Rv3813c Family assigned · medium auto-curated
H37Rv Rv3813c · MTBC0 mtbc0_004042 ·
273 aa · 4302504–4303325 (-) ·
RefSeq NP_218330.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | Cof-type HAD-IIB family hydrolase |
| Revised (this work) | Cof-type HAD-IIB family hydrolase. Pfam: Hydrolase_3 (PF08282.19), S6PP (PF05116.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07810
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 | hydrolase |
| Orthologous group | COG0561 |
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 | 0.268 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 6 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 |
|---|---|---|---|---|
Hydrolase_3 | PF08282.19 | 1.9e-58 | 9–268 | haloacid dehalogenase-like hydrolase |
S6PP | PF05116.20 | 5.2e-06 | 170–257 | Sucrose-6F-phosphate phosphohydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3816c (acyltransferase), high confidence from genomic context alone (score 852 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) |
|---|---|---|---|---|
Rv3816c |
acyltransferase | 851 | 852 ctx | neighborhood:852 |
Rv3814c |
acyltransferase | 776 | 776 ctx | neighborhood:776 |
Rv3815c |
acyltransferase | 771 | 771 ctx | neighborhood:742 |
Rv3818 hyp |
hypothetical protein | 581 | 566 ctx | neighborhood:565 |
Rv3817 |
phosphotransferase | 563 | 563 ctx | neighborhood:558 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 532 | 456 ctx | neighborhood:438 |
Rv3013 hyp |
hypothetical protein | 465 | 446 | |
Rv3819 hyp |
hypothetical protein | 428 | 429 ctx | neighborhood:425 |
Rv3264c manB |
D-alpha-D-mannose-1-phosphate guanylyltransferase ManB | 522 | 390 | |
Rv2584c apt |
adenine phosphoribosyltransferase | 417 | 383 | |
Rv0946c pgi |
glucose-6-phosphate isomerase | 427 | 335 | |
Rv3255c manA |
mannose-6-phosphate isomerase | 405 | 223 | |
Rv2870c dxr |
1-deoxy-D-xylulose 5-phosphate reductoisomerase | 491 | 65 | 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: hypothetical protein
- MTBC0 PGAP product: Cof-type HAD-IIB family hydrolase
- Pfam (hmmscan --cut_ga): Hydrolase_3 PF08282.19 (E=2e-58), S6PP PF05116.20 (E=5e-06)
- (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_218330.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase_3 (PF08282.19), S6PP (PF05116.20)
- 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
COG0561 - Curated reference: UniProt O07810 (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 —
13 functional partner(s); context anchor
Rv3816c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004042|Rv3813c| MKPTVPALVACDVDGTLLDDGETVTKRTRDAVHAAVDAGTHFILATGRPPRWVRPIVDALGFAPMAVCANGAVIYDPGTDRVMSVRTLPVDALATLAEVATRVIPGAGLAVERIGERAHDTATPQFVSSPGYEHAWLNPDNTEVSIDHLLSAPAIKLLIRKAGAASADMAAELAKHVGFEGDITYSTNNGLVEIVPLGISKATGVDEIARPLGISDAEVVAFGDMPNDVPMLLRAGLGVAMGNAHPDALAVADEVTAPNSEDGVARVLERWWS