hisB Resolved · high auto-curated
H37Rv Rv1601 · MTBC0 mtbc0_001707 ·
210 aa · 1813999–1814631 (+) ·
RefSeq NP_216117.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | imidazole glycerol-phosphate dehydratase |
|---|---|
| MTBC0 PGAP re-annotation | imidazoleglycerol-phosphate dehydratase HisB |
| Revised (this work) | Imidazoleglycerol-phosphate dehydratase HisB. Pfam: IGPD (PF00475.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WML9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Imidazoleglycerol-phosphate dehydratase |
| EC (curated) |
EC 4.2.1.19
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | hisB |
| eggNOG description | imidazoleglycerol-phosphate dehydratase |
| Orthologous group | COG0131 |
| EC number |
EC 3.1.3.15, EC 4.2.1.19
|
| KEGG orthology |
K01089, K01693
|
| KEGG pathways |
map00340, map01100, map01110, map01230
|
| KEGG modules |
M00026
|
| Gene Ontology (40) |
GO:0000105, GO:0003674, GO:0003824, GO:0004424, GO:0006082, GO:0006520, GO:0006547, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0008652 +28 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
IGPD | PF00475.25 | 8.5e-57 | 40–190 | Imidazoleglycerol-phosphate dehydratase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hisH (imidazole glycerol phosphate synthase subunit HisH), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:958 database:900 textmining:617 |
Rv1599 hisD |
histidinol dehydrogenase | 999 | 1000 ctx | neighborhood:881 fusion:809 cooccurence:774 coexpression:957 textmining:938 |
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 999 | 1000 ctx | neighborhood:876 cooccurence:774 coexpression:884 database:900 textmining:697 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 999 | 1000 ctx | neighborhood:882 fusion:851 cooccurence:729 coexpression:937 database:900 textmining:711 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 999 | 999 ctx | neighborhood:876 cooccurence:770 coexpression:967 textmining:822 |
Rv1606 hisI |
phosphoribosyl-AMP cyclohydrolase | 999 | 997 ctx | neighborhood:876 cooccurence:774 coexpression:887 textmining:759 |
Rv3772 hisC2 |
histidinol-phosphate aminotransferase | 997 | 997 ctx | fusion:860 coexpression:692 database:900 |
Rv2231c cobC |
aminotransferase | 979 | 977 | coexpression:693 database:900 |
Rv1604 impA |
inositol-monophosphatase ImpA | 973 | 970 ctx | neighborhood:876 coexpression:770 |
Rv2121c hisG |
ATP phosphoribosyltransferase | 994 | 969 ctx | cooccurence:764 coexpression:857 textmining:843 |
Rv2122c hisE |
phosphoribosyl-ATP pyrophosphatase | 981 | 885 | coexpression:857 textmining:848 |
Rv1598c hyp |
hypothetical protein | 672 | 672 ctx | neighborhood:670 |
Rv3859c gltB |
glutamate synthase large subunit | 735 | 639 ctx | neighborhood:448 |
Rv2483c plsC |
bifunctional L-3-phosphoserine phosphatase/1-acyl-sn-glycerol-3-phosphate acyltransferase | 579 | 513 | coexpression:468 |
Rv3661 hyp |
hypothetical protein | 526 | 488 | coexpression:471 |
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: imidazole glycerol-phosphate dehydratase
- MTBC0 PGAP product: imidazoleglycerol-phosphate dehydratase HisB
- Pfam (hmmscan --cut_ga): IGPD PF00475.25 (E=8e-57)
- (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_216117.1)
- Domains: Pfam-A via hmmscan --cut_ga — IGPD (PF00475.25)
- 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
COG0131 - Curated reference: UniProt P9WML9 (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 —
53 functional partner(s); context anchor
hisH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001707|Rv1601|hisB MTTTQTAKASRRARIERRTRESDIVIELDLDGTGQVAVDTGVPFYDHMLTALGSHASFDLTVRATGDVEIEAHHTIEDTAIALGTALGQALGDKRGIRRFGDAFIPMDETLAHAAVDLSGRPYCVHTGEPDHLQHTTIAGSSVPYHTVINRHVFESLAANARIALHVRVLYGRDPHHITEAQYKAVARALRQAVEPDPRVSGVPSTKGAL