifiedproteinsislowerinthemixedsamplesrelative tothesinglespeciescontrolasthepercentageofthe extractedproteinsoriginatingfrom S.gordonii islower inthemixedcommunitythaninapureSgsample. Proteinlevels,asmeasuredbyspectralcounting (seeMethods),werecomparedamongallsamples.Proteinswereconsideredsignificantlyalteredbetweenconditionsat q valuesof0.005andlower.Table2shows numbersofincreased,decreased,andunchangedproteins forallsixcomparisons.Relativeabundancecalculations wereonlycarriedoutforproteinsdetectedinbothconditionsbeingcompared,i.e.noartificialbaselinesinplaceof missingdatawereused.Thereforeincreasedand decreasedproteinlevelsarealsoexpressedasapercentage ofthesharedproteinsdetectedinbothstates.The S.gordonii proteomeundergoessubstantialchangeswhen exposedtoFnorPgwith45to54%ofthedetectedproteinsshowingalteredlevelscomparedtoSgalone(SgFn vsSg,SgPgvsSg,andSgPgFnvsSg).WhileSgshowed manyrelativeabundancechangeswitheitherFnorPg, theresponsesaredistinctandspeciesspecificasseenin thelargedifferencesbetweentheSgPgandSgFnpreparations(SgPgvsSgFn).However,theresponsetoPgappears tobedominant.SginacommunitywithbothPgandFn showssignificantdifferencescomparedtotheSgFncommunitybutisverysimilartotheSgPgcommunity(SgPgFn vsSgFn,SgPgFnvsSgPg).Thisisinkeepingwithmodels ofdentalplaquedevelopmentwherebythepathogenicpotentialaltersaslatercolonizersbecomeestablished[16].A shortformatsummarytableofalldatapresentedinthis reportcanbefoundinAdditionalfile1.Additionalfiles2, 3,4,5,6,7presentthedatainsomewhatgreaterdetailfor eachproteomequantitativecomparison,includingboth rawandnormalizedspectralcountsandassociatedstatistics.QualitativeproteincoverageinformationissummarizedinAdditionalfile8.Additionalfile9showsawhole genomeplotoftheSgPgFnvsSgcomparison.Plotscomparingspectralcountsfortechnicalreplicatesandspectral countsforeachbiologicalrepl icatearefoundinAdditional file10,aswellasadditionalremarksaboutdatareproducibilityandtheeffectsofnormalization.Thehighcorrelationsshownsuggestthatthedetectedchangesaredue primarilytodifferencesbetweentheconditionsbeingcomparedratherthanrandomvariabilityinthemeasurements. TheoriginalFileMaker™databasefromwhichadditional files1,2,3,4,5,6,7,8werederivedisavailablefromthe correspondingauthor.Therawdatahasbeenarchivedina remotesecurelocationaspartoftheUniversityof Washington ’ s lolo fileretrievalsystem,andwillalsobe madeavailablethroughtheUnitedStatesDepartmentof Energy ’ sJointGenomeInstitute(JGI),andpossiblyother sitespendingongoingdiscussionsintheproteomicscommunitywithrespecttobestpracticesforpermanentarchivalstorage.EnergymetabolismandsugartransportChangestopathwaysforenergymetabolismandsugar transportinthemultispeciescommunitieswereconsistentwithahigherlevelofavailableenergymetabolites andalowerpH.Oralstreptococcalspeciesprimarilyderivetheirenergyfromthebreakdownofcarbohydrates. Figures2,3,4,5,6,7compareenergymetabolismpathwayproteinsbetweenthedifferentcommunities(2SgFn vsSg,3SgPgvsSg,4SgPgFnvsSg,5SgPgvsSgFn,6 SgPgFnvsSgFn,7SgPgFnvsSgPg).ComparedtoSg alonethemultispeciescommunitiesshowedincreased levelsforboththeglycolysispathwayandthepentose phosphatepathway,implyinghigherenergyavailability (Figures2,3,4).ThepresenceofPgappearedtobe dominantasSgPgFnwasverysimilartoSgPg(Figure7). EventhoughbothpathwayswereincreasedinthepresenceofFnorPgtherewasadifferenceinemphasis Table1 S.gordonii proteinsdetectedincommunitiesOrganism(s)Proteinsdetected S.gordonii 1122 SgFn915 SgPg849 SgPgFn649 Table2Relativeabundancechangesobservedforthe S. gordonii expressedproteomeComparisonUnchangedIncreasedDecreased SgFnvs S.gordonii 421188(24%)160(21%) SgPgvs S.gordonii 389212(25%)200(26%) SgPgFnvs S.gordonii 287163(26%)174(28%) SgPgvsSgFn375161(23%)177(25%) SgPgFnvsSgFn327111(19%)146(25%) SgPgFnvsSgPg55615(2%)56(9%) Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page3of23 http://www.biomedcentral.com/1471-2180/12/211

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D-Glucose D-Fructose a-D-GlucoseB-D-Glucose ATP ATP a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P Fructose-1-P B-DFructose-1,6-P Glyceraldehyde-3-P D-Glucano-d-lactano-6-P D-Glucanate-6-P D-Ribulose-5-P D-Xylose-5-P Glycerone-P ATP ATP acetyl phosphate Glycerate-1-3-P Glycerate-3-P Glycerate-2-P phosphoenol pyruvate pyruvate ATP Acetyl-CoA 2-Hydroxyethyl-ThPP Thiamine diphosphate Lipoamide-E Dihydrolipodamide-E S-Aceyl dihydrolipoamide-E Acetaldehyde Ethanol L-lactate acetyl phosphate Acetate ATP ADP ADP ADP ADP ATP ADP ATP ATP ADP ADP ADP ADP SGO_1144 glcK SGO_1144 glcK SGO_0505 SGO_0049 galM SGO_0154 pgi SGO_0154 pgi SGO_0154 pgi SGO_1113 fruA SGO_1755 scrK SGO_1340 pfk SGO_0813 fbp SGO_1745 fba SGO_1112 fruB SGO_0762 tpiA SGO_0207 gap SGO_0209 pgk SG O_0391, SGO_0392, SGO_0704 gpmA, SGO_07 54 SGO_1426 eno SGO_1339 pyk SGO_1132 aco, SGO_1133 acoA SGO_1130 dld SGO_1132 aco, SGO_1133 acoA SGO_1131 sucB SGO_0292 spxB SGO_1916 ackA SGO_1369 hicdh, SGO_ 1232 ldh SGO_0247 pfl, SGO_1788 pfl SGO_0788 zwf SGO_1422 hypothetical pgls SGO_0503 gnd SGO_0198 rpe SGO_0312 xfp SGO_1219 pta SGO_0113 acdH SGO_0113 acdH SGO_0372 Malate CoA Formate Figure2 SgFnvsSgEnergymetabolismandendproducts. Thediagramshowsaschematicoftheglycolysisandpentosephosphate pathwaysforSgincludingtheendproductsofthemetabolism,formate,acetate,L-lactate,andethanolforthe S.gordonii with F.nucleatum samplecomparedto S.gordonii .Proteinscatalyzingeachstepareshownbytheir S.gordonii SGOdesignation,someincludeaprotein abbreviation.Rednumbersindicateincreasedlevelsinthefirstconditioncomparedtothesecondcondition,greendecreasedlevels,yellowno statisticalchange,andblackundetectedinatleastoneoftheconditions.Abbreviations:acdH:alcohol-acetaldehydedehydrogenase;ackA: acetatekinaseA;acoA:acetoindehydrogenase;dld:dihydrolipoamidedehydrogenase;eno:enolase;fba:fructose-1,6-bisphosphatealdolase;fb p: fructose-bisphosphatase;fruA:fructosespecificphosphoenolpyruvate-dependentphosphotransferasesystemscomponentII;fruB:1phosphofructokinase;galM:aldose1-epimerase;gap:glyceraldehydes-3-phosphatedehydrogenase;glcK:glucokinase;gnd:6-phosphogluconate dehydrogenase;gpmA:2,3-bisphosphoglycerate-dependentphosphoglyceratemutase;hicdh:L-2-hydroxyisocaproatedehydrogenase;ldh:lactat e dehydrogenase;pfk:phosphofructokinase;pfl:pyruvateformatelyase;pgi:glucose-6-phosphateisomerase;pgk:phosphoglyceratekinase;pgls :6phosphogluconolactonase;pta:phosphateacetlytransferase;pyk:pyruvatekinase;rpe:ribulose-phosphate3-epimerase;scrK:fructokinase;s pxB: pyruvateoxidase;sucB:dihydrolipoamideS-acetyltransferase;tpiA:triosephosphateisomerase;xfp:D-xululose5-phosphate/D-fructose6phosphatephosphoketolase;zwf:glucose-6-phosphate1-dehydrogenase. Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page4of23 http://www.biomedcentral.com/1471-2180/12/211

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(Figure5).SgincontactwithPghadlargerincreasesin theglycolysispathwaywhileSgwithFnhadlarger increasesinthepentosephosphatepathway.SgFnand SgPgalsoshowedincreasedlevelsofmalateoxidoreductasethatconvertsmalatetopyruvate(Figures2,3)with SgFnshowingalargerincrease(Figure5). Higherlevelsofavailablesugarscouldexplaintheincreaseinenergypathways,butwouldrequireimporting thesugarsintothecell.Oralstreptococcitransport sugarusingtwoprimarysystems:thephosphoenolpyruvatemediatedphosphotransferase(PTS)system,which movessugarsacrossthemembranewithconcomitant phosphorylation;andtheprotonmotiveforce(PMF) system[8,17],thoughthespecificproteinsforthePMF systemhavenotyetbeenidentified.Bothsystemsare knowntoberegulated.Whilethelactose-PTSin S. mutans isinducedbylactose,PTSactivityisgenerally repressedundersugarexcess.ThePTSisalsorepressed atlowpHwhilethePMFsystemisinducedunderlow pH.Togetherthesystemsarebelievedtoprovide Streptococcus specieswithahighaffinityscavengersystemundersugarlimitedconditions,andalowaffinity systemtakingadvantageoftheprotonmotiveforce availableunderlowenvironmentalpH. D-Glucose D-Fructose a-D-GlucoseB-D-Glucose ATP ATP a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P Fructose-1-P B-DFructose-1,6-P Glyceraldehyde-3-P D-Glucano-d-lactano-6-P D-Glucanate-6-P D-Ribulose-5-P D-Xylose-5-P Glycerone-P ATP ATP acetyl phosphate Glycerate-1-3-P Glycerate-3-P Glycerate-2-P phosphoenol pyruvate pyruvate ATP Acetyl-CoA 2-Hydroxyethyl-ThPP Thiamine diphosphate Lipoamide-E Dihydrolipodamide-E S-Aceyl dihydrolipoamide-E Acetaldehyde Ethanol L-lactate acetyl phosphate Acetate ATP ADP ADP ADP ADP ATP ADP ATP ATP ADP ADP ADP ADP SGO_1144 glcK SGO_1144 glcK SGO_0505 SGO_0049 galM SGO_0154 pgi SGO_0154 pgi SGO_0154 pgi SGO_1113 fruA SGO_1755 scrK SGO_1340 pfk SGO_0813 fbp SGO_1745 fba SGO_1112 fruB SGO_0762 tpiA SGO_0207 gap SGO_0209 pgk SGO_0391, SGO_0392, SGP_0704 gpmA SGO_0754 SGO_1426 eno SGO_1339 pyk SGO_1132 aco SGO_1133 acoA SGO_1130 dld SGO_1132 aco SGO_1133 acoA SGO_1131 sucB SGO_0292 spxB SGO_1916 ackA SGO_1369 ,hicdh, SGO_ 1232 ldh SGO_0247 pfl, SGO_1788 pfl SGO_0788 zwf SGO_1422 hypothetical pgls SGO_0503 gnd SGO_0198 rpe SGO_0312 xfp SGO_1219 pta SGO_0113 acdH SGO_0113 acdH SGO_0372 Malate CoA Formate Figure3 SgPgvsSgEnergymetabolismandendproducts. Labels,abbreviationsandcolorcodingasdescribedforFigure2,forthe S. gordonii with P.gingivalis comparisonto S.gordonii Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page5of23 http://www.biomedcentral.com/1471-2180/12/211

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Figures8,9,10,11,12,13showcomparisonsbetween thecommunitiesforPTStransportsystemsandpathwaysfeedingsugarsintoglycolysis.Theseareasubset ofannotatedsystemsincludingonlythosewith detectedproteins.Themultispeciescommunitiesshow areductioninalmostalldetectedPTScomponents comparedtoSgalone(Figures8,9,10).Theexceptions areoneproteininthemultipleproteincomplexfor transportingmannose,eitherSGO_1680(SgPgFnvsSg) orSGO_1892(SgFnvsSg,SgPgvsSg)dependingon thecomparison,andSGO_1555,PtsI,thesugarnonspecificcomponentofthePTSthatprovidesthephosphorylgroupforthereactiontoacarrierprotein.These areincreasedinSgFnandshownochangeinSgPgand SgPgFn(Figures8,9,10).Overall,theindicationisareductionintransportfromthePTSsystem,consistent withsugarexcessand/orlowpH. IncontrasttothePTSsystemproteins,manyofthe proteinsfeedingsugarsintotheglycolysisandpentose phosphatepathwaysshowincreasedlevelsinmixed communities(Figures8,9,10).Thisisconsistentwith thehigherproteinlevelsintheenergypathwaysaswell D-Glucose D-Fructose a-D-GlucoseB-D-Glucose ATP ATP a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P Fructose-1-P B-DFructose-1,6-P Glyceraldehyde-3-P D-Glucano-d-lactano-6-P D-Glucanate-6-P D-Ribulose-5-P D-Xylose-5-P Glycerone-P ATP ATP acetyl phosphate Glycerate-1-3-P Glycerate-3-P Glycerate-2-P phosphoenol pyruvate pyruvate ATP Acetyl-CoA 2-Hydroxyethyl-ThPP Thiamine diphosphate Lipoamide-E Dihydrolipodamide-E S-Aceyl dihydrolipoamide-E Acetaldehyde Ethanol L-lactate acetyl phosphate Acetate ATP ADP ADP ADP ADP ATP ADP ATP ATP ADP ADP ADP ADP SGO_1144 glcK SGO_1144 glcK SGO_0505 SGO_0049 galM SGO_0154 pgi SGO_0154 pgi SGO_0154 pgi SGO_1113 fruA SGO_1755 scrK SGO_1340 pfk SGO_0813 fbp SGO_1745 fba SGO_1112 fruB SGO_0762 tpiA SGO_0207 gap SGO_0209 pgk SG O_0391, SGO_0392, SGO_0704 gpmA SGO_07 54 SGO_1426 eno SGO_1339 pyk SGO_1132 aco, SGO_1133 acoA SGO_1130 dld SGO_1132 aco, SGO_1133 acoA SGO_1131 sucB SGO_0292 spxB SGO_1916 ackA SGO_1369 ,hicdh, SGO_ 1232 ldh SGO_0247 pfl, SGO_1788 pfl SGO_0788 zwf SGO_1422 hypothetical pgls SGO_0503 gnd SGO_0198 rpe SGO_0312 xfp SGO_1219 pta SGO_0113 acdH SGO_0113 acdH SGO_0372 Malate CoA Formate Figure4 SgPgFnvsSgenergymetabolismandendproducts. Labels,abbreviationsandcolorcodingasdescribedforFigure2,forthe S. gordonii with P.gingivalis and F.nucleatum comparisonto S.gordonii Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page6of23 http://www.biomedcentral.com/1471-2180/12/211

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ashighlevelsofavailablesugar.Theimplicationisthat thesecond,lowpHinduced,pathwayhashighactivity underthemixedcommunityconditions.Inductionof thesecondsugartransportsystemwouldagainbeconsistentwithalowpHenvironment.WhileSgdoesnot commonlyreducepHtolevelswheredemineralization occurs,itcanproduceacidatpH ’ saslowas5.5andso couldberesponsibleforalowerpHinthemixedcommunities[9].Itisimportanttonotethattheseexperiments wereconductedinmediawithoutexogenousnutrientsand thusSgmaybeundergoingaprogrammedresponsetothe presenceoftheotherspecies,ratherthanaresponseto alterednutrientlevels.AlcoholsandacidicendproductsInmixedspeciescommunitiesSgshowedanextensive shiftinpathwaysforbyproductproduction.Theendproductsofenergymetabolismareoftenimportantcomponentsofpathogenicityandcommunitydevelopment. ChangesinpHcanselectfordifferentorganisms[3].End productscanalsoprovidenutrientsforothercommunity members. S.gordonii hasbeenshowntoincrease A. D-Glucose D-Fructose a-D-GlucoseB-D-Glucose ATP ATP a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P Fructose-1-P B-DFructose-1,6-P Glyceraldehyde-3-P D-Glucano-d-lactano-6-P D-Glucanate-6-P D-Ribulose-5-P D-Xylose-5-P Glycerone-P ATP ATP acetyl phosphate Glycerate-1-3-P Glycerate-3-P Glycerate-2-P phosphoenol pyruvate pyruvate ATP Acetyl-CoA 2-Hydroxyethyl-ThPP Thiamine diphosphate Lipoamide-E Dihydrolipodamide-E S-Aceyl dihydrolipoamide-E Acetaldehyde Ethanol L-lactate acetyl phosphate Acetate ATP ADP ADP ADP ADP ATP ADP ATP ATP ADP ADP ADP ADP SGO_1144 glcK SGO_1144 glcK SGO_0505 SGO_0049 galM SGO_0154 pgi SGO_0154 pgi SGO_0154 pgi SGO_1113 fruA SGO_1755 scrK SGO_1340 pfk SGO_0813 fbp SGO_1745 fba SGO_1112 fruB SGO_0762 tpiA SGO_0207 gap SGO_0209 pgk SG O_0391, SGO_0392, SGO_0704 gpmA, SGO_0754 SGO_1426 eno SGO_1339 pyk SGO_1132 aco, SGO_1133 acoA SGO_1130 dld SGO_1132 aco, SGO_1133 acoA SGO_1131 sucB SGO_0292 spxB SGO_1916 ackA SGO_1369 ,hicdh, SGO_ 1232 ldh SGO_0247 pfl, SGO_1788 pfl SGO_0788 zwf SGO_1422 hypothetical pgls SGO_0503 gnd SGO_0198 rpe SGO_0312 xfp SGO_1219 pta SGO_0113 acdH SGO_0113 acdH SGO_0372 Malate CoA Formate Figure5 SgPgvsSgFnEnergymetabolismandendproducts. Labels,abbreviationsandcolorcodingasdescribedforFigure2,forthe S. gordonii with P.gingivalis comparisonto S.gordonii with F.nucleatum Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page7of23 http://www.biomedcentral.com/1471-2180/12/211

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actinomycetemcomitans pathogenicitythroughmetabolic cross-feedingofL-lactate[7]. Figures2,3,4,5,6,7showtheendproductsofSgenergymetabolism,formate,acetate,L-lactate,andethanol. ComparedtoSgalone,SgFnshowedareductioninthe proteinsforethanolandacetateproductionandanincreaseinthoseforlactate(Figure2).SgPgandSgPgFn alsohadanincreaseinproteinsforlactateproduction andadecreaseintheethanolpathway(Figures3,4). However,neitherwasasstrongasthatseeninSgFn (Figure5).Incontrast,SgPgandSgPgFndisplayedan increaseratherthanadecreaseinthepathwaytoacetate (Figures3,4).Thesecombinationsalsoshowedadecreaseintheenzymefordecarboxylationofpyruvate thatproducesformateasabyproduct(Figures3,4). Overall,exposuretoPgcausedashiftawayfromethanolandformatetowardsacetateandlactate,whileSgFn shiftedawayfromacetateandethanolheavilytowards lactateformation.Whileanasaccharolyticorganismlike PgisunlikelytomakeuseofL-lactateitisinterestingto seeashiftinallthemixedculturestowardslactateproduction.Giventheincreased A.actinomycetemcomitans D-Glucose D-Fructose a-D-GlucoseB-D-Glucose ATP ATP a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P Fructose-1-P B-DFructose-1,6-P Glyceraldehyde-3-P D-Glucano-d-lactano-6-P D-Glucanate-6-P D-Ribulose-5-P D-Xylose-5-P Glycerone-P ATP ATP acetyl phosphate Glycerate-1-3-P Glycerate-3-P Glycerate-2-P phosphoenol pyruvate pyruvate ATP Acetyl-CoA 2-Hydroxyethyl-ThPP Thiamine diphosphate Lipoamide-E Dihydrolipodamide-E S-Aceyl dihydrolipoamide-E Acetaldehyde Ethanol L-lactate acetyl phosphate Acetate ATP ADP ADP ADP ADP ATP ADP ATP ATP ADP ADP ADP ADP SGO_1144 glcK SGO_1144 glcK SGO_0505 SGO_0049 galM SGO_0154 pgi SGO_0154 pgi SGO_0154 pgi SGO_1113 fruA SGO_1755 scrK SGO_1340 pfk SGO_0813 fbp SGO_1745 fba SGO_1112 fruB SGO_0762 tpiA SGO_0207 gap SGO_0209 pgk SG O_0391, SGO_0392, SGO_0704 gpmA, SGO_07 54 SGO_1426 eno SGO_1339 pyk SGO_1132 aco, SGO_1133 acoA SGO_1130 dld SGO_1132 aco, SGO_1133 acoA SGO_1131 sucB SGO_0292 spxB SGO_1916 ackA SGO_1369 ,hicdh, SGO_ 1232 ldh SGO_0247 pfl, SGO_1788 pfl SGO_0788 zwf SGO_1422 hypothetical pgls SGO_0503 gnd SGO_0198 rpe SGO_0312 xfp SGO_1219 pta SGO_0113 acdH SGO_0113 acdH SGO_0372 Malate CoA Formate Figure6 SgPgFnvsSgFnEnergyMetabolismandEndProducts. Labels,abbreviationsandcolorcodingasdescribedforFigure2,forthe S. gordonii with P.gingivalis and F.nucleatum comparisonto S.gordonii with F.nucleatum Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page8of23 http://www.biomedcentral.com/1471-2180/12/211

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pathogenicityinSgco-culturefromL-lactatetransfer [7],shiftingtohigherlactateproductionmightbeatypicalSgresponsetothepresenceofotheroralspecies. Thepresenceofexcesssugarsandrapidgrowthhave alsobeenassociatedwithashifttowardslactatein S. mutans [18].However,asmentionedabove,thecultureswerenotprovidedwithexogenousnutrientsso thelikelihoodofrapidgrowthunderourexperimental conditionswaslow.Hence,theseresultsaremoreconsistentwith S.gordonii utilizingthepresenceofother organismsasaproxyfornutritionalavailabilityin developingplaque.AdhesionProteinsthatenhancebacterialbindingtodentalsurfaces andotherbacteriaareimportantfortheformationofdentalplaque[19].Table3showstheproteinratiosforadhesionproteinsacrossthesixcomparisons.Almostall detectedproteinsshowedstatisticallysignificantdecreases comparedtolevelsinSgalone.Thisincludesamylase bindingprotein,SGO_2105,whichplaysanimportantrole inplaqueformationbybindingsalivaryamylase[20]. Streptococcalsurfaceproteins(Ssp)AandB,SGO_0210 andSGO_0211,areimportantforbindingPgviatheMfa1 receptor[5].Table3showsthatSspAisdowninSgPgvs D-Glucose D-Fructose a-D-GlucoseB-D-Glucose ATP ATP a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P Fructose-1-P B-DFructose-1,6-P Glyceraldehyde-3-P D-Glucano-d-lactano-6-P D-Glucanate-6-P D-Ribulose-5-P D-Xylose-5-P Glycerone-P ATP ATP acetyl phosphate Glycerate-1-3-P Glycerate-3-P Glycerate-2-P phosphoenol pyruvate pyruvate ATP Acetyl-CoA 2-Hydroxyethyl-ThPP Thiamine diphosphate Lipoamide-E Dihydrolipodamide-E S-Aceyl dihydrolipoamide-E Acetaldehyde Ethanol L-lactate acetyl phosphate Acetate ATP ADP ADP ADP ADP ATP ADP ATP ATP ADP ADP ADP ADP SGO_1144 glcK SGO_1144 glcK SGO_0505 SGO_0049 galM SGO_0154 pgi SGO_0154 pgi SGO_0154 pgi SGO_1113 fruA SGO_1755 scrK SGO_1340 pfk SGO_0813 fbp SGO_1745 fba SGO_1112 fruB SGO_0762 tpiA SGO_0207 gap SGO_0209 pgk SG O_0391, SGO_0392, SGO_0704 gpmA SGO_07 54 SGO_1426 eno SGO_1339 pyk SGO_1132 aco, SGO_1133 acoA SGO_1130 dld SGO_1132 aco, SGO_1133 acoA SGO_1131 sucB SGO_0292 spxB SGO_1916 ackA SGO_1369 ,hicdh, SGO_ 1232 ldh SGO_0247 pfl, SGO_1788 pfl SGO_0788 zwf SGO_1422 hypothetical pgls SGO_0503 gnd SGO_0198 rpe SGO_0312 xfp SGO_1219 pta SGO_0113 acdH SGO_0113 acdH SGO_0372 Malate CoA Formate Figure7 SgPgFnvsSgPgEnergymetabolismandendproducts. Labels,abbreviationsandcolorcodingasdescribedforFigure2,forthe S. gordonii with P.gingivalis and F.nucleatum comparisonto S.gordonii with P.gingivalis Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page9of23 http://www.biomedcentral.com/1471-2180/12/211

