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6  structures 3397  species 2  interactions 5028  sequences 10  architectures

Family: BATS (PF06968)

Summary: Biotin and Thiamin Synthesis associated domain

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Biotin and Thiamin Synthesis associated domain Provide feedback

Biotin synthase (BioB), EC:2.8.1.6 , catalyses the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer [1]. Thiamin synthesis if a complex process involving at least six gene products (ThiFSGH, ThiI and ThiJ). Two of the proteins required for the biosynthesis of the thiazole moiety of thiamine (vitamin B(1)) are ThiG and ThiH (this family) and form a [2]. Both of these reactions are thought of involve the binding of co-factors, and both function as dimers [1,2]. This domain therefore may be involved in co-factor binding or dimerisation (Finn, RD personal observation).

Literature references

  1. Ollagnier-de-Choudens S, Mulliez E, Fontecave M; , FEBS Lett 2002;532:465-468.: The PLP-dependent biotin synthase from Escherichia coli: mechanistic studies. PUBMED:12482614 EPMC:12482614

  2. Leonardi R, Fairhurst SA, Kriek M, Lowe DJ, Roach PL; , FEBS Lett 2003;539:95-99.: Thiamine biosynthesis in Escherichia coli: isolation and initial characterisation of the ThiGH complex. PUBMED:12650933 EPMC:12650933


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010722

Biotin synthase (BioB), EC, catalyses the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer [PUBMED:12482614]. Thiamin synthesis if a complex process involving at least six gene products (ThiFSGH, ThiI and ThiJ). Two of the proteins required for the biosynthesis of the thiazole moiety of thiamine (vitamin B(1)) are ThiG and ThiH (this entry) and form a heterodimer[PUBMED:12650933]. Both of these reactions are thought of involve the binding of co-factors, and both function as dimers [PUBMED:12482614, PUBMED:12650933]. This domain therefore may be involved in co-factor binding or dimerisation.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(127)
Full
(5028)
Representative proteomes NCBI
(3436)
Meta
(382)
RP15
(421)
RP35
(778)
RP55
(1014)
RP75
(1177)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(127)
Full
(5028)
Representative proteomes NCBI
(3436)
Meta
(382)
RP15
(421)
RP35
(778)
RP55
(1014)
RP75
(1177)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(127)
Full
(5028)
Representative proteomes NCBI
(3436)
Meta
(382)
RP15
(421)
RP35
(778)
RP55
(1014)
RP75
(1177)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_5417 (release 10.0)
Previous IDs: none
Type: Domain
Author: Finn RD
Number in seed: 127
Number in full: 5028
Average length of the domain: 97.40 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 26.94 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 93
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 2 interactions for this family. More...

BATS Radical_SAM

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the BATS domain has been found. There are 6 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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