Rv2026c Resolved · high auto-curated
H37Rv Rv2026c · MTBC0 mtbc0_002159 ·
294 aa · 2300476–2301360 (-) ·
RefSeq NP_216542.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | universal stress protein |
|---|---|
| MTBC0 PGAP re-annotation | universal stress protein |
| 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.
Curated reference (UniProt)
| UniProt |
P9WFD1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Universal stress protein Rv2026c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | Belongs to the universal stress protein A family |
| Orthologous group | COG0589 |
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.341 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (245) · 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 | 3.4e-29 | 161–292 | Universal stress protein family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dosT (two component sensor histidine kinase DosT), high confidence from genomic context alone (score 928 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2027c dosT |
two component sensor histidine kinase DosT | 944 | 928 ctx | neighborhood:659 coexpression:731 |
Rv2028c |
universal stress protein | 664 | 640 ctx | neighborhood:504 |
Rv2032 acg |
NAD(P)H nitroreductase | 586 | 571 | |
Rv2031c hspX |
alpha-crystallin | 646 | 523 ctx | neighborhood:479 |
Rv2025c |
cation efflux system protein | 523 | 523 ctx | neighborhood:517 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 517 | 517 ctx | neighborhood:512 |
Rv2030c hyp |
hypothetical protein | 522 | 503 ctx | neighborhood:500 |
Rv1316c ogt |
methylated-DNA--protein-cysteine methyltransferase | 424 | 424 | coexpression:415 |
Rv3127 hyp |
hypothetical protein | 442 | 422 ctx | cooccurence:409 |
Rv3314c deoA |
thymidine phosphorylase | 414 | 415 | coexpression:412 |
Rv3241c raiA hyp |
hypothetical protein | 402 | 375 | |
Rv0079 hyp |
hypothetical protein | 400 | 372 | |
Rv3132c devS |
two component sensor histidine kinase DevS | 447 | 250 | |
Rv0998 |
acetyltransferase Pat | 694 | 103 | textmining:673 |
Rv0995 rimJ |
ribosomal-protein-alanine acetyltransferase RimJ | 661 | 61 | textmining:654 |
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: universal stress protein
- MTBC0 PGAP product: universal stress protein
- Pfam (hmmscan --cut_ga): Usp PF00582.33 (E=3e-29)
- (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_216542.1)
- 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 P9WFD1 (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 —
20 functional partner(s); context anchor
dosT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002159|Rv2026c| MSAATAKYGILVGVDGSAQSNAAVAWAAREAVMRQLPITLLHIVAPVVVGWPVGQLYANMTEWQKDNAQQVIEQAREALTNSLGESKPPQVHTELVFSNVVPTLIDASQQAWLMVVGSQGMGALGRLLLGSISTALLHHARCPVAIIHSGNGATPDSDAPVLVGIDGSPASEAATALAFDEASRRRVDLVALHAWTDLGMFPVLGMDWREREKREAEVLAERLAGWQEQYPDVRVHRSLVCDKPARWLLEHSEQAQLVVVGSHGRGGFSGMLLGSVSSAVAHSVRIPVIVVRPS