bioA Resolved · high auto-curated
H37Rv Rv1568 · MTBC0 mtbc0_001676 ·
437 aa · 1787356–1788669 (+) ·
RefSeq NP_216084.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA |
|---|---|
| MTBC0 PGAP re-annotation | adenosylmethionine--8-amino-7-oxononanoate transaminase |
| Revised (this work) | Adenosylmethionine--8-amino-7-oxononanoate transaminase. Pfam: Aminotran_3 (PF00202.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ81
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase |
| EC (curated) |
EC 2.6.1.62
|
| Curated function | Catalyzes the reversible transfer of the alpha-amino group from S-adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only aminotransferase known to utilize SAM as an amino donor. Can also use sinefungin but not S-adenosylhomocysteine as substrate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | bioA |
| eggNOG description | Catalyzes the transfer of the alpha-amino group from S- adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only animotransferase known to utilize SAM as an amino donor |
| Orthologous group | COG0161 |
| EC number |
EC 2.6.1.62
|
| KEGG orthology |
K00833
|
| KEGG pathways |
map00780, map01100
|
| KEGG modules |
M00123, M00573, M00577
|
| Gene Ontology (47) |
GO:0003674, GO:0003824, GO:0004015, GO:0006082, GO:0006732, GO:0006766, GO:0006767, GO:0006768, GO:0006790, GO:0006807, GO:0008150, GO:0008152 +35 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 | 0.157 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 4 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_3 | PF00202.28 | 2.4e-110 | 35–428 | Aminotransferase class-III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: bioD (ATP-dependent dethiobiotin synthetase BioD), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1570 bioD |
ATP-dependent dethiobiotin synthetase BioD | 999 | 999 ctx | neighborhood:881 cooccurence:762 coexpression:695 database:900 textmining:965 |
Rv1569 bioF1 |
8-amino-7-oxononanoate synthase | 999 | 998 ctx | neighborhood:881 cooccurence:667 coexpression:473 database:900 textmining:946 |
Rv1589 bioB |
biotin synthetase | 999 | 976 ctx | fusion:633 cooccurence:756 coexpression:693 textmining:963 |
Rv0032 bioF2 |
8-amino-7-oxononanoate synthase | 989 | 974 ctx | cooccurence:510 coexpression:451 database:900 textmining:596 |
Rv1571 hyp |
hypothetical protein | 975 | 882 ctx | neighborhood:881 textmining:803 |
Rv1567c |
membrane protein | 718 | 719 ctx | neighborhood:719 |
Rv1563c treY |
maltooligosyl trehalose synthase | 635 | 625 ctx | neighborhood:623 |
Rv1565c |
acyltransferase | 439 | 439 ctx | neighborhood:439 |
Rv1564c treX |
maltooligosyl trehalose synthase | 440 | 428 ctx | neighborhood:426 |
Rv1590 hyp |
hypothetical protein | 401 | 370 | |
Rv2794c pptT |
4'-phosphopantetheinyl transferase | 668 | 260 | textmining:571 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 887 | 189 | textmining:867 |
Rv0089 |
methyltransferase | 828 | 134 | textmining:811 |
Rv3602c panC |
pantothenate synthetase | 808 | 106 | textmining:795 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 768 | 102 | textmining:753 |
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: adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA
- MTBC0 PGAP product: adenosylmethionine--8-amino-7-oxononanoate transaminase
- Pfam (hmmscan --cut_ga): Aminotran_3 PF00202.28 (E=2e-110)
- (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_216084.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_3 (PF00202.28)
- 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
COG0161 - Curated reference: UniProt P9WQ81 (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 —
22 functional partner(s); context anchor
bioD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001676|Rv1568|bioA MAAATGGLTPEQIIAVDGAHLWHPYSSIGREAVSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGGMHSLWTDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLVGSLP