cyp136 Resolved · high auto-curated
H37Rv Rv3059 · MTBC0 mtbc0_003251 ·
492 aa · 3440788–3442266 (+) ·
RefSeq NP_217575.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytochrome P450 Cyp136 |
|---|---|
| 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 |
P9WPM7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative cytochrome P450 136 |
| EC (curated) |
EC 1.14.-.-
|
UniProt still lists this protein as Putative cytochrome P450 136; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | cyp136A2 |
| eggNOG description | cytochrome p450 |
| Orthologous group | COG2124 |
| Gene Ontology (13) |
GO:0003674, GO:0003824, GO:0006629, GO:0008150, GO:0008152, GO:0008202, GO:0016125, GO:0016491, GO:0044238, GO:0055114, GO:0071704, GO:1901360 +1 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 | 0.391 · 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 |
|---|---|---|---|---|
p450 | PF00067.28 | 1.7e-64 | 62–466 | Cytochrome P450 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3057c (short chain alcohol dehydrogenase/reductase), high confidence from genomic context alone (score 767 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3800c pks13 |
polyketide synthase | 943 | 938 | experimental:891 |
Rv2380c mbtE |
peptide synthetase | 809 | 800 | experimental:689 |
Rv1937 |
oxygenase | 813 | 786 | experimental:478 |
Rv3057c |
short chain alcohol dehydrogenase/reductase | 767 | 767 ctx | neighborhood:725 |
Rv3058c |
TetR family transcriptional regulator | 755 | 754 ctx | neighborhood:751 |
Rv1629 polA |
DNA polymerase I | 709 | 690 | database:638 |
Rv0719 rplF |
50S ribosomal protein L6 | 690 | 690 | experimental:412 database:493 |
Rv1777 cyp144 |
cytochrome P450 Cyp144 | 850 | 682 ctx | cooccurence:680 textmining:550 |
Rv2946c pks1 |
polyketide synthase | 715 | 680 | experimental:460 |
Rv3554 fdxB |
electron transfer protein FdxB | 703 | 666 | |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 681 | 661 | experimental:460 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 694 | 660 | |
Rv1527c pks5 |
polyketide synthase | 693 | 660 | |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 692 | 658 | |
Rv2048c pks12 |
polyketide synthase | 692 | 658 |
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 Cyp136
- MTBC0 PGAP product: cytochrome P450
- Pfam (hmmscan --cut_ga): p450 PF00067.28 (E=2e-64)
- (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_217575.1)
- 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 P9WPM7 (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 —
121 functional partner(s); context anchor
Rv3057c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003251|Rv3059|cyp136 MATIHPPAYLLDQAKRRFTPSFNNFPGMSLVEHMLLNTKFPEKKLAEPPPGSGLKPVVGDAGLPILGHMIEMLRGGPDYLMFLYKTKGPVVFGDSAVLPGVAALGPDAAQVIYSNRNKDYSQQGWVPVIGPFFHRGLMLLDFEEHMFHRRIMQEAFVRSRLAGYLEQMDRVVSRVVADDWVVNDARFLVYPAMKALTLDIASMVFMGHEPGTDHELVTKVNKAFTITTRAGNAVIRTSVPPFTWWRGLRARELLENYFTARVKERREASGNDLLTVLCQTEDDDGNRFSDADIVNHMIFLMMAAHDTSTSTATTMAYQLAAHPEWQQRCRDESDRHGDGPLDIESLEQLESLDLVMNESIRLVTPVQWAMRQTVRDTELLGYYLPKGTNVIAYPGMNHRLPEIWTDPLTFDPERFTEPRNEHKRHRYAFTPFGGGVHKCIGMVFGQLEIKTILHRLLRRYRLELSRPDYQPRWDYSAMPIPMDGMPIVLRPR