| Phosphoglucomutase | pgm CE10_0678 | A0A0E0V338 | 3 |
| Phosphoglucosamine mutase (EC 5.4.2.10) | glmM PA4749 | Q9HV50 | 3 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk PA0552 | Q9I5Y4 | 3 |
| Phospholipase (Phospholipase A) (EC 3.1.1.32) (EC 3.1.1.4) | A4T50_13445 APU18_23080 BE932_18380 SY51_21735 WM48_21070 | E2QHZ4 | 3 |
| Phosphoribosylamine--glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide synthetase) (Phosphoribosylglycinamide synthetase) | purD ECED1_4712 | B7N2K7 | 3 |
| Phosphoribosylformylglycinamidine synthase (FGAM synthase) (FGAMS) (EC 6.3.5.3) (Formylglycinamide ribonucleotide amidotransferase) (FGAR amidotransferase) (FGAR-AT) | purL BE932_10570 SY51_14640 | A0A066T7J4 | 3 |
| Phosphoserine aminotransferase (EC 2.6.1.52) (Phosphohydroxythreonine aminotransferase) (PSAT) | serC ECED1_0934 | B7MS22 | 3 |
| Pneumococcal surface protein A | pspA SPCG_0120 | B2IRK1 | 3 |
| Polar amino acid uptake transporter | FTN_0191 | A0Q4D6 | 3 |
| Polyamine-transporting ATPase (EC 3.6.3.31) | PA0603 | Q9I5T5 | 3 |
| Polyphosphate kinase (EC 2.7.4.1) (ATP-polyphosphate phosphotransferase) (Polyphosphoric acid kinase) | ppk PA5242 | Q9S646 | 3 |
| Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) (Polynucleotide phosphorylase) (PNPase) | pnp E2348C_3445 | B7UJ59 | 3 |
| Porin | oprB-I PP_1019 | Q88P34 | 3 |
| Porin | oprB-III PP_3570 | Q88GZ5 | 3 |
| Porin | rpfN Smlt2559 | B2FSS7 | 3 |
| Positive alginate biosynthesis regulatory protein | algR PA5261 | P26275 | 3 |
| Potassium-transporting ATPase ATP-binding subunit (EC 3.6.3.12) (ATP phosphohydrolase [potassium-transporting] B chain) (Potassium-binding and translocating subunit B) (Potassium-translocating ATPase B chain) | kdpB FTN_1717 | A0Q8K9 | 3 |
| Potassium-transporting ATPase ATP-binding subunit (EC 3.6.3.12) (ATP phosphohydrolase [potassium-transporting] B chain) (Potassium-binding and translocating subunit B) (Potassium-translocating ATPase B chain) | kdpB PA1634 | P57698 | 3 |
| Potential aminotransferase (EC 2.6.1.1) | aspC spr1808 | Q8DNC7 | 3 |
| Predicted type I restriction-modification enzyme M subunit | E2348C_4610 | B7UQU3 | 3 |
| Predicted type I restriction-modification enzyme S subunit | E2348C_4609 | B7UQU2 | 3 |
| Primosomal replication protein N | BE932_25960 SY51_02435 | A0A061KQ46 | 3 |
| Probable 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD (EC 3.5.1.n3) | arnD A4T40_16615 BK334_03330 ECONIH1_13180 MS6198_25910 | A0A0A1AA63 | 3 |
| Probable AGCS sodium/alanine/glycine symporter | PA2252 | Q9I1L7 | 3 |
| Probable aldehyde dehydrogenase | PA4022 | Q9HX05 | 3 |
| Probable ATP-binding component of ABC dipeptide transporter | PA4506 | Q9HVR5 | 3 |
| Probable ATP-binding component of ABC transporter | PA4505 | Q9HVR6 | 3 |
| Probable ATP-binding component of ABC transporter | PA4595 | Q9HVJ1 | 3 |
| Probable bacteriophage protein | PA0638 | Q9I5S8 | 3 |
| Probable chemotaxis protein | PA3349 | Q9HYP7 | 3 |
| Probable chemotaxis transducer | PA1608 | Q9I3B3 | 3 |