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SgandSspBisdowninSgFnvsSg.CellsurfaceproteinCshA,SGO_0854,hasbeenshowntobeimportantinbindingtheoralmicrobes Actinomyces naeslundii and Streptococcusoralis aswellasthehost adhesiontargethumanfibronectin[21].CshAwas downinSgFn,SgPg,andSgPgFncomparedtoSg. MutationsinCshB,SGO_1148,alsodecreasedbindingbutreducedCshAlevelsandthatmayaccount forthebindingdifferences[21].CshBwasdownin SgFnvsSgandundetectedintheothersamples.In Phosphoenolpyruvate Pyruvate SGO_1555 ptsI a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P SGO_0154 pgi B-D Fructose-1,6-P a-D-Glucose-1-P Mannose Fructose Fructose-1-P Mannose-6-P SGO_1113 fruA SGO_0045, SGO_1680, SGO_1891 manY SGO_0044, SGO_0047, SGO_1679, SGO_1892 manX SGO_0046, SGO_1681 manZ SGO_1890 levG D-Fructose SGO_1113 fruA Fructan SGO_0385 D-Mannose-1-P SGO_1215 manB SGO_1749 manA SGO_1112 fruB SGO_1755 scrK Trehalose Trehalose-6-P SGO_0505, SGO_1653 treP SGO_1652 a-D-Glucose B-D-Glucose SGO_1144 glcK SGO_0049 galM SGO_1144 glcK Glucose Maltose Maltose-6-P SGO_0505 SGO_0505 unknownMaltoseSGO_0105 malQ Galactan D-Galactose Lactose a-D-Galactose-1-P SGO_0932 galK UDP-galactose SGO_0933 galT UDP-glucose SGO_0163 galU SGO_0934 galE-2, SGO_1012 galE-1, SGO_2022 unknown SGO_0043 -gal SGO_1486 -galGlycolysisD-sorbitol SGO_0440 SGO_0043 -gal SGO_1486 -gal Figure8 SgFnvsSgSugartransport. Thediagramshowsaschematicofsugartransportacrossthecellmembraneandreactionsfeedinginto theglycolysispathwayforSgforthe S.gordonii with F.nucleatum samplescomparedto S.gordonii .Proteinscatalyzingeachstepareshownby their S.gordonii SGOdesignation,someincludeaproteinabbreviation.Thepurpleboxrepresentstheglycolysispathwayandthebluelinethe cellmembrane.Rednumbersindicateincreasedlevelsinthefirstconditioncomparedtothesecondcondition,greendecreasedlevels,yellowno statisticalchange,andblackundetectedinatleastoneoftheconditions.Abbreviations: -gal: -galactosidase;fruA:fructosespecific phosphoenolpyruvate-dependentphosphotransferasesystemscomponentII;fruB:1-phosphofructokinase;galE-1:UDP-glucose4-epimerase;galE 2:UDP-glucose4-epimerase;galK:galactokinase;galM:aldose1-epimerase;galT:galactose-1-phosphateuridylytransferase;galU:UTP-glucos e-1phosphateuridylytransferase;glcK:glucokinase;malQ:4-alpha-glucanotransferase;manA:mannose-6-phosphateisomerase;manB: phosphomannomutase;manX:mannose-specificphosphoenolpyruvate-dependentphosphotransferasesystemscomponentIIB;manY:mannosespecificphosphoenolpyruvate-dependentphosphotransferasesystemscomponentIIC;manZ:mannose-specificphosphoenolpyruvate-dependent phosphotransferasesystemscomponentIID;ptsI:phosphoenolpyruvate-proteinphosphotransferase;scrK:fructokinase;treP:trehalose phosphoenolpyruvate-dependentphosphotransferasesystemscomponentII. Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page10of23 http://www.biomedcentral.com/1471-2180/12/211

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contrast,thefibronectinbindingproteinSGO_0855 showednostatisticaldifferencesbetweensamples. Streptococcalhemagglutinin,HsaSGO_0966,which bindstoerythrocytesandplaysaroleininfective endocarditis[22],wasdown-regulatedintheone comparisonwhereitwasdetected,SgFnvsSg. WhiletheshortfimbriaeofPghavebeenfoundto bindtoSgviaSspB,thelongfimbriaebindtostreptococciusingthemetabolicproteinglyceraldehyde3-phosphatedehydrogenase,Gap[23].SgGAPDH, SGO_0207,showsincreasedproteinlevelswithSgFn, SgPg,andSgPgFnvsSgandmayindicateanincreased needforGapmediatedinter-speciesadhesioninthe mixedsamples.However,Gapfunctionsnotonlyas anadhesinbutisalsopartoftheglycolysispathway. Therestofthepathwayshowedincreasedlevelsand theincreasesinGAPDHmayberelatedtoitsmetabolicfunctionratherthanbinding.Thiswouldbe consistentwiththereducedlevelsseenwiththeother adhesins. Despitetheinconsistentdetectionofmanyofthe knownadhesins,overall,adhesionproteinlevelsappeartobedowninthemixedspeciessamples.This isconsistentwithearlierstudiesshowingthatafter initialcontact,organismsincommunitiesdownregulateadhesinexpression[24]. Phosphoenolpyruvate Pyruvate SGO_1555 ptsI a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P SGO_0154 pgi B-D Fructose-1,6-P a-D-Glucose-1-P Mannose Fructose Fructose-1-P Mannose-6-P SGO_1113 fruA SGO_0045, SGO_1680, SGO_1891 manY SGO_0044, SGO_0047, SGO_1679, SGO_1892 manX SGO_0046, SGO_1681 manZ SGO_1890 levG D-Fructose SGO_1113 fruA Fructan SGO_0385 D-Mannose-1-P SGO_1215 manB SGO_1749 manA SGO_1112 fruB SGO_1755 scrK Trehalose Trehalose-6-P SGO_0505, SGO_1653 treP SGO_1652 a-D-Glucose B-D-Glucose SGO_1144 glcK SGO_0049 galM SGO_1144 glcK Glucose Maltose Maltose-6-P SGO_0505 SGO_0505 unknownMaltoseSGO_0105 malQ Galactan D-Galactose Lactose a-D-Galactose-1-P SGO_0932 galK UDP-galactose SGO_0933 galT UDP-glucose SGO_0163 galU SGO_0934 galE-2, SGO_1012 galE-1, SGO_2022 unknown SGO_0043 -gal SGO_1486 -galGlycolysisD-sorbitol SGO_0440 SGO_0043 -gal SGO_1486 -gal Figure9 SgPgvsSgSugartransport. Labels,abbreviationsandcolorcodingasdescribedforFigure8,forthe S.gordonii with P.gingivalis comparisonto S.gordonii Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page11of23 http://www.biomedcentral.com/1471-2180/12/211

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SurfaceproteinsandcellwallsynthesisInadditiontoproteinswithknownfunctionsinbinding,manyproteinspredictedtobelocatedonthecell surfacewerefoundatsignificantlydifferentlevelsin thecommunitysamples.Table4showssignificantdifferences,mostlylower,inmanyofthedetectedsurfaceproteinsbetweenthecommunitysamplesandSg alone.Therearealsonumerouschangesinproteins predictedtoparticipateincellwallbiosynthesis (Table4).ComparingcommunitytoSgsamplesboth increasedanddecreasedproteinlevelsareseen, thoughSgPgFnvsSgwasskewedtowardsreduced levels.Proteinsforsynthesisandattachmentofthe cellmembranesugarrhamnoseshowaninteresting pattern.Theresultsfortheseproteinsareshownin Table5.RhamnosesynthesizingproteinsshowgenerallyincreasedlevelswithSgFn,SgPg,andSgPgFn comparedtoSgalonewithevenhigherlevelsinthe FncommunitythanwithPgorPgFn.However,the rhamnosyltransferase,SGO_1026,whichwouldattach rhamnosetothecellmembrane,isdowncompared toSg.Onepossibleexplanationisashiftbetweendifferentrhamnosyltransferases.Sghasthree,SGO_1021, SGO_1022,andSGO_1026.Wefailedtodetect SGO_1021orSGO_1022inallbuttheSgsinglespeciescontrols. Phosphoenolpyruvate Pyruvate SGO_1555 ptsI a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P SGO_0154 pgi B-D Fructose-1,6-P a-D-Glucose-1-P Mannose Fructose Fructose-1-P Mannose-6-P SGO_1113 fruA SGO_0045, SGO_1680, SGO_1891 manY SGO_0044, SGO_0047, SGO_1679, SGO_1892 manX SGO_0046, SGO_1681 manZ SGO_1890 levG D-Fructose SGO_1113 fruA Fructan SGO_0385 D-Mannose-1-P SGO_1215 manB SGO_1749 manA SGO_1112 fruB SGO_1755 scrK Trehalose Trehalose-6-P SGO_0505, SGO_1653 treP SGO_1652 a-D-Glucose B-D-Glucose SGO_1144 glcK SGO_0049 galM SGO_1144 glcK Glucose Maltose Maltose-6-P SGO_0505 SGO_0505 unknownMaltoseSGO_0105 malQ Galactan D-Galactose Lactose a-D-Galactose-1-P SGO_0932 galK UDP-galactose SGO_0933 galT UDP-glucose SGO_0163 galU SGO_0934 galE-2, SGO_1012 galE-1, SGO_2022 unknown SGO_0043 -gal SGO_1486 -galGlycolysisD-sorbitol SGO_0440 SGO_0043 -gal SGO_1486 -gal Figure10 SgPgFnvsSgEnergymetabolismandendproducts. Labels,abbreviationsandcolorcodingasdescribedforFigure8,forthe S. gordonii with P.gingivalis and F.nucleatum comparisonto S.gordonii Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page12of23 http://www.biomedcentral.com/1471-2180/12/211

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TransportandexportAsmentionedabove,PTSsugartransportsystemsare almostallreducedinthemixedorganismsamples.The othertransportandexportproteinsarealsogenerally reducedinthemixedsamplesasshowninTable6. SomeexceptionsshowincreasescomparedtoSgalone andareshownindetailinTable7.Two,SGO_0006and SGO_2100,areABCtransporterproteinswithunknown substrates.SGO_1059isaphosphatetransportprotein showingsignificantlylowerlevelsinSgFnvsSgbut higherlevelswithSgPgorSgPgFn.Interestingly,the phosphatetransportsystemregulatoryprotein,SGO_1060, issignificantlydowninSgFnandSgPgFnimplyinganother levelofregulationforSGO_1059.Incontrasttothephosphatetransporter,thepredictedTrkpotassiumuptakesystemprotein,SGO_1666,isupinSgFnbutsignificantly reducedinSgPgFn. Thesignalrecognitionparticleprotein,FfhSGO_1123, isalsoincreasedinallofthemixedcommunities.Ffh bindstoprotein ’ ssignalsequenceswhentheyemerge fromtheribosomeandisnecessaryforefficientextracytoplasmicproteinexport.BothSecA,SGO_0415,the onlydetectedsecprotein,andSGO_0255,oneoftwo detectedsignalpeptidases,showedsignificantreduction inthemixedcommunities(Table7).SGO_1338,the otherdetectedsignalpeptidase,showedreducedlevels Phosphoenolpyruvate Pyruvate SGO_1555 ptsI a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P SGO_0154 pgi B-D Fructose-1,6-P a-D-Glucose-1-P Mannose Fructose Fructose-1-P Mannose-6-P SGO_1113 fruA SGO_0045, SGO_1680, SGO_1891 manY SGO_0044, SGO_0047, SGO_1679, SGO_1892 manX SGO_0046, SGO_1681 manZ SGO_1890 levG D-Fructose SGO_1113 fruA Fructan SGO_0385 D-Mannose-1-P SGO_1215 manB SGO_1749 manA SGO_1112 fruB SGO_1755 scrK Trehalose Trehalose-6-P SGO_0505, SGO_1653 treP SGO_1652 a-D-Glucose B-D-Glucose SGO_1144 glcK SGO_0049 galM SGO_1144 glcK Glucose Maltose Maltose-6-P SGO_0505 SGO_0505 unknownMaltoseSGO_0105 malQ Galactan D-Galactose Lactose a-D-Galactose-1-P SGO_0932 galK UDP-galactose SGO_0933 galT UDP-glucose SGO_0163 galU SGO_0934 galE-2, SGO_1012 galE-1, SGO_2022 unknown SGO_0043 -gal SGO_1486 -galGlycolysisD-sorbitol SGO_0440 SGO_0043 -gal SGO_1486 -gal Figure11 SgPgvsSgFnEnergymetabolismandendproducts. Labels,abbreviationsandcolorcodingasdescribedforFigure8,forthe S. gordonii with P.gingivalis comparisonto S.gordonii with F.nucleatum Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page13of23 http://www.biomedcentral.com/1471-2180/12/211

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butdidnotmakethestatisticalcutoff.Theimplication isthatthemixedcommunitieshadanincreaseinintegralmembraneproteins,primarilythoseprocessedby FfhandoftenSecAindependent,butadecreaseinperiplasmicandextracellularproteins,primarilythoseprocessedviathesecpathway[25]. Bacteriocins,toxinsthatkillorinhibitcloselyrelated species,mayexperienceincreasedexport.Thepredicted bacteriocintransportaccessoryprotein,SGO_1216, showedincreasedlevelsinallmixedcommunities.Bacteriocinproductioncouldbepartofastrategyadopted bySgtoinfluenceitsmixedspeciesenvironment, explainingtheincreaseinallmixedorganismsamples. However,noneoftheotherannotatedbacteriocinproteinsweredetected.Also,SGO_1216isnotassociated withtheotherbacteriocinproteinsandmaybeamisannotation.TranscriptionalregulationTable8summarizestheresultsforpredictedtranscriptionalregulators.Approximatelyathirdofthedetected regulatorsshowstatisticallyalteredlevelsinthemixed communities.Asubsetoftheregulatoryproteins,those discussedbelow,isshowninTable9.Mostoftheseproteinshaveonlyageneralpredictionoftranscriptional Phosphoenolpyruvate Pyruvate SGO_1555 ptsI a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P SGO_0154 pgi B-D Fructose-1,6-P a-D-Glucose-1-P Mannose Fructose Fructose-1-P Mannose-6-P SGO_1113 fruA SGO_0045, SGO_1680, SGO_1891 manY SGO_0044, SGO_0047, SGO_1679, SGO_1892 manX SGO_0046, SGO_1681 manZ SGO_1890 levG D-Fructose SGO_1113 fruA Fructan SGO_0385 D-Mannose-1-P SGO_1215 manB SGO_1749 manA SGO_1112 fruB SGO_1755 scrK Trehalose Trehalose-6-P SGO_0505, SGO_1653 treP SGO_1652 a-D-Glucose B-D-Glucose SGO_1144 glcK SGO_0049 galM SGO_1144 glcK Glucose Maltose Maltose-6-P SGO_0505 SGO_0505 unknownMaltoseSGO_0105 malQ Galactan D-Galactose Lactose a-D-Galactose-1-P SGO_0932 galK UDP-galactose SGO_0933 galT UDP-glucose SGO_0163 galU SGO_0934 galE-2, SGO_1012 galE-1, SGO_2022 unknown SGO_0043 -gal SGO_1486 -galGlycolysisD-sorbitol SGO_0440 SGO_0043 -gal SGO_1486 -gal Figure12 SgPgFnvsSgFnEnergymetabolismandendproducts. Labels,abbreviationsandcolorcodingasdescribedforFigure8,forthe S. gordonii with P.gingivalis and F.nucleatum comparisonto S.gordonii with F.nucleatum Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page14of23 http://www.biomedcentral.com/1471-2180/12/211

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Phosphoenolpyruvate Pyruvate SGO_1555 ptsI a-D-Glucose-6-P B-D-Glucose-6-P B-D-Fructose-6 -P SGO_0154 pgi B-D Fructose-1,6-P a-D-Glucose-1-P Mannose Fructose Fructose-1-P Mannose-6-P SGO_1113 fruA SGO_0045, SGO_1680, SGO_1891 manY SGO_0044, SGO_0047, SGO_1679, SGO_1892 manX SGO_0046, SGO_1681 manZ SGO_1890 levG D-Fructose SGO_1113 fruA Fructan SGO_0385 D-Mannose-1-P SGO_1215 manB SGO_1749 manA SGO_1112 fruB SGO_1755 scrK Trehalose Trehalose-6-P SGO_0505, SGO_1653 treP SGO_1652 a-D-Glucose B-D-Glucose SGO_1144 glcK SGO_0049 galM SGO_1144 glcK Glucose Maltose Maltose-6-P SGO_0505 SGO_0505 unknownMaltoseSGO_0105 malQ Galactan D-Galactose Lactose a-D-Galactose-1-P SGO_0932 galK UDP-galactose SGO_0933 galT UDP-glucose SGO_0163 galU SGO_0934 galE-2, SGO_1012 galE-1, SGO_2022 unknown SGO_0043 -gal SGO_1486 -galGlycolysisD-sorbitol SGO_0440 SGO_0043 -gal SGO_1486 -gal Figure13 SgPgFnvsSgPgEnergymetabolismandendproducts. Labels,abbreviationsandcolorcodingasdescribedforFigure8,forthe S. gordonii with P.gingivalis and F.nucleatum comparisonto S.gordonii with P.gingivalis Table3RegulationofadhesionproteinsProteinSgFnvsSgSgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg SGO_0210 1.0 5.4 nd 4.5 ndnd SGO_0211 4.1 ndndndndnd SGO_0854 2.7 5.3 5.4 2.6 2.7 0.1 SGO_0855 0.7 0.5nd0.3ndnd SGO_0966 1.3 ndndndndnd SGO_1148 2.7 ndndndndnd SGO_2105 1.9 6.9 6.4 5.0 4.40.6Bold:statisticallysignificantdifference,allratiosarelog2. nd:notdetectedinoneormoreofthecomparedsamples.Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page15of23 http://www.biomedcentral.com/1471-2180/12/211

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regulatoryfunction,thoughtheymaybeinterestingtargetsforfurtherinvestigation. Twoofthoseproteinswithfunctionalpredictions fromtheannotation,SGO_0237andSGO_0773,have homologytocatabolitecontrolproteinA,CcpA.CcpA isatranscriptionalregulatorprimarilyinvolvedincontrollingcarbonmetabolism,especiallycatabolicrepression[26],thougha ccpA mutantin S.mutans wasfound tohave60%impairmentinbiofilmformation[27]. SGO_0237showsincreasedlevelsinSgPgcomparedto SgbutSGO_0773showsdecreasedlevelsinallmixed communities(Table9).GiventhereductionseeninPTS sugartransportandtheformationofcommunities,a CcpAproteinwouldbeexpectedtobeincreasedacross allofthecommunities.Itisunlikelythatboth SGO_0237andSGO_0773arefunctioningasclassical CcpAregulatoryproteins.TheincreasedSGO_0237may betheactualcatabolitecontrolproteinAforSg.However,thePTStransportsystemsdonotseemtobe respondingtoatraditionalcatabolicrepressionandthe bindingproteinsthatplayanimportantroleinbiofilm formationaredownaswell.Aswiththebindingproteins,CcpAmayplayanearlyroleinbiofilmformation andbereducedat18hourswhenthesampleswerecollected.ItisalsopossiblethatdespitethehomologyneitherproteinactslikeCcpAinSg. SGO_1816encodesforScaR,amanganesedependent regulatorofahighaffinityABCmanganesetransporter, SGO_1800-1802[28].However,thenameScaactually referstostreptococcalcoaggregationadherencebecause oneoftheregulatedtransporterproteins,ScaA, SGO_1801,wasoriginallyidentifiedasanadhesinimportantforaggregationwith A.neaslundii [29].ScaA wasnotdetectedinanyofthesamples,thoughthatis notunusualforamembraneprotein,butScaRshowed increasedlevelsinSgFnwhiletheothermembersofthe operonwithScaA,SGO_1800andSGO_1802,showed reducedlevelsinallthemixedcommunities.Itseems unlikelythatSgisseeinghigherlevelsofmanganesein themixedcommunitiestoaccountfordown-regulation oftheABCtransporter.However,therearesomeindicationsthat,likethePTSsugartransporters,Sghasasecondmanganesetransportsystemdrivenbytheproton motiveforce[28].Thiswouldonceagainbeconsistent withalowpHenvironment.Also,weseeasignificant reductioninotheradhesinproteinsandtheScaoperon maybedown-regulatedtoreducetheadhesinScaA. SGO_1072andSGO_1073havehomologytothesensorandkinaseproteinsofthetwo-componentsignalingtransducingsystemCiaR-CiaHfrom S.pneumoniae [30]. In S.pneumoniae Ciahasbeenshowntoregulatea numberofgenesinvolvedinthebiochemicalmakeupof thecellwall,includingactivationofthegenesforD-alanylationoflipoteichoicacid, dlt .Detectionofthe regulatoryproteinCiaR,SGO_1072,waspoorandstatisticalsignificancecouldonlybecalculatedfortheSgFn Table4PredictedsurfaceandcellwallbiosynthesisproteinsCategoryChangeSgFnvs Sg SgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg OtherSurfaceProteinsaTotal271612171212 Unchanged164211911 Increase331210 Decrease899421 CellWallMetabolismbTotal362623292323 Unchanged16158171518 Increase1165400 Decrease9510885aCoversSGO_0004,0068,0208,0233,0388,0430,0455,0494,0502,0521,0707,0721,0825,0890,1069,1082,1110,1189,1347,1355,1381,1487,1651,18 98, 2004,2005,2082.bCoversSGO_0054,0056,0057,0327,0393,0515,0586,0631,0671,0672,0763,0804,0886,0948,0969,0975,1009,1010,1011,1013,1020,1025,1026,14 00, 1446,1447,1623,1624,1638,1676,1717,1768,1854,2010,2104,2037. Table5ProteinratiosforrhamnosesynthesisandattachmentProteinSgFnvsSgSgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg SGO_1009 2.11.51.1 0.6 0.9 0.4 SGO_1010 0.80.90.9 0.10.10 SGO_1011 2.41.2 0.6 1.2 1.7 0.5 SGO_1020 1.1 0.7 0.5 0.5 0.6 0.1 SGO_1026 1.9 2.2 3.2 0.2 1.3 1.0Bold:statisticallysignificantdifference,allratiosarelog2.Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page16of23 http://www.biomedcentral.com/1471-2180/12/211

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vsSgandSgPgvsSgFncomparisons.CiaRshowedasignificantincreaseinSgFnvsSgandadecreaseinSgPgvs SgFnimplyingalargeincreaseinthepresenceofFn. Thesensorkinase,SGO_1073,remainedstatisticallyunchanged.DespitethehighlevelsofCiaRinSgFntheDtl proteinsdidnotshowanycoherentchange.CiaRmay controladifferentsetofgenesinSgthan S.pneumoniae .Increasesintheamountsoftheregulatorprotein alsodonotnecessarilycauseregulatoryeffects.However, giventhechangestocellwallbiosynthesisproteinsitis interestingthatacellwallbiosyntheticregulatorshowed increasedlevelsinthepresenceofFn.Translation,ribosomalproteins,andtRNAsynthetasesInapreviousreporton P.gingivalis resultsfromthese sameexperimentswenotedthatPghadsignificant increasesintranslationalmachineryandribosomalproteinlevelsinacommunitywithSgandFn[11].Table10 showsasummaryofthetranslationalmachineryproteins,ribosomalandaccessoryproteins,andtRNA synthetasesforSg.Thetranslationalproteinsshowed someincreaseinthemixedcommunitieswithincreases inapproximatelyhalfofthedetectedproteins.SgFnvs Sgshowedonereducedprotein.Theribosomalproteins showedageneralincreasecomparedtoSgintheSgPg andSgPgFncommunities,againapproximatelyhalfof thedetectedproteins,withasmallnumbershowinga decrease.Incontrast,ribosomalproteinsinSgFnwere mostlyunchangedandmostofthechangedproteins showeddecreasedlevelscomparedtoSg.Similarresults wereseenwithtRNAsynthetaseswhereSgPgand SgPgFnshowedasignificantnumberofincreasedproteinsandfewornodecreasedproteins.SgFnshowed fewchangesoftRNAsynthetaseproteinlevels.Taken togetherthedataimplythattranslationisincreasedin Sg,similartowhatwasseenwithPgwhenexposedto SgFn,butonlyincommunitieswithPgorPgFnandnot withFnalone.HenceFn-Sginteractionsmaybeless synergisticthanoccurinthethreespeciescommunity.StressproteinsAsyntropiccommunitymightbeexpectedtobeless stressfultotheorganismsinvolvedduetosupportfrom otherspecies.OneresultofstressfulconditionsisDNA damage.Table11showsasummaryoftheDNArepair proteins.MostremainunchangedbutanumberofDNA repairproteinsshowreducedlevelsinthemixedcommunities,andintheSgPgandSgPgFncommunities comparedtoSgFn.Thereisonestrikingexceptionhowever,recombinaseA.RecA,SGO_2045,issignificantly downinSgFnbutupinSgPgandSgPgFncomparedto Sgalone(Table12).RecAisimportantforbothDNArecombinationandDNArepair.AnincreaseinRecAbut adecreaseinotherDNArepairproteinsmightindicate Table6Exportandnon-PTStransportproteinsaSgFnvsSgSgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg Total615845584544 Unchanged18156261938 Increased35424181 Decreased403835885aProteinscoveredSGO_0006,0015,0104,0255,0291,0352,0353,0398,0415,0457,0458,0460,0488,0505,0538,0548,0579,0750,0751,0767,0798,080 5,0808, 0851,0856,0955,0982,1024,1036,1037,1059,1060,1118,1123,1216,1338,1342,1458,1465,1572,1580,1605,1619,1626,1630,1634,1666,1708,17 09,1711, 1712,1713,1715,1716,1727,1728,1744,1763,1802,1936,2100. Table7ProteinratiosofselectedexportandtransportproteinsProteinSgFnvsSgSgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg SGO_00060.2 0.5 0.10.3 0.1 0..4 SGO_0255 1.9 1.6 2.2 0.3 0.2 0.1 SGO_0415 1.1 1.0 1.2 0.1 0.1 0.1 SGO_1059 1.60.50.82.12.40.3 SGO_1060 1.6 0.2 1.31.4 0.4 1.0 SGO_1123 1.01.21.00.3 0.0 0.2 SGO_1216 1.41.81.2 0.4 0.2 0.6 SGO_1338 0.7 3.0nd 2.3 ndnd SGO_1666 0.8 1.0 2.5 1.8 3.3 1.5 SGO_2100 0.92.62.73.53.6 0.1Bold:statisticallysignificantdifference,allratiosarelog2. nd:notdetectedinoneormoreofthecomparedsamples.Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page17of23 http://www.biomedcentral.com/1471-2180/12/211

