| COG0068 | Hydrogenase maturation factor |
| COG0071 | Molecular chaperone (small heat shock protein) |
| COG0109 | Polyprenyltransferase (cytochrome oxidase assembly factor) |
| COG0225 | Peptide methionine sulfoxide reductase |
| COG0229 | Conserved domain frequently associated with peptide methionine sulfoxide reductase |
| COG0234 | Co-chaperonin GroES (HSP10) |
| COG0265 | Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain |
| COG0278 | Glutaredoxin-related protein |
| COG0298 | Hydrogenase maturation factor |
| COG0309 | Hydrogenase maturation factor |
| COG0326 | Molecular chaperone, HSP90 family |
| COG0330 | Membrane protease subunits, stomatin/prohibitin homologs |
| COG0378 | Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase |
| COG0386 | Glutathione peroxidase |
| COG0396 | ABC-type transport system involved in Fe-S cluster assembly, ATPase component |
| COG0409 | Hydrogenase maturation factor |
| COG0425 | Predicted redox protein, regulator of disulfide bond formation |
| COG0435 | Predicted glutathione S-transferase |
| COG0443 | Molecular chaperone |
| COG0450 | Peroxiredoxin |
| COG0459 | Chaperonin GroEL (HSP60 family) |
| COG0464 | ATPases of the AAA+ class |
| COG0465 | ATP-dependent Zn proteases |
| COG0466 | ATP-dependent Lon protease, bacterial type |
| COG0484 | DnaJ-class molecular chaperone with C-terminal Zn finger domain |
| COG0492 | Thioredoxin reductase |
| COG0501 | Zn-dependent protease with chaperone function |
| COG0526 | Thiol-disulfide isomerase and thioredoxins |
| COG0533 | Metal-dependent proteases with possible chaperone activity |
| COG0542 | ATPases with chaperone activity, ATP-binding subunit |
| COG0544 | FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) |
| COG0545 | FKBP-type peptidyl-prolyl cis-trans isomerases 1 |
| COG0555 | ABC-type sulfate transport system, permease component |
| COG0576 | Molecular chaperone GrpE (heat shock protein) |
| COG0602 | Organic radical activating enzymes |
| COG0606 | Predicted ATPase with chaperone activity |
| COG0616 | Periplasmic serine proteases (ClpP class) |
| COG0625 | Glutathione S-transferase |
| COG0638 | 20S proteasome, alpha and beta subunits |
| COG0652 | Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family |
| COG0678 | Peroxiredoxin |
| COG0691 | tmRNA-binding protein |
| COG0694 | Thioredoxin-like proteins and domains |
| COG0695 | Glutaredoxin and related proteins |
| COG0719 | ABC-type transport system involved in Fe-S cluster assembly, permease component |
| COG0740 | Protease subunit of ATP-dependent Clp proteases |
| COG0755 | ABC-type transport system involved in cytochrome c biogenesis, permease component |
| COG0760 | Parvulin-like peptidyl-prolyl isomerase |
| COG0785 | Cytochrome c biogenesis protein |
| COG0826 | Collagenase and related proteases |
| COG0829 | Urease accessory protein UreH |
| COG0830 | Urease accessory protein UreF |
| COG1025 | Secreted/periplasmic Zn-dependent peptidases, insulinase-like |
| COG1030 | Membrane-bound serine protease (ClpP class) |
| COG1047 | FKBP-type peptidyl-prolyl cis-trans isomerases 2 |
| COG1066 | Predicted ATP-dependent serine protease |
| COG1067 | Predicted ATP-dependent protease |
| COG1076 | DnaJ-domain-containing proteins 1 |
| COG1138 | Cytochrome c biogenesis factor |
| COG1180 | Pyruvate-formate lyase-activating enzyme |
| COG1214 | Inactive homolog of metal-dependent proteases, putative molecular chaperone |
| COG1219 | ATP-dependent protease Clp, ATPase subunit |
| COG1220 | ATP-dependent protease HslVU (ClpYQ), ATPase subunit |
| COG1222 | ATP-dependent 26S proteasome regulatory subunit |
| COG1225 | Peroxiredoxin |
| COG1261 | Flagellar basal body P-ring biosynthesis protein |
| COG1281 | Disulfide bond chaperones of the HSP33 family |
| COG1331 | Highly conserved protein containing a thioredoxin domain |
| COG1333 | ResB protein required for cytochrome c biosynthesis |
| COG1370 | Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit |
