recX Resolved · high auto-curated
H37Rv Rv2736c · MTBC0 mtbc0_002910 ·
174 aa · 3070977–3071501 (-) ·
RefSeq NP_217252.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | regulatory protein RecX |
|---|---|
| MTBC0 PGAP re-annotation | recombination regulator RecX |
| Revised (this work) | Recombination regulator RecX. Pfam: RecX_HTH1 (PF21982.3), RecX_HTH2 (PF02631.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHI1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Regulatory protein RecX |
| Curated function | Binds to RecA inhibiting ATP hydrolysis and the generation of heteroduplex DNA. It might act as an anti-recombinase to quell inappropriate recombinational repair during normal DNA metabolism. It is essential for cell survival. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | recX |
| eggNOG description | regulatory protein RecX |
| Orthologous group | COG2137 |
| KEGG orthology |
K03565
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 1.13 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
RecX_HTH1 | PF21982.3 | 1.8e-12 | 17–56 | RecX, first three-helix domain |
RecX_HTH2 | PF02631.23 | 2.8e-12 | 63–104 | RecX, second three-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recA (recombinase A), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2737c recA |
recombinase A | 999 | 998 ctx | neighborhood:881 coexpression:984 textmining:865 |
Rv3585 radA |
DNA repair protein RadA | 990 | 968 | coexpression:957 textmining:711 |
Rv2735c hyp |
hypothetical protein | 960 | 889 ctx | neighborhood:882 textmining:655 |
Rv2594c ruvC |
crossover junction endodeoxyribonuclease RuvC | 859 | 674 | coexpression:663 textmining:588 |
Rv2737A |
Rv2737A, len: 57 aa. Conserved hypothetical cys-rich protein (possibly gene fragment), similar to central part of AJ243803_1|glgA from Strep | 561 | 560 ctx | neighborhood:558 |
Rv2977c thiL |
thiamine-monophosphate kinase | 559 | 560 | coexpression:524 |
Rv2738c hyp |
hypothetical protein | 546 | 546 ctx | neighborhood:544 |
Rv2739c |
transferase | 536 | 537 ctx | neighborhood:532 |
Rv1696 recN |
DNA repair protein RecN | 714 | 431 | coexpression:413 textmining:518 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 419 | 420 | coexpression:408 |
Rv2593c ruvA |
Holliday junction ATP-dependent DNA helicase RuvA | 701 | 418 | textmining:509 |
Rv1460 sufR |
transcriptional regulator | 418 | 418 ctx | cooccurence:413 |
Rv2362c recO |
DNA repair protein RecO | 700 | 394 | textmining:526 |
Rv1901 cinA |
competence damage-inducible protein CinA | 687 | 390 | textmining:508 |
Rv2720 lexA |
repressor LexA | 668 | 338 | textmining:520 |
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: regulatory protein RecX
- MTBC0 PGAP product: recombination regulator RecX
- Pfam (hmmscan --cut_ga): RecX_HTH1 PF21982.3 (E=2e-12), RecX_HTH2 PF02631.23 (E=3e-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_217252.1)
- Domains: Pfam-A via hmmscan --cut_ga — RecX_HTH1 (PF21982.3), RecX_HTH2 (PF02631.23)
- 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
COG2137 - Curated reference: UniProt P9WHI1 (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 —
44 functional partner(s); context anchor
recA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002910|Rv2736c|recX MTVSCPPPSTSEREEQARALCLRLLTARSRTRAELAGQLAKRGYPEDIGNRVLDRLAAVGLVDDTDFAEQWVQSRRANAAKSKRALAAELHAKGVDDDVITTVLGGIDAGAERGRAEKLVRARLRREVLIDDGTDEARVSRRLVAMLARRGYGQTLACEVVIAELAAERERRRV