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0  structures 3614  species 0  interactions 33622  sequences 38  architectures

Family: BPD_transp_2 (PF02653)

Summary: Branched-chain amino acid transport system / permease component

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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.

Branched-chain amino acid transport system / permease component Provide feedback

This is a large family mainly comprising high-affinity branched-chain amino acid transporter proteins such as E. coli LivH P08340 and LivM P22729 both of which are form the LIV-I transport system [3]. Also found with in this family are proteins from the galactose transport system permease [2] and a ribose transport system [1].

Literature references

  1. Woodson K, Devine KM; , Microbiology 1994;140:1829-1838.: Analysis of a ribose transport operon from Bacillus subtilis. PUBMED:7921236 EPMC:7921236

  2. Hogg RW, Voelker C, Von Carlowitz I; , Mol Gen Genet 1991;229:453-459.: Nucleotide sequence and analysis of the mgl operon of Escherichia coli K12. PUBMED:1719366 EPMC:1719366

  3. Adams MD, Wagner LM, Graddis TJ, Landick R, Antonucci TK, Gibson AL, Oxender DL; , J Biol Chem 1990;265:11436-11443.: Nucleotide sequence and genetic characterization reveal six essential genes for the LIV-I and LS transport systems of Escherichia coli. PUBMED:2195019 EPMC:2195019


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001851

This is a large family mainly comprising high-affinity branched-chain amino acid transporter proteins such as Escherichia coli LivH SWISSPROT and LivM SWISSPROT both of which are form the LIV-I transport system [PUBMED:2195019]. Also found with in this family are proteins from the galactose transport system permease [PUBMED:1719366] and a ribose transport system [PUBMED:7921236].

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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Pfam Clan

This family is a member of clan Membrane_trans (CL0142), which has the following description:

This clan contains membrane proteins involved in the transport of molecules including amino acids sugars and signalling molecules. It also includes integral membrane cell cycle proteins and some putative ammonia monooxygenases.

The clan contains the following 6 members:

ABC-3 AmoA BPD_transp_2 FecCD FTSW_RODA_SPOVE Pam17

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
(51)
Full
(33622)
Representative proteomes NCBI
(25680)
Meta
(15397)
RP15
(2466)
RP35
(5546)
RP55
(7467)
RP75
(9346)
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PP/heatmap 1   View           
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(51)
Full
(33622)
Representative proteomes NCBI
(25680)
Meta
(15397)
RP15
(2466)
RP35
(5546)
RP55
(7467)
RP75
(9346)
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
(51)
Full
(33622)
Representative proteomes NCBI
(25680)
Meta
(15397)
RP15
(2466)
RP35
(5546)
RP55
(7467)
RP75
(9346)
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: COG0559 & Pfam-B_654 (Release 7.5)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 51
Number in full: 33622
Average length of the domain: 275.60 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 80.62 %

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 23.8 23.8
Trusted cut-off 23.8 23.8
Noise cut-off 23.7 23.7
Model length: 267
Family (HMM) version: 11
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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Tree controls

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