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increasedhomologousrecombinationratherthanDNA repair.However,theproteinsassociatedwithbacterial competencethatwedetectedshowedmanysignificant reductionsinallmixedpellets(Table12). Sgalsohasanumberofproteinstodealwithoxidative stress.Mostoftheseproteinsshowedincreasedlevelsin themixedcommunitiescomparedtoSgalone(Table11). Thismayindicateanincreasedexposuretooxidative stress.However,whileSgcangrowaerobicallyandanaerobically,otheroralmicrobeslikePgarestrictanaerobes.Theincreasedproteinlevelsmayservethe purposeofprovidingoxygenprotectionforanaerobic communitymembers. Otherstressresponseproteinsincludechaperonessuch asGroES,SGO_1886,andproteasessuchasClpprotease P(ClpP),SGO_1632,thatdegradesmisfoldedproteins. Table11summarizesthechangesinotherstressproteins. Bothincreasedanddecreasedproteinlevelswereseenin allofthemultispeciessamplescomparedtotheSgcontrol, thoughtherewasageneraltrendtowardslowerlevelsin SgPgandevenlowerlevelsinSgPgFncomparedtoSgFn.ConclusionsBothdentalcariesandperiodontaldiseasearecommunity diseasesthatensuefromtheactionofcomplexmultispeciesbiofilms.Bothsynergisticandcompetitiveinteractions occuramongthebiofilmconstituentspecies,andbiofilm developmentisacomplexinteractioninvolvingattachment,recruitment,maturationanddetachment.Inthis studyweusedquantitativewholecellproteomicstocompareproteomesinasimplifiedmodelofdentalplaque, fromamono-cultureoftheearlycolonizer S.gordonii ,toa mixedcommunityof S.gordonii withtheintermediatecolonizer F.nucleatum ,toathree-speciesmodelnascent communityof S.gordonii F.nucleatum ,andthelatecolonizingperiodontalpathogen P.gingivalis S.gordonii displayedextensivechangesincommunitieswith F.nucleatum and P.gingivalis ,especially relatedtopathwaysformetaboliteutilizationandproduction.Theobservedchangeswerespeciesspecificdependingontheinteractionpartner.The P.gingivalis interactionappearedtobedominantasproteinlevelsin S.gordonii pairedwith P.gingivalis and F.nucleatum wereverysimilartothoseobservedwith P.gingivalis only.Allofthemixedspeciessamplesshowedevidence ofincreasedenergymetabolismanddecreasedPTS sugartransportcomparedto S.gordonii alone,consistent withhighmetaboliteavailabilityinmixedcommunities invivo.Therewasalsoashiftinendproductpathways forenergymetabolism,alteringtheproductsavailable from S.gordonii tothecommunityawayfromethanol andtowardsL-lactate.Suchashiftwouldbeconsistent withtheproductionofamoreacidicenvironment invivo. Whilecontactwithboth F.nucleatum and P.gingivalis resultedinextensivechangestotheproteomeof S.gordonii ,thedominant P.gingivalis interactionwasconsistentwithmodelswhereby P.gingivalis caninfluencethe Table8TranscriptionalRegulatorsaSgFnvsSgSgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg Total312414241414 Unchanged201710141014 Increased931210 Decreased243830aCoversproteinsSGO_0042,0100,0182,0202,0237,0252,0374,0400,0431,0484,0508,0535,0603,0755,0773,0779,0981,1072,1073,1228,1257,1281 ,1365, 1699,1731,1739,1792,1814,1816,1878,1993. Table9ProteinRatiosofSelectedTranscriptionalRegulatorsandRegulatedProteinsProteinSgFnvsSgSgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg SGO_0237 0.81.3 0.20.5 0.6 1.1 SGO_0773 2.3 2.4 2.5 0.1 0.2 0.1 SGO_1072 3.9 1.3*nd 2.6 ndnd SGO_1073 0.8 2.1nd 1.3ndnd SGO_1800nd 2.2 2.8 ndnd 0.7 SGO_1801ndndndndndnd SGO_1802 6.2 2.7 3.43.42.8 0.6 SGO_1816 0.9 0.1nd 0.7ndndBold:statisticallysignificantdifference,allratiosarelog2. nd:notdetectedinoneormoreofthecomparedsamples. *insufficientdetectiontodeterminesignificance.Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page18of23 http://www.biomedcentral.com/1471-2180/12/211

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virulencepropertiesofthemicrobialcommunityasa whole[31,32].Themixedcommunitiesshowedsignificantquantitativechangesin45to54%ofthedetected proteomecomparedtothe S.gordonii singleorganism control.The F.nucleatum or P.gingivalis interactions appearedtobequitedistinct,withapproximately48%of thedetectedproteomedifferingbetweenthetwotwospeciescommunities.However,onlyasmallquantitative relativeabundancedifference,11%ofthedetectedproteome,occurredbetweenpelletscontaining P.gingivalis andpelletswith P.gingivalis and F.nucleatum ,implying thatinthepresentexperimentalmodelthecontribution of P.gingivalis toanascentheterotypiccommunity supersedesthatofothergram-negativeanaerobes,such as F.nucleatum .MethodsBacteriaandcultureconditionsFusobacteriumnucleatum subsp. nucleatum ATCC 25586and Porphyromonasgingivalis ATCC33277were grownanaerobically(85%N2,10%H2,5%CO2)at37C intrypticasesoybrothsupplementedwith1mg/mlyeast extract,1 g/mlmenadioneand5 g/mlhemin(TSB).S. gordonii DL1wasgrownanaerobicallyat37CinToddHewittbroth(THB). Table10Translation,ribosomal,andtRNAsynthetaseproteinsSgFnvsSgSgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg TranslationaTotal101091099 Unchanged555559 Increased454320 Decreased100220 RibosomalProteinsbTotal585753575352 Unchanged432621272544 Increased5283028285 Decreased1022203 tRNASynthetasescTotal222221222121 Unchanged1899111317 Increased2139860 Decreased203324acoversSGO_0206,0321,0546,0761,1090,1154,1441,1617,1863,2000.bcoversSGO_0027,0183,0204,0205,0333,0355,0358,0359,0523,0573,0610,0719,0818,0820,0848,1033,1034,1191,1192,1234,1276,1316,1323,13 64, 1383,1451,1455,1456,1669,1824,1879,1881,1958,1960,1961,1966,1967,1968,1969,1970,1971,1973,1974,1975,1976,1977,1978,1979,1980,19 81,1982, 1983,1984,1985,1986,2001,2066,2088.ccoversSGO_0007,0174,0349,0407,0434,0568,0569,0639,0681,0753,0778,0859,0861,1293,1570,1683,1784,1851,1929,2058,2060,2062. Table11StressproteinsSgFnvsSgSgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg DNARepairaTotal211712171211 Unchanged131261189 Increased221110 Decreased635532 OxidativeStressbTotal766666 Unchanged113236 Increased653210 Decreased000220 OtherStressProteinscTotal181715171514 Unchanged9858810 Increased764200 Decreased236774aCoversSGO_0105,0171,0260,0286,0626,0685,0698,0830,1000,1038,1044,1250,1390,1413,1414,1531,1865,2045,2050,2053,2056.bCoversSGO_0263,0278,0749,1599,1685,1803,1990.cCoversSGO_0368,0401,0402,0404,0495.0688,0722,1140,1625,1632,1736,1862,1885,1886,1991,1998,2150.Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page19of23 http://www.biomedcentral.com/1471-2180/12/211

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ChemicalsHPLCgradeacetonitrilewasfromBurdick&Jackson (Muskegon,MI,USA);highpurityaceticacid(99.99%) andammoniumacetate(99.99%),fromAldrich (Milwaukee,WI,USA).Highpuritywaterwasgenerated withaNANOpureUVsystem(Barnstead,Dubuque, IA,USA).ProteomicsofmodelbacterialcommunitiesHarvestingandpelletingofbacteria,proteomicanalysis,massspectrometryandstatisticalmethodswere handledasdescribedinKuboniwa etal. [11].Inbrief, bacteriawereculturedtomid-logphase,harvestedby centrifugationandresuspendedinpre-reducedPBS (rPBS).1x109cellsof S.gordonii weremixedwithan equalnumberof P.gingivalis F.nucleatum ,orbothas combinationsofthespecies. S.gordonii cellsalonewere alsousedasacontrol.Twoindependentbiologicalreplicatesfromseparateexperimentscomprisedofatleasttwo technicalreplicateswereanalyzed.Bacteriawerecentrifugedat3000gfor5min,andpelletedmixturesofbacteria wereheldin1mlpre-reducedPBSinananaerobicchamberat37Cfor18h[10].Bacterialcellswerelysedinresuspensionbuffer(15mMTrisHClpH9.5,0.02%RapigesttmWaters,Milford,MA)inaboilingwaterbathfollowedby sonicationandbeadbeatingandproteinsweredigested withtrypsinthenfractionatedintofivepre-fractions[33]. The2DcapillaryHPLC/MS/MSanalyseswereconducted onaThermoLTQmassspectrometer(ThermoFisher Corp.SanJose,CA,USA).Peptideswereelutedwitha sevenstepsaltgradient(0,10,25,50,100,250and 500mMammoniumacetate)followedbyanacetonitrile gradientelution(SolventA:99.5%water,0.5%aceticacid. SolventB:99.5%acetonitrile,0.5%aceticacid).TheMS1scanrangeforallsampleswas400 – 2000 m/z .EachMS1scanwasfollowedby10MS2scansinadatadependent mannerforthe10mostintenseionsintheMS1scan.DefaultparametersunderXcalibur1.4dataacquisitionsoftware(ThermoFisher)wereused,withtheexceptionofan isolationwidthof3.0 m/z unitsandnormalizedcollision energyof40%.DataprocessingandproteinidentificationDataprocessingwashandledasdescribedinKuboniwa etal. [11].Inbrief,rawdataweresearchedbySEQUEST [34]againstaFASTAproteinORFdatabaseconsisting ofthe P.gingivalis W83(2006,TIGR-CMR[35])[GenBank:AE015924], S.gordonii ChallisNCTC7868(2007, TIGR-CMR[36])[GenBank:CP00725.1], F.nucleatum ATCC25586(2002,TIGR-CMR[37])[GenBank: AE009951.1],bovine(2005,UCSantaCruz),nrdb humansubset(NCBI,asprovidedwithThermoBioworksver.3.3)andtheMGC(MammalianGenecollection,2004curation,NIH-NCI[38])concatenatedwith thereversedsequences.Thereversedsequenceswere usedforpurposesofcalculatingaqualitativeFDRusing thepublishedmethod[39,40].TheSEQUESTpeptide levelsearchresultswerefilteredandgroupedbyprotein usingDTASelect[41],theninputintoaFileMakerscript developedin-house[42,43]forfurtherprocessing,includingpeaklistgeneration.Onlypeptidesthatwere uniquetoagivenORFwereusedinthecalculations,ignoringtrypticfragmentsthatwerecommontomore thanoneORFormorethanoneorganism,orboth.The qualitativepeptidelevelFDRwascontrolledtoapproximately5%forallconditionsbyselectingaminimum non-redundantspectralcount(uniquepeptide)cut-off numberappropriatetothecomplexityofeachcondition. Usingourmethods,thisimpliesaproteinlevelqualitativeFDRintherangeofapproximately0.01to2%,dependingonthespecificexperiment.Aminimumof threeuniquepeptideswereusedforanyqualitativeproteinidentification.Substitutionofadatabasebasedon P. gingivalis 33277[GenBank:AP009380]ratherthanW83 hadnosubstantiveeffectonthecalculations[44],sothe originalW83entrieswereretainedinthedatabasefor purposesoftheworkdescribedhere.ProteinabundanceratiocalculationsProteinrelativeabundanceswereestimatedonthebasis ofspectralcountvaluesforproteinsmeetingthe requirementsforqualitativeidentificationdescribed above[42,43].Forspectralcounts,theredundant Table12RecAandcompetenceproteinsProteinSgFnvsSgSgPgvsSgSgPgFnvsSgSgPgvsSgFnSgPgFnvsSgFnSgPgFnvsSgPg SGO_0200 1.4 1.2 1.80.3 0.3 0.6 SGO_0981 1.1 0.8nd0.3Ndnd SGO_1924nd 2.0 2.5 ndNd 0.5 SGO_2045 2.30.80.93.23.2 0.1 SGO_2097nd 5.5 6.6 ndNd 1.1 SGO_2145nd 0.3 0.3 ndNd0.0 SGO_2146nd 1.7 2.7ndNd 1.0Bold:statisticallysignificantdifference,allratiosarelog2. nd:notdetectedinoneormoreofthecomparedsamples.Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page20of23 http://www.biomedcentral.com/1471-2180/12/211

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numbersofpeptidesuniquelyassociatedwitheachORF weretakenfromtheDTAselectfiltertable(t=0).Spectralcountingisafrequencymeasurementthathasbeen demonstratedintheliteraturetocorrelatewithprotein abundance[45].Tocalculateproteinabundanceratios,a normalizationschemewasappliedsuchthatthetotal spectralcountsforall S.gordonii proteinsineachconditionweresetequalforeachcomparison.Thenormalized dataforeachabundanceratiocomparisonwastestedfor significanceusingaglobalpaired t -testforeachcondition,thedetailsofwhichhavebeenpublishedforthis typeofproteomicsdatainwhichallbiologicalreplicates arecomparedagainsteachother[33,46],seealsotheexplanatorynotesinKuboniwa etal .[11].Thetestingprocedureweighsdeviationfromthenullhypothesisofzero abundancechangeandrandomscatterinthedatatoderiveaprobabilityor p -valuethattheobservedchangeis arandomevent,i.e.thatthenullhypothesisofnoabundancechangeistrue.Eachhypothesistestgenerateda p -valuethatinturnwasusedtogeneratea q -valueas described[42,47],usingtheRpackageQVALUE[48]. The q -valueinthiscontextisameasureofquantitative FDR[49]thatcontainsacorrectionformultiplehypothesistesting.A q cut-offvalueof0.005wasusedforall ratiosreportedintherelativeabundancetablesshownin Additionalfiles1,2,3,4,5,6,7.AllstatisticalcalculationsweredoneusingR(Ver.2.5.0).Onlyproteinswith dataconsistingofconfirmedhighscoringMS2mass spectra(highscoringqualitativedatabasematchesas describedabove)presentinboththenumeratoranddenominatoroftheabundanceratiocomparisonwere listedassignificantlychangedintherelativeabundance datatables(seeAdditionalfiles1,2,3,4,5,6,7).OntologyanalysisAnoveralllistofdetectedproteins,aswellaslistsofproteinsthatshowedincreasedordecreasedlevelsinthe communitycomparisons,werepreparedusingEntrezgene identifiers.Ontologyanalyseswerethenconductedusing theDAVID[50]functionalannotationclusteringfeature withthedefaultdatabases.Bothincreasedanddecreased proteinlevellistswereanalyzedusingtheoveralllistof detectedproteinsasthebackground.PotentiallyinterestingclustersidentifiedbyDAVIDwerethenexamined manually.ConfocalmicroscopyS.gordonii stainedwithhexidiumiodide15 gml-1, (MolecularProbes,Carlsbad,CA), F.nucleatum stained5(and6-)carboxyfluorescein(4 gml-1,MolecularProbes) and P.gingivalis (2x108cellsofeachspecies)wereadded together,centrifugedandincubatedunderanaerobicconditionsfor18hbeforeremovalofthesupernatantandgentle re-suspensionofthecells.Thecellsuspension(0.5ml)was addedtoaglasscoverslipbeforefixingwith4%paraformaldehyde.Detectionof P.gingivalis wasachievedusinga specificanti-wholecell P.gingivalis antibodyandantirabbitalexa547(MolecularProbes)conjugatedsecondary. CoverslipswereimagedusinganOlympusFV500laser scanningconfocalmicroscope.AseriesofXYZimage stacksweredigitallyreconstructedusingVolocityimage analysisprogram(Improvision,Waltham,MA).AdditionalfilesAdditionalfile1: Summary. Thisfilecontainsashortsummaryofall therelativeabundanceratiosmentionedinthisreport.Priorto permanentarchivingatJGI(http://www.jgi.doe.gov/)andLANL(http:// semiglobe.lanl.gov/)withthemassspectraldatainXMLcompatible format,summariesoftheproteinidentificationsintheformoftabdelimitedtextfileswillbeavailableonaUniversityofWashingtonserver (http://depts.washington.edu/mhlab/),ratherthanontheBMC Microbiologywebsiteduetotheirlargesize.Requestapasswordfrom thecorrespondingauthor.ThesefilesincludedetailssuchasSEQUEST scores,peptidesequence,percentageofpeptidecoveragebyobserved ionsintheCIDspectrum,spectralcounts,andotherinformationatthe individualpeptideandproteinlevelascalculatedusingDTASelect[41]. Spectralcountsandcoverageinformationforeachproteincanalsobe foundinthefileslistedbelow.Ratiosforproteincomparisonswith statisticallyincreasedlevelsareshowninredhighlight,ratiosfor statisticallydecreasedlevelsareshowningreenhighlight.Thepalered andgreenhighlightsindicatethe q -valuesforstatisticallyincreasedor decreasedlevelsrespectively. Additionalfile2: SgFn_vs_Sg. Amoredetailedpresentationofthe relativeabundanceratiosforthecomparisonofSgFnandtheSg controls,includingbothrawandnormalizedspectralcounts.Redand greenhighlightsareusedasinAdditionalfile1. Additionalfile3: SgPg_vs_Sg. Amoredetailedpresentationofthe relativeabundanceratiosforthecomparisonofSgPgandtheSg controls,includingbothrawandnormalizedspectralcounts.Redand greenhighlightsareusedasinAdditionalfile1. Additionalfile4: SgPgFn_vs_Sg. Amoredetailedpresentationofthe relativeabundanceratiosforthecomparisonofSgPgFnandtheSg controls,includingbothrawandnormalizedspectralcounts.Redand greenhighlightsareusedasinAdditionalfile1. Additionalfile5: SgPg_vs_SgFn. Amoredetailedpresentationofthe relativeabundanceratiosforthecomparisonofSgPgandSgFn, includingbothrawandnormalizedspectralcounts.Redandgreen highlightsareusedasinAdditionalfile1. Additionalfile6: SgPgFn_vs_SgFn. Amoredetailedpresentationof therelativeabundanceratiosforthecomparisonofSgPgFnandSgFn, includingbothrawandnormalizedspectralcounts.Redandgreen highlightsareusedasinAdditionalfile1. Additionalfile7: SgPgFn_vs_SgPg. Amoredetailedpresentationof therelativeabundanceratiosforthecomparisonofSgPgFnandSgPg, includingbothrawandnormalizedspectralcounts.Redandgreen highlightsareusedasinAdditionalfile1. Additionalfile8: Coverage. Coveragestatisticsforindividualproteins basedonrecoveredtrypticfragmentsandtheinferredsequencesfrom theannotatedgenomefor S.gordonii [36].Grayshadingindicatesthe percentageoftheproteincoveredbythedetectedpeptides.Black shadingindicatestheundetectedpercentage. Additionalfile9: Geneplot_SgPgFn_vs_Sg. Agenomicplotofalldata collectedfor S.gordonii proteinrelativeabundancecalculationsusedin thecomparisonofSgPgFnandtheSgcontrols.Thecolorcodeforeach SGOnumber[36]followsthatusedinthedatatables(seeAdditionalfiles 1,2,3,4,5,6,7),wheredatawasacquired.ORFscodedblackwereeitherHendrickson etal.BMCMicrobiology 2012, 12 :211 Page21of23 http://www.biomedcentral.com/1471-2180/12/211

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notusedintheannotationornotrypticfragmentswereobserved.Grey indicatesqualitativedetectiononly. Additionalfile10: Regressplots.pdf. XYregressionplots demonstratingthereproducibilityofthespectralcountingmass spectrometrydataforthetechnicalandbiologicalreplicates,withan explanatorynote. Abbreviations ATCC:Americantypeculturecollection;DAVID:Databaseforannotation, visualizationandintegrateddiscovery;FDR:Falsediscoveryrate; Fn: Fusobacteriumnucleatum ;LANL:LosAlamosNationalLaboratory; MS:Massspectrometry;ORF:Openreadingframe;Pg: Porphyromonas gingivalis ;PTS:Phosphoenolpyruvatedependentphosphotransferasesystem; Sg: Streptococcusgordonii ;TIGR-CMR:TheInstituteforGenomicResearch ComprehensiveMicrobialResource,nowpartoftheJ.CraigVenterInstitute. Competinginterests Theauthorsdeclarethattheyhavenocompetinginterests. Authors ’ contributions ELHcalculatedtheproteinabundanceratios,abundancechangestatistics, andperformedthepathwayandontologyanalyses.TWperformedthemass spectrometrymeasurements.BCDandSEWperformedinvitroexperiments. CJWperformedtheconfocalmicroscopy.MHandRJLconceivedthe experiments.ELH,MHandRJLwrotethemanuscript.Allauthorsreadand approvedthemanuscript. Acknowledgements ThisworkwassupportedbytheNIHNIDCRundergrantsDE014372, DE12505andDE11111.AdditionalfundingwasprovidedbytheUWOffice ofResearch,CollegeofEngineeringandtheDepartmentofChemical Engineering.WethankQiangweiXiaandFredTaubfortheFileMaker database,DavidA.C.Beckforhelpwiththecomputations. Authordetails1DepartmentofChemicalEngineering,UniversityofWashington,Box 355014,Seattle,WA98195,USA.2DepartmentofMicrobiology,Universityof Washington,Box357242,Seattle,WA98195,USA.3DepartmentofOral Biology,UniversityofFlorida,Gainesville,FL32610,USA.4CenterforOral HealthandSystemicDisease,UniversityofLouisville,Louisville,KY40292, USA. Received:15May2012Accepted:17September2012 Published:18September2012 References1.NyvadB,KilianM: Microbiologyoftheearlycolonizationofhuman enamelandrootsurfacesinvivo. ScandJDentRes 1987, 95: 369 – 380. 2.KolenbranderPE,LondonJ: Adheretoday,heretomorrow:oralbacterial adherence. JBacteriol 1993, 175: 3247 – 3252. 3.BradshawDJ,MarshPD: AnalysisofpH-DrivenDisruptionofOral MicrobialCommunitiesinvitro. CariesRes 1998, 32: 456 – 462. 4.KolenbranderPE,AndersenRN,MooreLV: Coaggregationof Fusobacterium nucleatum Selenomonasflueggei Selenomonasinfelix Selenomonas noxia ,and Selenomonassputigena withstrainsfrom11generaoforal bacteria. InfectImmun 1989, 57: 3194 – 3203. 5.ParkY,SimionatoMR,SekiyaK,MurakamiY,JamesD,ChenW,HackettM, YoshimuraF,DemuthDR,LamontRJ: ShortFimbriaeof Porphyromonas gingivalis andTheirRoleinCoadhesionwith Streptococcusgordonii Infect Immun 2005, 73: 3983 – 3989. 6.PeriasamyS,KolenbranderPE: Mutualisticbiofilmcommunitiesdevelop with Porphyromonasgingivalis andinitial,early,andlatecolonizersof enamel. JBacteriol 2009, 191: 6804 – 6811. 7.RamseyMM,RumbaughKP,WhiteleyM: MetaboliteCross-Feeding EnhancesVirulenceinaModelPolymicrobialInfection. PLoSPathogens 2011, 7: e1002012. 8.LoescheWJ: Roleof Streptococcusmutans inHumanDentalDecay. MicrobiolRev 1986, 50: 353 – 380. 9.deSoetJJ,NyvadB,KilianM: Strain-RelatedAcidProductionbyOral Streptococci. CariesRes2000 1999, 34: 486 – 490.10.MerrittJ,KrethJ,ShiW,QiF: LuxScontrolsbacteriocinproductionin Streptococcusmutans throughanovelregulatorycomponent. Mol Microbiol 2005, 57: 960 – 969. 11.KuboniwaM,HendricksonEL,XiaQ,WangT,XieH,HackettM,LamontRJ: Proteomicsof Porphyromonasgingivalis withinamodeloralmicrobial community. BMCMicrobiol 2009, 9: 98. 12.KuboniwaM,LamontRJ: Subgingivalbiofilmformation. Periodontol 2010, 52: 38 – 52. 13.KuramitsuHK,HeX,LuxR,AndersonMH,ShiW: Interspeciesinteractions withinoralmicrobialcommunities. MicrobiolMolBiolRev 2007, 71: 653 – 670. 14.KolenbranderPE,PalmerRJJr,PeriasamyS,JakubovicsNS: Oral multispeciesbiofilmdevelopmentandthekeyroleofcell-celldistance. NatRevMicrobiol 2010, 8: 471 – 480. 15.JenkinsonHF,LamontRJ: Oralmicrobialcommunitiesinsicknessandin health. TrendsMicrobiol 2005, 13: 589 – 595. 16.WhitmoreSE,LamontRJ: Thepathogenicpersonaofcommunityassociatedoralstreptococci. MolMicrobiol 2011, 81: 305 – 314. 17.JacobsonGR,LodgeJ,PoyF: Carbohydrateuptakeintheoralpathogen Streptococcusmutans: mechanismsandregulationbyprotein phosphorylation. Biochimie 1989, 71: 997 – 1004. 18.MikxFHM,vanderHoevenJS: Symbiosisof Streptococcusmutans and Veillonellaalcalescens inMixedContinuousCultures. ArchsOralBiol 1975, 20: 407 – 410. 19.RosanB,LamontRJ: Dentalplaqueformation. MicrobesInfect 2000, 2: 1599 – 1607. 20.ScannapieceFA,SolomonL,WadenyaRO: EmergenceinHumanDental PlaqueandHostDistributionofAmylase-bindingStreptococci. JDentRes 1994, 73:1627 – 1635. 21.McNabR,HolmesAR,ClarkeJM,TannockGW,JenkinsonHF: CellSurface PolypeptideCshAMediatesBindingof Streptococcusgordonii toOther OralBacteriaandtoImmobilizedFibronectin. InfectImmun 1996, 64: 4204 – 4210. 22.YajimaA,Urano-TashiroY,ShimazuK,TakashimaE,TakahashiY,KonishiK: Hsa,anadhesinof Streptococcusgordonii DL1,bindstoa2-3-linkedsialic acidonglycophorinAoftheerythrocytemembrane. MicrobiolImmunol 2008, 52: 69 – 77. 23.MaedaK,NagataH,YamamotoY,TanakaM,TanakaJ,MinaminoN, ShizukuishiS: Glyceraldehyde-3-PhosphateDehydrogenaseof Streptococcusoralis FunctionsasaCoadhesinfor Porphyromonas gingivalis MajorFimbriae. InfectImmun 2004, 72: 1341 – 1348. 24.ParkY,JamesCE,YoshimuraF,LamontRJ: Expressionoftheshortfimbriae of Porphyromonasgingivalis isregulatedinoralbacterialconsortia. FEMS MicrobiolLett 2006, 262: 65 – 71. 25.FrekkesP,DriessenAJM: ProteinTargetingtotheBacterialCytoplasmic Membrane. MicrobiolMolBiolRev 1999, 63: 161 – 173. 26.MorenoMS,SchneiderBL,MaileRR,WeylerW,SaierMHJr: Catabolite repressionmediatedbytheCcpAproteinin Bacillussubtilis :novel modesofregulationrevealedbywhole-genomeanalyses. MolMicrobiol 2001, 39: 1366 – 1381. 27.WenZT,BurneRA: FunctionalGenomicsApproachtoIdentifyingGenes RequiredforBiofilmDevelopmentby Streptococcusmutans ApplEnviron Microbiol 2002, 68: 1196 – 1203. 28.KolenbranderPE,AndersenRN,BakerRA,JenkinsonHF: TheAdhesionAssociated sca Operonin Streptococcusgordonii EncodesanInducible High-AffinityABCTransporterforMn2+Uptake. JBact 1998, 180: 290 – 295. 29.AndersenRN,GaneshkumarN,KolenbranderPE: Cloningofthe Streptococcusgordonii PK488Gene,EncodinganAdhesinWhich MediatesCoaggregationwith Actinomycesnaeslundii PK606. InfectImmun 1993, 61: 981 – 987. 30.MascherT,ZahnerD,MeraiM,BalmelleN,deSaizieuAB,HakenbeckR: The Streptococcuspneumoniaecia Regulon:CiaRTargetSitesand TranscriptionProfileAnalysis. JBacteriol 2003, 185: 60 – 70. 31.DarveauRP,BeltonCM,ReifeRA,LamontRJ: LocalChemokineParalysis,a NovelPathogenicMechanismfor Porphyromonasgingivalis InfectImmun 1998, 66: 1660 – 1665. 32.HajishengallisG,LiangS,PayneMA,HashimA,JotwaniR,EskanMA, McIntoshML,AlsamA,KirkwoodKL,LambrisJD,DarveauRP,CurtisMA: Low-abundancebiofilmspeciesorchestratesinflammatoryperiodontalHendrickson etal.BMCMicrobiology 2012, 12 :211 Page22of23 http://www.biomedcentral.com/1471-2180/12/211

