| Protease III (EC 3.4.24.55) | ptr YPO1019 | Q7CH00 | 1 |
| Protease PfpI | pfpI PA0355 | Q9I6D8 | 1 |
| Protease, insulinase family/protease, insulinase family | VC_0554 | Q9KUG7 | 1 |
| Protease, membrane-associated | yibP KPN_03958 | A6TFK9 | 1 |
| Proteasome subunit alpha (EC 3.4.25.1) (20S proteasome alpha subunit) (Proteasome core protein PrcA) | prcA Rv2109c | P9WHU1 | 1 |
| Proteasome subunit beta (EC 3.4.25.1) (20S proteasome beta subunit) (Proteasome core protein PrcB) | prcB Rv2110c | P9WHT9 | 1 |
| Protein ClpV1 | clpV1 PA0090 | Q9I742 | 1 |
| Protein CreA (Catabolite regulation protein A) | creA STM4587 | Q7CP64 | 1 |
| Protein CsuA | ABAYE1320 | B0V7M3 | 1 |
| Protein CsuA/B putative secreted protein related to type I pili | ABAYE1319 | B0V7M2 | 1 |
| Protein CsuB putative secreted protein related to type I pili | ABAYE1321 | B0V7M4 | 1 |
| Protein DedA (Protein DSG-1) | dedA b2317 JW2314 | P0ABP6 | 1 |
| Protein deglycase 1 (EC 3.1.2.-) (EC 3.5.1.124) (Glyoxalase III) (EC 4.2.1.130) (Holding molecular chaperone) (Hsp31) | hchA yedU yzzC b1967 JW1950 | P31658 | 1 |
| Protein DltD | dltD SAOUHSC_00872 | Q2FZW3 | 1 |
| Protein DltD | LMRG_02070 | A0A0H3GAT9 | 1 |
| Protein ElaB | elaB yfbD b2266 JW2261 | P0AEH5 | 1 |
| Protein F-related protein | VSAK1_15362 | A6D703 | 1 |
| Protein FhaE | fhaE fimD BP1883 | Q00879 | 1 |
| Protein FixC | fixC yaaS b0043 JW0042 | P68644 | 1 |
| Protein FtsN | B195_02583 | M5QZM5 | 1 |
| Protein GltL | B195_11246 | M5QHD4 | 1 |
| Protein GrpE (HSP-70 cofactor) | grpE Fphi_1402 | B0TYF1 | 1 |
| Protein GrpE (HSP-70 cofactor) | grpE B195_04322 | M5QNQ5 | 1 |
| Protein GrpE (HSP-70 cofactor) | grpE spr0454 | Q8CWT4 | 1 |
| Protein GrpE (HSP-70 cofactor) | grpE | Q8L399 | 1 |
| Protein GrpE (HSP-70 cofactor) | grpE ACL_0549 | A9NFN7 | 1 |
| Protein GrpE (HSP-70 cofactor) | grpE Rv0351 MTCY13E10.11 | P9WMT5 | 1 |
| Protein GrpE (HSP-70 cofactor) | grpE SPy_1761 M5005_Spy1499 | P68892 | 1 |
| Protein HemY | hemY b3802 JW3774 | P0ACB7 | 1 |
| Protein HflC | SC1083_0408 | G4A6G8 | 1 |
| Protein HflC | Smlt3595 | B2FQG3 | 1 |
| Protein HflC | OOM_1330 | I2AZZ5 | 1 |
| Protein HflC | hflC SCH_4240 | Q57GL6 | 1 |
| Protein HflC | hflC FTT_0634 | Q5NH37 | 1 |
| Protein HflK | hflK SCH_4239 | Q57GL7 | 1 |
| Protein HflK | hflK FTT_0633 | Q5NH38 | 1 |
| Protein IpgB | ipgB CP0130 | P33548 | 1 |
| Protein kinase | AC1_2162 | B1R8F9 | 1 |
| Protein kinase (EC 2.7.11.1) | yeaG PP_0397 | Q88QU0 | 1 |
| Protein MvaT | B195_10121 | M5QGQ4 | 1 |
| Protein MxiC | mxiC CP0146 | Q04640 | 1 |
| Protein NirF | nirF PA0516 | Q51480 | 1 |
| Protein of uncharacterised function (DUF3186) | SAMEA3375004_00125 | A0A160WYR6 | 1 |
| Protein of uncharacterised function (DUF3798) (Putative lipoprotein) | BN1095_250021 BN1096_680020 BN1097_690010 SAMEA3375004_04156 SAMEA3375059_00025 | A0A069AK17 | 1 |
| Protein PhnA | phnA yjdM b4108 JW4069 | P0AFJ1 | 1 |
| Protein phosphatase CheZ (EC 3.1.3.-) (Chemotaxis protein CheZ) | cheZ PA1457 | Q51434 | 1 |
| Protein phosphatase CheZ (EC 3.1.3.-) (Chemotaxis protein CheZ) | VSAK1_03139 | A6CXC0 | 1 |
| Protein PrgI | prgI STM2873 | P41784 | 1 |
