Rv1106c Resolved · high auto-curated
H37Rv Rv1106c · MTBC0 mtbc0_001188 ·
370 aa · 1241284–1242396 (-) ·
RefSeq NP_215622.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase |
|---|---|
| MTBC0 PGAP re-annotation | 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase |
| Revised (this work) | 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase. Pfam: KR (PF08659.17), RmlD_sub_bind (PF04321.24), NmrA (PF05368.20), Epimerase (PF01370.28), Polysacc_synt_2 (PF02719.22), 3Beta_HSD (PF01073.26), GDP_Man_Dehyd (PF16363.12), NAD_binding_10 (PF13460.13), NAD_binding_4 (PF07993.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQP7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase |
| EC (curated) |
EC 1.1.1.145, EC 5.3.3.1
|
| Curated function | 3-beta-HSD is a bifunctional enzyme, that catalyzes the oxidation and isomerization of cholesterol, pregnenolone, and dehydroepiandrosterone (DHEA) into cholest-4-en-3-one, progesterone, and androsterone, respectively. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | 3-beta hydroxysteroid dehydrogenase isomerase |
| Orthologous group | COG0451 |
| EC number |
EC 1.1.1.145, EC 1.1.1.412, EC 5.3.3.1
|
| KEGG orthology |
K16045, K22320
|
| KEGG pathways |
map00984, map01120
|
| Gene Ontology (44) |
GO:0000166, GO:0003674, GO:0003824, GO:0003854, GO:0004769, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886 +32 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 | 0.112 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.62% of strains (905) · 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 |
|---|---|---|---|---|
KR | PF08659.17 | 6.2e-06 | 15–139 | KR domain |
RmlD_sub_bind | PF04321.24 | 3.2e-12 | 16–273 | RmlD substrate binding domain |
NmrA | PF05368.20 | 5.5e-09 | 16–131 | NmrA-like family |
Epimerase | PF01370.28 | 2.1e-31 | 17–238 | NAD dependent epimerase/dehydratase family |
Polysacc_synt_2 | PF02719.22 | 5.5e-07 | 17–136 | Polysaccharide biosynthesis protein |
3Beta_HSD | PF01073.26 | 3.0e-57 | 18–277 | 3-beta hydroxysteroid dehydrogenase/isomerase family |
GDP_Man_Dehyd | PF16363.12 | 1.1e-15 | 18–342 | GDP-mannose 4,6 dehydratase |
NAD_binding_10 | PF13460.13 | 2.5e-15 | 21–134 | NAD(P)H-binding |
NAD_binding_4 | PF07993.19 | 1.1e-09 | 53–221 | Male sterility protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: xseB (exodeoxyribonuclease VII small subunit), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3518c cyp142 |
cytochrome P450 monooxygenase Cyp142 | 968 | 917 | database:900 textmining:633 |
Rv3545c cyp125 |
steroid C26-monooxygenase | 960 | 917 | database:900 textmining:546 |
Rv3409c choD |
cholesterol oxidase | 987 | 900 | database:900 textmining:875 |
Rv1107c xseB |
exodeoxyribonuclease VII small subunit | 888 | 884 ctx | neighborhood:882 |
Rv1108c xseA |
exodeoxyribonuclease VII large subunit | 883 | 883 ctx | neighborhood:882 |
Rv1109c hyp |
hypothetical protein | 882 | 882 ctx | neighborhood:882 |
Rv0705 rpsS |
30S ribosomal protein S19 | 817 | 817 | experimental:463 database:574 |
Rv0682 rpsL |
30S ribosomal protein S12 | 814 | 806 | experimental:463 database:573 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 804 | 798 | experimental:463 database:578 |
Rv0707 rpsC |
30S ribosomal protein S3 | 803 | 796 | experimental:463 database:578 |
Rv0721 rpsE |
30S ribosomal protein S5 | 797 | 790 | experimental:463 database:575 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 788 | 788 | experimental:436 database:548 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 788 | 788 | experimental:436 database:548 |
Rv0718 rpsH |
30S ribosomal protein S8 | 793 | 786 | experimental:463 database:578 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 789 | 785 | experimental:463 database:557 |
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: 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase
- MTBC0 PGAP product: 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase
- Pfam (hmmscan --cut_ga): KR PF08659.17 (E=6e-06), RmlD_sub_bind PF04321.24 (E=3e-12), NmrA PF05368.20 (E=5e-09), Epimerase PF01370.28 (E=2e-31), Polysacc_synt_2 PF02719.22 (E=6e-07), 3Beta_HSD PF01073.26 (E=3e-57), GDP_Man_Dehyd PF16363.12 (E=1e-15), NAD_binding_10 PF13460.13 (E=2e-15), NAD_binding_4 PF07993.19 (E=1e-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_215622.1)
- Domains: Pfam-A via hmmscan --cut_ga — KR (PF08659.17), RmlD_sub_bind (PF04321.24), NmrA (PF05368.20), Epimerase (PF01370.28), Polysacc_synt_2 (PF02719.22), 3Beta_HSD (PF01073.26), GDP_Man_Dehyd (PF16363.12), NAD_binding_10 (PF13460.13), NAD_binding_4 (PF07993.19)
- 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
COG0451 - Curated reference: UniProt P9WQP7 (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 —
92 functional partner(s); context anchor
xseB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001188|Rv1106c| MLRRMGDASLTTELGRVLVTGGAGFVGANLVTTLLDRGHWVRSFDRAPSLLPAHPQLEVLQGDITDADVCAAAVDGIDTIFHTAAIIELMGGASVTDEYRQRSFAVNVGGTENLLHAGQRAGVQRFVYTSSNSVVMGGQNIAGGDETLPYTDRFNDLYTETKVVAERFVLAQNGVDGMLTCAIRPSGIWGNGDQTMFRKLFESVLKGHVKVLVGRKSARLDNSYVHNLIHGFILAAAHLVPDGTAPGQAYFINDAEPINMFEFARPVLEACGQRWPKMRISGPAVRWVMTGWQRLHFRFGFPAPLLEPLAVERLYLDNYFSIAKARRDLGYEPLFTTQQALTECLPYYVSLFEQMKNEARAEKTAATVKP