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55  structures 1475  species 1  interaction 1857  sequences 10  architectures

Family: Peptidase_S58 (PF03576)

Summary: Peptidase family S58

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Peptidase family S58 Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005321

This group of serine peptidases belong to MEROPS peptidase family S58 (DmpA aminopeptidase family, clan PB(S)). The protein fold of the peptidase unit for members of this family resembles that of archaean proteasome subunit B, the type example of clan PB. The type example is aminopeptidase DmpA from Ochrobactrum anthropi. This family also contains proteins that have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the family.

L-aminopeptidase D-Ala-esterase/amidase (DmpA) from O. anthropi releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. DmpA active form is an alphabeta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide. DmpA shows structural homology to N-terminal nucleophile (Ntn) hydrolase family members, and may work by a similar catalytic mechanism, however their secondary structure elements differ significantly [PUBMED:10673442].

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 DmpA_ArgJ (CL0635), which has the following description:

This superfamily includes the ArgJ protein and members of peptidase family S58. According to SCOP these proteins have a fold which resembles but is unrelated to that of the NTN hydrolases.

The clan contains the following 2 members:

ArgJ Peptidase_S58

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
(236)
Full
(1857)
Representative proteomes UniProt
(4983)
NCBI
(9557)
Meta
(477)
RP15
(296)
RP35
(985)
RP55
(1853)
RP75
(2913)
Jalview View  View  View  View  View  View  View  View  View 
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
(236)
Full
(1857)
Representative proteomes UniProt
(4983)
NCBI
(9557)
Meta
(477)
RP15
(296)
RP35
(985)
RP55
(1853)
RP75
(2913)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(236)
Full
(1857)
Representative proteomes UniProt
(4983)
NCBI
(9557)
Meta
(477)
RP15
(296)
RP35
(985)
RP55
(1853)
RP75
(2913)
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: MEROPS
Previous IDs: Peptidase_T4;
Type: Family
Author: Griffiths-Jones SR
Number in seed: 236
Number in full: 1857
Average length of the domain: 311.40 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 90.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.9 23.9
Trusted cut-off 24.4 24.7
Noise cut-off 23.8 23.7
Model length: 299
Family (HMM) version: 13
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 is 1 interaction for this family. More...

Peptidase_S58

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_S58 domain has been found. There are 55 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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