ctaD Family assigned · medium auto-curated
H37Rv Rv3043c · MTBC0 mtbc0_003235 ·
573 aa · 3424510–3426231 (-) ·
RefSeq NP_217559.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytochrome C oxidase cytochrome 1 |
|---|---|
| MTBC0 PGAP re-annotation | cytochrome c oxidase subunit I |
| Revised (this work) | Cytochrome c oxidase subunit I. Pfam: COX1 (PF00115.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP71
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable cytochrome c oxidase subunit 1 |
| EC (curated) |
EC 7.1.1.9
|
| Curated function | Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits 1-3 form the functional core of the enzyme complex. CO I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit 2 and heme A of subunit 1 to the bimetallic center formed by heme A3 and copper B (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | ctaD |
| eggNOG description | Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits 1- 3 form the functional core of the enzyme complex. CO I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit 2 and heme A of subunit 1 to the bimetallic center formed by heme A3 and copper B |
| Orthologous group | COG0843 |
| EC number |
EC 1.9.3.1
|
| KEGG orthology |
K02274
|
| KEGG pathways |
map00190, map01100
|
| KEGG modules |
M00155
|
| Gene Ontology (38) |
GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0006091, GO:0006810, GO:0006811, GO:0006812, GO:0008150, GO:0008152, GO:0009060, GO:0009987 +26 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 | 0.081 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 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 |
|---|---|---|---|---|
COX1 | PF00115.26 | 9.7e-163 | 40–483 | Cytochrome C and Quinol oxidase polypeptide I |
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:773 coexpression:911 experimental:999 database:984 textmining:960 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 999 | 1000 ctx | cooccurence:774 coexpression:875 experimental:999 database:984 textmining:964 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 999 | 1000 | experimental:999 textmining:919 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 999 | 1000 ctx | cooccurence:604 coexpression:858 experimental:999 textmining:762 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 999 | 1000 | coexpression:663 experimental:999 textmining:809 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 999 | 1000 | experimental:999 textmining:597 |
Rv2876 |
transmembrane protein | 999 | 999 | experimental:999 |
Rv1451 ctaB |
protoheme IX farnesyltransferase | 999 | 997 ctx | cooccurence:773 coexpression:820 database:900 textmining:928 |
Rv2468A hyp |
hypothetical protein | 997 | 997 | experimental:997 |
Rv0863 hyp |
hypothetical protein | 987 | 987 | experimental:987 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 981 | 975 | coexpression:858 experimental:794 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 973 | 966 | coexpression:804 experimental:794 |
Rv3584 lpqE |
lipoprotein LpqE | 924 | 924 | experimental:902 |
Rv3158 nuoN |
NADH-quinone oxidoreductase subunit N | 946 | 923 | coexpression:671 experimental:775 |
Rv2782c pepR |
zinc protease | 929 | 920 | experimental:917 |
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 cytochrome 1
- MTBC0 PGAP product: cytochrome c oxidase subunit I
- Pfam (hmmscan --cut_ga): COX1 PF00115.26 (E=1e-162)
- (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_217559.1)
- Domains: Pfam-A via hmmscan --cut_ga — COX1 (PF00115.26)
- 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
COG0843 - Curated reference: UniProt P9WP71 (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 —
106 functional partner(s); context anchor
ctaC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003235|Rv3043c|ctaD MTAEAPPLGELEAIRPYPARTGPKGSLVYKLITTTDHKMIGIMYCVACISFFFIGGLLALLMRTELAAPGLQFLSNEQFNQLFTMHGTIMLLFYATPIVFGFANLVLPLQIGAPDVAFPRLNAFSFWLFVFGATIGAAGFITPGGAADFGWTAYTPLTDAIHSPGAGGDLWIMGLIVAGLGTILGAVNMITTVVCMRAPGMTMFRMPIFTWNIMVTSILILIAFPLLTAALFGLAADRHLGAHIYDAANGGVLLWQHLFWFFGHPEVYIIALPFFGIVSEIFPVFSRKPIFGYTTLVYATLSIAALSVAVWAHHMFATGAVLLPFFSFMTYLIAVPTGIKFFNWIGTMWKGQLTFETPMLFSVGFMVTFLLGGLTGVLLASPPLDFHVTDSYFVVAHFHYVLFGTIVFATFAGIYFWFPKMTGRLLDERLGKLHFWLTFIGFHTTFLVQHWLGDEGMPRRYADYLPTDGFQGLNVVSTIGAFILGASMFPFVWNVFKSWRYGEVVTVDDPWGYGNSLEWATSCPPPRHNFTELPRIRSERPAFELHYPHMVERLRAEAHVGRHHDEPAMVTSS