Rv3548c Family assigned · medium auto-curated
H37Rv Rv3548c · MTBC0 mtbc0_003765 ·
304 aa · 4011059–4011973 (-) ·
RefSeq NP_218065.1
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), 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 |
P71853
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 |
| Gene Ontology (62) |
GO:0003674, GO:0003824, GO:0004303, GO:0005488, GO:0005515, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005777, GO:0006066, GO:0006629 +50 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 | 0.228 · 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 | 1.6e-41 | 7–215 | short chain dehydrogenase |
KR | PF08659.17 | 1.2e-13 | 9–185 | KR domain |
adh_short_C2 | PF13561.13 | 5.5e-34 | 13–260 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3549c (short-chain type dehydrogenase/reductase), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3549c |
short-chain type dehydrogenase/reductase | 988 | 983 ctx | neighborhood:853 coexpression:839 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 983 | 968 ctx | neighborhood:716 coexpression:785 textmining:498 |
Rv3538 |
dehydrogenase | 962 | 963 ctx | fusion:900 cooccurence:478 |
Rv3389c htdY |
3-hydroxyacyl-thioester dehydratase HtdY | 958 | 959 ctx | fusion:900 cooccurence:422 |
Rv3552 |
CoA-transferase subunit beta | 957 | 956 ctx | neighborhood:588 cooccurence:455 coexpression:800 |
Rv3551 |
CoA-transferase subunit alpha | 963 | 947 ctx | neighborhood:588 cooccurence:486 coexpression:770 |
Rv3553 |
oxidoreductase | 979 | 895 ctx | neighborhood:449 coexpression:751 textmining:812 |
Rv2524c fas |
fatty acid synthase | 826 | 800 | coexpression:506 experimental:475 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 802 | 759 ctx | cooccurence:615 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 756 | 744 ctx | cooccurence:592 |
Rv3485c |
short-chain type dehydrogenase/reductase | 682 | 682 ctx | cooccurence:679 |
Rv3573c fadE34 |
acyl-CoA dehydrogenase FadE34 | 724 | 656 ctx | cooccurence:475 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 701 | 638 ctx | cooccurence:441 |
Rv3541c chsH1 hyp |
hypothetical protein | 631 | 612 ctx | cooccurence:430 |
Rv0271c fadE6 |
acyl-CoA dehydrogenase FadE6 | 614 | 601 |
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=2e-41), KR PF08659.17 (E=1e-13), adh_short_C2 PF13561.13 (E=6e-34)
- (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_218065.1)
- 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 P71853 (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 —
104 functional partner(s); context anchor
Rv3549c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003765|Rv3548c| MGLVDGRVVIVTGAGGGIGRAHALAFAAEGARVVVNDIGVGLDGSPASGGSAAQDVVDEILAAGGQAVADGSDISDWDQAANLIQAAVETYGGVDVLVNNAGIVRDRMIANTSEEEFDAVIAVHLKGHFATMRHAASHWRGLSKAGKAPKDIDARIINTSSGAGLQGSVGQGNYSAAKAGIAALTLVGAAEMRRYGVTVNAIAPAARTRMTETVFAEMMAKPQEGFDAMAPENVSPLVVWLGSAESRDVTGKVFEVEGGIIRVAEGWAHGPQVDKGVKWDPAELGPVVSDLLAKSRPPVPVYGA