Rv3085 Family assigned · medium auto-curated
H37Rv Rv3085 · MTBC0 mtbc0_003279 ·
276 aa · 3472284–3473114 (+) ·
RefSeq NP_217601.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase SadH |
|---|---|
| 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 |
P9WGP9
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Putative oxidoreductase SadH |
| EC (curated) |
EC 1.-.-.-
|
| Curated function | Required for maintaining the appropriate mycolic acid composition and permeability of the envelope on its exposure to acidic pH. |
UniProt still lists this protein as Putative oxidoreductase SadH; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Belongs to the short-chain dehydrogenases reductases (SDR) family |
| Orthologous group | COG4221 |
| Gene Ontology (13) |
GO:0008150, GO:0009268, GO:0009628, GO:0010447, GO:0040007, GO:0044110, GO:0044116, GO:0044117, GO:0044119, GO:0044403, GO:0044419, GO:0050896 +1 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 | 0.337 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.19% of strains (272) · clonal |
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 | 1.7e-47 | 7–198 | short chain dehydrogenase |
KR | PF08659.17 | 3.4e-13 | 10–174 | KR domain |
adh_short_C2 | PF13561.13 | 1.5e-33 | 13–215 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mymA (FAD-containing monooxygenase MymA), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3083 mymA |
FAD-containing monooxygenase MymA | 997 | 989 ctx | neighborhood:882 coexpression:860 textmining:803 |
Rv3084 lipR |
acetyl-hydrolase LipR | 997 | 983 ctx | neighborhood:882 coexpression:860 textmining:870 |
Rv3086 adhD |
alcohol dehydrogenase D | 991 | 959 ctx | neighborhood:721 coexpression:860 textmining:810 |
Rv3088 tgs4 |
diacyglycerol O-acyltransferase | 975 | 951 ctx | neighborhood:616 coexpression:860 textmining:510 |
Rv3089 fadD13 |
long chain-fatty-acid--CoA ligase FadD13 | 973 | 945 ctx | neighborhood:616 coexpression:863 textmining:542 |
Rv3087 |
diacyglycerol O-acyltransferase | 970 | 941 ctx | neighborhood:590 coexpression:862 textmining:511 |
Rv0233 nrdB |
ribonucleoside-diphosphate reductase subunit beta NrdB | 687 | 687 | coexpression:687 |
Rv0242c fabG4 |
3-oxoacyl-ACP reductase FabG | 680 | 681 ctx | cooccurence:672 |
Rv3549c |
short-chain type dehydrogenase/reductase | 674 | 674 ctx | cooccurence:665 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 658 | 657 ctx | neighborhood:602 |
Rv1714 |
oxidoreductase | 644 | 645 ctx | cooccurence:632 |
Rv1483 fabG1 |
3-oxoacyl-ACP reductase FabG | 535 | 536 ctx | cooccurence:526 |
Rv3502c |
3-oxoacyl-ACP reductase | 486 | 486 ctx | cooccurence:472 |
Rv3049c |
monooxygenase | 459 | 459 ctx | cooccurence:400 |
Rv0976c hyp |
hypothetical protein | 466 | 439 |
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 SadH
- MTBC0 PGAP product: SDR family NAD(P)-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=2e-47), KR PF08659.17 (E=3e-13), adh_short_C2 PF13561.13 (E=2e-33)
- (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_217601.1)
- 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
COG4221 - Curated reference: UniProt P9WGP9 (SwissProt, reviewed; Evidence at transcript 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 —
21 functional partner(s); context anchor
mymA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003279|Rv3085| MSSFEGKVAVITGAGSGIGRALALNLSEKRAKLALSDVDTDGLAKTVRLAQALGAQVKSDRLDVAEREAVLAHADAVVAHFGTVHQVYNNAGIAYNGNVDKSEFKDIERIIDVDFWGVVNGTKAFLPHVIASGDGHIVNISSLFGLIAVPGQSAYNAAKFAVRGFTEALRQEMLVARHPVKVTCVHPGGIKTAVARNATVADGEDQQTFAEFFDRRLALHSPEMAAKTIVNGVAKGQARVVVGLEAKAVDVLARIMGSSYQRLVAAGVAKFFPWAK