Rv2028c Resolved · high auto-curated
H37Rv Rv2028c · MTBC0 mtbc0_002161 ·
279 aa · 2303182–2304021 (-) ·
RefSeq NP_216544.1
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 |
P9WFD9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Universal stress protein Rv2028c |
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 (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, 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 | 0.557 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 | 3.3e-20 | 10–141 | Universal stress protein family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pfkB (6-phosphofructokinase PfkB), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2029c pfkB |
6-phosphofructokinase PfkB | 993 | 983 ctx | neighborhood:882 coexpression:860 textmining:630 |
Rv2030c hyp |
hypothetical protein | 986 | 962 ctx | neighborhood:808 coexpression:810 textmining:665 |
Rv2032 acg |
NAD(P)H nitroreductase | 934 | 913 ctx | neighborhood:483 cooccurence:407 coexpression:738 |
Rv2624c |
universal stress protein | 885 | 883 | coexpression:860 |
Rv2625c rip3 |
zinc metalloprotease Rip3 | 902 | 882 | coexpression:860 |
Rv1997 ctpF |
cation transporter ATPase F | 908 | 873 | coexpression:869 |
Rv1736c narX |
nitrate reductase-like protein NarX | 860 | 860 | coexpression:860 |
Rv1733c |
transmembrane protein | 881 | 833 | coexpression:740 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 809 | 810 | coexpression:803 |
Rv3132c devS |
two component sensor histidine kinase DevS | 888 | 809 | coexpression:748 textmining:440 |
Rv3128c |
Rv3128c, (MTCY164.38c), len: 337 aa. Conserved hypothetical protein, similar to other conserved hypothetical proteins. This ORF corresponds | 793 | 793 | coexpression:793 |
Rv1737c narK2 |
nitrate/nitrite transporter | 847 | 783 | coexpression:783 |
Rv1996 |
universal stress protein | 796 | 772 ctx | cooccurence:754 |
Rv2627c hyp |
hypothetical protein | 765 | 765 | coexpression:734 |
Rv2031c hspX |
alpha-crystallin | 917 | 762 ctx | neighborhood:727 textmining:667 |
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-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_216544.1)
- 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 P9WFD9 (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 —
59 functional partner(s); context anchor
pfkB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002161|Rv2028c| MNQSHKPPSIVVGIDGSKPAVQAALWAVDEAASRDIPLRLLYAIEPDDPGYAAHGAAARKLAAAENAVRYAFTAVEAADRPVKVEVEITQERPVTSLIRASAAAALVCVGAIGVHHFRPERVGSTAAALALSAQCPVAIVRPHRVPIGRDAAWIVVEADGSSDIGVLLGAVMAEARLRDSPVRVVTCRQSGVGDTGDDVRASLDRWLARWQPRYPDVRVQSAAVHGELLDYLAGLGRSVHMVVLSASDQEHVEQLVGAPGNAVLQEAGCTLLVVGQQYL