| COG0201 | Preprotein translocase subunit SecY |
| COG0341 | Preprotein translocase subunit SecF |
| COG0342 | Preprotein translocase subunit SecD |
| COG0541 | Signal recognition particle GTPase |
| COG0552 | Signal recognition particle GTPase |
| COG0597 | Lipoprotein signal peptidase |
| COG0616 | Periplasmic serine proteases (ClpP class) |
| COG0630 | Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis |
| COG0653 | Preprotein translocase subunit SecA (ATPase, RNA helicase) |
| COG0681 | Signal peptidase I |
| COG0690 | Preprotein translocase subunit SecE |
| COG0706 | Preprotein translocase subunit YidC |
| COG0740 | Protease subunit of ATP-dependent Clp proteases |
| COG0758 | Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake |
| COG0805 | Sec-independent protein secretion pathway component TatC |
| COG0811 | Biopolymer transport proteins |
| COG0823 | Periplasmic component of the Tol biopolymer transport system |
| COG0848 | Biopolymer transport protein |
| COG1157 | Flagellar biosynthesis/type III secretory pathway ATPase |
| COG1298 | Flagellar biosynthesis pathway, component FlhA |
| COG1314 | Preprotein translocase subunit SecG |
| COG1317 | Flagellar biosynthesis/type III secretory pathway protein |
| COG1338 | Flagellar biosynthesis pathway, component FliP |
| COG1377 | Flagellar biosynthesis pathway, component FlhB |
| COG1400 | Signal recognition particle 19 kDa protein |
| COG1450 | Type II secretory pathway, component PulD |
| COG1459 | Type II secretory pathway, component PulF |
| COG1516 | Flagellin-specific chaperone FliS |
| COG1538 | Outer membrane protein |
| COG1585 | Membrane protein implicated in regulation of membrane protease activity |
| COG1677 | Flagellar hook-basal body protein |
| COG1684 | Flagellar biosynthesis pathway, component FliR |
| COG1705 | Muramidase (flagellum-specific) |
| COG1766 | Flagellar biosynthesis/type III secretory pathway lipoprotein |
| COG1826 | Sec-independent protein secretion pathway components |
| COG1862 | Preprotein translocase subunit YajC |
| COG1886 | Flagellar motor switch/type III secretory pathway protein |
| COG1952 | Preprotein translocase subunit SecB |
| COG1955 | Archaeal flagella assembly protein J |
| COG1987 | Flagellar biosynthesis pathway, component FliQ |
| COG1989 | Type II secretory pathway, prepilin signal peptidase PulO and related peptidases |
| COG2064 | Flp pilus assembly protein TadC |
| COG2095 | Multiple antibiotic transporter |
| COG2165 | Type II secretory pathway, pseudopilin PulG |
| COG2443 | Preprotein translocase subunit Sss1 |
| COG2747 | Negative regulator of flagellin synthesis (anti-sigma28 factor) |
| COG2804 | Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB |
| COG2805 | Tfp pilus assembly protein, pilus retraction ATPase PilT |
| COG2831 | Hemolysin activation/secretion protein |
| COG2874 | Predicted ATPases involved in biogenesis of archaeal flagella |
| COG2882 | Flagellar biosynthesis chaperone |
| COG2948 | Type IV secretory pathway, VirB10 components |
| COG3031 | Type II secretory pathway, component PulC |
| COG3063 | Tfp pilus assembly protein PilF |
| COG3114 | Heme exporter protein D |
| COG3121 | P pilus assembly protein, chaperone PapD |
| COG3149 | Type II secretory pathway, component PulM |
| COG3156 | Type II secretory pathway, component PulK |
| COG3166 | Tfp pilus assembly protein PilN |
| COG3167 | Tfp pilus assembly protein PilO |
| COG3168 | Tfp pilus assembly protein PilP |
| COG3170 | Tfp pilus assembly protein FimV |
| COG3188 | P pilus assembly protein, porin PapC |
| COG3210 | Large exoproteins involved in heme utilization or adhesion |
| COG3215 | Tfp pilus assembly protein PilZ |
| COG3267 | Type II secretory pathway, component ExeA (predicted ATPase) |
| COG3297 | Type II secretory pathway, component PulL |
| COG3418 | Flagellar biosynthesis/type III secretory pathway chaperone |
| COG3419 | Tfp pilus assembly protein, tip-associated adhesin PilY1 |
| COG3451 | Type IV secretory pathway, VirB4 components |
| COG3468 | Type V secretory pathway, adhesin AidA |
| COG3504 | Type IV secretory pathway, VirB9 components |
| COG3505 | Type IV secretory pathway, VirD4 components |
| COG3539 | P pilus assembly protein, pilin FimA |
| COG3678 | P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein |
| COG3701 | Type IV secretory pathway, TrbF components |
| COG3702 | Type IV secretory pathway, VirB3 components |
| COG3704 | Type IV secretory pathway, VirB6 components |
| COG3736 | Type IV secretory pathway, component VirB8 |
| COG3745 | Flp pilus assembly protein CpaB |
