| Phosphoglucosamine mutase (EC 5.4.2.10) | glmM OOM_0574 | I2AY45 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk FTN_1331 | A0Q7J1 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk CPR_1300 | Q0STD5 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk STM3069 | P65702 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk YPO0921 y3308 YP_3519 | Q8ZHH3 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk SC1083_1544 | G4A9M5 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk b2926 JW2893 | P0A799 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk SFV_2972 | Q0T0X4 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk SPy_1881 M5005_Spy1599 | P68897 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk CD630_31730 | Q181T8 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk SCH_3011 | Q57K45 | 1 |
| Phosphoglycerate kinase (EC 2.7.2.3) | pgk FTT_1367c | Q5NF76 | 1 |
| Phosphoglycerate mutase domain protein | FSU_2641 | C9RJI1 | 1 |
| Phosphoglycerate mutase family protein | FSU_2082 | C9RRK4 | 1 |
| Phosphoglycerate transport: outer membrane protein E | pgtE SCH_2396 | Q57LW0 | 1 |
| Phosphoheptose isomerase (EC 5.-.-.-) | lpcA FTT_1681c | Q5NEF5 | 1 |
| Phosphoheptose isomerase (EC 5.3.1.28) (Sedoheptulose 7-phosphate isomerase) | gmhA lpcA NMB2090 | P0A0Y6 | 1 |
| Phosphoheptose isomerase (EC 5.3.1.28) (Sedoheptulose 7-phosphate isomerase) | gmhA lpcA YPO3243 y0947 YP_0689 | Q8ZBY7 | 1 |
| Phosphoheptose isomerase (EC 5.3.1.28) (Sedoheptulose 7-phosphate isomerase) | gmhA VSAK1_07339 | A6D3E5 | 1 |
| Phosphohexosemutase | jhp_1196 | Q9ZJV2 | 1 |
| Phospholipase A1 (EC 3.1.1.32) (EC 3.1.1.4) (Detergent-resistant phospholipase A) (DR-phospholipase A) (Outer membrane phospholipase A) (OM PLA) (OMPLA) (Phosphatidylcholine 1-acylhydrolase) | pldA b3821 JW3794 | P0A921 | 1 |
| Phospholipase A1 (EC 3.1.1.32) (EC 3.1.1.4) (Detergent-resistant phospholipase A) (DR-phospholipase A) (Outer membrane phospholipase A) (OM PLA) (OMPLA) (Phosphatidylcholine 1-acylhydrolase) | pldA SF3899 S3856 | P0A923 | 1 |
| Phospholipase D family protein (EC 3.1.1.-) | FTT_0490c | Q5NHG4 | 1 |
| Phospholipid ABC transporter | mlaE PP_0959 | Q88P93 | 1 |
| Phosphomannomutase | VSAK1_21279 | A6CZQ0 | 1 |
| Phosphomannomutase | VSAK1_09608 | A6D0G2 | 1 |
| Phosphomevalonate kinase | mvaK2 SPy_0878 | Q9A096 | 1 |
| Phosphonate ABC transporter, substrate-binding protein, putative | SAOUHSC_00105 | Q2G1L7 | 1 |
| Phosphonate uptake transporter | VSAK1_00787 | A6D1B8 | 1 |
| Phosphonates import ATP-binding protein PhnC (EC 3.6.3.28) | phnC VSAK1_20089 | A6CWU8 | 1 |
| Phosphonates import ATP-binding protein PhnC (EC 3.6.3.28) | phnC VSAK1_00777 | A6D1B6 | 1 |
| Phosphonates transport ATP-binding protein | phnK VSAK1_19829 | A6CWP6 | 1 |
| Phosphopantetheine adenylyltransferase (EC 2.7.7.3) (Dephospho-CoA pyrophosphorylase) (Pantetheine-phosphate adenylyltransferase) (PPAT) | coaD PA0363 | Q9I6D1 | 1 |
| Phosphopantetheine adenylyltransferase (EC 2.7.7.3) (Dephospho-CoA pyrophosphorylase) (Pantetheine-phosphate adenylyltransferase) (PPAT) | coaD VSAK1_09703 | A6D0I1 | 1 |
| Phosphopantetheine adenylyltransferase (EC 2.7.7.3) (Dephospho-CoA pyrophosphorylase) (Pantetheine-phosphate adenylyltransferase) (PPAT) | coaD kdtB SPy_1537 M5005_Spy1267 | P63821 | 1 |
