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93  structures 7333  species 0  interactions 345769  sequences 236  architectures

Family: BPD_transp_1 (PF00528)

Summary: Binding-protein-dependent transport system inner membrane component

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

This is the Wikipedia entry entitled "Bacterial binding protein-dependent transporter". More...

Bacterial binding protein-dependent transporter Edit Wikipedia article

BPD_transp_1
Identifiers
SymbolBPD_transp_1
PfamPF00528
Pfam clanCL0404
InterProIPR000515
PROSITEPDOC00364
TCDB3.A.1
OPM superfamily17
OPM protein3puz

Bacterial binding protein-dependent transport systems,[1] [2] are multicomponent systems typically composed of a periplasmic substrate-binding protein, one or two reciprocally homologous integral inner-membrane proteins and one or two peripheral membrane ATP-binding proteins that couple energy to the active transport system. The integral inner-membrane proteins translocate the substrate across the membrane. It has been shown,[3] [4] that most of these proteins contain a conserved region located about 80 to 100 residues from their C-terminal extremity. This region seems [5] to be located in a cytoplasmic loop between two transmembrane domains. Apart from the conserved region, the sequence of these proteins is quite divergent, and they have a variable number of transmembrane helices, however they can be classified into seven families which have been respectively termed: araH, cysTW, fecCD, hisMQ, livHM, malFG and oppBC.

References

  1. ^ Ames GF (1986). "Bacterial periplasmic transport systems: structure, mechanism, and evolution". Annu. Rev. Biochem. 55: 397–425. doi:10.1146/annurev.bi.55.070186.002145. PMID 3527048. {{cite journal}}: C1 control character in |pages= at position 5 (help)
  2. ^ Higgins CF, Hyde SC, Mimmack MM, Gileadi U, Gill DR, Gallagher MP (1990). "Binding protein-dependent transport systems". J. Bioenerg. Biomembr. 22 (4): 571–92. PMID 2229036. {{cite journal}}: C1 control character in |pages= at position 5 (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ Dassa E, Hofnung M (1985). "Sequence of gene malG in E. coli K12: homologies between integral membrane components from binding protein-dependent transport systems". EMBO J. 4 (9): 2287–93. PMC 554499. PMID 3000770. {{cite journal}}: C1 control character in |pages= at position 6 (help); Unknown parameter |month= ignored (help)
  4. ^ Saurin W, Köster W, Dassa E (1994). "Bacterial binding protein-dependent permeases: characterization of distinctive signatures for functionally related integral cytoplasmic membrane proteins". Mol. Microbiol. 12 (6): 993–1004. PMID 7934906. {{cite journal}}: C1 control character in |pages= at position 5 (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  5. ^ Pearce SR, Mimmack ML, Gallagher MP, Gileadi U, Hyde SC, Higgins CF (1992). "Membrane topology of the integral membrane components, OppB and OppC, of the oligopeptide permease of Salmonella typhimurium". Mol. Microbiol. 6 (1): 47–57. PMID 1738314. {{cite journal}}: C1 control character in |pages= at position 4 (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR000515

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Binding-protein-dependent transport system inner membrane component Provide feedback

The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have a variable number of transmembrane helices.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000515

ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein (mostly in eukaryotes and bacterial exporters) or on two different ones (mostly bacterial importers) [ PUBMED:9873074 ]. In importers, the TMD displays a distinctive signature, the EAA motif, a 20 amino acid conserved sequence located about 100 residues from the C terminus. The motif is hydrophilic and has been found to reside in a cytoplasmic loop located between the penultimate and the antepenultimate transmembrane segment in all proteins with a known topology [ PUBMED:7934906 ]. It appears to play an important role in ensuring the correct assembly of the prokaryotic ABC transport complex [ PUBMED:9640644 ] and constituting an interaction site with the so-called helical domain of the ABC module [ PUBMED:10809785 , PUBMED:9214624 ].

