| Quinol oxidase subunit 2 (EC 1.10.3.-) (Oxidase aa(3)-600 subunit 2) (Quinol oxidase aa3-600, subunit QoxA) (Quinol oxidase polypeptide II) | qoxA BSU38170 ipa-37d | P34957 | 3 |
| Receptor family ligand-binding protein | MXAN_1262 | Q1DCV4 | 3 |
| Recombinase (Recombination protein bet) | AM266_24395 EL75_2097 EL79_2408 | A0A086V0N7 | 3 |
| Recombination-associated protein RdgC | rdgC BE932_25585 SY51_02070 | A0A061YF08 | 3 |
| Regulator protein FrmR | frmR AML07_16520 APZ14_02825 ERS150876_00540 | A0A0F3WCZ6 | 3 |
| Repressor protein C2 | CE10_2482 | A0A0E0V778 | 3 |
| Respiratory nitrate reductase alpha chain | narG PA3875 | G3XCX1 | 3 |
| Response regulator | sirA BY96_17205 | A0A027TS78 | 3 |
| Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)] | ribA ribBA spr0162 | Q8DRF1 | 3 |
| Riboflavin synthase alpha chain | ribC PA4055 | Q9HWX3 | 3 |
| Ribonuclease E (RNase E) (EC 3.1.26.12) | rne FTN_1246 | A0Q7B2 | 3 |
| Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | nrdB PA1155 | Q9I4I2 | 3 |
| Ribose import binding protein RbsB | rbsB prlB rbsP b3751 JW3730 | P02925 | 3 |
| Ribose-phosphate pyrophosphokinase (RPPK) (EC 2.7.6.1) (5-phospho-D-ribosyl alpha-1-diphosphate) (Phosphoribosyl diphosphate synthase) (Phosphoribosyl pyrophosphate synthase) (P-Rib-PP synthase) (PRPP synthase) (PRPPase) | prs prsA Cj0918c | Q9PP15 | 3 |
| Ribose-phosphate pyrophosphokinase 2 (RPPK 2) (EC 2.7.6.1) (5-phospho-D-ribosyl alpha-1-diphosphate 2) (Phosphoribosyl diphosphate synthase 2) (Phosphoribosyl pyrophosphate synthase 2) (P-Rib-PP synthase 2) (PRPP synthase 2) (PRPPase 2) | prs2 prs spr1002 | P65242 | 3 |
| Ribosomal RNA large subunit methyltransferase G (EC 2.1.1.174) (23S rRNA m2G1835 methyltransferase) (rRNA (guanine-N(2)-)-methyltransferase RlmG) | rlmG APU18_16900 BE932_14355 BXT93_22215 SY51_17870 | A0A066SX35 | 3 |
| Ribosomal RNA large subunit methyltransferase I (EC 2.1.1.191) (23S rRNA m5C1962 methyltransferase) (rRNA (cytosine-C(5)-)-methyltransferase RlmI) | rlmI BX51_11055 | A0A025CK37 | 3 |
| Ribosome-binding ATPase YchF | ychF engD Z1974 ECs1708 | P0ABU3 | 3 |
| Ribosome-binding ATPase YchF | ychF ECBD_2418 | A0A140NAR5 | 3 |
| Ribosome-recycling factor (RRF) (Ribosome-releasing factor) | frr PA3653 | O82853 | 3 |
| Ribulose-5-phosphate reductase (Ribulose-5-P reductase) (EC 1.1.1.405) (Ribitol-5-phosphate dehydrogenase) | tarJ spr1148 | Q8DPI3 | 3 |
| Right origin-binding protein | rob Z5999 ECs5354 | P0ACI1 | 3 |
| RNA polymerase sigma factor RpoS (Sigma S) (Sigma-38) | rpoS AC789_1c30620 | A0A0E1LFA8 | 3 |
| RNA polymerase sigma-54 factor | BX23_10445 | A0A028ECH1 | 3 |
| RNA polymerase-associated protein RapA (EC 3.6.4.-) (ATP-dependent helicase HepA) | rapA hepA PA3308 | Q9HYT6 | 3 |
| RNA-binding protein | A4T50_21345 BE932_29920 SY51_06270 | A0A066SN32 | 3 |
| RNA-binding transcriptional accessory protein (Transcription accessory protein) | BE932_15990 SY51_19490 | A0A061YNY0 | 3 |
| RND efflux transporter, AcrB/AcrD/AcrF family | FTN_1610 | A0Q8A5 | 3 |
| S-adenosylmethionine decarboxylase proenzyme (AdoMetDC) (SAMDC) (EC 4.1.1.50) [Cleaved into: S-adenosylmethionine decarboxylase beta chain; S-adenosylmethionine decarboxylase alpha chain] | speD EcE24377A_0122 | A7ZHK9 | 3 |