| Probable chemotaxis transducer | PA4633 | Q9HVF8 | 3 |
| Probable ClpA/B protease ATP binding subunit | PA0459 | Q9I659 | 3 |
| Probable cold-shock protein | PA0456 | Q9I662 | 3 |
| Probable cytosol aminopeptidase (EC 3.4.11.1) (Leucine aminopeptidase) (LAP) (EC 3.4.11.10) (Leucyl aminopeptidase) | pepA BX23_11600 | A0A028E6T3 | 3 |
| Probable efflux pump membrane transporter TtgB | ttgB PP_1385 | Q88N31 | 3 |
| Probable efflux pump outer membrane protein TtgC | ttgC PP_1384 | Q88N32 | 3 |
| Probable efflux pump periplasmic linker TtgA | ttgA PP_1386 | Q88N30 | 3 |
| Probable enoyl-CoA hydratase/isomerase | PA0745 | Q9I5I4 | 3 |
| Probable glyceraldehyde-3-phosphate dehydrogenase | PA2323 | Q9I1F5 | 3 |
| Probable GTP-binding protein EngB | engB EcE24377A_4383 | A7ZU66 | 3 |
| Probable L,D-transpeptidase YbiS (EC 2.-.-.-) | ybiS Z1041 ECs0896 | P0AAY0 | 3 |
| Probable L-asparaginase (L-ASNase) (EC 3.5.1.1) (L-asparagine amidohydrolase) | ansA asn HP_0723 | O25424 | 3 |
| Probable lipoprotein YiaD | yiaD b3552 JW5657 | P37665 | 3 |
| Probable outer membrane protein | opmD PA4208 | Q9HWH3 | 3 |
| Probable outer membrane protein | PA1048 | Q9I4S6 | 3 |
| Probable oxidoreductase | PA1833 | Q9I2R2 | 3 |
| Probable phospholipid import ATP-binding protein MlaF (EC 3.6.3.-) | mlaF Z4558 ECs4074 | P63388 | 3 |
| Probable purine-binding chemotaxis protein | PA1464 | G3XD72 | 3 |
| Probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein | PA4374 | Q9HW28 | 3 |
| Probable Resistance-Nodulation-Cell Division (RND) efflux transporter | mexI PA4207 | Q9HWH4 | 3 |
| Probable septum site-determining protein MinC | minC BX23_12090 | A0A028E633 | 3 |
| Probable siderophore-binding lipoprotein YfiY | yfiY BSU08440 | O31567 | 3 |
| Probable thioredoxin | PA0953 | Q9I505 | 3 |
| Probable TonB-dependent receptor | PA5505 | Q9HT68 | 3 |
| Protease 7 (EC 3.4.23.49) | ompT ECDEC1D_0931 | H4J4S0 | 3 |
| Protease B (EC 3.4.-.-) | prtB MXAN_2791 | Q1D8L5 | 3 |
| Protease HtpX (EC 3.4.24.-) (Heat shock protein HtpX) | htpX PP_1871 | Q88LQ8 | 3 |
| Protein CyaE | tolC Smlt3928 | B2FTS5 | 3 |
| Protein TolB | tolB FTN_0355 | A0Q4U6 | 3 |
| Protein TolB | tolB Cj0112 | Q9PJ14 | 3 |
| Protein TolB | tolB PP_1222 | P0A173 | 3 |
| Protein TolB | tolB HP_1126 | O25751 | 3 |
| Protein TolR | tolR PA0970 | P50599 | 3 |
| Protein TonB | AC789_1c05620 ACN002_0554 APT94_07960 APU18_12400 BET08_30795 BK373_12420 BMT94_24345 BN17_22271 HMPREF3040_04526 SM09_05063 SY51_06410 WM48_06000 | E2QKQ2 | 3 |
| Protein translocase subunit SecA | secA spr1544 | Q8DNT8 | 3 |
| Protein translocase subunit SecA | secA E2348C_0103 | B7UIE8 | 3 |
| Protein translocase subunit SecDF | secDF BSU27650 | O32047 | 3 |
| Protein transporter, outer bacterial membrane secretin (Secretin) family | MXAN_3106 | Q1D7R4 | 3 |
| Protein YebF | yebF b1847 JW1836 | P33219 | 3 |
| Protein-disulfide isomerase | FTN_0771 | A0Q5Z7 | 3 |
| Protein-disulfide isomerase | FTN_0597 | A0Q5H7 | 3 |
