Supporting Information for Proteomics DOI 10.1002/pmic.200500112

Bindu Nanduri, Mark L. Lawrence, Sucharith Vanguri and Shane C. Burgess

Proteomic analysis using an unfinished bacterial genome: The effects of subminimum inhibitory concentrations of antibiotics on Mannheimia haemolytica virulence factor expression

ยช 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de Supplementary Material. List of all identified M. haemolytica proteins

GI #a % AAb COGc Protein/COG#d Protein description identity M. haemolytica proteins in the nrpd database 56788308 C Mdh Malic 56606831 E Asd Aspartate-semialdehyde dehydrogenase 38046578 E LapT Arginine-binding periplasmic protein 2 56606845 G GalE UDP-glucose 4-epimerase 97190 G O-sialoglycoprotein endopeptidase 2645727 I FabI Short-chain alcohol dehydrogenase homolog (enoyl-acyl-carrier-protein ) 2731435 K FIS Factor for inversion stimulation Fis, transcriptional activator 28974007 L Tnp 279565 M Ssa1 Serotype-specific antigen precursor 1683632 M KdsA 3-deoxy-D-manno-octulosonic acid synthetase KdsA 3283200 M PlpD Lipoprotein Plp4 6424988 M CpxD 6424993 M UDP-N-acetylglucosamine-2-epimerase 6424995 M PhyA Capsule polysaccharide export protein 45758047 M OmpA Heat-modifiable outer membrane protein 541237 M Outer membrane 30K protein 6424994 M WecC UDP-N-acetylmannosamine dehydrogenase 2738813 O DnaK Molecular chaperone 15987895 O LktC Leukotoxin C 11762018 O LktA Leukotoxin A 3978164 P FbpA Iron binding protein FbpA precursor 1353671 R GS60 antigen 282115 NAe Hypothetical protein 2 3947938 NA PlpE Outer membrane lipoprotein PlpE 6424991 NA Unknown

Proteins confirmed by gene/protein name or COG number from draft genome 15602146 87 C SucD Succinyl-CoA synthetase, alpha subunit 15602586 65 C TtrA Anaerobic dehydrogenases, typically selenocysteine-containing 15603357 83 C AtpA F0F1-type ATP synthase, alpha subunit 15603471 90 C Idp Isocitrate dehydrogenases 32033610 80 C Ppc Phosphoenolpyruvate carboxylase 32033738 82 C GlcD FAD/FMN-containing dehydrogenases 32034038 98 C IscU NifU homolog involved in Fe-S cluster formation 32034767 87 C SucA 2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) co 32034775 71 C LldP L-lactate permease 32035015 84 C PckA Phosphoenolpyruvate carboxykinase (ATP) 32035743 86 C COG1139 Uncharacterized conserved protein containing a ferredoxin-l domain PM1854 46143536 90 C SdhA Succinate dehydrogenase/fumarate reductase, flavoprotein su 46143581 84 C BisC Anaerobic dehydrogenases, typically selenocysteine-containing 52424094 77 C OadA Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, alpha subunit 52424975 48 C NqrA Na+-transporting NADHubiquinone alpha subunit 52425391 80 C AceE Pyruvate dehydrogenase complex, dehydrogenase (E1) component 52426187 33 C PutA Delta 1-pyrroline-5-carboxylate dehydrogenase 53728869 84 C NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF 53728986 90 C Lpd Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component 53728987 76 C AceF Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component 53729160 86 C AckA Acetate 32033425 76 CH HemG Flavodoxin 15603350 81 D GidA NAD/FAD-utilizing enzyme apparently involved in cell divisi 32033984 83 D Mrp ATPases involved in chromosome partitioning 46143719 81 D MukB Uncharacterized protein involved in chromosome partitioning 581456 70 E AroA 3-phosphoshikimate-1-carboxyvinyltransferase 15603060 80 E HisG ATP phosphoribosyltransferase 15603295 83 E CysE Serine acetyltransferase 15603439 78 E AsnA Asparagine synthetase A 15603490 75 E IlvD Dihydroxyacid /phosphogluconate dehydratase 15603633 58 E SelA Selenocysteine synthase 15603772 99 E OppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component 32033631 83 E MetC Cystathionine beta-/cystathionine gamma-synthases 32034037 94 E NifS Cysteine sulfinate desulfinase/cysteine desulfurase and rel 32034165 90 E ArgF Ornithine carbamoyltransferase 32034923 81 E GlnB regulatory protein PII 32035348 86 E AroG 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase 32035370 84 E LysC Aspartokinases 32035395 92 E DppB ABC-type dipeptide/oligopeptide/nickel transport systems, p 46143264 91 E PotD