| Ribosome-binding factor A | rbfA PA4743 | Q9HV56 | 1 |
| Ribosome-binding factor A | rbfA VSAK1_10988 | A6D245 | 1 |
| Ribosome-binding factor A | rbfA SPy_1719 M5005_Spy1408 | P65971 | 1 |
| Ribosome-recycling factor (RRF) (Ribosome-releasing factor) | frr CPF_1951 | Q0TPQ6 | 1 |
| Ribosome-recycling factor (RRF) (Ribosome-releasing factor) | frr YPO1047 y3133 YP_2804 | Q8ZH63 | 1 |
| Ribosome-recycling factor (RRF) (Ribosome-releasing factor) | frr SF0162 S0165 | P0A808 | 1 |
| Ribosome-recycling factor (RRF) (Ribosome-releasing factor) | frr HPSD74_0083 | U4SPB7 | 1 |
| Ribulokinase | KPN_02547 | A6TBJ4 | 1 |
| Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | Fphi_1467 | B0TYU6 | 1 |
| Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | rpe PA0607 | Q9I5T1 | 1 |
| Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | rpe SPy_0264 | Q9A1H8 | 1 |
| Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | rpe1 CD630_25750 | Q182R3 | 1 |
| RmuC family protein | FTN_1024 | A0Q6P6 | 1 |
| RmuC family protein | OOM_1356 | I2B016 | 1 |
| RNA chaperone ProQ | proQ VSAK1_05305 | A6D6G5 | 1 |
| RNA polymerase sigma factor | VSAK1_03239 | A6CXE0 | 1 |
| RNA polymerase sigma factor RpoD (Sigma-70) | rpoD B195_13965 | M5QTQ1 | 1 |
| RNA polymerase sigma factor RpoD (Sigma-70) | alt rpoD YPO0643 | Q0WJ27 | 1 |
| RNA polymerase sigma factor RpoD (Sigma-70) | rpoD HPSD74_1172 | U4SIE0 | 1 |
| RNA polymerase sigma factor RpoE | rpoE KW89_1205 | A0A0K2DWH4 | 1 |
| RNA polymerase sigma factor RpoH (Heat shock regulatory protein F33.4) (RNA polymerase sigma-32 factor) | rpoH fam hin htpR b3461 JW3426 | P0AGB3 | 1 |
| RNA polymerase sigma factor RpoS (Sigma S) (Sigma-38) | rpoS KW89_1518 | A0A0K2DWU8 | 1 |
| RNA polymerase sigma factor SigA | rpoD sigA SPy_0782 | Q9A0G8 | 1 |
| RNA polymerase sigma factor SigA | sigA plaC rpoD SAOUHSC_01662 | P0A0J0 | 1 |
| RNA polymerase sigma factor SigA (Sigma-43) (Sigma-A) | sigA rpoD BSU25200 | P06224 | 1 |
| RNA polymerase-associated protein RapA (EC 3.6.4.-) (ATP-dependent helicase HepA) | rapA SSON_0065 | Q3Z5V2 | 1 |
| RNA polymerase-binding transcription factor DksA | dksA PA4723 | G3XD14 | 1 |
| RNA-binding protein Hfq | hfq Fphi_1538 | B0TZB1 | 1 |
| RNA-binding protein Hfq | hfq PA4944 | Q9HUM0 | 1 |
| RNA-binding protein Hfq | hfq CD630_19740 | Q187T2 | 1 |
| RNA-binding protein Hfq | hfq OOM_1325 | I2AZZ0 | 1 |
| RNA-binding protein Hfq | hfq FTT_0630 | Q5NH41 | 1 |
| RNA-binding protein YhbY | yhbY b3180 JW3147 | P0AGK4 | 1 |
| Rna-binding protein, yhby family | CD630_11650 | Q18B26 | 1 |
| RNase adapter protein RapZ | rapZ YPO3586 y0158 YP_3840 | Q8ZB41 | 1 |
| RNase I (EC 3.1.27.6) | rna STM0617 | Q8ZR16 | 1 |
| RND efflux system outer membrane lipoprotein | NSU_4717 | G6EK46 | 1 |
| RND efflux system outer membrane lipoprotein | NSU_2605 | G6EE34 | 1 |
| RND efflux system, outer membrane lipoprotein,NodT | NSU_1588 | G6EB67 | 1 |
| RND efflux transporter | PP_1517 | Q88MQ3 | 1 |
| RND efflux transporter | PP_5173 | Q88CK7 | 1 |
| Rod shape-determining protein MreB | B195_04911 | M5QYM9 | 1 |
| Rod shape-determining protein MreB | mreB BSU28030 | Q01465 | 1 |
| Rod shape-determining protein MreB | envB YPO3665 | Q7CL65 | 1 |
| Rod shape-determining protein MreB | VSAK1_08271 | A6D037 | 1 |
| Rod shape-determining protein MreB | mreB2 CD630_11450 | Q18B05 | 1 |
| ROK family protein | FTN_0617 | A0Q5J6 | 1 |
| ROK family protein | cscK FTN_0646 | A0Q5M4 | 1 |
| ROK family protein | VSAK1_22089 | A6D6M6 | 1 |
| Rough colony protein B | SC1083_1233 | G4A8T1 | 1 |
| RoxR | roxR PA4493 | Q9HVS8 | 1 |
| RsbR protein | RsbR | Q8Y8K9 | 1 |
| RsbT co-antagonist protein RsbRA (Stressosome protein RsbRA) | rsbRA rsbR ycxR BSU04670 | P42409 | 1 |
| RsbT co-antagonist protein RsbRB (Stressosome protein RsbRB) | rsbRB ykoB BSU13200 | O34860 | 1 |
| Rubredoxin-NAD(+) reductase (RdxR) (EC 1.18.1.1) | alkT PA5349 | Q9HTK9 | 1 |
