Rv2624c Resolved · high auto-curated
H37Rv Rv2624c · MTBC0 - ·
272 aa · 2950489–2951307 (-) ·
RefSeq NP_217140.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | universal stress protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Universal stress protein. Pfam: Usp (PF00582.33). |
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 |
P9WFD5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Universal stress protein Rv2624c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | Universal stress protein |
| Orthologous group | COG0589 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 1.746 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 1.29% of strains (1868) · 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 |
|---|---|---|---|---|
Usp | PF00582.33 | 3.9e-21 | 9–140 | Universal stress protein family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rip3 (zinc metalloprotease Rip3), high confidence from genomic context alone (score 971 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2625c rip3 |
zinc metalloprotease Rip3 | 975 | 971 ctx | neighborhood:748 coexpression:857 |
Rv2626c hrp1 |
hypoxic response protein | 920 | 908 ctx | neighborhood:586 coexpression:788 |
Rv2028c |
universal stress protein | 885 | 883 | coexpression:860 |
Rv1997 ctpF |
cation transporter ATPase F | 877 | 873 | coexpression:869 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 857 | 857 | coexpression:855 |
Rv2032 acg |
NAD(P)H nitroreductase | 834 | 828 | coexpression:730 |
Rv1736c narX |
nitrate reductase-like protein NarX | 822 | 822 | coexpression:822 |
Rv3132c devS |
two component sensor histidine kinase DevS | 845 | 814 | coexpression:744 |
Rv2623 TB31.7 |
universal stress protein | 829 | 806 | coexpression:735 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 803 | 804 | coexpression:797 |
Rv2005c |
universal stress protein | 802 | 803 | coexpression:738 |
Rv2003c hyp |
hypothetical protein | 800 | 800 | coexpression:800 |
Rv3128c |
Rv3128c, (MTCY164.38c), len: 337 aa. Conserved hypothetical protein, similar to other conserved hypothetical proteins. This ORF corresponds | 838 | 799 | coexpression:799 |
Rv2628 hyp |
hypothetical protein | 830 | 796 | coexpression:796 |
Rv1733c |
transmembrane protein | 772 | 773 ctx | cooccurence:481 coexpression:580 |
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): universal stress protein
- Pfam (hmmscan --cut_ga): Usp PF00582.33 (E=4e-21)
- (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_217140.1)
- Domains: Pfam-A via hmmscan --cut_ga — Usp (PF00582.33)
- 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
COG0589 - Curated reference: UniProt P9WFD5 (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 —
49 functional partner(s); context anchor
rip3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2624c| MSGRGEPTMKTIIVGIDGSHAAITAALWGVDEAISRAVPLRLVSVIKPTHPSPDDYDRDLAHAERSLREAQSAVEAAGKLVKIETDIPRGPAGPVLVEASRDAEMICVGSVGIGRYASSILGSTATELAEKAHCPVAVMRSKVDQPASDINWIVVRMTDAPDNEAVLEYAAREAKLRQAPILALGGRPEELREIPDGEFERRVQDWHHRHPDVRVYPITTHTGIARFLADHDERVQLAVIGGGEAGQLARLVGPSGHPVFRHAECSVLVVRR