Summary: Peptidase family C25
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Peptidase family C25 Provide feedback
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This tab holds annotation information from the InterPro database.
InterPro entry IPR001769
This domain is found in cysteine peptidases belonging to MEROPS peptidase family C25 (gingipain). Gingipains are cysteine proteinases acting as key virulence factors of the bacterium Porphyromonas gingivalis (Bacteroides gingivalis), a Gram-negative anaerobic bacterial species strongly associated with adult periodontitis [PUBMED:10523290].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||cysteine-type peptidase activity (GO:0008234)|
|Biological process||proteolysis (GO:0006508)|
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The members of this clan are all endopeptidase that have the catalytic dyad histidine followed by cysteine. The catalytic histidine is preceded by a block of hydrophobic residues and a glycine, where as the cysteine is preceded by a block of hydrophobic residues and a glutamine and an alanine. The members with a know structure adopt an alpha/beta fold .
The clan contains the following 9 members:CHAT GVQW Peptidase_C11 Peptidase_C13 Peptidase_C14 Peptidase_C25 Peptidase_C50 Peptidase_C80 Raptor_N
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Curation and family details
|Seed source:||Pfam-B_516 (release 3.0)|
|Author:||Bateman A, Griffiths-Jones SR|
|Number in seed:||77|
|Number in full:||705|
|Average length of the domain:||318.40 aa|
|Average identity of full alignment:||19 %|
|Average coverage of the sequence by the domain:||35.91 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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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 Peptidase_C25 domain has been found. There are 7 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 seqence.
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