bioB Resolved · high auto-curated
H37Rv Rv1589 · MTBC0 mtbc0_001695 ·
349 aa · 1802248–1803297 (+) ·
RefSeq NP_216105.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | biotin synthetase |
|---|---|
| MTBC0 PGAP re-annotation | biotin synthase BioB |
| Revised (this work) | Biotin synthase BioB. Pfam: Radical_SAM (PF04055.28), BATS (PF06968.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPQ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Biotin synthase |
| EC (curated) |
EC 2.8.1.6
|
| Curated function | Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | bioB |
| eggNOG description | Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism |
| Orthologous group | COG0502 |
| EC number |
EC 2.8.1.6
|
| KEGG orthology |
K01012
|
| KEGG pathways |
map00780, map01100
|
| KEGG modules |
M00123, M00573, M00577
|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, 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 | 0.515 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
Radical_SAM | PF04055.28 | 2.6e-20 | 82–239 | Radical SAM superfamily |
BATS | PF06968.19 | 1.7e-19 | 250–339 | Biotin and Thiamin Synthesis associated domain |
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 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1570 bioD |
ATP-dependent dethiobiotin synthetase BioD | 999 | 997 ctx | cooccurence:770 coexpression:856 database:900 textmining:954 |
Rv1568 bioA |
adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA | 999 | 976 ctx | fusion:633 cooccurence:756 coexpression:693 textmining:963 |
Rv1590 hyp |
hypothetical protein | 959 | 956 ctx | neighborhood:881 cooccurence:556 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 985 | 912 | database:900 textmining:840 |
Rv1569 bioF1 |
8-amino-7-oxononanoate synthase | 990 | 910 ctx | cooccurence:629 coexpression:672 textmining:902 |
Rv1591 |
transmembrane protein | 906 | 906 ctx | neighborhood:881 |
Rv1442 bisC |
biotin sulfoxide reductase BisC | 900 | 900 | database:900 |
Rv0032 bioF2 |
8-amino-7-oxononanoate synthase | 923 | 810 | coexpression:669 textmining:613 |
Rv3329 |
aminotransferase | 764 | 733 | coexpression:693 |
Rv0423c thiC |
phosphomethylpyrimidine synthase | 641 | 507 | |
Rv1596 nadC |
nicotinate-nucleotide pyrophosphatase | 481 | 448 | |
Rv1594 nadA |
quinolinate synthetase A | 537 | 447 | coexpression:415 |
Rv2213 pepB |
cytosol aminopeptidase | 464 | 386 | |
Rv1571 hyp |
hypothetical protein | 485 | 342 | |
Rv2524c fas |
fatty acid synthase | 532 | 245 | textmining:406 |
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: biotin synthetase
- MTBC0 PGAP product: biotin synthase BioB
- Pfam (hmmscan --cut_ga): Radical_SAM PF04055.28 (E=3e-20), BATS PF06968.19 (E=2e-19)
- (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_216105.1)
- Domains: Pfam-A via hmmscan --cut_ga — Radical_SAM (PF04055.28), BATS (PF06968.19)
- 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
COG0502 - Curated reference: UniProt P9WPQ7 (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 —
39 functional partner(s); context anchor
bioD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001695|Rv1589|bioB MTQAATRPTNDAGQDGGNNSDILVVARQQVLQRGEGLNQDQVLAVLQLPDDRLEELLALAHEVRMRWCGPEVEVEGIISLKTGGCPEDCHFCSQSGLFASPVRSAWLDIPSLVEAAKQTAKSGATEFCIVAAVRGPDERLMAQVAAGIEAIRNEVEINIACSLGMLTAEQVDQLAARGVHRYNHNLETARSFFANVVTTHTWEERWQTLSMVRDAGMEVCCGGILGMGETLQQRAEFAAELAELGPDEVPLNFLNPRPGTPFADLEVMPVGDALKAVAAFRLALPRTMLRFAGGREITLGDLGAKRGILGGINAVIVGNYLTTLGRPAEADLELLDELQMPLKALNASL