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Table 2 Protein families with high fraction of conserved and variable positions

From: Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions

csCOG identifier COG Func Gene Description Comment
flavo9.00376 COG1158 K Rho Transcription termination factor Rho Mostly Bacteroidetes
flavo9.00582 COG1314 U SecG Protein translocase subunit SecG All bacteroidetes, but also in some other bacteria such as Chlorobia, some Proteobacteria, Spirochaetes; others do not possess the variable tail
flavo9.00756 xre family HTH (N-terminal), the loop is present mostly in Bacteroidetes, but seen in some Bacilli too
flavo9.00944 COG4807 S YehS Uncharacterized conserved protein YehS, DUF1456 family Specific for Flavobacterium
deino9.00350 An artefact: wrong ORFs start in some of these genes
deino9.00475 COG1722 L XseB Exonuclease VII small subunit Variable tail in other bacteria too
deino9.00842 COG0511 I AccB Biotin carboxyl carrier protein PA-rich, present in most bacteria
deino9.01337 Uncharacterized, small, Deinococcus specific
deino9.01490 COG0568 K RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) Specific N-terminal extension in Deinococci and Truepera, although partially low complexity region is present in Thermus
deino9.03407 COG0199 J RpsN Ribosomal protein S14 Xenologous gene displacement by zinc finger variant in some Deinococci
paen9.00611 COG1937 K FrmR DNA-binding transcriptional regulator, FrmR family Copper-sensitive operon repressor, variable N-terminal region is present in many other Firmicutes
paen9.00802 YycC-like protein, PF14174.7 Paenibacillus specific variable tail
paen9.00805 COG3874 S YtfJ Uncharacterized spore protein YtfJ Sporulation protein YtfJ; variable region is present in many sporulating Bacilli, but variable tail is rather specific for Paenibacillus
paen9.00958 COG1674 D FtsK DNA segregation ATPase FtsK/SpoIIIE or related protein Variable insertion is present in all Bacilli and other bacteria, in Paenibacillus these regions are longer
paen9.01226 COG0323 L MutL DNA mismatch repair ATPase MutL Common feature among some archaea and some bacteria
paen9.01699 COG4467 L YabA Regulator of replication initiation timing YabA Variable insertion is present in all Firmicutes and other bacteria, in Paenibacillus these regions is longer [66]
paen9.02368 COG0532 J InfB Translation initiation factor IF-2, a GTPase Variable insertion is present in all Firmicutes (very different lengths), in Paenibacillus these regions are longer, but not the longest among Firmicutes. In many other bacteria the insertion is much smaller [67]
rhodo7.000637 COG1826 U TatA Twin-arginine protein secretion pathway components TatA and TatB Variable tail is specific for at least actinobacteria
rhodo7.001015 COG5416 S YrvD Uncharacterized integral membrane protein YrvD Variable N-terminal region specific for actinobacteria, but not others
rhodo7.001149 COG2409 S YdfJ Predicted lipid transporter YdfJ, MMPL/SSD domain, RND superfamily Variable tail region specific for actinobacteria, but not others, sometime the tail is missing in actinobacteria too
rhodo7.001169 lipid droplet-associated protein Found in lipid droplets in Mycobacterium tuberculosis [68]; two variable internal regions specific for actinobacteria
rhodo7.001269 COG1158 K Rho Transcription termination factor Rho N-terminal variable region specific for actinobacteria
rhodo7.001344 COG0328 L RnhA Ribonuclease HI Variable region is present in many bacteria
rhodo7.001562 COG1862 U YajC Protein translocase subunit YajC Variable region is present in many bacteria
rhodo7.001949 COG0305 L DnaB Replicative DNA helicase Some contain intein
thermo9.00277 (arCOG04026) Pilin/Flagellin, contains class III signal peptide Thermococcus specific, not present elsewhere
halo9.00332 COG0323 L MutL DNA mismatch repair enzyme (predicted ATPase) Common feature among some archaea and some bacteria
halo9.00351 COG1885 S Uncharacterized protein, DUF555 family Uncharacterized, variable tail present in Methanosarcina, but not in a few other euryarchaea
halo9.00421 COG4530 S Uncharacterized protein Uncharacterized DUF5806, specific for Halobacteria variable N-terminal region, some have CxxCxHxxH motif, variable N-terminal region
halo9.00587 COG0805 U Sec-independent protein translocase protein TatC Specific for Halobacteria variable N-terminal region
halo9.00602 COG0552 U Signal recognition particle-docking protein FtsY N-terminal variable region present in many euryarchaea
halo9.00879 COG1474 L orc1/cdc6 family replication initiation protein N-terminal region specific for Haloferacales
halo9.00317 COG0358 L DnaG DNA primase (bacterial type) Common feature among euryarchaea
methano7.000496 COG1311 L HYS2 Archaeal DNA polymerase II, small subunit/DNA polymerase delta, subunit B Specific for Methanosarcina