Rv0785 Resolved · high auto-curated
H37Rv Rv0785 · MTBC0 mtbc0_000835 ·
566 aa · 883766–885466 (+) ·
RefSeq NP_215299.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | KsdD-like steroid dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | FAD-binding dehydrogenase |
| Revised (this work) | FAD-binding dehydrogenase. Pfam: FAD_binding_3 (PF01494.26), FAD_binding_2 (PF00890.31), NAD_binding_8 (PF13450.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71838
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | KsdD-like steroid dehydrogenase Rv0785 |
| EC (curated) |
EC 1.3.99.-
|
| Curated function | Able to catalyze the elimination of the C-1 and C-2 hydrogen atoms of the A-ring from the polycyclic ring structure of 3-ketosteroids. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Dehydrogenase |
| Orthologous group | COG3573 |
| KEGG orthology |
K07077
|
| Gene Ontology (25) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006629, GO:0006694, GO:0008150, GO:0008152, GO:0008202, GO:0008610, GO:0009058 +13 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) pseudogene candidate
| pN/pS | 0.573 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 11.99% of strains (17405) · 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 |
|---|---|---|---|---|
FAD_binding_3 | PF01494.26 | 1.6e-05 | 22–62 | FAD binding domain |
FAD_binding_2 | PF00890.31 | 2.0e-88 | 23–547 | FAD binding domain |
NAD_binding_8 | PF13450.13 | 2.0e-08 | 26–62 | NAD(P)-binding Rossmann-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: emrB (multidrug resistance protein EmrB), high confidence from genomic context alone (score 727 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0784 hyp |
hypothetical protein | 863 | 864 ctx | neighborhood:863 |
Rv0783c emrB |
multidrug resistance protein EmrB | 726 | 727 ctx | neighborhood:723 |
Rv1769 hyp |
hypothetical protein | 443 | 444 ctx | cooccurence:442 |
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: KsdD-like steroid dehydrogenase
- MTBC0 PGAP product: FAD-binding dehydrogenase
- Pfam (hmmscan --cut_ga): FAD_binding_3 PF01494.26 (E=2e-05), FAD_binding_2 PF00890.31 (E=2e-88), NAD_binding_8 PF13450.13 (E=2e-08)
- (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_215299.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_3 (PF01494.26), FAD_binding_2 (PF00890.31), NAD_binding_8 (PF13450.13)
- 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
COG3573 - Curated reference: UniProt P71838 (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 —
3 functional partner(s); context anchor
emrB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000835|Rv0785| MALTCTDMSDAVAGSDAEGLTADAIVVGAGLAGLVAACELADRGLRVLILDQENRANVGGQAFWSFGGLFLVNSPEQRRLGIRDSHELALQDWLGTAAFDRPEDYWPEQWAHAYVDFAAGEKRSWLRARGLKIFPLVGWAERGGYDAQGHGNSVPRFHITWGTGPALVDIFVRQLRDRPTVRFAHRHQVDKLIVEGNAVTGVRGTVLEPSDEPRGAPSSRKSVGKFEFRASAVIVASGGIGGNHELVRKNWPRRMGRIPKQLLSGVPAHVDGRMIGIAQKAGAAVINPDRMWHYTEGITNYDPIWPRHGIRIIPGPSSLWLDAAGKRLPVPLFPGFDTLGTLEYITKSGHDYTWFVLNAKIIEKEFALSGQEQNPDLTGRRLGQLLRSRAHAGPPGPVQAFIDRGVDFVHANSLRELVAAMNELPDVVPLDYETVAAAVTARDREVVNKYSKDGQITAIRAARRYRGDRFGRVVAPHRLTDPKAGPLIAVKLHILTRKTLGGIETDLDARVLKADGTPLAGLYAAGEVAGFGGGGVHGYRALEGTFLGGCIFSGRAAGRGAAEDIR