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28  structures 106  species 4  interactions 194  sequences 106  architectures

Family: Peptidase_M10_C (PF08548)

Summary: Peptidase M10 serralysin C terminal

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Peptidase M10 serralysin C terminal Provide feedback

Serralysins are peptidases related to mammalian matrix metallopeptidases (MMPs). The peptidase unit is found at the N terminal while this domain at the C terminal forms a corkscrew and is thought to be important for secretion of the protein through the bacterial cell wall. This domain contains the calcium ion binding domain PF00353.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013858

Serralysins are peptidases related to mammalian matrix metallopeptidases (MMPs). The peptidase unit is found at the N-terminal, while this domain at the C-terminal forms a corkscrew and is thought to be important for secretion of the protein through the bacterial cell wall. This domain contains the hemolysin-type calcium-binding repeat.

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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Pfam Clan

This family is a member of clan beta_Roll (CL0592), which has the following description:

This superfamily is characterised by families of a short nonarepeat unit. The beta-roll is made up of a super-helix of beta-strand-turns of two short strands each, and the loops are stabilised by Ca2+ ions. The region of a protein with this beta-roll is often termed the R-module, and it can frequently be found in metalloproteases of the serralysin type and in epimerases [1]. The nonarepeat is also found multiple times in haemolysins, where the structure is again stabilised by binding Ca2+ ions.

The clan contains the following 2 members:

HemolysinCabind Peptidase_M10_C

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
(16)
Full
(194)
Representative proteomes UniProt
(1510)
NCBI
(3361)
Meta
(178)
RP15
(30)
RP35
(136)
RP55
(211)
RP75
(368)
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HTML View  View               
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
(16)
Full
(194)
Representative proteomes UniProt
(1510)
NCBI
(3361)
Meta
(178)
RP15
(30)
RP35
(136)
RP55
(211)
RP75
(368)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(16)
Full
(194)
Representative proteomes UniProt
(1510)
NCBI
(3361)
Meta
(178)
RP15
(30)
RP35
(136)
RP55
(211)
RP75
(368)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: Rawlings ND
Previous IDs: none
Type: Domain
Author: Mistry J, Rawlings ND
Number in seed: 16
Number in full: 194
Average length of the domain: 188.70 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 23.15 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.7 20.7
Trusted cut-off 20.7 20.8
Noise cut-off 20.5 20.6
Model length: 193
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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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Interactions

There are 4 interactions for this family. More...

Reprolysin_2 Peptidase_M10 HemolysinCabind Inh

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 Peptidase_M10_C domain has been found. There are 28 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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