Spermidine/putrescine-binding periplasmic protein 46143274 95 E ArgG Argininosuccinate synthase 46143474 90 E ThrB 46143532 88 E LysA Diaminopimelate decarboxylase 46143754 78 E DapD Tetrahydrodipicolinate N-succinyltransferase 46143847 91 E PotA ABC-type spermidine/putrescine transport systems, ATPase co 46143854 80 E DdpA ABC-type dipeptide transport system, periplasmic component 46143878 91 E DapA Dihydrodipicolinate synthase/N-acetylneuraminate 52424921 88 E AroC Chorismate synthase 52425089 72 E PepN Aminopeptidase N 52425157 67 E TyrA Chorismate mutase 52425659 68 E ProA Gamma-glutamyl phosphate reductase 52425712 72 E PheA Prephenate dehydratase 52426248 62 E TrpE Anthranilate/para-aminobenzoate synthases component I 53728921 40 E HisM ABC-type amino acid transport system, permease component 53728984 72 E SstT Na+/serine symporter 53729180 77 E KamA Lysine 2,3-aminomutase 15602089 80 F PurD Phosphoribosylamine-glycine 15602485 71 F PurK Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) 15602743 57 F Dgt dGTP triphosphohydrolase 15603676 45 F CyaA Adenylate cyclase 32033968 63 F NupC Nucleoside permease 32033969 71 F DeoC Deoxyribose-phosphate aldolase 32033970 92 F DeoD Purine-nucleoside 32034124 76 F CpdB 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases 32034191 62 F Cdd Cytidine deaminase 32034313 85 F PurL Phosphoribosylformylglycinamidine (FGAM) synthase, syntheta 32035815 92 F Apt Adenine/guanine phosphoribosyltransferases and related PRPP 46143444 98 F Adk 46143460 95 F PurA Adenylosuccinate synthase 46143605 88 F Upp Uracil phosphoribosyltransferase 46143710 85 F GuaB IMP dehydrogenase/GMP reductase 46143711 93 F GuaA GMP synthase, PP-ATPase domain/subunit 52424682 67 F PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN 52425378 81 F PurU Formyltetrahydrofolate 53728853 79 F ThyA Thymidylate synthase 53728876 88 F NrdF Ribonucleotide reductase, beta subunit 15601934 74 G PfkA 6- 15602035 46 G PtsN system mannitol/fructose-specific IIA domain (Ntr-type) 15602900 55 G GalK 15602903 77 G MglB ABC-type sugar transport system, periplasmic component MglB 15603237 22 G RbsK Sugar , family 15603371 91 G GpmA Phosphoglycerate mutase 1 32034150 96 G GmhA Phosphoheptose 32034170 81 G FruB Phosphotransferase system, HPr-related proteins 32034172 88 G NagE Phosphotransferase system IIA components 32034335 51 G ManZ Phosphotransferase system, mannose/fructose/N-acetylgalacto 32034786 82 G TpiA Triosephosphate isomerase 32035456 83 G AraD Ribulose-5-phosphate 4-epimerase and related epimerases and 32035526 91 G Eno 32035646 65 G MalQ 4-alpha-glucanotransferase 46143450 89 G Gnd 6-phosphogluconate dehydrogenase 46143685 93 G RpiA Ribose 5-phosphate isomerase 46143789 91 G TktA Transketolase 46143806 70 G GlgB 1,4-alpha-glucan branching enzyme 52424113 75 G AraA L-arabinose isomerase 52424299 85 G Fba Fructose/tagatose bisphosphate aldolase 52424592 82 G UxuA D-mannonate dehydratase 52424698 80 G RbsB ABC-type sugar transport system, periplasmic component 52425466 57 G XylB 53728742 75 G ProP Permeases of the major facilitator superfamily 53728801 95 G Pgk 3- 53728880 26 G GntT H+/gluconate symporter and related permeases 53728901 81 G SuhB Archaeal fructose-1,6-bisphosphatase and related of 53729272 84 G MtlD Mannitol-1-phosphate/altronate dehydrogenases 53729273 72 G mtlA Phosphotransferase system, mannitol-specific IIBC component 15602961 90 H MenB Dihydroxynaphthoic acid synthase 15603097 53 H Snz1 Pyridoxine biosynthesis enzyme 15603526 58 H RibF FAD synthase 15603551 89 H UbiE Methylase involved in ubiquinone/menaquinone biosynthesis 15603766 96 H BioF 7-keto-8-aminopelargonate synthetase and related enzymes 15603795 86 H LipA Lipoate synthase 32033744 85 H MoaE Molybdopterin converting factor, large subunit 32033974 87 H HemC Porphobilinogen deaminase 32034922 90 H MoaB Molybdopterin biosynthesis enzymes 46143459 83 H ThiI Thiamine biosynthesis ATP pyrophosphatase 52424724 85 H MetK S-adenosylmethionine synthetase 52424860 73 H PdxK Pyridoxal/pyridoxine/pyridoxamine kinase 52425228 55 H FolC Folylpolyglutamate synthase 53729101 80 H NadR Predicted ATPase/kinase involved in NAD