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diseasethroughthecommensalmicrobiotaandcomplement. CellHost Microbe 2011, 10: 497 – 506. 33.BoschG,SkovranE,XiaQ,WangT,TaubF,MillerJA,LidstromME,Hackett M: Comprehensiveproteomicsof Methylobacteriumextorquens AM1 metabolismundersinglecarbonandnonmethylotrophicconditions. Proteomics 2008, 8: 3494 – 3505. 34.EngJK,McCormackAL,YatesJR: Anapproachtocorrelatetandemmassspectraldataofpeptideswithamino-acid-sequencesinaprotein database. JAmericanSocMassSpectrom 1994, 5: 976 – 989. 35. PorphyromonasgingivalisW83GenomePage .[http://cmr.jcvi.org/tigr-scripts/ CMR/GenomePage.cgi?org=gpg]. 36. StreptococcusgordoniiChallisNCTC7868GenomePage .[ cmr.jcvi.org/cgi-bin/ CMR/GenomePage.cgi?org=gsg ]. 37. FusobacteriumnucleatumATCC25586GenomePage .[ cmr.jcvi.org/cgi-bin/ CMR/GeneomePage.cgi?org=ntfn01 ]. 38. MammalianGeneCollection .[http://mgc.nci.nih.gov]. 39.PengJ,EliasJE,ThoreenCC,LickliderLJ,GygiSP: Evaluationof multidimensionalchromatographycoupledwithtandemmass spectrometry(LC/LC-MS/MS)forlarge-scaleproteinanalysis:theyeast proteome. JProteomeRes 2003, 2: 43 – 50. 40.EliasJE,GibbonsFD,KingOD,RothFP,GygiSP: Intensity-basedprotein identificationbymachinelearningfromalibraryoftandemmass spectra. NatBiotechnol 2004, 22: 214 – 219. 41.TabbDL,McDonaldWH,YatesJR3rd: DTASelectandContrast:toolsfor assemblingandcomparingproteinidentificationsfromshotgun proteomics. JProteomeRes 2002, 1: 21 – 26. 42.XiaQ,WangT,ParkY,LamontRJ,HackettM: Differentialquantitative proteomicsof Porphyromonasgingivalis bylineariontrapmass spectrometry:non-labelmethodscomparison,q-valuesandLOWESS curvefitting. IntJMassSpectrom 2007, 259: 105 – 116. 43.XiaQ,WangT,TaubF,ParkY,CapestanyCA,LamontRJ,HackettM: Quantitativeproteomicsofintracellular Porphyromonasgingivalis Proteomics 2007, 7: 4323 – 4337.44.HendricksonEL,XiaQ,WangT,LamontRJ,HackettM: Pathwayanalysisfor intracellular Porphyromonasgingivalis usingastrainATCC33277specific database. BMCMicrobiol 2009, 9: 185. 45.LiuH,SadygovRG,YatesJR3rd: Amodelforrandomsamplingand estimationofrelativeproteinabundanceinshotgunproteomics. Anal Chem 2004, 76: 4193 – 4201. 46.SokalRR,RohlfFJ: Biometry,theprinciplesandpracticeofstatisticsin biologicalresearch .NewYork:WHFreeman;1995:715 – 724. 47.StoreyJD,TibshiraniR: Statisticalsignificanceforgenomewidestudies. ProcNatlAcadSciUSA 2003, 100: 9440 – 9445. 48.StoreyResearchGroup: Qvalue .[http://genomics.princeton.edu/storeylab/ qvalue/]. 49.BenjaminiY,YekutieliD: QuantitativetraitLocianalysisusingthefalse discoveryrate. Genetics 2005, 171: 783 – 790. 50.daHuangW,ShermanBT,TanQ,KirJ,LiuD,BryantD,GuoY,StephensR, BaselerMW,LaneHC, etal : DAVIDBioinformaticsResources:expanded annotationdatabaseandnovelalgorithmstobetterextractbiology fromlargegenelists. NucleicAcidsRes 2007, 35: W169 – W175.doi:10.1186/1471-2180-12-211 Citethisarticleas: Hendrickson etal. : Proteomicsof Streptococcus gordonii withinamodeldevelopingoralmicrobialcommunity. BMC Microbiology 2012 12 :211. Submit your next manuscript to BioMed Central and take full advantage of: € Convenient online submission € Thorough peer review € No space constraints or color “gure charges € Immediate publication on acceptance € Inclusion in PubMed, CAS, Scopus and Google Scholar € Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Hendrickson etal.BMCMicrobiology 2012, 12 :211 Page23of23 http://www.biomedcentral.com/1471-2180/12/211



