Rv3031 Family assigned · medium auto-curated
H37Rv Rv3031 · MTBC0 mtbc0_003222 ·
526 aa · 3411232–3412812 (+) ·
RefSeq NP_217547.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 1,4-alpha-glucan-branching protein |
|---|---|
| MTBC0 PGAP re-annotation | glycoside hydrolase family 57 protein |
| Revised (this work) | Glycoside hydrolase family 57 protein. Pfam: Glyco_hydro_57 (PF03065.21), BE_C (PF09210.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ27
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable 1,4-alpha-glucan branching enzyme Rv3031 |
| EC (curated) |
EC 2.4.1.18
|
| Curated function | Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position (Probable). Is probably involved in the biosynthesis of 6-O-methylglucosyl lipopolysaccharides (MGLP). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Belongs to the glycosyl hydrolase 57 family |
| Orthologous group | COG1543 |
| EC number |
EC 2.4.1.18
|
| KEGG orthology |
K16149
|
| KEGG pathways |
map00500, map01100, map01110
|
| KEGG modules |
M00565
|
| CAZy family |
GH57
|
| Gene Ontology (9) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, 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 | 0.234 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 6 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_hydro_57 | PF03065.21 | 4.0e-11 | 13–244 | Glycosyl hydrolase family 57 |
BE_C | PF09210.17 | 5.8e-18 | 444–522 | 1,4-alpha-glucan branching enzyme, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3032 (glycogen synthase), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3032 |
glycogen synthase | 999 | 999 ctx | neighborhood:732 fusion:757 cooccurence:749 coexpression:449 database:900 textmining:875 |
Rv3030 |
S-adenosylmethionine-dependent methyltransferase | 991 | 957 ctx | neighborhood:881 cooccurence:553 textmining:809 |
Rv1328 glgP |
glycogen phosphorylase | 976 | 907 | database:900 textmining:759 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 987 | 903 | database:900 textmining:875 |
Rv1327c glgE |
alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | 981 | 901 | database:900 textmining:824 |
Rv1564c treX |
maltooligosyl trehalose synthase | 949 | 901 | database:900 textmining:511 |
Rv0126 treS |
trehalose synthase/amylase TreS | 936 | 901 | database:900 |
Rv1781c malQ |
4-alpha-glucanotransferase | 943 | 900 | database:900 textmining:456 |
Rv2418c octT hyp |
hypothetical protein | 907 | 761 ctx | cooccurence:760 textmining:627 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 750 | 750 ctx | neighborhood:748 |
Rv2186c hyp |
hypothetical protein | 749 | 749 ctx | cooccurence:749 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 720 | 721 ctx | neighborhood:718 |
Rv2695 hyp |
hypothetical protein | 705 | 706 ctx | cooccurence:704 |
Rv3038c hyp |
hypothetical protein | 688 | 688 ctx | cooccurence:676 |
Rv3415c hyp |
hypothetical protein | 684 | 685 ctx | cooccurence:684 |
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: 1,4-alpha-glucan-branching protein
- MTBC0 PGAP product: glycoside hydrolase family 57 protein
- Pfam (hmmscan --cut_ga): Glyco_hydro_57 PF03065.21 (E=4e-11), BE_C PF09210.17 (E=6e-18)
- (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_217547.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_hydro_57 (PF03065.21), BE_C (PF09210.17)
- 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
COG1543 - Curated reference: UniProt P9WQ27 (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 —
42 functional partner(s); context anchor
Rv3032 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003222|Rv3031| MNTSASPVPGLFTLVLHTHLPWLAHHGRWPVGEEWLYQSWAAAYLPLLQVLAALADENRHRLITLGMTPVVNAQLDDPYCLNGVHHWLANWQLRAEEAASVRYARQSKSADYPSCTPEALRAFGIRECADAARALDNFATRWRHGGSPLLRGLIDAGTVELLGGPLAHPFQPLLAPRLREFALREGLADAQLRLAHRPKGIWAPECAYAPGMEVDYATAGVSHFMVDGPSLHGDTALGRPVGKTDVVAFGRDLQVSYRVWSPKSGYPGHAAYRDFHTYDHLTGLKPARVTGRNVPSEQKAPYDPERADRAVDVHVADFVDVVRNRLLSESERIGRPAHVIAAFDTELFGHWWYEGPTWLQRVLRALPAAGVRVGTLSDAIADGFVGDPVELPPSSWGSGKDWQVWSGAKVADLVQLNSEVVDTALTTIDKALAQTASLDGPLPRDHVADQILRETLLTVSSDWPFMVSKDSAADYARYRAHLHAHATREIAGALAAGRRDTARRLAEGWNRADGLFGALDARRLPK