Rv2953 Resolved · high auto-curated
H37Rv Rv2953 · MTBC0 mtbc0_003135 ·
418 aa · 3326454–3327710 (+) ·
RefSeq NP_217469.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | trans-acting enoyl reductase |
|---|---|
| MTBC0 PGAP re-annotation | trans-acting enoyl reductase |
| Revised (this work) | Trans-acting enoyl reductase. Pfam: Sacchrp_dh_NADP (PF03435.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGV5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Trans-acting enoyl reductase |
| EC (curated) |
EC 1.3.1.-
|
| Curated function | Involved in the reduction of the double bond between C-4 and C-5 during phthiocerol dimycocerosates (DIM A) and glycosylated phenolphthiocerol dimycocerosates (PGL) biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | LYS1 |
| eggNOG description | Involved in the reduction of the double bond between C-4 and C-5 during phthiocerol dimycocerosates (DIM A) and glycosylated phenolphthiocerol dimycocerosates (PGL) biosynthesis |
| Orthologous group | COG3268 |
| KEGG orthology |
K12445
|
| Gene Ontology (36) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006629, GO:0006643, GO:0006664, GO:0008150, GO:0008152, GO:0008610, GO:0009058, GO:0009247 +24 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 | 0.364 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Sacchrp_dh_NADP | PF03435.25 | 8.2e-08 | 10–135 | Saccharopine dehydrogenase NADP binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2952 (phthiotriol/phenolphthiotriol dimycocerosates methyltransferase), high confidence from genomic context alone (score 923 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2952 |
phthiotriol/phenolphthiotriol dimycocerosates methyltransferase | 945 | 923 ctx | neighborhood:724 coexpression:733 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 963 | 730 ctx | neighborhood:469 database:500 textmining:870 |
Rv0241c htdX |
3-hydroxyacyl-thioester dehydratase HtdX | 409 | 408 | |
Rv3854c ethA |
monooxygenase EthA | 544 | 303 | |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 406 | 224 | |
Rv1254 |
acyltransferase | 530 | 81 | textmining:510 |
Rv1484 inhA |
NADH-dependent enoyl-[ACP | 795 | 57 | textmining:792 |
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 444 | 54 | textmining:437 |
Rv2960c hyp |
hypothetical protein | 630 | 46 | textmining:629 |
Rv2956 hyp |
hypothetical protein | 513 | 46 | textmining:511 |
Rv3060c |
GntR family transcriptional regulator | 511 | 41 | textmining:511 |
Rv0854 hyp |
hypothetical protein | 443 | 41 | textmining:443 |
Rv2382c mbtC |
polyketide synthetase | 414 | 41 | textmining:414 |
Rv2961 |
transposase | 403 | 41 | textmining:403 |
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: trans-acting enoyl reductase
- MTBC0 PGAP product: trans-acting enoyl reductase
- Pfam (hmmscan --cut_ga): Sacchrp_dh_NADP PF03435.25 (E=8e-08)
- (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_217469.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sacchrp_dh_NADP (PF03435.25)
- 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
COG3268 - Curated reference: UniProt P9WGV5 (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 —
14 functional partner(s); context anchor
Rv2952 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003135|Rv2953| MSPAEREFDIVLYGATGFSGKLTAEHLAHSGSTARIALAGRSSERLRGVRMMLGPNAADWPLILADASQPLTLEAMAARAQVVLTTVGPYTRYGLPLVAACAKAGTDYADLTGELMFCRNSIDLYHKQAADTGARIILACGFDSIPSDLNVYQLYRRSVEDGTGELCDTDLVLRSFSQRWVSGGSVATYSEAMRTASSDPEARRLVTDPYTLTTDRGAEPELGAQPDFLRRPGRDLAPELAGFWTGGFVQAPFNTRIVRRSNALQEWAYGRRFRYSETMSLGKSMAAPILAAAVTGTVAGTIGLGNKYFDRLPRRLVERVTPKPGTGPSRKTQERGHYTFETYTTTTTGARYRATFAHNVDAYKSTAVLLAQSGLALALDRDRLAELRGVLTPAAAMGDALLARLPGAGVVMGTTRLS