Table 1 Protein components of CASS
| Â | Family | SubfamilyA | Phyletic distributionB | Comments |
|---|---|---|---|---|
1 | COG1518 | COG1518 (cas1) | All | Putative novel nuclease/integrase; Mostly α-helical protein |
2 | COG1343 | COG1343 (cas2), COG3512, ygbF-like; MTH324-like; y1723_N-like; | All | Small protein related to VapD, fused to helicase (COG1203) in y1723-like proteins |
3 | COG1203 | COG1203 (cas3) | All | DNA helicase; Most proteins have fusion to HD nuclease |
4 | RecB-like nuclease | COG1468 (cas4), COG4343 | All | RecB-like nuclease; Contains three-cysteine C-terminal cluster |
5 | RAMP | COG1688, COG1769, COG1583, COG1567, COG1336, COG1367, COG1604, COG1337, COG1332, COG5551, BH0337-like, MJ0978-like, YgcH-like, y1726-like, y1727-like | All | Belong to "RAMP" superfamily, possibly RNA-binding protein, structurally related to a duplicated ferredoxin fold (PDB: 1WJ9) |
6 | COG1857 | COG1857, COG3649, YgcJ-like, y1725-like | All | α/β protein; probable enzymatic activity, possibly, a nuclease |
7 | HD-like nuclease | COG1203 (N-terminus), COG2254 | All | HD-like nuclease |
8 | BH0338 | BH0338-like MTH1090-like | All, mostly archaea and FIRM | Large Zn-finger-containing proteins, possibly, nucleases (nuclease activity has been reported for MTH1090 [75]. |
9 | ygcL | ygcL | Bacteria, mostly PROTEO | Large Zn-finger containing proteins; |
10 | COG1353 | COG1353, MTH326-like, alr1562, slr7011 | All, mostly Archaea | Putative novel polymerase; Multidomain protein with permuted HD nuclease domain, palm domain, polymerase-thumb-like domain and Zn-ribbon; MTH326-like has inactivated polymerase catalytic domain; alr1562 and slr7011 – predicted only on the basis of size, presence of HD domain, and location with RAMPs in one operon |
11 | COG1517/HTH | COG2462 | Archaea | Former COG2462; Fusion of COG1517-like domain to HTH-type transcriptional regulator; Possible regulator of the system expression in archaea |
12 | COG1421 | COG1421 | All, mostly Archaea | ~150 aa protein; Has a few motifs similar to ygcK-like; mostly α-helical protein |
13 | ygcK | ygcK-like | Bacteria, mostly PROTEO | ~180 aa protein; has a few motifs similar to COG1421; mostly α-helical protein |
14 | COG3337 | COG3337 | All, mostly Archaea | ~110 aa; mostly α-helical protein |
15 | COG1517 | COG1517 COG4006 | All, mostly Archaea | Some are fused to HTH domain (see COG1517/HTH), some proteins have the domain duplication; structure is available (1XMX); domain appears to have a Rossmann-like fold. |
16 | COG3513 | COG3513 | Bacteria, mostly PROTEO | Huge protein; contains McrA/HNH-nuclease related domain and RuvC-like nuclease domain |
17 | PH0918 | PH0918-like | All, mostly Archaea | Specific for Pyrococcus and Thermococcus. The pair ST0031/SSO1401 and AF1873, most likely, belong to the same family because have similar length and located in the identical place in an operon but due to low conservation are not alignable |
18 | AF1870 | AF1870-like | Archaea | Former COG3574; ~150 aa protein. |
19 | AF0070 | AF0070-like | Archaea | ~420 aa protein, no prediction |
20 | y1724 | y1724-like | Bacteria, mostly PROTEO | ~450 aa protein, no prediction |
21 | SPy1049 | Spy1049-like | Bacteria, mostly FIRM | ~220 aa protein, no prediction |
22 | TTE2665 | TTE2665-like | Bacteria, mostly CHLOR | ~130 aa protein, no prediction |
23 | LA3191 | LA3191-like | Few bacteria | ~650 aa, no prediction |