| Putative phthiocerol dimycocerosate transporter LppX (Lipoprotein LppX) | lppX Rv2945c MTCY24G1.04 | P9WK65 | 1 |
| Putative pilus biogenesis operon protein | MXAN_0362 | Q1DFD7 | 1 |
| Putative pilus biogenesis protein PilJ/methyl accepting chemotaxis protein | pilJ Smlt3671 | B2FR34 | 1 |
| Putative PilW protein (Type 4 fimbrial biogenesis protein PilW) | pilW Smlt1623 | B2FJB5 | 1 |
| Putative pit accessory protein | Smlt1705 | B2FK78 | 1 |
| Putative poly-hydroxy-butyrate synthesis protein | Smlt3326 | B2FN33 | 1 |
| Putative polymerase/proteinase | yajG S0385 SF0378 AJR25_006310 AJR27_019305 | A0A0H2VTD9 | 1 |
| Putative polymerase/proteinase | yajG ECs0488 Z0537 | Q8XE62 | 1 |
| Putative polysaccharide biosynthesis protein | FSU_1440 | D9SAA0 | 1 |
| Putative polysaccharide deacetylase | CD630_15220 | Q18C42 | 1 |
| Putative polysaccharide deacetylase | CD630_27190 | Q183F4 | 1 |
| Putative polysaccharide deacetylase family protein | VSAK1_24960 | A6CZ48 | 1 |
| Putative polysaccharide-degrading enzyme | MXAN_6236 | Q1CZ08 | 1 |
| Putative pore-forming peptide | SPy_0800 | Q9A0F3 | 1 |
| Putative porin | KPN_04773 | A6THT5 | 1 |
| Putative Porin | PP_4465 | Q88EJ7 | 1 |
| Putative porin D | ACIN5021_0233 | L9MEG5 | 1 |
| Putative positive transcriptional regulator | mutR SPy_0496 | Q9A132 | 1 |
| Putative pre-16S rRNA nuclease (EC 3.1.-.-) | spr0176 | Q8DRE2 | 1 |
| Putative pre-16S rRNA nuclease (EC 3.1.-.-) | SPy_2113 M5005_Spy1796 | Q99XP4 | 1 |
| Putative primosome component (Helicase loader) | dnaI SPy_0340 | Q9A1D1 | 1 |
| Putative pristinamycin I synthase 3 | MXAN_1023 | Q1DDI9 | 1 |
| Putative processin peptidase (EC 3.4.24.-) | PP_5112 | Q88CR8 | 1 |
| Putative PROCESSING PROTEASE | jhp_0602 | Q9ZLH7 | 1 |
| Putative prolyl aminopeptidase | VSAK1_01422 | A6D2H0 | 1 |
| Putative protease | VS_2565 | B7VK36 | 1 |
| Putative protease | VSAK1_14177 | A6D729 | 1 |
| Putative protease | SPy_0590 | Q9A0W0 | 1 |
| Putative protease | SPy_0591 | Q9A0V9 | 1 |
| Putative PTS system enzyme II | SPy_2097 | Q99XQ4 | 1 |
| Putative PTS system, enzyme IIB component | SPy_1710 | Q99YG9 | 1 |
| Putative PTS system, lactose-specific component IIA | lacF SPy_1918 | Q99Y16 | 1 |
| Putative PTS system, lactose-specific component IIBC (EC 2.7.1.69) | lacE SPy_1917 | Q99Y17 | 1 |
| Putative PTS system, N-acetylglucosamine-specific IIA component | CPC_0098 | B1BFR7 | 1 |
| Putative PTS transport protein | manX YPO0834 | Q7CGX3 | 1 |
| Putative pullulanase | VSAK1_23704 | A6CWE7 | 1 |
| Putative pullulanase | pulA SPy_1972 | Q99XX8 | 1 |
| Putative purine operon repressor | purR SPy_0268 | Q9A1H4 | 1 |
| Putative PydP transporter, NCS1 nucleoside transporter family | pydP PP_4035 | Q88FQ2 | 1 |
| Putative pyridine nucleotide-disulphide oxidoreductase | Cj0559 | Q0PAV7 | 1 |
| Putative pyruvate carboxylase B subunit (EC 6.4.1.1) | pycB Cj0933c | Q0P9W6 | 1 |
| Putative pyruvate carboxylase, B subunit | FSU_1289 | C9RNK8 | 1 |
| Putative pyruvate formate-lyase | pfl SPy_1849 | Q99Y65 | 1 |
| Putative pyruvate formate-lyase 2 (EC 2.3.1.54) | pflD SPy_2049 | Q99XT3 | 1 |
| Putative pyruvate formate-lyase activating enzyme | SPy_2055 | Q99XS7 | 1 |
| Putative reductase / dehydrogenase | SPy_1693 | Q99YI1 | 1 |
| Putative regulator AbrB (AidB regulator) | abrB ybgN b0715 JW5097 ECK0704 | P75747 | 1 |
| Putative regulator of flagellation | ycfJ PP_0837 | Q88PL3 | 1 |
| Putative regulatory protein | Cj1507c | Q0P8B1 | 1 |
| Putative regulatory protein | B195_16809 | M5QEB3 | 1 |
| Putative regulatory protein-RofA related | SPy_0216 | Q9A1L0 | 1 |
