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