| Protein rarD | KW89_2307 | A0A0K2DZM2 | 1 |
| Protein RecA (Recombinase A) | recA jhp_0141 | Q9ZMS7 | 1 |
| Protein RecA (Recombinase A) | recA KPN78578_29710 KPN_03031 | A6TCW1 | 1 |
| Protein RecA (Recombinase A) | recA FTN_0122 | A0Q468 | 1 |
| Protein RecA (Recombinase A) | recA Cj1673c | Q0P7V6 | 1 |
| Protein RecA (Recombinase A) | recA B195_10806 | M5QUQ3 | 1 |
| Protein RecA (Recombinase A) | recA PP_1629 | Q88ME4 | 1 |
| Protein RecA (Recombinase A) | recA HPSD74_1181 | U4SHB4 | 1 |
| Protein RecA (Recombinase A) | recA SPy_2116 M5005_Spy1799 | P0C095 | 1 |
| Protein RecA (Recombinase A) | recA CD630_13280 | Q18BJ4 | 1 |
| Protein RecA (Recombinase A) | recA Smlt1741 | B2FL31 | 1 |
| Protein RecA (Recombinase A) | recA SCH_2762 | Q57KU4 | 1 |
| Protein RecA (Recombinase A) | recA SAOUHSC_01262 | Q2FZ09 | 1 |
| Protein RecA (Recombinase A) | recA LMRG_00850 | G2JZ14 | 1 |
| Protein rep (Replication protein) | rep SPD_2300 | O52776 | 1 |
| Protein Rv1269c | Rv1269c MTCY50.13 | P9WM45 | 1 |
| Protein SanA | sanA yeiF b2144 JW2132 | P0AFY2 | 1 |
| Protein Smg homolog | smg VSAK1_24385 | A6D3X4 | 1 |
| Protein SopA (Plasmid partition protein A) | sopA A ECOK12F046 | P62556 | 1 |
| Protein TolA | tolA HPSD74_0018 | U4SP58 | 1 |
| Protein TolB | tolB MXAN_5756 | Q1D0D0 | 1 |
| Protein TolB | tolB jhp_1055 | Q9ZK86 | 1 |
| Protein TolB | tolB KPN_00744 | A6T6G6 | 1 |
| Protein TolB | tolB ABSDF0908 | B0VT82 | 1 |
| Protein TolB | tolB B195_07300 | M5QKD1 | 1 |
| Protein TolB | tolB VC_1836 | Q9KR11 | 1 |
| Protein TolB | tolB VS_1116 | B7VMJ2 | 1 |
| Protein TolB | tolB YPO1124 y3055 YP_1032 | Q8ZGZ1 | 1 |
| Protein TolB | tolB SF0557 S0570 | Q83MM7 | 1 |
| Protein TolB | tolB J804_0074 | A0A014EKM2 | 1 |
| Protein TolB | tolB SC1083_1318 | G4A912 | 1 |
| Protein TolB | tolB NSU_1019 | G6E9J8 | 1 |
| Protein TolB | tolB OOM_0338 | I2AXI5 | 1 |
| Protein TolQ | SC1083_1315 | G4A909 | 1 |
| Protein TolQ | tolQ HPSD74_0016 | U4SM55 | 1 |
| Protein TonB | tonB NMB1730 | P57004 | 1 |
| Protein TonB | Smlt4506 | B2FMI9 | 1 |
| Protein TonB | tonB exbA b1252 JW5195 | P02929 | 1 |
| Protein translocase subunit SecA | secA KPN78578_01010 KPN_00102 | A6T4P1 | 1 |
| Protein translocase subunit SecA | secA CPC_2474 | B1BKC4 | 1 |
| Protein translocase subunit SecA | secA SPJ_1595 | C1CFS1 | 1 |
| Protein translocase subunit SecA | secA div+ BSU35300 | P28366 | 1 |
| Protein translocase subunit SecA | secA SC1083_0071 | G4A5I6 | 1 |
| Protein translocase subunit SecA | secA azi pea prlD b0098 JW0096 | P10408 | 1 |
| Protein translocase subunit SecA | secA SSON_0106 | Q3Z5R1 | 1 |
| Protein translocase subunit SecA | secA SPy_1805 M5005_Spy1534 | Q99Y96 | 1 |
| Protein translocase subunit SecA | secA KW89_3048 | A0A0K2E1P2 | 1 |
| Protein translocase subunit SecA | secA FTT_0769 | Q5NGR3 | 1 |
| Protein translocase subunit SecA 1 | secA1 SAOUHSC_00769 | O06446 | 1 |
| Protein translocase subunit SecA 2 | secA2 SAOUHSC_02985 | Q2FUW6 | 1 |
| Protein translocase subunit SecA 2 | secA2 LMRG_00265 | G2K3V6 | 1 |
| Protein translocase subunit SecD | secD MBMO_EB0-39H12.0040 | A4GHV3 | 1 |