recO Resolved · high auto-curated
H37Rv Rv2362c · MTBC0 mtbc0_002514 ·
265 aa · 2667654–2668451 (-) ·
RefSeq NP_216878.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA repair protein RecO |
|---|---|
| MTBC0 PGAP re-annotation | DNA repair protein RecO |
| Revised (this work) | DNA repair protein RecO. Pfam: RecO_N (PF11967.15), RecO_C (PF02565.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHI5
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | DNA repair protein RecO |
| Curated function | Involved in DNA repair and RecF pathway recombination. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | recO |
| eggNOG description | Involved in DNA repair and RecF pathway recombination |
| Orthologous group | COG1381 |
| KEGG orthology |
K03584
|
| KEGG pathways |
map03440
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.186 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
RecO_N | PF11967.15 | 2.2e-26 | 1–79 | Recombination protein O N terminal |
RecO_C | PF02565.22 | 5.5e-31 | 86–237 | Recombination protein O C terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uppS (decaprenyl diphosphate synthase), high confidence from genomic context alone (score 890 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3715c recR |
recombination protein RecR | 984 | 940 | experimental:912 textmining:746 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 932 | 890 ctx | neighborhood:882 textmining:411 |
Rv2360c hyp |
hypothetical protein | 902 | 887 ctx | neighborhood:882 |
Rv2363 amiA2 |
amidase | 810 | 787 ctx | neighborhood:786 |
Rv2368c phoH1 |
phosphate starvation-inducible protein PhoH | 790 | 783 | coexpression:730 |
Rv3644c |
DNA polymerase | 649 | 602 ctx | cooccurence:424 |
Rv3859c gltB |
glutamate synthase large subunit | 544 | 544 ctx | neighborhood:544 |
Rv2364c era |
GTPase Era | 769 | 543 | coexpression:431 textmining:517 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 504 | 504 | |
Rv2478c hyp |
hypothetical protein | 537 | 475 | |
Rv2903c lepB |
signal peptidase | 467 | 467 ctx | cooccurence:401 |
Rv0343 iniC |
iIsoniazid inductible protein IniC | 526 | 463 | coexpression:432 |
Rv2365c hyp |
hypothetical protein | 461 | 440 | |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 424 | 425 | |
Rv3195 hyp |
hypothetical protein | 412 | 413 ctx | cooccurence:407 |
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 RecO
- MTBC0 PGAP product: DNA repair protein RecO
- Pfam (hmmscan --cut_ga): RecO_N PF11967.15 (E=2e-26), RecO_C PF02565.22 (E=5e-31)
- (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_216878.1)
- Domains: Pfam-A via hmmscan --cut_ga — RecO_N (PF11967.15), RecO_C (PF02565.22)
- 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
COG1381 - Curated reference: UniProt P9WHI5 (SwissProt, reviewed; Inferred from homology)
- 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 —
70 functional partner(s); context anchor
uppS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002514|Rv2362c|recO MRLYRDRAVVLRQHKLGEADRIVTLLTRDHGLVRAVAKGVRRTRSKFGARLEPFAHIEVQLHPGRNLDIVTQVVSVDAFATDIVADYGRYTCGCAILETAERLAGEERAPAPALHRLTVGALRAVADGQRPRDLLLDAYLLRAMGIAGWAPALTECARCATPGPHRAFHIATGGSVCAHCRPAGSTTPPLGVVDLMSALYDGDWEAAEAAPQSARSHVSGLVAAHLQWHLERQLKTLPLVERFYQADRSVAERRAALIGQDIAGG