radA Resolved · high auto-curated
H37Rv Rv3585 · MTBC0 mtbc0_003804 ·
480 aa · 4050121–4051563 (+) ·
RefSeq NP_218102.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA repair protein RadA |
|---|---|
| MTBC0 PGAP re-annotation | DNA repair protein RadA |
| Revised (this work) | DNA repair protein RadA. Pfam: Zn_ribbon_LapB (PF18073.8), ATPase (PF06745.20), DUF7125 (PF23442.2), DnaB_C (PF03796.22), AAA_25 (PF13481.13), AAA (PF00004.36), Lon_C (PF05362.20), ChlI (PF13541.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHJ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA repair protein RadA |
| EC (curated) |
EC 3.6.4.-
|
| Curated function | DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | radA |
| eggNOG description | DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function |
| Orthologous group | COG1066 |
| KEGG orthology |
K04485
|
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.162 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 3 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Zn_ribbon_LapB | PF18073.8 | 4.3e-08 | 8–35 | Rubredoxin metal binding domain |
ATPase | PF06745.20 | 3.5e-12 | 70–141 | KaiC |
DUF7125 | PF23442.2 | 2.9e-11 | 71–244 | Family of unknown function (DUF7125) |
DnaB_C | PF03796.22 | 2.4e-07 | 71–181 | DnaB-like helicase C terminal domain |
AAA_25 | PF13481.13 | 3.9e-17 | 75–222 | AAA domain |
AAA | PF00004.36 | 8.2e-06 | 92–192 | ATPase family associated with various cellular activities (AAA) |
Lon_C | PF05362.20 | 8.0e-05 | 365–428 | Lon protease (S16) C-terminal proteolytic domain |
ChlI | PF13541.13 | 1.4e-07 | 367–427 | Subunit ChlI of Mg-chelatase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: disA (DNA integrity scanning protein DisA), high confidence from genomic context alone (score 991 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3586 disA |
DNA integrity scanning protein DisA | 997 | 991 ctx | neighborhood:881 coexpression:929 textmining:758 |
Rv2736c recX |
regulatory protein RecX | 990 | 968 | coexpression:957 textmining:711 |
Rv2977c thiL |
thiamine-monophosphate kinase | 943 | 943 | coexpression:943 |
Rv2737c recA |
recombinase A | 979 | 939 | coexpression:926 textmining:686 |
Rv3202c adnA |
ATP-dependent DNA helicase | 836 | 821 | coexpression:811 |
Rv3296 lhr |
ATP-dependent helicase | 793 | 793 | coexpression:793 |
Rv3714c hyp |
hypothetical protein | 791 | 791 | coexpression:791 |
Rv0185 hyp |
hypothetical protein | 761 | 761 | coexpression:761 |
Rv2191 hyp |
hypothetical protein | 812 | 741 | coexpression:734 |
Rv2978c tnpB |
transposase | 738 | 738 | coexpression:738 |
Rv0184 hyp |
hypothetical protein | 738 | 737 | coexpression:732 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 735 | 735 | coexpression:735 |
Rv3584 lpqE |
lipoprotein LpqE | 698 | 699 ctx | neighborhood:697 |
Rv3582c ispD |
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 710 | 665 ctx | neighborhood:453 coexpression:412 |
Rv2979c |
resolvase | 553 | 553 | coexpression:553 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: DNA repair protein RadA
- MTBC0 PGAP product: DNA repair protein RadA
- Pfam (hmmscan --cut_ga): Zn_ribbon_LapB PF18073.8 (E=4e-08), ATPase PF06745.20 (E=4e-12), DUF7125 PF23442.2 (E=3e-11), DnaB_C PF03796.22 (E=2e-07), AAA_25 PF13481.13 (E=4e-17), AAA PF00004.36 (E=8e-06), Lon_C PF05362.20 (E=8e-05), ChlI PF13541.13 (E=1e-07)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_218102.1)
- Domains: Pfam-A via hmmscan --cut_ga — Zn_ribbon_LapB (PF18073.8), ATPase (PF06745.20), DUF7125 (PF23442.2), DnaB_C (PF03796.22), AAA_25 (PF13481.13), AAA (PF00004.36), Lon_C (PF05362.20), ChlI (PF13541.13)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG1066 - Curated reference: UniProt P9WHJ9 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
66 functional partner(s); context anchor
disA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003804|Rv3585|radA MANARSQYRCSECRHVSAKWVGRCLECGRWGTVDEVAVLSAVGGTRRRSVAPASGAVPISAVDAHRTRPCPTGIDELDRVLGGGIVPGSVTLLAGDPGVGKSTLLLEVAHRWAQSGRRALYVSGEESAGQIRLRADRIGCGTEVEEIYLAAQSDVHTVLDQIETVQPALVIVDSVQTMSTSEADGVTGGVTQVRAVTAALTAAAKANEVALILVGHVTKDGAIAGPRSLEHLVDVVLHFEGDRNGALRMVRGVKNRFGAADEVGCFLLHDNGIDGIVDPSNLFLDQRPTPVAGTAITVTLDGKRPLVGEVQALLATPCGGSPRRAVSGIHQARAAMIAAVLEKHARLAIAVNDIYLSTVGGMRLTEPSADLAVAIALASAYANLPLPTTAVMIGEVGLAGDIRRVNGMARRLSEAARQGFTIALVPPSDDPVPPGMHALRASTIVAALQYMVDIADHRGTTLATPPSHSGTGHVPLGRGT