metabolism 15602110 60 I IspE 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate synthase 32034925 89 I LytB Penicillin tolerance protein 46143750 92 I AccC Biotin carboxylase 46143902 80 I FabD (acyl-carrier-protein) S-malonyltransferase 53728816 85 I AccA Acetyl-CoA carboxylase alpha subunit 46143558 91 I FabB 3-oxoacyl-(acyl-carrier-protein) synthase 46143901 89 I FabG Dehydrogenases with different specificities 2500221 96 J RpL2 Ribosomal protein L2 2500232 94 J RpL4 Ribosomal protein L4 13274359 25 J DcbE Seryl-tRNA synthetase 15602028 95 J COG0012 Predicted GTPase, probable translation factor 15602458 88 J ThrS Threonyl-tRNA synthetase 15602963 89 J GlyQ Glycyl-tRNA synthetase, alpha subunit 15603007 92 J RpL31 Ribosomal protein L31 15603268 96 J RpL5 Ribosomal protein L5 15603436 83 J MiaB 2-methylthioadenine synthetase 15603527 78 J IleS Isoleucyl-tRNA synthetase 22795549 97 J InfB Translation initiation factor IF2 32033514 94 J LeuS Leucyl-tRNA synthetase 32033553 76 J PcnB tRNA /poly(A) 32033623 J PrfB Protein chain release factor B 32033728 J AsnS Aspartyl/asparaginyl-tRNA synthetases 32033731 J GlnS Glutamyl- and glutaminyl-tRNA synthetases 32033887 J RpL9 Ribosomal protein L9 32033979 J RpL15 Ribosomal protein L15 32034120 J QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase 32034388 J Frr Ribosome recycling factor Frr 32034392 87 J RpS2 Ribosomal protein S2 32034689 85 J RpL19 Ribosomal protein L19 32034693 J RpL17 Ribosomal protein L17 32034695 J RpS4 Ribosomal protein S4 32034699 J RpS15 Ribosomal protein L15 32034701 J RpL18 Ribosomal protein L18 32034702 J RpL6 Ribosomal protein L6 32034814 J RpL1 Ribosomal protein L1 32034867 J SecB Preprotein subunit SecB 32034872 J RpS7 Ribosomal protein S7 32035006 93 J LysU Lysyl-tRNA synthetase (class II) 32035070 J RpL25 Ribosomal protein L25 32035109 92 J ProS Prolyl-tRNA synthetase 32035250 J RpS9 Ribosomal protein S9 32035256 J PheS Phenylalanyl-tRNA synthetase alpha subunit 32035264 J Rnd Ribonuclease D 32035471 J RpL27 Ribosomal protein L27 32035713 J RpL3 Ribosomal protein L3 32035715 J RpL23 Ribosomal protein L23 32035718 J RpL22 Ribosomal protein L22 32035720 J RpL16 Ribosomal protein L16 46143217 J TufB Traslation elongation factor TufB 46143380 J Tgt Queuine/archaeosine tRNA-ribosyltransferase 46143391 J LasT rRNA methylase 46143575 J Rne Ribonucleases G and E 46143638 J RpS5 Ribosomal protein S5 46143699 J TyrS Tyrosyl-tRNA synthetase 46143730 J Tsf Translation elongation factor Ts 46143827 J COG0042 tRNA-dihydrouridine synthase 46143889 86 J CysS Cysteinyl-tRNA synthetase 52424295 J TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase 53728751 J RpS1 Ribosomal protein S1 53728774 J RluA Pseudouridylate synthases, 23S RNA-specific 53728830 J FusA Traslation elongation factors FusA 53729050 85 J AspS Aspartyl-tRNA synthetase 53729064 J RpS6 Ribosomal protein S6 53729104 88 J ArgS Arginyl-tRNA synthetase 53729108 J Pth Peptidyl-tRNA hydrolase 53729237 84 J Fmt Methionyl-tRNA formyltransferase 15602046 K Rnb II 15603020 K AcrR Transcriptional regulator 15603106 K RpoZ DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) 15603785 90 K Rho Transcription termination factor Rho 32033691 76 K NusA Transcription elongation factor NusA 32034024 K GreA Transcription elongation factor GreA 32034036 K COG1959 Predicted transcriptional regulator 32034812 82 K NusG Transcription antiterminator 32035105 K RpoD DNA-directed RNA polymerase, subunit K/omega 32035110 K RpoE DNA-directed RNA polymerase specialized sigma subunit/sigma 24 homolog 32035265 86 K Lrp Transcriptional regulators 46143282 K MalT ATP-dependent transcriptional regulator 46143635 K RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit 46143661 K Rnc dsRNA-specific ribonuclease 46143682 K RpoC DNA-directed RNA polymerase beta' subunit/160 kD 46143701 K VacB Exoribonuclease R 52426430 K PurR Transcriptional regulators 53728886 K LysR Transcriptional regulator 15602548 K NagC Transcriptional regulator/sugar kinase 15602381 L RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains and exonuclease domains) 15602512 L COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase 