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4  structures 90  species 0  interactions 90  sequences 1  architecture

Family: Peripla_BP_7 (PF18610)

Summary: Periplasmic binding protein domain

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Periplasmic binding protein domain Provide feedback

Treponema pallidum, the bacterium that causes syphilis, is an obligate human parasite. T. pallidum lacks the machinery for the de novo synthesis of many key nutrients therefore it acquires these nutrients from its human host. MglB-2 from T. pallidum has been shown to act as the ligand-binding element of an ABC transporter for D-glucose. The overall fold of MglB-2 resembles those of LBPs (Ligand-binding proteins sometimes called 'Periplasmic Binding Proteins') that serve as receptors for nutrients and cofactors in bacterial ABC transporters. Furthermore, structural analysis of MglB-2 i found in Treponema pallidum shows it to be one of the founding member of a family of proteins related to the 'Type I' or 'Cluster B' LBPs [1]. This domain can also be found on the C-terminal region of PF13407.

Literature references

  1. Brautigam CA, Deka RK, Liu WZ, Norgard MV;, PLoS One. 2016;11:e0161022.: The Tp0684 (MglB-2) Lipoprotein of Treponema pallidum: A Glucose-Binding Protein with Divergent Topology. PUBMED:27536942 EPMC:27536942


This tab holds annotation information from the InterPro database.

InterPro entry IPR040740

Treponema pallidum, the bacterium that causes syphilis, is an obligate human parasite. T. pallidum lacks the machinery for the de novo synthesis of many key nutrients therefore it acquires these nutrients from its human host. MglB-2 from T. pallidum has been shown to act as the ligand-binding element of an ABC transporter for D-glucose. The overall fold of MglB-2 resembles those of LBPs (Ligand-binding proteins sometimes called 'Periplasmic Binding Proteins') that serve as receptors for nutrients and cofactors in bacterial ABC transporters. Furthermore, structural analysis of MglB-2 found in Treponema pallidum shows it to be one of the founding member of a family of proteins related to the 'Type I' or 'Cluster B' LBPs [PUBMED:27536942].

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 Periplas_BP (CL0144), which has the following description:

This clan includes proteins involved in chemotaxis, membrane transport of sugars and allocrites, and the LacI family transcriptional regulators. It also includes some antigenic basic membrane lipoproteins.

The clan contains the following 11 members:

ABC_sub_bind ANF_receptor Bmp DUF3798 LppC Peripla_BP_1 Peripla_BP_3 Peripla_BP_4 Peripla_BP_5 Peripla_BP_6 Peripla_BP_7

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(5)
Full
(90)
Representative proteomes UniProt
(391)
NCBI
(342)
Meta
(3)
RP15
(16)
RP35
(61)
RP55
(88)
RP75
(157)
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PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(5)
Full
(90)
Representative proteomes UniProt
(391)
NCBI
(342)
Meta
(3)
RP15
(16)
RP35
(61)
RP55
(88)
RP75
(157)
Alignment:
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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
(5)
Full
(90)
Representative proteomes UniProt
(391)
NCBI
(342)
Meta
(3)
RP15
(16)
RP35
(61)
RP55
(88)
RP75
(157)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: ECOD:PF01453
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S
Number in seed: 5
Number in full: 90
Average length of the domain: 71.00 aa
Average identity of full alignment: 80 %
Average coverage of the sequence by the domain: 16.50 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 36.8 36.8
Trusted cut-off 59.3 105.1
Noise cut-off 34.0 22.2
Model length: 71
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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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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 Peripla_BP_7 domain has been found. There are 4 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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