Summary: Serpin (serine protease inhibitor)
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This is the Wikipedia entry entitled "Serpin". More...
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Serpin (serine protease inhibitor) Provide feedback
Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.
Literature references
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Wright HT; , Bioessays 1996;18:453-464.: The structural puzzle of how serpin serine proteinase inhibitors work. PUBMED:8787534 EPMC:8787534
External database links
HOMSTRAD: | serpin |
PROSITE: | PDOC00256 |
SCOP: | 1hle |
This tab holds annotation information from the InterPro database.
InterPro entry IPR023796
Serpins (SERine Proteinase INhibitors) belong to MEROPS inhibitor family I4, clan ID. Most serpin family members are indeed serine protease inhibitors, but several have additional cross-class inhibition functions and inhibit cysteine protease family members such as the caspases and cathepsins [PUBMED:8034697, PUBMED:7851535]. Others, such as ovalbumin, are incapable of protease inhibition and serve other functions [PUBMED:8417965].
Serpins share a highly conserved core structure that is critical for their functioning as serine protease inhibitors [PUBMED:21781239]. Inhibitory serpins comprise several alpha-helix and beta-strands together with an external reactive centre loop (RCL) containing the active site recognised by the target enzyme. Serpins form covalent complexes with target proteases. Their mechanism of protease inhibition is known as irreversible "trapping" , in which a rapid conformational change traps the cognate protease in a covalent complex.
This entry represents the structural domain of serpins.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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...
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 (125) |
Full (13416) |
Representative proteomes | UniProt (28678) |
NCBI (39200) |
Meta (69) |
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RP15 (2069) |
RP35 (5106) |
RP55 (9710) |
RP75 (14322) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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Format an alignment
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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 (125) |
Full (13416) |
Representative proteomes | UniProt (28678) |
NCBI (39200) |
Meta (69) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (2069) |
RP35 (5106) |
RP55 (9710) |
RP75 (14322) |
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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: | Overington and HMM_iterative_training |
Previous IDs: | serpin; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Eddy SR |
Number in seed: | 125 |
Number in full: | 13416 |
Average length of the domain: | 299.20 aa |
Average identity of full alignment: | 23 % |
Average coverage of the sequence by the domain: | 83.94 % |
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: | 371 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
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
There are 7 interactions for this family. More...
Trypsin Thrombin_light Trypsin Asp Asp Serpin Somatomedin_BStructures
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 Serpin domain has been found. There are 478 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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