Rv1829 Family assigned · medium auto-curated
H37Rv Rv1829 · MTBC0 - ·
164 aa · 2073943–2074437 (+) ·
RefSeq NP_216345.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains BFN_dom (PF02577.20) 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 |
P9WLR5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1829 |
UniProt still lists this protein as Uncharacterized protein Rv1829; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Bifunctional nuclease |
| Orthologous group | COG1259 |
| KEGG orthology |
K08999
|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.988 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
BFN_dom | PF02577.20 | 1.3e-42 | 20–127 | Bifunctional nuclease domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1828 (HTH-type transcriptional regulator), high confidence from genomic context alone (score 769 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) |
|---|---|---|---|---|
Rv1828 |
HTH-type transcriptional regulator | 829 | 769 ctx | neighborhood:763 |
Rv1827 garA |
glycogen accumulation regulator GarA | 777 | 766 ctx | neighborhood:763 |
Rv2115c mpa |
proteasome-associated ATPase | 729 | 730 | coexpression:729 |
Rv1826 gcvH |
glycine cleavage system protein H | 647 | 647 ctx | neighborhood:643 |
Rv1824 hyp |
hypothetical protein | 640 | 641 ctx | neighborhood:632 |
Rv1830 |
HTH-type transcriptional regulator | 845 | 569 ctx | neighborhood:544 textmining:656 |
Rv1823 hyp |
hypothetical protein | 904 | 537 ctx | neighborhood:527 textmining:803 |
Rv1825 hyp |
hypothetical protein | 925 | 451 ctx | neighborhood:442 textmining:870 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 449 | 449 ctx | neighborhood:446 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 | 573 | 429 ctx | neighborhood:402 |
Rv1832 gcvB |
glycine dehydrogenase | 404 | 405 | |
Rv1023 eno |
enolase | 403 | 404 | experimental:402 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 580 | 289 | textmining:434 |
Rv2531c |
amino acid decarboxylase | 634 | 272 | textmining:519 |
Rv2534c efp |
elongation factor P | 714 | 235 | textmining:642 |
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): BFN_dom PF02577.20 (E=1e-42)
- (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_216345.1)
- Domains: Pfam-A via hmmscan --cut_ga — BFN_dom (PF02577.20)
- 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
COG1259 - Curated reference: UniProt P9WLR5 (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 —
37 functional partner(s); context anchor
Rv1828 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1829| MGEVRVVGIRVEQPQNQPVLLLREANGDRYLPIWIGQSEAAAIALEQQGVEPPRPLTHDLIRDLIAALGHSLKEVRIVDLQEGTFYADLIFDRNIKVSARPSDSVAIALRVGVPIYVEEAVLAQAGLLIPDESDEEATTAVREDEVEKFKEFLDSVSPDDFKAT