recR Resolved · high auto-curated
H37Rv Rv3715c · MTBC0 mtbc0_003938 ·
203 aa · 4184010–4184621 (-) ·
RefSeq NP_218232.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | recombination protein RecR |
|---|---|
| MTBC0 PGAP re-annotation | recombination mediator RecR |
| Revised (this work) | Recombination mediator RecR. Pfam: RecR_HhH (PF21176.4), RecR_ZnF (PF02132.22), Toprim_4 (PF13662.13), Toprim (PF01751.29), RecR_C (PF21175.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHI3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Recombination protein RecR |
| Curated function | May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | recR |
| eggNOG description | May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO |
| Orthologous group | COG0353 |
| KEGG orthology |
K06187
|
| KEGG pathways |
map03440
|
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 | 0.362 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
RecR_HhH | PF21176.4 | 1.8e-16 | 6–48 | RecR, helix-hairpin-helix |
RecR_ZnF | PF02132.22 | 2.2e-08 | 53–73 | RecR, Cys4-zinc finger domain |
Toprim_4 | PF13662.13 | 1.1e-23 | 79–175 | Toprim domain |
Toprim | PF01751.29 | 1.3e-13 | 81–165 | Toprim domain |
RecR_C | PF21175.3 | 5.6e-12 | 177–200 | RecR, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uvrD1 (ATP-dependent DNA helicase UvrD), medium confidence from genomic context alone (score 661 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3716c hyp |
hypothetical protein | 983 | 973 ctx | neighborhood:876 coexpression:792 |
Rv2362c recO |
DNA repair protein RecO | 984 | 940 | experimental:912 textmining:746 |
Rv3717 hyp |
hypothetical protein | 873 | 774 ctx | neighborhood:772 textmining:465 |
Rv3880c espL |
ESX-1 secretion-associated protein EspL | 776 | 748 | coexpression:734 |
Rv0949 uvrD1 |
ATP-dependent DNA helicase UvrD | 761 | 661 ctx | cooccurence:650 |
Rv3714c hyp |
hypothetical protein | 635 | 636 ctx | neighborhood:632 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 628 | 615 | |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 652 | 605 | coexpression:435 |
Rv2524c fas |
fatty acid synthase | 587 | 587 ctx | neighborhood:544 |
Rv2442c rplU |
50S ribosomal protein L21 | 624 | 580 | coexpression:484 |
Rv2154c ftsW |
lipid II flippase FtsW | 615 | 578 | |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 596 | 571 ctx | cooccurence:471 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 639 | 520 ctx | cooccurence:479 |
Rv0017c rodA |
cell division protein RodA | 532 | 486 | |
Rv3100c smpB |
SsrA-binding protein | 510 | 479 ctx | cooccurence:419 |
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: recombination protein RecR
- MTBC0 PGAP product: recombination mediator RecR
- Pfam (hmmscan --cut_ga): RecR_HhH PF21176.4 (E=2e-16), RecR_ZnF PF02132.22 (E=2e-08), Toprim_4 PF13662.13 (E=1e-23), Toprim PF01751.29 (E=1e-13), RecR_C PF21175.3 (E=6e-12)
- (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_218232.1)
- Domains: Pfam-A via hmmscan --cut_ga — RecR_HhH (PF21176.4), RecR_ZnF (PF02132.22), Toprim_4 (PF13662.13), Toprim (PF01751.29), RecR_C (PF21175.3)
- 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
COG0353 - Curated reference: UniProt P9WHI3 (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 —
71 functional partner(s); context anchor
uvrD1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003938|Rv3715c|recR MFEGPVQDLIDELGKLPGIGPKSAQRIAFHLLSVEPSDIDRLTGVLAKVRDGVRFCAVCGNVSDNERCRICSDIRRDASVVCIVEEPKDIQAVERTREFRGRYHVLGGALDPLSGIGPDQLRIRELLSRIGERVDDVDVTEVIIATDPNTEGEATATYLVRMLRDIPGLTVTRIASGLPMGGDLEFADELTLGRALAGRRVLA