Rv2319c Resolved · high auto-curated
H37Rv Rv2319c · MTBC0 mtbc0_002467 ·
292 aa · 2616597–2617475 (-) ·
RefSeq NP_216835.1
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 |
P9WLB5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Universal stress protein Rv2319c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| Preferred name | uspA4 |
| eggNOG description | Universal stress protein |
| 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) pseudogene candidate
| pN/pS | 0.871 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 17.63% of strains (25598) · 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 | 2.3e-20 | 2–140 | Universal stress protein family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rocE (cationic amino acid transporter permease RocE), high confidence from genomic context alone (score 975 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2320c rocE |
cationic amino acid transporter permease RocE | 983 | 975 ctx | neighborhood:800 coexpression:861 |
Rv2323c hyp |
hypothetical protein | 978 | 963 ctx | neighborhood:780 coexpression:840 textmining:433 |
Rv2322c rocD1 |
Rv2322c, (MTCY3G12.12), len: 221 aa. Probable rocD1,ornithine aminotransferase, highly similar to N-terminal region of other ornithine amino | 962 | 961 ctx | neighborhood:783 coexpression:826 |
Rv2321c rocD2 |
Rv2321c, (MTCY3G12.13), len: 181 aa. Probable rocD2,ornithine aminotransferase, highly similar to C-terminal region of other ornithine amino | 984 | 954 ctx | neighborhood:783 coexpression:797 textmining:667 |
Rv2324 |
AsnC family transcriptional regulator | 713 | 615 ctx | neighborhood:613 |
Rv1921c lppF |
lipoprotein LppF | 531 | 531 ctx | cooccurence:529 |
Rv0295c stf0 hyp |
hypothetical protein | 460 | 460 ctx | cooccurence:460 |
Rv1288 hyp |
hypothetical protein | 463 | 444 ctx | cooccurence:440 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 443 | 443 ctx | cooccurence:443 |
Rv2226 hyp |
hypothetical protein | 438 | 438 ctx | cooccurence:421 |
Rv1316c ogt |
methylated-DNA--protein-cysteine methyltransferase | 424 | 424 | coexpression:415 |
Rv3637 |
Possible transposase; Rv3637, (MTCY15C10.15c), len: 166 aa. Possible transposase. C-terminal end highly similar to Q9RLQ9|ISTA putative tran | 413 | 413 | |
Rv3636 |
Possible transposase; Rv3636, (MTCY15C10.16c), len: 115 aa. Possible transposase, weakly similar to others e.g. O69924|SC3C8.12 putative tra | 410 | 410 | |
Rv3314c deoA |
thymidine phosphorylase | 409 | 409 | coexpression:406 |
Rv0049 hyp |
hypothetical protein | 734 | 229 | textmining:670 |
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=2e-20)
- (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_216835.1)
- 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 P9WLB5 (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 —
21 functional partner(s); context anchor
rocE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002467|Rv2319c| MTIVVGYLAGKVGPSALHLAVRVARMHKTSLTVATIVRRHWPTPSLARVDAEYELWSEQLAAASAREAQRYLRRLADGIEVSYHHRAHRSVSAGLLDVVEELEAEVLVLGSFPSGRRARVLIGSTADRLLHSSPVPVAITPRRYRCYTDRLTRLSCGYSATSGSVDVVRRCGHLASRYGVPMRVITFAVRGRTMYPPEVGLHAEASVLEAWAAQARELLEKLRINGVVSEDVVLQVVTGNGWAQALDAADWQDGEILALGTSPFGDVARVFLGSWSGKIIRYSPVPVLVLPG