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257  structures 4823  species 0  interactions 24530  sequences 329  architectures

Family: Peptidase_M28 (PF04389)

Summary: Peptidase family M28

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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 family M28 Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007484

Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site [ PUBMED:7674922 ]. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases [ PUBMED:7674922 ].

This domain is found in metallopeptidases belonging to the MEROPS peptidase family M28 (aminopeptidase Y, clan MH) [ PUBMED:7674922 ]. They also contain a transferrin receptor-like dimerisation domain ( INTERPRO ) and a protease-associated PA domain ( 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 Peptidase_MH (CL0035), which has the following description:

This clan contains peptidases belonging to MEROPS clan MH, MC and MF. We also include Nicastrin that is part of the gamma secretase complex and not known to be a peptidase.

The clan contains the following 17 members:

Amidase_3 AstE_AspA DUF2817 DUF4910 FGase Gamma_PGA_hydro Glycolytic Ncstrn_small Nicastrin Peptidase_M14 Peptidase_M17 Peptidase_M18 Peptidase_M20 Peptidase_M28 Peptidase_M42 Peptidase_M99 SpoIIP

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...

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
(55)
Full
(24530)
Representative proteomes UniProt
(78468)
RP15
(3479)
RP35
(10471)
RP55
(22027)
RP75
(35167)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(55)
Full
(24530)
Representative proteomes UniProt
(78468)
RP15
(3479)
RP35
(10471)
RP55
(22027)
RP75
(35167)
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
(55)
Full
(24530)
Representative proteomes UniProt
(78468)
RP15
(3479)
RP35
(10471)
RP55
(22027)
RP75
(35167)
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: Bateman A
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 55
Number in full: 24530
Average length of the domain: 201.90 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 36.43 %

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 198
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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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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_M28 domain has been found. There are 257 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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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
A0A0B4KEL4 View 3D Structure Click here
A0A0B4KEU8 View 3D Structure Click here
A0A0B4KFC9 View 3D Structure Click here
A0A0G2KE94 View 3D Structure Click here
A0A0P0V7Z3 View 3D Structure Click here
A0A0P0V830 View 3D Structure Click here
A0A0P0WCM5 View 3D Structure Click here
A0A0P0X4T3 View 3D Structure Click here
A0A0R0HR10 View 3D Structure Click here
A0A1D6L709 View 3D Structure Click here
A0A1D6NCY3 View 3D Structure Click here
A0A1D6NCY9 View 3D Structure Click here
A0A1D6NWK9 View 3D Structure Click here
A0A1D8PDD4 View 3D Structure Click here
A0A1D8PI95 View 3D Structure Click here
A0A1D8PKX5 View 3D Structure Click here
A0A1D8PQI1 View 3D Structure Click here
A0A1P8ASM6 View 3D Structure Click here
A0A2R8RRX1 View 3D Structure Click here
A0A368ULZ9 View 3D Structure Click here
A1Z8X5 View 3D Structure Click here
A1Z8X9 View 3D Structure Click here
A1ZBK1 View 3D Structure Click here
A2BGQ8 View 3D Structure Click here
A4HSL7 View 3D Structure Click here
A4HSL7 View 3D Structure Click here
B2GUY2 View 3D Structure Click here
B5DFI7 View 3D Structure Click here
B7ZZ74 View 3D Structure Click here
D4A2Y7 View 3D Structure Click here
D4AC85 View 3D Structure Click here
E7F131 View 3D Structure Click here
E7F8H4 View 3D Structure Click here
E9QEV8 View 3D Structure Click here
F1QYJ7 View 3D Structure Click here
F1RD57 View 3D Structure Click here
G5EBT9 View 3D Structure Click here
I1JQD5 View 3D Structure Click here
I1K3L0 View 3D Structure Click here
I1KS06 View 3D Structure Click here
I1NAY2 View 3D Structure Click here
K7LKM1 View 3D Structure Click here
K7MGF1 View 3D Structure Click here
K7MRT3 View 3D Structure Click here
K7V8V3 View 3D Structure Click here
O06803 View 3D Structure Click here
O35409 View 3D Structure Click here
O43023 View 3D Structure Click here
O54697 View 3D Structure Click here
O94479 View 3D Structure Click here
O94702 View 3D Structure Click here
P02786 View 3D Structure Click here
P10423 View 3D Structure Click here
P37302 View 3D Structure Click here
P38244 View 3D Structure Click here
P43599 View 3D Structure Click here
P47161 View 3D Structure Click here
P70627 View 3D Structure Click here
P76482 View 3D Structure Click here
P91406 View 3D Structure Click here
P96264 View 3D Structure Click here
Q04033 View 3D Structure Click here
Q04609 View 3D Structure Click here
Q058X1 View 3D Structure Click here
Q08693 View 3D Structure Click here
Q09216 View 3D Structure Click here
Q0WVZ7 View 3D Structure Click here
Q16769 View 3D Structure Click here
Q18600 View 3D Structure Click here
Q1LWV0 View 3D Structure Click here
Q3UVK0 View 3D Structure Click here
Q4DQ87 View 3D Structure Click here
Q4DQ87 View 3D Structure Click here
Q4DZX1 View 3D Structure Click here
Q4DZX1 View 3D Structure Click here
Q4DZX1 View 3D Structure Click here
Q4U2G8 View 3D Structure Click here
Q4V5E4 View 3D Structure Click here
Q54B14 View 3D Structure Click here
Q54MN6 View 3D Structure Click here
Q550Q3 View 3D Structure Click here
Q58DX5 View 3D Structure Click here
Q59RF7 View 3D Structure Click here
Q5AA00 View 3D Structure Click here
Q5JKV3 View 3D Structure Click here
Q5MPX4 View 3D Structure Click here
Q5XIA1 View 3D Structure Click here
Q62351 View 3D Structure Click here
Q6IRK9 View 3D Structure Click here
Q6NZ07 View 3D Structure Click here
Q6UPR8 View 3D Structure Click here
Q7M758 View 3D Structure Click here
Q7Y228 View 3D Structure Click here
Q7Z2K6 View 3D Structure Click here
Q852M4 View 3D Structure Click here
Q86PD7 View 3D Structure Click here
Q8BH73 View 3D Structure Click here
Q8I936 View 3D Structure Click here
Q8MKL0 View 3D Structure Click here
Q8MT48 View 3D Structure Click here
Q8VCM8 View 3D Structure Click here
Q93332 View 3D Structure Click here
Q969V3 View 3D Structure Click here
Q99376 View 3D Structure Click here
Q9CYK2 View 3D Structure Click here
Q9CZR2 View 3D Structure Click here
Q9HBA9 View 3D Structure Click here
Q9JKX3 View 3D Structure Click here
Q9M1S8 View 3D Structure Click here
Q9N516 View 3D Structure Click here
Q9NXS2 View 3D Structure Click here
Q9UP52 View 3D Structure Click here
Q9UQQ1 View 3D Structure Click here
Q9VRQ9 View 3D Structure Click here
Q9VTH7 View 3D Structure Click here
Q9WVJ3 View 3D Structure Click here
Q9XH28 View 3D Structure Click here
Q9Y3Q0 View 3D Structure Click here
Q9Y646 View 3D Structure Click here