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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 1 -0.902 7.046 0.0183 0.0240 0.0189 6.882 SGO_0001 0.0101 0.0398 0.0038 5.838 -1.455 -0.702 -0.702 5.838 0.0183 0.0240 0.0183 0.0240 5.838 -0.702 -0.553 5.134 0.0078 0.0292 0.0183 0.0240 5.838 -0.702 0.148 6.069 0.0468 0.3152 0.0586 7.101 0.0159 -0.754 dnaA; chromosomal replication initiator protein DnaA 0.640 7.258 0.0067 0.0043 0.5301 6.846 SGO_0002 0.0146 0.0633 0.0591 6.614 -0.140 -0.691 -0.691 6.614 0.0067 0.0043 0.0067 0.0043 6.614 -0.691 -0.780 6.060 0.0016 0.0035 0.0067 0.0043 6.614 -0.691 -0.090 6.961 0.0299 0.1843 0.0969 7.204 0.0242 0.550 dnaN; DNA polymerase III, beta subunit -1.661 8.780 0.2009 0.7232 0.0028 8.695 SGO_0004 0.0020 0.0050 0.0009 6.879 -2.017 -0.038 -0.038 6.879 0.2009 0.7232 0.2009 0.7232 6.879 -0.038 -0.356 6.431 0.0274 0.1457 0.2009 0.7232 6.879 -0.038 -0.318 7.080 0.0514 0.3501 0.0040 8.713 0.0019 -1.979 putative lipoprotein 4.640 4.640 SGO_0005 4.640 hypothetical protein SGO_0005 0.158 7.655 0.0348 0.0653 0.4541 7.626 SGO_0006 0.0485 0.2750 0.0516 7.354 0.100 -0.362 -0.362 7.354 0.0348 0.0653 0.0348 0.0653 7.354 -0.362 -0.058 6.587 0.1084 0.7696 0.0348 0.0653 7.354 -0.362 0.304 7.378 0.0161 0.0882 0.0033 7.817 0.0017 0.462 ABC transporter, ATP-binding protein -0.294 6.164 0.0012 0.0001 0.0012 6.734 SGO_0007 0.0417 0.2311 0.0005 6.754 0.785 -0.368 -0.368 6.754 0.0012 0.0001 0.0012 0.0001 6.754 -0.368 1.079 5.516 0.0015 0.0031 0.0012 0.0001 6.754 -0.368 1.447 6.385 0.0006 0.0008 0.0002 6.977 0.0003 1.153 trpS; tryptophanyl-tRNA synthetase 0.310 9.371 0.0397 0.0811 0.0008 9.763 SGO_0008 0.0149 0.0651 0.0004 9.703 0.961 -0.103 -0.103 9.703 0.0397 0.0811 0.0397 0.0811 9.703 -0.103 0.651 8.752 0.0013 0.0020 0.0397 0.0811 9.703 -0.103 0.755 9.426 0.0009 0.0014 0.0007 9.833 0.0005 1.064 inosine-5'-monophosphate dehydrogenase -0.863 5.257 0.1464 0.4687 0.0486 5.581 SGO_0011 0.0270 0.1369 0.0082 4.509 -0.825 0.238 0.238 4.509 0.1464 0.4687 0.1464 0.4687 4.509 0.238 0.038 3.580 0.1191 0.8484 0.1464 0.4687 4.509 0.238 -0.201 4.002 0.0922 0.6812 0.0090 5.482 0.0036 -1.064 proteinase, M16 family 1.455 4.510 1.807 SGO_0012 0.0205 0.0948 3.145 3.756 1.807 mpp; peptidase, M16 family 4.813 4.813 SGO_0013 2.648 2.648 2.648 2.648 2.648 0.1881 5.212 0.0434 -0.643 hypothetical protein SGO_0013 -2.771 6.426 0.0283 0.0484 0.0197 6.428 SGO_0015 0.0058 0.0196 0.0039 3.996 -2.738 -0.482 -0.482 3.996 0.0283 0.0484 0.0283 0.0484 3.996 -0.482 0.033 2.445 0.0283 0.0484 3.996 -0.482 0.514 3.987 0.0097 0.0458 0.0000 6.598 0.0001 -2.256 ABC transporter (ATP-binding protein) 3.787 3.787 SGO_0016 3.028 3.028 3.028 3.028 3.028 0.1825 4.669 0.0423 -0.241 cbiO; ABC transporter, ATP-binding protein 2.351 2.351 SGO_0017 2.351 ABC-type putative cobalt transport system, permease 2.807 2.807 SGO_0019 2.807 sdhA; L-serine dehydratase, iron-sulfur-dependent, alpha subunit -0.115 4.222 2.585 SGO_0020 0.1386 0.9320 2.538 3.149 2.585 sdhB; L-serine dehydratase, iron-sulfur-dependent, beta subunit 3.662 7.860 0.0037 0.0010 0.8591 5.176 SGO_0022 0.0001 0.0000 0.0906 5.357 0.104 -1.137 -1.137 5.357 0.0037 0.0010 0.0037 0.0010 5.357 -1.137 -3.558 6.740 0.0001 0.0000 0.0037 0.0010 5.357 -1.137 -2.421 7.479 0.0000 0.0000 0.0057 5.854 0.0025 1.241 trmU; tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins tRNA Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 2 -0.570 5.781 0.2382 0.9134 0.2749 6.230 SGO_0025 0.0268 0.1355 0.0332 5.892 0.343 0.005 0.005 5.892 0.2382 0.9134 0.2382 0.9134 5.892 0.005 0.913 4.918 0.0230 0.1173 0.2382 0.9134 5.892 0.005 0.908 5.502 0.0157 0.0846 0.2100 6.207 0.0477 0.338 gidA; glucose inhibited division protein A 7.420 0.2247 0.8413 0.0718 7.463 SGO_0026 0.0109 3.561 -4.015 -0.039 -0.039 3.561 0.2247 0.8413 0.2247 0.8413 3.561 -0.039 1.272 0.2247 0.8413 3.561 -0.039 3.020 0.0007 7.514 0.0005 -3.976 DHH subfamily 1 protein -0.380 6.937 0.1271 0.3931 0.0722 7.410 SGO_0027 0.0100 0.0393 0.0109 7.060 0.520 0.144 0.144 7.060 0.1271 0.3931 0.1271 0.3931 7.060 0.144 0.900 6.144 0.0071 0.0259 0.1271 0.3931 7.060 0.144 0.756 6.646 0.0011 0.0021 0.0126 7.312 0.0046 0.376 rplI; ribosomal protein L9 -1.442 5.255 0.1982 0.7084 0.2993 5.208 SGO_0028 0.0034 0.0101 0.0357 4.394 -0.610 -0.159 -0.159 4.394 0.1982 0.7084 0.1982 0.7084 4.394 -0.159 0.832 3.141 0.0235 0.1219 0.1982 0.7084 4.394 -0.159 0.991 4.452 0.0119 0.0590 0.2268 5.614 0.0507 -0.451 dnaC; replicative DNA helicase 2.151 7.906 0.0184 0.0244 0.0069 6.851 SGO_0030 0.0001 0.0000 0.0018 6.784 0.689 -0.278 -0.278 6.784 0.0184 0.0244 0.0184 0.0244 6.784 -0.278 -1.462 6.935 0.0001 0.0000 0.0184 0.0244 6.784 -0.278 -1.184 7.625 0.0001 0.0000 0.0011 7.027 0.0008 0.967 aspB; aspartate transaminase -0.944 7.088 0.0188 0.0254 0.1364 7.365 SGO_0032 0.0028 0.0077 0.0180 6.860 -0.245 -0.269 -0.269 6.860 0.0188 0.0254 0.0188 0.0254 6.860 -0.269 0.699 5.805 0.0031 0.0086 0.0188 0.0254 6.860 -0.269 0.968 6.584 0.0006 0.0007 0.8926 7.492 0.1697 0.024 plsX; fatty acid/phospholipid synthesis protein PlsX 3.725 0.0935 0.2631 0.0517 5.651 SGO_0033 0.0085 5.472 1.403 0.409 0.409 5.472 0.0935 0.2631 0.0935 0.2631 5.472 0.409 4.086 0.0935 0.2631 5.472 0.409 4.205 0.0102 5.306 0.0039 0.994 acpP; acyl carrier protein 2.367 5.314 1.807 SGO_0035 0.0174 0.0779 0.585 0.585 0.585 4.058 0.585 -3.076 4.751 0.0137 0.0713 2.496 -0.709 phosphoribosylformylglycinamidine synthase 0.918 6.144 0.1627 0.5485 0.0752 5.283 SGO_0042 0.0003 0.0002 0.0113 5.007 0.243 -0.112 -0.112 5.007 0.1627 0.5485 0.1627 0.5485 5.007 -0.112 -0.675 4.801 0.0136 0.0616 0.1627 0.5485 5.007 -0.112 -0.563 5.766 0.0019 0.0045 0.0260 5.804 0.0083 0.355 transcription regulator, GntR family SGO_0044 PTS system, IIB component 4.640 4.640 SGO_0050 4.640 hypothetical protein SGO_0050 3.351 3.351 SGO_0051 3.351 hypothetical protein SGO_0051 1.565 8.469 0.0031 0.0007 0.0031 7.186 SGO_0054 0.0001 0.0001 0.0010 6.823 -0.677 -0.915 -0.915 6.823 0.0031 0.0007 0.0031 0.0007 6.823 -0.915 -2.242 7.201 0.0001 0.0000 0.0031 0.0007 6.823 -0.915 -1.327 8.019 0.0002 0.0001 0.0480 7.609 0.0136 0.238 dltA; D-alanine-activating enzyme 2.058 2.058 SGO_0055 2.058 dltB; integral membrane protein -0.711 3.805 3.420 SGO_0056 0.0112 0.0452 0.585 1.196 3.420 dltC; D-alanyl carrier protein -1.818 8.223 0.0050 0.0020 0.0010 8.108 SGO_0057 0.0010 0.0018 0.0005 6.092 -2.415 -0.316 -0.316 6.092 0.0050 0.0020 0.0050 0.0020 6.092 -0.316 -0.596 5.653 0.0078 0.0291 0.0050 0.0020 6.092 -0.316 -0.280 6.397 0.0215 0.1239 0.0012 8.163 0.0008 -2.098 dltD protein 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Cell Wall Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 3 -2.492 11.167 0.0058 0.0034 0.0015 13.189 SGO_0059 0.0067 0.0235 0.0006 12.958 1.992 0.895 0.895 12.958 0.0058 0.0034 0.0058 0.0034 12.958 0.895 4.484 11.789 0.0004 0.0002 0.0058 0.0034 12.958 0.895 3.589 11.564 0.0007 0.0009 0.0222 12.538 0.0073 1.097 pXO1; hypothetical protein SGO_0059 -4.809 8.069 8.043 SGO_0060 0.0112 0.0455 1.107 1.717 8.043 hypothetical protein SGO_0060 1.379 1.380 SGO_0062 1.380 hypothetical protein SGO_0062 -1.969 7.830 0.1104 0.3266 0.0000 7.907 SGO_0063 0.0001 0.0000 0.0000 6.304 -1.618 0.146 0.146 6.304 0.1104 0.3266 0.1104 0.3266 6.304 0.146 0.350 5.597 0.0071 0.0258 0.1104 0.3266 6.304 0.146 0.204 6.135 0.0400 0.2615 0.0001 7.875 0.0002 -1.765 hypothetical protein SGO_0063 -2.780 8.948 0.0120 0.0121 0.0000 8.988 SGO_0064 0.0001 0.0000 0.0001 7.241 -2.484 -0.837 -0.837 7.241 0.0120 0.0121 0.0120 0.0121 7.241 -0.837 0.296 6.006 0.0101 0.0407 0.0120 0.0121 7.241 -0.837 1.133 7.144 0.0027 0.0079 0.0002 9.154 0.0003 -1.647 FtsK/SpoIIIE family protein 0.041 7.328 0.0094 0.0077 0.0020 7.386 SGO_0065 0.0927 0.5936 0.0007 7.043 0.159 -0.179 -0.179 7.043 0.0094 0.0077 0.0094 0.0077 7.043 -0.179 0.118 6.285 0.0397 0.2305 0.0094 0.0077 7.043 -0.179 0.298 6.991 0.0071 0.0294 0.0013 7.484 0.0009 0.339 hypothetical protein SGO_0065 2.446 0.0661 0.1647 4.900 SGO_0066 5.198 0.388 0.388 5.198 0.0661 0.1647 0.0661 0.1647 5.198 0.388 1.422 4.018 0.0352 0.2001 0.0661 0.1647 5.198 0.388 1.034 4.293 0.0278 0.1684 4.494 D-3-phosphoglycerate dehydrogenase, putative -1.326 6.056 0.0122 0.0126 0.0489 6.487 SGO_0067 0.0003 0.0004 0.0082 6.452 -0.170 -0.954 -0.954 6.452 0.0122 0.0126 0.0122 0.0126 6.452 -0.954 1.156 4.815 0.0012 0.0019 0.0122 0.0126 6.452 -0.954 2.110 6.156 0.0015 0.0035 0.0173 7.024 0.0059 0.784 protein with prophage function domain -1.848 6.075 0.0051 0.0023 0.0009 6.537 SGO_0068 0.0116 0.0478 0.0004 5.719 -0.815 -0.305 -0.305 5.719 0.0051 0.0023 0.0051 0.0023 5.719 -0.305 1.033 4.262 0.0063 0.0223 0.0051 0.0023 5.719 -0.305 1.338 5.123 0.0075 0.0324 0.0031 6.655 0.0016 -0.510 lipoprotein, putative 5.402 0.0396 0.0796 0.0015 5.980 SGO_0069 0.0006 5.023 -1.033 -0.305 -0.305 5.023 0.0396 0.0796 0.0396 0.0796 5.023 -0.305 3.258 0.0396 0.0796 5.023 -0.305 4.162 0.0009 6.084 0.0007 -0.728 hypothetical protein SGO_0069 5.452 0.1261 0.3884 0.0470 6.637 SGO_0070 0.0080 6.244 0.351 0.087 0.087 6.244 0.1261 0.3884 0.1261 0.3884 6.244 0.087 4.678 0.1261 0.3884 6.244 0.087 5.199 0.0667 6.588 0.0177 0.264 merozoite surface protein 1 1.379 1.380 SGO_0075 1.380 hypothetical protein SGO_0075 -2.233 5.972 5.830 SGO_0078 0.0356 0.1899 4.038 4.038 4.038 1.429 4.038 0.966 4.360 0.0387 0.2518 0.0292 6.328 0.0090 -1.267 hypothetical protein SGO_0078 1.379 1.380 SGO_0079 1.380 hypothetical protein SGO_0079 -1.239 7.315 0.2181 0.8060 0.0007 7.490 SGO_0080 0.0013 0.0026 0.0004 6.581 -0.691 0.021 0.021 6.581 0.2181 0.8060 0.2181 0.8060 6.581 0.021 0.548 5.745 0.0105 0.0445 0.2181 0.8060 6.581 0.021 0.527 6.346 0.0125 0.0629 0.0018 7.484 0.0011 -0.712 hypothetical protein SGO_0080 1.176 4.906 3.266 SGO_0081 0.0041 0.0126 3.740 3.740 3.740 3.224 3.740 -0.142 4.788 0.0913 0.6734 0.0685 4.842 0.0181 1.034 hypothetical protein SGO_0081 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Unknown Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 4 6.401 SGO_0095 4.758 4.758 4.758 5.277 4.758 -1.125 6.431 0.0009 0.0016 5.271 mccF; microcin immunity protein MccF, putative 6.097 6.097 SGO_0097 6.097 hypothetical protein SGO_0097 4.012 4.012 SGO_0098 5.487 5.487 5.487 5.487 5.487 0.1448 6.324 0.0344 0.979 ribonucleotide reductase-like protein 4.372 0.0956 0.2721 2.396 SGO_0099 3.686 -0.310 -0.310 3.686 0.0956 0.2721 0.0956 0.2721 3.686 -0.310 -0.792 3.575 0.0732 0.4882 0.0956 0.2721 3.686 -0.310 -0.483 4.566 0.0416 0.2746 3.712 pulA-2; pullulanase, type I 0.845 4.371 3.499 SGO_0100 0.0570 0.3329 2.000 2.000 2.000 2.107 2.000 -0.717 3.403 0.9834 4.089 0.1827 0.127 maltose operon transcription repressor 4.874 4.874 SGO_0101 4.874 malA; Maltodextrose utilization protein malA -0.242 9.829 0.0450 0.0968 0.0024 9.703 SGO_0104 0.0207 0.0962 0.0008 8.825 -0.524 0.165 0.165 8.825 0.0450 0.0968 0.0450 0.0968 8.825 0.165 -0.282 8.448 0.0219 0.1109 0.0450 0.0968 8.825 0.165 -0.447 8.985 0.0077 0.0334 0.0000 9.636 0.0001 -0.689 Maltose/maltodextrin-binding protein precursor 1.097 6.362 0.0067 0.0043 0.8746 5.689 SGO_0105 0.0042 0.0127 0.0920 5.676 -0.043 -0.915 -0.915 5.676 0.0067 0.0043 0.0067 0.0043 5.676 -0.915 -1.140 5.228 0.0045 0.0140 0.0067 0.0043 5.676 -0.915 -0.225 6.182 0.0330 0.2061 0.0019 6.200 0.0011 0.873 malQ; 4-alpha-glucanotransferase 2.848 8.574 0.0238 0.0370 0.0001 7.794 SGO_0106 0.0005 0.0007 0.0001 7.963 1.923 -0.046 -0.046 7.963 0.0238 0.0370 0.0238 0.0370 7.963 -0.046 -0.925 7.869 0.0018 0.0039 0.0238 0.0370 7.963 -0.046 -0.879 8.496 0.0019 0.0044 0.0001 7.831 0.0002 1.969 glgP-2; maltodextrin phosphorylase 2.907 SGO_0107 2.394 2.394 2.394 1.783 2.394 LPXTG cell wall surface protein, collagen binding domain -1.035 6.092 5.505 SGO_0108 0.0022 0.0058 3.387 3.998 5.505 ruvB; Holliday junction DNA helicase RuvB 2.231 SGO_0110 2.385 2.385 2.385 1.107 2.385 0.668 3.090 2.898 phosphotyrosine protein phosphatase 4.115 4.115 SGO_0111 4.115 MORN motif family protein 5.366 5.366 SGO_0112 5.366 putative acyltransferase -2.089 13.012 0.0405 0.0836 0.0001 13.107 SGO_0113 0.0001 0.0000 0.0001 11.620 -1.648 -0.143 -0.143 11.620 0.0405 0.0836 0.0405 0.0836 11.620 -0.143 0.441 10.731 0.0011 0.0015 0.0405 0.0836 11.620 -0.143 0.584 11.427 0.0014 0.0031 0.0001 13.143 0.0002 -1.505 acdH; alcohol-acetaldehyde dehydrogenase 3.170 3.170 SGO_0128 3.170 hypothetical protein SGO_0128 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 5 6.741 6.741 SGO_0129 2.937 2.937 2.937 2.937 2.937 0.0001 6.881 0.0002 -3.290 atpI; v-type sodium ATP synthase, chain I -0.135 6.282 5.425 SGO_0131 0.0858 0.5442 4.000 4.611 5.425 v-type sodium ATP synthase, chain E 3.524 3.524 SGO_0132 3.020 3.020 3.020 3.020 3.020 0.2205 4.528 0.0494 -1.088 ATP synthase (C/AC39) subunit -0.328 4.635 4.154 SGO_0134 0.0580 0.3390 3.779 3.779 3.779 1.692 3.779 0.434 4.222 0.0641 0.4482 0.5924 5.225 0.1182 0.106 acetyltransferase, GNAT family -0.017 8.321 0.0532 0.1238 0.0008 7.825 SGO_0135 0.1433 0.9713 0.0004 6.712 -1.286 -0.332 -0.332 6.712 0.0532 0.1238 0.0532 0.1238 6.712 -0.332 -1.269 6.698 0.0026 0.0068 0.0532 0.1238 6.712 -0.332 -0.937 7.410 0.0031 0.0095 0.0003 7.926 0.0003 -0.954 v-type sodium ATP synthase, subunit A -0.696 8.587 0.0664 0.1660 0.0011 8.309 SGO_0136 0.0016 0.0037 0.0005 6.942 -1.600 -0.291 -0.291 6.942 0.0664 0.1660 0.0664 0.1660 6.942 -0.291 -0.904 6.696 0.0022 0.0052 0.0664 0.1660 6.942 -0.291 -0.613 7.410 0.0019 0.0047 0.0010 8.383 0.0007 -1.309 v-type sodium ATP synthase, chain B 3.653 3.653 SGO_0137 3.653 V-type ATPase, D subunit 0.579 3.778 2.459 SGO_0138 1.914 2.525 2.459 LysM domain protein 0.506 7.391 0.0063 0.0038 0.0555 6.896 SGO_0139 0.0013 0.0027 0.0090 6.748 -0.511 -1.092 -1.092 6.748 0.0063 0.0038 0.0063 0.0038 6.748 -1.092 -1.017 6.088 0.0023 0.0056 0.0063 0.0038 6.748 -1.092 0.074 7.146 0.0368 0.2375 0.0010 7.434 0.0007 0.581 thrC; threonine synthase 1.585 1.585 SGO_0142 1.585 hypothetical protein SGO_0142 -1.032 5.671 5.092 SGO_0144 0.0020 0.0050 1.063 1.063 1.063 2.951 1.063 -1.478 3.796 0.0265 0.1585 0.0651 5.213 0.0174 -2.511 hypothetical protein SGO_0144 0.275 8.112 0.0224 0.0329 0.0009 7.593 SGO_0145 0.0341 0.1807 0.0004 6.743 -0.848 -0.282 -0.282 6.743 0.0224 0.0329 0.0224 0.0329 6.743 -0.282 -1.124 6.669 0.0048 0.0153 0.0224 0.0329 6.743 -0.282 -0.841 7.372 0.0061 0.0248 0.0009 7.699 0.0007 -0.566 polI; DNA polymerase I 1.056 6.377 0.1828 0.6415 0.4436 5.991 SGO_0146 0.0048 0.0152 0.0505 5.791 0.244 -0.416 -0.416 5.791 0.1828 0.6415 0.1828 0.6415 5.791 -0.416 -0.812 5.412 0.0355 0.2024 0.1828 0.6415 5.791 -0.416 -0.397 6.110 0.0195 0.1112 0.0278 6.116 0.0087 0.659 CoA-binding domain protein 4.387 4.387 SGO_0148 1.648 1.648 1.648 1.648 1.648 0.0492 4.667 0.0139 -1.225 hypothetical protein SGO_0148 1.379 1.380 SGO_0150 1.380 fucA1; alpha-L-fucosidase 0.387 5.773 0.0019 0.0003 0.0119 5.291 SGO_0152 0.0519 0.2961 0.0027 5.438 -0.431 -1.441 -1.441 5.438 0.0019 0.0003 0.0019 0.0003 5.438 -1.441 -0.818 4.490 0.0268 0.1420 0.0019 0.0003 5.438 -1.441 0.622 5.762 0.0322 0.1998 0.0003 6.079 0.0003 1.009 tgt; queuine tRNA-ribosyltransferase 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins tRNA Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 6 1.787 11.314 0.0256 0.0417 0.0018 10.628 SGO_0154 0.0007 0.0010 0.0007 10.324 0.826 0.309 0.309 10.324 0.0256 0.0417 0.0256 0.0417 10.324 0.309 -0.961 10.418 0.0014 0.0025 0.0256 0.0417 10.324 0.309 -1.270 10.934 0.0011 0.0022 0.0367 10.445 0.0109 0.517 pgi; glucose-6-phosphate isomerase 8.348 8.348 SGO_0155 3.118 3.118 3.118 3.118 3.118 0.0014 8.402 0.0009 -4.703 hypothetical protein SGO_0155 7.444 0.0319 0.0567 0.0003 7.620 SGO_0156 0.0003 5.181 -2.949 -0.369 -0.369 5.181 0.0319 0.0567 0.0319 0.0567 5.181 -0.369 3.370 0.0319 0.0567 5.181 -0.369 4.357 0.0004 7.668 0.0004 -2.580 hypothetical protein SGO_0156 3.357 3.357 SGO_0157 3.357 hypothetical protein SGO_0157 2.802 8.548 0.0376 0.0735 0.0050 7.756 SGO_0158 0.0003 0.0002 0.0014 7.674 1.833 0.454 0.454 7.674 0.0376 0.0735 0.0376 0.0735 7.674 0.454 -0.969 7.832 0.0020 0.0047 0.0376 0.0735 7.674 0.454 -1.423 8.300 0.0006 0.0007 0.0014 7.403 0.0009 1.379 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative 1.294 3.787 2.000 SGO_0159 1.063 1.063 1.063 2.170 1.063 -1.718 3.164 2.804 -0.424 hippurate hydrolase 0.563 7.521 0.0007 0.0000 0.9909 7.216 SGO_0163 0.0030 0.0085 0.1026 7.118 0.009 -0.737 -0.737 7.118 0.0007 0.0000 0.0007 0.0000 7.118 -0.737 -0.555 6.398 0.0013 0.0022 0.0007 0.0000 7.118 -0.737 0.182 7.353 0.0069 0.0286 0.0016 7.631 0.0010 0.746 galU; UTP-glucose-1-phosphate uridylyltransferase 0.296 7.639 0.0594 0.1433 0.0071 7.239 SGO_0164 0.0213 0.0992 0.0018 6.572 -0.524 -0.244 -0.244 6.572 0.0594 0.1433 0.0594 0.1433 6.572 -0.244 -0.821 6.303 0.0038 0.0111 0.0594 0.1433 6.572 -0.244 -0.577 7.010 0.0080 0.0354 0.1009 7.349 0.0252 -0.280 Glycerol-3-phosphate dehydrogenase [NAD(P)+] (NAD(P)H-dependent glycerol-3-phosphate dehydrogenase) 4.275 4.275 SGO_0165 4.275 ABC transporter, permease/ATP-binding protein SP2075 6.237 6.237 SGO_0166 2.000 2.000 2.000 2.000 2.000 0.0256 6.342 0.0082 -2.723 ABC transporter, permease/ATP-binding protein SP2073 4.020 4.020 SGO_0167 4.020 glutamine amidotransferase -0.600 4.566 4.156 SGO_0168 0.0250 0.1212 1.429 2.039 4.156 hydrolase, NUDIX family 1.929 6.595 0.1609 0.5407 0.0364 5.680 SGO_0169 0.0023 0.0059 0.0064 5.383 0.646 0.144 0.144 5.383 0.1609 0.5407 0.1609 0.5407 5.383 0.144 -1.283 5.622 0.0033 0.0094 0.1609 0.5407 5.383 0.144 -1.427 6.200 0.0032 0.0101 0.1490 5.611 0.0352 0.502 dut; dUTP diphosphatase -0.989 5.628 0.0664 0.1664 0.1728 5.530 SGO_0171 0.0409 0.2246 0.0219 4.672 -1.565 -1.163 -1.163 4.672 0.0664 0.1664 0.0664 0.1664 4.672 -1.163 -0.576 2.911 0.0664 0.1664 4.672 -1.163 0.587 4.795 0.0400 0.2623 0.1424 6.118 0.0338 -0.402 radA; DNA repair protein RadA -0.682 6.005 5.614 SGO_0172 0.0089 0.0337 2.807 3.418 5.614 conserved hypothetical protein TIGR00266 -1.237 7.924 7.412 SGO_0173 0.0003 0.0002 3.790 3.790 3.790 5.058 3.790 -1.884 6.016 0.0008 0.0013 0.0000 7.570 0.0001 -3.121 Carbonic anhydrase 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Homeostasis Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 7 0.758 8.458 0.0055 0.0029 0.0023 8.400 SGO_0174 0.0073 0.0266 0.0008 8.419 0.684 -0.429 -0.429 8.419 0.0055 0.0029 0.0055 0.0029 8.419 -0.429 -0.073 7.627 0.0875 0.6035 0.0055 0.0029 8.419 -0.429 0.356 8.459 0.0157 0.0841 0.0000 8.678 0.0001 1.114 gltX; glutamyl-tRNA synthetase 2.585 2.585 SGO_0179 2.585 Membrane protein oxaA 1 precursor -0.946 6.660 0.0521 0.1201 0.0809 6.647 SGO_0180 0.0122 0.0506 0.0120 6.054 -1.123 -0.991 -0.991 6.054 0.0521 0.1201 0.0521 0.1201 6.054 -0.991 -0.177 4.949 0.1287 0.9284 0.0521 0.1201 6.054 -0.991 0.815 6.068 0.0151 0.0803 0.7291 7.007 0.1414 -0.132 jag; hypothetical protein SGO_0180 5.217 5.217 SGO_0181 5.217 lipoprotein, putative 0.723 4.937 2.700 SGO_0182 0.0798 0.4978 3.469 4.080 2.700 sapR; sakacin A production response regulator -0.017 5.264 4.272 SGO_0188 0.1383 0.9279 2.000 2.000 2.000 3.132 2.000 -0.729 4.120 0.0340 0.2137 0.2076 4.646 0.0473 -0.745 hydrolase, TatD family 1.585 1.585 SGO_0189 1.585 primase-related protein 5.130 0.2040 0.7382 0.2689 5.410 SGO_0190 0.0326 3.791 -1.173 0.512 0.512 3.791 0.2040 0.7382 0.2040 0.7382 3.791 0.512 1.783 0.2040 0.7382 3.791 0.512 3.103 0.0370 5.563 0.0110 -1.685 hypothetical protein SGO_0190 4.351 4.351 SGO_0191 1.063 1.063 1.063 1.063 1.063 0.0179 4.548 0.0060 -1.774 hypothetical protein SGO_0191 0.004 4.805 3.820 SGO_0193 0.1428 0.9653 3.887 3.887 3.887 2.666 3.887 0.840 4.614 0.0309 0.1910 0.2304 5.139 0.0514 0.844 ksgA; dimethyladenosine transferase 4.429 0.0520 0.1190 3.170 SGO_0197 3.854 0.637 0.637 3.854 0.0520 0.1190 0.0520 0.1190 3.854 0.637 -0.253 3.809 0.0515 0.3175 0.0520 0.1190 3.854 0.637 -0.890 4.539 0.0020 0.0048 3.541 predicted ribosome small subunit-dependent GTPase A 2.600 8.472 0.0089 0.0068 0.0827 6.853 SGO_0198 0.0001 0.0001 0.0122 6.794 0.364 -0.532 -0.532 6.794 0.0089 0.0068 0.0089 0.0068 6.794 -0.532 -2.236 7.405 0.0002 0.0001 0.0089 0.0068 6.794 -0.532 -1.704 8.123 0.0002 0.0001 0.0017 7.170 0.0011 0.896 rpe; ribulose-phosphate 3-epimerase -1.421 7.784 0.0165 0.0202 0.0003 7.706 SGO_0200 0.0001 0.0001 0.0003 6.391 -1.758 -0.591 -0.591 6.391 0.0165 0.0202 0.0165 0.0202 6.391 -0.591 -0.337 5.633 0.0212 0.1059 0.0165 0.0202 6.391 -0.591 0.255 6.525 0.0010 0.0018 0.0001 7.858 0.0002 -1.166 competence-induced protein Ccs50 1.296 8.289 0.0048 0.0017 0.0034 7.048 SGO_0201 0.0028 0.0079 0.0011 6.416 -1.090 -0.917 -0.917 6.416 0.0048 0.0017 0.0048 0.0017 6.416 -0.917 -2.387 6.927 0.0016 0.0032 0.0048 0.0017 6.416 -0.917 -1.470 7.726 0.0022 0.0060 0.1122 7.404 0.0277 -0.173 cmp-binding-factor 1 0.149 5.698 4.619 SGO_0202 0.0870 0.5536 3.983 3.983 3.983 3.648 3.983 -0.250 5.128 0.0384 0.2496 0.5282 5.559 0.1063 -0.101 pur operon repressor 2.700 2.700 SGO_0203 2.700 hypothetical protein SGO_0203 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 8 -0.081 8.109 0.0830 0.2217 0.2491 8.092 SGO_0204 0.1339 0.8941 0.0304 7.633 -0.064 -0.158 -0.158 7.633 0.0830 0.2217 0.0830 0.2217 7.633 -0.158 0.016 6.952 0.1239 0.8855 0.0830 0.2217 7.633 -0.158 0.174 7.649 0.0829 0.6053 0.4380 8.177 0.0899 0.094 rpsL; ribosomal protein S12 0.380 9.252 0.2016 0.7269 0.0174 9.499 SGO_0205 0.0236 0.1119 0.0036 9.299 0.797 0.071 0.071 9.299 0.2016 0.7269 0.2016 0.7269 9.299 0.071 0.417 8.530 0.0214 0.1072 0.2016 0.7269 9.299 0.071 0.345 9.103 0.0281 0.1707 0.0269 9.456 0.0085 0.726 rpsG; ribosomal protein S7 0.449 12.222 0.0590 0.1419 0.0015 12.576 SGO_0206 0.0005 0.0006 0.0006 12.413 1.012 0.140 0.140 12.413 0.0590 0.1419 0.0590 0.1419 12.413 0.140 0.564 11.617 0.0024 0.0061 0.0590 0.1419 12.413 0.140 0.424 12.143 0.0008 0.0013 0.0001 12.482 0.0002 0.873 fusA; translation elongation factor G 1.189 12.534 0.0248 0.0399 0.0034 12.724 SGO_0207 0.0005 0.0007 0.0010 12.579 1.446 0.375 0.375 12.579 0.0248 0.0399 0.0248 0.0399 12.579 0.375 0.257 12.020 0.0183 0.0872 0.0248 0.0399 12.579 0.375 -0.118 12.434 0.0006 0.0008 0.0010 12.454 0.0007 1.071 gap; glyceraldehyde-3-phosphate dehydrogenase, type I 0.596 6.284 4.996 SGO_0208 0.0337 0.1782 4.400 5.011 4.996 LPXTG cell wall surface protein, glycosyl hydrolase family 1.455 12.630 0.0050 0.0022 0.0000 12.819 SGO_0209 0.0002 0.0001 0.0001 13.183 1.708 -0.484 -0.484 13.183 0.0050 0.0022 0.0050 0.0022 13.183 -0.484 0.252 12.189 0.0031 0.0085 0.0050 0.0022 13.183 -0.484 0.736 13.083 0.0007 0.0009 0.0001 13.204 0.0002 2.191 pgk; phosphoglycerate kinase -0.950 8.543 7.943 SGO_0210 0.0059 0.0198 2.024 2.024 2.024 5.865 2.024 -4.474 6.540 0.0009 0.0016 0.0020 7.976 0.0012 -5.424 sspA; streptococcal surface protein A -4.047 9.262 9.177 SGO_0211 0.0003 0.0003 4.003 4.614 9.177 sspB; streptococcal surface protein B 1.322 1.322 SGO_0214 1.322 transcription regulator, MerR family 0.153 8.746 0.0562 0.1327 0.0555 8.481 SGO_0215 0.0017 0.0040 0.0090 7.921 -0.427 -0.339 -0.339 7.921 0.0562 0.1327 0.0562 0.1327 7.921 -0.339 -0.579 7.445 0.0059 0.0205 0.0562 0.1327 7.921 -0.339 -0.240 8.195 0.0085 0.0389 0.3407 8.628 0.0722 -0.087 glnA; glutamine synthetase, type I -0.136 8.107 0.0050 0.0021 0.1387 8.101 SGO_0219 0.0278 0.1417 0.0183 7.715 -0.152 -0.389 -0.389 7.715 0.0050 0.0021 0.0050 0.0021 7.715 -0.389 -0.016 6.905 0.1133 0.8056 0.0050 0.0021 7.715 -0.389 0.373 7.721 0.0007 0.0008 0.0251 8.297 0.0080 0.237 metallo-beta-lactamase superfamily protein 1 3.446 SGO_0220 3.781 3.781 3.781 2.322 3.781 -0.171 4.418 0.0848 0.6214 4.294 Protein of unknown function (DUF1447) superfamily 0.818 4.028 3.118 SGO_0223 0.0150 0.0659 3.087 3.087 3.087 1.807 3.087 0.669 3.791 0.0279 4.380 0.0087 1.487 glycoproteinase family protein -0.275 5.406 0.1672 0.5724 0.1203 5.967 SGO_0230 0.1056 0.6858 0.0163 5.720 0.773 0.108 0.108 5.720 0.1672 0.5724 0.1672 0.5724 5.720 0.108 1.048 4.788 0.0233 0.1196 0.1672 0.5724 5.720 0.108 0.940 5.270 0.0117 0.0564 0.0141 5.843 0.0050 0.665 Protein of unknown function, DUF536 family 3.111 3.111 SGO_0231 3.111 glycerophosphoryl diester phosphodiesterase family protein 1.807 0.1775 0.6200 0.1289 4.606 SGO_0232 0.0173 4.947 1.561 -0.102 -0.102 4.947 0.1775 0.6200 0.1775 0.6200 4.947 -0.102 3.258 0.1775 0.6200 4.947 -0.102 4.022 0.2527 4.738 0.0558 1.663 conserved hypothetical protein TIGR00103 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 9 -1.071 6.570 5.976 SGO_0233 0.0111 0.0442 3.881 4.491 5.976 lipoprotein, putative 0.223 7.887 0.0178 0.0227 0.0009 7.449 SGO_0234 0.0036 0.0108 0.0004 6.807 -0.741 -0.522 -0.522 6.807 0.0178 0.0227 0.0178 0.0227 6.807 -0.522 -0.964 6.469 0.0008 0.0008 0.0178 0.0227 6.807 -0.522 -0.442 7.280 0.0043 0.0153 0.0849 7.669 0.0216 -0.219 pepX; X-Pro dipeptidyl-peptidase 6.742 6.742 SGO_0235 4.642 4.642 4.642 4.642 4.642 0.0133 7.157 0.0048 -1.563 glycerol uptake facilitator protein-like protein 4.509 4.509 SGO_0236 4.509 hypothetical protein SGO_0236 0.811 5.501 0.0099 0.0084 0.7214 5.141 SGO_0237 0.0302 0.1571 0.0774 5.325 0.200 -1.119 -1.119 5.325 0.0099 0.0084 0.0099 0.0084 5.325 -1.119 -0.611 4.436 0.0348 0.1970 0.0099 0.0084 5.325 -1.119 0.508 5.557 0.0255 0.1510 0.0097 5.790 0.0038 1.319 ccpA; CcpA protein (proteinase) 2.836 2.836 SGO_0240 2.836 mvaD; diphosphomevalonate decarboxylase 1.066 2.687 1.058 SGO_0242 1.000 1.611 1.058 FMN-dependent dehydrogenase family protein 4.989 0.0166 0.0206 3.755 SGO_0243 4.260 0.965 0.965 4.260 0.0166 0.0206 0.0166 0.0206 4.260 0.965 -0.226 4.377 0.0612 0.3979 0.0166 0.0206 4.260 0.965 -1.190 4.998 0.0013 0.0029 3.791 hydroxymethylglutaryl-CoA reductase, degradative 2.219 5.446 0.0935 0.2633 0.0095 4.551 SGO_0244 0.0014 0.0029 0.0023 5.193 2.049 -0.203 -0.203 5.193 0.0935 0.2633 0.0935 0.2633 5.193 -0.203 -0.170 4.570 0.0834 0.5695 0.0935 0.2633 5.193 -0.203 0.032 5.664 0.1189 0.9011 0.0002 5.461 0.0003 2.252 hydroxymethylglutaryl-CoA synthase -0.232 11.349 0.0316 0.0559 0.0007 11.037 SGO_0247 0.0506 0.2878 0.0004 9.898 -0.986 0.100 0.100 9.898 0.0316 0.0559 0.0316 0.0559 9.898 0.100 -0.755 9.779 0.0088 0.0343 0.0316 0.0559 9.898 0.100 -0.854 10.354 0.0067 0.0274 0.0006 11.004 0.0005 -1.086 pfl; formate acetyltransferase 0.478 5.107 0.1586 0.5274 0.3739 4.382 SGO_0252 0.0169 0.0754 0.0432 3.562 -0.114 0.427 0.427 3.562 0.1586 0.5274 0.1586 0.5274 3.562 0.427 -0.593 3.619 0.0510 0.3132 0.1586 0.5274 3.562 0.427 -1.020 4.417 0.0086 0.0395 0.1218 4.617 0.0297 -0.542 possible TetR-type transcriptional regulator 5.655 5.655 SGO_0253 5.655 hypothetical protein SGO_0253 4.018 4.018 SGO_0254 2.622 2.622 2.622 2.622 2.622 0.1228 4.643 0.0299 -0.810 helicase, RecD/TraA family -1.915 7.565 0.0073 0.0051 0.0045 7.519 SGO_0255 0.0021 0.0053 0.0013 5.836 -2.151 -0.533 -0.533 5.836 0.0073 0.0051 0.0073 0.0051 5.836 -0.533 -0.236 5.062 0.0282 0.1521 0.0073 0.0051 5.836 -0.533 0.297 5.938 0.0082 0.0371 0.0065 7.630 0.0027 -1.618 Signal peptidase I 0.549 4.962 4.191 SGO_0256 0.0603 0.3566 2.566 3.177 4.191 rnhC; ribonuclease HIII 1.231 3.328 3.585 SGO_0258 2.657 1.585 2.657 2.657 0.355 2.880 2.657 2.302 1.585 hypothetical protein SGO_0258 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Unknown Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 10 -0.703 6.887 0.0045 0.0014 0.0008 6.661 SGO_0260 0.0044 0.0135 0.0004 6.073 -1.380 -1.274 -1.274 6.073 0.0045 0.0014 0.0045 0.0014 6.073 -1.274 -0.677 5.083 0.0123 0.0543 0.0045 0.0014 6.073 -1.274 0.597 6.310 0.0062 0.0249 0.1609 7.135 0.0376 -0.106 DNA mismatch binding protein MutS2 1.585 1.585 SGO_0261 1.585 acetyltransferase, GNAT family 0.568 6.914 0.0019 0.0003 0.0017 6.228 SGO_0262 0.0032 0.0094 0.0006 6.302 -0.877 -1.706 -1.706 6.302 0.0019 0.0003 0.0019 0.0003 6.302 -1.706 -1.445 5.499 0.0010 0.0014 0.0019 0.0003 6.302 -1.706 0.261 6.793 0.0115 0.0553 0.0012 7.073 0.0008 0.829 dipeptidase 0.095 7.290 0.0306 0.0536 0.0199 7.973 SGO_0263 0.0900 0.5751 0.0040 7.637 1.216 0.690 0.690 7.637 0.0306 0.0536 0.0306 0.0536 7.637 0.690 1.121 6.893 0.0087 0.0340 0.0306 0.0536 7.637 0.690 0.431 7.051 0.0237 0.1383 0.0020 7.504 0.0012 0.527 trx-1; thioredoxin 5.055 5.055 SGO_0268 1.585 1.585 1.585 1.585 1.585 0.1082 5.229 0.0268 -1.945 mechanosensitive transport protein 4.194 4.194 SGO_0269 4.194 hypothetical protein SGO_0269 0.119 6.592 0.0212 0.0303 0.2548 6.586 SGO_0272 0.0674 0.4081 0.0310 5.959 0.120 0.368 0.368 5.959 0.0212 0.0303 0.0212 0.0303 5.959 0.368 0.001 5.530 0.1304 0.9477 0.0212 0.0303 5.959 0.368 -0.367 5.966 0.0163 0.0892 0.0009 6.402 0.0007 -0.248 hypothetical protein SGO_0272 0.718 9.428 0.1104 0.3263 0.0143 9.271 SGO_0276 0.0029 0.0083 0.0031 8.931 0.460 0.077 0.077 8.931 0.1104 0.3263 0.1104 0.3263 8.931 0.077 -0.258 8.496 0.0206 0.1025 0.1104 0.3263 8.931 0.077 -0.334 9.070 0.0083 0.0379 0.0034 9.225 0.0017 0.383 gdhA; glutamate dehydrogenase (NADP) 0.354 6.057 4.856 SGO_0277 0.0447 0.2509 3.945 3.945 3.945 4.110 3.945 -0.766 5.384 0.0153 0.0815 0.1820 5.671 0.0422 -0.412 pyrA; Dihydroorotate dehydrogenase 1.709 3.094 1.000 SGO_0278 1.585 2.196 1.000 msrA; Peptide methionine sulfoxide reductase msrA/msrB 3.902 3.902 SGO_0279 3.902 lipoprotein, putative 0.678 7.016 5.584 SGO_0280 0.0256 0.1260 4.531 4.531 4.531 5.224 4.531 -1.269 6.326 0.0124 0.0620 0.0629 6.340 0.0170 -0.591 trzA; ethylammeline chlorohydrolase 5.347 5.347 SGO_0282 5.347 cell wall polysaccharide biosynthesis protein 1.058 1.058 SGO_0284 1.058 transcriptional regulator -1.447 5.729 0.0419 5.668 SGO_0286 0.0117 0.0484 0.0073 2.072 -1.900 2.072 2.072 -0.453 2.705 2.072 2.525 5.487 DNA mismatch repair protein MutS, putative 3.231 SGO_0288 2.494 2.494 2.494 2.107 2.494 -1.232 3.610 0.0111 0.0536 3.007 GDSL-like lipase/acylhydrolase 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 11 5.411 0.2458 0.9518 0.3152 5.657 SGO_0290 0.0373 4.065 -1.342 0.001 0.001 4.065 0.2458 0.9518 0.2458 0.9518 4.065 0.001 1.857 0.2458 0.9518 4.065 0.001 3.486 0.0519 5.871 0.0144 -1.343 copper -translocating P-type ATPase -1.699 7.622 0.0057 0.0032 0.0006 7.507 SGO_0291 0.0005 0.0008 0.0004 5.946 -2.286 -0.884 -0.884 5.946 0.0057 0.0032 0.0057 0.0032 5.946 -0.884 -0.587 5.151 0.0046 0.0146 0.0057 0.0032 5.946 -0.884 0.297 6.175 0.0019 0.0045 0.0011 7.697 0.0008 -1.402 copper-translocating P-type ATPase -1.515 8.103 0.0391 0.0774 0.0005 9.282 SGO_0292 0.0001 0.0000 0.0003 9.120 1.040 0.159 0.159 9.120 0.0391 0.0774 0.0391 0.0774 9.120 0.159 2.555 7.814 0.0003 0.0001 0.0391 0.0774 9.120 0.159 2.395 8.289 0.0002 0.0001 0.0005 9.177 0.0004 0.881 spxB; pyruvate oxidase 4.271 4.271 SGO_0294 4.271 ABC transporter, putative 2.180 5.828 2.459 SGO_0297 0.0348 0.1852 4.557 5.168 2.459 6-phospho-beta-glucosidase 0.585 0.585 SGO_0299 0.585 putative histidine kinase 1.981 SGO_0301 1.468 1.468 1.468 0.857 1.468 ABC transporter ATP-binding protein-like protein 3.886 3.886 SGO_0306 3.886 ABC transporter ATP-binding protein-like protein 2.718 2.718 SGO_0307 2.718 pabB; chorismate binding enzyme 2.302 4.772 2.202 SGO_0310 0.0011 0.0022 2.063 2.063 2.063 3.382 2.063 -0.916 4.329 0.0290 0.1782 0.0522 3.401 0.0144 1.387 metE; 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 1.214 11.377 0.0042 0.0012 0.0000 11.225 SGO_0312 0.0002 0.0002 0.0001 11.002 0.992 0.258 0.258 11.002 0.0042 0.0012 0.0042 0.0012 11.002 0.258 -0.222 10.630 0.0039 0.0115 0.0042 0.0012 11.002 0.258 -0.479 11.127 0.0008 0.0013 0.0000 11.059 0.0001 0.735 xfp; D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase 8.639 0.0481 8.661 SGO_0317 0.0082 2.072 -5.050 2.072 2.072 1.461 2.072 8.639 LPXTG cell wall surface protein, serine protease, subtilase family 1.577 7.033 0.0650 0.1584 0.1194 6.384 SGO_0321 0.0012 0.0024 0.0162 6.267 0.594 -0.292 -0.292 6.267 0.0650 0.1584 0.0650 0.1584 6.267 -0.292 -0.983 6.071 0.0015 0.0030 0.0650 0.1584 6.267 -0.292 -0.690 6.785 0.0021 0.0052 0.0322 6.560 0.0098 0.887 polypeptide deformylase 1.000 1.000 SGO_0323 1.063 1.063 1.063 1.063 1.063 2.317 0.576 pseudouridine synthase rRNA-specific 5.618 5.618 SGO_0324 5.618 hypothetical protein SGO_0324 3.058 3.058 SGO_0325 3.058 probable membrane protein, putative 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 12 6.681 6.681 SGO_0326 1.871 1.871 1.871 1.871 1.871 0.0317 6.752 0.0097 -3.296 probable membrane protein, putative 0.798 3.924 3.025 SGO_0327 0.0200 0.0913 0.648 0.648 0.648 1.692 0.648 -1.654 2.700 0.1462 3.376 0.0346 -0.856 Lipopolysaccharide N-acetylglucosaminyltransferase 4.383 4.383 SGO_0328 4.383 transmembrane protein, putative 6.839 6.839 SGO_0329 0.585 0.585 0.585 0.585 0.585 0.0718 6.866 0.0187 -4.732 hypothetical protein SGO_0329 5.031 5.031 SGO_0330 5.031 hypothetical protein SGO_0330 5.455 5.455 SGO_0331 5.455 hypothetical protein SGO_0331 5.722 5.722 SGO_0332 5.722 hypothetical protein SGO_0332 -0.323 8.323 0.1089 0.3178 0.7503 8.488 SGO_0333 0.0334 0.1757 0.0801 7.930 0.039 0.128 0.128 7.930 0.1089 0.3178 0.1089 0.3178 7.930 0.128 0.362 7.225 0.0310 0.1718 0.1089 0.3178 7.930 0.128 0.234 7.759 0.0419 0.2768 0.2989 8.419 0.0644 -0.089 rpsO; ribosomal protein S15 1.000 1.000 SGO_0337 2.648 2.648 2.648 2.648 2.648 3.452 2.161 trx-2; thioredoxin 3.050 5.724 1.585 SGO_0339 0.0138 0.0594 0.648 0.648 0.648 4.516 0.648 -3.474 5.190 0.0118 0.0574 2.389 -0.424 hypothetical protein SGO_0339 1.201 8.387 0.0330 0.0606 0.0143 7.819 SGO_0342 0.0004 0.0004 0.0031 7.594 0.291 -0.280 -0.280 7.594 0.0330 0.0606 0.0330 0.0606 7.594 -0.280 -0.909 7.359 0.0009 0.0010 0.0330 0.0606 7.594 -0.280 -0.629 8.075 0.0021 0.0050 0.0093 7.982 0.0036 0.572 pepF-2; oligoendopeptidase 0.219 9.215 0.0735 0.1898 0.0326 9.053 SGO_0344 0.0124 0.0516 0.0059 8.477 -0.094 0.030 0.030 8.477 0.0735 0.1898 0.0735 0.1898 8.477 0.030 -0.313 8.048 0.0061 0.0214 0.0735 0.1898 8.477 0.030 -0.343 8.646 0.0046 0.0170 0.0139 9.039 0.0049 -0.124 pnpA; polyribonucleotide nucleotidyltransferase 3.663 3.663 SGO_0345 3.663 cysE; serine O-acetyltransferase -0.407 4.511 3.700 SGO_0348 2.839 2.839 2.839 2.170 2.839 -0.942 3.810 0.0043 0.0151 0.0090 4.537 0.0036 -1.348 reductase 0.798 7.081 0.0419 0.0871 0.1270 6.710 SGO_0349 0.0084 0.0315 0.0171 6.196 0.188 0.186 0.186 6.196 0.0419 0.0871 0.0419 0.0871 6.196 0.186 -0.611 6.029 0.0125 0.0552 0.0419 0.0871 6.196 0.186 -0.796 6.568 0.0072 0.0301 0.9875 6.611 0.1832 0.002 cysS; cysteinyl-tRNA synthetase -0.349 7.992 0.1733 0.6020 0.0003 7.816 SGO_0352 0.0015 0.0032 0.0003 6.880 -0.788 -0.043 -0.043 6.880 0.1733 0.6020 0.1733 0.6020 6.880 -0.043 -0.438 6.480 0.0007 0.0007 0.1733 0.6020 6.880 -0.043 -0.396 7.112 0.0042 0.0144 0.0022 7.834 0.0012 -0.745 ABC transporter, ATP-binding protein SP1580 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins ABC Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 13 1.406 4.544 2.619 SGO_0353 0.0136 0.0580 3.040 3.040 3.040 2.979 3.040 -0.501 4.341 0.0414 0.2728 0.0639 4.160 0.0171 0.905 transport protein 0.730 5.564 4.154 SGO_0355 0.0047 0.0149 4.612 4.612 4.612 3.759 4.612 0.236 5.496 0.0349 0.2222 0.0127 5.720 0.0046 0.966 RNA methyltransferase, TrmH family, group 3 1.379 1.380 SGO_0356 1.380 hypothetical protein SGO_0356 1.098 7.238 0.0627 0.1523 0.0041 7.388 SGO_0357 0.0022 0.0058 0.0012 7.442 1.313 -0.137 -0.137 7.442 0.0627 0.1523 0.0627 0.1523 7.442 -0.137 0.214 6.658 0.0091 0.0360 0.0627 0.1523 7.442 -0.137 0.351 7.343 0.0025 0.0070 0.0025 7.485 0.0013 1.449 degV; DegV family fatty acid binding protein 0.443 9.550 0.0116 0.0115 0.0498 9.490 SGO_0358 0.0112 0.0451 0.0083 9.027 0.343 0.221 0.221 9.027 0.0116 0.0115 0.0116 0.0115 9.027 0.221 -0.100 8.576 0.0520 0.3226 0.0116 0.0115 9.027 0.221 -0.321 9.085 0.0082 0.0369 0.3765 9.371 0.0784 0.122 rplM; ribosomal protein L13 -0.649 8.262 0.0120 0.0122 0.9422 8.546 SGO_0359 0.0156 0.0689 0.0981 7.813 0.022 0.488 0.488 7.813 0.0120 0.0122 0.0120 0.0122 7.813 0.488 0.671 7.145 0.0101 0.0418 0.0120 0.0122 7.813 0.488 0.184 7.477 0.0730 0.5246 0.0485 8.319 0.0137 -0.466 rpsI; ribosomal protein S9 0.296 4.951 3.789 SGO_0361 0.0570 0.3323 2.740 2.740 2.740 2.972 2.740 -0.849 4.222 0.0132 0.0679 0.1384 4.546 0.0329 -0.553 immunity repressor protein 1.733 4.471 0.1064 3.371 SGO_0368 0.0048 0.0150 0.0148 1.883 1.075 1.883 1.883 -0.659 3.359 0.0554 0.3497 1.883 3.583 2.345 merA; mercury(II) reductase 2.000 2.000 SGO_0371 2.000 putative transcriptional regulator 1.711 6.450 0.0055 0.0029 0.0319 5.806 SGO_0372 0.0017 0.0040 0.0059 5.811 0.792 -0.374 -0.374 5.811 0.0055 0.0029 0.0055 0.0029 5.811 -0.374 -0.919 5.539 0.0025 0.0064 0.0055 0.0029 5.811 -0.374 -0.545 6.289 0.0048 0.0177 0.0062 6.049 0.0026 1.166 malate oxidoreductase 0.739 6.858 0.0145 0.0161 0.0094 6.002 SGO_0374 0.0028 0.0079 0.0022 5.376 -1.123 -0.954 -0.954 5.376 0.0145 0.0161 0.0145 0.0161 5.376 -0.954 -1.862 5.419 0.0013 0.0022 0.0145 0.0161 5.376 -0.954 -0.908 6.283 0.0019 0.0047 0.1547 6.358 0.0363 -0.169 Response regulator of the LytR/AlgR family 3.322 3.932 SGO_0376 1.883 -0.926 1.883 1.883 1.272 1.883 3.322 ABC transporter ATP-binding protein 4.294 SGO_0378 3.170 3.781 hypothetical protein SGO_0378 4.594 4.594 SGO_0379 4.594 Protein of unknown function (DUF421) family 3.459 3.459 SGO_0380 3.459 hypothetical protein SGO_0380 -0.291 5.820 0.1416 0.4514 0.3577 5.827 SGO_0384 0.0649 0.3905 0.0418 5.090 -0.243 0.142 0.142 5.090 0.1416 0.4514 0.1416 0.4514 5.090 0.142 0.048 4.532 0.1293 0.9361 0.1416 0.4514 5.090 0.142 -0.094 5.081 0.0912 0.6706 0.2637 5.773 0.0578 -0.385 putative carboxylate-amine/thiol ligase 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins Unknown Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary Table SgPgFn vs Sg Protein qVal pVal SgFn vs Sg Ratio Sum Ratio SgPg vs Sg qVal pVal Ratio Sum qVal pVal Ratio Sum Log 2 Ratios 0 2 4 6 -2 -4 -6 qVal pVal Ratio Sum SgPgFn vs SgPg qVal pVal Ratio Sum SgPgFn vs SgFn qVal pVal Sum SgPg vs SgFn Spectral Counts Sg Summary Table Page 14 0.670 7.728 6.351 SGO_0385 0.0026 0.0070 5.903 6.514 6.351 exo-beta-D-fructosidase 4.194 4.194 SGO_0387 4.194 hypothetical protein SGO_0387 0.224 7.351 6.251 SGO_0388 0.0555 0.3217 5.320 5.931 6.251 LPXTG cell wall surface protein, zinc carboxypeptidase family 3.458 5.613 1.000 SGO_0389 0.0418 0.2326 4.429 5.039 1.000 possible phosphoserine phosphatase 1.938 8.321 0.0236 0.0363 0.0005 7.757 SGO_0390 0.0014 0.0028 0.0003 7.920 1.196 -0.369 -0.369 7.920 0.0236 0.0363 0.0236 0.0363 7.920 -0.369 -0.742 7.537 0.0050 0.0165 0.0236 0.0363 7.920 -0.369 -0.374 8.298 0.0161 0.0876 0.0015 8.027 0.0010 1.564 glycerol-3-phosphate dehydrogenase (NAD(P)+) 3.821 6.458 0.0830 0.2216 4.127 SGO_0392 0.0090 0.0344 5.365 2.271 -0.604 -0.604 5.365 0.0830 0.2216 0.0830 0.2216 5.365 -0.604 -1.550 5.511 0.0113 0.0485 0.0830 0.2216 5.365 -0.604 -0.946 6.501 0.0011 0.0021 0.0922 5.566 0.0232 2.875 phosphoglycerate mutase -0.858 5.430 5.105 SGO_0393 0.0702 0.4299 2.000 2.611 5.105 D-alanyl-D-alanine carboxypeptidase 2.322 2.322 SGO_0396 2.322 Transcriptional regulator, PadR family -1.902 7.059 0.2021 0.7300 0.0028 6.912 SGO_0398 0.0021 0.0053 0.0009 4.508 -2.749 -0.054 -0.054 4.508 0.2021 0.7300 0.2021 0.7300 4.508 -0.054 -0.848 4.338 0.0119 0.0517 0.2021 0.7300 4.508 -0.054 -0.794 4.991 0.0183 0.1028 0.0033 6.928 0.0017 -2.695 ABC transporter ATP-binding protein 0.608 4.887 3.423 SGO_0400 0.0421 0.2346 3.113 3.724 3.423 hrcA; heat-inducible transcription repressor HrcA 0.727 7.007 0.0127 0.0135 0.0835 7.096 SGO_0401 0.0294 0.1511 0.0122 6.598 0.875 0.708 0.708 6.598 0.0127 0.0135 0.0127 0.0135 6.598 0.708 0.148 6.218 0.0233 0.1210 0.0127 0.0135 6.598 0.708 -0.561 6.510 0.0076 0.0327 0.9248 6.709 0.1742 0.166 grpE; co-chaperone GrpE 1.202 11.615 0.1603 0.5363 0.0019 11.157 SGO_0402 0.0001 0.0001 0.0007 10.853 0.487 0.026 0.026 10.853 0.1603 0.5363 0.1603 0.5363 10.853 0.026 -0.715 10.656 0.0003 0.0001 0.1603 0.5363 10.853 0.026 -0.741 11.257 0.0002 0.0001 0.0022 11.142 0.0013 0.461 dnaK; DnaK chaperone protein -2.009 7.978 0.0769 0.2007 0.0147 7.910 SGO_0404 0.0052 0.0171 0.0032 5.889 -2.460 -0.415 -0.415 5.889 0.0769 0.2007 0.0769 0.2007 5.889 -0.415 -0.451 5.300 0.0313 0.1735 0.0769 0.2007 5.889 -0.415 -0.036 6.073 0.0706 0.5026 0.0167 7.970 0.0057 -2.045 dnaJ; DnaJ chaparone protein 1.455 4.510 1.807 SGO_0407 0.0205 0.0948 1.063 1.063 1.063 3.145 1.063 -1.686 3.963 0.0161 0.0876 2.696 -0.231 truA; tRNA pseudouridine synthase A 8.890 0.0117 8.913 SGO_0408 0.0027 2.394 -4.983 2.394 2.394 1.783 2.394 8.890 zmpB; zinc metalloproteinase B 7.517 9.176 0.643 SGO_0409 0.0184 0.0834 2.735 2.735 2.735 8.048 2.735 -5.919 8.682 0.0007 0.0010 0.0929 3.467 0.0233 1.598 pyridoxine kinase 1179 Proteins found: .005 q -Value p -Value Test Cutoff Signif Direction Applies To yes yes yes yes no + + n/a ratios, bars ratios, bars bars p q -Values SgPg vs Sg SgPgFn vs Sg SgPgFn vs SgFn Dot Plots Dot Plots SgFn vs Sg SgPgFn vs SgPg SgPg vs SgFn ABC Transporter Filter by category: Show detected proteins only Show all proteins B6 Hendrickson et al.

