| Peptide/nickel transport system ATP-binding protein | LMRG_01639 | A0A0H3GMC5 | 4 |
| Peptide/nickel transport system permease | LMRG_01638 | A0A0H3GE46 | 4 |
| Peptide/nickel transport system substrate-binding protein | LMRG_02699 | A0A0H3GFV1 | 4 |
| Peptide/nickel transport system substrate-binding protein | LMRG_02384 | A0A0H3GCP2 | 4 |
| Peptide/nickel transport system substrate-binding protein | LMRG_02397 | A0A0H3GH20 | 4 |
| Peptide/nickel transport system substrate-binding protein | LMRG_01636 | A0A0H3GJB6 | 4 |
| Peptidoglycan N-acetylglucosamine deacetylase | LMRG_00107 | A0A0H3GDH9 | 4 |
| Peptidoglycan-associated lipoprotein | pal excC b0741 JW0731 | P0A912 | 4 |
| Peptidoglycan-binding protein LysM | NGO_1873 | Q5F5P4 | 4 |
| Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | NGO_1225 | Q5F7F3 | 4 |
| Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | Smlt1559 | B2FIF8 | 4 |
| Peptidylprolyl isomerase | NGO_1655 | Q5F6A5 | 4 |
| Peptidylprolyl isomerase | NGO_0766 | Q5F8K6 | 4 |
| Peptidylprolyl isomerase (EC 5.2.1.8) | NMB0345 | Q7DDR0 | 4 |
| Peptidylprolyl isomerase (EC 5.2.1.8) | NGO_1656 | Q5F6A4 | 4 |
| Peptidylprolyl isomerase (EC 5.2.1.8) | NGO_1714 | Q5F652 | 4 |
| Periplasmic protein | NGO_0416 | Q5F9H8 | 4 |
| Periplasmic protein | NGO_0757 | Q5F8L5 | 4 |
| Phage tail protein (Tail protein) | BE932_30150 SY51_06485 | A0A061KGU5 | 4 |
| Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase alpha subunit) (PheRS) | pheS NGO0299 | Q5F9U0 | 4 |
| Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase beta subunit) (PheRS) | pheT NGO0304 | Q5F9T6 | 4 |
| Pheromone lipoprotein | LMRG_02182 | A0A0H3GKQ3 | 4 |
| Phosphate acetyltransferase | NGO_0214 | Q5FA20 | 4 |
| Phosphate acyltransferase (EC 2.3.1.n2) (Acyl-ACP phosphotransacylase) (Acyl-[acyl-carrier-protein]--phosphate acyltransferase) (Phosphate-acyl-ACP acyltransferase) | plsX NGO2171 | Q5F4X3 | 4 |
| Phosphoenolpyruvate carboxylase (PEPC) (PEPCase) (EC 4.1.1.31) | ppc NGO2020 | Q5F5A9 | 4 |
| Phosphoenolpyruvate carboxylase (PEPC) (PEPCase) (EC 4.1.1.31) | ppc spr0974 | Q8DPW5 | 4 |
| Phosphoenolpyruvate synthase (PEP synthase) (EC 2.7.9.2) (Pyruvate, water dikinase) | NGO_0200 | Q5FA34 | 4 |
| Phosphofructokinase | BE932_04070 SY51_09590 | A0A061KZW9 | 4 |
| Phosphoglucomutase | NGO_0375 | Q5F9L8 | 4 |
| Phosphogluconate dehydratase | NGO_0714 | Q5F8Q3 | 4 |
| Phosphogluconate dehydratase (EC 4.2.1.12) (6-phosphogluconate dehydratase) | edd PA3194 | P31961 | 4 |
| Phosphoglucosamine mutase (EC 5.4.2.10) | glmM NGO1341 | Q5F746 | 4 |
| Phospholipase A(2) (EC 3.1.1.4) | ECBD_4217 | A0A140NHI4 | 4 |
| Phospholipase A1 | NGO_1492 | Q5F6Q7 | 4 |
