Rv3530c Family assigned · medium auto-curated
H37Rv Rv3530c · MTBC0 mtbc0_003747 ·
260 aa · 3990715–3991497 (-) ·
RefSeq NP_218047.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | SDR family oxidoreductase |
| Revised (this work) | SDR family 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 |
I6Y3S9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Dehydrogenase |
| Orthologous group | COG1028 |
| Gene Ontology (33) |
GO:0003674, GO:0003824, GO:0004799, GO:0006725, GO:0006807, GO:0006950, GO:0006979, GO:0008150, GO:0008152, GO:0008168, GO:0009987, GO:0016491 +21 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 | 0.802 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 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 | 1.4e-40 | 8–199 | short chain dehydrogenase |
KR | PF08659.17 | 1.7e-08 | 11–184 | KR domain |
adh_short_C2 | PF13561.13 | 7.3e-53 | 15–256 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3502c (3-oxoacyl-ACP reductase), high confidence from genomic context alone (score 769 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3529c hyp |
hypothetical protein | 996 | 996 ctx | neighborhood:881 fusion:487 cooccurence:630 coexpression:826 |
Rv3531c hyp |
hypothetical protein | 996 | 972 ctx | neighborhood:882 cooccurence:646 textmining:870 |
Rv2524c fas |
fatty acid synthase | 826 | 800 | coexpression:506 experimental:475 |
Rv3502c |
3-oxoacyl-ACP reductase | 768 | 769 ctx | cooccurence:766 |
Rv1865c |
short-chain type dehydrogenase | 776 | 768 ctx | cooccurence:736 |
Rv0945 |
oxidoreductase | 635 | 621 ctx | cooccurence:570 |
Rv3570c hsaA |
flavin-dependent monooxygenase oxygenase subunit HsaA | 585 | 585 | |
Rv1882c |
short-chain type dehydrogenase/reductase | 575 | 575 ctx | cooccurence:566 |
Rv2509 cmrA |
short-chain type dehydrogenase/reductase | 587 | 572 ctx | cooccurence:514 |
Rv1937 |
oxygenase | 604 | 557 | |
Rv0310c hyp |
hypothetical protein | 562 | 544 ctx | cooccurence:460 |
Rv3541c chsH1 hyp |
hypothetical protein | 552 | 533 | |
Rv2299c htpG |
chaperone protein HtpG | 539 | 520 | database:450 |
Rv3526 kshA |
3-ketosteroid-9-alpha-monooxygenase oxygenase subunit | 529 | 512 | |
Rv0073 |
glutamine ABC transporter ATP-binding protein | 532 | 510 | database:431 |
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 oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=1e-40), KR PF08659.17 (E=2e-08), adh_short_C2 PF13561.13 (E=7e-53)
- (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_218047.1)
- 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 I6Y3S9 (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 —
91 functional partner(s); context anchor
Rv3502c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003747|Rv3530c| MTGMLKRKVIVVSGVGPGLGTTLAHRCARDGADLVLAARSAERLDDVAKQIIDTGRRAVAVRTDITDDDDVSNLVQATLAAYGKADVLINNAFRVPSMKPLAGTTFEHIRDAIELSALGTLRLIQAFTPALAQSHGAIVNVNSMVIRHSQPKYGTYKMAKSVLLAMSHSLATELGEQGIRVNSVAPGYIWGDTLKSYFDHQAGKYGTTVDQIYQATAANSDLKRLPTEDEVASAILFLASDLASGITGQTLDVNCGEYHT