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Hackett Laboratory UW Streptococcus gordonii SgFn vs Sg SgPg vs Sg SgPgFn vs Sg SgPg v SgFn SgPgFn v SgFn SgPgFn vs SgPg Coverage Summary
STANDARD VIEW MARC VIEW
Permanent Link: http://ufdc.ufl.edu/UF00099918/00001
 Material Information
Title: Proteomics of Porphyromonas gingivalis within a model oral microbial community
Physical Description: Book
Language: English
Creator: Kuboniwa, Masae
Hendrickson, Erik
Xia, Qiangwei
Wang, Tiansong
Xie, Hua
Hackett, Murray
Lamont, Richard
Publisher: BMC Microbiology
Publication Date: 2009
 Notes
Abstract: BACKGROUND:Porphyromonas gingivalis is a periodontal pathogen that resides in a complex multispecies microbial biofilm community known as dental plaque. Confocal laser scanning microscopy showed that P. gingivalis can assemble into communities in vitro with Streptococcus gordonii and Fusobacterium nucleatum, common constituents of dental plaque. Whole cell quantitative proteomics, along with mutant construction and analysis, were conducted to investigate how P. gingivalis adapts to this three species community.RESULTS:1156 P. gingivalis proteins were detected qualitatively during comparison of the three species model community with P. gingivalis incubated alone under the same conditions. Integration of spectral counting and summed signal intensity analyses of the dataset showed that 403 proteins were down-regulated and 89 proteins up-regulated. The proteomics results were inspected manually and an ontology analysis conducted using DAVID. Significant decreases were seen in proteins involved in cell shape and the formation of the cell envelope, as well as thiamine, cobalamin, and pyrimidine synthesis and DNA repair. An overall increase was seen in proteins involved in protein synthesis. HmuR, a TonB dependent outer membrane receptor, was up-regulated in the community and an hmuR deficient mutant was deficient in three species community formation, but was unimpaired in its ability to form mono- or dual-species biofilms.CONCLUSION:Collectively, these results indicate that P. gingivalis can assemble into a heterotypic community with F. nucleatum and S. gordonii, and that a community lifestyle provides physiologic support for P. gingivalis. Proteins such as HmuR, that are up-regulated, can be necessary for community structure.
General Note: Start page 98
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Full Text



BMC Microbiology Bioled Central


Research article

Proteomics of Porphyromonas gingivalis within a model oral


microbial community
Masae Kuboniwal, Erik L Hendrickson2, Qiangwei Xia2,3,6, Tiansong Wang2,3,
Hua Xie4, Murray Hackett2 and Richard J Lamont*5


Address: 'Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan, 2Department of Chemical
Engineering, University of Washington, Seattle, WA, USA, 3Department of Microbiology, University of Washington, Seattle, WA, USA, 4School of
Dentistry, Meharry Medical College, Nashville, TN, USA, 5Department of Oral Biology, University of Florida, Gainesville, FL, USA and 6University
of Wisconsin-Madison, Department of Chemistry, Madison, WI, USA
Email: Masae Kuboniwa kuboniwa@dent.osaka-u.ac.jp; Erik L Hendrickson elh@u.washington.edu; Qiangwei Xia qxia@chem.wisc.edu;
Tiansong Wang tswang@u.washington.edu; Hua Xie hxie@mmc.edu; Murray Hackett mhackett@u.washington.edu;
Richard J Lamont* rlamont@dental.ufl.edu
* Corresponding author



Published: 19 May 2009 Received: 30 January 2009
BMC Microbiology 2009, 9:98 doi:10.1 186/1471-2180-9-98 Accepted: 19 May 2009
This article is available from: http://www.biomedcentral.com/1471-2180/9/98
2009 Kuboniwa et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.ore/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.



Abstract
Background: Porphyromonas gingivalis is a periodontal pathogen that resides in a complex
multispecies microbial biofilm community known as dental plaque. Confocal laser scanning
microscopy showed that P. gingivalis can assemble into communities in vitro with Streptococcus
gordonii and Fusobacterium nucleatum, common constituents of dental plaque. Whole cell
quantitative proteomics, along with mutant construction and analysis, were conducted to
investigate how P. gingivalis adapts to this three species community.
Results: I 1156 P. gingivalis proteins were detected qualitatively during comparison of the three
species model community with P. gingivalis incubated alone under the same conditions. Integration
of spectral counting and summed signal intensity analyses of the dataset showed that 403 proteins
were down-regulated and 89 proteins up-regulated. The proteomics results were inspected
manually and an ontology analysis conducted using DAVID. Significant decreases were seen in
proteins involved in cell shape and the formation of the cell envelope, as well as thiamine,
cobalamin, and pyrimidine synthesis and DNA repair. An overall increase was seen in proteins
involved in protein synthesis. HmuR, a TonB dependent outer membrane receptor, was up-
regulated in the community and an hmuR deficient mutant was deficient in three species community
formation, but was unimpaired in its ability to form mono- or dual-species biofilms.
Conclusion: Collectively, these results indicate that P. gingivalis can assemble into a heterotypic
community with F. nucleatum and S. gordonii, and that a community lifestyle provides physiologic
support for P. gingivalis. Proteins such as HmuR, that are up-regulated, can be necessary for
community structure.








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Background
The microbial communities that exist on oral surfaces are
complex and dynamic biofilms that develop through tem-
porally distinct patterns of microbial colonization [1,2].
For example, initial colonizers of the salivary pellicle on
the coronal tooth surface are principally commensal oral
streptococci such as S. gordonii and related species. Estab-
lishment of these organisms facilitates the subsequent col-
onization of additional gram-positives along with gram-
negatives such as Fusobacterium nucleatum. As the biofilm
extends below the gum line and becomes subgingival
plaque, further maturation is characterized by the coloni-
zation of more pathogenic gram-negative anaerobes
including Porphyromonas gingivalis [2-4]. While organisms
such as P. gingivalis are considered responsible for destruc-
tion of periodontal tissues, pathogenicity is only
expressed in the context of mixed microbial communities.
Periodontal diseases, therefore, are essentially microbial
community diseases, and the interactions among the con-
stituents of these communities and between the commu-
nities and host cells and tissues, are of fundamental
importance for determining the health or disease status of
the periodontium.

Oral biofilm developmental pathways are driven by coad-
hesive, signaling and metabolic interactions among the
participating organisms. Pioneer bacteria provide a sub-
stratum and appropriate metabolic support for succeed-
ing organisms. Complex consortia then accumulate
through recognition and communication systems. These
interbacterial signaling processes can be based on cell-cell
contact, short range soluble mediators, AI-2, or nutri-
tional stimuli [2,5-8]. In general, bacterial adaptation to
the community lifestyle is accompanied by distinct pat-
terns of gene and protein expression [9,10]. In S. gordonii
for example, arginine biosynthesis genes are regulated in
communities with Actinomyces naeslundii which enables
aerobic growth when exogenous arginine is limited [11].
Over 30 genes are differentially regulated in P. gingivalis
following community formation with S. gordonii but not
with S. mutans [12], whereas in monospecies P. gingivalis
biofilm communities there are changes in abundance of
over 80 envelope proteins [13].

While over 700 species or phylotypes of bacteria can be
recovered from the oral cavity, in any one individual there
are closer to 200 species [14] and the diversity of bacteria
assembled in dense consortia will be further limited by
nutritional and other compatibility constraints. P. gingiva-
lis can accumulate into single species biofilms and mixed
species consortia with S. gordonii and related oral strepto-
cocci [15-17]. Moreover, introduction of P. gingivalis into
the mouths of human volunteers results in almost exclu-
sive localization in areas of streptococcal-rich plaque [18].
Development of more complex multi-species communi-


ties in aerated environments such as supragingival tooth
surfaces may require oxygen scavenging by F. nucleatum
[19]. F. nucleatum is also able to coaggregate with P. gingi-
valis and with oral streptococci [19-21]. Hence communi-
ties of S. gordonii, F. nucleatum and P. gingivalis are likely
to be favored in vivo; however, community formation by
these three organisms has not been investigated. The aim
of this study was to examine the ability of S. gordonii, F.
nucleatum and P. gingivalis to form multispecies commu-
nities in vitro, and to utilize a global proteomic approach
to investigate differential protein expression in P. gingiva-
lis in response to presence of these organisms.

Results and discussion
Assembly of P. gingivalis-F. nucleatum-S. gordonii
communities in vitro
Confocal laser scanning microscopy (CLSM) was used to
investigate the ability of P. gingivalis to assemble into
communities with S. gordonii and F. nucleatum. In order to
mimic the temporal progression of events in vivo, S. gor-
donii cells were first cultured on a glass surface and this
streptococcal substratum was then reacted in succession
with F. nucleatum and P. gingivalis. The F. nucleatum and P.
gingivalis cells were maintained in the absence of growth
media in order to be able to detect any metabolic support
being provided by the other organisms in the community.
A 3D reconstruction of the heterotypic community is
shown in Fig. 1. Both P. gingivalis and F. nucleatum formed
discrete accumulations and could be either separate from
each other or interdigitated, consistent with the concept
that the later gram-negative colonizers such as P. gingivalis
and F. nucleatum initially establish themselves on the
streptococcal rich supragingival plaque [4,18]. The results
demonstrate the mutual compatibility of these three
organisms for heterotypic community development, an
early step in the overall process of plaque biofilm accumu-
lation. Participation in multispecies communities may
provide a basis for synergistic interactions in virulence.
For example, mixed infections of P. gingivalis and F. nucle-
atum are more pathogenic in animal models than either
species alone [22], and F. nucleatum can enhance the abil-
ity of P. gingivalis to invade host cells [23].

