Summary: Receptor family ligand binding region
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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.
Receptor family ligand binding region Provide feedback
This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
Literature references
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Kuryatov A, Laube B, Betz H, Kuhse J; , Neuron 1994;12:1291-1300.: Mutational analysis of the glycine-binding site of the NMDA receptor: structural similarity with bacterial amino acid-binding proteins. PUBMED:8011339 EPMC:8011339
Internal database links
SCOOP: | ABC_sub_bind CRT10 Fe-ADH Lig_chan-Glu_bd LppC NCD3G Peripla_BP_1 Peripla_BP_3 Peripla_BP_4 Peripla_BP_5 Peripla_BP_6 |
Similarity to PfamA using HHSearch: | LppC Peripla_BP_5 Peripla_BP_6 |
External database links
HOMSTRAD: | aminobp |
PROSITE: | PDOC00430 |
SCOP: | 2liv |
Transporter classification: | 3.A.1 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001828
This describes a ligand binding domain and includes extracellular ligand binding domains of a wide range of receptors, as well as the bacterial amino acid binding proteins of known structure [PUBMED:8011339].
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_7Alignments
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...
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 (71) |
Full (25562) |
Representative proteomes | UniProt (40484) |
NCBI (177829) |
Meta (2724) |
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RP15 (4281) |
RP35 (10298) |
RP55 (19045) |
RP75 (26920) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (71) |
Full (25562) |
Representative proteomes | UniProt (40484) |
NCBI (177829) |
Meta (2724) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (4281) |
RP35 (10298) |
RP55 (19045) |
RP75 (26920) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Prosite |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 71 |
Number in full: | 25562 |
Average length of the domain: | 315.90 aa |
Average identity of full alignment: | 16 % |
Average coverage of the sequence by the domain: | 39.57 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 354 | ||||||||||||
Family (HMM) version: | 29 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
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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...
Tree controls
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Interactions
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 ANF_receptor domain has been found. There are 632 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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