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5  structures 631  species 0  interactions 957  sequences 18  architectures

Family: Ceramidse_alk_C (PF17048)

Summary: Neutral/alkaline non-lysosomal ceramidase, 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.

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

This family represents C-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 C-terminal tail of the enzyme is highly conserved across all species and may play a role in the interaction of the enzyme with the plasma membranes [4]. The tail is also vital for the stabilisation of the enzyme as a whole [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 IPR031331

This family represents the C-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 C-terminal tail of the enzyme is highly conserved across all species and may play a role in the interaction of the enzyme with the plasma membranes. The tail is also vital for the stabilisation of the enzyme as a whole [PUBMED:19088069].

Domain organisation

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Alignments

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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
(154)
Full
(957)
Representative proteomes UniProt
(1649)
NCBI
(2581)
Meta
(10)
RP15
(190)
RP35
(518)
RP55
(786)
RP75
(1050)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(154)
Full
(957)
Representative proteomes UniProt
(1649)
NCBI
(2581)
Meta
(10)
RP15
(190)
RP35
(518)
RP55
(786)
RP75
(1050)
Alignment:
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Sequence:
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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
(154)
Full
(957)
Representative proteomes UniProt
(1649)
NCBI
(2581)
Meta
(10)
RP15
(190)
RP35
(518)
RP55
(786)
RP75
(1050)
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: PF04734
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 154
Number in full: 957
Average length of the domain: 159.40 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 22.97 %

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 27.8 27.8
Trusted cut-off 27.9 27.8
Noise cut-off 27.5 27.6
Model length: 167
Family (HMM) version: 4
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

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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 Ceramidse_alk_C 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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