15602784 L RecG RecG-like helicase 15603010 L Fpg Formamidopyrimidine-DNA glycosylase 32034137 L Ssb Single-stranded DNA-binding protein 32034579 L HimA Bacterial nucleoid DNA-binding protein 32035303 L DnaE DNA polymerase III, alpha subunit 46143317 L COG0116 Predicted N6-adenine-specific DNA methylase 46143331 L COG2189 Adenine specific DNA methylase Mod 46143431 89 L GyrB DNA Gyrase B 46143544 L XerD Site-specific recombinase XerD 46143793 L XthA Exonuclease III 46143842 L GyrA DNA Gyrase A 46143849 L UvrC Nuclease subunit of the excinuclease complex 52424926 50 L DnaX DNA polymerase III, gamma/tau subunits 52425571 54 L MutL DNA mismatch repair enzyme (predicted ATPase) 52426136 L RecQ Superfamily II DNA helicase 53729134 L DnaA ATPase involved in DNA replication initiation 53729175 L UvrB Helicase subunit of the DNA excision repair complex 53729177 L Mug G:T/U mismatch-specific DNA glycosylase 53729191 84 L TopA Topoisomerase IA 53729249 L MutS Mismatch repair ATPase (MutS family) 15602003 60 M MurF UDP-N-acetylmuramyl pentapeptide synthase 15602581 M DacB D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) 15602895 M RffG dTDP-D-glucose 4,6-dehydratase 15603207 M RfaD Nucleoside-diphosphate-sugar epimerases RfaD 32033515 M RplB Rare lipoprotein B 32033957 M COG3306 Glycosyltransferase involved in LPS biosynthesis 32034276 76 M MurB UDP-N-acetylmuramate dehydrogenase 46143310 M KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase 46143602 M LpxA Acyl-[acyl carrier protein]--UDP-N-acetylglucosamine O-acyltransferase 46143698 M WcaJ Sugar involved in lipopolysaccharide synthesis 46143831 M TolA Membrane protein involved in colicin uptake 46143879 M HtrB Lauroyl/myristoyl acyltransferase 52425237 54 M Alr Alanine racemase 52425570 M AmiC N-acetylmuramoyl-L-alanine amidase 52426314 59 M RfaF ADP-heptose:LPS heptosyltransferase 53728769 69 M KdtA 3-deoxy-D-manno-octulosonic-acid 53729090 M BetT Choline-glycine betaine transporter 53729122 M MraY UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N-a 12963881 69 O YeaA Methionine sulfoxide reductase 15602098 O COG0826 Collagenase and related proteases 15603569 O ClpB ATPases with chaperone activity, ATP-binding subunit 15603840 O Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) 32033971 90 O GroES Co-chaperonin GroES (HSP10) 32033972 O GroEL Chaperonin GroEL (HSP60 family) 32034480 O SlpA FKBP-type peptidyl-prolyl cis-trans 2 32034501 O AhpI Peroxiredoxin 32034721 O SurA Parvulin-like peptidyl-prolyl isomerase 32035049 O ClpX ATP-dependent protease Clp, ATPase subunit 32035169 O ClpA ATPases with chaperone activity, ATP-binding subunit 32035197 O QRI7 Metal-dependent proteases with possible chaperone activity 32035457 O FkpA FKBP-type peptidyl-prolyl cis-trans isomerases 1 32035579 O COG3118 Thioredoxin domain-containing protein 32035737 O HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit 46143226 O AprE Subtilisin-like serine proteases 46143420 O COG0606 Predicted ATPase with chaperone activity 46143492 O DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain 46143749 O TrxA Thiol-disulfide isomerase and thioredoxins 53728847 O DsbG Protein-disulfide isomerase 53728970 79 O CcmF Cytochrome c biogenesis factor 53729084 O HtpG Molecular chaperone, HSP90 family 11095368 89 P TbpA Transferrin binding protein A 11095369 76 P TbpB Transferrin binding protein B 15602265 P YfeA ABC-type metal ion transport system, periplasmic component/surface adhesin 15602301 P PstS ABC-type phosphate transport system, periplasmic component 15602820 P AfuA ABC-type Fe3+ transport system, periplasmic component 15603217 P DsrF Uncharacterized protein involved in the oxidation of intracellular sulfur Pm1352 32034900 P HugZ Putative heme iron utilization protein 32034901 P CirA Outer membrane receptor proteins, mostly Fe transport 32034997 P ZntA Cation transport ATPase 32035378 P COG1392 Phosphate transport regulator (distant homolog of PhoU) 32035412 P LraI ABC-type metal ion transport system, periplasmic component/ 32035844 P CynT 46143573 P ZnuA ABC-type Zn2+ transport system, periplasmic component/surfa 46143759 P CysA ABC-type