| S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC 2.4.99.17) (Queuosine biosynthesis protein QueA) | queA EcE24377A_0435 | A7ZIF7 | 3 |
| S-ribosylhomocysteine lyase (EC 4.4.1.21) (AI-2 synthesis protein) (Autoinducer-2 production protein LuxS) | luxS EcE24377A_2970 | A7ZQC0 | 3 |
| Sec-independent protein translocase protein TatA | tatA PGD_00134 SK85_04164 | A0A024L616 | 3 |
| Second ferric pyoverdine receptor FpvB | fpvB PA4168 | Q9HWL3 | 3 |
| Septum site-determining protein DivIVA (Cell division initiation protein DivIVA) (Minicell-associated protein DivIVA) | divIVA ylmJ BSU15420 | P71021 | 3 |
| Serine hydroxymethyltransferase (SHMT) (Serine methylase) (EC 2.1.2.1) | glyA Z3827 ECs3417 | Q8XA55 | 3 |
| Serine hydroxymethyltransferase 3 (SHMT 3) (Serine methylase 3) (EC 2.1.2.1) | glyA2 PA4602 | Q9HVI7 | 3 |
| Serine protease | sphtra spr2045 | Q8DMW2 | 3 |
| Serine protease (EC 3.4.21.-) | MXAN_6352 | Q1CYP7 | 3 |
| Serine protease (EC 3.4.21.-) | MXAN_0587 | Q1DER8 | 3 |
| Serine protease (Protease DO) (EC 3.4.21.-) | htrA Cj1228c | Q0P928 | 3 |
| Serine-type D-Ala-D-Ala carboxypeptidase | FTN_0917 | A0Q6E0 | 3 |
| Signal recognition particle protein (Fifty-four homolog) | ffh PA3746 | Q9HXP8 | 3 |
| Signal recognition particle protein (Fifty-four homolog) | ffh Z3904 ECs3473 | P0AGD9 | 3 |
| Signal recognition particle protein (Fifty-four homolog) | ffh CE10_3044 | A0A0E0V8D2 | 3 |
| Site-determining protein | minD Smlt1251 | B2FTA7 | 3 |
| Skp-like protein | PP_1600 | Q88MH1 | 3 |
| Sodium/proline symporter PutP | putP PA0783 | Q9I5F5 | 3 |
| Soluble lytic murein transglycosylase | slt FTN_0496 | A0Q577 | 3 |
| SopB | sopB | D9Z554 | 3 |
| Spermidine/putrescine ABC transporter-periplasmic subunit | spuD PP_5181 | Q88CJ9 | 3 |
| Starvation-inducible DNA-binding protein | LMRG_02041 | A0A0H3GFE0 | 3 |
| Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | sdhA FTN_1637 | A0Q8D0 | 3 |
| Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | sdhA PP_4191 | Q88FA7 | 3 |
| Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | sdhA Smlt1798 | B2FL86 | 3 |
| Succinate dehydrogenase hydrophobic membrane anchor subunit | sdhD PA1582 | Q9I3D6 | 3 |
| Succinate dehydrogenase iron-sulfur subunit (EC 1.3.5.1) | sdhB PP_4190 | Q88FA8 | 3 |
| Succinate--CoA ligase [ADP-forming] subunit alpha (EC 6.2.1.5) (Succinyl-CoA synthetase subunit alpha) (SCS-alpha) | sucD Z0883 ECs0754 | P0AGF1 | 3 |
| Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) (Succinyl-CoA synthetase subunit beta) (SCS-beta) | sucC PP_4186 PP4186 | Q88FB2 | 3 |
| Sugar phosphatase | BX52_19210 | A0A0E2U1H2 | 3 |
| Sulfate ABC transporter | sbp-I PP_4305 | Q88EZ5 | 3 |
| Superoxide dismutase (EC 1.15.1.1) | LMRG_00891 | A0A0H3GC36 | 3 |
| Surface protein PspA | SP70585_0197 | C1CAE6 | 3 |
| Tagatose 1,6-diphosphate aldolase (EC 4.1.2.40) (D-tagatose-1,6-bisphosphate aldolase) (Tagatose-bisphosphate aldolase) | lacD spr1073 | Q8DPP2 | 3 |
| TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase (EC 2.4.1.325) (4-alpha-L-fucosyltransferase) (TDP-Fuc4NAc:lipid II Fuc4NAc transferase) (Fuc4NAc transferase) | wecF rffT BE932_18215 SY51_21580 | A0A066T2U8 | 3 |
| Tetratricopeptide repeat protein | MXAN_2541 | Q1D9B3 | 3 |
| Thiol:disulfide interchange protein | dsbA-2 NMB0294 | Q7DDR6 | 3 |
| Thiol:disulfide interchange protein | dsbA PP_0127 | Q88RK2 | 3 |
