cyp123 Resolved · high auto-curated
H37Rv Rv0766c · MTBC0 mtbc0_000815 ·
402 aa · 863288–864496 (-) ·
RefSeq NP_215280.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytochrome P450 Cyp123 |
|---|---|
| MTBC0 PGAP re-annotation | cytochrome P450 |
| Revised (this work) | Cytochrome P450. Pfam: p450 (PF00067.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPP5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative cytochrome P450 123 |
| EC (curated) |
EC 1.14.-.-
|
UniProt still lists this protein as Putative cytochrome P450 123; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | cyp123A3 |
| eggNOG description | cytochrome p450 |
| Orthologous group | COG2124 |
| Gene Ontology (38) |
GO:0003674, GO:0003824, GO:0004497, GO:0005575, GO:0005623, GO:0005886, GO:0006066, GO:0006629, GO:0006706, GO:0006707, GO:0008150, GO:0008152 +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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 7 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 7.67% of strains (11133) · clonal |
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 |
|---|---|---|---|---|
p450 | PF00067.28 | 2.9e-24 | 205–372 | Cytochrome P450 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cyp51 (lanosterol 14-alpha demethylase), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0764c cyp51 |
lanosterol 14-alpha demethylase | 999 | 994 ctx | neighborhood:882 cooccurence:690 coexpression:839 textmining:860 |
Rv0765c |
oxidoreductase | 982 | 983 ctx | neighborhood:882 coexpression:836 |
Rv0768 aldA |
aldehyde dehydrogenase AldA | 953 | 952 ctx | neighborhood:758 coexpression:807 |
Rv0762c hyp |
hypothetical protein | 952 | 952 ctx | neighborhood:882 coexpression:431 |
Rv3800c pks13 |
polyketide synthase | 943 | 938 | experimental:891 |
Rv0763c |
ferredoxin | 931 | 928 ctx | neighborhood:882 |
Rv2776c |
oxidoreductase | 920 | 916 ctx | fusion:740 |
Rv0767c |
HTH-type transcriptional regulator | 914 | 914 ctx | neighborhood:881 |
Rv0770 |
oxidoreductase | 895 | 895 ctx | neighborhood:677 coexpression:687 |
Rv2380c mbtE |
peptide synthetase | 809 | 800 | experimental:689 |
Rv0769 |
oxidoreductase | 795 | 795 ctx | neighborhood:731 |
Rv1937 |
oxygenase | 814 | 787 | experimental:478 |
Rv0771 |
4-carboxymuconolactone decarboxylase | 790 | 784 ctx | neighborhood:677 |
Rv0761c adhB |
alcohol dehydrogenase B | 778 | 776 ctx | neighborhood:774 |
Rv1175c fadH |
NADPH dependent 2,4-dienoyl-CoA reductase FadH | 759 | 745 ctx | neighborhood:522 database:485 |
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 P450 Cyp123
- MTBC0 PGAP product: cytochrome P450
- Pfam (hmmscan --cut_ga): p450 PF00067.28 (E=3e-24)
- (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_215280.1)
- Domains: Pfam-A via hmmscan --cut_ga — p450 (PF00067.28)
- 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
COG2124 - Curated reference: UniProt P9WPP5 (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 —
136 functional partner(s); context anchor
cyp51 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000815|Rv0766c|cyp123 MTVRVGDPELVLDPYDYDFHEDPYPYYRRLRDEAPLYRNEERNFWAVSRHHDVLQGFRDSTALSNAYGVSLDPSSRTSEAYRVMSMLAMDDPAHLRMRTLVSKGFTPRRIRELEPQVLELARIHLDSALQTESFDFVAEFAGKLPMDVISELIGVPDTDRARIRALADAVLHREDGVADVPPPAMAASIELMRYYADLIAEFRRRPANNLTSALLAAELDGDRLSDQEIMAFLFLMVIAGNETTTKLLANAVYWAAHHPGQLARVFADHSRIPMWVEETLRYDTSSQILARTVAHDLTLYDTTIPEGEVLLLLPGSANRDDRVFDDPDDYRIGREIGCKLVSFGSGAHFCLGAHLARMEARVALGALLRRIRNYEVDDDNVVRVHSSNVRGFAHLPISVQAR