ctaC Family assigned · medium auto-curated
H37Rv Rv2200c · MTBC0 mtbc0_002336 ·
363 aa · 2489817–2490908 (-) ·
RefSeq NP_216716.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytochrome C oxidase subunit II |
|---|---|
| MTBC0 PGAP re-annotation | cytochrome c oxidase subunit II |
| Revised (this work) | Cytochrome c oxidase subunit II. Pfam: COX2 (PF00116.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP69
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cytochrome c oxidase subunit 2 |
| EC (curated) |
EC 7.1.1.9
|
| Curated function | Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B) (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | ctaC |
| eggNOG description | cytochrome C oxidase (Subunit |
| Orthologous group | COG1622 |
| EC number |
EC 1.9.3.1
|
| KEGG orthology |
K02275
|
| KEGG pathways |
map00190, map01100
|
| KEGG modules |
M00155
|
| Gene Ontology (72) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0005887, GO:0006091, GO:0006119, GO:0006139, GO:0006163, GO:0006725, GO:0006753, GO:0006793 +60 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 | 0.189 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
COX2 | PF00116.27 | 5.2e-13 | 235–311 | Cytochrome C oxidase subunit II, periplasmic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ctaD (cytochrome C oxidase cytochrome 1), 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 ctx | cooccurence:773 coexpression:911 experimental:999 database:984 textmining:960 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 999 | 1000 ctx | cooccurence:637 coexpression:401 experimental:999 textmining:850 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 999 | 1000 ctx | cooccurence:627 coexpression:445 experimental:999 textmining:889 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 999 | 1000 ctx | neighborhood:882 cooccurence:611 experimental:999 textmining:902 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 999 | 1000 ctx | cooccurence:718 coexpression:857 experimental:999 textmining:846 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 999 | 1000 ctx | cooccurence:774 coexpression:866 experimental:999 database:984 textmining:968 |
Rv2876 |
transmembrane protein | 999 | 999 | experimental:999 |
Rv1451 ctaB |
protoheme IX farnesyltransferase | 999 | 994 ctx | cooccurence:770 coexpression:751 database:900 textmining:853 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 979 | 973 | coexpression:859 experimental:771 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 974 | 967 | coexpression:862 experimental:771 |
Rv3145 nuoA |
NADH-quinone oxidoreductase subunit A | 950 | 926 | coexpression:690 experimental:771 |
Rv2782c pepR |
zinc protease | 930 | 923 | experimental:919 |
Rv3584 lpqE |
lipoprotein LpqE | 919 | 919 | experimental:902 |
Rv1304 atpB |
ATP synthase subunit A | 913 | 886 | coexpression:886 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 900 | 878 | coexpression:484 experimental:773 |
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 subunit II
- MTBC0 PGAP product: cytochrome c oxidase subunit II
- Pfam (hmmscan --cut_ga): COX2 PF00116.27 (E=5e-13)
- (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_216716.1)
- Domains: Pfam-A via hmmscan --cut_ga — COX2 (PF00116.27)
- 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
COG1622 - Curated reference: UniProt P9WP69 (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 —
103 functional partner(s); context anchor
ctaD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002336|Rv2200c|ctaC MTPRGPGRLQRLSQCRPQRGSGGPARGLRQLALAAMLGALAVTVSGCSWSEALGIGWPEGITPEAHLNRELWIGAVIASLAVGVIVWGLIFWSAVFHRKKNTDTELPRQFGYNMPLELVLTVIPFLIISVLFYFTVVVQEKMLQIAKDPEVVIDITSFQWNWKFGYQRVNFKDGTLTYDGADPERKRAMVSKPEGKDKYGEELVGPVRGLNTEDRTYLNFDKVETLGTSTEIPVLVLPSGKRIEFQMASADVIHAFWVPEFLFKRDVMPNPVANNSVNVFQIEEITKTGAFVGHCAEMCGTYHSMMNFEVRVVTPNDFKAYLQQRIDGKTNAEALRAINQPPLAVTTHPFDTRRGELAPQPVG