gmhB Resolved · medium auto-curated
H37Rv Rv0114 · MTBC0 mtbc0_000124 ·
190 aa · 138106–138678 (+) ·
RefSeq NP_214628.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | D-glycero-alpha-D-manno-heptose-1,7-bisphosphate 7-phosphatase |
|---|---|
| MTBC0 PGAP re-annotation | D-glycero-alpha-D-manno-heptose-1%2C7-bisphosphate 7-phosphatase |
| Revised (this work) | D-glycero-alpha-D-manno-heptose-1%2C7-bisphosphate 7-phosphatase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMV3
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | D-glycero-alpha-D-manno-heptose-1,7-bisphosphate 7-phosphatase |
| EC (curated) |
EC 3.1.3.83
|
| Curated function | Converts the D-glycero-alpha-D-manno-heptose 1,7-bisphosphate intermediate into D-glycero-alpha-D-manno-heptose 1-phosphate by removing the phosphate group at the C-7 position. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | gmhB |
| eggNOG description | D,D-heptose 1,7-bisphosphate phosphatase |
| Orthologous group | COG0241 |
| EC number |
EC 3.1.3.82, EC 3.1.3.83
|
| KEGG orthology |
K03273
|
| KEGG pathways |
map00540, map01100
|
| KEGG modules |
M00064
|
| Gene Ontology (21) |
GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0006793, GO:0006796, GO:0008150, GO:0008152, GO:0008270, GO:0009987, GO:0016311, GO:0016787 +9 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 | 0.806 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.29% of strains (416) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hddA (D-alpha-D-heptose-7-phosphate kinase HddA), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0115 hddA |
D-alpha-D-heptose-7-phosphate kinase HddA | 999 | 999 ctx | neighborhood:802 cooccurence:699 coexpression:860 database:900 |
Rv0113 gmhA |
phosphoheptose isomerase | 999 | 993 ctx | neighborhood:713 cooccurence:774 coexpression:907 textmining:895 |
Rv0112 gca |
GDP-mannose 4,6-dehydratase | 937 | 934 ctx | neighborhood:509 coexpression:829 |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 771 | 749 | database:597 |
Rv3062 ligB |
DNA ligase | 762 | 738 | database:597 |
Rv3731 ligC |
DNA ligase C | 761 | 737 | database:597 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 742 | 703 | coexpression:679 |
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 740 | 672 | coexpression:645 |
Rv1599 hisD |
histidinol dehydrogenase | 748 | 671 | coexpression:644 |
Rv3264c manB |
D-alpha-D-mannose-1-phosphate guanylyltransferase ManB | 714 | 671 ctx | fusion:571 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 746 | 669 | coexpression:642 |
Rv2231c cobC |
aminotransferase | 605 | 564 | coexpression:547 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 605 | 564 | coexpression:547 |
Rv3772 hisC2 |
histidinol-phosphate aminotransferase | 605 | 564 | coexpression:547 |
Rv2121c hisG |
ATP phosphoribosyltransferase | 653 | 548 | coexpression:511 |
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: D-glycero-alpha-D-manno-heptose-1,7-bisphosphate 7-phosphatase
- MTBC0 PGAP product: D-glycero-alpha-D-manno-heptose-1%2C7-bisphosphate 7-phosphatase
- (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_214628.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0241 - Curated reference: UniProt P9WMV3 (SwissProt, reviewed; Inferred from homology)
- 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 —
23 functional partner(s); context anchor
hddA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000124|Rv0114|gmhB MVAERAGHQWCLFLDRDGVINRQVVGDYVRNWRQFEWLPGAARALKKLRAWAPYIVVVTNQQGVGAGLMSAVDVMVIHRHLQMQLASDGVLIDGFQVCPHHRSQRCGCRKPRPGLVLDWLGRHPDSEPLLSIVVGDSLSDLELAHNVAAAAGACASVQIGGASSGGVADASFDSLWEFAVAVGHARGERG