Rv1543 Family assigned · medium auto-curated
H37Rv Rv1543 · MTBC0 mtbc0_001650 ·
341 aa · 1754873–1755898 (+) ·
RefSeq NP_216059.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | SDR family NAD(P)-dependent oxidoreductase |
| Revised (this work) | SDR family NAD(P)-dependent oxidoreductase. Pfam: adh_short (PF00106.32), KR (PF08659.17), adh_short_C2 (PF13561.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGS1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized oxidoreductase Rv1543 |
| EC (curated) |
EC 1.-.-.-
|
UniProt still lists this protein as Uncharacterized oxidoreductase Rv1543; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Belongs to the short-chain dehydrogenases reductases (SDR) family |
| Orthologous group | COG1028 |
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, 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 | 1.001 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
adh_short | PF00106.32 | 1.1e-45 | 54–246 | short chain dehydrogenase |
KR | PF08659.17 | 5.5e-13 | 56–225 | KR domain |
adh_short_C2 | PF13561.13 | 5.4e-31 | 63–249 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1544 (ketoacyl reductase), high confidence from genomic context alone (score 967 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1544 |
ketoacyl reductase | 974 | 967 ctx | neighborhood:801 coexpression:813 |
Rv1546 hyp |
hypothetical protein | 792 | 792 ctx | neighborhood:685 |
Rv1545 hyp |
hypothetical protein | 745 | 745 ctx | neighborhood:739 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 748 | 739 | coexpression:734 |
Rv3734c tgs2 |
diacyglycerol O-acyltransferase | 941 | 731 ctx | cooccurence:720 textmining:791 |
Rv3740c |
diacyglycerol O-acyltransferase | 728 | 729 ctx | cooccurence:722 |
Rv0895 |
diacyglycerol O-acyltransferase | 831 | 713 ctx | cooccurence:699 textmining:437 |
Rv3480c |
diacyglycerol O-acyltransferase | 857 | 711 ctx | cooccurence:695 textmining:528 |
Rv2285 |
diacylglycerol acyltransferase | 826 | 707 ctx | cooccurence:690 textmining:433 |
Rv3088 tgs4 |
diacyglycerol O-acyltransferase | 775 | 658 ctx | cooccurence:656 |
Rv0242c fabG4 |
3-oxoacyl-ACP reductase FabG | 612 | 598 ctx | cooccurence:540 |
Rv3087 |
diacyglycerol O-acyltransferase | 686 | 591 ctx | cooccurence:570 |
Rv1882c |
short-chain type dehydrogenase/reductase | 583 | 583 ctx | cooccurence:573 |
Rv1760 |
diacylglycerol acyltransferase | 825 | 568 ctx | cooccurence:556 textmining:612 |
Rv1425 |
diacyglycerol O-acyltransferase | 769 | 548 ctx | cooccurence:532 textmining:511 |
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: oxidoreductase
- MTBC0 PGAP product: SDR family NAD(P)-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=1e-45), KR PF08659.17 (E=5e-13), adh_short_C2 PF13561.13 (E=5e-31)
- (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_216059.1)
- Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), KR (PF08659.17), adh_short_C2 (PF13561.13)
- 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
COG1028 - Curated reference: UniProt P9WGS1 (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 —
37 functional partner(s); context anchor
Rv1544 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001650|Rv1543| MNLGDLTNFVEKPLAAVSNIVNTPNSAGRYRPFYLRNLLDAVQGRNLNDAVKGKVVLITGGSSGIGAAAAKKIAEAGGTVVLVARTLENLENVANDIRAIRGNGGTAHVYPCDLSDMDAIAVMADQVLGDLGGVDILINNAGRSIRRSLELSYDRIHDYQRTMQLNYLGAVQLILKFIPGMRERHFGHIVNVSSVGVQTRAPRFGAYIASKAALDSLCDALQAETVHDNVRFTTVHMALVRTPMISPTTIYDKFPTLTPDQAAGVITDAIVHRPRRASSPFGQFAAVADAVNPAVMDRVRNRAFNMFGDSSAAKGSESQTDTSELDKRSETFVRATRGIHW