hspX Resolved · high auto-curated
H37Rv Rv2031c · MTBC0 mtbc0_002164 ·
144 aa · 2307111–2307545 (-) ·
RefSeq NP_216547.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | alpha-crystallin |
|---|---|
| MTBC0 PGAP re-annotation | alpha-crystallin HspX |
| Revised (this work) | Alpha-crystallin HspX. Pfam: HSP20 (PF00011.28), ArsA_HSP20 (PF17886.8). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMK1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alpha-crystallin |
| Curated function | Acts as a chaperone, as it has a significant ability to suppress the thermal denaturation of alcohol dehydrogenase. Cells overexpressing this gene grow more slowly than wild-type cells, and are less susceptible to autolysis following saturation of the culture in vitro, suggesting this protein may slow down the growth rate of M.tuberculosis in culture and by extension during macrophage infection. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | hspX |
| eggNOG description | Belongs to the small heat shock protein (HSP20) family |
| Orthologous group | COG0071 |
| KEGG orthology |
K13993
|
| KEGG pathways |
map04141
|
| Gene Ontology (89) |
GO:0001666, GO:0003674, GO:0005488, GO:0005515, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006457 +77 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 | 0.321 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
HSP20 | PF00011.28 | 1.4e-24 | 45–140 | Hsp20/alpha crystallin family |
ArsA_HSP20 | PF17886.8 | 1.8e-06 | 48–125 | HSP20-like domain found in ArsA |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: acg (NAD(P)H nitroreductase), high confidence from genomic context alone (score 932 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2030c hyp |
hypothetical protein | 980 | 966 ctx | neighborhood:792 coexpression:804 textmining:452 |
Rv2032 acg |
NAD(P)H nitroreductase | 967 | 932 ctx | neighborhood:531 coexpression:860 textmining:548 |
Rv1738 hyp |
hypothetical protein | 963 | 906 | coexpression:860 textmining:630 |
Rv1996 |
universal stress protein | 916 | 893 | coexpression:864 |
Rv3134c |
universal stress protein | 941 | 871 | coexpression:843 textmining:564 |
Rv3131 |
NAD(P)H nitroreductase | 918 | 864 | coexpression:860 textmining:429 |
Rv0079 hyp |
hypothetical protein | 910 | 864 | coexpression:862 |
Rv2626c hrp1 |
hypoxic response protein | 950 | 863 | coexpression:859 textmining:654 |
Rv3130c tgs1 |
diacyglycerol O-acyltransferase | 942 | 862 | coexpression:861 textmining:602 |
Rv3127 hyp |
hypothetical protein | 909 | 861 | coexpression:860 |
Rv2007c fdxA |
ferredoxin | 947 | 860 | coexpression:860 textmining:640 |
Rv2623 TB31.7 |
universal stress protein | 971 | 856 | coexpression:827 textmining:812 |
Rv1733c |
transmembrane protein | 936 | 837 | coexpression:804 textmining:625 |
Rv0080 hyp |
hypothetical protein | 872 | 833 | coexpression:829 |
Rv2627c hyp |
hypothetical protein | 810 | 810 | coexpression:805 |
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: alpha-crystallin
- MTBC0 PGAP product: alpha-crystallin HspX
- Pfam (hmmscan --cut_ga): HSP20 PF00011.28 (E=1e-24), ArsA_HSP20 PF17886.8 (E=2e-06)
- (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_216547.1)
- Domains: Pfam-A via hmmscan --cut_ga — HSP20 (PF00011.28), ArsA_HSP20 (PF17886.8)
- 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
COG0071 - Curated reference: UniProt P9WMK1 (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 —
89 functional partner(s); context anchor
acg - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002164|Rv2031c|hspX MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEVRAELPGVDPDKDVDIMVRDGQLTIKAERTEQKDFDGRSEFAYGSFVRTVSLPVGADEDDIKATYDKGILTVSVAVSEGKPTEKHIQIRSTN