| Thiol:disulfide interchange protein | dsbA AC789_1c42430 | A0A0E1LES4 | 3 |
| Thiol:disulfide interchange protein DsbA | dsbA-1 NMB0278 | Q9K189 | 3 |
| Thiol:disulfide interchange protein DsbA | dsbA E2348C_4167 | P0A4L6 | 3 |
| Thiol:disulfide interchange protein DsbE (Cytochrome c biogenesis protein CcmG) | dsbE ccmG PA1481 | Q9I3N1 | 3 |
| Thioredoxin reductase (EC 1.8.1.9) | BE932_28155 SY51_04550 | A0A066T755 | 3 |
| Threonine synthase | BE932_23025 SY51_00020 | A0A066SPL1 | 3 |
| Toluene tolerance protein | ttg2D PP_0961 | Q88P91 | 3 |
| TonB-dependent receptor | MXAN_6911 | Q1CX48 | 3 |
| TonB-dependent receptor | PP_1446 | Q88MX2 | 3 |
| Toxin expression-transcriptional accessory protein | tex spr0808 | Q8DQ79 | 3 |
| TPR repeat-containing protein NMB0313 | NMB0313 | Q9K165 | 3 |
| Transaldolase (EC 2.2.1.2) | tal O3O_03880 | K0BE10 | 3 |
| Transaldolase 1 (EC 2.2.1.2) | tal1 SSON_0009 | Q3Z606 | 3 |
| Transcription elongation factor GreA (Transcript cleavage factor GreA) | greA BY96_04470 | A0A027U3E8 | 3 |
| Transcription termination/antitermination protein NusG | nusG spr1820 | Q8DNB8 | 3 |
| Transcriptional regulator | nanR ECUMN_3378 | B7NCN8 | 3 |
| Transcriptional regulator | nhaR SY51_00105 | A0A061YHB9 | 3 |
| Transcriptional regulatory protein PhoP | UMNK88_1461 | A0A0E0TX07 | 3 |
| Transferrin-binding protein 1 | tbp1 NMB0461 | Q9K0U9 | 3 |
| Transferrin-binding protein 2 (TBP-2) | tbpB tbp2 NMB0460 | Q9K0V0 | 3 |
| Translation initiation factor IF-2 | infB FTN_1660 | A0Q8F3 | 3 |
| Translation initiation factor IF-2 | infB spr0481 | Q8DQV2 | 3 |
| Trehalose-6-phosphate synthase (EC 2.4.1.15) (Osmoregulatory trehalose synthesis protein A) (UDP-glucose-glucosephosphate glucosyltransferase) | otsA A4T40_14230 BK334_13095 ECONIH1_10875 MS6198_21280 | A0A086V237 | 3 |
| Tributyrin esterase | estA spr0539 | Q8DQR2 | 3 |
| tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ (EC 2.1.1.200) (tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase) (tRNA Cm32/Um32 methyltransferase) | trmJ BY96_10455 | A0A027TYH4 | 3 |
| tRNA 2-thiocytidine biosynthesis protein TtcA | ttcA ECS88_1488 | B7MM21 | 3 |
| tRNA 2-thiocytidine biosynthesis protein TtcA | ttcA ECED1_1555 | B7MUI7 | 3 |
| tRNA dimethylallyltransferase (EC 2.5.1.75) (Dimethylallyl diphosphate:tRNA dimethylallyltransferase) (DMAPP:tRNA dimethylallyltransferase) (DMATase) (Isopentenyl-diphosphate:tRNA isopentenyltransferase) (IPP transferase) (IPPT) (IPTase) | miaA EcE24377A_4729 | A7ZV40 | 3 |
| tRNA sulfurtransferase (EC 2.8.1.4) (Sulfur carrier protein ThiS sulfurtransferase) (Thiamine biosynthesis protein ThiI) (tRNA 4-thiouridine synthase) | thiI BE932_25730 SY51_02215 | A0A066T5U9 | 3 |
| tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase (EC 2.8.4.3) ((Dimethylallyl)adenosine tRNA methylthiotransferase MiaB) (tRNA-i(6)A37 methylthiotransferase) | miaB EC958_0779 UG58_01325 | W8ZNP1 | 3 |
| tRNA-dihydrouridine(20/20a) synthase (EC 1.3.1.-) (EC 1.3.1.91) (U20-specific dihydrouridine synthase) (U20-specific Dus) (tRNA-dihydrouridine synthase A) | dusA_2 dusA ECRM12581_25810 | A0A023Z651 | 3 |
| Tryptophanase (EC 4.1.99.1) (L-tryptophan indole-lyase) (TNase) | tnaA BX06_13805 | A0A028AFZ4 | 3 |
| Tryptophanase (EC 4.1.99.1) (L-tryptophan indole-lyase) (TNase) | tnaA Z5203 ECs4645 | Q8XB34 | 3 |