Proteome of P. gingivalis in a three species community
To begin to investigate the mechanisms of adaptation of
P. gingivalis to a community environment, the proteome
of non-growing P. gingivalis cells incorporated into a com-
munity with F. nucleatum and S. gordonii was compared to
the proteome of non-growing P. gingivalis cells alone. The
expressed proteome of P. gingivalis in a community con-
sisted of 1156 annotated gene products detected qualita-
tively. Based on spectral counting, 271 gene products
showed evidence of relative abundance change at a q-
value of 0.01: 109 proteins at higher relative abundance
and 162 at lower relative abundance, using P. gingivalis


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higher relative abundance. For purposes of examining the
totals for combined trends, if an abundance change was
called as significant (red or green in Additional file 1:
Table ST1) in one measurement, it was considered signif-
icant for the above combined totals only if the ratio of the
other measurement showed the same direction of abun-
dance change, with a log2 ratio of + 0.1 or greater regard-
less of the q-value in the second measurement. The
experimental data for differential protein abundance are
shown in Fig. 2 as a pseudo M/A plot [28,29] with a LOW-
ESS curve fit [30]. The same data are plotted in Fig. 3 as
open reading frames according to PGN numbers from the
ATCC 33277 genome annotation [31]. A complete listing
of all proteins, their abundance ratios relative to P. gingi-
valis controls incubated alone under the same conditions
as determined by spectral counting and summed signal


Figure I
Confocal laser scanning microscopy of P. gingivalis-F.
nucleatum-S. gordonii community. S. gordonii cells (red,
stained with hexidium iodide) were cultured on a glass plate.
FITC-labeled F. nucleatum cells (green), followed by DAPI
labeled P. gingivalis cells (blue), were reacted sequentially with
the S. gordonii substratum. Bacterial accumulations were
examined on a Bio-Rad Radiance 2100 confocal laser scan-
ning microscope. A series of fluorescent optical x-y sections
in the z-plane to the maximum vertical extent of the accumu-
lation were collected with Laser Sharp software. Images
were digitally reconstructed with Imaris software. Image is
representative of three independent experiments.


alone as a reference state. Spectral counting is a conserva-
tive measure of protein abundance change that tends to
generate low FDRs [24-26] but that often suffers from
high FNRs in studies of the kind described here [27]. Less
conservative calculations based on intensity measure-
ments [27] found 458 gene products with evidence of rel-
ative abundance change at a q-value of 0.01: 72 proteins
at higher relative abundance, and 386 proteins at lower
relative abundance. Spectral counting and protein inten-
sity measurements were examined for common trends.
Trends tended to be consistent across both biological rep-
licates, but the magnitudes of the abundance ratios
showed significant scatter, similar to most published
expression data at either the mRNA or protein level [27].
In most cases the abundance ratio trends were the same,
using both quantitation methods, although not necessar-
ily significantly so. In only eight cases were the spectral
counting trend and summed intensity trend significantly
in opposite directions for the same protein (PGN 0329,
0501, 1094, 1341, 1637, 1733, 2065). The integrated rel-
ative abundance trends found 403 gene products with evi-
dence of lower relative abundance change and 89 at


log2 spectral counts

Figure 2
Pseudo M versus A plot [28,29] of the average protein
abundance ratios over all replicates for the P. gingiva-
lis-F. nucleatum-S. gordoniilP. gingivalis comparison
versus total abundance as estimated by spectral
counting. Color codes: red, P. gingivalis protein is over-
expressed in the P. gingivalis-F. nucleatum-S. gordonii commu-
nity relative to P. gingivalis alone; green, P. gingivalis protein is
under-expressed in the community relative to P. gingivalis
alone; black, no significant abundance change. Solid black lines
represent a LOWESS curve fit [30] to the biological repli-
cates of P. gingivalis alone, and represent the upper and lower
boundaries of the experimentally observed error regions or
null distributions associated with the relative abundance ratio
calculations. Proteins coded as either red or green were
determined to be significantly changed at the q-value [24]
cut-off value of 0.01. Thus, the G-test predictions [56] were
in good agreement with the curve fitting procedure. Details
regarding hypothesis testing procedures can be found in
Methods and in the explanatory notes to the data tables [see
Additional File I].



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Figure 3
Genomic representation of the P. gingivalis proteome, showing changes in relative abundance for the P. gingiva-
lis-F. nucleatum-S. gordoniilP. gingivalis comparison by spectral counting. Each dot represents a PGN ORF number in
the order followed by the ATCC 33277 strain annotation. Color codes: red, over-expression in the P. gingivalis-F. nucleatum-S.
gordonii community relative to P. gingivalis alone; green, under-expression in the community relative to P. gingivalis alone; yellow,
protein was detected qualitatively, but did not change in abundance; gray, proteins that were qualitative non-detects; gaps indi-
cate ORFs that were not common to both the ATCC 33277 and W83 annotations according to a master cross-reference
compiled by LANL (G. Xie, personal communication).





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intensity [27,32,33], and q-values, are given in Additional
file 1: Table ST1. Qualitative identifications for proteins
secreted by P. gingivalis in the 3-species community but
not by P. gingivalis alone are given Additional file 1: Table
ST2. Additional file 1: Figs. SF1, SF2, SF3, SF4, SF5 and SF6
and explanatory notes provide more detailed technical
information regarding reproducibility of the biological
replicates and the adequacy of sampling depth. To assess
global sampling depth, average spectral counts were calcu-
lated by summing all spectral count numbers for all P. gin-
givalis proteins in the FileMaker script output described
under Methods and dividing by the total number of P. gin-
givalis proteins in that file. The average redundant spectral
count number for peptides unique to a given ORF for P.
gingivalis alone was 80, for P. gingivalis in the community
it was 64. The lower number of counts observed for P. gin-
givalis proteins in the community is consistent with the
added sampling demands placed on the analytical system
by sequence overlaps in the proteomes of all three
microbes and thus the smaller number of unique proteo-
lytic fragments predicted. More discussion of this topic is
given in the explanatory notes [see Additional File 1].
Spectral count values for individual proteins are given in
data Additional file 1: Table ST1. Details regarding access
to mass spectrometry data for individual peptides and
their SEQUEST database searching scores [34], p-values
and q-values are given in the notes to the data tables [see
Additional File 1].

Proteins and functions differentially regulated by P.
gingivalis in a community
Cell envelope and cell structure
In bacterial communities significant surface-surface con-
tact occurs both within and among accumulations of the
constituent species, as was also observed in the P. gingiva-
lis-F. nucleatum-S. gordonii consortia. Regulation of outer
membrane constituents of P. gingivalis would thus be pre-
dicted in the context of a community and this was borne
out by the proteomic results. Overall, 84 proteins anno-
tated as involved in the cell envelope were detected, and
40 of these showed reduced abundance in the three spe-
cies community, indicating an extensive change to the cell
envelope. Only four proteins showed increased abun-
dance, two OmpH proteins (PGN0300, PGN0301) and
two lipoproteins (PGN1037, PGN1998). MreB
(PGN0234), a bacterial actin homologue that plays a role
in determining cell shape, showed almost a 2-fold
decrease in community derived P. gingivalis. Expression of
MreB has been found to decrease under stress or during
stationary phase in Vibrio paraheamolyticus [35]. However,
stress-related proteins were generally reduced in P. gingi-
valis cells in the community (see below) so stress is an
unlikely explanation for the change in MreB. Rather, the
decrease in MreB abundance may be due to the P. gingiva-
lis cells entering a state resembling stationary phase or


responding in a previously unseen way to the formation
of the three species community.

Protein synthesis
Extensive changes were observed in ribosomal proteins
and in translation elongation and initiation proteins.
While overall more proteins showed reduced abundance
in the three species community, the changes to the trans-
lational machinery were almost exclusively increases in
abundance. Of 49 ribosomal proteins detected, 27
showed increased abundance, while only one showed
decreased abundance. Of nine translation elongation and
initiation proteins detected, none showed significant
abundance decreases but five showed increased abun-
dance (EfG (PGN1870), putative EfG (PGN1014), EfTs
(PGN1587), EfTu (PGN1578), and If2 (PGN0255)). This
represents not only a substantial portion of the transla-
tional machinery but also a large portion, 366%, of the pro-
teins showing increased abundance. It is well known that
ribosomal content is generally proportional to growth
rate [36]; however, given that the cells were not in culture
medium during the assay, rapid growth is an unlikely
explanation for these results. The increased ribosomal
content presumably indicates increased translation, con-
sistent with the community providing physiologic sup-
port to P. gingivalis and allowing higher levels of protein
synthesis.

Vitamin synthesis
Pathways for synthesizing several vitamins showed
reduced protein abundance in the three species commu-
nity. Most of the proteins involved in thiamine diphos-
phate (vitamin B 1) biosynthesis were downregulated (Fig.
4). Thiamine is a cofactor for the 2-oxoglutarate dehydro-
genase complex that converts 2-oxoglutarate to succinyl-
CoA and for the transketolase reactions of the anaerobic
pentose phosphate pathway [37]. However, transketolase
(PGN1689, Tkt) showed no abundance change while of
the three components of the 2-oxoglutarate dehydroge-
nase complex (PGN1755, KorB) only the beta subunit
showed an abundance increase.

Only incomplete pathways have been identified for many
of the other vitamin biosynthesis activities in P. gingivalis.
However, cobalamin (vitamin B12) synthesis [38] can be
predicted to be decreased in the community, with five
(PGN0010, CobC; PGN0316, CbiG; PGN0317, CobL;
PGN0318, CobH/CbiC; PGN0735, CobU) of the seven
identified proteins having statistically significant reduc-
tions. Less complete population of pathways was
observed for pyridoxal phosphate (vitamin B6) and biotin
synthesis. Only two of the four detected proteins for vita-
min B6 synthesis showed reduced abundance (PGN1359,
PdxB and PGN2055, PdxA). For biotin synthesis, three of
the six detected proteins showed reduced abundance


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5-aminoimidazole
Ribonucleotide Hydroxymethylpyrimidine

PGN0160 PGN0159
ThiC / ThiD/E
Hydroxymethylpyrimidine Phosphate


PGN0159
ThiD/E


4-am ino-5-hyd roxym ethyl-
2-methylpyrimidine- pyrophosphate


D-Glyceraldehyde-
3-Phosphate Pyruvate


PGN2081
Dxs

1-Deoxy-D-Xylulose-
5-Phosphate
PGN0157 tyrosine
ThiH Y e+ThiS-COSH
PGN0158 ThiS
ThiG
4-Methyl-5-(B-hydroxyethyl)-
- thiazole Phosphate


PGN0159
ThiD/E


PGN0678
ThiL


PGN1516
D
ThiS + ATP ThiS-COAMP + diphosphate

ThiS-COAMP + L- cysteine TbiS-COSH + L- alanine + AMP


Thiamine Diphosphate

Figure 4
Thiamine biosynthetic pathway, showing protein abundance changes for the P. gingivalis-F. nucleatum-S. gordo-
nil/P. gingivalis comparison. Proteins catalyzing each step in the pathway are shown by their P. gingivalis ATCC 33277 gene
designation (PGN number) and protein name, where applicable. Green downward arrows indicate decreased abundance in the
three species community. Yellow squares indicate no statistically significant abundance change. Empty squares indicate that the
protein was not detected in the proteomic analysis. Thiamine diphosphate is shown in bold.


(PGN0133, BioA; PGN1721, BioF; PGN1997, BioD).
None of the vitamin/cofactor synthesis pathways showed
any indication of increased protein levels in the three spe-
cies community.

The decrease in several vitamin/cofactor pathways could
be due to a decreased utilization of those cofactors. How-
ever, in the case of thiamine, the proteins that utilize this
cofactor showed no decrease, and a possible increase in
abundance, implying that demand for vitamin B1 was
unchanged. A more likely explanation for the reduced
cofactor pathways is therefore nutrient transfer. Either one
or both of the other organisms in the three species com-
munity could be providing P. gingivalis with cofactors,
allowing reduced cofactor synthesis without reducing
expression of the cofactor dependent pathways. Nutri-
tional cross-feeding among members of oral biofilms is
well established [5], and indeed P. gingivalis has been
found to utilize succinate produced by T. denticola [39].


Nucleotide synthesis
Pyrimidine biosynthesis appeared to be reduced in the
three species community (Fig. 5) as many of the proteins
leading to the production of finished pyrimidine nucle-
otides have decreased abundance. However, the proteins
responsible for incorporating finished ribonucleotides
into RNA show unchanged or increased abundance. As
with vitamin biosynthesis this may be the result of nutri-
ent transfer from the other organisms in the community.
P. gingivalis can acquire nucleosides and nucleobases and
it has even been suggested that they may represent an
important nutrient source for P. gingivalis [40]. Consistent
with uptake of nucleosides and their precursors, uracil
permease (PGN1223) shows increased expression in the
three species community.

Purine biosynthesis does not appear to be significantly
effected in the three species community (Fig. 6). A few
proteins showed reduced abundance, but the central bio-
synthesis pathway was primarily unchanged.



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PGN1027" PGN0905,
N-Carbamoyl PyrC Y PyrD
I- t Dihdroorotate + Orotate


PGN1604
PyrB
PGN1603,
Pyrl


Carbamoyl-P
IPGN1443
CarB
PGN1444
CarA r
L-Glutamine De

PGN0026
Cdd

Deoxycytidine


PGN1140A
PyrE
+-- Orotidine-5P


dUDP


PGN2021 PC
PyrF V PC


PGN0207 PGN0646
PGN1158 SurE Y Cmk
Uracil 4 Uridine UMP 4 UDP
PG D'M 170 ....


N1226
N1232
TrxB


AL T 'U'-,' PGN1833J PGN0792
PGN1412Y U2'k PnpA
IIkPnpA
PGN0026 PGN0207 PGN0646 PGN0792
SCdd SurE Y Cmk Y PnpA
oxyuridine Cytidine P I- CMP 4 CDP + RNA
PGN1022 PGN1722' PG1226 GN1570
Tmk Udk v PGN1226 / RpoC
PGN1232 PGN1570 / PGN1571
PGN1789V1 PGN0646m T RpoC7 RpoB
I PGN1789 Cmk P PGN1571 PGN1841
dUMP dCMP dCDP RpoB V RpoA


PGN2062
TS

dTMP

PGN1022
Tmk II

Thymidine


PGN0997Y


dUTP 4
PGN1369
PGN1232
TrxB


PGN1841 CTP
RpoA -
RPoA GN1447 PGN136S[]
PPyrG GN1232
PyrG TrxB
PGN1786 dCTP
DnaN f
PGN1770YPGN1015
PolA HolA
PGN0034 PGN0894
DnaE DnaX
dTTP 4I DNA


Figure 5
Pyrimidine biosynthetic pathway, showing protein abundance changes for the P. gingivalis-F. nucleatum-S. gor-
donilP. gingivalis comparison. The protein names follow the same conventions as in Fig. 4. Green downward arrows indi-
cate decreased abundance in the three species community. Red upward arrows indicate increased abundance. Yellow squares
indicate no statistically significant abundance change. Empty squares indicate that the protein was not detected in the pro-
teomic analysis. RNA and DNA are shown in bold.


Stress proteins
The ability of the community to provide physiologic sup-
port to constituent species might result in P. gingivalis
experiencing lower levels of environmental stress than
occurs in monoculture. Consistent with this concept,
community derived P. gingivalis showed a significant
reduction in abundance of DNA repair proteins
(PGN0333, RadA; PGN0342, Ung; PGN0367, Xth;
PGN1168, MutS; PGN1316, UvrA; PGN1388, LigA;
PGN1567, RecF; PGN1585, UvrB; PGN1712, Nth;
PGN1714, Mfd; PGN1771, Poll). DNA repair genes are
generally induced in the presence of damaged DNA [41],
and lower abundance of DNA repair proteins is consistent
with the monoculture experiencing more DNA damage


than P. gingivalis in the three species community where
the presence of the partner organisms provides protection
against DNA damage.

Only two stress proteins showed increased abundance,
and then only 30% increases, the molecular chaperone
DnaK (PGN1208) and a PhoH family protein possibly
involved in oxidation protection (PGN0090).

Role of the differentially regulated P. gingivalis protein
HmuR
To begin to test the functional relevance of proteins iden-
tified as differentially regulated in the three species com-
munity, we undertook a mutational analysis. For this


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CAIR --ISAICAR
I PGN0976
HemH TPGN12201
PGN0999 PurB
PurE AICAR


AI



FGA



FGA


CA

t
Ribosy


Deoxyadenosine Adenosine

PGN1412Y IPGN1412Y

Adenine


dAMP


R PGN0865 PGN0815 PGN0814
PGN2023 PurH PGN1220 Htp Adk
PurM Adenylo- PurB Y
FAICAR succinate P AMP dADP
M PGN0865 PGN0814
NPurH ./PGN1504 PGN1460 G Adk PGN1226
PGN1666 7 PurA Gmk P / Nrd
PurL IMP PGN1449 PGN1226 ADP PGN0792
R A GuaB Nrd PnpA
PGN1706 PGN0815 PGN0635 PGN1460 PGN0792
PurN Htp XMP GuaA GMP mk GDP PnpA RNA
R t PGN1570 ,,,PGN1841
PGN1148 Hypoxanthine PGN0815 PGN0815 RpoC GN1571 oA A
PurD AL Htp Htp ^ RpoB
lamine-5P Xanthine DDGDD 4- GTP ATP


PGN1412Y/ PGN1412y
Deoxyinos

Inosine


I PGN1412-f


ine


PGN
S


1757
poT *
PGN1396


Xanthosine Guanine
PGN142 J PGN1412" PGN1948
GN osine DeoxyguosineDg
Guanosine Deoxyguosine


PGN1396

PGN1770 1
PolA v dATP
PGN0034 fl


PGN1015 '"V""e PGN0894
HolA DNA DnaX


Figure 6
Purine biosynthetic pathway, showing protein abundance changes for the P. gingivalis-F. nucleatum-S. gordoniilP.
gingivalis comparison. The protein names and arrows/squares follow the same conventions as in Fig. 5. RNA and DNA are
shown in bold. GAR: 5-Phosphoribosyl glycinamide; FGAM: 5-phosphoribosyl-N-formylglycineamidine; FGAR: I -(5'-Phosphori-
bosyl)-N-formylglycinamide; AICAR: 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole; AIR: I-(5'-Phophoribo-
syl)-5-aminoimidazole; CAIR: 5'P-Ribosyl-4-carboxy-5-aminoimidazole; SAICAR: 5'P-Ribosyl-4-(N-succinocarboximide)-5-
aminoimidazole; FAICAR: I (5'-Phosphoribosyl)-5-formamido-4-imidazole carboxamide.


purpose it was important to target a protein that directly
effectuates a biological function and lacks homologs in
the genome. HmuR, a major hemin uptake protein, and
potential adhesin [421, was selected. As shown in Fig. 7A,
while wild type P. gingivalis cells are abundant within a S.
gordonii-F. nucleatum-P. gingivalis community, P. gingivalis
cells lacking HmuR are deficient in community forma-
tion. Biovolume analysis showed a 70% reduction in
community formation by the HmuR mutant (Fig. 7C).
Furthermore, this effect was specific for the three species
community as a decrease in accumulation by the HmuR
deficient mutant was not observed in monospecies bio-
films, or in two species communities of P. gingivalis with


either S. gordonii or F. nucleatum (Fig. 7B, D-G). Hence
loss of HmuR, that is up-regulated by P. gingivalis when
the organism is associated with S. gordonii and F. nuclea-
turn, results in a phenotype that is restricted to three spe-
cies community formation. P. gingivalis cells were first
cultured in hemin excess, under which conditions the hmu
operon is expressed at a basal level [42]. As the three spe-
cies model system involves metabolically quiescent P. gin-
givalis cells in buffer, it is unlikely that the role of HmuR
is related to its hemin uptake capacity. However, TonB
dependent receptors can exhibit functions distinct from
transport across the outer membrane. For example, in E.
coli the TonB dependent catecholate siderophore receptor


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A)
S. gordonii F nucleatum P gingivalis merged


Com nity wth y (189.4 pm)



II z (29.9 pm)




Community with y(189.4 pm)
P gingivalis AhmuR


[ z (24 1 pm)
B)
P gingivalis P gingivalis
WT AhmuR


E ly y(1894pm)


x x (189,4 Mm)

(21.4 pm) (19.8 pm)

C) D)
4.0E+05 4.0E+05

3 .0E+05 ^ 3.0E05
3 0E+05 3 0E+05


d 1.OE.05 i 1. 0E+05

0.0E+00 O.OE 0+00
WT AhmuR WT AhmuR


E) F)
0.5 4.0E+05
04 0E+05
0 .3
m E 2.0E+05
0 02

01 fi 10E+05
0 O.OE+00
WT AhmuR WT AhmuR

G)
05]
0.4


0 0.2
001

WT AhmuR

Figure 7
HmuR mutant of P. gingivalis is deficient in community accumulation. A) Confocal microscopy showing x-y and x-z
projections of communities of S. gordonii (red), F. nucleatum (green) and P. gingivalis (blue) wild type (WT) or AhmuR mutant
strains. Representative image from three independent experiments. B) Confocal microscopy showing x-y and x-z projections
of single species P. gingivalis WT or AhmuR mutant accumulations. Representative image from three independent experiments.
C) Biovolume analysis of P. gingivalis WT or AhmuR mutant accumulation in the P. gingivalis-F. nucleatum-S. gordonii communities
shown in A. D) Biovolume analysis of P. gingivalis WT or AhmuR single species accumulations shown in B. E) Biomass of P. gingi-
valis WT or AhmuR single species accumulations measured by crystal violet staining and release. F) Biovolume analysis of P. gin-
givalis WT or AhmuR accumulation in two species P. gingivalis-S. gordonii communities. G) Biomass of P. gingivalis WT or AhmuR
two species accumulation with F. nucleatum measured with P. gingivalis antibodies. ** denotes p < 0.01 (n = 3) compared to
WT.


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Iha confers an adhesin function and contributes to colo-
nization and virulence in the mouse urinary tract [43].
Hence, HmuR may have a cohesive function in commu-
nity formation by P. gingivalis although further studies are
necessary to resolve this issue.

Conclusion
Complex multi-species biofilms such as pathogenic den-
tal plaque accumulate through a series of developmental
steps involving attachment, recruitment, maturation and
detachment. Choreographed patterns of gene and protein
expression characterize each of these steps. In this study
we developed a model of the early stages of plaque devel-
opment whereby three compatible species accreted into
simple communities. P. gingivalis increased in biomass
due to attachment and recruitment, and this allowed us to
catalog differential protein expression in P. gingivalis con-
sequent to contact dependent interbacterial signaling and
communication through short range soluble mediators.
The proteomic analysis indicated that around 40% of P.
gingivalis proteins exhibit changes in abundance in a com-
munity with F. nucleatum and S. gordonii, implying exten-
sive interactions among the organisms. The proteomic
results were consistent with the formation of a favorable
environment in a P. gingivalis-F. nucleatum-S. gordonii
community, wherein P. gingivalis showed evidence of
increased protein synthesis and decreased stress. Moreo-
ver, nutrient transfer may occur among the constituents of
the community. As evidenced by HmuR, these proteins
may have a functional role in the development of multi-
species communities and ultimately shape the pathogenic
potential of plaque.

Methods
Bacteria and culture conditions
Fusobacterium nucleatum subsp. nucleatum ATCC 25586
and Porphyromonas gingivalis ATCC 33277 were grown
anaerobically (85% N2, 10% H2, 5% CO2) at 37C in
trypticase soy broth supplemented with 1 mg/ml yeast
extract, 1 lig/ml menadione and 5 lig/ml hemin (TSB). S.
gordonii DL1 was grown anaerobically at 37C in Todd-
Hewitt broth (THB).

Chemicals
HPLC grade acetonitrile was from Burdick & Jackson
(Muskegon, MI, USA); high purity acetic acid (99.99%)
and ammonium acetate (99.99%), from Aldrich (Milwau-
kee, WI, USA). High purity water was generated with a
NANOpure UV system (Barnstead, Dubuque, IA, USA).

Proteomics of model bacterial communities
High density bacterial communities were generated by the
method of Merritt et al. [44]. Bacteria were cultured to
mid-log phase, harvested by centrifugation and resus-
pended in pre-reduced PBS (rPBS). 1 x 109 cells of P. gin-


givalis were mixed with an equal number of S. gordonii and
F. nucleatum as a combination of the three species. P. gin-
givalis cells alone were also used as a control. Two inde-
pendent biological replicates from separate experiments
comprised of at least two technical replicates were ana-
lyzed. Bacteria were centrifuged at 3000 g for 5 min, and
pellets were held in 1 ml pre-reduced PBS in an anaerobic
chamber at 37C for 18 h. The bacterial cells remain via-
ble under these conditions, as determined by both colony
counts and live/dead fluorescent staining. Supernatant
and bacterial cells were separated and processed sepa-
rately. Bacterial cells were lysed with ice cold sterile dis-
tilled water and proteins were digested with trypsin as
previously described for P. gingivalis [33], then fraction-
ated on a 2.0 mm x 150 mm YMC polymer C18 column.
There were five pre-fractions collected for each cellular
sample, with a final volume of 50 il for each fraction. The
2D capillary HPLC/MS/MS analyses [32,45,46] were con-
ducted using an in-house fabricated semi-automated sys-
tem, consisting of a Thermo LTQ mass spectrometer
(Thermo Fisher Corp. San Jose, CA, USA), a Magic 2002
HPLC (Michrom BioResouces, Inc., Auburn, CA, USA), a
Pump 11 Plus syringe pump (Harvard Apparatus, Inc.,
Holliston, MA, USA), an Alcott 718 autosampler (Alcott
Chromatography, Inc., Norcross, GA, USA) and a micro-
electrospray interface built in-house. About 2 jil of sample
solution was loaded into a 75 jim i.d. x 360 jim o.d. cap-
illary column packed with 11 cm of AQUA C18 (5 jim,
Phenomenex, Torrance, CA, USA) and 4 cm of polysulfoe-
thyl aspartamide SCX (strong cation exchange) resin
(PSEA, 5 jim, Michrom BioResouces, Inc.). The peptides
were eluted with a seven step salt gradient (0, 10, 25, 50,
100, 250 and 500 mM ammonium acetate) followed by
an acetonitrile gradient elution (Solvent A: 99.5% water,
0.5% acetic acid. Solvent B: 99.5% acetonitrile, 0.5% ace-
tic acid), 5% B hold 13 min, 5-16% B in 1 min, hold 6
min, 16-45% B in 45 min, 40-80% B in 1 min, hold 9
min, 80-5% B in 5 min, then hold 10 min. For the
secreted proteins in the supernatant no pre-fractionation
or SCX was performed, and 4 jil of digested sample was
loaded into a 75 im i.d. x 360 jim o.d. column packed
with 11 cm AQUA C18 for a single dimension of capillary
HPLC/tandem MS analysis. After 20 min of flushing with
5% acetonitrile, peptides were eluted by an acetonitrile
gradient (5-12% B in 1 min, hold 9 min, 12-40% B in 50
min, 40-80% B in 1 min, hold 10 min, 80-5% B in 5 min,
hold 14 min). The MS1 scan range for all samples was
400-2000 m/z. Each MS1 scan was followed by 10 MS2
scans in a data dependent manner for the 10 most intense
ions in the MS1 scan. Default parameters under Xcalibur
1.4 data acquisition software (Thermo Fisher) were used,
with the exception of an isolation width of 3.0 m/z units
and a normalized collision energy of 40%.




