Rv3796 Family assigned · medium auto-curated
H37Rv Rv3796 · MTBC0 - ·
375 aa · 4249878–4251005 (+) ·
RefSeq YP_178016.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Lactamase_B (PF00753.34), Anti-Pycsar_Apyc1 (PF23023.2), Lactamase_B_2 (PF12706.14) domain(s); putative function inferred from the domain architecture. |
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 |
P72062
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Zinc phosphodiesterase, which displays some tRNA 3'- processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA |
| Orthologous group | COG1234 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 8 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 |
|---|---|---|---|---|
Lactamase_B | PF00753.34 | 7.6e-05 | 81–126 | Metallo-beta-lactamase superfamily |
Anti-Pycsar_Apyc1 | PF23023.2 | 6.8e-08 | 84–126 | Anti-Pycsar protein Apyc1 |
Lactamase_B_2 | PF12706.14 | 1.5e-07 | 230–342 | Beta-lactamase superfamily domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: embB (arabinosyltransferase B), medium confidence from genomic context alone (score 630 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) |
|---|---|---|---|---|
Rv3795 embB |
arabinosyltransferase B | 630 | 630 ctx | neighborhood:625 |
Rv3794 embA |
arabinosyltransferase A | 590 | 590 ctx | neighborhood:586 |
Rv3797 fadE35 |
acyl-CoA dehydrogenase FadE35 | 584 | 584 ctx | neighborhood:577 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 469 | 469 | coexpression:400 |
Rv3791 dprE2 |
decaprenylphosphoryl-D-2-keto erythropentose reductase | 439 | 439 ctx | neighborhood:434 |
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 426 | 426 ctx | neighborhood:418 |
Rv3793 embC |
arabinosyltransferase C | 425 | 425 ctx | neighborhood:418 |
Rv3792 aftA |
arabinofuranosyltransferase | 420 | 420 ctx | neighborhood:418 |
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): Lactamase_B PF00753.34 (E=8e-05), Anti-Pycsar_Apyc1 PF23023.2 (E=7e-08), Lactamase_B_2 PF12706.14 (E=1e-07)
- (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 YP_178016.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lactamase_B (PF00753.34), Anti-Pycsar_Apyc1 (PF23023.2), Lactamase_B_2 (PF12706.14)
- 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
COG1234 - Curated reference: UniProt P72062 (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 —
8 functional partner(s); context anchor
embB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3796| MLLGMHQAGHVGTHERRAAATRRSALTAAGLAVVGAGVLGASACSPQKSPQPSSPRLPDNALITLGVAAGPPPTPSRVGISSVLKIGRDLYVIDCGLGSLNAFTNAGLQFDDLKAMFITHLHTDHIVDYYNFFLSGGFLAPPGRAPVLVYGPGPAGGLPPSEVGNPNPATVNPANPTPGLAAATEALHRAFAYTSNIFIRDYGIDNVADLVKVTEIGLPPGSDYRNRAPKMSPFSVASDDNVSVTATLVSHYDVYPAFGFRFDLKKSGVSVTFSGDTTKSDNLITLAQGTDILVHEAVFSLDTAYFGNAFPPNYLVNSHTSAEQVGEVAAAAKPKQLILSHYAPDDLPDSQWLDKIKKNYSGMTTIARDGQVFAL