| Nucleotide sugar epimerase/dehydratase WbpM | wbpM PA3141 | Q9HZ86 | 3 |
| Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein (OppA) | HP_1252 | O25845 | 3 |
| Oligopeptide-binding protein OppA (Stage 0 sporulation protein KA) | oppA spo0KA BSU11430 | P24141 | 3 |
| OmpA domain protein | MXAN_5598 | Q1D0T6 | 3 |
| OmpA family protein | fopA FTN_0756 | A0Q5Y2 | 3 |
| OmpA family protein | FTN_0346 | A0Q4T7 | 3 |
| OmpA family protein | PP_1121 | Q88NT3 | 3 |
| OmpA family protein | PP_1502 | Q88MR7 | 3 |
| OmpA family protein | PP_4198 | Q88FA0 | 3 |
| OmpA family protein | PP_4669 | Q88DZ9 | 3 |
| OmpA family protein | PP_1122 | Q88NT2 | 3 |
| OmpA/MotB domain-containing protein | yiaD PP_0773 | Q88PS5 | 3 |
| Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) | pyrF BE932_02265 SY51_07890 | A0A061YJC8 | 3 |
| Osmotically-inducible putative lipoprotein OsmE (Activator of ntr-like gene protein) | osmE anr b1739 JW1728 | P0ADB1 | 3 |
| Outer membrane copper receptor OprC | oprC PP_4838 | Q88DI7 | 3 |
| Outer membrane efflux protein | PP_4923 | Q88DA4 | 3 |
| Outer membrane efflux protein, tolC | tolC FTN_1703 | A0Q8J5 | 3 |
| Outer membrane ferripyoverdine receptor FpvA, TonB-dependent | fpvA PP_4217 | Q88F81 | 3 |
| Outer membrane fibronectin-binding protein | cadF Cj1478c | Q0P8D9 | 3 |
| Outer membrane lipoprotein | slyB PP_1131 | Q88NS3 | 3 |
| Outer membrane lipoprotein SlyB | slyB b1641 JW1633 | P0A905 | 3 |
| Outer membrane porin F | oprF PP_2089 | Q88L46 | 3 |
| Outer membrane protein (Omp2) | HP_0025 | O24870 | 3 |
| Outer membrane protein (Omp3) | HP_0079 | O24908 | 3 |
| Outer membrane protein 3b (A), protease VII (Protease) | ompT EC958_0673 UG58_01860 | W8ZNZ0 | 3 |
| Outer membrane protein assembly factor BamA | bamA Cj0129c | Q0PC08 | 3 |
| Outer membrane protein assembly factor BamA | bamA bamA-I PP_1599 | Q88MH2 | 3 |
| Outer membrane protein assembly factor BamA | bamA Smlt1498 | B2FIA0 | 3 |
| Outer membrane protein assembly factor BamA (Omp85) | bamA yaeT yzzN yzzY b0177 JW0172 | P0A940 | 3 |
| Outer membrane protein assembly factor BamB | bamB PP_0856 | Q88PJ4 | 3 |
| Outer membrane protein assembly factor BamD | bamD yfiO b2595 JW2577 | P0AC02 | 3 |
| Outer membrane protein assembly factor BamD | bamD PP_0622 | Q88Q73 | 3 |
| Outer membrane protein assembly factor BamD | bamD yfiO Z3889 ECs3458 | P0AC04 | 3 |
| Outer membrane protein assembly factor BamE | bamE PP_4731 | Q88DT8 | 3 |
| Outer membrane protein assembly factor BamE | bamE smpA b2617 JW2598 | P0A937 | 3 |
| Outer membrane protein C (Outer membrane protein 1B) (Porin OmpC) | ompC Z3473 ECs3104 | Q8XE41 | 3 |
| Outer membrane protein F (Outer membrane protein 1A) (Outer membrane protein B) (Outer membrane protein IA) (Porin OmpF) | ompF cmlB coa cry tolF b0929 JW0912 | P02931 | 3 |
| Outer membrane protein H.8 | NMB1533 | P57026 | 3 |
| Outer membrane protein H1 | oprH PP_1185 | Q88NM2 | 3 |
| Outer membrane protein induced after carbon starvation (Slp family outer membrane lipoprotein) | slp slp_1 AC789_1c38740 ERS150876_00023 | A0A0E1LDD5 | 3 |
| Outer membrane protein Omp38 | omp38 A1S_2840 | A3M8K2 | 3 |
| Outer membrane protein OmpH | ompH FTN_1481 | A0Q7Y3 | 3 |
| Outer membrane protein OprG | oprG PP_0504 | Q88QI8 | 3 |
| Outer membrane protein slp | slp b3506 JW3474 | P37194 | 3 |
