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5  structures 1645  species 0  interactions 3497  sequences 66  architectures

Family: Ceramidase_alk (PF04734)

Summary: Neutral/alkaline non-lysosomal ceramidase, N-terminal

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

Neutral/alkaline non-lysosomal ceramidase, N-terminal Provide feedback

This family represents N-terminal domain of a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes [1,2,3]. The EC classification is EC:3.5.1.23. The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This N-terminal domain carries two metal-binding sites, the first for Zn2+ residing within the domain, and the second, for Mg2+/Ca2+ lying at the interface between the two domains [4].

Literature references

  1. Tani M, Okino N, Mori K, Tanigawa T, Izu H, Ito M; , J Biol Chem 2000;275:11229-11234.: Molecular cloning of the full-length cDNA encoding mouse neutral ceramidase. A novel but highly conserved gene family of neutral/alkaline ceramidases. PUBMED:10753931 EPMC:10753931

  2. El Bawab S, Roddy P, Qian T, Bielawska A, Lemasters JJ, Hannun YA; , J Biol Chem 2000;275:21508-21513.: Molecular cloning and characterization of a human mitochondrial ceramidase. PUBMED:10781606 EPMC:10781606

  3. Okino N, Ichinose S, Omori A, Imayama S, Nakamura T, Ito M; , J Biol Chem 1999;274:36616-36622.: Molecular cloning, sequencing, and expression of the gene encoding alkaline ceramidase from Pseudomonas aeruginosa. Cloning of a ceramidase homologue from Mycobacterium tuberculosis. PUBMED:10593963 EPMC:10593963

  4. Inoue T, Okino N, Kakuta Y, Hijikata A, Okano H, Goda HM, Tani M, Sueyoshi N, Kambayashi K, Matsumura H, Kai Y, Ito M;, J Biol Chem. 2009;284:9566-9577.: Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase. PUBMED:19088069 EPMC:19088069


This tab holds annotation information from the InterPro database.

InterPro entry IPR031329

This entry represents the N-terminal domain of a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes [ PUBMED:10753931 , PUBMED:10781606 , PUBMED:10593963 ]. The EC classification is ( EC ). The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This N-terminal domain carries two metal-binding sites, the first for Zn2+ residing within the domain, and the second, for Mg2+/Ca2+ lying at the interface between the two domains [ PUBMED:19088069 ].

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 5 members:

ArgJ Ceramidase_alk MoCoBD_1 MoCoBD_2 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 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
(113)
Full
(3497)
Representative proteomes UniProt
(10015)
RP15
(652)
RP35
(1719)
RP55
(2997)
RP75
(4343)
Jalview 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
(113)
Full
(3497)
Representative proteomes UniProt
(10015)
RP15
(652)
RP35
(1719)
RP55
(2997)
RP75
(4343)
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
(113)
Full
(3497)
Representative proteomes UniProt
(10015)
RP15
(652)
RP35
(1719)
RP55
(2997)
RP75
(4343)
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: Pfam-B_3385 (release 7.5)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mifsud W
Number in seed: 113
Number in full: 3497
Average length of the domain: 387.5 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 65.02 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 32.1 32.1
Trusted cut-off 32.1 32.1
Noise cut-off 32.0 32.0
Model length: 509
Family (HMM) version: 16
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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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 Ceramidase_alk domain has been found. There are 5 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
A0A096T3A1 View 3D Structure Click here
A0A0D2G7R9 View 3D Structure Click here
A0A0R0F8U3 View 3D Structure Click here
A0A0R0GS00 View 3D Structure Click here
A0A0R0IW53 View 3D Structure Click here
A0A175W3N0 View 3D Structure Click here
A0A175W6M4 View 3D Structure Click here
A0A1C1C664 View 3D Structure Click here
A0A1D6LH26 View 3D Structure Click here
A0A1D6LTQ1 View 3D Structure Click here
A0A3Q0KPD2 View 3D Structure Click here
A0A5K4ERM4 View 3D Structure Click here
C0NGI0 View 3D Structure Click here
C1HAQ2 View 3D Structure Click here
F4HQM3 View 3D Structure Click here
F4KHQ8 View 3D Structure Click here
I1JJN8 View 3D Structure Click here
I1M6B9 View 3D Structure Click here
K0EPA9 View 3D Structure Click here
K7MQD2 View 3D Structure Click here
K7MQD4 View 3D Structure Click here
O06769 View 3D Structure Click here
Q0JL46 View 3D Structure Click here
Q29C43 View 3D Structure Click here
Q304B9 View 3D Structure Click here
Q54BK2 View 3D Structure Click here
Q55G11 View 3D Structure Click here
Q5W7F1 View 3D Structure Click here
Q91XT9 View 3D Structure Click here
Q9I596 View 3D Structure Click here
Q9JHE3 View 3D Structure Click here
Q9NR71 View 3D Structure Click here
Q9VA70 View 3D Structure Click here
U7Q0G1 View 3D Structure Click here
U7Q1D5 View 3D Structure Click here
X8FGM5 View 3D Structure Click here
X8FII4 View 3D Structure Click here