This entry recognises ABC transmembrane domains where the TMD is on a separate protein, such as the D-methionine transport system permease protein MetI. The crystal structure of the high-affinity Escherichia coli MetNI methionine uptake transporter has been solved. Each MetI subunit is organised around a core of five transmembrane helices that correspond to a subset of the helices observed in the larger membrane-spanning subunits of the molybdate (ModBC) and maltose (MalFGK) ABC transporters, which contain six helices [ PUBMED:18621668 , PUBMED:29240795 ].

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 BPD_transp_1 (CL0404), which has the following description:

This clan contains families that are involved in transport of molecules across membranes. It includes the bacterial binding protein-dependent transport system inner membrane component, Pfam:PF00528, which is ATP dependent system involved in transport of a range of substrates [1-2].

The clan contains the following 4 members:

BPD_transp_1 DUF1430 FtsX LptF_LptG

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...

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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
(81)
Full
(345769)
Representative proteomes UniProt
(1593253)
RP15
(30611)
RP35
(155897)
RP55
(366531)
RP75
(664281)
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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
(81)
Full
(345769)
Representative proteomes UniProt
(1593253)
RP15
(30611)
RP35
(155897)
RP55
(366531)
RP75
(664281)
Alignment:
Format:
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Sequence:
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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
(81)
Full
(345769)
Representative proteomes UniProt
(1593253)
RP15
(30611)
RP35
(155897)
RP55
(366531)
RP75
(664281)
Raw Stockholm Download     Download          
Gzipped 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: LMB bacterial genome group and Prosite
Previous IDs: BPD_transp;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 81
Number in full: 345769
Average length of the domain: 197.5 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 65.36 %

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 26.4 26.4
Trusted cut-off 26.4 26.4
Noise cut-off 26.3 26.3
Model length: 185
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 BPD_transp_1 domain has been found. There are 93 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 sequence.

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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
A0A077Z514 View 3D Structure Click here
A0A077ZH25 View 3D Structure Click here
A0A077ZHK6 View 3D Structure Click here
A0A077ZJ97 View 3D Structure Click here
A0A077ZJB1 View 3D Structure Click here
A0A077ZJG8 View 3D Structure Click here
A0A077ZK14 View 3D Structure Click here
A0A077ZL76 View 3D Structure Click here
A0A077ZLA9 View 3D Structure Click here
A0A077ZM60 View 3D Structure Click here
A0A0H3GGU7 View 3D Structure Click here
A0A0H3GIE8 View 3D Structure Click here
A0A0H3GIV6 View 3D Structure Click here
A0A0H3GIW5 View 3D Structure Click here
A0A0H3GJ62 View 3D Structure Click here
A0A0H3GJ82 View 3D Structure Click here
A0A0H3GJT0 View 3D Structure Click here
A0A0H3GJT5 View 3D Structure Click here
A0A0H3GK73 View 3D Structure Click here
A0A0H3GKV9 View 3D Structure Click here
A0A0H3GL23 View 3D Structure Click here
A0A0H3GLE7 View 3D Structure Click here
A0A0H3GLJ9 View 3D Structure Click here
A0A0H3GLZ7 View 3D Structure Click here
A0A0H3GM52 View 3D Structure Click here
A0A0H3GME0 View 3D Structure Click here
A0A0H3GN83 View 3D Structure Click here
A0A0H3GN93 View 3D Structure Click here
A0A0H3GNF7 View 3D Structure Click here
A0A0H3GP90 View 3D Structure Click here
A0A0H3GPE6 View 3D Structure Click here
A0A0H3GPL3 View 3D Structure Click here
A0A0H3GPQ4 View 3D Structure Click here
A0A0H3GPX4 View 3D Structure Click here
A0A0H3GQ49 View 3D Structure Click here
A0A0H3GQB0 View 3D Structure Click here
A0A0H3GQC7 View 3D Structure Click here
A0A0H3GQD0 View 3D Structure Click here
A0A0H3GQI9 View 3D Structure Click here
A0A0H3GQJ0 View 3D Structure Click here