| Aminopeptidase | pepC/pepN/pepN | 0 | 3 |
| Aminopeptidase p family protein | ypdF | 2 | 1 |
| ATP-dependent clp endopeptidase proteolytic subunit | | 1 | 0 |
| ATP-dependent clp protease ATP-binding subunit | clpC/clpE/clpX | 4 | 3 |
| ATP-dependent protease clp protease protease proteolytic subunit | clpP | 0 | 2 |
| ATP-dependent protease ATPase subunit | clpY | 1 | 2 |
| ATP-dependent protease subnit HslV | hslV | 0 | 1 |
| ATP-dependent zinc metalloprotease | ftsH | 0 | 1 |
| Beta-barrel assembly-enhancing protease | bepA | 0 | 1 |
| C1/C40/C69 family peptidase | pepE/pepD | 7 | 0 |
| Carboxy-terminal processing protease CtpA | ctpA | 0 | 1 |
| Clp protease | | 2 | 0 |
| Cpbp family intramembrane metalloprotease | | 13 | 0 |
| D-alanyl-d-alanine carboxypeptidase/D-alanyl-D-alanine dipeptidase | dacA/ddpX | 2 | 2 |
| Dipeptidase | pepD/pepDA | 2 | 4 |
| Extracellular zinc metalloproteinase | | 1 | 0 |
| Family deacylase | | 2 | 0 |
| Family metallo-endopeptidase | | 2 | 0 |
| Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase | ykfC | 0 | 1 |
| Gamma-d-glutamyl-meso-diaminopimelate peptidase | | 1 | 0 |
| Gnat family n-acetyltransferase | | 1 | 0 |
| Guanosine monophosphate reductase | | 1 | 0 |
| ld-carboxypeptidase | mccF | 2 | 0 |
| Lipoprotein signal peptidase | IspA | 0 | 1 |
| m1/m15 family metallopeptidase | pepN/ddpX | 3 | 0 |
| m3 family oligoendopeptidase | | 1 | 0 |
| Matrixin family metalloprotease | | 3 | 0 |
| Methionine aminopeptidase | Map | 0 | 1 |
| Neutral endopeptidase | pepO | 0 | 1 |
| Oligoendopeptidase F_ plasmid | pepF1 | 1 | 1 |
| Peptidase E/m13/m23 | pepE/pepO | 2 | 1 |
| Peptidase propeptide and ypeb domain protein | | 1 | 0 |
| Peptidase proteolytic subunit | | 1 | 0 |
| Peptidase s41 | | 1 | 0 |
| Peptidase t | prpT | 1 | 1 |
| Peptide cleavage export abc transporter | | 1 | 0 |
| Peptidoglycan endopeptidase | | 1 | 0 |
| Phage endopeptidase | | 1 | 0 |
| Prepilin peptidase | comC | 1 | 0 |
| Proline iminopeptidase | fpaP/peplP | 1 | 1 |
| Proline-specific peptidase family protein | | 1 | 0 |
| Protease HtpX | htpX | 0 | 1 |
| Putative dipeptidase | | 0 | 1 |
| Putative L_D-transpeptidase YciB | yciB | 0 | 3 |
| Putative protease YdeA | ydeA | 0 | 1 |
| Regulator of sigma-W protease RasP | rasP | 0 | 1 |
| Rhomboid family intramembrane serine protease | gluP | 1 | 1 |
| Ribosomal-processing cysteine protease Prp | | 1 | 0 |
| Rip metalloprotease | rasP | 1 | 0 |
| Serine hydrolase | | 2 | 0 |
| Serine protease Do-like HtrA | htrA | 0 | 1 |
| Signal peptidase I/Signal peptidase II | spsB / ispA | 4 | 2 |
| Transpeptidase/transpeptidase family protein | | 5 | 0 |
| Xaa-pro dipeptidyl-peptidase | pepX | 1 | 1 |
| Zinc metallopeptidase | | 2 | 0 |
| Number of proteolytic genes | | 81 | 41 |