glmS Resolved · high auto-curated
H37Rv Rv3436c · MTBC0 mtbc0_003655 ·
624 aa · 3880901–3882775 (-) ·
RefSeq NP_217953.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glucosamine--fructose-6-phosphate aminotransferase |
|---|---|
| MTBC0 PGAP re-annotation | glutamine--fructose-6-phosphate transaminase (isomerizing) |
| Revised (this work) | Glutamine--fructose-6-phosphate transaminase (isomerizing). Pfam: GATase_6 (PF13522.12), GATase_7 (PF13537.12), 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 |
P9WN49
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutamine--fructose-6-phosphate aminotransferase [isomerizing] |
| EC (curated) |
EC 2.6.1.16
|
| Curated function | Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | glmS |
| eggNOG description | Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source |
| Orthologous group | COG0449 |
| EC number |
EC 2.6.1.16
|
| KEGG orthology |
K00820
|
| KEGG pathways |
map00250, map00520, map01100, map01130, map04931
|
| Gene Ontology (62) |
GO:0003674, GO:0003824, GO:0004360, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006002, GO:0006040, GO:0006047 +50 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 | 0.224 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 7 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 |
|---|---|---|---|---|
GATase_6 | PF13522.12 | 2.5e-20 | 67–200 | Glutamine amidotransferase domain |
GATase_7 | PF13537.12 | 2.3e-13 | 84–204 | Glutamine amidotransferase domain |
SIS | PF01380.28 | 6.5e-37 | 301–427 | SIS domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gltB (glutamate synthase large subunit), high confidence from genomic context alone (score 958 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3859c gltB |
glutamate synthase large subunit | 981 | 958 ctx | neighborhood:544 database:900 textmining:589 |
Rv3441c mrsA |
phosphoglucosamine mutase | 992 | 943 | database:900 textmining:871 |
Rv2222c glnA2 |
glutamine synthetase | 930 | 924 | database:900 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 937 | 919 | database:900 |
Rv2220 glnA1 |
glutamine synthetase | 931 | 917 | database:900 |
Rv1878 glnA3 |
glutamine synthetase GlnA | 923 | 916 | database:900 |
Rv2860c glnA4 |
glutamine synthetase | 923 | 916 | database:900 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 921 | 909 | database:900 |
Rv3332 nagA |
N-acetylglucosamine-6-phosphate deacetylase NagA | 987 | 908 | database:900 textmining:870 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 958 | 908 | database:900 textmining:562 |
Rv0808 purF |
amidophosphoribosyltransferase | 918 | 908 | database:900 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 913 | 908 | database:900 |
Rv3255c manA |
mannose-6-phosphate isomerase | 957 | 904 | database:900 textmining:574 |
Rv3858c gltD |
glutamate synthase small subunit | 916 | 904 | database:900 |
Rv1018c glmU |
bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase | 962 | 823 ctx | fusion:590 coexpression:464 textmining:798 |
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: glucosamine--fructose-6-phosphate aminotransferase
- MTBC0 PGAP product: glutamine--fructose-6-phosphate transaminase (isomerizing)
- Pfam (hmmscan --cut_ga): GATase_6 PF13522.12 (E=2e-20), GATase_7 PF13537.12 (E=2e-13), SIS PF01380.28 (E=7e-37)
- (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_217953.1)
- Domains: Pfam-A via hmmscan --cut_ga — GATase_6 (PF13522.12), GATase_7 (PF13537.12), 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
COG0449 - Curated reference: UniProt P9WN49 (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 —
73 functional partner(s); context anchor
gltB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003655|Rv3436c|glmS MCGIVGYVGRRPAYVVVMDALRRMEYRGYDSSGIALVDGGTLTVRRRAGRLANLEEAVAEMPSTALSGTTGLGHTRWATHGRPTDRNAHPHRDAAGKIAVVHNGIIENFAVLRRELETAGVEFASDTDTEVAAHLVARAYRHGETADDFVGSVLAVLRRLEGHFTLVFANADDPGTLVAARRSTPLVLGIGDNEMFVGSDVAAFIEHTREAVELGQDQAVVITADGYRISDFDGNDGLQAGRDFRPFHIDWDLAAAEKGGYEYFMLKEIAEQPAAVADTLLGHFVGGRIVLDEQRLSDQELREIDKVFVVACGTAYHSGLLAKYAIEHWTRLPVEVELASEFRYRDPVLDRSTLVVAISQSGETADTLEAVRHAKEQKAKVLAICNTNGSQIPRECDAVLYTRAGPEIGVASTKTFLAQIAANYLLGLALAQARGTKYPDEVEREYHELEAMPDLVARVIAATGPVAELAHRFAQSSTVLFLGRHVGYPVALEGALKLKELAYMHAEGFAAGELKHGPIALIEDGLPVIVVMPSPKGSATLHAKLLSNIREIQTRGAVTIVIAEEGDETVRPYADHLIEIPAVSTLLQPLLSTIPLQVFAASVARARGYDVDKPRNLAKSVTVE