Rv3032 Resolved · high auto-curated
H37Rv Rv3032 · MTBC0 mtbc0_003223 ·
414 aa · 3412844–3414088 (+) ·
RefSeq NP_217548.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycogen synthase |
|---|---|
| MTBC0 PGAP re-annotation | glycogen synthase |
| Revised (this work) | Glycogen synthase. Pfam: Glyco_transf_5 (PF08323.18), Glyco_transf_4 (PF13439.13), Glyco_trans_4_4 (PF13579.13), 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 |
P9WMY9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycogen synthase |
| EC (curated) |
EC 2.4.1.11
|
| Curated function | Glucosyltransferase that uses UDP-glucose as the sugar donor to elongate alpha-(1->4)-glucans. Is involved in the biosynthesis of both 6-O-methylglucosyl lipopolysaccharides (MGLP) and glycogen. May also use ADP-glucose as substrate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Glycosyl transferase, group 1 |
| Orthologous group | COG0297 |
| EC number |
EC 2.4.1.11
|
| KEGG orthology |
K16150
|
| KEGG pathways |
map00500, map01100
|
| CAZy family |
GT4
|
| Gene Ontology (43) |
GO:0000271, GO:0003674, GO:0003824, GO:0005975, GO:0005976, GO:0005977, GO:0005978, GO:0006073, GO:0006091, GO:0006112, GO:0006629, GO:0008150 +31 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 | 0.256 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 5 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_5 | PF08323.18 | 6.3e-25 | 2–192 | Starch synthase catalytic domain |
Glyco_transf_4 | PF13439.13 | 2.4e-28 | 15–204 | Glycosyltransferase Family 4 |
Glyco_trans_4_4 | PF13579.13 | 6.8e-27 | 16–199 | Glycosyl transferase 4-like domain |
GT4-conflict | PF20706.4 | 4.8e-26 | 22–384 | Family 4 Glycosyltransferase in conflict systems |
Glycos_transf_1 | PF00534.27 | 1.5e-45 | 212–372 | Glycosyl transferases group 1 |
Glyco_trans_1_4 | PF13692.13 | 1.2e-32 | 218–358 | Glycosyl transferases group 1 |
Glyco_trans_1_2 | PF13524.13 | 1.4e-10 | 239–385 | Glycosyl transferase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3031 (1,4-alpha-glucan-branching protein), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3031 |
1,4-alpha-glucan-branching protein | 999 | 999 ctx | neighborhood:732 fusion:757 cooccurence:749 coexpression:449 database:900 textmining:875 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 997 | 977 | coexpression:410 database:955 textmining:890 |
Rv3030 |
S-adenosylmethionine-dependent methyltransferase | 991 | 936 ctx | neighborhood:827 cooccurence:641 textmining:875 |
Rv1327c glgE |
alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | 984 | 914 | database:900 textmining:829 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 948 | 904 | database:900 textmining:482 |
Rv3490 otsA |
trehalose-phosphate synthase | 947 | 903 | database:900 textmining:479 |
Rv1781c malQ |
4-alpha-glucanotransferase | 965 | 900 | database:900 textmining:664 |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 978 | 809 | database:800 textmining:891 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 929 | 782 | coexpression:411 database:572 textmining:688 |
Rv3032A hyp |
hypothetical protein | 752 | 752 ctx | neighborhood:752 |
Rv2418c octT hyp |
hypothetical protein | 883 | 698 ctx | cooccurence:693 textmining:630 |
Rv2186c hyp |
hypothetical protein | 692 | 692 ctx | cooccurence:683 |
Rv2529 hyp |
hypothetical protein | 674 | 662 | database:516 |
Rv3038c hyp |
hypothetical protein | 649 | 649 ctx | cooccurence:646 |
Rv3034c |
acetyltransferase | 948 | 627 ctx | cooccurence:590 textmining:868 |
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 synthase
- MTBC0 PGAP product: glycogen synthase
- Pfam (hmmscan --cut_ga): Glyco_transf_5 PF08323.18 (E=6e-25), Glyco_transf_4 PF13439.13 (E=2e-28), Glyco_trans_4_4 PF13579.13 (E=7e-27), GT4-conflict PF20706.4 (E=5e-26), Glycos_transf_1 PF00534.27 (E=2e-45), Glyco_trans_1_4 PF13692.13 (E=1e-32), Glyco_trans_1_2 PF13524.13 (E=1e-10)
- (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_217548.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_transf_5 (PF08323.18), Glyco_transf_4 (PF13439.13), Glyco_trans_4_4 (PF13579.13), 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 P9WMY9 (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 —
60 functional partner(s); context anchor
Rv3031 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003223|Rv3032| MRILMVSWEYPPVVIGGLGRHVHHLSTALAAAGHDVVVLSRCPSGTDPSTHPSSDEVTEGVRVIAAAQDPHEFTFGNDMMAWTLAMGHAMIRAGLRLKKLGTDRSWRPDVVHAHDWLVAHPAIALAQFYDVPMVSTIHATEAGRHSGWVSGALSRQVHAVESWLVRESDSLITCSASMNDEITELFGPGLAEITVIRNGIDAARWPFAARRPRTGPAELLYVGRLEYEKGVHDAIAALPRLRRTHPGTTLTIAGEGTQQDWLIDQARKHRVLRATRFVGHLDHTELLALLHRADAAVLPSHYEPFGLVALEAAAAGTPLVTSNIGGLGEAVINGQTGVSCAPRDVAGLAAAVRSVLDDPAAAQRRARAARQRLTSDFDWQTVATATAQVYLAAKRGERQPQPRLPIVEHALPDR