Rv1456c Resolved · high auto-curated
H37Rv Rv1456c · MTBC0 mtbc0_001558 ·
310 aa · 1651245–1652177 (-) ·
RefSeq NP_215972.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antibiotic ABC transporter permease |
|---|---|
| MTBC0 PGAP re-annotation | heme A synthase |
| Revised (this work) | Heme A synthase. Pfam: COX15-CtaA (PF02628.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53148
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable unidentified antibiotic-transport integral membrane ABC transporter |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | ctaA |
| eggNOG description | cytochrome oxidase assembly |
| Orthologous group | COG1612 |
| KEGG orthology |
K02259
|
| KEGG pathways |
map00190, map00860, map01100, map01110, map02020, map04714
|
| KEGG modules |
M00154
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
COX15-CtaA | PF02628.21 | 4.0e-10 | 17–291 | Cytochrome oxidase assembly protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ctaB (protoheme IX farnesyltransferase), high confidence from genomic context alone (score 990 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1451 ctaB |
protoheme IX farnesyltransferase | 996 | 990 ctx | cooccurence:440 coexpression:664 experimental:471 database:900 textmining:646 |
Rv1457c |
antibiotic ABC transporter permease | 998 | 989 ctx | neighborhood:767 cooccurence:568 database:900 textmining:870 |
Rv1458c |
antibiotic ABC transporter ATP-binding protein | 996 | 978 ctx | neighborhood:746 database:900 textmining:865 |
Rv2235 |
transmembrane protein | 927 | 905 ctx | cooccurence:495 coexpression:674 experimental:425 |
Rv1459c mptB |
alpha-(1->6)-mannopyranosyltransferase | 957 | 784 ctx | neighborhood:699 textmining:810 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 828 | 762 ctx | cooccurence:703 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 828 | 756 ctx | cooccurence:728 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 748 | 710 ctx | cooccurence:697 |
Rv1460 sufR |
transcriptional regulator | 662 | 662 ctx | neighborhood:662 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 658 | 658 ctx | cooccurence:656 |
Rv1462 sufD hyp |
hypothetical protein | 601 | 601 ctx | neighborhood:600 |
Rv1463 sufC |
ABC transporter ATP-binding protein | 601 | 601 ctx | neighborhood:600 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 693 | 600 ctx | cooccurence:494 |
Rv1464 csd |
cysteine desulfurase | 587 | 587 ctx | neighborhood:586 |
Rv1466 hyp |
hypothetical protein | 586 | 586 ctx | neighborhood:585 |
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: antibiotic ABC transporter permease
- MTBC0 PGAP product: heme A synthase
- Pfam (hmmscan --cut_ga): COX15-CtaA PF02628.21 (E=4e-10)
- (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_215972.1)
- Domains: Pfam-A via hmmscan --cut_ga — COX15-CtaA (PF02628.21)
- 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
COG1612 - Curated reference: UniProt O53148 (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 —
41 functional partner(s); context anchor
ctaB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001558|Rv1456c| MPYDRAVSPSLRVQRVIAAIVILTQGGIAVTGAIVRVTASGLGCPTWPQCFPGSFTPVVVAEVPRVHQAVEFGNRMVTFAVVIAAALAVLVVTRARRRTEVLAYAWLMPVSTVVQAMIGGITVRTGLLWWTVAIHLLASMTMVWLAVLLYVKIGQPDDGVVHELVVSPLRALTALSALNLAAVLVTGTLVTAAGPHAGDRSPSRTVPRLKVEITTLVHMHSSLLVAYLALLIGLGFGLLAVGATRAILVRLAVLLALVATQAAVGTTQYFTGVPAALVAIHVAGAAAVTAATAALWASMGERAQPQPLQR