| Protein-export membrane protein SecG (P12) (Preprotein translocase band 1 subunit) | secG Z4537 ECs4054 | P0AGA1 | 3 |
| Protein-export protein SecB | secB PA5128 | Q9HU56 | 3 |
| Protoporphyrinogen IX dehydrogenase [menaquinone] (Protoporphyrinogen IX oxidase HemG) (Protoporphyrinogen oxidase) (EC 1.3.3.4) (EC 1.3.5.3) | hemG AA102_11500 ACN77_18125 ACN81_23910 ACU90_13925 AML07_08265 APZ14_07770 AUS26_26115 BE957_02840 BHF46_22510 BHS81_23030 BK400_20800 BMT53_14410 BMT61_12715 BW690_25260 ERS085374_03145 ERS150876_04184 FORC28_5937 GJ11_24465 GJ12_23730 HW42_00740 PGD_00121 PU06_16905 RG28_24565 SK85_04176 | A0A024L7L1 | 3 |
| Protoporphyrinogen oxidase (EC 1.3.3.4) | hemG EcSMS35_4231 | B1LM36 | 3 |
| Pseudouridine synthase (EC 5.4.99.-) | rsuA CE10_2557 | A0A0E0V7W2 | 3 |
| Pseudouridine synthase (EC 5.4.99.-) | rluD A5958_17240 AA102_04920 ACN77_02865 ACN81_10225 ACU90_01895 AM270_24195 AMK83_27920 BE957_09685 BMT61_22580 ERS085374_05138 GJ12_17190 PU06_25505 UN86_25225 WQ89_15875 | A0A066RC26 | 3 |
| PTS system glucose-specific EIICBA component (EC 2.7.1.199) (EII-Glc/EIII-Glc) (EIICBA-Glc) (EIICBA-Glc 1) [Includes: Glucose permease IIC component (PTS system glucose-specific EIIC component); Glucose-specific phosphotransferase enzyme IIB component (PTS system glucose-specific EIIB component); Glucose-specific phosphotransferase enzyme IIA component (PTS system glucose-specific EIIA component)] | ptsG crr ptsX BSU13890 | P20166 | 3 |
| Purine nucleoside phosphorylase DeoD-type (PNP) (EC 2.4.2.1) | deoD EcE24377A_4983 | A7ZVS7 | 3 |
| Putative 2',3'-cyclic-nucleotide 2'-phosphodiesterase | MXAN_6266 | Q1CYX8 | 3 |
| Putative 28 kDa outer membrane protein | MXAN_7203 | Q1CWA7 | 3 |
| Putative ACR family protein | Smlt3869 | B2FT31 | 3 |
| Putative acyl-CoA thioester hydrolase YbhC (EC 3.1.2.-) | ybhC b0772 JW0755 | P46130 | 3 |
| Putative alkaline phosphatase | MXAN_1389 | Q1DCH7 | 3 |
| Putative alkyl hydroperoxide reductase subunit c (EC 1.11.1.15) | ahpC Smlt0841 | B2FPY7 | 3 |
| Putative amino-acid transporter periplasmic solute-binding protein | cjaA Cj0982c | Q0P9S0 | 3 |
| Putative autotransporter subtilisin-like protease | sphB Smlt3524 | B2FPV5 | 3 |
| Putative cell division protein | PP_5090 | Q88CU0 | 3 |
| Putative cytochrome C551 peroxidase (EC 1.11.1.5) | Cj0358 | Q0PBF1 | 3 |
| Putative endonuclease P1 (EC 3.1.30.1) | Smlt3806 | B2FSF8 | 3 |
| Putative fibronectin domain-containing lipoprotein | Cj1279c | Q0P8X7 | 3 |
| Putative fimbria adhesin protein | Smlt0709 | B2FNJ3 | 3 |
| Putative glycosyltransferase | SP70585_0422 | C1CBD7 | 3 |
| Putative GMC oxidoreductase subunit | Cj0415 | Q0PB95 | 3 |
| Putative intercellular spreading VacJ lipoprotein | Smlt4675 | B2FP87 | 3 |
| Putative iron transporter | Smlt2858 | B2FHT9 | 3 |
| Putative iron-uptake ABC transport system,periplasmic iron-binding protein | cfbpA Cj0175c | Q0PBW4 | 3 |
| Putative lipoprotein | MXAN_5684 | Q1D0K1 | 3 |
| Putative lipoprotein | MXAN_7333 | Q1CVX7 | 3 |