TABLE 3.
Novel REC-associated domains in archaeal response regulators
| Domaina | Pfam IDb | Length (aa) | No. of proteins containing domainc | Accession no. of representative example in: |
Domain architecture(s) | Phylogenetic distribution | |
|---|---|---|---|---|---|---|---|
| GenBank | UniProt | ||||||
| AcidOD1 | NA | 70 | 2 | ADD08891 | B5IH54 | REC-AcidOD1 | Aciduliprofundum |
| HalOD1 | PF18545 | 80 | >2,000 | ADE02288 | I3R6Z3 | REC-HalOD1, HalOD1-PAS, HalOD1-iKaiC | Halobacteria, haloviruses |
| HalOD2 | PF18547 | 130 | 14 | ACV46423 | C7NX58 | REC-HalOD2 | Halobacteria |
| MetOD1 | PF18546 | 140 | >100 | AAM05831 | Q8TN48 | MetOD1, REC-MetOD1, REC-PAS-MetOD1 | Methanobacteria, Methanomicrobia |
| MetOD2 | PF18548 | 80 | >70 | ABD41349 | Q2FRF9 | REC-MetOD2, MetOD3-REC-MetOD2 | Methanocellales, Methanomicrobiales |
| MetOD3 | NA | 180 | 4 | ABS55483 | A7I6X2 | MetOD3-REC-MetOD2 | Methanoregula |
| MetOD4 | NA | 80 | 3 | ADZ10090 | F0TAL8 | MetOD4, REC-MetOD4 | Methanobacterium |
| MetOD5 | NA | 300 | 3 | ABS56126 | A7I8R5 | MetOD5, MetOD5-REC | Methanoregula |
| NitrOD1 | PF18549 | 70 | 12 | AFS82515 | K0BBZ3 | NitrOD1, REC-NitrOD1 | Nitrosopumilus |
| NitrOD2 | PF18550 | 90 | 13 | AIF82253 | A0A075MLY6 | NitrOD2, NitrOD2-REC | Nitrososphaera |
| NitrOD3 | NA | 120 | 3 | AIF83507 | A0A075MRR1 | NitrOD3-REC | Nitrososphaera |
| NitrOD4 | NA | 75 | 4 | AFS80878 | K0B452 | NitrOD4, NitrOD4-REC | Nitrosopumilus |
| NitrOD5 | PF11537 | 100 | 16 | ABX12603 | A9A4B4 | NitrOD5, REC-NitrOD5 | Nitrosopumilus, “Candidatus Nitrosotalea,” “Candidatus Nitrosotenuis” |
| TackOD1 | PF18551 | 200 | 12 | AFS80801 | K0B8K6 | TackOD1, REC-TackOD1, REC-wHTH-TackOD1 | TACK group |
a
Tentative domain names, constructed by combining an abbreviated taxon name with “OD” (output domain). These names are expected to be replaced as soon as these domains are experimentally characterized. Details of the analyses of remote sequence similarities of these domains are presented in Table S5 in the supplemental material.
b
NA, not available. The numbered domains are expected to be included in Pfam release 33 [2018]).
c
The number of archaeal proteins containing the domain (with any domain architecture) in the NCBI protein database as of 1 July 2017.