| COG1382 | Prefoldin, chaperonin cofactor |
| COG1391 | Glutamine synthetase adenylyltransferase |
| COG1397 | ADP-ribosylglycohydrolase |
| COG1404 | Subtilisin-like serine proteases |
| COG1474 | Cdc6-related protein, AAA superfamily ATPase |
| COG1495 | Disulfide bond formation protein DsbB |
| COG1516 | Flagellin-specific chaperone FliS |
| COG1585 | Membrane protein implicated in regulation of membrane protease activity |
| COG1612 | Uncharacterized protein required for cytochrome oxidase assembly |
| COG1651 | Protein-disulfide isomerase |
| COG1730 | Predicted prefoldin, molecular chaperone implicated in de novo protein folding |
| COG1764 | Predicted redox protein, regulator of disulfide bond formation |
| COG1765 | Predicted redox protein, regulator of disulfide bond formation |
| COG1899 | Deoxyhypusine synthase |
| COG1928 | Dolichyl-phosphate-mannose--protein O-mannosyl transferase |
| COG1973 | Hydrogenase maturation factor |
| COG1975 | Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family |
| COG1989 | Type II secretory pathway, prepilin signal peptidase PulO and related peptidases |
| COG2020 | Putative protein-S-isoprenylcysteine methyltransferase |
| COG2039 | Pyrrolidone-carboxylate peptidase (N-terminal pyroglutamyl peptidase) |
| COG2077 | Peroxiredoxin |
| COG2143 | Thioredoxin-related protein |
| COG2192 | Predicted carbamoyl transferase, NodU family |
| COG2214 | DnaJ-class molecular chaperone |
| COG2332 | Cytochrome c-type biogenesis protein CcmE |
| COG2360 | Leu/Phe-tRNA-protein transferase |
| COG2370 | Hydrogenase/urease accessory protein |
| COG2371 | Urease accessory protein UreE |
| COG2377 | Predicted molecular chaperone distantly related to HSP70-fold metalloproteases |
| COG2386 | ABC-type transport system involved in cytochrome c biogenesis, permease component |
| COG2518 | Protein-L-isoaspartate carboxylmethyltransferase |
| COG2844 | UTP:GlnB (protein PII) uridylyltransferase |
| COG2882 | Flagellar biosynthesis chaperone |
| COG2924 | Fe-S cluster protector protein |
| COG2935 | Putative arginyl-tRNA:protein arginylyltransferase |
| COG2994 | ACP:hemolysin acyltransferase (hemolysin-activating protein) |
| COG2999 | Glutaredoxin 2 |
| COG3058 | Uncharacterized protein involved in formate dehydrogenase formation |
| COG3088 | Uncharacterized protein involved in biosynthesis of c-type cytochromes |
| COG3118 | Thioredoxin domain-containing protein |
| COG3175 | Cytochrome oxidase assembly factor |
| COG3187 | Heat shock protein |
| COG3278 | Cbb3-type cytochrome oxidase, subunit 1 |
| COG3418 | Flagellar biosynthesis/type III secretory pathway chaperone |
| COG3484 | Predicted proteasome-type protease |
| COG3526 | Uncharacterized protein conserved in bacteria |
| COG3531 | Predicted protein-disulfide isomerase |
| COG3555 | Aspartyl/asparaginyl beta-hydroxylase and related dioxygenases |
| COG3590 | Predicted metalloendopeptidase |
| COG3634 | Alkyl hydroperoxide reductase, large subunit |
| COG3751 | Predicted proline hydroxylase |
| COG3823 | Glutamine cyclotransferase |
| COG3914 | Predicted O-linked N-acetylglucosamine transferase, SPINDLY family |
| COG3951 | Rod binding protein |
| COG4067 | Uncharacterized protein conserved in archaea |
| COG4070 | Predicted peptidyl-prolyl cis-trans isomerase (rotamase), cyclophilin family |
| COG4133 | ABC-type transport system involved in cytochrome c biogenesis, ATPase component |
| COG4232 | Thiol:disulfide interchange protein |
| COG4233 | Uncharacterized protein predicted to be involved in C-type cytochrome biogenesis |
| COG4235 | Cytochrome c biogenesis factor |
| COG4346 | Predicted membrane-bound dolichyl-phosphate-mannose-protein mannosyltransferase |
| COG4512 | Membrane protein putatively involved in post-translational modification of the autoinducing quorum-sensing peptide |
| COG4545 | Glutaredoxin-related protein |
| COG4736 | Cbb3-type cytochrome oxidase, subunit 3 |
