Summary: Peptidase family S41
Peptidase family S41 Provide feedback
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This tab holds annotation information from the InterPro database.
InterPro entry IPR005151
This entry represents a domain found in the tail-specific proteases, such as retinol-binding protein 3 (also known as IRBP) from animals, C-terminal processing peptidases from algae and tricorn proteases from archaea. This domain share structural similarity with the crotonase fold that is formed from repeated beta/beta/alpha units, which comprises two perpendicular beta-sheet surrounded by alpha-helices.
The C-terminal processing peptidases have different substrates in different species, including processing of D1 protein of the photosystem II reaction centre in higher plants [PUBMED:8702985], and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in Escherichia coli [PUBMED:1856173].
The tricorn protease is responsible for degrading oligopeptides, probably derived from the proteasome. Its crystal structure has been resolved to 2 A resolution [PUBMED:11719810].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||serine-type peptidase activity (GO:0008236)|
|Biological process||proteolysis (GO:0006508)|
- the number of sequences which exhibit this architecture
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This example describes an architecture with one
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This family includes several peptidases of peptidase clan SK as well as crotonase like proteins.
The clan contains the following 10 members:ACCA Carboxyl_trans CLP_protease ECH_1 ECH_2 MdcE Peptidase_S41 Peptidase_S49 Peptidase_S49_N SDH_sah
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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Curation and family details
|Author:||Griffiths-Jones SR, Finn RD|
|Number in seed:||120|
|Number in full:||27996|
|Average length of the domain:||170.40 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||32.81 %|
|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_S41 domain has been found. There are 58 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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