glgP Family assigned · medium auto-curated
H37Rv Rv1328 · MTBC0 mtbc0_001425 ·
863 aa · 1505266–1507857 (+) ·
RefSeq NP_215844.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycogen phosphorylase |
|---|---|
| MTBC0 PGAP re-annotation | glycosyltransferase family 1 protein |
| Revised (this work) | Glycosyltransferase family 1 protein. Pfam: DUF3417 (PF11897.14), Phosphorylase (PF00343.27), GlgP_C (PF28476.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMW1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycogen phosphorylase |
| EC (curated) |
EC 2.4.1.1
|
| Curated function | Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | glgP |
| eggNOG description | phosphorylase |
| Orthologous group | COG0058 |
| EC number |
EC 2.4.1.1
|
| KEGG orthology |
K00688
|
| KEGG pathways |
map00500, map01100, map01110, map02026, map04217, map04910, map04922, map04931
|
| CAZy family |
GT35
|
| Gene Ontology (11) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0044424, GO:0044444, GO:0044464, GO:0071944
|
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 | 1.974 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 17 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 |
|---|---|---|---|---|
DUF3417 | PF11897.14 | 1.2e-34 | 13–126 | Protein of unknown function (DUF3417) |
Phosphorylase | PF00343.27 | 6.7e-21 | 237–632 | Carbohydrate phosphorylase |
GlgP_C | PF28476.1 | 1.0e-29 | 751–862 | Glycogen phosphorylase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glgB (1,4-alpha-glucan branching protein), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1326c glgB |
1,4-alpha-glucan branching protein | 999 | 995 ctx | neighborhood:768 coexpression:732 database:900 textmining:937 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 988 | 983 | coexpression:818 database:900 |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 999 | 982 | coexpression:765 database:900 textmining:948 |
Rv1564c treX |
maltooligosyl trehalose synthase | 997 | 969 | coexpression:631 database:900 textmining:936 |
Rv1781c malQ |
4-alpha-glucanotransferase | 984 | 966 | coexpression:648 database:900 textmining:548 |
Rv0126 treS |
trehalose synthase/amylase TreS | 979 | 947 | database:900 textmining:636 |
Rv1212c glgA |
capsular glucan synthase | 991 | 946 | database:900 textmining:857 |
Rv3031 |
1,4-alpha-glucan-branching protein | 976 | 907 | database:900 textmining:759 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 942 | 900 | database:900 textmining:446 |
Rv1327c glgE |
alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | 990 | 858 ctx | neighborhood:772 textmining:936 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 930 | 802 | coexpression:729 textmining:663 |
Rv1023 eno |
enolase | 800 | 740 | coexpression:699 |
Rv3010c pfkA |
6-phosphofructokinase | 790 | 727 | coexpression:676 |
Rv3257c pmmA |
phosphomannomutase PmmA | 752 | 725 ctx | fusion:672 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 755 | 680 | coexpression:654 |
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: glycogen phosphorylase
- MTBC0 PGAP product: glycosyltransferase family 1 protein
- Pfam (hmmscan --cut_ga): DUF3417 PF11897.14 (E=1e-34), Phosphorylase PF00343.27 (E=7e-21), GlgP_C PF28476.1 (E=1e-29)
- (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_215844.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3417 (PF11897.14), Phosphorylase (PF00343.27), GlgP_C (PF28476.1)
- 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
COG0058 - Curated reference: UniProt P9WMW1 (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 —
67 functional partner(s); context anchor
glgB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001425|Rv1328|glgP MKALRRFTVRAHLPERLAALDQLSTNLRWSWDKPTQDLFAAIDPALWEQCGHDPVALLGAVNPARLDELALDAEFLGALDELAADLNDYLSRPLWYQEQQDAGVAAQALPTGIAYFSLEFGVAEVLPNYSGGLGILAGDHLKSASDLGVPLIAVGLYYRSGYFRQSLTADGWQHETYPSLDPQGLPLRLLTDANGDPVLVEVALGDNAVLRARIWVAQVGRVPLLLLDSDIPENEHDLRNVTDRLYGGDQEHRIKQEILAGIGGVRAIRAYTAVEKLTPPEVFHMNEGHAGFLGIERIRELVTDAGLDFDTALTVVRSSTVFTTHTPVPAGIDRFPLEMVQRYVNDQRGDGRSRLLPGLPADRIVALGAEDDPAKFNMAHMGLRLAQRANGVSLLHGRVSRAMFNELWAGFDPDEVPIGSVTNGVHAPTWAAPQWLQLGRELAGSDSLREPVVWQRLHQVDPAHLWWIRSQLRSMLVEDVRARLRQSWLERGATDAELGWIATAFDPNVLTVGFARRVPTYKRLTLMLRDPDRLEQLLLDEQRPIQLIVAGKSHPADDGGKALIQQVVRFADRPQVRHRIAFLPNYDMSMARLLYWGCDVWLNNPLRPLEACGTSGMKSALNGGLNLSIRDGWWDEWYDGENGWEIPSADGVADENRRDDLEAGALYDLLAQAVAPKFYERDERGVPQRWVEMVRHTLQTLGPKVLASRMVRDYVEHYYAPAAQSFRRTAGAQFDAARELADYRRRAEEAWPKIEIADVDSTGLPDTPLLGSQLTLTATVRLAGLRPNDVTVQGVLGRVDSGDVLMDPVTVEMAHTGTGDGGYEIFSTTTPLPLAGPVGYTVRVLPRHPMLAASNELGLVTLA