cydA Family assigned · medium auto-curated
H37Rv Rv1623c · MTBC0 - ·
485 aa · 1824430–1825887 (-) ·
RefSeq YP_177824.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytochrome D ubiquinol oxidase subunit I CydA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Cytochrome D ubiquinol oxidase subunit I CydA. Pfam: Cyt_bd_oxida_I (PF01654.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
L7N662
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable integral membrane cytochrome D ubiquinol oxidase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | cydA |
| eggNOG description | ubiquinol oxidase (Subunit I) |
| Orthologous group | COG1271 |
| EC number |
EC 1.10.3.14
|
| KEGG orthology |
K00425
|
| KEGG pathways |
map00190, map01100, map02020
|
| KEGG modules |
M00153
|
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 | 0.4 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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_bd_oxida_I | PF01654.23 | 1.1e-156 | 6–460 | Cytochrome bd terminal oxidase subunit I |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cydB (cytochrome D ubiquinol oxidase subunit II CydB), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1622c cydB |
cytochrome D ubiquinol oxidase subunit II CydB | 999 | 1000 ctx | neighborhood:841 cooccurence:774 coexpression:976 experimental:999 database:540 textmining:966 |
Rv1621c cydD |
cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydD | 999 | 991 ctx | neighborhood:731 cooccurence:746 coexpression:877 textmining:918 |
Rv1620c cydC |
cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydC | 998 | 974 ctx | neighborhood:756 cooccurence:497 coexpression:807 textmining:934 |
Rv1624c |
membrane protein | 781 | 781 ctx | neighborhood:768 |
Rv1625c cya |
adenylate cyclase | 534 | 534 ctx | neighborhood:527 |
Rv3601c panD |
aspartate 1-decarboxylase | 494 | 446 | coexpression:446 |
Rv0558 menH |
demethylmenaquinone methyltransferase | 495 | 435 ctx | cooccurence:421 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 411 | 389 | |
Rv3239c |
transmembrane transport protein | 417 | 335 | |
Rv3728 |
membrane protein | 414 | 332 | |
Rv1854c ndh |
NADH dehydrogenase | 505 | 266 | |
Rv1161 narG |
nitrate reductase subunit alpha | 545 | 160 | textmining:481 |
Rv1736c narX |
nitrate reductase-like protein NarX | 428 | 160 | |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 473 | 138 | textmining:414 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 476 | 120 | textmining:429 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): cytochrome D ubiquinol oxidase subunit I CydA
- Pfam (hmmscan --cut_ga): Cyt_bd_oxida_I PF01654.23 (E=1e-156)
- (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 YP_177824.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cyt_bd_oxida_I (PF01654.23)
- 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
COG1271 - Curated reference: UniProt L7N662 (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 —
29 functional partner(s); context anchor
cydB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1623c|cydA MNVVDISRWQFGITTVYHFIFVPLTIGLAPLIAVMQTLWVVTDNPAWYRLTKFFGKLFLINFAIGVATGIVQEFQFGMNWSEYSRFVGDVFGAPLAMEGLAAFFFESTFIGLWIFGWNRLPRLVHLACIWIVAIAVNVSAFFIIAANSFMQHPVGAHYNPTTGRAELSSIVVLLTNNTAQAAFTHTVSGALLTAGTFVAAVSAWWLVRSSTTHADSDTQAMYRPATILGCWVALAATAGLLFTGDHQGKLMFQQQPMKMASAESLCDTQTDPNFSVLTVGRQNNCDSLTRVIEVPYVLPFLAEGRISGVTLQGIRDLQQEYQQRFGPNDYRPNLFVTYWSFRMMIGLMAIPVLFALIALWLTRGGQIPNQRWFSWLALLTMPAPFLANSAGWVFTEMGRQPWVVVPNPTGDQLVRLTVKAGVSDHSATVVATSLLMFTLVYAVLAVIWCWLLKRYIVEGPLEHDAEPAAHGAPRDDEVAPLSFAY