bioF1 Resolved · high auto-curated
H37Rv Rv1569 · MTBC0 - ·
386 aa · 1776702–1777862 (+) ·
RefSeq YP_177822.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 8-amino-7-oxononanoate synthase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 8-amino-7-oxononanoate synthase. Pfam: Aminotran_1_2 (PF00155.28), Aminotran_5 (PF00266.26), 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WQ87
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 8-amino-7-oxononanoate synthase 1 |
| EC (curated) |
EC 2.3.1.47
|
| Curated function | Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide (By similarity). Can also use pimeloyl-CoA instead of pimeloyl-ACP as substrate. To a lesser extent, can also utilize D-alanine instead of L-alanine as substrate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | bioF |
| eggNOG description | Catalyzes the decarboxylative condensation of pimeloyl- acyl-carrier protein and L-alanine to produce 8-amino-7- oxononanoate (AON), acyl-carrier protein , and carbon dioxide |
| Orthologous group | COG0156 |
| EC number |
EC 2.3.1.47, EC 6.2.1.14
|
| KEGG orthology |
K00652, K01906
|
| KEGG pathways |
map00780, map01100
|
| KEGG modules |
M00123, M00573, M00577
|
| Gene Ontology (55) |
GO:0003674, GO:0003824, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006082, GO:0006732, GO:0006766, GO:0006767, GO:0006768, GO:0006790 +43 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 | 0.546 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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_1_2 | PF00155.28 | 1.9e-58 | 43–374 | Aminotransferase class I and II |
Aminotran_5 | PF00266.26 | 1.0e-06 | 81–210 | Aminotransferase class-V |
DegT_DnrJ_EryC1 | PF01041.24 | 3.1e-06 | 85–217 | DegT/DnrJ/EryC1/StrS aminotransferase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: bioA (adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1568 bioA |
adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA | 999 | 998 ctx | neighborhood:881 cooccurence:667 coexpression:473 database:900 textmining:946 |
Rv1570 bioD |
ATP-dependent dethiobiotin synthetase BioD | 999 | 990 ctx | neighborhood:882 cooccurence:711 coexpression:723 textmining:964 |
Rv0032 bioF2 |
8-amino-7-oxononanoate synthase | 932 | 918 | database:900 |
Rv1589 bioB |
biotin synthetase | 990 | 910 ctx | cooccurence:629 coexpression:672 textmining:902 |
Rv1571 hyp |
hypothetical protein | 985 | 895 ctx | neighborhood:882 textmining:870 |
Rv1567c |
membrane protein | 741 | 741 ctx | neighborhood:741 |
Rv1563c treY |
maltooligosyl trehalose synthase | 625 | 625 ctx | neighborhood:623 |
Rv2211c gcvT |
aminomethyltransferase | 618 | 571 | coexpression:428 |
Rv3329 |
aminotransferase | 519 | 474 | coexpression:454 |
Rv3726 |
dehydrogenase | 486 | 453 | coexpression:422 |
Rv1895 |
zinc-binding alcohol dehydrogenase | 481 | 449 | coexpression:417 |
Rv1530 adh |
alcohol dehydrogenase | 481 | 449 | coexpression:417 |
Rv2947c pks15 |
polyketide synthase | 425 | 403 | |
Rv2048c pks12 |
polyketide synthase | 569 | 397 | |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 568 | 396 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): 8-amino-7-oxononanoate synthase
- Pfam (hmmscan --cut_ga): Aminotran_1_2 PF00155.28 (E=2e-58), Aminotran_5 PF00266.26 (E=1e-06), DegT_DnrJ_EryC1 PF01041.24 (E=3e-06)
- (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 YP_177822.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_1_2 (PF00155.28), Aminotran_5 (PF00266.26), 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
COG0156 - Curated reference: UniProt P9WQ87 (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 —
30 functional partner(s); context anchor
bioA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1569|bioF1 MKAATQARIDDSPLAWLDAVQRQRHEAGLRRCLRPRPAVATELDLASNDYLGLSRHPAVIDGGVQALRIWGAGATGSRLVTGDTKLHQQFEAELAEFVGAAAGLLFSSGYTANLGAVVGLSGPGSLLVSDARSHASLVDACRLSRARVVVTPHRDVDAVDAALRSRDEQRAVVVTDSVFSADGSLAPVRELLEVCRRHGALLLVDEAHGLGVRGGGRGLLYELGLAGAPDVVMTTTLSKALGSQGGVVLGPTPVRAHLIDAARPFIFDTGLAPAAVGAARAALRVLQAEPWRPQAVLNHAGELARMCGVAAVPDSAMVSVILGEPESAVAAAAACLDAGVKVGCFRPPTVPAGTSRLRLTARASLNAGELELARRVLTDVLAVARR