Rv2449c Family assigned · medium auto-curated
H37Rv Rv2449c · MTBC0 mtbc0_002608 ·
419 aa · 2774561–2775820 (-) ·
RefSeq NP_216965.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | trans-acting enoyl reductase |
|---|---|
| MTBC0 PGAP re-annotation | trans-acting enoyl reductase family protein |
| Revised (this work) | Trans-acting enoyl reductase family protein. 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 |
O53176
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative trans-acting enoyl reductase Rv2449c |
| EC (curated) |
EC 1.3.1.-
|
UniProt still lists this protein as Putative trans-acting enoyl reductase Rv2449c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | LYS1 |
| eggNOG description | Saccharopine dehydrogenase |
| Orthologous group | COG3268 |
| KEGG orthology |
K12445
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.45 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 6 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 | 2.0e-11 | 10–136 | Saccharopine dehydrogenase NADP binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpfE (resuscitation-promoting factor RpfE), medium confidence from genomic context alone (score 659 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2450c rpfE |
resuscitation-promoting factor RpfE | 659 | 659 ctx | neighborhood:596 |
Rv2448c valS |
valine--tRNA ligase | 608 | 609 ctx | neighborhood:599 |
Rv2447c folC |
folylpolyglutamate synthase FolC | 603 | 603 ctx | neighborhood:599 |
Rv2446c |
integral membrane protein | 599 | 599 ctx | neighborhood:599 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 523 | 523 ctx | neighborhood:523 |
Rv0241c htdX |
3-hydroxyacyl-thioester dehydratase HtdX | 420 | 420 ctx | cooccurence:403 |
Rv2451 hyp |
hypothetical protein | 402 | 402 ctx | neighborhood:402 |
Rv1484 inhA |
NADH-dependent enoyl-[ACP | 427 | 57 | textmining:418 |
Rv1544 |
ketoacyl reductase | 603 | 55 | textmining:598 |
Rv2928 tesA |
thioesterase TesA | 431 | 41 | textmining:431 |
Rv2382c mbtC |
polyketide synthetase | 414 | 41 | textmining:414 |
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 family protein
- Pfam (hmmscan --cut_ga): Sacchrp_dh_NADP PF03435.25 (E=2e-11)
- (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_216965.1)
- 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 O53176 (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 —
11 functional partner(s); context anchor
rpfE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002608|Rv2449c| MTATPREFDIVLYGATGFVGKLTAEYLARAGGDARIALAGRSTQRVLAVREALGESAQTWPILTADASLPSTLQAMAARAQVVVTTVGPYTRYGLPLVAACAAAGTDYADLTGEPMFMRNSIDLYHKQAADTGARIVHACGFDSVPSDLSVYALYHAAREDGAGELTDTNCVVRSFKGGFSGGTIASMLEVLSTASNDPDARRQLSDPYMLSPDRGAEPELGPQPDLPSRRGRRLAPELAGVWTAGFIMAPTNTRIVRRSNALLDWAYGRRFRYSETMSVGSTVLAPVVSVVGGGVGNAMFGLASRYIRLLPRGLVKRVVPKPGTGPSAAARERGYYRIETYTTTTTGARYLARMAQDGDPGYKATSVLLGECGLALALDRDKLSDMRGVLTPAAAMGDALLERLPAAGVSLQTTRLAS