Summary: WD40-like Beta Propeller Repeat
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WD40-like Beta Propeller Repeat Provide feedback
This family appears to be related to the PF00400 repeat. This repeat corresponds to the RIVW repeat identified in cell surface proteins [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16.
Literature references
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Neer EJ, Schmidt CJ, Nambudripad R, Smith TF; , Nature 1994;371:297-300.: The ancient regulatory-protein family of WD-repeat proteins. PUBMED:8090199 EPMC:8090199
Internal database links
SCOOP: | Cytochrom_D1 DPPIV_N DUF5050 DUF839 eIF2A Gmad1 Pectate_lyase22 Peptidase_S9_N SGL |
External database links
SCOP: | 1crz |
This tab holds annotation information from the InterPro database.
InterPro entry IPR011659
WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [PUBMED:11814058, PUBMED:10322433]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.
This region appears to be related to the INTERPRO repeat. This model is likely to miss copies within a sequence.
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 Beta_propeller (CL0186), which has the following description:
This large clan contains proteins that contain beta propellers. These are composed of between 6 and 8 repeats. The individual repeats are composed of a four stranded sheet. The clan includes families such as WD40 Pfam:PF00400 where the individual repeats are modeled. The clan also includes families where the entire propeller is modeled such as Pfam:PF02239 usually because the individual repeats are not discernible. These proteins carry out a very wide diversity of functions including catalysis.
The clan contains the following 80 members:
ANAPC4_WD40 Arylesterase Arylsulfotran_2 Arylsulfotrans BBS2_Mid Beta_propel Coatomer_WDAD CPSF_A CyRPA Cytochrom_D1 DPPIV_N DUF1513 DUF1668 DUF2415 DUF4221 DUF4933 DUF4934 DUF5046 DUF5050 DUF5122 DUF5128 DUF5711 DUF839 eIF2A FG-GAP FG-GAP_2 Frtz Ge1_WD40 Glu_cyclase_2 Gmad1 GSDH Hyd_WA IKI3 Itfg2 Kelch_1 Kelch_2 Kelch_3 Kelch_4 Kelch_5 Kelch_6 Lactonase Ldl_recept_b LGFP Lgl_C LVIVD Me-amine-dh_H MRJP Nbas_N Neisseria_PilC NHL Nucleoporin_N Nup160 PALB2_WD40 PD40 Pectate_lyase22 Peptidase_S9_N PHTB1_N Phytase-like PQQ PQQ_2 PQQ_3 RAG2 RCC1 RCC1_2 Reg_prop SBBP SBP56 SdiA-regulated SGL Str_synth TcdB_toxin_midN Tectonin TolB_like VCBS VID27 WD40 WD40_2 WD40_3 WD40_4 WD40_likeAlignments
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 (94) |
Full (45889) |
Representative proteomes | UniProt (213092) |
NCBI (304377) |
Meta (9025) |
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RP15 (6607) |
RP35 (21125) |
RP55 (45772) |
RP75 (75800) |
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HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (94) |
Full (45889) |
Representative proteomes | UniProt (213092) |
NCBI (304377) |
Meta (9025) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (6607) |
RP35 (21125) |
RP55 (45772) |
RP75 (75800) |
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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: | Yeats C |
Previous IDs: | none |
Type: | Repeat |
Sequence Ontology: | SO:0001068 |
Author: |
Yeats C |
Number in seed: | 94 |
Number in full: | 45889 |
Average length of the domain: | 34.40 aa |
Average identity of full alignment: | 24 % |
Average coverage of the sequence by the domain: | 13.39 % |
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: | 38 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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...
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Interactions
There are 11 interactions for this family. More...
Tricorn_PDZ TolB_N TolB_N DPPIV_N Cloacin Peptidase_S41 Tricorn_PDZ OmpA DPPIV_N Peptidase_S41 PD40Structures
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 PD40 domain has been found. There are 179 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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