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Data processing and protein identification
Raw data were searched by SEQUEST [34] against a FASTA
protein ORF database consisting of the Ver. 3.1 curation
of P. gingivalis W83 (2006, TIGR-CMR [47]), S. gordonii
Challis NCTC7868 (2007, TIGR-CMR [48], F. nucleatum
ATCC 25586 (2002, TIGR-CMR [49]), bovine (2005, UC
Santa Cruz), nrdb human subset (NCBI, as provided with
Thermo Bioworks ver. 3.3) and the MGC (Mammalian
Gene collection, 2004 curation, NIH-NCI [50]) concate-
nated with the reversed sequences. After data processing,
the genome sequence for strain 33277 became available
[31] and the data were subsequently cross-referenced to
PGN numbers from the 33277 specific FASTA database
provided by LANL (personal communication with G.
Xie). Although Naito et al. [31] reported extensive
genome re-arrangements between W83 and ATCC 33277,
the actual protein amino acid sequences are sufficiently
similar across the proteome that the use of a database
based on W83 was not expected to greatly impact the anal-
ysis. Our proteomic methods are not sensitive to genome
re-arrangements, only to changes in amino acid sequence
for a given protein. The reversed sequences were used for
purposes of calculating a peptide level qualitative FDR
using the published method [51,52]. The SEQUEST pep-
tide level search results were filtered and grouped by pro-
tein using DTASelect [53], then input into a FileMaker
script developed in-house [32,33] for further processing.
The DTASelect Ver. 1.9 filter parameters were: peptides
were fully tryptic; ACn/Xcorr values for different peptide
charge states were 0.08/1.9 for +1, 0.08/2.0 for + 2, and
0.08/3.3 for +3; all spectra detected for each sequence
were retained (t = 0). Only peptides that were unique to a
given ORF were used in the calculations, ignoring tryptic
fragments that were common to more than one ORF or
more than one organism, or both. In practice this had the
consequence of reducing our sampling depth from what
we have achieved with single organism studies [27,32,33 ],
because the gene sequence overlap among the three
organisms is significant. A bioinformatic analysis (data
not shown) of inferred protein sequence overlaps
between P. gingivalis and S. gordonii or F. nucleatum sug-
gested the reduction in the number of predicted tryptic
fragments unique to P. gingivalis would not be sufficient
to impact the analysis of more than a small number of
proteins. The qualitative peptide level FDR was controlled
to approximately 5% for all conditions by selecting a min-
imum non-redundant spectral count cut-off number
appropriate to the complexity of each condition, P. gingi-
valis alone or the P. gingivalis-F. nucleatum-S. gordonii com-
munity.

Protein abundance ratio calculations
Protein relative abundances were estimated on the basis
of summed intensity or spectral count values [27,32,33]


for proteins meeting the requirements for qualitative
identification described above. Summed intensity refers
to the summation of all processed parent ion (peptide)
intensity measurements (MSI) for which a confirming
CID spectrum (MS2) was acquired according to the
DTASelect filter files. For spectral counts, the redundant
numbers of peptides uniquely associated with each ORF
were taken from the DTAselect filter table (t = 0). Spectral
counting is a frequency measurement that has been dem-
onstrated in the literature to correlate with protein abun-
dance [54]. These two ways of estimating protein relative
abundance, that avoid the need for stable isotope labe-
ling, have been discussed in a recent review [27] with spe-
cific reference to microbial systems. To calculate protein
abundance ratios, a normalization scheme was applied
such that the total spectral counts or total intensities for
all P. gingivalis proteins in each condition were set equal
for each comparison. This normalization also had the
effect of zero centering the log2 transformed relative abun-
dance ratios, see Fig. 2 (and also the frequency histograms
in Additional file 1: Figs. SF5 and SF6). The normalized
data for each abundance ratio comparison was tested for
significance using either a global G-test or a global paired
t-test for each condition, the details of which have been
published for this type of proteomics data in which all
biological replicates are compared against each other
[55,56], and are also described in the explanatory notes
[see Additional File 1]. Both of these testing procedures
weigh deviation from the null hypothesis of zero abun-
dance change and random scatter in the data to derive a
probability or p-value that the observed change is a ran-
dom event, i.e. that the null hypothesis of no abundance
change is true. Each hypothesis test generated a p-value
that in turn was used to generate a q-value as described
[24,32], using the R package QVALUE [26]. The q-value in
this context is a measure of quantitative FDR [25] that
contains a correction for multiple hypothesis testing. A q
cut-off value of 0.01 was used for all ratios reported in
Additional file 1: Table ST1. All statistical calculations
were done in R (Ver. 2.5.0), using source code that has
been published [32,33,55]. Only proteins with data con-
sisting of confirmed high scoring MS2 mass spectra (high
scoring qualitative database matches as described above)
present in both the numerator and denominator of the
abundance ratio comparison were listed as significantly
changed in Additional file 1. Certain proteins listed in the
tables with q-values = 0.01 are still coded yellow for no
significant abundance change due to missing data in
either the numerator or the denominator.

Ontology analysis
An overall list of detected proteins as well as lists of pro-
teins that showed increased or decreased levels in the
three species community were prepared using Entrez gene



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identifiers. Ontology analyses were then conducted using
the DAVID [57] functional annotation clustering feature
with the default databases. Both increased and decreased
protein level lists were analyzed using the overall list of
detected proteins as the background. Potentially interest-
ing clusters identified by DAVID were then examined
manually.

Construction of P. gingivalis HmuR mutant
A mutation in the hmuR gene was generated using liga-
tion-independent cloning of PCR mediated mutagenesis
(LIC-PCR) [58]. A 2.1-kb ermF-ermAM cassette was intro-
duced into the hmuR gene by three steps of PCR to yield a
hmuR-erm-hmuR DNA fragment as described previously
[59]. The fragment was then introduced into P. gingivalis
33277 by electroporation. The hmuR deficient mutant
(AhmuR) was generated via a double crossover event that
replaces hmuR with the hmuR-erm-hmuR DNA fragment in
the 33277 chromosome. The mutants were selected on
TSB plates containing erythromycin (5 ig/ml), and the
mutation was confirmed by PCR analysis. Growth rates of
mutant and parent strains were equivalent.

Quantitative community development assays
i) Crystal violet assay. Homotypic community formation
by P. gingivalis was quantified by a microtiter plate assay
[60], as adapted for P. gingivalis [61]. Parental and mutant
strains in early log phase (2 x 108 cells) were incubated at
37C anaerobically for 24 h. Wells were washed, stained
with 1% crystal violet and destined with 95% ethanol.
Absorbance at 595 nm was determined in a Benchmark
microplate reader. ii) ELISA. F. nucleatum was incubated at
37 C anaerobically for 36 h in microtiter plate wells. After
washing, parental and mutant P. gingivalis strains (2 x 106
cells) were incubated with the fusobacterial biofilm at
37C anaerobically for 24 h. P. gingivalis accumulation
was detected with antibodies to whole cells (1:10,000)
followed by peroxidase-conjugated secondary antibody
(1:3,000), each for 1 h at 37 C. Antigen-antibody binding
was determined by a colorimetric reaction using the
3,3',5,5'-tetramethylbenzidine (TMB) liquid substrate,
and absorbance at 655 nm. P. gingivalis antibody binding
to the fusobacterial biofilm alone was subtracted as back-
ground. iii) Confocal microscopy assay. A. Single species.
P. gingivalis was stained with 4',6-diamidino-2-phenylin-
dole (50 |ig ml-1) and 2 x 106 cells in rPBS incubated
anaerobically at 37C for 16 h with rocking in individual
chambers of the CultureWell coverglass system (Grace Bio
Labs). Chambers were washed three times in rPBS. B. Dual
species. Heterotypic P. gingivalis-S. gordonii communities
were generated as described previously [15]. S. gordonii
cells were labeled with hexidium iodide (15 |ig ml-1), then
cultured anaerobically at 37 C for 16 h with rocking in
CultureWell chambers. P. gingivalis was stained with 5-


(and-6)-carboxyfluorescein, succinimidyl ester (10 |ig ml-
1), and 2 x 106 cells in rPBS were reacted with the surface
attached S. gordonii for 24 h anaerobically at 37C with
rocking. C) Three species. Surface attached hexidium
iodide-stained S. gordonii were generated as above. Fluo-
rescein stained F. nucleatum (2 x 106 cells in rPBS) reacted
with S. gordonii for 24 h anaerobically at 37C with rock-
ing. The coverglass was then washed with rPBS to remove
non-attached bacteria. P. gingivalis was stained with 4',6-
diamidino-2-phenylindole (50 |ig ml-1) and 2 x 106 cells
in rPBS were added and further incubated for 24 h anaer-
obically at 37C with rocking. Communities were
observed on a Bio-Rad Radiance 2100 confocal laser scan-
ning microscope (Blue Diode/Ar/HeNe) system with an
Nicon ECLIPSE TE300 inverted light microscope and 40 x
objective using reflected laser light of combined 405, 488
and 543 nm wavelengths where appropriate. A series of
fluorescent optical x-y sections were collected to create
digitally reconstructed images (z-projection of x-y sec-
tions) of the communities with Image I V1.34s (National
Institutes of Health) or Laser Sharp software (Bio-Rad). Z
stacks of the x-y sections of CLSM were converted to com-
posite images with "Iso Surface" functions of the "Sur-
pass" option on Imaris 5.0.1 (Bitplane AG; Zurich,
Switzerland) software. Iso Surface images of P. gingivalis
were created at threshold of 20 and smoothed with Gaus-
sian Filter function at 0.5 width, and P. gingivalis biovol-
ume was calculated.

Biofilm assays were repeated independently three times
with each strain in triplicate. Crystal violet results were
compared by t-tests. Biovolume calculations were com-
pared with a t-test using the SPSS statistics software.

Abbreviations
ATCC: American Type Culture Collection; DAVID: Data-
base for Annotation, Visualization and Integrated Discov-
ery; FDR: false discovery rate; FNR: false negative rate;
LANL: Los Alamos National Laboratory; LOWESS: Locally
weighted scatterplot smoothing; MS: Mass spectrometry;
MS1: First stage of tandem mass spectrometry; MS2: Sec-
ond stage of tandem mass spectrometry; SCX: strong cat-
ion exchange; TIGR-CMR: The Institute for Genomic
Research Comprehensive Microbial Resource, now part of
the J. Craig Venter Institute.

Authors' contributions
MK carried out the community construction and analysis
by confocal microscopy; ELH did the pathway analysis;
QX and TW performed the protein biochemistry, separa-
tions and mass spectrometry; HX constructed the hmuR
mutant; MH and RJL conceived the experiments. MH,
ELH, MK and RJL wrote the manuscript. MK and ELH con-
tributed equally.



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BMC Microbiology 2009, 9:98




Additional material


Acknowledgements
This work was supported by NIDCR research grants DE14372, DEI2505
and DE I I I 11, and by a Grant-in-Aid for Scientific Research (C)(20592453)
from the Ministry of Education, Culture, Sports, Science and Technology of
Japan. We thank the Institute for Systems Biology and Nittin Baliga for the
use of Gaggle and assistance with the pathway analysis. We thank Fred Taub
for the FileMaker database and assistance with the figures. We thank LAN L
(Los Alamos National Laboratory) and Gary Xie in particular for bioinfor-
matics support.

References
I. Diaz PI, Chalmers NI, Rickard AH, Kong C, Milburn CL, Palmer RJ Jr,
Kolenbrander PE: Molecular characterization of subject-spe-
cific oral microflora during initial colonization of enamel.
AppI Environ Microbiol 2006, 72:2837-2848.
2. Rosan B, Lamont RJ: Dental plaque formation. Microbes Infect
2000, 2:1599-1607.
3. Ximenez-Fyvie LA, Haffajee AD, Socransky SS: Comparison of the
microbiota of supra- and subgingival plaque in health and
periodontitis. J Clin Periodontol 2000, 27:648-657.
4. Socransky SS, Haffajee AD, Ximenez-Fyvie LA, Feres M, Mager D:
Ecological considerations in the treatment of Actinobacillus
actinomycetemcomitans and Porphyromonas gingivalis perio-
dontal infections. Periodontol 2000 1999, 20:341-362.
5. Kolenbrander PE, Andersen RN, Blehert DS, Egland PG, Foster JS,
Palmer RJ Jr: Communication among oral bacteria. Microbiol
Mol Biol Rev 2002, 66:486-505.
6. Kolenbrander PE, Palmer RJ Jr, Rickard AH, Jakubovics NS, Chalmers
NI, Diaz PI: Bacterial interactions and successions during
plaque development. Periodontol 2000 2006, 42:47-79.
7. Marsh PD: Dental plaque as a biofilm and a microbial commu-
nity implications for health and disease. BMC Oral Health
2006, 6(Suppl 1):S14.
8. Jenkinson HF, Lamont RJ: Oral microbial communities in sick-
ness and in health. Trends Microbiol 2005, 13:589-595.
9. Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM,
Lory S, Greenberg EP: Gene expression in Pseudomonas aerugi-
nosa biofilms. Nature 2001, 413:860-864.
10. Stoodley P, Sauer K, Davies DG, Costerton JW: Biofilms as com-
plex differentiated communities. Annu Rev Microbiol 2002,
56:187-209.
II. Jakubovics NS, Gill SR, lobst SE, Vickerman MM, Kolenbrander PE:
Regulation of gene expression in a mixed-genus community:
stabilized arginine biosynthesis in Streptococcus gordonii by
coaggregation with Actinomyces naeslundii. J Bacteriol 2008,
190:3646-3657.
12. Simionato MR, Tucker CM, Kuboniwa M, Lamont G, Demuth DR,
Tribble GD, Lamont RJ: Porphyromonas gingivalis genes involved
in community development with Streptococcus gordonii.
Infect Immun 2006, 74:6419-6428.
13. Ang CS, Veith PD, Dashper SG, Reynolds EC: Application of 160/
180 reverse proteolytic labeling to determine the effect of
biofilm culture on the cell envelope proteome of Porphyrom-
onas gingivalis W50. Proteomics 2008, 8:1645-1660.


http://www.biomedcentral.com/1471-2180/9/98


Additional file 1
DataTables. Data tables, explanatory notes and supporting figures. This
file contains the proteomic data tables ST1 and ST2, explanatory notes for
each heading in the tables, a note regarding the handling of missing data
and additional figures informative of proteome coverage for the model
community described in data tables ST1 and ST2.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1471 -
2180-9-98-Sl.pdf]


14. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE: Defining the
normal bacterial flora of the oral cavity. J Clin Microbiol 2005,
43:5721-5732.
15. Kuboniwa M, Tribble GD, James CE, Kilic AO, Tao L, Herzberg MC,
Shizukuishi S, Lamont RJ: Streptococcus gordonii utilizes several
distinct gene functions to recruit Porphyromonas gingivalis
into a mixed community. Mol Microbiol 2006, 60:121-139.
16. Lamont RJ, EI-Sabaeny A, Park Y, Cook GS, Costerton JW, Demuth
DR: Role of the Streptococcus gordonii SspB protein in the
development of Porphyromonas gingivalis biofilms on strepto-
coccal substrates. Microbiology 2002, 148:1627-1636.
17. Capestany CA, Tribble GD, Maeda K, Demuth DR, Lamont RJ: Role
of the CIp system in stress tolerance, biofilm formation, and
intracellular invasion in Porphyromonas gingivalis. J Bacteriol
2008, 190:1436-1446.
18. Slots J, Gibbons RJ: Attachment of Bacteroides melaninogenicus
subsp. asaccharolyticus to oral surfaces and its possible role in
colonization of the mouth and of periodontal pockets. Infect
Immun 1978, 19:254-264.
19. Bradshaw DJ, Marsh PD, Watson GK, Allison C: Role of Fusobacte-
rium nucleatum and coaggregation in anaerobe survival in
planktonic and biofilm oral microbial communities during
aeration. Infect Immun 1998, 66:4729-4732.
20. Yao ES, Lamont RJ, Leu SP, Weinberg A: Interbacterial binding
among strains of pathogenic and commensal oral bacterial
species. Oral Microbiol Immunol 1996, I 1:35-4 1.
21. Foster JS, Kolenbrander PE: Development of a multispecies oral
bacterial community in a saliva-conditioned flow cell. AppI
Environ Microbiol 2004, 70:4340-4348.
22. EbersoleJL, Feuille F, Kesavalu L, HoltSC: Host modulation of tis-
sue destruction caused by periodontopathogens: effects on a
mixed microbial infection composed of Porphyromonas gingi-
valis and Fusobacterium nucleatum. Microb Pathog 1997,
23:23-32.
23. Saito A, Inagaki S, Kimizuka R, Okuda K, Hosaka Y, Nakagawa T, Ishi-
hara K: Fusobacterium nucleatum enhances invasion of human
gingival epithelial and aortic endothelial cells by Porphyrom-
onas gingivalis. FEMS Immunol Med Microbiol 2008, 54:349-355.
24. Storey JD, Tibshirani R: Statistical significance for genomewide
studies. Proc Natl Acad Sci USA 2003, 100:9440-9445.
25. Benjamini Y, Yekutieli D: Quantitative trait Loci analysis using
the false discovery rate. Genetics 2005, 171:783-790.
26. Storey Research Group, Qvalue [http://genomics.prince
ton.edu/storeylab/qvalue/]
27. Xia Q, Hendrickson EL, Wang T, Lamont RJ, Leigh JA, Hackett M:
Protein abundance ratios for global studies of prokaryotes.
Proteomics 2007, 7:2904-2919.
28. Knudsen S: Guide to analysis of DNA microarray data. Hobo-
ken NJ: Wiley-Liss; 2004:33-55.
29. Hendrickson EL, Lamont RJ, Hackett M: Tools for interpreting
large-scale protein profiling in microbiology. J Dent Res 2008,
87:1004-1015.
30. Cleveland WS: A program for smoothing scatterplots by
robust locally weighted regression. American Statistician 1981,
35:54.
31. Naito M, Hirakawa H, Yamashita A, Ohara N, Shoji M, Yukitake H,
Nakayama K, Toh H, Yoshimura F, Kuhara S, et al.: Determination
of the genome sequence of Porphyromonas gingivalis strain
ATCC 33277 and genomic comparison with strain W83
revealed extensive genome rearrangements in P. gingivalis.
DNA Res 2008, 15:215-225.
32. Xia Q, Wang T, Park Y, Lamont RJ, Hackett M: Differential quan-
titative proteomics of Porphyromonas gingivalis by linear ion
trap mass spectrometry: non-label methods comparison, q-
values and LOWESS curve fitting. International journal of Mass
Spectrometry 2007, 259:105- 16.
33. Xia Q, Wang T, Taub F, Park Y, Capestany CA, Lamont RJ, Hackett
M: Quantitative proteomics of intracellular Porphyromonas
gingivalis. Proteomics 2007, 7:4323-4337.
34. EngJK, McCormack AL, Yates JR: An approach to correlate tan-
dem mass-spectral data of peptides with amino-acid-
sequences in a protein database. journal of the American Society of
Mass Spectrometry 1994, 5:976-989.
35. Chiu SW, Chen SY, Wong HC: Localization and expression of
MreB in Vibrio parahaemolyticus under different stresses. AppI
Environ Microbiol 2008, 74:7016-7022.



Page 13 of 14
(page number not for citation purposes)








http://www.biomedcentral.com/1471-2180/9/98


36. Nomura M, Gourse R, Baughman G: Regulation of the synthesis
of ribosomes and ribosomal components. Annu Rev Biochem
1984, 53:75-117.
37. Schenk G, Duggleby RG, Nixon PF: Properties and functions of
the thiamin diphosphate dependent enzyme transketolase.
Intj Biochem Cell Biol 1998, 30:1297-1318.
38. Roper JM, Raux E, Brindley AA, Schubert HL, Gharbia SE, Shah HN,
Warren MJ: The enigma of cobalamin (Vitamin B 12) biosyn-
thesis in Porphyromonas gingivalis. Identification and charac-
terization of a functional corrin pathway. j Biol Chem 2000,
275:40316-40323.
39. Grenier D: Nutritional interactions between two suspected
periodontopathogens, Treponema denticola and Porphyrom-
onas gingivalis. Infect Immun 1992, 60:5298-5301.
40. Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen
JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, et al.: Complete
genome sequence of the oral pathogenic bacterium Porphy-
romonas gingivalis strain W83. j Bacteriol 2003, 185:5591-560 1.
41. Volkert MR, Landini P: Transcriptional responses to DNA dam-
age. Curr Opin Microbiol 2001, 4:178-185.
42. Lewis JP, Plata K, Yu F, Rosato A, Anaya C: Transcriptional organ-
ization, regulation and role of the Porphyromonas gingivalis
W83 hmu haemin-uptake locus. Microbiology 2006,
152:3367-3382.
43. Leveille S, Caza M, Johnson JR, Clabots C, Sabri M, Dozois CM: Iha
from an Escherichia coli urinary tract infection outbreak
clonal group A strain is expressed in vivo in the mouse uri-
nary tract and functions as a catecholate siderophore recep-
tor. Infect Immun 2006, 74:3427-3436.
44. Merrittj, Kreth J, Shi W, Qi F: LuxS controls bacteriocin produc-
tion in Streptococcus mutans through a novel regulatory com-
ponent. Mol Microbiol 2005, 57:960-969.
45. Washburn MP, Ulaszek R, Deciu C, Schieltz DM, Yates JR 3rd: Anal-
ysis of quantitative proteomic data generated via multidi-
mensional protein identification technology. Anal Chem 2002,
74:1650-1657.
46. Washburn MP, Wolters D, Yates JR 3rd: Large-scale analysis of
the yeast proteome by multidimensional protein identifica-
tion technology. Nat Biotechnol 2001, 19:242-247.
47. Porphyromonas gingivalis W83 Genome Page [http://
cmr.icvi.org/tigr-scripts/CMR/GenomePage.cgi?org=gpg]
48. Streptococcus gordonii Challis NCTC7868 Genome Page
[http://cmr.icvi.org/tigr-scripts/CMR/GenomePage.ci ?org=gsg]
49. Fusobacterium nucleatum ATCC 25586 Genome Page [http:/
/cmr.icvi.org/cgi-bin/CMR/GenomePage.cgi?org=ntfn01]
50. Mammalian Gene Collection [http://mgc.nci.nih.gov]
51. Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP: Evaluation of
multidimensional chromatography coupled with tandem
mass spectrometry (LC/LC-MS/MS) for large-scale protein
analysis: the yeast proteome. j Proteome Res 2003, 2:43-50.
52. Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP: Intensity-based
protein identification by machine learning from a library of
tandem mass spectra. Nat Biotechnol 2004, 22:214-219.
53. Tabb DL, McDonald WH, Yates JR 3rd: DTASelect and Contrast:
tools for assembling and comparing protein identifications
from shotgun proteomics. j Proteome Res 2002, 1:21-26.
54. Liu H, Sadygov RG, Yates JR 3rd: A model for random sampling
and estimation of relative protein abundance in shotgun pro-
teomics. Anal Chem 2004, 76:4193-420 1.
55. Bosch G, Skovran E, Xia Q, Wang T, Taub F, Miller JA, Lidstrom ME,
Hackett M: Comprehensive proteomics of Methylobacterium
extorquens AM I metabolism under single carbon and non-
methylotrophic conditions. Proteomics 2008, 8:3494-3505.
56. Sokal RR, Rohlf FJ: Biometry, the principles and practice of sta-
tistics in biological research. New York: WH Freeman;
1995:715-724.
57. Huang da W, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y,
Stephens R, Baseler MW, Lane HC, et al.: DAVID Bioinformatics
Resources: expanded annotation database and novel algo-
rithms to better extract biology from large gene lists. Nucleic
Acids Res 2007, 35:WI 69-175.
58. Aslanidis C, de Jong PJ: Ligation-independent cloning of PCR
products (LIC-PCR). Nucleic Acids Res 1990, 18:6069-6074.
59. Wu J, Lin X, Xie H: Regulation of hemin binding proteins by a
novel transcriptional activator in Porphyromonas gingivalis. j
Bacterial 2009, 191:1 15-122.


60. O'Toole GA, Kolter R: Initiation of biofilm formation in Pseu-
domonas fluorescens WCS365 proceeds via multiple, conver-
gent signalling pathways: a genetic analysis. Mol Microbiol 1998,
28:449-461.
61. Capestany CA, Kuboniwa M, Jung IY, Park Y, Tribble GD, Lamont RJ:
Role of the Porphyromonas gingivalis InlJ protein in homo-
typic and heterotypic biofilm development. Infect Immun 2006,
74:3002-3005.


Page 14 of 14
(page number not for citation purposes)


BMC Microbiology 2009, 9:98


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