| COG3838 | Type IV secretory pathway, VirB2 components (pilins) |
| COG3843 | Type IV secretory pathway, VirD2 components (relaxase) |
| COG3846 | Type IV secretory pathway, TrbL components |
| COG3847 | Flp pilus assembly protein, pilin Flp |
| COG3946 | Type IV secretory pathway, VirJ component |
| COG4023 | Preprotein translocase subunit Sec61beta |
| COG4473 | Predicted ABC-type exoprotein transport system, permease component |
| COG4537 | Competence protein ComGC |
| COG4669 | Type III secretory pathway, lipoprotein EscJ |
| COG4726 | Tfp pilus assembly protein PilX |
| COG4789 | Type III secretory pathway, component EscV |
| COG4790 | Type III secretory pathway, component EscR |
| COG4791 | Type III secretory pathway, component EscT |
| COG4792 | Type III secretory pathway, component EscU |
| COG4794 | Type III secretory pathway, component EscS |
| COG4795 | Type II secretory pathway, component PulJ |
| COG4796 | Type II secretory pathway, component HofQ |
| COG4940 | Competence protein ComGF |
| COG4959 | Type IV secretory pathway, protease TraF |
| COG4960 | Flp pilus assembly protein, protease CpaA |
| COG4961 | Flp pilus assembly protein TadG |
| COG4962 | Flp pilus assembly protein, ATPase CpaF |
| COG4963 | Flp pilus assembly protein, ATPase CpaE |
| COG4964 | Flp pilus assembly protein, secretin CpaC |
| COG4965 | Flp pilus assembly protein TadB |
| COG4966 | Tfp pilus assembly protein PilW |
| COG4967 | Tfp pilus assembly protein PilV |
| COG4968 | Tfp pilus assembly protein PilE |
| COG4969 | Tfp pilus assembly protein, major pilin PilA |
| COG4970 | Tfp pilus assembly protein FimT |
| COG4972 | Tfp pilus assembly protein, ATPase PilM |
| COG5008 | Tfp pilus assembly protein, ATPase PilU |
| COG5010 | Flp pilus assembly protein TadD, contains TPR repeats |
| COG5028 | Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 |
| COG5030 | Clathrin adaptor complex, small subunit |
| COG5032 | Phosphatidylinositol kinase and protein kinases of the PI-3 kinase family |
| COG5043 | Vacuolar protein sorting-associated protein |
| COG5047 | Vesicle coat complex COPII, subunit SEC23 |
| COG5052 | Protein involved in membrane traffic |
| COG5058 | Protein transporter of the TRAM (translocating chain-associating membrane) superfamily, longevity assurance factor |
| COG5061 | Oxidoreductin, endoplasmic reticulum membrane-associated protein involved in disulfide bond formation |
| COG5064 | Karyopherin (importin) alpha |
| COG5066 | VAMP-associated protein involved in inositol metabolism |
| COG5070 | Nucleotide-sugar transporter |
| COG5073 | Vacuolar import and degradation protein |
| COG5074 | t-SNARE complex subunit, syntaxin |
| COG5079 | Nuclear protein export factor |
| COG5080 | Rab GTPase interacting factor, Golgi membrane protein |
| COG5082 | Arginine methyltransferase-interacting protein, contains RING Zn-finger |
| COG5096 | Vesicle coat complex, various subunits |
| COG5101 | Importin beta-related nuclear transport receptor |
| COG5102 | Membrane protein involved in ER to Golgi transport |
| COG5117 | Protein involved in the nuclear export of pre-ribosomes |
| COG5120 | Membrane protein involved in Golgi transport |
| COG5122 | Transport protein particle (TRAPP) complex subunit |
| COG5128 | Transport protein particle (TRAPP) complex subunit |
| COG5130 | Prenylated rab acceptor 1 and related proteins |
| COG5143 | Synaptobrevin/VAMP-like protein |
| COG5153 | Putative lipase essential for disintegration of autophagic bodies inside the vacuole |
| COG5158 | Proteins involved in synaptic transmission and general secretion, Sec1 family |
| COG5167 | Protein involved in vacuole import and degradation |
| COG5171 | Ran GTPase-activating protein (Ran-binding protein) |
| COG5173 | Exocyst complex subunit SEC6 |
| COG5196 | ER lumen protein retaining receptor |
| COG5215 | Karyopherin (importin) beta |
| COG5232 | Preprotein translocase subunit Sec62 |
| COG5233 | Peripheral Golgi membrane protein |
| COG5240 | Vesicle coat complex COPI, gamma subunit |
| COG5249 | Golgi protein involved in Golgi-to-ER retrieval |
| COG5268 | Type IV secretory pathway, TrbD component |
| COG5295 | Autotransporter adhesin |
| COG5308 | Nuclear pore complex subunit |
| COG5314 | Conjugal transfer/entry exclusion protein |
| COG5325 | t-SNARE complex subunit, syntaxin |
| COG5347 | GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport |
| COG5391 | Phox homology (PX) domain protein |
| COG5407 | Preprotein translocase subunit Sec63 |
| COG5538 | Preprotein translocase subunit Sec66 |
