Rv0372c Family assigned · medium auto-curated
H37Rv Rv0372c · MTBC0 mtbc0_000392 ·
251 aa · 451992–452747 (-) ·
RefSeq NP_214886.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | XdhC family protein |
| Revised (this work) | XdhC family protein. Pfam: XdhC_CoxI (PF02625.22), XdhC_C (PF13478.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53707
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Carbon monoxide dehydrogenase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | XdhC Rossmann domain |
| Orthologous group | COG1975 |
| KEGG orthology |
K07402
|
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 | 0.253 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.21% of strains (299) · 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 |
|---|---|---|---|---|
XdhC_CoxI | PF02625.22 | 3.9e-16 | 11–75 | XdhC and CoxI family |
XdhC_C | PF13478.13 | 1.2e-19 | 117–229 | XdhC Rossmann domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0375c (carbon monoxyde dehydrogenase medium subunit), high confidence from genomic context alone (score 992 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0375c |
carbon monoxyde dehydrogenase medium subunit | 993 | 992 ctx | neighborhood:811 cooccurence:772 coexpression:835 |
Rv0371c hyp |
hypothetical protein | 981 | 981 ctx | neighborhood:882 cooccurence:704 coexpression:488 |
Rv0373c |
carbon monoxyde dehydrogenase large subunit | 980 | 978 ctx | neighborhood:852 cooccurence:773 |
Rv0374c |
carbon monoxyde dehydrogenase small subunit | 974 | 972 ctx | neighborhood:861 cooccurence:752 |
Rv0368c hyp |
hypothetical protein | 944 | 945 ctx | neighborhood:773 cooccurence:748 |
Rv0370c |
oxidoreductase | 928 | 928 ctx | neighborhood:882 cooccurence:400 |
Rv0369c |
membrane oxidoreductase | 925 | 926 ctx | neighborhood:773 cooccurence:684 |
Rv0377 |
HTH-type transcriptional regulator | 882 | 883 ctx | neighborhood:635 cooccurence:687 |
Rv0376c hyp |
hypothetical protein | 799 | 800 ctx | neighborhood:719 |
Rv0365c hyp |
hypothetical protein | 619 | 620 ctx | neighborhood:620 |
Rv0345 hyp |
hypothetical protein | 589 | 563 | coexpression:409 |
Rv0367c hyp |
hypothetical protein | 432 | 432 ctx | neighborhood:427 |
Rv3646c topA |
DNA topoisomerase I | 479 | 110 | textmining:439 |
Rv0195 |
two component transcriptional regulator | 465 | 91 | textmining:436 |
Rv1656 argF |
ornithine carbamoyltransferase | 541 | 83 | textmining:521 |
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: hypothetical protein
- MTBC0 PGAP product: XdhC family protein
- Pfam (hmmscan --cut_ga): XdhC_CoxI PF02625.22 (E=4e-16), XdhC_C PF13478.13 (E=1e-19)
- (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_214886.1)
- Domains: Pfam-A via hmmscan --cut_ga — XdhC_CoxI (PF02625.22), XdhC_C (PF13478.13)
- 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
COG1975 - Curated reference: UniProt O53707 (TrEMBL, unreviewed; Predicted)
- 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 —
19 functional partner(s); context anchor
Rv0375c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000392|Rv0372c| MSISDRAAQLVAARTPFVRATVVRAQQPTSARPGDEAILLADGTIEGFVGGHCAQNSVRKAAMGVLQAGESVLLRVLPDGDVHFPEAPGACVVVNPCLAGGSLEIFLTPQLPAPLIQIYGETPIADALIELCGLLGYDARRDTDPADTDALPTAIVIASHGGPEAEIIRTALDNGVGYVGLVASTVRGASILDSLDLSDAERARVHTPVGLAIGAKTPAEIAVSIAAELIATLRGGGPRGRKALADENGGA