| Phosphopentomutase (EC 5.4.2.7) (Phosphodeoxyribomutase) | deoB FTN_1602 | A0Q897 | 1 |
| Phosphopentomutase (EC 5.4.2.7) (Phosphodeoxyribomutase) | deoB spr0732 | Q8DQD0 | 1 |
| Phosphopentomutase (EC 5.4.2.7) (Phosphodeoxyribomutase) | deoB SFV_4417 | Q0SX28 | 1 |
| Phosphopentomutase (EC 5.4.2.7) (Phosphodeoxyribomutase) | deoB SPy_0890 M5005_Spy0696 | P63927 | 1 |
| Phosphopentomutase (EC 5.4.2.7) (Phosphodeoxyribomutase) | deoB OOM_0606 | I2AY71 | 1 |
| Phosphoporin PhoE (Putative outer membrane porin protein C precurser) | nmpC S2073 SF1977 AJR25_008510 AJR27_008620 | Q83KN4 | 1 |
| Phosphoribosyl-AMP cyclohydrolase (PRA-CH) (EC 3.5.4.19) | hisI LMRG_00244 | A0A0H3GDW2 | 1 |
| Phosphoribosylamine--glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide synthetase) (Phosphoribosylglycinamide synthetase) | purD PA4855 | Q9HUV8 | 1 |
| Phosphoribosylamine--glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide synthetase) (Phosphoribosylglycinamide synthetase) | purD VSAK1_13473 | A6D4I6 | 1 |
| Phosphoribosylamine--glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide synthetase) (Phosphoribosylglycinamide synthetase) | purD SPy_0032 M5005_Spy0029 | Q9A1Y7 | 1 |
| Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) (SAICAR synthetase) | purC SSON_2557 | Q3YZ76 | 1 |
| Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) (SAICAR synthetase) | purC VSAK1_06165 | A6CZM3 | 1 |
| Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) (AIR synthase) (AIRS) (Phosphoribosyl-aminoimidazole synthetase) | purM NMB1252 | Q9JZ80 | 1 |
| Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) (AIR synthase) (AIRS) (Phosphoribosyl-aminoimidazole synthetase) | purM PA0945 | Q9I513 | 1 |
| Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) (AIR synthase) (AIRS) (Phosphoribosyl-aminoimidazole synthetase) | purM HPSD74_1092 | U4SJ87 | 1 |
| Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) (AIR synthase) (AIRS) (Phosphoribosyl-aminoimidazole synthetase) | purM VSAK1_07354 | A6D3E8 | 1 |
| Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) (AIR synthase) (AIRS) (Phosphoribosyl-aminoimidazole synthetase) | purM FSU_1946 | C9RR83 | 1 |
| Phosphoribosylformylglycinamidine synthase (FGAM synthase) (FGAMS) (EC 6.3.5.3) (Formylglycinamide ribonucleotide amidotransferase) (FGAR amidotransferase) (FGAR-AT) | purL Fphi_0905 | B0TWM0 | 1 |
| Phosphoribosylformylglycinamidine synthase (FGAM synthase) (FGAMS) (EC 6.3.5.3) (Formylglycinamide ribonucleotide amidotransferase) (FGAR amidotransferase) (FGAR-AT) | purL FTN_1699 | A0Q8J1 | 1 |
| Phosphoribosylformylglycinamidine synthase (FGAM synthase) (FGAMS) (EC 6.3.5.3) (Formylglycinamide ribonucleotide amidotransferase) (FGAR amidotransferase) (FGAR-AT) | purL B195_05590 | M5QJD2 | 1 |
| Phosphoribosylformylglycinamidine synthase (FGAM synthase) (FGAMS) (EC 6.3.5.3) (Formylglycinamide ribonucleotide amidotransferase) (FGAR amidotransferase) (FGAR-AT) | purL PP_1037 | Q88P16 | 1 |
| Phosphorylase family protein | ACIN5021_0831 | L9M616 | 1 |
| Phosphoserine aminotransferase (EC 2.6.1.52) (Phosphohydroxythreonine aminotransferase) (PSAT) | serC Fphi_1843 | B0U152 | 1 |
| Phosphoserine aminotransferase (EC 2.6.1.52) (Phosphohydroxythreonine aminotransferase) (PSAT) | serC FTN_0955 | A0Q6H8 | 1 |
