Summary: Periplasmic binding protein domain
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Periplasmic binding protein domain Provide feedback
This domain is found in a variety of bacterial periplasmic binding proteins.
Internal database links
|Similarity to PfamA using HHSearch:||Bmp ABC_sub_bind ABC_sub_bind Peripla_BP_1 Peripla_BP_3 Peripla_BP_6|
External database links
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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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 9 members:ABC_sub_bind ANF_receptor Bmp LppC Peripla_BP_1 Peripla_BP_3 Peripla_BP_4 Peripla_BP_5 Peripla_BP_6
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||173|
|Number in full:||12924|
|Average length of the domain:||255.70 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||75.86 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||1|
|Download:||download the raw HMM for this family|
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How the sunburst is generated
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Anomalies in the taxonomy tree
Missing taxonomic levels
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The tree shows the occurrence of this domain across different species. More...
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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_4 domain has been found. There are 86 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 seqence.
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