Rv1269c Family assigned · low
H37Rv Rv1269c · MTBC0 mtbc0_001359 ·
124 aa · 1427562–1427936 (-) ·
RefSeq NP_215785.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF4189 domain-containing protein |
| Revised (this work) | DUF4189; same fold as Rv1813c (PDB 7NHZ); secreted DUF4189-family protein. |
Curated reference (UniProt)
| UniProt |
P9WM45
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein Rv1269c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF4189) |
| Orthologous group | 2DE1B |
| Gene Ontology (7) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, 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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 14.02% of strains (20353) · 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 |
|---|---|---|---|---|
DUF4189 | PF13827.12 | 1.7e-18 | 39–115 | Domain of unknown function (DUF4189) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 94.4 (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 |
|---|---|---|---|---|
7nhz-assembly1_A |
1.00 | 0.70 | 6.5e-08 sig | 7nhz-assembly1_A NMR structure of Rv1813c from Mycobacterium tuberculosis |
8wr4-assembly1_B |
0.23 | 0.46 | 6.3e-01 | 8wr4-assembly1_B Structure of CbCas9-PcrIIC1 complex bound to 62-bp DNA substrate (non-targeting complex) |
2le2-assembly1_A |
0.03 | 0.42 | 9.6e+00 | 2le2-assembly1_A Novel dimeric structure of phage phi29-encoded protein p56: Insights into Uracil-DNA glycosylase inhibition |
1wj4-assembly1_A |
0.01 | 0.19 | 8.0e+00 | 1wj4-assembly1_A Solution structure of the UBX domain of KIAA0794 protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lprA (lipoprotein LprA), medium confidence from genomic context alone (score 669 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) |
|---|---|---|---|---|
Rv1270c lprA |
lipoprotein LprA | 668 | 669 ctx | neighborhood:669 |
Rv1268c hyp |
hypothetical protein | 491 | 491 ctx | neighborhood:491 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 457 | 385 | |
Rv0450c mmpL4 |
transmembrane transport protein MmpL4 | 571 | 153 | textmining:515 |
Rv3283 sseA |
thiosulfate sulfurtransferase SseA | 811 | 51 | textmining:809 |
Rv3005c hyp |
hypothetical protein | 651 | 41 | textmining:651 |
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
- MTBC0 PGAP product: DUF4189 domain-containing protein
- Pfam: DUF4189 PF13827.12
- Foldseek best: 7nhz-assembly1_A NMR structure of Rv1813c from Mycobacterium tuberculosis (prob 1.00, E=6e-08, TM=0.70)
- (structure-only promotion reviewed by hand, 2026-06-01)
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_215785.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4189 (PF13827.12)
- 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
2DE1B - Curated reference: UniProt P9WM45 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 94.4, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
6 functional partner(s); context anchor
lprA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001359|Rv1269c| MTTMITLRRRFAVAVAGVATAAATTVTLAPAPANAADVYGAIAYSGNGSWGRSWDYPTRAAAEATAVKSCGYSDCKVLTSFTACGAVAANDRAYQGGVGPTLAAAMKDALTKLGGGYIDTWACN