sulfate/molybdate transport systems, ATPase compon 46143785 88 P KatE Catalase 51292063 P SodA Superoxide dismutase 53729098 P Fur Fe2+/Zn2+ uptake regulation proteins 15602205 86 Q SmtA SAM-dependent methyltransferases 46143494 Q Ttg2D ABC-type transport system involved in resistance to organic 15601929 R COG3445 Acid-induced glycyl radical enzyme 15603031 R ThdF Predicted GTPase 15603376 R COG0218 Predicted GTPase PM1511 32033508 R COG3106 Predicted ATPase 32034590 R GloB Zn-dependent , including glyoxylases 32034654 R Era GTPase Era 32034718 R COG1160 Predicted GTPases PM0105 32035045 R Uup ATPase components of ABC transporters with duplicated ATPase domains 46143782 R COG1408 Predicted phosphohydrolases 53728766 R COG0802 Predicted ATPase or kinase 53728783 R MazG Predicted pyrophosphatase 15602256 S COG2840 Uncharacterized protein conserved in bacteria 15602774 S COG3768 Predicted membrane protein 15603185 S COG2924 Fe-S cluster protector protein PM1320 15603230 S COG3395 Uncharacterized protein conserved in bacteria PM1365 15603373 S COG2861 Uncharacterized protein conserved in bacteria Pm1508 15603475 S COG0585 Uncharacterized conserved protein Pm1610 15603767 S COG2830 Uncharacterized protein conserved in bacteria PM1902 32033607 S LemA Uncharacterized conserved protein 32034567 S SanA Uncharacterized membrane protein 32035634 S COG1666 Uncharacterized protein conserved in bacteria 52425753 S SprT Uncharacterized protein conserved in bacteria SprT 46143322 89 T TypA Predicted membrane GTPase involved in stress response 46143604 82 T SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases 32035561 82 T CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 52424382 75 U SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) 53728959 61 U FtsY Signal recognition particle GTPase 15603406 46 V HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related 32035511 70 V COG3587 Restriction endonuclease 46143394 33 V CcmA ABC-type multidrug transport system, ATPase component 15603307 28 C GlpA Glycerol-3-phosphate dehydrogenase 52424317 87 E GlnA Glutamine synthetase 32035180 88 G Pgi Glucose-6-phosphate isomerase 15602782 58 M MurI Glutamate racemase 15603416 33 O Gst Glutathione S-transferase

Proteins that BLAST against M. haemolytica genome 32034053 100 J RpL28 Ribosomal protein L28 33149179 100 J RpS19 Ribosomal protein S19 15603764 99 I Psd Phosphatidylserine decarboxylase 32034692 98 J RpS16 Ribosomal protein S16 32034697 98 J RpS13 Ribosomal protein S13 32035637 98 J InfA Translation initiation factor 1 (IF-1) 33149096 98 J RpL11 Ribosomal protein L11 32034233 97 C Ppa Inorganic pyrophosphatase 15603043 97 J RpS18 Ribosomal protein S18 52426104 97 J RpS10 Ribosomal protein S10 53728990 96 F PrsA Phosphoribosylpyrophosphate synthetase 2641641 96 J RpS12 Ribosomal protein S12 15603266 96 J RpS8 Ribosomal protein S8 32034700 96 J RpL30 Ribosomal protein L30 34499998 95 C AtpD ATP synthase F1 subunit beta 32034493 95 J RpS21 Ribosomal protein S21 32035721 95 J RpL29 Ribosomal protein L29 33149169 95 J RpL14 Ribosomal protein L14 2500396 94 J RpS3 Ribosomal protein S3 53729024 94 J RpL33 Ribosomal protein L33 32033552 92 O PpiB Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin 53729148 91 E HisB Imidazoleglycerol-phosphate dehydratase 46143302 91 L RecR Recombinational DNA repair protein (RecF pathway) 53729096 91 T LuxS LuxS protein involved in autoinducer AI2 synthesis 2500469 90 J RpS17 Ribosomal protein S17 32035724 90 J RpL24 Ribosomal protein L24 52424244 90 M GlmS Glucosamine 6-phosphate synthetase, contains amidotransferase and phosphosugar isomerase domains 52425814 90 NA Hypothetical protein MS1759 32033521 90 O Sms Predicted ATP-dependent serine protease 52424326 90 O HslV ATP-dependent protease HslVU (ClpYQ), peptidase subunit 15603257 89 J RpS11 Ribosomal protein S11 52424264 88 J RpL10 Ribosomal protein L10 53729187 87 R Predicted SAM-dependent methyltransferase 32034933 87 J COG2269 Truncated, possibly inactive, lysyl-tRNA synthetase (class II) 52426244 87 R TdcF Putative translation initiation inhibitor 15602789 86 G GapDH Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase 15602385 86 J RpL13 Ribosomal protein L13 32035042 86 M MurA UDP-N-acetylglucosamine enolpyruvyl transferase 53728968 85 R Predicted methyltransferases 15602273 85 C FdxG Anaerobic dehydrogenases, typically selenocysteine-containing 52424371 85 NA Hypothetical protein MS0316 52426426 85 H GltA Glutamyl-tRNA reductase 46143757 84 E COG1305 Transglutaminase-like enzymes, putative cysteine proteases 52425043 84 NA Hypothetical protein MS0988 46143794 84 R COG2056 Predicted permease 53728834 83 M LolA Outer membrane lipoprotein-sorting protein 52425041 83 NA Hypothetical protein MS0986 32033986 83 Q COG2931 RTX toxins and related Ca2+-binding proteins 15603658 83 T TorA Carbon storage regulator (could also regulate swarming and quorum sensing) 52425350 82 E GlyA Glycine/serine hydroxymethyltransferase 52425098 82 H FolE GTP cyclohydrolase I 15602420 82 J PrfA Protein chain release factor A 46143328 82 L XseA Exonuclease VII, large subunit 52426004 82 M GlmU N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) 15602682 82 P Dps DNA-binding ferritin-like protein (oxidative damage protectant) 15602591 81 E DapB Dihydrodipicolinate reductase 32034816 81 J RpL7/L12 Ribosomal protein L7/L12 46143821 81 K HepA Superfamily II DNA/RNA helicases, SNF2 family 32033564 81 R AarF Predicted unusual 32033951 80 E Dcp Zn-dependent oligopeptidases 15603117 80 G DctP TRAP-type C4-dicarboxylate transport system, periplasmic component 52424265 80 J RpL12 Ribosomal protein L12 15603597 80 L HupA Bacterial nucleoid DNA-binding protein 52424790 79 NA Hypothetical protein MS0735 15602629 78 G Hypothetical protein PM0764 15602761 78 G Crr Phosphotransferase system IIA components 53728781 78 L Dam Site-specific DNA methylase 32034582 78 NA Hypothetical protein Aple02001143 32034022 78 R COG2388 Predicted acetyltransferase 15603385 77 D FtsE Predicted ATPase involved in cell division 53728788 77 K LexA SOS-response transcriptional repressors (RecA-mediated auto 52424398 77 NA Hypothetical protein MS0343 52425852 77 NA AvtA PLP-dependent aminotransferases 52426245 77 NA EutG Alcohol dehydrogenase IV 15602337 77 R Imp TRAP-type uncharacterized transport system, periplasmic component 15603099 77 R OrfJ Protein involved in catabolism of external DNA 15602397 76 H Dxs Deoxyxylulose-5-phosphate synthase 52424538 76 J RnpA RNase P protein component 52424375 76 P CorA Mg2+ and Co2+ transporters 52425649 76 R Obg Predicted GTPase ObG 15603348 76 S COG3074 Uncharacterized protein conserved in bacteria PM1483 52425252 75 C PykF 53728763 75 C COG5016 Pyruvate/oxaloacetate carboxyltransferase 32035656 75 M COG4775 Outer membrane protein/protective antigen OMA87 52426121 75 NA Hypothetical protein MS2066 15603777 74 J RpL32 Ribosomal protein L32 46143344 74 J RpL21 Ribosomal protein L21 53729278 74 O Spy Predicted O-linked N-acetylglucosamine transferase, SPINDLY 32034741 74 C GlpQ Glycerophosphoryl diester phosphodiesterase 52426002 73 NA Hypothetical protein MS1948 52425738 72 H GshA Gamma-glutamylcysteine synthetase 52425801 72 H HemN Coproporphyrinogen III oxidase and related Fe-S 15602906 72 L Mfd Transcription-repair coupling factor (superfamily II helicase 53728752 71 F Cmk 15602762 71 G PtsI Phosphoenolpyruvate-protein kinase (PTS system EI component) 15603018 69 H Dfp DNA/pantothenate metabolism flavoprotein 15602468 69 J RpL35 Ribosomal protein L35 52425509 69 NA Hypothetical protein MS1454 52425046 68 NA Hypothetical protein MS0991 53728902 67 I PgpA Phosphatidylglycerophosphatase A and related proteins 15602424 66 C LdhA Lactate dehydrogenase and related dehydrogenases 15603047 66 I PlsB Glycerol-3-phosphate O-acyltransferase 52424676 66 R COG0121 Predicted glutamine amidotransferase 15603520 66 S Uncharacterized protein conserved in bacteria PM1655 38488592 65 NA oxyR like protein 52424706 65 NA Hypothetical protein MS0651 15602503 65 R COG4667 Predicted esterase of the alpha-beta hydrolase superfamily 46143601 64 M HlpA Outer membrane protein HlpA 15602378 63 M MltB Membrane-bound lytic murein transglycosylase B 52425091 63 R Predicted metal-dependent phosphoesterases (PHP family) 15603329 62 E PabB