Rv3549c Family assigned · medium auto-curated
H37Rv Rv3549c · MTBC0 mtbc0_003766 ·
259 aa · 4011996–4012775 (-) ·
RefSeq NP_218066.1
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), Epimerase (PF01370.28), adh_short_C2 (PF13561.13), SDR (PF23441.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YCE1
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 | Dehydrogenase |
| 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 0 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 | 4.3e-43 | 17–191 | short chain dehydrogenase |
KR | PF08659.17 | 3.8e-05 | 19–172 | KR domain |
Epimerase | PF01370.28 | 1.9e-05 | 19–112 | NAD dependent epimerase/dehydratase family |
adh_short_C2 | PF13561.13 | 2.3e-52 | 26–245 | Enoyl-(Acyl carrier protein) reductase |
SDR | PF23441.1 | 6.3e-09 | 63–202 | SDR-like rossmann domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA20 (enoyl-CoA hydratase EchA20), high confidence from genomic context alone (score 985 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 995 | 985 ctx | neighborhood:787 cooccurence:422 coexpression:849 textmining:698 |
Rv3548c |
short-chain type dehydrogenase/reductase | 988 | 983 ctx | neighborhood:853 coexpression:839 |
Rv3552 |
CoA-transferase subunit beta | 984 | 983 ctx | neighborhood:787 cooccurence:593 coexpression:807 |
Rv3551 |
CoA-transferase subunit alpha | 983 | 981 ctx | neighborhood:787 cooccurence:584 coexpression:806 |
Rv3553 |
oxidoreductase | 982 | 955 ctx | neighborhood:713 coexpression:815 textmining:625 |
Rv2524c fas |
fatty acid synthase | 826 | 800 | coexpression:506 experimental:475 |
Rv3561 fadD3 |
fatty-acid--CoA ligase FadD3 | 798 | 794 | coexpression:735 |
Rv3502c |
3-oxoacyl-ACP reductase | 774 | 774 ctx | cooccurence:773 |
Rv2214c ephD |
oxidoreductase EphD | 748 | 693 ctx | cooccurence:629 |
Rv1245c |
short-chain type dehydrogenase/reductase | 680 | 680 ctx | cooccurence:673 |
Rv3085 sadH |
oxidoreductase SadH | 674 | 674 ctx | cooccurence:665 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 850 | 657 | textmining:581 |
Rv3541c chsH1 hyp |
hypothetical protein | 658 | 644 ctx | cooccurence:478 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 796 | 613 | textmining:496 |
Rv3554 fdxB |
electron transfer protein FdxB | 646 | 611 ctx | neighborhood:416 |
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=4e-43), KR PF08659.17 (E=4e-05), Epimerase PF01370.28 (E=2e-05), adh_short_C2 PF13561.13 (E=2e-52), SDR PF23441.1 (E=6e-09)
- (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_218066.1)
- Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), KR (PF08659.17), Epimerase (PF01370.28), adh_short_C2 (PF13561.13), SDR (PF23441.1)
- 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 I6YCE1 (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 —
119 functional partner(s); context anchor
echA20 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003766|Rv3549c| MTLAEAADAINFGLAGRVVLVTGGVRGVGAGISSVFAEQGATVITCARRAVDGQPYEFHRCDIRDEDSVKRLVGEIGERHGRLDMLVNNAGGSPYALAAEATHNFHRKIVELNVLAPLLVSQHANVLMQAQPNGGSIVNICSVSGRRPTPGTAAYGAAKAGLENLTTTLAVEWAPKVRVNAVVVGMVETERSELFYGDAESIARVAATVPLGRLARPADIGWAAAFLASDAASYISGATLEVHGGGEPPPYLGASSANK