| Phosphoserine aminotransferase (EC 2.6.1.52) (Phosphohydroxythreonine aminotransferase) (PSAT) | serC YPO1389 y2784 YP_1204 | Q8ZGB4 | 1 |
| Phosphoserine aminotransferase (EC 2.6.1.52) (Phosphohydroxythreonine aminotransferase) (PSAT) | serC PG_1278 | Q7MV30 | 1 |
| Phosphoserine aminotransferase (EC 2.6.1.52) (Phosphohydroxythreonine aminotransferase) (PSAT) | serC Rv0884c MTCY31.12c | P9WQ73 | 1 |
| Phosphoserine aminotransferase (EC 2.6.1.52) (Phosphohydroxythreonine aminotransferase) (PSAT) | serC FSU_1007 | C9RM31 | 1 |
| Phosphoserine aminotransferase (EC 2.6.1.52) (Phosphohydroxythreonine aminotransferase) (PSAT) | serC Cj0326 | Q9PIH3 | 1 |
| Phosphothreonine lyase OspF (EC 4.2.3.-) (Effector protein OspF) | ospF mkaD SSON_P009 | Q3YTY3 | 1 |
| Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) | VSAK1_00587 | A6D178 | 1 |
| Phosphotransferase system sugar-specific EII component | PTS-EII spr1969 | Q8DN20 | 1 |
| Phosphotransferase system sugar-specific EII component (EC 2.7.1.69) | PTS-EII spr0425 | Q8DQZ0 | 1 |
| Phosphotransferase system sugar-specific EIID component | PTS-EIID spr0062 | Q8DRL1 | 1 |
| Phosphotransferase system transporter enzyme I, FruI | fruI PA3562 | Q9HY55 | 1 |
| Phosphotransferase system, fructose-specific IIC component | VSAK1_22759 | A6CVV8 | 1 |
| Phosphotransferase system, mannose-specific EIID (EC 2.7.1.69) | manN spr0259 | Q8DR99 | 1 |
| PilA | pilA | Q93PL8 | 1 |
| PilC | pilC | P72083 | 1 |
| PilC2 protein | pilC2 | O05925 | 1 |
| PilD-dependent protein pddA | xcpT SAMEA3374989_03389 SAMEA3375059_03068 | A0A160X422 | 1 |
| PilF protein | pilF | Q51526 | 1 |
| Pilin glycosylation protein | NMBB_2078 | E3D2E0 | 1 |
| Pilin protein | CDIF1296T_02416 | A0A125V797 | 1 |
| PilO protein (Pilus assembly protein, PilO) | pilO PAERUG_E15_London_28_01_14_03389 PAERUG_P32_London_17_VIM_2_10_11_01500 | Q51353 | 1 |
| PilS cassette | NMB0026 | Q4W585 | 1 |
| PilS cassette | NMB0019 | Q4W592 | 1 |
| PilS2 (Sensor histidine kinase) | pilS2 MXAN_5778 | Q306N8 | 1 |
| Pimeloyl-[acyl-carrier protein] methyl ester esterase (EC 3.1.1.85) (Biotin synthesis protein BioH) (Carboxylesterase BioH) | bioH KPN78578_37450 KPN_03782 | A6TF35 | 1 |
| PIN/TRAM domain protein | CPC_2773 | B1BK22 | 1 |
| Plasmid addiction system poison protein | SPJ_0034 | C1CHA7 | 1 |
| PLD-like domain protein | KW89_2208 | A0A0K2DZA3 | 1 |
| PmrB: two-component regulator system signal sensor kinase PmrB | pmrB PA4777 | Q9HV31 | 1 |
| Pneumococcal histidine triad protein D | phtD spr0907 | Q8DQ08 | 1 |
| Pneumococcal histidine triad protein E | phtE spr0908 | Q8DQ07 | 1 |
| Pneumococcal vaccine antigen A | pvaA spr0930 | Q8DPY9 | 1 |
| Pneumococcal vaccine antigen A homolog | pvaA SPy_1147 M5005_Spy0869 | Q99ZN9 | 1 |
| Polar amino acid transport system substrate-binding protein | LMRG_02533 | A0A0H3GKX3 | 1 |
| Polar flagellar hook-length control protein FliK | VS_0828 | B7VL10 | 1 |
| Poly(3-hydroxyalkanoic acid) synthase 1 | phaC1 PA5056 | G3XCV5 | 1 |
| Poly(A) polymerase I (PAP I) (EC 2.7.7.19) | pcnB PA4727 | Q9HV72 | 1 |
| Polyamine ABC transporter, periplasmic polyamine-binding protein | PP_0412 | Q88QS6 | 1 |
| Polyamine transport protein PotH | spuG PA0303 | Q9I6I8 | 1 |
| Polyamine transport protein PotI | spuH PA0304 | Q9I6I7 | 1 |
| Polyamine-transporting ATPase (EC 3.6.3.31) | potG FTN_0739 | A0Q5W5 | 1 |