Rv3559c Family assigned · medium auto-curated
H37Rv Rv3559c · MTBC0 mtbc0_003776 ·
262 aa · 4023324–4024112 (-) ·
RefSeq NP_218076.1
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 |
I6YCF0
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | (5R,7aS)-5-hydroxy-7a-methyl-1-oxo-2,3,5,6,7,7a-hexahydro-1H-indene-carboxyl-CoA reductase |
| EC (curated) |
EC 1.1.1.-
|
| Curated function | Involved in the final steps of cholesterol and steroid degradation. Probably catalyzes the oxidation of the 5-OH group of (5R,7aS)-5-hydroxy-7a-methyl-1-oxo-2,3,5,6,7,7a-hexahydro-1H-indene-carboxyl-CoA, leading to the formation of HIEC-CoA (Probable). |
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 |
| EC number |
EC 1.1.1.100
|
| KEGG orthology |
K00059
|
| KEGG pathways |
map00061, map00333, map00780, map01040, map01100, map01130, map01212
|
| KEGG modules |
M00083, M00572
|
| 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 | 0.133 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 4 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 | 2.3e-50 | 19–205 | short chain dehydrogenase |
KR | PF08659.17 | 7.8e-12 | 22–182 | KR domain |
adh_short_C2 | PF13561.13 | 2.6e-58 | 26–257 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE30 (acyl-CoA dehydrogenase FadE30), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 996 | 995 ctx | neighborhood:882 cooccurence:425 coexpression:796 database:622 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 988 | 980 ctx | neighborhood:788 cooccurence:505 coexpression:736 textmining:478 |
Rv2524c fas |
fatty acid synthase | 981 | 979 | coexpression:508 experimental:475 database:918 |
Rv3561 fadD3 |
fatty-acid--CoA ligase FadD3 | 969 | 969 ctx | neighborhood:588 coexpression:815 database:500 |
Rv3564 fadE33 |
acyl-CoA dehydrogenase FadE33 | 954 | 953 ctx | neighborhood:770 coexpression:710 |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 945 | 943 | database:900 |
Rv3552 |
CoA-transferase subunit beta | 943 | 941 ctx | cooccurence:709 coexpression:783 |
Rv3553 |
oxidoreductase | 962 | 933 | coexpression:813 database:500 textmining:462 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 961 | 929 ctx | neighborhood:788 textmining:479 |
Rv0769 |
oxidoreductase | 924 | 925 | database:900 |
Rv3551 |
CoA-transferase subunit alpha | 955 | 919 ctx | cooccurence:706 coexpression:730 textmining:479 |
Rv1350 fabG2 |
3-oxoacyl-ACP reductase FabG | 916 | 916 | database:900 |
Rv0242c fabG4 |
3-oxoacyl-ACP reductase FabG | 913 | 914 | database:900 |
Rv0649 fabD2 |
malonyl CoA-acyl carrier protein transacylase | 900 | 901 | database:900 |
Rv3550 echA20 |
enoyl-CoA hydratase EchA20 | 942 | 894 ctx | cooccurence:561 database:591 textmining:478 |
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=2e-50), KR PF08659.17 (E=8e-12), adh_short_C2 PF13561.13 (E=3e-58)
- (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_218076.1)
- 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 I6YCF0 (SwissProt, reviewed; 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 —
117 functional partner(s); context anchor
fadE30 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003776|Rv3559c| MNLSVAPKEIAGHGLLDGKVVVVTAAAGTGIGSATARRALAEGADVVISDHHERRLGETAAELSALGLGRVEHVVCDVTSTAQVDALIDSTTARMGRLDVLVNNAGLGGQTPVADMTDDEWDRVLDVSLTSVFRATRAALRYFRDAPHGGVIVNNASVLGWRAQHSQSHYAAAKAGVMALTRCSAIEAAEYGVRINAVSPSIARHKFLDKTASAELLDRLAAGEAFGRAAEPWEVAATIAFLASDYSSYLTGEVISVSCQHP