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53  structures 8367  species 0  interactions 18727  sequences 209  architectures

Family: Peptidase_M41 (PF01434)

Summary: Peptidase family M41

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Peptidase family M41 Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000642

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 group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH.

The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.

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...

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
(27)
Full
(18727)
Representative proteomes UniProt
(68027)
RP15
(2947)
RP35
(9425)
RP55
(17638)
RP75
(27392)
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
(27)
Full
(18727)
Representative proteomes UniProt
(68027)
RP15
(2947)
RP35
(9425)
RP55
(17638)
RP75
(27392)
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
(27)
Full
(18727)
Representative proteomes UniProt
(68027)
RP15
(2947)
RP35
(9425)
RP55
(17638)
RP75
(27392)
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: Swiss-Prot
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 27
Number in full: 18727
Average length of the domain: 181.60 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 26.76 %

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 29.9 29.9
Trusted cut-off 29.9 29.9
Noise cut-off 29.8 29.8
Model length: 191
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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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_M41 domain has been found. There are 53 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
A0A096S2Q4 View 3D Structure Click here
A0A0P0V4Q4 View 3D Structure Click here
A0A0R0EFV6 View 3D Structure Click here
A0A0R0GL56 View 3D Structure Click here
A0A0R0I7T2 View 3D Structure Click here
A0A0R0K458 View 3D Structure Click here
A0A0R4IJC7 View 3D Structure Click here
A0A1D6FLN2 View 3D Structure Click here
A0A1D6LPZ6 View 3D Structure Click here
A0A1D6NJI2 View 3D Structure Click here
A0A1D6NK09 View 3D Structure Click here
A0A1D6P5R0 View 3D Structure Click here
A0A1D8PME0 View 3D Structure Click here
A0A2R8PVN0 View 3D Structure Click here
A2ZVG7 View 3D Structure Click here
A4HXT7 View 3D Structure Click here
A4HYI8 View 3D Structure Click here
A4I6G4 View 3D Structure Click here
A4I809 View 3D Structure Click here
A4I9Q6 View 3D Structure Click here
A4ICH8 View 3D Structure Click here
A8MPR5 View 3D Structure Click here
A9JRG9 View 3D Structure Click here
B4F988 View 3D Structure Click here
C4J917 View 3D Structure Click here
D3ZZ20 View 3D Structure Click here
E7EZJ5 View 3D Structure Click here
E7F2S4 View 3D Structure Click here
E7F6D6 View 3D Structure Click here
F1LN92 View 3D Structure Click here
F3YDF1 View 3D Structure Click here
F4J3N2 View 3D Structure Click here
F6M9W9 View 3D Structure Click here
G5EDB6 View 3D Structure Click here
G5EGR7 View 3D Structure Click here
I1J3Y7 View 3D Structure Click here
I1JHB5 View 3D Structure Click here
I1JSX4 View 3D Structure Click here
I1K360 View 3D Structure Click here
I1K7F0 View 3D Structure Click here
I1KPL2 View 3D Structure Click here
I1KRI0 View 3D Structure Click here
I1LQN8 View 3D Structure Click here
I1M5H4 View 3D Structure Click here
I1M934 View 3D Structure Click here
I1MB96 View 3D Structure Click here
I1N4D7 View 3D Structure Click here
K7KDX3 View 3D Structure Click here
K7KUR7 View 3D Structure Click here
K7L8H2 View 3D Structure Click here
K7LFQ9 View 3D Structure Click here
K7LJT5 View 3D Structure Click here
K7LPM7 View 3D Structure Click here
K7LTB1 View 3D Structure Click here
K7LXZ1 View 3D Structure Click here
K7M5W8 View 3D Structure Click here
K7M5X0 View 3D Structure Click here
K7M918 View 3D Structure Click here
K7MNG0 View 3D Structure Click here
K7MQB0 View 3D Structure Click here
K7MQX4 View 3D Structure Click here
K7TYZ8 View 3D Structure Click here
K7V321 View 3D Structure Click here
K7V3I7 View 3D Structure Click here
K7V5A0 View 3D Structure Click here
K7VGG8 View 3D Structure Click here
O22993 View 3D Structure Click here
O59824 View 3D Structure Click here
O80860 View 3D Structure Click here
O80983 View 3D Structure Click here
O88967 View 3D Structure Click here
P0AAI3 View 3D Structure Click here
P32795 View 3D Structure Click here
P39925 View 3D Structure Click here
P40341 View 3D Structure Click here
P54813 View 3D Structure Click here
P9WQN3 View 3D Structure Click here
Q0DDE7 View 3D Structure Click here
Q0DHL4 View 3D Structure Click here
Q1PDW5 View 3D Structure Click here
Q2G0R0 View 3D Structure Click here
Q39102 View 3D Structure Click here
Q3ULF4 View 3D Structure Click here
Q4CZ68 View 3D Structure Click here
Q4DAV1 View 3D Structure Click here
Q4DB84 View 3D Structure Click here
Q4DBP0 View 3D Structure Click here
Q4DEY4 View 3D Structure Click here
Q4DJU4 View 3D Structure Click here
Q4DM81 View 3D Structure Click here
Q4DMG4 View 3D Structure Click here
Q4DZT3 View 3D Structure Click here
Q4E303 View 3D Structure Click here
Q4E5H7 View 3D Structure Click here
Q54BW7 View 3D Structure Click here
Q54PX1 View 3D Structure Click here
Q55GV8 View 3D Structure Click here
Q5AD10 View 3D Structure Click here
Q5AJC2 View 3D Structure Click here
Q5Z974 View 3D Structure Click here
Q655S1 View 3D Structure Click here
Q67WJ2 View 3D Structure Click here
Q6H6R9 View 3D Structure Click here
Q75JS8 View 3D Structure Click here
Q7TT47 View 3D Structure Click here
Q84WU8 View 3D Structure Click here
Q8I526 View 3D Structure Click here
Q8IIH1 View 3D Structure Click here
Q8IKI9 View 3D Structure Click here
Q8JZQ2 View 3D Structure Click here
Q8LQJ8 View 3D Structure Click here
Q8LQJ9 View 3D Structure Click here
Q8S2A7 View 3D Structure Click here
Q8T4G5 View 3D Structure Click here
Q8VZI8 View 3D Structure Click here
Q8W585 View 3D Structure Click here
Q920A7 View 3D Structure Click here
Q925S8 View 3D Structure Click here
Q96TA2 View 3D Structure Click here
Q9FGM0 View 3D Structure Click here
Q9FH02 View 3D Structure Click here
Q9FIM2 View 3D Structure Click here
Q9HGM3 View 3D Structure Click here
Q9N3T5 View 3D Structure Click here
Q9SAJ3 View 3D Structure Click here
Q9SD67 View 3D Structure Click here
Q9UQ90 View 3D Structure Click here
Q9W4W8 View 3D Structure Click here
Q9Y4W6 View 3D Structure Click here