bioF2 Family assigned · medium auto-curated
H37Rv Rv0032 · MTBC0 mtbc0_000037 ·
771 aa · 34281–36596 (+) ·
RefSeq NP_214546.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 8-amino-7-oxononanoate synthase |
|---|---|
| MTBC0 PGAP re-annotation | pyridoxal phosphate-dependent aminotransferase family protein |
| Revised (this work) | Pyridoxal phosphate-dependent aminotransferase family protein. Pfam: Acetyltransf_6 (PF13480.14), Aminotran_1_2 (PF00155.28), Beta_elim_lyase (PF01212.28), 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 |
P9WQ85
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative 8-amino-7-oxononanoate synthase 2 |
| 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. |
UniProt still lists this protein as Putative 8-amino-7-oxononanoate synthase 2; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | bioF2 |
| eggNOG description | Could be involved in biotin biosynthesis (at the first step) catalytic activity 6-carboxyhexanoyl-CoA L- alanine 8-amino-7-oxononanoate CoA CO2 |
| Orthologous group | COG0156 |
| EC number |
EC 2.3.1.47
|
| KEGG orthology |
K00652
|
| KEGG pathways |
map00780, map01100
|
| KEGG modules |
M00123, M00573, M00577
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, 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 | 0.665 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 17 missense, 1 nonsense, 7 frameshift |
| Disruption | 8 distinct premature-stop/frameshift site(s); most common in 7.52% of strains (10913) · convergent |
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 |
|---|---|---|---|---|
Acetyltransf_6 | PF13480.14 | 1.8e-06 | 190–307 | Acetyltransferase (GNAT) domain |
Aminotran_1_2 | PF00155.28 | 1.9e-53 | 418–756 | Aminotransferase class I and II |
Beta_elim_lyase | PF01212.28 | 2.1e-08 | 465–636 | Beta-eliminating lyase |
DegT_DnrJ_EryC1 | PF01041.24 | 7.4e-05 | 465–588 | 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 974 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1568 bioA |
adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA | 989 | 974 ctx | cooccurence:510 coexpression:451 database:900 textmining:596 |
Rv0033 acpA |
acyl carrier protein AcpA | 973 | 972 ctx | neighborhood:781 coexpression:860 |
Rv0034 hyp |
hypothetical protein | 971 | 972 ctx | neighborhood:781 coexpression:860 |
Rv0035 fadD34 |
fatty-acid--CoA ligase FadD34 | 970 | 970 ctx | neighborhood:781 coexpression:863 |
Rv1569 bioF1 |
8-amino-7-oxononanoate synthase | 932 | 918 | database:900 |
Rv1570 bioD |
ATP-dependent dethiobiotin synthetase BioD | 931 | 869 ctx | cooccurence:513 coexpression:709 textmining:500 |
Rv1589 bioB |
biotin synthetase | 923 | 810 | coexpression:669 textmining:613 |
Rv1918c PPE35 |
PPE family protein PPE35 | 761 | 761 | coexpression:761 |
Rv2211c gcvT |
aminomethyltransferase | 608 | 560 | coexpression:422 |
Rv3329 |
aminotransferase | 518 | 472 | coexpression:454 |
Rv1895 |
zinc-binding alcohol dehydrogenase | 488 | 456 | coexpression:425 |
Rv3726 |
dehydrogenase | 486 | 453 | coexpression:422 |
Rv1530 adh |
alcohol dehydrogenase | 483 | 451 | coexpression:419 |
Rv1826 gcvH |
glycine cleavage system protein H | 489 | 435 | |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 567 | 394 |
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: 8-amino-7-oxononanoate synthase
- MTBC0 PGAP product: pyridoxal phosphate-dependent aminotransferase family protein
- Pfam (hmmscan --cut_ga): Acetyltransf_6 PF13480.14 (E=2e-06), Aminotran_1_2 PF00155.28 (E=2e-53), Beta_elim_lyase PF01212.28 (E=2e-08), DegT_DnrJ_EryC1 PF01041.24 (E=7e-05)
- (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_214546.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acetyltransf_6 (PF13480.14), Aminotran_1_2 (PF00155.28), Beta_elim_lyase (PF01212.28), 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
COG0156 - Curated reference: UniProt P9WQ85 (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 —
29 functional partner(s); context anchor
bioA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000037|Rv0032|bioF2 MPTGLGYDFLRPVEDSGINDLKHYYFMADLADGQPLGRANLYSVCFDLATTDRKLTPAWRTTIKRWFPGFMTFRFLECGLLTMVSNPLALRSDTDLERVLPVLAGQMDQLAHDDGSDFLMIRDVDPEHYQRYLDILRPLGFRPALGFSRVDTTISWSSVEEALGCLSHKRRLPLKTSLEFRERFGIEVEELDEYAEHAPVLARLWRNVKTEAKDYQREDLNPEFFAACSRHLHGRSRLWLFRYQGTPIAFFLNVWGADENYILLEWGIDRDFEHYRKANLYRAALMLSLKDAISRDKRRMEMGITNYFTKLRIPGARVIPTIYFLRHSTDPVHTATLARMMMHNIQRPTLPDDMSEEFCRWEERIRLDQDGLPEHDIFRKIDRQHKYTGLKLGGVYGFYPRFTGPQRSTVKAAELGEIVLLGTNSYLGLATHPEVVEASAEATRRYGTGCSGSPLLNGTLDLHVSLEQELACFLGKPAAVLCSTGYQSNLAAISALCESGDMIIQDALNHRSLFDAARLSGADFTLYRHNDMDHLARVLRRTEGRRRIIVVDAVFSMEGTVADLATIAELADRHGCRVYVDESHALGVLGPDGRGASAALGVLARMDVVMGTFSKSFASVGGFIAGDRPVVDYIRHNGSGHVFSASLPPAAAAATHAALRVSRREPDRRARVLAAAEYMATGLARQGYQAEYHGTAIVPVILGNPTVAHAGYLRLMRSGVYVNPVAPPAVPEERSGFRTSYLADHRQSDLDRALHVFAGLAEDLTPQGAAL