| Rubredoxin/flavodoxin/oxidoreductase | CPC_1265 | B1BEV4 | 1 |
| Rubrerythrin | CPR_2638 | C6UAS6 | 1 |
| Rubrerythrin | rbr FSU_0915 | C9RLG2 | 1 |
| Rz lysis protein | enpP SCH_0350 | Q57SQ5 | 1 |
| S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284) | Fphi_0427 | B0U016 | 1 |
| S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284) | adhC FTN_0409 | A0Q4Z7 | 1 |
| S-(Hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284) | B195_06095 | M5R188 | 1 |
| S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284) | VSAK1_11845 | A6D2U5 | 1 |
| S-adenosylmethionine decarboxylase proenzyme (AdoMetDC) (SAMDC) (EC 4.1.1.50) [Cleaved into: S-adenosylmethionine decarboxylase beta chain; S-adenosylmethionine decarboxylase alpha chain] | speH PA4773 | Q9HV35 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK NMB1799 | Q9JY09 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK spr0671 | Q8DQH0 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK YPO0931 y3314 YP_3512 | Q8ZHG7 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK SF2933 S3137 | P0A820 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK Rv1392 MTCY21B4.09 | P9WGV1 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK KPR_4645 | R4YFG0 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK metX b2942 JW2909 | P0A817 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK SSON_3096 | Q3YXS9 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK SPy_1359 M5005_Spy1108 | Q99Z77 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK CD630_01300 | Q18CL7 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK FSU_0038 | C9RNB7 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK SCH_3030 | Q57K26 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK SAOUHSC_01909 | Q2G1W4 | 1 |
| S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (MAT) (Methionine adenosyltransferase) | metK FTT_0149c | Q5NIC7 | 1 |
| S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC 2.4.99.17) (Queuosine biosynthesis protein QueA) | queA SPy_1400 M5005_Spy1140 | Q99Z49 | 1 |
| S-formylglutathione hydrolase (EC 3.1.2.12) | VSAK1_11850 | A6D2U6 | 1 |
| S-layer protein | slpA | Q9AEM3 | 1 |
| S-layer protein | CDIF1296T_02929 | A0A125V960 | 1 |
| S-methyl-5-thioadenosine phosphorylase (EC 2.4.2.28) | Fphi_1715 | B0U0B0 | 1 |
| S-ribosylhomocysteine lyase (EC 4.4.1.21) (AI-2 synthesis protein) (Autoinducer-2 production protein LuxS) | luxS YPO3300 y0888 YP_0386 | Q8ZBU3 | 1 |
| S-ribosylhomocysteine lyase (EC 4.4.1.21) (AI-2 synthesis protein) (Autoinducer-2 production protein LuxS) | luxS SSON_2831 | Q3YYH1 | 1 |
| S-ribosylhomocysteine lyase (EC 4.4.1.21) (AI-2 synthesis protein) (Autoinducer-2 production protein LuxS) | luxS SPy_1642 M5005_Spy1349 | P0C0C8 | 1 |
| S1 RNA binding domain protein | SAOUHSC_02297 | Q2FWJ5 | 1 |
| S41 family peptidase | B195_20148 | M5QCZ5 | 1 |
| SapA-like protein | sapA SCH_0307 | Q57SU8 | 1 |
| Scaffolding protein for murein-synthesising holoenzyme | mipA KPN_01194 | A6T7Q6 | 1 |
| Scaffolding protein for murein-synthesizing holoenzyme | mipA SCH_1298 | Q57Q07 | 1 |
| Sco1-related protein | VSAK1_19069 | A6CXZ1 | 1 |
| SCP-2 sterol transfer family protein | KW89_379 | A0A0K2DU56 | 1 |
| Sec translocon accessory complex subunit YajC | yajC b0407 JW0397 | P0ADZ7 | 1 |
| Sec-independent protein translocase protein TatA | tatA Rv2094c MTCY49.34c | P9WGA1 | 1 |
| Sec-independent protein translocase protein TatA | tatA PA5068 | Q9HUB5 | 1 |
| Sec-independent protein translocase protein TatA | tatA mttA1 yigT b3836 JW3813 | P69428 | 1 |
| Sec-independent protein translocase protein TatC | tatC VSAK1_13195 | A6D2C8 | 1 |
| Sec-independent protein translocase protein TatE | tatE ybeC b0627 JW0622 | P0A843 | 1 |
| Secreted chorismate mutase (*MtCM) (CM) (EC 5.4.99.5) | pheA2 y2828 YP_1243 YPO1353 | Q7CHH5 | 1 |