glpK Resolved · high auto-curated
H37Rv Rv3696c · MTBC0 mtbc0_003917 ·
517 aa · 4162150–4163703 (-) ·
RefSeq NP_218213.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycerol kinase |
|---|---|
| MTBC0 PGAP re-annotation | glycerol kinase GlpK |
| Revised (this work) | Glycerol kinase GlpK. Pfam: FGGY_N (PF00370.28), FGGY_C (PF02782.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPK1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycerol kinase |
| EC (curated) |
EC 2.7.1.30
|
| Curated function | Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn-glycerol 3-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | glpK |
| eggNOG description | Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn- glycerol 3-phosphate |
| Orthologous group | COG0554 |
| EC number |
EC 2.7.1.30
|
| KEGG orthology |
K00864
|
| KEGG pathways |
map00561, map01100, map03320, map04626
|
| Gene Ontology (24) |
GO:0003674, GO:0003824, GO:0004370, GO:0005975, GO:0006066, GO:0006071, GO:0006793, GO:0006796, GO:0008150, GO:0008152, GO:0009987, GO:0016301 +12 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) pseudogene candidate
| pN/pS | 0.683 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 2.14% of strains (3102) · 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 |
|---|---|---|---|---|
FGGY_N | PF00370.28 | 3.2e-68 | 17–268 | FGGY family of carbohydrate kinases, N-terminal domain |
FGGY_C | PF02782.23 | 1.7e-49 | 278–467 | FGGY family of carbohydrate kinases, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glpD2 (glycerol-3-phosphate dehydrogenase), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3302c glpD2 |
glycerol-3-phosphate dehydrogenase | 998 | 994 ctx | fusion:796 cooccurence:741 coexpression:726 database:500 textmining:691 |
Rv2115c mpa |
proteasome-associated ATPase | 990 | 989 | experimental:916 database:844 |
Rv1334 mec |
[CysO | 988 | 986 | experimental:908 database:844 |
Rv2249c glpD1 |
glycerol-3-phosphate dehydrogenase | 991 | 984 ctx | fusion:516 cooccurence:744 coexpression:725 database:500 textmining:469 |
Rv2110c prcB |
proteasome subunit beta | 936 | 929 | experimental:791 database:662 |
Rv2109c prcA |
proteasome subunit alpha | 936 | 928 | experimental:791 database:662 |
Rv3045 adhC |
NADP-dependent alcohol dehydrogenase | 916 | 911 | database:900 |
Rv1692 |
phosphatase | 913 | 905 | database:900 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 922 | 900 | database:900 |
Rv1551 plsB1 |
acyltransferase PlsB | 913 | 900 | database:900 |
Rv1043c hyp |
hypothetical protein | 769 | 754 | experimental:402 database:589 |
Rv0125 pepA |
serine protease PepA | 767 | 753 | experimental:402 database:589 |
Rv0983 pepD |
serine protease PepD | 767 | 753 | experimental:402 database:589 |
Rv3671c marP |
serine protease | 767 | 753 | experimental:402 database:589 |
Rv1223 htrA |
serine protease HtrA | 766 | 752 | experimental:402 database:589 |
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: glycerol kinase
- MTBC0 PGAP product: glycerol kinase GlpK
- Pfam (hmmscan --cut_ga): FGGY_N PF00370.28 (E=3e-68), FGGY_C PF02782.23 (E=2e-49)
- (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_218213.1)
- Domains: Pfam-A via hmmscan --cut_ga — FGGY_N (PF00370.28), FGGY_C (PF02782.23)
- 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
COG0554 - Curated reference: UniProt P9WPK1 (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 —
134 functional partner(s); context anchor
glpD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003917|Rv3696c|glpK MSDAILGEQLAESSDFIAAIDQGTTSTRCMIFDHHGAEVARHQLEHEQILPRAGWVEHNPVEIWERTASVLISVLNATNLSPKDIAALGITNQRETTLVWNRHTGRPYYNAIVWQDTRTDRIASALDRDGRGNLIRRKAGLPPATYFSGGKLQWILENVDGVRAAAENGDALFGTPDTWVLWNLTGGPRGGVHVTDVTNASRTMLMDLETLDWDDELLSLFSIPRAMLPEIASSAPSEPYGVTLATGPVGGEVPITGVLGDQHAAMVGQVCLAPGEAKNTYGTGNFLLLNTGETIVRSNNGLLTTVCYQFGNAKPVYALEGSIAVTGSAVQWLRDQLGIISGAAQSEALARQVPDNGGMYFVPAFSGLFAPYWRSDARGAIVGLSRFNTNAHLARATLEAICYQSRDVVDAMEADSGVRLQVLKVDGGITGNDLCMQIQADVLGVDVVRPVVAETTALGAAYAAGLAVGFWAAPSDLRANWREDKRWTPTWDDDERAAGYAGWRKAVQRTLDWVDVS