ctaB Resolved · high auto-curated
H37Rv Rv1451 · MTBC0 mtbc0_001553 ·
308 aa · 1644631–1645557 (+) ·
RefSeq NP_215967.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | protoheme IX farnesyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | heme o synthase |
| Revised (this work) | Heme o synthase. Pfam: UbiA (PF01040.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFR7
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Protoheme IX farnesyltransferase |
| EC (curated) |
EC 2.5.1.141
|
| Curated function | Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | ctaB |
| eggNOG description | Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group |
| Orthologous group | COG0109 |
| EC number |
EC 2.5.1.141
|
| KEGG orthology |
K02257
|
| KEGG pathways |
map00190, map00860, map01100, map01110, map04714
|
| KEGG modules |
M00154
|
| Gene Ontology (47) |
GO:0003674, GO:0003824, GO:0004311, GO:0004659, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006091, GO:0006725, GO:0006778, GO:0006779 +35 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 | 0.209 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 4 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 |
|---|---|---|---|---|
UbiA | PF01040.24 | 2.4e-60 | 35–282 | UbiA prenyltransferase family |
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 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 999 | 997 ctx | cooccurence:773 coexpression:820 database:900 textmining:928 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 999 | 997 ctx | cooccurence:773 coexpression:851 database:900 textmining:940 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 999 | 994 ctx | cooccurence:770 coexpression:751 database:900 textmining:853 |
Rv1456c |
antibiotic ABC transporter permease | 996 | 990 ctx | cooccurence:440 coexpression:664 experimental:471 database:900 textmining:646 |
Rv1485 hemZ |
ferrochelatase | 927 | 906 | database:900 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 863 | 677 ctx | cooccurence:618 textmining:595 |
Rv2235 |
transmembrane protein | 750 | 674 | coexpression:423 |
Rv1448c tal |
transaldolase | 630 | 607 ctx | neighborhood:544 |
Rv1449c tkt |
transketolase | 587 | 561 ctx | neighborhood:544 |
Rv1447c zwf2 |
glucose-6-phosphate 1-dehydrogenase | 563 | 536 ctx | neighborhood:533 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 669 | 531 | coexpression:467 |
Rv1444c hyp |
hypothetical protein | 523 | 523 ctx | neighborhood:523 |
Rv3339c icd1 |
isocitrate dehydrogenase | 538 | 512 | coexpression:512 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 658 | 508 ctx | cooccurence:430 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 724 | 491 ctx | cooccurence:423 textmining:480 |
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: protoheme IX farnesyltransferase
- MTBC0 PGAP product: heme o synthase
- Pfam (hmmscan --cut_ga): UbiA PF01040.24 (E=2e-60)
- (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_215967.1)
- Domains: Pfam-A via hmmscan --cut_ga — UbiA (PF01040.24)
- 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
COG0109 - Curated reference: UniProt P9WFR7 (SwissProt, reviewed; Inferred from homology)
- 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 —
46 functional partner(s); context anchor
ctaD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001553|Rv1451|ctaB MNVRGRVAPRRVTGRAMSTLLAYLALTKPRVIELLLVTAIPAMLLADRGAIHPLLMLNTLVGGMMAAAGANTLNCVADADIDKVMKRTARRPLAREAVPTRNALALGLTLTVISFFWLWCATNLLAGVLALVTVAFYVFVYTLWLKRRTSQNVVWGGAAGCMPVMIGWSAITGTIAWPALAMFAIIFFWTPPHTWALAMRYKQDYQVAGVPMLPAVATERQVTKQILIYTWLTVAATLVLALATSWLYGAVALVAGGWFLTMAHQLYAGVRAGEPVRPLRLFLQSNNYLAVVFCALAVDSVIALPTLH