Rv1882c Family assigned · medium auto-curated
H37Rv Rv1882c · MTBC0 mtbc0_001996 ·
277 aa · 2150409–2151242 (-) ·
RefSeq NP_216398.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | short-chain type dehydrogenase/reductase |
|---|---|
| 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 |
O07749
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable short-chain type dehydrogenase/reductase |
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 | 0.669 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
adh_short | PF00106.32 | 1.2e-43 | 2–194 | short chain dehydrogenase |
adh_short_C2 | PF13561.13 | 2.3e-32 | 8–194 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cyp140 (cytochrome P450 Cyp140), high confidence from genomic context alone (score 772 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1883c hyp |
hypothetical protein | 866 | 866 ctx | neighborhood:844 |
Rv1880c cyp140 |
cytochrome P450 Cyp140 | 772 | 772 ctx | neighborhood:771 |
Rv1881c lppE |
lipoprotein LppE | 702 | 702 ctx | neighborhood:688 |
Rv1714 |
oxidoreductase | 698 | 699 ctx | cooccurence:688 |
Rv3485c |
short-chain type dehydrogenase/reductase | 689 | 690 ctx | cooccurence:673 |
Rv2766c |
short-chain type dehydrogenase/reductase | 681 | 682 ctx | cooccurence:675 |
Rv1884c rpfC |
resuscitation-promoting factor RpfC | 658 | 648 ctx | neighborhood:606 |
Rv1543 |
oxidoreductase | 583 | 583 ctx | cooccurence:573 |
Rv1885c |
chorismate mutase | 582 | 583 ctx | neighborhood:577 |
Rv1006 hyp |
hypothetical protein | 579 | 579 ctx | cooccurence:573 |
Rv3549c |
short-chain type dehydrogenase/reductase | 576 | 577 ctx | cooccurence:565 |
Rv3530c |
oxidoreductase | 575 | 575 ctx | cooccurence:566 |
Rv1886c fbpB |
diacylglycerol acyltransferase/mycolyltransferase Ag85B | 566 | 566 ctx | neighborhood:561 |
Rv2509 cmrA |
short-chain type dehydrogenase/reductase | 553 | 553 ctx | cooccurence:544 |
Rv0547c |
oxidoreductase | 552 | 552 ctx | cooccurence:542 |
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/reductase
- MTBC0 PGAP product: SDR family oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=1e-43), adh_short_C2 PF13561.13 (E=2e-32)
- (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_216398.1)
- 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 O07749 (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 —
22 functional partner(s); context anchor
cyp140 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001996|Rv1882c| MKAIFITGAGSGMGREGATLFHANGWRVGAIDRNEDGLAALRVQLGAERLWARAVDVTDKAALEGALADFCAGNVGGGLDMMWNNAGIGEGGWFEDVPYEAAVRVVDVNFKAVLTGAYAALPYLKKAPGSLMFSTSSSSGTYGMPRIAVYSATKHAVKGLTEALSVEWQRHGVRVADVLPGLIDTAILTSTRQHSDEGPYTISAEQIRAAAPKKGMFRLMPSSSVAEAAWRAYQHPTRLHWYVPRSIRWIDRLKGVSPEFVRRHIAKSLATLEPKRK