qcrC Resolved · high auto-curated
H37Rv Rv2194 · MTBC0 mtbc0_002330 ·
280 aa · 2483560–2484402 (+) ·
RefSeq NP_216710.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ubiquinol-cytochrome C reductase cytochrome subunit C |
|---|---|
| MTBC0 PGAP re-annotation | cytochrome c |
| Revised (this work) | Cytochrome c. Pfam: Cytochrom_C (PF00034.27), Cytochrome_CBB3 (PF13442.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP35
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cytochrome bc1 complex cytochrome c subunit |
| EC (curated) |
EC 7.1.1.8
|
| Curated function | Cytochrome b subunit of the cytochrome bc1 complex, an essential component of the respiratory electron transport chain required for ATP synthesis. The bc1 complex catalyzes the oxidation of ubiquinol and the reduction of cytochrome c in the respiratory chain. The bc1 complex operates through a Q-cycle mechanism that couples electron transfer to generation of the proton gradient that drives ATP synthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | qcrC |
| eggNOG description | cytochrome C |
| Orthologous group | COG2010 |
| KEGG orthology |
K03889
|
| KEGG pathways |
map00190, map01100
|
| KEGG modules |
M00151
|
| Gene Ontology (14) |
GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0008150, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0040007, GO:0044425, GO:0044459 +2 more
|
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 | 0.712 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 |
|---|---|---|---|---|
Cytochrom_C | PF00034.27 | 4.4e-08 | 64–137 | Cytochrome c |
Cytochrome_CBB3 | PF13442.12 | 1.4e-08 | 163–235 | Cytochrome C oxidase, cbb3-type, subunit III |
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) |
|---|---|---|---|---|
Rv2200c ctaC |
cytochrome C oxidase subunit II | 999 | 1000 ctx | cooccurence:637 coexpression:401 experimental:999 textmining:850 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 999 | 1000 | experimental:999 textmining:919 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 999 | 1000 ctx | neighborhood:881 cooccurence:773 coexpression:816 experimental:999 database:900 textmining:933 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 999 | 1000 ctx | neighborhood:881 cooccurence:773 coexpression:929 experimental:999 database:900 textmining:965 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 999 | 1000 ctx | cooccurence:774 experimental:999 textmining:434 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 999 | 1000 ctx | neighborhood:822 cooccurence:559 coexpression:823 experimental:999 textmining:879 |
Rv2876 |
transmembrane protein | 999 | 999 | experimental:999 |
Rv0685 tuf |
elongation factor Tu | 941 | 931 | experimental:921 |
Rv3584 lpqE |
lipoprotein LpqE | 962 | 913 | experimental:902 textmining:592 |
Rv0432 sodC |
superoxide dismutase | 871 | 872 | experimental:870 |
Rv2468A hyp |
hypothetical protein | 870 | 870 | experimental:870 |
Rv0863 hyp |
hypothetical protein | 867 | 868 | experimental:848 |
Rv1162 narH |
nitrate reductase subunit beta | 859 | 811 | experimental:790 |
Rv1161 narG |
nitrate reductase subunit alpha | 854 | 801 | experimental:788 |
Rv1736c narX |
nitrate reductase-like protein NarX | 828 | 801 | experimental:788 |
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: ubiquinol-cytochrome C reductase cytochrome subunit C
- MTBC0 PGAP product: cytochrome c
- Pfam (hmmscan --cut_ga): Cytochrom_C PF00034.27 (E=4e-08), Cytochrome_CBB3 PF13442.12 (E=1e-08)
- (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_216710.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cytochrom_C (PF00034.27), Cytochrome_CBB3 (PF13442.12)
- 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
COG2010 - Curated reference: UniProt P9WP35 (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 —
104 functional partner(s); context anchor
ctaC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002330|Rv2194|qcrC MTKLGFTRSGGSKSGRTRRRLRRRLSGGVLLLIALTIAGGLAAVLTPTPQVAVADESSSALLRTGKQLFDTSCVSCHGANLQGVPDHGPSLIGVGEAAVYFQVSTGRMPAMRGEAQAPRKDPIFDEAQIDAIGAYVQANGGGPTVVRNPDGSIATQSLRGNDLGRGGDLFRLNCASCHNFTGKGGALSSGKYAPDLAPANEQQILTAMLTGPQNMPKFSNRQLSFEAKKDIIAYVKVATEARQPGGYLLGGFGPAPEGMAMWIIGMVAAIGLALWIGARS