| Putative repressor protein | adcR SPy_0092 | Q9A1U7 | 1 |
| Putative repressor protein PhnR | VSAK1_17747 | A6CVB0 | 1 |
| Putative repressor-phage associated | SPy_1861 | Q99Y57 | 1 |
| Putative resistance protein | ylcB SSON_0523 | Q3Z4M0 | 1 |
| Putative respiratory nitrate reductase alpha chain (EC 1.7.99.4) | narG Smlt2774 | B2FUL2 | 1 |
| Putative respiratory nitrate reductase subunit | narH Smlt2773 | B2FUL1 | 1 |
| Putative response regulator | VSAK1_01297 | A6D2E5 | 1 |
| Putative response regulator | SPy_0245 | Q9A1J5 | 1 |
| Putative response regulator | SPy_1237 | Q99ZG8 | 1 |
| Putative response regulator (Activator) in two-component regulatory system (OmpR family) | ACIAD0726 | Q6FE74 | 1 |
| Putative rhamnosyltransferase-possibly involved in cell wall localization and side chain formation of rhamnose-glucose polysaccharide | rgpBc SPy_0787 | Q9A0G4 | 1 |
| Putative ribonucleotide reductase 2 | nrdF.1 SPy_0425 | Q9A177 | 1 |
| Putative ribosomal protein S1-like DNA-binding protein | SPy_0913 | Q9A066 | 1 |
| Putative RmuC family protein | Smlt4678 | B2FP90 | 1 |
| Putative RNA helicase | deaD2 SPy_1369 | Q99Z69 | 1 |
| Putative RNA-binding Sun protein | sunL SPy_1627 | Q99YM8 | 1 |
| Putative RND family (AdeB-like) | ACIAD2944 | Q6F8F6 | 1 |
| Putative RND/Acr family transmembrane transporter | smeO Smlt3925 | B2FTS2 | 1 |
| Putative rod shape-determining protein | mreB Smlt4059 | B2FUU0 | 1 |
| Putative rRNA methylase | SPy_0356 | Q9A1C1 | 1 |
| Putative rubrerythrin | CD630_15240 | Q18C45 | 1 |
| Putative rubrerythrin (Rr) | CD630_14740 | Q18BZ4 | 1 |
| Putative salt-induced outer membrane protein | NSU_0049 | G6E6S8 | 1 |
| Putative secreted serine protease (EC 3.4.21.-) | Cj1365c | Q0P8P4 | 1 |
| Putative secretion protein | NMB1737 | Q7DD87 | 1 |
| Putative sensor histidine kinase | CPC_2708 | B1BMM0 | 1 |
| Putative sensory box-containing diguanylate cyclase | CPC_1163 | B1BJA8 | 1 |
| Putative serine protein kinase PrkA | B195_20245 | M5QD22 | 1 |
| Putative serine-pyruvate aminotransferase (EC 2.6.1.-) | CD630_09940 | Q18AJ4 | 1 |
| Putative shikimate 5-dehydrogenase (EC 1.1.1.25) | aroE.2 SPy_0534 | Q9A102 | 1 |
| Putative short-chain type dehydrogenase/reductase Rv0148 (EC 1.1.1.-) | Rv0148 | P96825 | 1 |
| Putative SI family secreted trypsin-like serine protease | VS_II0815 | B7VSJ8 | 1 |
| Putative siderophore receptor | fhuA | Q7AX11 | 1 |
| Putative sigma 54 modulation protein | yfiA YPO3279 | Q0WC09 | 1 |
| Putative signal peptide peptidase SppA (EC 3.4.21.-) | sppA yteI BSU29530 | O34525 | 1 |
| Putative single-strand DNA-specific exonuclease | recJ SPy_0926 | Q9A054 | 1 |
| Putative SNF helicase | snf SPy_0342 | Q9A1C9 | 1 |
| Putative sodium/solute symporter | VSAK1_26655 | A6D8U8 | 1 |
| Putative sodium:dicarboxylate symport transport protein | Smlt3462 | B2FP32 | 1 |
| Putative SpoIIIJ-associated RNA/ssDNA-binding protein Jag | jag CD630_36770 | Q181S9 | 1 |
| Putative spore protein | CD630_00070 | Q18C91 | 1 |
| Putative sporulation initiation inhibitor protein | MXAN_5815 | Q1D071 | 1 |
| Putative sporulation transcription regulator WhiA | whiA SPy_0654 M5005_Spy0541 | Q9A0R6 | 1 |
| Putative structural protein-phage associated | SPy_1457 | Q99Z07 | 1 |
| Putative succinate dehydrogenase iron-sulfur protein (EC 1.3.5.1) | sdhB Cj0438 | Q0PB72 | 1 |
| Putative succinate dehydrogenase subunit C (EC 1.3.99.1) | sdhC Cj0439 | Q0PB71 | 1 |
| Putative succinic semialdehyde dehydrogenase | gabD SPy_1067 | Q99ZU4 | 1 |
| Putative succinyl-diaminopimelate desuccinylase | MXAN_6777 | Q1CXH9 | 1 |
| Putative sucrose operon repressor | scrR SPy_1817 | Q99Y89 | 1 |