TB15.3 Resolved · high auto-curated
H37Rv Rv1636 · MTBC0 mtbc0_001744 ·
146 aa · 1854415–1854855 (+) ·
RefSeq NP_216152.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | iron-regulated 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 |
P9WFC9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Universal stress protein Rv1636 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| Preferred name | uspA3 |
| eggNOG description | Universal stress protein |
| Orthologous group | COG0589 |
| Gene Ontology (12) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0042221, GO:0044464, GO:0046677, GO:0050896, 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
Usp | PF00582.33 | 1.7e-27 | 4–144 | Universal stress protein family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1635c (mannosyltransferase), medium confidence from genomic context alone (score 619 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 687 | 688 | coexpression:687 |
Rv1635c |
mannosyltransferase | 618 | 619 ctx | neighborhood:617 |
Rv1318c |
adenylate cyclase | 551 | 548 ctx | cooccurence:548 |
Rv1319c |
adenylate cyclase | 544 | 541 ctx | cooccurence:541 |
Rv1320c |
adenylate cyclase | 541 | 524 ctx | cooccurence:523 |
Rv3645 |
transmembrane protein | 529 | 522 ctx | cooccurence:514 |
Rv3584 lpqE |
lipoprotein LpqE | 448 | 449 | |
Rv3718c hyp |
hypothetical protein | 446 | 446 ctx | cooccurence:443 |
Rv1316c ogt |
methylated-DNA--protein-cysteine methyltransferase | 427 | 428 | coexpression:419 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 422 | 423 ctx | cooccurence:412 |
Rv3314c deoA |
thymidine phosphorylase | 412 | 413 | coexpression:410 |
Rv3241c raiA hyp |
hypothetical protein | 407 | 380 | |
Rv0079 hyp |
hypothetical protein | 400 | 372 | |
Rv1240 mdh |
malate dehydrogenase | 499 | 295 | |
Rv3369 hyp |
hypothetical protein | 757 | 249 | textmining:690 |
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: iron-regulated universal stress protein
- MTBC0 PGAP product: universal stress protein
- Pfam (hmmscan --cut_ga): Usp PF00582.33 (E=2e-27)
- (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_216152.1)
- 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 P9WFC9 (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 —
35 functional partner(s); context anchor
Rv1635c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001744|Rv1636|TB15.3 MSAYKTVVVGTDGSDSSMRAVDRAAQIAGADAKLIIASAYLPQHEDARAADILKDESYKVTGTAPIYEILHDAKERAHNAGAKNVEERPIVGAPVDALVNLADEEKADLLVVGNVGLSTIAGRLLGSVPANVSRRAKVDVLIVHTT