| COG4745 | Predicted membrane-bound mannosyltransferase |
| COG4759 | Uncharacterized protein conserved in bacteria containing thioredoxin-like domain |
| COG4826 | Serine protease inhibitor |
| COG4846 | Membrane protein involved in cytochrome C biogenesis |
| COG4862 | Negative regulator of genetic competence, sporulation and motility |
| COG4870 | Cysteine protease |
| COG4930 | Predicted ATP-dependent Lon-type protease |
| COG4934 | Predicted protease |
| COG4935 | Regulatory P domain of the subtilisin-like proprotein convertases and other proteases |
| COG4959 | Type IV secretory pathway, protease TraF |
| COG4960 | Flp pilus assembly protein, protease CpaA |
| COG4987 | ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components |
| COG4988 | ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components |
| COG5021 | Ubiquitin-protein ligase |
| COG5029 | Prenyltransferase, beta subunit |
| COG5044 | RAB proteins geranylgeranyltransferase component A (RAB escort protein) |
| COG5046 | Protein involved in Mod5 protein sorting |
| COG5054 | Mitochondrial sulfhydryl oxidase involved in the biogenesis of cytosolic Fe/S proteins |
| COG5061 | Oxidoreductin, endoplasmic reticulum membrane-associated protein involved in disulfide bond formation |
| COG5070 | Nucleotide-sugar transporter |
| COG5071 | 26S proteasome regulatory complex component |
| COG5077 | Ubiquitin carboxyl-terminal hydrolase |
| COG5078 | Ubiquitin-protein ligase |
| COG5082 | Arginine methyltransferase-interacting protein, contains RING Zn-finger |
| COG5110 | 26S proteasome regulatory complex component |
| COG5113 | Ubiquitin fusion degradation protein 2 |
| COG5116 | 26S proteasome regulatory complex component |
| COG5131 | Ubiquitin-like protein |
| COG5140 | Ubiquitin fusion-degradation protein |
| COG5148 | 26S proteasome regulatory complex, subunit RPN10/PSMD4 |
| COG5155 | Separase, a protease involved in sister chromatid separation |
| COG5156 | Anaphase-promoting complex (APC), subunit 10 |
| COG5159 | 26S proteasome regulatory complex component |
| COG5160 | Protease, Ulp1 family |
| COG5187 | 26S proteasome regulatory complex component, contains PCI domain |
| COG5193 | La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation |
| COG5194 | Component of SCF ubiquitin ligase and anaphase-promoting complex |
| COG5201 | SCF ubiquitin ligase, SKP1 component |
| COG5206 | Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 |
| COG5207 | Isopeptidase T |
| COG5227 | Ubiquitin-like protein (sentrin) |
| COG5234 | Beta-tubulin folding cofactor D |
| COG5243 | HRD ubiquitin ligase complex, ER membrane component |
| COG5264 | Vacuolar transporter chaperone |
| COG5265 | ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components |
| COG5269 | Ribosome-associated chaperone zuotin |
| COG5272 | Ubiquitin |
| COG5371 | Golgi nucleoside diphosphatase |
| COG5380 | Lipase chaperone |
| COG5387 | Chaperone required for the assembly of the mitochondrial F1-ATPase |
| COG5405 | ATP-dependent protease HslVU (ClpYQ), peptidase subunit |
| COG5494 | Predicted thioredoxin/glutaredoxin |
| COG5504 | Predicted Zn-dependent protease |
| COG5533 | Ubiquitin C-terminal hydrolase |
| COG5536 | Protein prenyltransferase, alpha subunit |
| COG5539 | Predicted cysteine protease (OTU family) |
| COG5540 | RING-finger-containing ubiquitin ligase |
| COG5541 | Vesicle coat complex COPI, zeta subunit |
| COG5549 | Predicted Zn-dependent protease |
| COG5550 | Predicted aspartyl protease |
| COG5560 | Ubiquitin C-terminal hydrolase |
| COG5574 | RING-finger-containing E3 ubiquitin ligase |
| COG5580 | Activator of HSP90 ATPase |
| COG5596 | Mitochondrial import inner membrane translocase, subunit TIM22 |
| COG5640 | Secreted trypsin-like serine protease |
| COG5647 | Cullin, a subunit of E3 ubiquitin ligase |
| COG5656 | Importin, protein involved in nuclear import |
| COG5661 | Predicted secreted Zn-dependent protease |
| COG5664 | Predicted secreted Zn-dependent protease |
