Table 2.
Top 20 most abundant uncharacterized arCOGs in “dark matter islands”
| arCOG | Number in islands | Annotation and comment |
|---|---|---|
| arCOG08821 | 18 | Membrane protein, expanded in Thaumarchaeota |
| arCOG10873 | 14 | Membrane protein |
| arCOG10027 | 12 | Thermococcus specific secreted protein, paralogs belong to arCOG10066 and arCOG10028, they form genes clusters |
| arCOG10864 | 11 | Predicted peptidase of C39 family; possibly associated with pseudo-murein binding domains |
| arCOG10897 | 10 | Small membrane protein |
| arCOG06558 | 10 | Likely a secreted protease, Propeptide PepSY and peptidase M4 |
| arCOG10066 | 9 | Thermococcus specific secreted protein, same as (see arCOG10027) |
| arCOG10865 | 9 | Methanobacterium specific |
| arCOG09441 | 8 | HJR family endonuclease, PD-DEXK superfamily, associated with arCOG07809, viral Primase fused to AAA DnaA-like ATPAse and Zn finger domain |
| arCOG10959 | 8 | Virus/plasmid associated, often co-occur with primase in particular arCOG06914 |
| arCOG09176 | 8 | Often associated with viruses or plasmids |
| arCOG09593 | 8 | Secreted protein with immunoglobulin-like domain |
| arCOG10866 | 8 | Methanosaeta specific |
| arCOG09761 | 8 | Large secreted protein; pyrobaculum specific expansion |
| arCOG11121 | 7 | Uncharacterized conserved membrane protein |
| arCOG03316 | 7 | Secreted enzyme present in bacteria and eukaryotes, duplication in methanosarcina acetivorans DUF3160 |
| arCOG03631 | 7 | Methanosarcina specific, present in bacteria |
| arCOG07691 | 7 | Secreted protein associated with membrane protein of a number of related arCOGs (e.g., arCOG09771), mostly beta stranded; pyrobaculum specific expansion |
| arCOG06827 | 7 | Membrane protein expansion in Methanosarcina, MGWCP motif, DUF1673 |
| arCOG10868 | 7 | PD-(D/E)XK nuclease family transposase |
| arCOG10363 | 7 | Associated with Zn-finger containing protein from arCOG08887 |
Genes that belong to the mobilome genes are highlighted by bold type