recC Family assigned · medium auto-curated
H37Rv Rv0631c · MTBC0 mtbc0_000664 ·
1097 aa · 728566–731859 (-) ·
RefSeq NP_215145.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | exonuclease V subunit gamma RecC |
|---|---|
| MTBC0 PGAP re-annotation | exodeoxyribonuclease V subunit gamma |
| Revised (this work) | Exodeoxyribonuclease V subunit gamma. Pfam: Exonuc_V_gamma (PF04257.21), RecC_4th (PF27451.1), RecC_C (PF17946.8). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIQ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | RecBCD enzyme subunit RecC |
| Curated function | A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit recognizes the wild-type Chi sequence, and when added to isolated RecB increases its ATP-dependent helicase processivity. Unlike the case in E.coli, suppresses RecA-dependent homologous recombination, is instead required for single-strand annealing pathway repair of DSB. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | recC |
| eggNOG description | A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit recognizes the wild- type Chi sequence, and when added to isolated RecB increases its ATP-dependent helicase processivity |
| Orthologous group | COG1330 |
| EC number |
EC 3.1.11.5
|
| KEGG orthology |
K03583
|
| KEGG pathways |
map03440
|
| Gene Ontology (60) |
GO:0003674, GO:0003678, GO:0003824, GO:0004003, GO:0004386, GO:0004518, GO:0004519, GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886 +48 more
|
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 | 0.483 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 14 synonymous, 18 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.19% of strains (279) · clonal |
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 |
|---|---|---|---|---|
Exonuc_V_gamma | PF04257.21 | 7.5e-63 | 3–321 | Exodeoxyribonuclease V, gamma subunit |
RecC_4th | PF27451.1 | 1.2e-59 | 418–617 | RecBCD enzyme subunit RecC fourth domain |
RecC_C | PF17946.8 | 4.2e-48 | 795–1020 | RecC C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recB (exonuclease V subunit beta RecB), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0630c recB |
exonuclease V subunit beta RecB | 999 | 998 ctx | neighborhood:881 cooccurence:774 experimental:829 textmining:831 |
Rv0629c recD |
exonuclease V subunit alpha RecD | 999 | 996 ctx | neighborhood:881 cooccurence:774 experimental:737 textmining:813 |
Rv2311 hyp |
hypothetical protein | 823 | 800 | experimental:737 |
Rv0628c hyp |
hypothetical protein | 557 | 557 ctx | neighborhood:553 |
Rv2037c |
transmembrane protein | 513 | 514 ctx | neighborhood:511 |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 449 | 448 ctx | neighborhood:445 |
Rv3731 ligC |
DNA ligase C | 850 | 240 | textmining:812 |
Rv1420 uvrC |
excinuclease ABC subunit UvrC | 452 | 163 | |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 484 | 160 | textmining:412 |
Rv2836c dinF |
DNA-damage-inducible protein DinF | 504 | 154 | textmining:438 |
Rv1317c alkA |
bifunctional regulatory protein/DNA repair enzyme AlkA | 600 | 102 | textmining:574 |
Rv1537 dinX |
DNA polymerase IV | 615 | 65 | textmining:606 |
Rv0711 atsA |
arylsulfatase AtsA | 447 | 57 | textmining:438 |
Rv1696 recN |
DNA repair protein RecN | 524 | 55 | textmining:518 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 447 | 54 | textmining:440 |
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: exonuclease V subunit gamma RecC
- MTBC0 PGAP product: exodeoxyribonuclease V subunit gamma
- Pfam (hmmscan --cut_ga): Exonuc_V_gamma PF04257.21 (E=8e-63), RecC_4th PF27451.1 (E=1e-59), RecC_C PF17946.8 (E=4e-48)
- (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_215145.1)
- Domains: Pfam-A via hmmscan --cut_ga — Exonuc_V_gamma (PF04257.21), RecC_4th (PF27451.1), RecC_C (PF17946.8)
- 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
COG1330 - Curated reference: UniProt P9WIQ5 (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 —
32 functional partner(s); context anchor
recB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000664|Rv0631c|recC MALHLHRAERTDLLADGLGALLADPQPDPFAQELVLVAARGVERWLSQRLSLVLGCGPGRADGVCAGIAFRNPQSLIAEITGTLDDDPWSPEALAWPLLAVIDASLDEPWCRTLASHLGHFATTDAEAELRRGRRYSVARRLAGLFASYARQRPGLLAAWLDGDLGELPGDLAWQPPLWRALVTTVGADPPHVRHDKTIARLRDGPADLPARLSLFGHTRLACTDVQLLDALAVHHDLHLWLPHPSDELWRALAGFQGADGLLPRRQDTSRRAAQHPLLETLGRDVRELQRALPAARATDEFLGATTKPDTLLGWLQADIAGNAPRPAGRSLSDADRSVQVHACHGPARQIDVLREVLLGLLEDDPTLQPRDIVVMCPDIDTYAPLIVAGFGLGEVAGDCHPAHRLRVRLADRALTQTNPLLSVAAELLTIAETRATASQLLNLAQAAPVRAKFGFADDDLDTITTWVRESNIRWGFDPTHRRRYGLDTVVHNTWRFGLDRILTGVAMSEDSQAWLDTALPLDDVGSNRVELAGRLAEFVERLHHVVGGLSGARPLVAWLDALATGIDLLTACNDGWQRAQVQREFADVLARAGSRAAPLLRLPDVRALLDAQLAGRPTRANFRTGTLTVCTMVPMRSVPHRVVCLVGLDDGVFPRLSHPDGDDVLAREPMTGERDIRSEDRQLLLDAIGAATQTLVITYTGADERTGQPRPPAVPLAELLDALDQTTSAPVRERILVTHPLQPFDRKNVTPGALLGAKPFTFDPAALAAAQAAAGKRCPPTAFISGRLPAPPAADVTLADLLDFFKDPVKGFFRALDYTLPWDVDTVEDSIPVQVDALAEWTVGERMLRDMLRGLHPDDAAHSEWRRGTLPPGRLGVRRAKEIRNRARDLAAAALAHRDGHGQAHDVDVDLGDGRRLSGTVTPVFGGRTVSVTYSKLAPKHVLPAWIGLVTLAAQEPGREWSALCIGRSKTRNHIARRLFVPPPDPVAVLRELVLLYDAGRREPLPLPLKTSCAWAQARRDGQDPYPPARECWQTNRFRPGDDDAPAHVRAWGPRAPFEVLLGKPRAGEEVAGEETRLGALAARLWLPLLAAEGSV