Rv1865c Family assigned · medium auto-curated
H37Rv Rv1865c · MTBC0 mtbc0_001978 ·
286 aa · 2130145–2131005 (-) ·
RefSeq NP_216381.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | short-chain type dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | SDR family oxidoreductase |
| Revised (this work) | SDR family oxidoreductase. Pfam: adh_short (PF00106.32), 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 |
P95150
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable short-chain type dehydrogenase |
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 |
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 | 0.226 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
adh_short | PF00106.32 | 7.3e-45 | 18–199 | short chain dehydrogenase |
adh_short_C2 | PF13561.13 | 1.9e-36 | 25–228 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0927c (oxidoreductase), high confidence from genomic context alone (score 785 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1864c hyp |
hypothetical protein | 840 | 840 ctx | neighborhood:834 |
Rv0927c |
oxidoreductase | 790 | 785 ctx | cooccurence:755 |
Rv1863c |
integral membrane protein | 781 | 781 ctx | neighborhood:781 |
Rv3530c |
oxidoreductase | 776 | 768 ctx | cooccurence:736 |
Rv1714 |
oxidoreductase | 738 | 731 ctx | cooccurence:695 |
Rv2509 cmrA |
short-chain type dehydrogenase/reductase | 527 | 527 ctx | cooccurence:527 |
Rv1866 hyp |
hypothetical protein | 518 | 518 ctx | neighborhood:511 |
Rv1867 hyp |
hypothetical protein | 426 | 414 | |
Rv3549c |
short-chain type dehydrogenase/reductase | 414 | 393 | |
Rv3485c |
short-chain type dehydrogenase/reductase | 412 | 389 | |
Rv2750 |
dehydrogenase | 410 | 388 | |
Rv2766c |
short-chain type dehydrogenase/reductase | 408 | 386 | |
Rv0769 |
oxidoreductase | 408 | 386 | |
Rv0687 |
NAD-dependent oxidoreductase | 408 | 385 | |
Rv3559c |
oxidoreductase | 406 | 383 |
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: short-chain type dehydrogenase
- MTBC0 PGAP product: SDR family oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=7e-45), adh_short_C2 PF13561.13 (E=2e-36)
- (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_216381.1)
- Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), 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 P95150 (TrEMBL, unreviewed; 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 —
15 functional partner(s); context anchor
Rv0927c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001978|Rv1865c| MPGRTSIGVKIRDKVQDKVIAITGGARGIGLATAAALHNLGAKVAIGDIDEAMAKESGADLDLDMYGKLDVTDPDSFSGFLDAVERQLGPIDVLVNNAGIMPVGRIVDEPDPVTRRILDINVYGVILGSKLAAQRMVPRGRGHVINVASLAGEIYAVGVATYCASKHAVVAFTDSARLEYRSAGVKFSMVLPSFVNTELIAGTGGIKGFKNAEPADIADAIVGLIVHPKPRVRVTKAAGSMIVAQRFMPRQVSEGLNRLLGGEHVFTDDVDMEKRRTYEARARGEE