Rv2199c Family assigned · medium auto-curated
H37Rv Rv2199c · MTBC0 mtbc0_002335 ·
139 aa · 2489390–2489809 (-) ·
RefSeq NP_216715.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytochrome c oxidase polypeptide 4 |
|---|---|
| MTBC0 PGAP re-annotation | cytochrome c oxidase subunit 4 |
| Revised (this work) | Cytochrome c oxidase subunit 4. Pfam: Cyt_c_ox_IV (PF12270.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP45
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable cytochrome c oxidase polypeptide 4 |
| EC (curated) |
EC 7.1.1.9
|
| Curated function | Part of cytochrome c oxidase, its function is unknown. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | ctaF |
| eggNOG description | Belongs to the cytochrome c oxidase bacterial subunit CtaF family |
| Orthologous group | 2D9MJ |
| 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 0 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 |
|---|---|---|---|---|
Cyt_c_ox_IV | PF12270.14 | 1.9e-50 | 1–137 | Cytochrome c oxidase subunit IV |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ctaC (cytochrome C oxidase subunit II), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 999 | 1000 | experimental:999 textmining:597 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 999 | 1000 ctx | neighborhood:882 cooccurence:611 experimental:999 textmining:902 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 999 | 1000 ctx | cooccurence:555 experimental:999 textmining:801 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 999 | 1000 ctx | cooccurence:774 experimental:999 textmining:434 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 999 | 1000 ctx | cooccurence:769 experimental:999 textmining:514 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 999 | 1000 ctx | cooccurence:768 coexpression:533 experimental:999 textmining:490 |
Rv2876 |
transmembrane protein | 999 | 999 | experimental:999 |
Rv0863 hyp |
hypothetical protein | 987 | 987 | experimental:987 |
Rv3584 lpqE |
lipoprotein LpqE | 898 | 895 | experimental:889 |
Rv0432 sodC |
superoxide dismutase | 871 | 872 | experimental:870 |
Rv2468A hyp |
hypothetical protein | 870 | 870 | experimental:870 |
Rv2468c hyp |
hypothetical protein | 829 | 829 | experimental:747 |
Rv0528 |
transmembrane protein | 763 | 763 ctx | cooccurence:761 |
Rv2197c |
transmembrane protein | 754 | 754 ctx | neighborhood:740 |
Rv2345 |
transmembrane protein | 750 | 751 | experimental:747 |
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: cytochrome c oxidase polypeptide 4
- MTBC0 PGAP product: cytochrome c oxidase subunit 4
- Pfam (hmmscan --cut_ga): Cyt_c_ox_IV PF12270.14 (E=2e-50)
- (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_216715.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cyt_c_ox_IV (PF12270.14)
- 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
2D9MJ - Curated reference: UniProt P9WP45 (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 —
72 functional partner(s); context anchor
ctaC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002335|Rv2199c| MHIEARLFEFVAAFFVVTAVLYGVLTSMFATGGVEWAGTTALALTGGMALIVATFFRFVARRLDSRPEDYEGAEISDGAGELGFFSPHSWWPIMVALSGSVAAVGIALWLPWLIAAGVAFILASAAGLVFEYYVGPEKH