Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aspartate aminotransferase |
|---|
| MTBC0 PGAP re-annotation | pyridoxal phosphate-dependent aminotransferase |
|---|
| Revised (this work) | Pyridoxal phosphate-dependent aminotransferase. Pfam: Aminotran_1_2 (PF00155.28), DegT_DnrJ_EryC1 (PF01041.24). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ91
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Alanine aminotransferase |
|---|
| EC (curated) |
EC 2.6.1.2
|
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|
| Preferred name | aspC |
|---|
| eggNOG description | Aminotransferase |
|---|
| Orthologous group | COG0436 |
|---|
| EC number |
EC 2.6.1.1, EC 2.6.1.17, EC 2.6.1.2, EC 2.6.1.66
|
|---|
| KEGG orthology |
K00812, K14260, K14267
|
|---|
| KEGG pathways |
map00220, map00250, map00270, map00290, map00300, map00330, map00350, map00360, map00400, map00401, map00950, map00960, map01100, map01110, map01120, map01130, map01210, map01230
|
|---|
| KEGG modules |
M00016
|
|---|
| Gene Ontology (8) |
GO:0005575, 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 |
0.336 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
3 synonymous, 3 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 |
|---|
Aminotran_1_2 | PF00155.28 |
1.4e-48 | 59–406 |
Aminotransferase class I and II |
DegT_DnrJ_EryC1 | PF01041.24 |
1.7e-04 | 134–232 |
DegT/DnrJ/EryC1/StrS aminotransferase family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0189c ilvD |
dihydroxy-acid dehydratase |
927 |
921 |
database:900 |
Rv3710 leuA |
2-isopropylmalate synthase |
914 |
910 |
database:900 |
Rv1653 argJ |
bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase |
913 |
906 |
database:900 |
Rv2210c ilvE |
branched-chain amino acid aminotransferase |
911 |
906 |
database:900 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase |
943 |
905 |
database:900 textmining:437 |
Rv2780 ald |
L-alanine dehydrogenase |
927 |
901 |
database:900 |
Rv2747 argA |
L-glutamate alpha-N-acetyltranferase |
906 |
901 |
database:900 |
Rv0428c |
GCN5-like N-acetyltransferase |
905 |
901 |
database:900 |
Rv3339c icd1 |
isocitrate dehydrogenase |
852 |
839 |
database:800 |
Rv1098c fum |
fumarate hydratase |
842 |
834 |
database:800 |
Rv1257c |
oxidoreductase |
829 |
823 |
coexpression:821 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA |
842 |
816 |
database:800 |
Rv0248c |
succinate dehydrogenase flavoprotein subunit |
820 |
813 |
database:800 |
Rv2454c korB |
2-oxoglutarate oxidoreductase subunit KorB |
820 |
809 |
database:800 |
Rv0247c |
succinate dehydrogenase iron-sulfur subunit |
815 |
808 |
database:800 |
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: aspartate aminotransferase
- MTBC0 PGAP product: pyridoxal phosphate-dependent aminotransferase
- Pfam (hmmscan --cut_ga): Aminotran_1_2 PF00155.28 (E=1e-48), DegT_DnrJ_EryC1 PF01041.24 (E=2e-04)
- (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_214851.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_1_2 (PF00155.28), DegT_DnrJ_EryC1 (PF01041.24)
- 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
COG0436
- Curated reference: UniProt
P9WQ91
(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 —
50 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000357|Rv0337c|aspC
MDNDGTIVDVTTHQLPWHTASHQRQRAFAQSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALPYAQGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQVLIPSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTGAVYSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAYRVAGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLPGGRLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKILVTQGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ
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