Summary: PAP2 superfamily C-terminal
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PAP2 superfamily C-terminal Provide feedback
This family is closely related to the C-terminal a region of PAP2.
Internal database links
SCOOP: | PAP2 PAP2_3 |
Similarity to PfamA using HHSearch: | PAP2 PAP2_3 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR025749
This domain is found in sphingomyelin synthase (also known as phosphatidylcholine:ceramide cholinephosphotransferase), and other proteins. Sphingomyelin synthase is a bidirectional lipid cholinephosphotransferase capable of converting phosphatidylcholine (PC) and ceramide to sphingomyelin (SM) and diacylglycerol (DAG) and vice versa [PUBMED:14685263]. This domain is closely related to the C-terminal a region of phosphatidic acid phosphatase type 2 (PAP2).
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 pap2 (CL0525), which has the following description:
The PAP2 superfamily is characterised by being mult-helical, with the core consisting of a 5-helical bundle. Normally the family will bind cofactor at the beginning of the third helix. The superfamily includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. The family also includes a variety of haloperoxidases [1,2] that function by oxidising halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.
The clan contains the following 5 members:
DUF212 PAP2 PAP2_3 PAP2_C Scs3pAlignments
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 (48) |
Full (1927) |
Representative proteomes | UniProt (2878) |
NCBI (4110) |
Meta (28) |
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RP15 (627) |
RP35 (1153) |
RP55 (1619) |
RP75 (1871) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (48) |
Full (1927) |
Representative proteomes | UniProt (2878) |
NCBI (4110) |
Meta (28) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (627) |
RP35 (1153) |
RP55 (1619) |
RP75 (1871) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Jackhmmer:Q56Y01 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Coggill P |
Number in seed: | 48 |
Number in full: | 1927 |
Average length of the domain: | 71.90 aa |
Average identity of full alignment: | 34 % |
Average coverage of the sequence by the domain: | 19.45 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 74 | ||||||||||||
Family (HMM) version: | 6 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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