Summary: Protein-arginine deiminase (PAD) middle domain
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Protein-arginine deiminase (PAD) middle domain Provide feedback
This family represents the central non-catalytic domain of protein-arginine deiminase. This domain has an immunoglobulin-like fold.
Literature references
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Rogers G, Winter B, McLaughlan C, Powell B, Nesci T; , J Invest Dermatol 1997;108:700-707.: Peptidylarginine deiminase of the hair follicle: characterization, localization, and function in keratinizing tissues. PUBMED:9129218 EPMC:9129218
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Asaga H, Ishigami A; , Neurosci Lett 2001;299:5-8.: Protein deimination in the rat brain after kainate administration: citrulline-containing proteins as a novel marker of neurodegeneration. PUBMED:11166924 EPMC:11166924
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Rus'd AA, Ikejiri Y, Ono H, Yonekawa T, Shiraiwa M, Kawada A, Takahara H; , Eur J Biochem 1999;259:660-669.: Molecular cloning of cDNAs of mouse peptidylarginine deiminase type I, type III and type IV, and the expression pattern of type I in mouse. PUBMED:10092850 EPMC:10092850
External database links
SCOP: | 1wd8 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013733
Peptidylarginine deiminase (PAD) enzymes catalyze the conversion of protein-bound arginine to citrulline. There are five types of PADs known in humans, PAD1-PAD4 and PAD6 [PUBMED:14579251]. This entry represents the central non-catalytic domain of protein-arginine deiminase. This domain has an immunoglobulin-like fold [PUBMED:16567635].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | cytoplasm (GO:0005737) |
Molecular function | calcium ion binding (GO:0005509) |
protein-arginine deiminase activity (GO:0004668) | |
Biological process | protein citrullination (GO:0018101) |
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 P53-like (CL0073), which has the following description:
This clan contains a variety of DNA-binding domains that contain an immunoglobulin-like fold. It includes the DNA-binding domains of NF-kappaB, NFAT, p53, STAT-1, the T-domain and the Runt domain [1].
The clan contains the following 9 members:
CEP1-DNA_bind LAG1-DNAbind NDT80_PhoG P53 PAD_M RHD_DNA_bind Runt STAT_bind T-boxAlignments
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 (559) |
Representative proteomes | UniProt (915) |
NCBI (1739) |
Meta (1) |
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RP15 (33) |
RP35 (138) |
RP55 (353) |
RP75 (590) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (71) |
Full (559) |
Representative proteomes | UniProt (915) |
NCBI (1739) |
Meta (1) |
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RP15 (33) |
RP35 (138) |
RP55 (353) |
RP75 (590) |
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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: | Pfam-B_2195 (release 6.4) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Mifsud W |
Number in seed: | 71 |
Number in full: | 559 |
Average length of the domain: | 154.70 aa |
Average identity of full alignment: | 46 % |
Average coverage of the sequence by the domain: | 24.53 % |
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: | 159 | ||||||||||||
Family (HMM) version: | 11 | ||||||||||||
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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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 PAD_M domain has been found. There are 40 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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