Rv0374c Family assigned · medium auto-curated
H37Rv Rv0374c · MTBC0 mtbc0_000394 ·
159 aa · 455162–455641 (-) ·
RefSeq NP_214888.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | carbon monoxyde dehydrogenase small subunit |
|---|---|
| MTBC0 PGAP re-annotation | (2Fe-2S)-binding protein |
| Revised (this work) | (2Fe-2S)-binding protein. Pfam: Fer2 (PF00111.33), Fer2_2 (PF01799.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53709
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable carbon monoxyde dehydrogenase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | coxS |
| eggNOG description | 2Fe-2S -binding domain |
| Orthologous group | COG2080 |
| EC number |
EC 1.2.5.3
|
| KEGG orthology |
K03518
|
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 | 0.482 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (213) · 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 |
|---|---|---|---|---|
Fer2 | PF00111.33 | 5.7e-08 | 6–53 | 2Fe-2S iron-sulfur cluster binding domain |
Fer2_2 | PF01799.26 | 5.6e-31 | 73–147 | [2Fe-2S] binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0373c (carbon monoxyde dehydrogenase large subunit), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0373c |
carbon monoxyde dehydrogenase large subunit | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:773 coexpression:577 experimental:928 textmining:895 |
Rv0375c |
carbon monoxyde dehydrogenase medium subunit | 999 | 999 ctx | neighborhood:869 cooccurence:773 coexpression:440 experimental:928 textmining:895 |
Rv0372c hyp |
hypothetical protein | 974 | 972 ctx | neighborhood:861 cooccurence:752 |
Rv0371c hyp |
hypothetical protein | 971 | 968 ctx | neighborhood:861 cooccurence:756 |
Rv0376c hyp |
hypothetical protein | 961 | 958 ctx | neighborhood:782 cooccurence:767 |
Rv0370c |
oxidoreductase | 896 | 891 ctx | neighborhood:861 |
Rv0368c hyp |
hypothetical protein | 870 | 870 ctx | neighborhood:760 cooccurence:452 |
Rv0369c |
membrane oxidoreductase | 841 | 841 ctx | neighborhood:760 |
Rv0377 |
HTH-type transcriptional regulator | 757 | 757 ctx | neighborhood:719 |
Rv0365c hyp |
hypothetical protein | 677 | 677 ctx | neighborhood:676 |
Rv0367c hyp |
hypothetical protein | 409 | 409 ctx | neighborhood:409 |
Rv0408 pta |
phosphate acetyltransferase | 413 | 171 |
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: carbon monoxyde dehydrogenase small subunit
- MTBC0 PGAP product: (2Fe-2S)-binding protein
- Pfam (hmmscan --cut_ga): Fer2 PF00111.33 (E=6e-08), Fer2_2 PF01799.26 (E=6e-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_214888.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fer2 (PF00111.33), Fer2_2 (PF01799.26)
- 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
COG2080 - Curated reference: UniProt O53709 (TrEMBL, unreviewed; 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 —
12 functional partner(s); context anchor
Rv0373c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000394|Rv0374c| MQVNMTVNGEPVTAEVEPRMLLVHFLRDQLRLTGTHWGCDTSNCGTCVVEVDGVPVKSCTMLAVMASGHSIRTVEGLAGPDGQLDPVQEGFMRCHGLQCGFCTPGMLITARALLDRNPDPDEQTIREAISGQICRCTGYTTIVRSIQWAAAHQTVKAQS