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0  structures 44  species 0  interactions 313  sequences 7  architectures

Family: Defensin_propep (PF00879)

Summary: Defensin propeptide

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Defensin propeptide Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002366

Defensins are 2-6kDa, cationic, microbicidal peptides active against many Gram-negative and Gram-positive bacteria, fungi, and enveloped viruses [ PUBMED:8528769 ], containing three pairs of intramolecular disulphide bonds [ PUBMED:12072367 ]. On the basis of their size and pattern of disulphide bonding, mammalian defensins are classified into alpha, beta and theta categories. Alpha-defensins, which have been identified in humans, monkeys and several rodent species, are particularly abundant in neutrophils, certain macrophage populations and Paneth cells of the small intestine. Every mammalian species explored thus far has beta-defensins. In cows, as many as 13 beta-defensins exist in neutrophils. However, in other species, beta-defensins are more often produced by epithelial cells lining various organs (e.g. the epidermis, bronchial tree and genitourinary tract). Theta-defensins are cyclic and have so far only been identified in primate phagocytes.

Defensins are produced constitutively and/or in response to microbial products or proinflammatory cytokines. Some defensins are also called corticostatins (CS) because they inhibit corticotropin-stimulated corticosteroid production. The mechanism(s) by which microorganisms are killed and/or inactivated by defensins is not understood completely. However, it is generally believed that killing is a consequence of disruption of the microbial membrane. The polar topology of defensins, with spatially separated charged and hydrophobic regions, allows them to insert themselves into the phospholipid membranes so that their hydrophobic regions are buried within the lipid membrane interior and their charged (mostly cationic) regions interact with anionic phospholipid head groups and water. Subsequently, some defensins can aggregate to form `channel-like' pores; others might bind to and cover the microbial membrane in a `carpet-like' manner. The net outcome is the disruption of membrane integrity and function, which ultimately leads to the lysis of microorganisms. Some defensins are synthesized as propeptides which may be relevant to this process - in neutrophils only the mature peptides have been identified but in Paneth cells, the propeptide is stored in vesicles [ PUBMED:12021776 ] and appears to be cleaved by trypsin on activation.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 and the UniProtKB 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
(31)
Full
(313)
Representative proteomes UniProt
(455)
RP15
(58)
RP35
(82)
RP55
(175)
RP75
(253)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(31)
Full
(313)
Representative proteomes UniProt
(455)
RP15
(58)
RP35
(82)
RP55
(175)
RP75
(253)
Alignment:
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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
(31)
Full
(313)
Representative proteomes UniProt
(455)
RP15
(58)
RP35
(82)
RP55
(175)
RP75
(253)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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 View help on the curation process

Seed source: Pfam-B_517 (release 3.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 31
Number in full: 313
Average length of the domain: 50.90 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 52.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.6 23.6
Trusted cut-off 23.6 23.6
Noise cut-off 23.5 23.3
Model length: 51
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
D3YX02 View 3D Structure Click here
D3YX03 View 3D Structure Click here
D3Z0J0 View 3D Structure Click here
D3Z1V9 View 3D Structure Click here
E9QLQ1 View 3D Structure Click here
E9QPZ2 View 3D Structure Click here
F1LSU5 View 3D Structure Click here
F2Z403 View 3D Structure Click here
K9J724 View 3D Structure Click here
L7N231 View 3D Structure Click here
P11477 View 3D Structure Click here
P12838 View 3D Structure Click here
P17533 View 3D Structure Click here
P17534 View 3D Structure Click here
P28309 View 3D Structure Click here
P28310 View 3D Structure Click here
P28311 View 3D Structure Click here
P28312 View 3D Structure Click here
P50704 View 3D Structure Click here
P50705 View 3D Structure Click here
P50706 View 3D Structure Click here
P50707 View 3D Structure Click here
P50708 View 3D Structure Click here
P50709 View 3D Structure Click here
P50711 View 3D Structure Click here
P50712 View 3D Structure Click here
P50713 View 3D Structure Click here
P50714 View 3D Structure Click here
P50715 View 3D Structure Click here
P50716 View 3D Structure Click here
P59665 View 3D Structure Click here
P59666 View 3D Structure Click here
P82106 View 3D Structure Click here
Q01523 View 3D Structure Click here
Q01524 View 3D Structure Click here
Q3L180 View 3D Structure Click here
Q45VN2 View 3D Structure Click here
Q4JEI2 View 3D Structure Click here
Q4JEI3 View 3D Structure Click here
Q4JEI5 View 3D Structure Click here
Q4JEI6 View 3D Structure Click here
Q4JEI8 View 3D Structure Click here
Q4JEI9 View 3D Structure Click here
Q5ERI8 View 3D Structure Click here
Q5ERJ0 View 3D Structure Click here
Q5G864 View 3D Structure Click here
Q5G865 View 3D Structure Click here
Q5G866 View 3D Structure Click here
Q62713 View 3D Structure Click here
Q62714 View 3D Structure Click here
Q62715 View 3D Structure Click here
Q62716 View 3D Structure Click here
Q64016 View 3D Structure Click here
Q64263 View 3D Structure Click here
Q8C1N8 View 3D Structure Click here
Q8C1P2 View 3D Structure Click here
Q9D848 View 3D Structure Click here
Q9Z1F1 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;