recB Family assigned · medium auto-curated
H37Rv Rv0630c · MTBC0 mtbc0_000663 ·
1094 aa · 725282–728566 (-) ·
RefSeq NP_215144.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | exonuclease V subunit beta RecB |
|---|---|
| MTBC0 PGAP re-annotation | exodeoxyribonuclease V subunit beta |
| Revised (this work) | Exodeoxyribonuclease V subunit beta. Pfam: UvrD-helicase (PF00580.28), AAA_19 (PF13245.13), UvrD_C (PF13361.13), PDDEXK_1 (PF12705.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMQ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | RecBCD enzyme subunit RecB |
| EC (curated) |
EC 3.1.11.5, EC 5.6.2.4
|
| 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. In the holoenzyme this subunit contributes ATPase, 3'-5' helicase, exonuclease activity and loads RecA onto ssDNA. 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 | recB |
| 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 contributes ATPase, 3'-5' helicase, exonuclease activity and loads RecA onto ssDNA |
| Orthologous group | COG1074 |
| EC number |
EC 3.1.11.5
|
| KEGG orthology |
K03582
|
| KEGG pathways |
map03440
|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0030312, GO:0044424, GO:0044444, GO:0044464 +1 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) pseudogene candidate
| pN/pS | 0.341 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 27 synonymous, 25 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.04% of strains (14578) · 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 |
|---|---|---|---|---|
UvrD-helicase | PF00580.28 | 1.3e-56 | 14–310 | UvrD/REP helicase N-terminal domain |
AAA_19 | PF13245.13 | 8.3e-15 | 15–299 | AAA domain |
UvrD_C | PF13361.13 | 1.2e-06 | 595–686 | UvrD-like helicase C-terminal domain |
PDDEXK_1 | PF12705.14 | 7.5e-07 | 831–1052 | PD-(D/E)XK nuclease superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recC (exonuclease V subunit gamma RecC), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0631c recC |
exonuclease V subunit gamma RecC | 999 | 998 ctx | neighborhood:881 cooccurence:774 experimental:829 textmining:831 |
Rv0629c recD |
exonuclease V subunit alpha RecD | 998 | 996 ctx | neighborhood:881 cooccurence:773 coexpression:460 experimental:510 database:540 textmining:707 |
Rv2311 hyp |
hypothetical protein | 649 | 602 | experimental:510 |
Rv0628c hyp |
hypothetical protein | 554 | 554 ctx | neighborhood:553 |
Rv2037c |
transmembrane protein | 513 | 513 ctx | neighborhood:511 |
Rv0955 |
integral membrane protein | 467 | 468 ctx | cooccurence:422 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 444 | 444 | |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 432 | 432 ctx | neighborhood:432 |
Rv2529 hyp |
hypothetical protein | 408 | 408 ctx | cooccurence:400 |
Rv3370c dnaE2 |
error-prone DNA polymerase | 614 | 374 | textmining:409 |
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 520 | 373 | |
Rv2737c recA |
recombinase A | 823 | 357 | textmining:737 |
Rv3014c ligA |
DNA ligase A | 761 | 348 | textmining:649 |
Rv0058 dnaB |
replicative DNA helicase | 646 | 334 | textmining:491 |
Rv1629 polA |
DNA polymerase I | 809 | 278 | textmining:747 |
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 beta RecB
- MTBC0 PGAP product: exodeoxyribonuclease V subunit beta
- Pfam (hmmscan --cut_ga): UvrD-helicase PF00580.28 (E=1e-56), AAA_19 PF13245.13 (E=8e-15), UvrD_C PF13361.13 (E=1e-06), PDDEXK_1 PF12705.14 (E=8e-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_215144.1)
- Domains: Pfam-A via hmmscan --cut_ga — UvrD-helicase (PF00580.28), AAA_19 (PF13245.13), UvrD_C (PF13361.13), PDDEXK_1 (PF12705.14)
- 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
COG1074 - Curated reference: UniProt P9WMQ3 (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 —
47 functional partner(s); context anchor
recC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000663|Rv0630c|recB MDRFELLGPLPREGTTTVLEASAGTGKTFALAGLVTRYLAETAATLDEMLLITFNRAASRELRERVRGQIVEAVGALQGDAPPSGELVEHLLRGSDAERAQKRSRLRDALANFDAATIATTHEFCGSVLKSLGVAGDNAADVELKESLTDLVTEIVDDRYLANFGRQETDPELTYAEALALALAVVDDPCAQLRPPDPEPGSKAAVRLRFAAEVLEELERRKGRLRAQGFNDLLIRLATALEAADSPARDRMRERWRIVLVDEFQDTDPMQWRVLERAFSRHSALILIGDPKQAIYGFRGGDIHTYLKAAGTADARYTLGVNWRSDRALVESLQTVLRDATLGHADIVVRGTDAHHAGHRLASAPRPAPFRLRVVKRHTLGYDGTAHVPIEALRRHIPDDLAADVAALLASGATFAGRPVVAADIAVIVEHHKDARACRNALAEAGIPAIYTGDTDVFASQAAKDWLCLLEAFDAPQRSGLVRAAACTMFFGETAESLAAEGDALTDRVAGTLREWADHARHRGVAAVFQAAQLAGMGRRVLSQRGGERDLTDLAHIAQLLHEAAHRERLGLPGLRDWLRRQAKAGAGPPEHNRRLDSDAAAVQIMTVFVAKGLQFPIVYLPFAFNRNVRSDDILLYHDDGTRCLYIGGKDGGAQRRTVEGLNRVEAAHDNLRLTYVALTRAQSQVVAWWAPTFDEVNGGLSRLLRGRRPGQSQVPDRCTPRVTDEQAWAVFAQWEAAGGPSVEESVIGARSSLEKPVPVPGFEVRHFHRRIDTTWRRTSYSDLVRGSEAVTVTSEPAAGGRADEVEIAVVAAPGSGADLTSPLAALPSGASFGSLVHAVLETADPAAPDLAAELEAQVRRHAPWWTVDVDHAQLAPELARALLPMHDTPLGPAAAALTLRQIGVRDRLRELDFEMPLAGGDLRGRSPDVSLADVGELLASHLPGDDPLSPYADRLGSAGLGDQPLRGYLAGSIDVVLRLPGQRYLVVDYKTNHLGDTAADYGFERLTEAMLHSDYPLQALLYVVVLHRFLRWRQRDYAPARHLGGVLYLFVRGMCGAATPVTAGHPAGVFTWNPPTALVVALSDLLDRGRLQS