Anthranilate/para-aminobenzoate synthases component I 15603712 62 K ScrR Transcriptional regulators ScrR 15601910 62 M COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino 52426170 61 C NfnB Dihydropteridine reductase; oxygen-insensitive NAD(P)H nitroreductase 52425957 61 O DjlA DnaJ-domain-containing proteins 1 15602410 60 G GlgP Glucan phosphorylase 15603148 60 K IlvY Transcriptional regulator IlvY 52425367 60 M MrcA Membrane carboxypeptidase (penicillin-binding protein) 52424553 60 NA Hypothetical protein MS0498 15602492 59 M Spr Cell wall-associated hydrolases (invasion-associated proteins) 13937107 59 Q ApxIIA RTX toxin IIA 52425068 58 H BtuC ABC-type cobalamin/Fe3+-siderophores transport syatems, permease components 4579742 58 M Omp29 52426408 58 M GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division 52424136 57 NA Hypothetical protein MS0081 52424479 57 P CitT Di- and tricarboxylate transporters 53729009 56 E OppA ABC-type oligopeptide transport system, periplasmic compone 52425727 56 M MurE UDP-N-acetylmuramyl tripeptide synthase 52424157 56 NA Hypothetical protein MS0102 52424229 56 NA Hypothetical protein MS0174 52424920 56 NA Hypothetical protein MS0865 52425765 55 NA MS1710 Uncharacterized periplasmic protein 53729035 55 NA Hypothetical protein Aple02000659 53728972 55 U CcmD Heme exporter protein D 15602250 54 C RnfC Predicted NADH:ubiquinone oxidoreductase, subunit RnfC 15602376 54 M WcaA Glycosyltransferases involved in cell wall biogenesis 52426037 54 NA Hypothetical protein MS1982 15603749 54 S COG3082 Uncharacterized protein conserved in bacteria PM1884 15602108 51 M NlpD Membrane proteins related to metalloendopeptidases 52425192 51 NA Hypothetical protein MS1137 52425980 51 NA MS1925 Predicted membrane-associated Zn-dependent proteases 1 52424872 51 R PqiB Paraquat-inducible protein B 52425812 50 NA Hypothetical protein MS1757 52424472 50 R WbbJ protein Acetyltransferases 52425747 49 NA Hypothetical protein MS1692 52424859 48 D MesJ Predicted ATPase of the PP-loop superfamily implicated in c 15603791 48 M RlpA Lipoproteins 52424625 47 L HolB ATPase involved in DNA replication 52424177 47 NA Hypothetical protein MS0122 52424567 46 NA Uncharacterized membrane protein, possible Na+ channel or pump 52425803 45 L ComEA DNA uptake protein and related DNA-binding proteins 52424769 45 NA Hypothetical protein MS0714 9587174 45 U PilB Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB 53729061 42 NA Hypothetical protein Aple02000476 40067371 42 S Hypothetical protein 32034626 41 NA Hypothetical protein Aple02001180 52424189 41 NA Hypothetical protein MS0134 53728791 41 NA Hypothetical protein Aple02001611 52425429 40 H RibD Pyrimidine reductase, riboflavin biosynthesis 52424067 40 NA Hypothetical protein MS0012 52426362 40 NA Hypothetical protein MS2307 15602633 39 NA Hypothetical protein PM0768 52425973 39 NA Hypothetical protein MS1918 52425138 37 NA Hypothetical protein MS1083 15602237 36 E Saccharopine dehydrogenase and related proteins 32033527 36 I PaaJ Acetyl-CoA acetyltransferase 52425976 36 NA Hypothetical protein MS1921 577527 36 P TfbA Outer membrane protein; transferrin-binding protein 52425399 36 R ModE N-terminal domain of molybdenum-binding protein 15603501 36 S COG3792 Uncharacterized protein conserved in bacteria Pm1636 53728894 35 NA Hypothetical protein Aple02000991 15603036 35 S COG3111 Uncharacterized conserved protein PM1171 52424123 34 E SerA Phosphoglycerate dehydrogenase and related dehydrogenases 15602805 34 F NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase 15603417 34 NA Hypothetical protein PM1552 52424604 33 E ProV ABC-type proline/glycine betaine transport systems, ATPase components 15603206 33 G UhpT Sugar phosphate permease 52424168 33 NA Hypothetical protein MS0113 52424576 33 NA Predicted Na+-dependent transporter 52425266 33 NA Hypothetical protein MS1211 21630237 32 M Cps1B Capsular polysaccharide synthesis-B 15602360 32 NA Hypothetical protein PM0495 13936954 31 H HgpA Hemoglobin binding protein A 15603003 31 M RfaG Glycosyltransferase 52425445 31 NA Hypothetical protein MS1390 52425485 31 NA Hypothetical protein MS1430 15603012 31 P FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components 15602579 31 U Hsf_1 Autotransporter adhesin 46143339 31 U CpaF Flp pilus assembly protein, ATPase CpaF 52424580 30 E Tdh Threonine dehydrogenase and related Zn-dependent dehydrogenases 52426228 30 K AraC AraC-type DNA-binding domain-containing proteins 52424749 30 K/T SrmR Regulator of polyketide synthase expression 4099386 30 M Outer membrane lipoprotein 4809236 30 M LbgA Putative LPS biosynthesis protein 52425443 30 R MviM Predicted dehydrogenases and related proteins 32033384 29 C COG1151 6Fe-6S prismane cluster-containing protein 52424234 29 K SoxR Predicted transcriptional regulators soxR 15603225 29 M WcaG Nucleoside-diphosphate-sugar epimerases 52424165 29 NA Hypothetical protein MS0110 52425690 29 NA Hypothetical protein MS1635 52425715 29 NA Hypothetical protein MS1660 53729000 29 NA Hypothetical protein Aple02000727 32035400 29 R MhpC Predicted hydrolases or acyltransferases (alpha/beta hydrol 32033541 28 J COG1544 Ribosome-associated protein Y (PSrp-1) 32035081 28 NA Hypothetical protein Aple02001600 50085568 28 NA Fragment of hypothetical protein PM0309 and/or PM0310 of Pasteurella m 52424967 28 NA Hypothetical protein MS0912 15603008 27 M LosA Glycosyltransferase involved in LPS biosynthesis LosA 46909860 27 M Cps7D 15602872 27 NA WbjB Unknown 52426341 27 T BaeS Sensory transduction histidine kinases 13345957 27 U Tag9 Transport associated protein 9 53729089 26 C AdhC Zn-dependent alcohol dehydrogenases, class III 4099400 26 M OmlA Outer membrane lipoprotein A 15602880 26 M Rfb Predicted nucleoside-diphosphate sugar epimerases 52424437 26 NA Hypothetical protein MS0382 5733704 26 P CbiK Putative periplasmic binding protein CbiK 52425533 26 R PfoR Predicted membrane protein, putative toxin regulator 15602992 26 S COG3513 Uncharacterized protein conserved in bacteria PM1127 32033900 25 NA Hypothetical protein Aple02000493 52426182 25 NA Hypothetical protein MS2127 15603572 25 S COG3055 Uncharacterized protein conserved in bacteria Pm1707 52425261 24 NA Hypothetical protein MS1206 15602717 24 U RcpA Flp pilus assembly protein, secretin CpaC 9309328 23 M Putative glycosyltransferase 52424502 23 M RfaJ Lipopolysaccharide biosynthesis proteins, LPSglycosyltransferases 15602669 23 R PqqL Predicted Zn-dependent peptidases 32035054 23 R COG0820 Predicted Fe-S-cluster redox enzyme 46143614 23 C GlpC Fe-S oxidoreductase 53729080 23 V Type I site-specific restriction-modification system, R (restriction) subunit and related helicases 13274365 22 M EcbK 7467535 22 NA Hypothetical protein 12 T00108 52424257 22 NA Hypothetical protein MS0202 52425941 22 NA Hypothetical protein MS1886 52425550 22 R RfbX Membrane protein involved in the export of O-antigen and teichoic acid 15601924 22 U PfhB2 Large exoproteins involved in heme utilization or adhesion 15602798 21 C DcuC C4-dicarboxylate transporter 52425283 21 G MelB Na+/melibiose symporter and related transporters 52426224 21 V HsdS Restriction endonuclease S subunits

Proteins that did not BLAST against the genome 46143458 D Maf Nucleotide-binding protein implicated in inhibition of septum formation 32035171 K ArsR Predicted transcriptional regulators 10955980 L Mobilization protein A 53728999 L SbcC ATPase involved in DNA repair 2996206 M Cps5C Region 2 capsular polysaccharide biosynthesis protein 13274370 M EcbG 46143762 P Sbp ABC-type sulfate transport system, periplasmic component 12025470 R Putative rhamnosyl transferase 15602715 U CpaE Flp pilus assembly protein, ATPase 10880911 NA Magb12 ATPase 15602562 NA Hypothetical protein PM0697 15603093 NA ComB 15603693 NA Hypothetical protein PM1828 46143650 NA Hypothetical protein Aple02001187 52424133 NA Hypothetical protein MS0078 52424225 NA Hypothetical protein MS0170 52425678 NA Hypothetical protein MS1623 52425870 NA Hypothetical protein MS1814 52426059 NA Hypothetical protein MS2004 52426110 NA Hypothetical protein MS2055 52426295 NA Hypothetical protein MS2240 a) Genbank accession number b) Percentage amino acid identity c) COG functional category d) Protein name or unique COG number e) Not assigned to a COG functional category