glgA Resolved · high auto-curated
H37Rv Rv1212c · MTBC0 mtbc0_001300 ·
387 aa · 1362940–1364103 (-) ·
RefSeq NP_215728.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | capsular glucan synthase |
|---|---|
| MTBC0 PGAP re-annotation | glycogen synthase |
| Revised (this work) | Glycogen synthase. Pfam: Glyco_transf_4 (PF13439.13), Glyco_trans_4_4 (PF13579.13), Glyco_transf_5 (PF08323.18), GT4-conflict (PF20706.4), Glycos_transf_1 (PF00534.27), Glyco_trans_1_4 (PF13692.13), Glyco_trans_1_2 (PF13524.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMZ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alpha-maltose-1-phosphate synthase |
| EC (curated) |
EC 2.4.1.342
|
| Curated function | Involved in the biosynthesis of the maltose-1-phosphate (M1P) building block required for alpha-glucan production by the key enzyme GlgE. Catalyzes the formation of an alpha-1,4 linkage between glucose from ADP-glucose and glucose 1-phosphate (G1P) to yield maltose-1-phosphate (M1P). Also able to catalyze the elongation of the non-reducing ends of glycogen, maltodextrin and maltoheptaose using ADP-glucose as sugar donor, however the rate of the reaction appears to be too low to be physiologically relevant. GlgM is also able to use UDP-glucose as sugar donor with G1P, however, it is less effici. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | glgA |
| eggNOG description | Glycogen synthase |
| Orthologous group | COG0297 |
| EC number |
EC 2.4.1.342
|
| KEGG orthology |
K16148
|
| KEGG pathways |
map00500, map01100
|
| CAZy family |
GT4
|
| Gene Ontology (28) |
GO:0000271, GO:0003674, GO:0003824, GO:0005975, GO:0005976, GO:0006073, GO:0008150, GO:0008152, GO:0009058, GO:0009059, GO:0009250, GO:0009987 +16 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 | 2.134 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 12 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 |
|---|---|---|---|---|
Glyco_transf_4 | PF13439.13 | 4.6e-27 | 15–176 | Glycosyltransferase Family 4 |
Glyco_trans_4_4 | PF13579.13 | 2.3e-13 | 16–172 | Glycosyl transferase 4-like domain |
Glyco_transf_5 | PF08323.18 | 3.6e-05 | 61–156 | Starch synthase catalytic domain |
GT4-conflict | PF20706.4 | 6.6e-13 | 126–376 | Family 4 Glycosyltransferase in conflict systems |
Glycos_transf_1 | PF00534.27 | 3.3e-29 | 193–364 | Glycosyl transferases group 1 |
Glyco_trans_1_4 | PF13692.13 | 4.6e-25 | 200–347 | Glycosyl transferases group 1 |
Glyco_trans_1_2 | PF13524.13 | 2.7e-08 | 270–380 | Glycosyl transferase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glgC (glucose-1-phosphate adenylyltransferase), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 999 | 987 ctx | neighborhood:765 cooccurence:465 database:900 textmining:965 |
Rv1327c glgE |
alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | 998 | 970 ctx | cooccurence:662 database:900 textmining:959 |
Rv1328 glgP |
glycogen phosphorylase | 991 | 946 | database:900 textmining:857 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 943 | 940 | database:900 |
Rv0127 mak |
maltokinase | 994 | 928 | database:900 textmining:933 |
Rv1781c malQ |
4-alpha-glucanotransferase | 968 | 914 | database:900 textmining:649 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 995 | 910 | coexpression:410 database:777 textmining:954 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 992 | 903 | database:900 textmining:922 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 987 | 834 | coexpression:407 database:572 textmining:925 |
Rv2529 hyp |
hypothetical protein | 673 | 661 | database:516 |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 556 | 528 | coexpression:443 |
Rv3809c glf |
UDP-galactopyranose mutase | 512 | 487 | coexpression:470 |
Rv3465 rmlC |
dTDP-4-dehydrorhamnose 3,5-epimerase | 503 | 473 | coexpression:455 |
Rv2627c hyp |
hypothetical protein | 481 | 456 | experimental:443 |
Rv2307c hyp |
hypothetical protein | 479 | 455 | experimental:443 |
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: capsular glucan synthase
- MTBC0 PGAP product: glycogen synthase
- Pfam (hmmscan --cut_ga): Glyco_transf_4 PF13439.13 (E=5e-27), Glyco_trans_4_4 PF13579.13 (E=2e-13), Glyco_transf_5 PF08323.18 (E=4e-05), GT4-conflict PF20706.4 (E=7e-13), Glycos_transf_1 PF00534.27 (E=3e-29), Glyco_trans_1_4 PF13692.13 (E=5e-25), Glyco_trans_1_2 PF13524.13 (E=3e-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_215728.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_transf_4 (PF13439.13), Glyco_trans_4_4 (PF13579.13), Glyco_transf_5 (PF08323.18), GT4-conflict (PF20706.4), Glycos_transf_1 (PF00534.27), Glyco_trans_1_4 (PF13692.13), Glyco_trans_1_2 (PF13524.13)
- 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
COG0297 - Curated reference: UniProt P9WMZ1 (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 —
35 functional partner(s); context anchor
glgC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001300|Rv1212c|glgA MRVAMLTREYPPEVYGGAGVHVTELVAYLRRLCAVDVHCMGAPRPGAFAYRPDPRLGSANAALSTLSADLVMANAASAATVVHSHTWYTALAGHLAAILYDIPHVLTAHSLEPLRPWKKEQLGGGYQVSTWVEQTAVLAANAVIAVSSAMRNDMLRVYPSLDPNLVHVIRNGIDTETWYPAGPARTGSVLAELGVDPNRPMAVFVGRITRQKGVVHLVTAAHRFRSDVQLVLCAGAADTPEVADEVRVAVAELARNRTGVFWIQDRLTIGQLREILSAATVFVCPSVYEPLGIVNLEAMACATAVVASDVGGIPEVVADGITGSLVHYDADDATGYQARLAEAVNALVADPATAERYGHAGRQRCIQEFSWAYIAEQTLDIYRKVCA