| Phosphomethylpyrimidine kinase | NGO_1160 | Q5F7L1 | 4 |
| Phosphopentomutase (EC 5.4.2.7) (Phosphodeoxyribomutase) | deoB Ecok1_44460 APECO1_1998 | A1AJV0 | 4 |
| Phosphoribosylglycinamide formyltransferase | NGO_1049 | Q5F7W6 | 4 |
| Pilin assembly protein | NGO_0095 | Q5FAD1 | 4 |
| Pilus assembly protein | NGO_0055 | Q5FAG7 | 4 |
| Pilus assembly protein PilF | NGO_1673 | Q5F689 | 4 |
| Pilus assembly protein PilM | NGO_0098 | Q5FAC8 | 4 |
| Pilus assembly protein PilO | NGO_0096 | Q5FAD0 | 4 |
| Pilus assembly protein PilW | NGO_0595 | Q5F912 | 4 |
| Pilus assembly protein PilW | NGO_0454 | Q5F9E4 | 4 |
| Plasminogen-binding protein PgbB | pgbB jhp_0797 | Q9ZKY5 | 4 |
| Polar amino acid transport system ATP-binding protein | LMRG_02271 | A0A0H3GF44 | 4 |
| Polar flagellin (FlaG) | HP_0751 | O25447 | 4 |
| Polyamine aminopropyltransferase (Putrescine aminopropyltransferase) (PAPT) (Spermidine synthase) (SPDS) (SPDSY) (EC 2.5.1.16) | speE E2348C_0124 | B7UIG9 | 4 |
| Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) (Polynucleotide phosphorylase) (PNPase) | pnp NGO0335 | Q5F9Q7 | 4 |
| Porphobilinogen deaminase (PBG) (EC 2.5.1.61) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyrinogen synthase) | hemC NGO_0146 | Q5FA83 | 4 |
| Probable ATP-binding component of ABC transporter | PA4461 | Q9HVV6 | 4 |
| Probable binding protein component of ABC transporter | PA1342 | Q9I402 | 4 |
| Probable binding protein component of ABC transporter | PA4500 | Q9HVS1 | 4 |
| Probable carbamoyl transferase | PA5005 | Q9HUG0 | 4 |
| Probable cold-shock protein | PA1159 | Q9I4H8 | 4 |
| Probable cold-shock protein | PA0961 | Q9I4Z8 | 4 |
| Probable DNA binding protein | PA3940 | Q9HX76 | 4 |
| Probable endonuclease 4 (EC 3.1.21.2) (Endodeoxyribonuclease IV) (Endonuclease IV) | nfo UMNK88_2704 | A0A0E0U0Z0 | 4 |
| Probable FKBP-type peptidyl-prolyl cis-trans isomerase FkpA (PPIase) (EC 5.2.1.8) (Rotamase) | fkpA NMB1567 | Q9JYI8 | 4 |
| Probable L,D-transpeptidase YbiS (EC 2.-.-.-) | ybiS b0819 JW0803 | P0AAX8 | 4 |
| Probable malate:quinone oxidoreductase (EC 1.1.5.4) (MQO) (Malate dehydrogenase [quinone]) | mqo NGO1980 | Q5F5E9 | 4 |
| Probable malate:quinone oxidoreductase 2 (EC 1.1.5.4) (MQO 2) (Malate dehydrogenase [quinone] 2) | mqo2 mqoB PA4640 | Q9HVF1 | 4 |
| Probable outer membrane protein | PA1041 | Q9I4T3 | 4 |
| Probable permease of ABC transporter | PA4503 | Q9HVR8 | 4 |
| Probable permease of ABC transporter | PA4455 | Q9HVW2 | 4 |
| Probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein | PA2528 | Q9I0V5 | 4 |
| Probable septum site-determining protein MinC | minC NGO1816 | Q5F5V4 | 4 |