| Outer membrane protein Slp (Outer membrane protein induced after carbon starvation) | slp ECs4377 Z4908 | Q8X5P5 | 3 |
| Outer membrane protein W | ompW yciD b1256 JW1248 | P0A915 | 3 |
| Outer membrane protein W (Putative outer membrane protein) | yciD ompW ECs1756 Z2034 | Q8XCB6 | 3 |
| Outer membrane protein X | ompX Z1036 ECs0892 | P0A919 | 3 |
| Outer-membrane lipoprotein LolB | lolB PP_0724 | Q88PX4 | 3 |
| Outer-membrane lipoprotein LolB | lolB Smlt0873 | B2FQ17 | 3 |
| Outer-membrane porin D (EC 3.4.21.-) | oprQ PP_0268 | Q88R66 | 3 |
| Outer-membrane porin E (EC 3.4.21.-) | oprE PP_0234 | Q88R99 | 3 |
| Oxidative stress defense protein | BE932_12665 ERS085366_00819 SY51_16390 | A0A061KYU0 | 3 |
| Oxidoreductase | BE932_03525 SY51_09070 | A0A066SVM5 | 3 |
| Oxygen-independent coproporphyrinogen III oxidase (CPO) (EC 1.3.98.3) (Coproporphyrinogen III dehydrogenase) (CPDH) | hemN PA1546 | P77915 | 3 |
| Paraquat-inducible protein B | PP_0599 | Q88Q96 | 3 |
| Penicillin acylase family protein | MXAN_2906 | Q1D8A6 | 3 |
| Penicillin-binding protein 1A/1B (PBP1) [Includes: Penicillin-insensitive transglycosylase (EC 2.4.1.129) (Peptidoglycan TGase); Penicillin-sensitive transpeptidase (EC 3.4.16.4) (DD-transpeptidase)] | ponA BSU22320 | P39793 | 3 |
| Penicillin-binding protein 1B (PBP-1b) (PBP1b) (Murein polymerase) | mrcB PA4700 | G3XD31 | 3 |
| Penicillin-binding protein 3 (PBP 3) (PSPB20) (Penicillin-binding protein C) | pbpC ycsM yzsA BSU04140 | P42971 | 3 |
| Penicillin-binding protein activator LpoA (PBP activator LpoA) (Lipoprotein activator of PBP from the outer membrane A) | lpoA yraM b3147 JW3116 | P45464 | 3 |
| Penicillin-binding protein activator LpoB (PBP activator LpoB) | lpoB BET08_26000 BK337_21960 BUE81_21320 | A0A0A6UCV4 | 3 |
| Peptidase U35 | PP_1566 | Q88MK5 | 3 |
| Peptidase, M36 (Fungalysin) family (EC 3.4.-.-) | MXAN_3564 | Q1D6G9 | 3 |
| Peptidase, S1A (Chymotrypsin) subfamily (EC 3.4.21.-) | MXAN_1650 | Q1DBS1 | 3 |
| Peptidase, S9C (Acylaminoacyl-peptidase) subfamily (EC 3.4.-.-) | MXAN_6601 | Q1CY03 | 3 |
| Peptide ABC transporter substrate-binding protein | BY96_03865 | A0A027U4C0 | 3 |
| Peptide deformylase (PDF) (EC 3.5.1.88) (Polypeptide deformylase) | def BET08_18245 BK337_16925 BUE81_25685 | A0A0A6R614 | 3 |
| Peptide methionine sulfoxide reductase MsrA/MsrB [Includes: Thioredoxin; Peptide methionine sulfoxide reductase MsrA (Protein-methionine-S-oxide reductase) (EC 1.8.4.11) (Peptide-methionine (S)-S-oxide reductase) (Peptide Met(O) reductase); Peptide methionine sulfoxide reductase MsrB (EC 1.8.4.12) (Peptide-methionine (R)-S-oxide reductase)] | msrAB pilB NMB0044 | Q9K1N8 | 3 |
| Peptidoglycan-associated lipoprotein | pal oprL pal1 PP_1223 | P0A138 | 3 |
| Peptidoglycan-associated lipoprotein | pal Z0909 ECs0776 | P0A913 | 3 |
| Peptidoglycan-associated lipoprotein, OmpA family | pal FTN_0357 | A0Q4U8 | 3 |
| Peptidoglycan-binding protein (Peptidoglycan-binding protein LysM) (Putative peptidoglycan-binding protein) (Putative uncharacterized protein) | ygaU A5958_16710 AA102_05120 ACN77_20570 ACN81_20545 ACN87_06915 ACU90_16385 AKG99_02960 AM270_01505 AMK83_09495 AML07_11840 AML35_05900 APZ14_09895 ARC77_09540 AU473_08610 AUS26_10540 BE957_09465 BHS81_16050 BK251_07065 BK292_15255 BMT53_21820 BMT61_21555 BMT91_21415 BWP17_12870 ECs3526 ERS085374_03231 ERS085379_00719 ERS085383_02332 ERS085386_03319 ERS085404_02124 ERS150876_01340 FORC28_1241 GJ12_17380 HW42_17915 PU06_25570 RG28_08305 UN86_27175 | C3SYE7 | 3 |
| Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | FTN_0921 | A0Q6E4 | 3 |
| Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | fklB-II PP_1714 | Q88M60 | 3 |
| Peptidyl-prolyl cis-trans isomerase (PPIase) (EC 5.2.1.8) | HMPREF3040_00561 UC41_08760 | A0A0D8WE88 | 3 |
| Peptidyl-prolyl cis-trans isomerase A (PPIase A) (EC 5.2.1.8) (Cyclophilin A) (Rotamase A) | ppiA Z4724 ECs4214 | P0AFL5 | 3 |
| Peptidyl-tRNA hydrolase (PTH) (EC 3.1.1.29) | pth BE932_30690 SY51_07025 | A0A066T103 | 3 |
| Peptidylprolyl isomerase (EC 5.2.1.8) | Smlt3182 | B2FLB8 | 3 |
| Peptidylprolyl isomerase (EC 5.2.1.8) | BE932_25825 SY51_02310 | A0A066T5W9 | 3 |
| Periplasmic cystine-binding protein | fliY PP_0227 | Q88RA6 | 3 |
| Periplasmic nitrate reductase (EC 1.7.99.4) | napA Cj0780 | Q9PPD9 | 3 |
| Periplasmic protein DcrB | dcrB A4T50_11545 APU18_01205 BE932_16325 BK373_21180 BMT49_24170 BV389_25590 ERS085406_01776 MJ49_12930 SY51_19815 UN91_22025 WM48_19205 | E2QFX6 | 3 |
| Periplasmic serine endoprotease DegP (EC 3.4.21.107) (Heat shock protein DegP) (Protease Do) | degP htrA ptd b0161 JW0157 | P0C0V0 | 3 |
| Peroxiredoxin (Thiol peroxidase) (EC 1.11.1.15) | bcp BV389_21970 UN91_14120 | A0A0F3UGQ5 | 3 |
| Persistence and stress-resistance toxin PasT (Ribosome association toxin RatA) | pasT ratA yfjG c3141 | Q8FEY4 | 3 |
| Phage minor tail protein G (Tail protein) | BE932_30155 SY51_06490 | A0A066SWW0 | 3 |
| Phage portal protein (Plasmid partitioning protein ParB) | BE932_30110 SY51_06445 | A0A061Y855 | 3 |
| Phage portal protein, HK97 family | PP_1565 | Q88MK6 | 3 |
| Phage protein (Prophage protein) | A5958_01720 AML07_04010 APT94_26570 APZ14_29570 AUS26_02580 BE957_11000 BWP17_26980 ERS085383_05319 ERS085386_05300 ERS085404_04777 FORC28_1805 FORC28_2485 | A0A066RBP1 | 3 |
| Phage tail protein | BE932_30195 SY51_06530 | A0A066T1C8 | 3 |
| Phage tail tape meausure protein, lambda family | PP_1577 | Q88MJ4 | 3 |
| Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase beta subunit) (PheRS) | pheT PA2739 | Q9I0A4 | 3 |
| Phosphatase NagD | ECSE_0735 | B6HYN3 | 3 |
| Phosphate acetyltransferase (EC 2.3.1.8) (Phosphotransacetylase) | pta E2348C_2437 | B7UFV5 | 3 |
| Phosphate acetyltransferase (EC 2.3.1.8) (Phosphotransacetylase) | pta A4T50_04540 APU18_03110 BE932_09095 ERS085406_01042 SY51_13135 | E2QPF8 | 3 |
| Phosphate import ATP-binding protein PstB 2 (EC 3.6.3.27) (ABC phosphate transporter 2) (Phosphate-transporting ATPase 2) | pstB2 spr1254 | Q8DPB4 | 3 |
| Phosphate-binding protein PstS | pstS A4T40_24515 AC067_07110 BK334_16130 ECONIH1_21940 MS6198_42910 | A0A0A1AC88 | 3 |
| Phosphate-specific transport system accessory protein PhoU | phoU A4T40_24535 AML35_24020 APT94_10120 ARC77_15530 AU473_02330 BE949_21380 BE963_09855 BHF46_03315 BIQ85_21170 BK248_08325 BK334_16150 BK375_10315 BK383_23325 BK400_01075 BMT94_11670 BMT97_04470 BUE82_25030 BV389_10035 BWP17_17305 BXT93_11130 ECONIH1_21920 ECs4660 ERS085366_03563 ERS085383_02594 ERS085404_03547 GJ11_23800 HMPREF3040_01853 JD73_04815 MS6198_42870 SM09_04711 UC41_07960 UN91_09845 | C3SLE7 | 3 |
| Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase) (DAHP synthase) (Phospho-2-keto-3-deoxyheptonate aldolase) | BE932_27430 BK248_02350 BK400_14395 SY51_03850 | A0A061KPI6 | 3 |