ccdA Resolved · medium auto-curated
H37Rv Rv0527 · MTBC0 - ·
259 aa · 617493–618272 (+) ·
RefSeq YP_177735.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytochrome C-type biogenesis protein CcdA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Cytochrome C-type biogenesis protein CcdA. |
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 |
L7N671
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible cytochrome C-type biogenesis protein CcdA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | ccdA |
| eggNOG description | cytochrome c biogenesis protein |
| Orthologous group | COG0785 |
| KEGG orthology |
K06196
|
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 | 0.826 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0526 (thioredoxin), high confidence from genomic context alone (score 991 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0526 |
thioredoxin | 996 | 991 ctx | neighborhood:882 cooccurence:464 coexpression:863 textmining:657 |
Rv0528 |
transmembrane protein | 988 | 984 ctx | neighborhood:833 coexpression:868 |
Rv0529 ccsA |
cytochrome C-type biogenesis protein CcsA | 995 | 982 ctx | neighborhood:833 coexpression:879 textmining:739 |
Rv0525 hyp |
hypothetical protein | 933 | 934 ctx | neighborhood:865 coexpression:530 |
Rv0524 hemL |
glutamate-1-semialdehyde 2,1-aminomutase | 970 | 915 ctx | neighborhood:865 textmining:661 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 719 | 719 | coexpression:651 |
Rv0530 hyp |
hypothetical protein | 612 | 613 ctx | neighborhood:609 |
Rv3673c |
membrane-anchored thioredoxin-like protein | 711 | 535 | textmining:404 |
Rv0523c hyp |
hypothetical protein | 531 | 531 ctx | neighborhood:531 |
Rv0514 |
transmembrane protein | 493 | 494 | coexpression:494 |
Rv0318c |
integral membrane protein | 463 | 464 | coexpression:462 |
Rv1677 dsbF |
lipoprotein DsbF | 463 | 436 | |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 447 | 427 | |
Rv2677c hemY |
protoporphyrinogen oxidase | 591 | 426 | |
Rv1586c |
phage integrase | 425 | 425 | coexpression:424 |
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 C-type biogenesis protein CcdA
- (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_177735.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0785 - Curated reference: UniProt L7N671 (TrEMBL, unreviewed; Predicted)
- 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 —
33 functional partner(s); context anchor
Rv0526 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0527|ccdA MTGFTEIAAVGPLLVAVGVCLLAGLVSFASPCVVPLVPGYLSYLAAVVGVDEQLPAGVVKPPVAARWRVAGSAALFVAGFTTVFVLGTVAVLGMTTTLITNQLLLQRVGGVLIVVMGLVFVGFIGALQRQARFTPRQLTSVAGAPVLGAVFALGWTPCLGPTLTGVITVASATEGASVARGIVLVIAYCLGLGIPFVLLAFGSAWAVAGLGWLRRHTRAIQIFGGALLIAVGAALVTGVWNDVVSWLRDAFVSDVRLPI