Rv1583c Still unknown · low auto-curated
H37Rv Rv1583c · MTBC0 mtbc0_001690 ·
132 aa · 1797872–1798270 (-) ·
RefSeq NP_216099.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phage protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2742 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2742. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLU1
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv1583c |
UniProt still lists this protein as Uncharacterized protein Rv1583c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2742) |
| Orthologous group | 2AYB0 |
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 | 0.363 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
DUF2742 | PF10888.15 | 5.8e-39 | 36–129 | Protein of unknown function (DUF2742) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1584c (phage protein), high confidence from genomic context alone (score 779 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1584c |
phage protein | 780 | 779 ctx | neighborhood:778 |
Rv1582c |
phage protein | 780 | 779 ctx | neighborhood:777 |
Rv1585c |
phage protein | 612 | 612 ctx | neighborhood:606 |
Rv1586c |
phage integrase | 612 | 611 ctx | neighborhood:606 |
Rv1588c hyp |
hypothetical protein | 609 | 609 ctx | neighborhood:605 |
Rv1587c hyp |
hypothetical protein | 608 | 607 ctx | neighborhood:605 |
Rv1581c |
phage protein | 456 | 456 ctx | neighborhood:453 |
Rv1579c |
phage protein | 438 | 438 ctx | neighborhood:436 |
Rv1580c |
phage protein | 437 | 437 ctx | neighborhood:436 |
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: phage protein
- MTBC0 PGAP product: DUF2742 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF2742 PF10888.15 (E=6e-39)
- (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_216099.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2742 (PF10888.15)
- 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
2AYB0 - Curated reference: UniProt P9WLU1 (SwissProt, reviewed; 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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
9 functional partner(s); context anchor
Rv1584c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001690|Rv1583c| MTAGAGGSPPTRRCPATEDRAPATVATPSSADPTASRAVSWWSVHEHVAPVLDAAGSWPMAGTPAWRQLDDADPRKWAAICDAARHWALRVETCQEAMAQASRDVSAAADWPGIAREIVRRRGVYIPRAGVA