aglA Family assigned · medium auto-curated
H37Rv Rv2471 · MTBC0 mtbc0_002633 ·
546 aa · 2797812–2799452 (+) ·
RefSeq NP_216987.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | alpha-glucosidase AglA |
|---|---|
| MTBC0 PGAP re-annotation | glycoside hydrolase family 13 protein |
| Revised (this work) | Glycoside hydrolase family 13 protein. Pfam: Alpha-amylase (PF00128.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53198
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable alpha-glucosidase AglA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | aglA |
| eggNOG description | alpha amylase, catalytic |
| Orthologous group | COG0366 |
| EC number |
EC 3.2.1.20
|
| KEGG orthology |
K01187
|
| KEGG pathways |
map00052, map00500, map01100
|
| CAZy family |
GH31
|
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 | 0.454 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 11 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 |
|---|---|---|---|---|
Alpha-amylase | PF00128.32 | 9.4e-107 | 39–482 | Alpha amylase, catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mak (maltokinase), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0127 mak |
maltokinase | 994 | 994 ctx | fusion:834 experimental:484 database:900 |
Rv2470 glbO |
hemoglobin GlbO | 950 | 950 ctx | neighborhood:881 fusion:596 |
Rv0126 treS |
trehalose synthase/amylase TreS | 936 | 935 | database:900 |
Rv1781c malQ |
4-alpha-glucanotransferase | 954 | 922 | database:900 textmining:439 |
Rv0186 bglS |
beta-glucosidase BglS | 945 | 922 | database:900 |
Rv2469c hyp |
hypothetical protein | 774 | 774 ctx | neighborhood:773 |
Rv1979c |
permease | 777 | 766 | experimental:451 database:577 |
Rv2320c rocE |
cationic amino acid transporter permease RocE | 776 | 765 | experimental:451 database:577 |
Rv3253c |
cationic amino acid transport integral membrane protein | 774 | 763 | experimental:451 database:577 |
Rv2690c |
integral membrane protein | 774 | 763 | experimental:451 database:577 |
Rv1999c |
transporter | 774 | 763 | experimental:451 database:577 |
Rv2468A hyp |
hypothetical protein | 742 | 742 ctx | neighborhood:742 |
Rv2468c hyp |
hypothetical protein | 742 | 742 ctx | neighborhood:742 |
Rv2472 hyp |
hypothetical protein | 692 | 693 ctx | neighborhood:691 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 785 | 635 | coexpression:410 textmining:436 |
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: alpha-glucosidase AglA
- MTBC0 PGAP product: glycoside hydrolase family 13 protein
- Pfam (hmmscan --cut_ga): Alpha-amylase PF00128.32 (E=9e-107)
- (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_216987.1)
- Domains: Pfam-A via hmmscan --cut_ga — Alpha-amylase (PF00128.32)
- 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
COG0366 - Curated reference: UniProt O53198 (TrEMBL, unreviewed; 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
mak - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002633|Rv2471|aglA MDQHQRPDPMGPGSPRASARRPEPDPMGEPWWSRAVFYQVYPRSFADSNGDGVGDLDGLASRLDHLQQLGVDAIWINPVTVSPMADHGYDVADPRDIDPLFGGMPAFERLVAAAHRQGIKVTMDVVPNHTSSAHPWFQAALADLPGSPARDRYFFRDGRGPDGSLPPNNWESVFGGPAWTRVREPDGNPGQWYLHLFDTEQPDLNWDNPEILDDFEKTLRFWLDRGVDGFRIDVAHGMAKPPGLPDSPDLGIEVLHHRDDDPRFNHPNVHAIHRDIRTVIDEYPGAVTVGEVWVHDNARWAEYLRPDELHLGFNFRLARTEFDAAEIRDAVANSLAAAALQNATPTWTLANHDVGREVSRYGGGEIGLRRAKAMAVVMLALPGVVFLYNGQELGLPDVDLPDEVLQDPTWERSGRTERGRDGCRVPIPWSGNIPPFGFSTCPDTWLPMPPEWAALTAEKQRADAGSTLSFFRLALRLRRERNEFDGDVDWLAAPDDALIFRRHGGGLVCALNAAERPLALPAGEPILASAPLTDATLPPNAAAWLV