Rv3134c Resolved · high auto-curated
H37Rv Rv3134c · MTBC0 mtbc0_003331 ·
268 aa · 3521308–3522114 (-) ·
RefSeq NP_217650.1
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 |
P9WFD3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Universal stress protein Rv3134c |
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 (15) |
GO:0001666, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006950, GO:0008150, GO:0009628, GO:0016020, GO:0030312, GO:0036293, GO:0044464 +3 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 | 0.501 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 | 5.1e-21 | 8–137 | Universal stress protein family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: devR (two component transcriptional regulator DevR), high confidence from genomic context alone (score 954 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3133c devR |
two component transcriptional regulator DevR | 991 | 954 ctx | neighborhood:744 coexpression:805 textmining:818 |
Rv3132c devS |
two component sensor histidine kinase DevS | 989 | 946 ctx | neighborhood:744 coexpression:730 textmining:809 |
Rv1733c |
transmembrane protein | 975 | 937 ctx | cooccurence:647 coexpression:829 textmining:626 |
Rv3127 hyp |
hypothetical protein | 933 | 911 ctx | cooccurence:403 coexpression:855 |
Rv2032 acg |
NAD(P)H nitroreductase | 936 | 906 ctx | cooccurence:404 coexpression:845 |
Rv3131 |
NAD(P)H nitroreductase | 946 | 892 | coexpression:827 textmining:529 |
Rv0080 hyp |
hypothetical protein | 915 | 891 | coexpression:823 |
Rv1996 |
universal stress protein | 894 | 887 | coexpression:850 |
Rv2623 TB31.7 |
universal stress protein | 898 | 886 | coexpression:853 |
Rv1738 hyp |
hypothetical protein | 975 | 882 ctx | cooccurence:424 coexpression:803 textmining:803 |
Rv2031c hspX |
alpha-crystallin | 941 | 871 | coexpression:843 textmining:564 |
Rv0079 hyp |
hypothetical protein | 954 | 869 | coexpression:868 textmining:671 |
Rv2626c hrp1 |
hypoxic response protein | 881 | 851 | coexpression:848 |
Rv2007c fdxA |
ferredoxin | 914 | 850 | coexpression:850 textmining:452 |
Rv2627c hyp |
hypothetical protein | 847 | 848 | coexpression:827 |
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=5e-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_217650.1)
- 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 P9WFD3 (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
devR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003331|Rv3134c| MSDPRPARAVVVGIDGSRAATHAALWAVDEAVNRDIPLRLVYVIDPSQLSAAGEGGGQSAARAALHDASRKVEATGQPVKIETEVLCGRPLTKLMQESRSAAMLCVGSVGLDHVRGRRGSVAATLAGSALCPVAVIHPSPAEPATTSQVSAVVAEVDNGVVLRHAFEEARLRGVPLRAVAVHAAETPDDVEQGSRLAHVHLSRRLAHWTRLYPEVRVDRAIAGGSACRHLAANAKPGQLFVADSHSAHELCGAYQPGCAVLTVRSANL