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 ª 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 Enzyme 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 Transposase 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 oxidoreductase 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 kinase 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 dehydratase/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-lyases/cystathionine gamma-synthases 32034037 94 E NifS Cysteine sulfinate desulfinase/cysteine desulfurase and rel 32034165 90 E ArgF Ornithine carbamoyltransferase 32034923 81 E GlnB Nitrogen 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 Homoserine kinase 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 lyase 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 ligase 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 phosphorylase 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 Adenylate kinase 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 hydrolase 53728853 79 F ThyA Thymidylate synthase 53728876 88 F NrdF Ribonucleotide reductase, beta subunit 15601934 74 G PfkA 6-phosphofructokinase 15602035 46 G PtsN Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) 15602900 55 G GalK Galactokinase 15602903 77 G MglB ABC-type sugar transport system, periplasmic component MglB 15603237 22 G RbsK Sugar kinases, ribokinase family 15603371 91 G GpmA Phosphoglycerate mutase 1 32034150 96 G GmhA Phosphoheptose isomerase 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 Enolase 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 Xylulokinase 53728742 75 G ProP Permeases of the major facilitator superfamily 53728801 95 G Pgk 3-phosphoglycerate kinase 53728880 26 G GntT H+/gluconate symporter and related permeases 53728901 81 G SuhB Archaeal fructose-1,6-bisphosphatase and related enzymes 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