| COG0630 | Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis |
| COG0643 | Chemotaxis protein histidine kinase and related kinases |
| COG0835 | Chemotaxis signal transduction protein |
| COG0840 | Methyl-accepting chemotaxis protein |
| COG1157 | Flagellar biosynthesis/type III secretory pathway ATPase |
| COG1256 | Flagellar hook-associated protein |
| COG1261 | Flagellar basal body P-ring biosynthesis protein |
| COG1291 | Flagellar motor component |
| COG1298 | Flagellar biosynthesis pathway, component FlhA |
| COG1317 | Flagellar biosynthesis/type III secretory pathway protein |
| COG1334 | Uncharacterized flagellar protein FlaG |
| COG1338 | Flagellar biosynthesis pathway, component FliP |
| COG1344 | Flagellin and related hook-associated proteins |
| COG1345 | Flagellar capping protein |
| COG1352 | Methylase of chemotaxis methyl-accepting proteins |
| COG1360 | Flagellar motor protein |
| COG1377 | Flagellar biosynthesis pathway, component FlhB |
| COG1406 | Predicted inhibitor of MCP methylation, homolog of CheC |
| COG1419 | Flagellar GTP-binding protein |
| COG1450 | Type II secretory pathway, component PulD |
| COG1459 | Type II secretory pathway, component PulF |
| COG1516 | Flagellin-specific chaperone FliS |
| COG1536 | Flagellar motor switch protein |
| COG1558 | Flagellar basal body rod protein |
| COG1580 | Flagellar basal body-associated protein |
| COG1582 | Uncharacterized protein, possibly involved in motility |
| COG1677 | Flagellar hook-basal body protein |
| COG1681 | Archaeal flagellins |
| COG1684 | Flagellar biosynthesis pathway, component FliR |
| COG1705 | Muramidase (flagellum-specific) |
| COG1706 | Flagellar basal-body P-ring protein |
| COG1724 | Predicted periplasmic or secreted lipoprotein |
| COG1749 | Flagellar hook protein FlgE |
| COG1766 | Flagellar biosynthesis/type III secretory pathway lipoprotein |
| COG1776 | Chemotaxis protein CheC, inhibitor of MCP methylation |
| COG1815 | Flagellar basal body protein |
| COG1843 | Flagellar hook capping protein |
| COG1868 | Flagellar motor switch protein |
| COG1871 | Chemotaxis protein; stimulates methylation of MCP proteins |
| COG1886 | Flagellar motor switch/type III secretory pathway protein |
| COG1955 | Archaeal flagella assembly protein J |
| COG1987 | Flagellar biosynthesis pathway, component FliQ |
| COG1989 | Type II secretory pathway, prepilin signal peptidase PulO and related peptidases |
| COG2063 | Flagellar basal body L-ring protein |
| COG2064 | Flp pilus assembly protein TadC |
| COG2165 | Type II secretory pathway, pseudopilin PulG |
| COG2201 | Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain |
| 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 |
| COG2874 | Predicted ATPases involved in biogenesis of archaeal flagella |
| COG2882 | Flagellar biosynthesis chaperone |
| COG3063 | Tfp pilus assembly protein PilF |
| COG3121 | P pilus assembly protein, chaperone PapD |
| COG3143 | Chemotaxis protein |
| COG3144 | Flagellar hook-length control protein |
| 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 |
| COG3190 | Flagellar biogenesis protein |
| COG3215 | Tfp pilus assembly protein PilZ |
| COG3225 | ABC-type uncharacterized transport system involved in gliding motility, auxiliary component |
| COG3351 | Putative archaeal flagellar protein D/E |
| COG3352 | Putative archaeal flagellar protein C |
| COG3353 | Putative archaeal flagellar protein F |
| COG3354 | Putative archaeal flagellar protein G |
| COG3418 | Flagellar biosynthesis/type III secretory pathway chaperone |
| COG3419 | Tfp pilus assembly protein, tip-associated adhesin PilY1 |
| COG3539 | P pilus assembly protein, pilin FimA |
| COG3678 | P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein |
| COG3951 | Rod binding protein |
| COG4726 | Tfp pilus assembly protein PilX |
| COG4786 | Flagellar basal body rod protein |
| COG4787 | Flagellar basal body rod protein |
| COG4862 | Negative regulator of genetic competence, sporulation and motility |
| 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 |
| COG5268 | Type IV secretory pathway, TrbD component |
| COG5442 | Flagellar biosynthesis regulator FlaF |
| COG5443 | Flagellar biosynthesis regulator FlbT |
| COG5461 | Type IV pili component |
| COG5491 | Conserved protein implicated in secretion |
| COG5492 | Bacterial surface proteins containing Ig-like domains |
| COG5555 | Cytolysin, a secreted calcineurin-like phosphatase |
| COG5567 | Predicted small periplasmic lipoprotein |
| COG5571 | Autotransporter protein or domain, integral membrane beta-barrel involved in protein secretion |
| COG5603 | Subunit of TRAPP, an ER-Golgi tethering complex |
| COG5622 | Protein required for attachment to host cells |
| COG5651 | PPE-repeat proteins |
