Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | universal stress protein |
|---|
| MTBC0 PGAP re-annotation | universal stress protein TB31.7 |
|---|
| Revised (this work) | Universal stress protein TB31.7. 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 |
P9WFD7
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Universal stress protein Rv2623 |
|---|
| Curated function | May play a role in the establishment of a persistent infection (latency) in the host, as strains without this gene are hypervirulent. Overexpression of the protein retards growth in culture; Glu-15 and Ala-117 mutant proteins which bind less ATP do not show this retardation, suggesting growth may be regulated through an ATP-dependent function. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|
| eggNOG description | Universal stress protein |
|---|
| Orthologous group | COG0589 |
|---|
| Gene Ontology (51) |
GO:0000166, GO:0001666, GO:0003674, GO:0005488, GO:0005524, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886 +39 more
|
|---|
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 |
2.947 · diversifying/relaxed
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
1 synonymous, 8 missense, 0 nonsense, 1 frameshift
|
|---|
| Disruption |
1 distinct premature-stop/frameshift site(s); most common in
0.19% of strains
(277) · 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 |
6.3e-27 | 162–293 |
Universal stress protein family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2032 acg |
NAD(P)H nitroreductase |
926 |
907 |
coexpression:860 |
Rv3134c |
universal stress protein |
898 |
886 |
coexpression:853 |
Rv3127 hyp |
hypothetical protein |
882 |
878 |
coexpression:803 |
Rv0080 hyp |
hypothetical protein |
912 |
877 |
coexpression:845 |
Rv2627c hyp |
hypothetical protein |
873 |
874 |
coexpression:853 |
Rv1996 |
universal stress protein |
869 |
865 |
coexpression:853 |
Rv2626c hrp1 |
hypoxic response protein |
949 |
862 |
coexpression:860 textmining:648 |
Rv2625c rip3 |
zinc metalloprotease Rip3 |
878 |
862 |
coexpression:803 |
Rv2031c hspX |
alpha-crystallin |
971 |
856 |
coexpression:827 textmining:812 |
Rv1733c |
transmembrane protein |
878 |
843 |
coexpression:843 |
Rv2030c hyp |
hypothetical protein |
878 |
839 |
coexpression:833 |
Rv2007c fdxA |
ferredoxin |
903 |
836 |
coexpression:831 textmining:433 |
Rv1813c hyp |
hypothetical protein |
836 |
836 |
coexpression:836 |
Rv1737c narK2 |
nitrate/nitrite transporter |
890 |
834 |
coexpression:805 |
Rv0079 hyp |
hypothetical protein |
865 |
825 |
coexpression:824 |
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 TB31.7
- Pfam (hmmscan --cut_ga): Usp PF00582.33 (E=6e-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_217139.1)
- 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
P9WFD7
(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 —
46 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002792|Rv2623|TB31.7
MSSGNSSLGIIVGIDDSPAAQVAVRWAARDAELRKIPLTLVHAVSPEVATWLEVPLPPGVLRWQQDHGRHLIDDALKVVEQASLRAGPPTVHSEIVPAAAVPTLVDMSKDAVLMVVGCLGSGRWPGRLLGSVSSGLLRHAHCPVVIIHDEDSVMPHPQQAPVLVGVDGSSASELATAIAFDEASRRNVDLVALHAWSDVDVSEWPGIDWPATQSMAEQVLAERLAGWQERYPNVAITRVVVRDQPARQLVQRSEEAQLVVVGSRGRGGYAGMLVGSVGETVAQLARTPVIVARESLT
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