gmhA Resolved · high auto-curated
H37Rv Rv0113 · MTBC0 mtbc0_000123 ·
196 aa · 137484–138074 (+) ·
RefSeq NP_214627.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoheptose isomerase |
|---|---|
| MTBC0 PGAP re-annotation | D-sedoheptulose 7-phosphate isomerase |
| Revised (this work) | D-sedoheptulose 7-phosphate isomerase. Pfam: SIS_2 (PF13580.12), SIS (PF01380.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGG1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphoheptose isomerase |
| EC (curated) |
EC 5.3.1.28
|
| Curated function | Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | gmhA |
| eggNOG description | Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate |
| Orthologous group | COG0279 |
| EC number |
EC 2.7.7.71, EC 5.3.1.28
|
| KEGG orthology |
K03271, K15669
|
| KEGG pathways |
map00540, map01100
|
| KEGG modules |
M00064
|
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) pseudogene candidate
| pN/pS | 1.017 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 2.71% of strains (3931) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
SIS_2 | PF13580.12 | 1.4e-24 | 35–148 | SIS domain |
SIS | PF01380.28 | 1.2e-08 | 111–166 | SIS domain |
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 | 998 | 999 ctx | neighborhood:710 cooccurence:736 coexpression:811 database:900 |
Rv0114 gmhB |
D-glycero-alpha-D-manno-heptose-1,7-bisphosphate 7-phosphatase | 999 | 993 ctx | neighborhood:713 cooccurence:774 coexpression:907 textmining:895 |
Rv0112 gca |
GDP-mannose 4,6-dehydratase | 954 | 952 ctx | neighborhood:579 coexpression:863 |
Rv0486 mshA |
D-inositol 3-phosphate glycosyltransferase | 800 | 788 ctx | fusion:776 |
Rv3032 |
glycogen synthase | 566 | 539 ctx | fusion:510 |
Rv0001 dnaA |
chromosomal replication initiator protein DnaA | 554 | 495 | experimental:469 |
Rv3465 rmlC |
dTDP-4-dehydrorhamnose 3,5-epimerase | 469 | 391 | |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 431 | 238 | |
Rv1514c |
glycosyltransferase | 542 | 186 | textmining:461 |
Rv2965c kdtB |
phosphopantetheine adenylyltransferase | 824 | 116 | textmining:809 |
Rv2538c aroB |
3-dehydroquinate synthase | 560 | 63 | textmining:550 |
Rv0059 darT hyp |
hypothetical protein | 554 | 55 | textmining:548 |
Rv0033 acpA |
acyl carrier protein AcpA | 628 | 49 | textmining:625 |
Rv1564c treX |
maltooligosyl trehalose synthase | 414 | 46 | textmining:411 |
Rv2732c |
transmembrane protein | 625 | 42 | textmining:625 |
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: phosphoheptose isomerase
- MTBC0 PGAP product: D-sedoheptulose 7-phosphate isomerase
- Pfam (hmmscan --cut_ga): SIS_2 PF13580.12 (E=1e-24), SIS PF01380.28 (E=1e-08)
- (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_214627.1)
- Domains: Pfam-A via hmmscan --cut_ga — SIS_2 (PF13580.12), SIS (PF01380.28)
- 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
COG0279 - Curated reference: UniProt P9WGG1 (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 —
17 functional partner(s); context anchor
hddA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000123|Rv0113|gmhA MCTARTAEEIFVETIAVKTRILNDRVLLEAARAIGDRLIAGYRAGARVFMCGNGGSAADAQHFAAELTGHLIFDRPPLGAEALHANSSHLTAVANDYDYDTVFARALEGSARPGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGESGGQLAEFADFLINVPSRDTGRIQESHIVFIHAISEHVEHALFAPRQ