Rv0784 Still unknown · low auto-curated
H37Rv Rv0784 · MTBC0 - ·
228 aa · 878638–879324 (+) ·
RefSeq NP_215298.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2334. Function unknown. Foldseek best (non-significant) hit: 3cqh-assembly1_A Crystal Structure of L-xylulose-5-phosphate 3-epimera (prob 0.21, TM 0.37). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P71837
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Deacetylase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Uncharacterized protein conserved in bacteria (DUF2334) |
| Orthologous group | COG3233 |
| KEGG orthology |
K06986
|
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 |
|---|---|---|---|---|
DUF2334 | PF10096.15 | 2.1e-20 | 9–133 | Uncharacterized protein conserved in bacteria (DUF2334) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 91.4 (very high). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
3cqh-assembly1_A |
0.21 | 0.37 | 3.0e-01 | 3cqh-assembly1_A Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE from the Anaerobic L-ascorbate Utilization Pathway of Escherichia coli |
5cew-assembly1_A |
0.18 | 0.29 | 8.6e-02 | 5cew-assembly1_A Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-(pyridin-4-yl)thiazolidine-4-carboxylic acid |
6c8p-assembly1_A |
0.15 | 0.26 | 9.7e-02 | 6c8p-assembly1_A Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-F-phenyldiketoacid |
3sad-assembly1_A |
0.14 | 0.24 | 6.7e-02 | 3sad-assembly1_A Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 4-(2-mehtylphenyl)-2,4-dioxobutanoic acid inhibitor |
6as6-assembly1_A |
0.14 | 0.24 | 4.7e-02 | 6as6-assembly1_A Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 3-Prop-6-Me-phenyldiketoacid |
5dri-assembly1_A |
0.13 | 0.22 | 4.7e-02 | 5dri-assembly1_A Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-hydroxy-4-(1H-indol-5-yl)-4-oxobut-2-enoic acid inhibitor |
5ccz-assembly1_A |
0.13 | 0.27 | 1.8e-01 | 5ccz-assembly1_A Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 3-(4-fluorophenyl)-4-methyl-1H-pyrazol-5-amine |
1n8i-assembly1_A |
0.12 | 0.27 | 1.7e-01 | 1n8i-assembly1_A Biochemical and Structural Studies of Malate Synthase from Mycobacterium tuberculosis |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0785 (KsdD-like steroid dehydrogenase), high confidence from genomic context alone (score 864 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0785 |
KsdD-like steroid dehydrogenase | 863 | 864 ctx | neighborhood:863 |
Rv0783c emrB |
multidrug resistance protein EmrB | 761 | 761 ctx | neighborhood:759 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 704 | 705 ctx | cooccurence:695 |
Rv3850 hyp |
hypothetical protein | 700 | 701 ctx | cooccurence:699 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 694 | 695 ctx | cooccurence:691 |
Rv0556 |
transmembrane protein | 693 | 694 ctx | cooccurence:693 |
Rv2342 hyp |
hypothetical protein | 677 | 677 ctx | cooccurence:673 |
Rv0358 hyp |
hypothetical protein | 653 | 653 ctx | cooccurence:650 |
Rv0996 |
transmembrane protein | 649 | 649 ctx | cooccurence:646 |
Rv1081c |
membrane protein | 649 | 649 ctx | cooccurence:647 |
Rv2138 lppL |
lipoprotein LppL | 645 | 646 ctx | cooccurence:644 |
Rv3438 hyp |
hypothetical protein | 633 | 633 ctx | cooccurence:633 |
Rv2732c |
transmembrane protein | 629 | 630 ctx | cooccurence:626 |
Rv2525c hyp |
hypothetical protein | 619 | 619 ctx | cooccurence:615 |
Rv3205c hyp |
hypothetical protein | 614 | 614 ctx | cooccurence:609 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): DUF2334 PF10096.15 (E=2e-20)
- Foldseek best: 3cqh-assembly1_A Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE fr (prob 0.21, E=3e-01, TM=0.37)
- (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_215298.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2334 (PF10096.15)
- 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
COG3233 - Curated reference: UniProt P71837 (TrEMBL, unreviewed; Predicted)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Model confidence: ESMFold per-residue pLDDT (mean 91.4, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
67 functional partner(s); context anchor
Rv0785 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0784| MSVSGIGESTLADVDAFCAEMDARSVPVSLLVAPRMRDDYRLDRDPRTVDWLTGRRAAGDALVLHGYDEAATKRRRGEFAMLRAHEANLRLMAADRVLEHLGLRTRLFAAPGWLVSPGVRTALPANGFRLLADLHGITDLVRLTTVRARVLGIGEGFLAEPWWCRMVVMSAERIARRGGVVRIAVAARHLRKSGPLQAMLDAVDLAMLQGCTPMVYRWRADAAVLDAA