| Probable siderophore receptor | PA1365 | Q9I3X9 | 4 |
| Probable transcriptional regulatory protein YebC | yebC b1864 JW1853 | P0A8A0 | 4 |
| Probable transcriptional regulatory protein YeeN | yeeN BY96_23695 | A0A027TFL6 | 4 |
| Probable zinc protease | PA0372 | Q9I6C2 | 4 |
| Prokaryotic membrane lipolipid attachment site family protein | NGO_1251 | Q5F7C7 | 4 |
| Proline--tRNA ligase (EC 6.1.1.15) (Prolyl-tRNA synthetase) (ProRS) | proS NGO0566 | Q5F938 | 4 |
| Proline--tRNA ligase (EC 6.1.1.15) (Prolyl-tRNA synthetase) (ProRS) | proS spr0243 | Q8DRB0 | 4 |
| Proline--tRNA ligase (EC 6.1.1.15) (Prolyl-tRNA synthetase) (ProRS) | proS PA0956 | Q9I502 | 4 |
| Protease | NGO_1314 | Q5F771 | 4 |
| Protease 7 (EC 3.4.23.49) (Omptin) (Outer membrane protein 3B) (Protease A) (Protease VII) | ompT b0565 JW0554 | P09169 | 4 |
| Protease HtpX homolog (EC 3.4.24.-) | htpX NGO0399 | Q5F9J4 | 4 |
| Protease LasA (EC 3.4.24.-) (Staphylolytic protease) | lasA PA1871 | P14789 | 4 |
| Protease TldD | tldD BX06_09880 | A0A028AIY8 | 4 |
| Protein DcrB | dcrB yhhR b3472 JW5682 | P0AEE1 | 4 |
| Protein GrpE (HSP-70 cofactor) | grpE NGO1422 | Q5F6X1 | 4 |
| Protein GrpE (HSP-70 cofactor) | grpE PA4762 | Q9HV42 | 4 |
| Protein hcp1 | hcp1 PA0085 | Q9I747 | 4 |
| Protein RecA (Recombinase A) | recA NGO0741 | Q5F8M9 | 4 |
| Protein TolB | tolB b0740 JW5100 | P0A855 | 4 |
| Protein TolB | tolB Smlt3704 | B2FRM9 | 4 |
| Protein translocase subunit SecA | secA NGO0996 | Q5F807 | 4 |
| Protein translocase subunit SecF | secF PA3820 | Q9HXI2 | 4 |
| Protein-export protein SecB | secB NGO0116 | Q5FAB1 | 4 |
| Pseudouridine synthase (EC 5.4.99.-) | rluC A4T40_09205 BK334_17110 ECONIH1_06675 MS6198_12210 | A0A0A1A469 | 4 |
| PTS IIA-like nitrogen regulatory protein PtsN (PTS system nitrogen regulatory protein IIA(Ntr)) (PTS system transporter subunit IIA-like nitrogen-regulatory protein PtsN) (EC 2.7.1.-) (Transcriptional regulator) | ptsN A4T50_10085 APU18_16335 BE932_14935 ERS085406_02946 SY51_18455 WM48_17810 | A0A066SXV7 | 4 |
| PTS system N,N'-diacetylchitobiose-specific transporter subunit IIB | UN91_27950 | A0A0F3UJH2 | 4 |
| Purine nucleoside phosphorylase DeoD-type (PNP) (EC 2.4.2.1) | deoD E2348C_4682 | B7UR12 | 4 |
| Purine nucleoside phosphorylase DeoD-type (PNP) (EC 2.4.2.1) | deoD UTI89_C5155 | Q1R259 | 4 |
| Putative adhesin complex protein | NMB2095 | Q9JXD8 | 4 |
| Putative alkaline phosphatase | Smlt3463 | B2FP33 | 4 |
| Putative biopolymer transport exbB protein | exbB1 Smlt0010 | B2FT88 | 4 |
| Putative exported endopeptidase | Smlt3450 | B2FP20 | 4 |
| Putative fatty acid transport system, membrane protein | Smlt0423 | B2FJY4 | 4 |