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0  structures 2228  species 0  interactions 2666  sequences 7  architectures

Family: BioY (PF02632)

Summary: BioY family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

BioY family Provide feedback

A number of bacterial genes are involved in bioconversion of pimelate into dethiobiotin [1]. BioY is a component of the BioMNY transport system involved in biotin uptake in prokaryotes [3].

Literature references

  1. Gloeckler R, Ohsawa I, Speck D, Ledoux C, Bernard S, Zinsius M, Villeval D, Kisou T, Kamogawa K, Lemoine Y; , Gene 1990;87:63-70.: Cloning and characterization of the Bacillus sphaericus genes controlling the bioconversion of pimelate into dethiobiotin. PUBMED:2110099 EPMC:2110099

  2. Rodionov DA, Mironov AA, Gelfand MS; , Genome Res. 2002;12:1507-1516.: Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. PUBMED:12368242 EPMC:12368242

  3. Hebbeln P, Rodionov DA, Alfandega A, Eitinger T; , Proc Natl Acad Sci U S A. 2007;104:2909-2914.: Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. PUBMED:17301237 EPMC:17301237


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003784

BioMNY proteins are considered to constitute tripartite biotin transporters in prokaryotes. One-third of the widespread bioY genes are linked to bioMN. Many bioY genes are located at loci encoding biotin biosynthesis, while others are unlinked to biotin metabolic or transport genes. BioY is a high-capacity transporter that is converted to a high-affinity system in the presence of BioMN. BioMNY-mediated biotin uptake is severely impaired by the replacement of the Walker A lysine residue in BioM, demonstrating the dependency of high-affinity transport on a functional ATPase [PUBMED:17301237].

Domain organisation

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

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Pfam Clan

This family is a member of clan Gx_transp (CL0315), which has the following description:

This superfamily includes a wide range of transporters that contain many conserved glycine residues in the presumed transmembrane regions.

The clan contains the following 12 members:

5TM-5TMR_LYT Bac_export_3 BioY CbiM DUF2232 DUF3816 ECF-ribofla_trS Hpre_diP_synt_I MreD QueT Thia_YuaJ ThiW

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
(153)
Full
(2666)
Representative proteomes NCBI
(1839)
Meta
(1577)
RP15
(205)
RP35
(400)
RP55
(503)
RP75
(579)
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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
(153)
Full
(2666)
Representative proteomes NCBI
(1839)
Meta
(1577)
RP15
(205)
RP35
(400)
RP55
(503)
RP75
(579)
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
(153)
Full
(2666)
Representative proteomes NCBI
(1839)
Meta
(1577)
RP15
(205)
RP35
(400)
RP55
(503)
RP75
(579)
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: COG1268
Previous IDs: none
Type: Family
Author: Mian N, Bateman A
Number in seed: 153
Number in full: 2666
Average length of the domain: 149.40 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 79.42 %

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 23.1 23.1
Trusted cut-off 23.1 23.3
Noise cut-off 23.0 23.0
Model length: 149
Family (HMM) version: 9
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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