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0  structures 5614  species 0  interactions 87777  sequences 76  architectures

Family: BPD_transp_2 (PF02653)

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

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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


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001851

ABC transporter 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 from the LIV-I transport system [ PUBMED:2195019 ]. Also found with in this family are proteins from the galactose, ribose, xylose, arabinose and fructose transport system permeases [ PUBMED:1719366 , PUBMED:7921236 , PUBMED:29150511 , PUBMED:11466273 ], as well as nucleoside transporters [ PUBMED:29150511 , PUBMED:20595258 ].

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 7 members:

ABC-3 AbrB BPD_transp_2 DUF1275 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(29)
Full
(87777)
Representative proteomes UniProt
(421227)
RP15
(9099)
RP35
(41052)
RP55
(92661)
RP75
(168348)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(29)
Full
(87777)
Representative proteomes UniProt
(421227)
RP15
(9099)
RP35
(41052)
RP55
(92661)
RP75
(168348)
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
(29)
Full
(87777)
Representative proteomes UniProt
(421227)
RP15
(9099)
RP35
(41052)
RP55
(92661)
RP75
(168348)
Raw Stockholm Download   Download   Download   Download        
Gzipped Download   Download   Download   Download        

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

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
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 29
Number in full: 87777
Average length of the domain: 278.8 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 79.7 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 27.0 26.8
Noise cut-off 26.7 26.7
Model length: 270
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A077ZFN7 View 3D Structure Click here
A0A077ZI57 View 3D Structure Click here
A0A0H3GGX1 View 3D Structure Click here
A0A0H3GHF5 View 3D Structure Click here
A0A0H3GHR5 View 3D Structure Click here
A0A0H3GIJ9 View 3D Structure Click here
A0A0H3GJW5 View 3D Structure Click here
A0A0H3GK64 View 3D Structure Click here
A0A0H3GKV2 View 3D Structure Click here
A0A0H3GL97 View 3D Structure Click here
A0A0H3GLD8 View 3D Structure Click here
A0A0H3GLK7 View 3D Structure Click here
A0A0H3GMP7 View 3D Structure Click here
A0A0H3GNV5 View 3D Structure Click here
A0A0H3GPH3 View 3D Structure Click here
A0A0H3GPM7 View 3D Structure Click here
A0A0H3GPT8 View 3D Structure Click here
A0A0H3GRP0 View 3D Structure Click here
A0A0H3GS32 View 3D Structure Click here
A0A0H3GSM2 View 3D Structure Click here
A0A0H3GTM7 View 3D Structure Click here
A0A0H3GTT9 View 3D Structure Click here
A0A0H3GUD3 View 3D Structure Click here
A0A0H3GV72 View 3D Structure Click here
A0A0H3GVG3 View 3D Structure Click here
A0A0H3GXV9 View 3D Structure Click here
A0A0H3GYQ1 View 3D Structure Click here
A0A0H3H460 View 3D Structure Click here
A0A0H3H4F0 View 3D Structure Click here
A6TEB6 View 3D Structure Click here
A6TEB7 View 3D Structure Click here
D4GPW1 View 3D Structure Click here
D4GPW2 View 3D Structure Click here
K0EN18 View 3D Structure Click here
K0ERD4 View 3D Structure Click here
K0ERF3 View 3D Structure Click here
K0ESK1 View 3D Structure Click here
K0EWH8 View 3D Structure Click here
K0EY02 View 3D Structure Click here
K0EY36 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;