Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 833  species 0  interactions 2724  sequences 53  architectures

Family: PAP2_C (PF14360)

Summary: PAP2 superfamily C-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.

PAP2 superfamily C-terminal Provide feedback

This family is closely related to the C-terminal a region of PAP2.

Internal database links

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...

Loading domain graphics...

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 Scs3p

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
(41)
Full
(2724)
Representative proteomes UniProt
(5415)
RP15
(612)
RP35
(1351)
RP55
(2406)
RP75
(3057)
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
(41)
Full
(2724)
Representative proteomes UniProt
(5415)
RP15
(612)
RP35
(1351)
RP55
(2406)
RP75
(3057)
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
(41)
Full
(2724)
Representative proteomes UniProt
(5415)
RP15
(612)
RP35
(1351)
RP55
(2406)
RP75
(3057)
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: Jackhmmer:Q56Y01
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 41
Number in full: 2724
Average length of the domain: 72.20 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 19.10 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 74
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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
A0A0N7KFG1 View 3D Structure Click here
A0A0R4IR05 View 3D Structure Click here
A0A0R4J2K6 View 3D Structure Click here
A0A143ZVB5 View 3D Structure Click here
A0A1D6L975 View 3D Structure Click here
A0A1D6N735 View 3D Structure Click here
A0A2R8QAS9 View 3D Structure Click here
A0A368UIV4 View 3D Structure Click here
A0JMN0 View 3D Structure Click here
A4IC70 View 3D Structure Click here
B4FD98 View 3D Structure Click here
B4FUI3 View 3D Structure Click here
B8A5Q0 View 3D Structure Click here
C4J4Z8 View 3D Structure Click here
C6KT86 View 3D Structure Click here
C6KT87 View 3D Structure Click here
I1JLW4 View 3D Structure Click here
I1KK80 View 3D Structure Click here
I1N2R0 View 3D Structure Click here
I1NH32 View 3D Structure Click here
K7U584 View 3D Structure Click here
K7W3A2 View 3D Structure Click here
Q0DJG3 View 3D Structure Click here
Q20696 View 3D Structure Click here
Q20735 View 3D Structure Click here
Q4DWW1 View 3D Structure Click here
Q4E4I4 View 3D Structure Click here
Q4JM44 View 3D Structure Click here
Q56Y01 View 3D Structure Click here
Q5N7A7 View 3D Structure Click here
Q641X0 View 3D Structure Click here
Q6DEI3 View 3D Structure Click here
Q6I647 View 3D Structure Click here
Q7TSX5 View 3D Structure Click here
Q7X8A2 View 3D Structure Click here
Q86VZ5 View 3D Structure Click here
Q8NHU3 View 3D Structure Click here
Q8VCQ6 View 3D Structure Click here
Q965Q4 View 3D Structure Click here
Q96LT4 View 3D Structure Click here
Q9D4B1 View 3D Structure Click here
Q9DA37 View 3D Structure Click here
Q9M325 View 3D Structure Click here
Q9SH93 View 3D Structure Click here
Q9TYV2 View 3D Structure Click here
Q9U3D4 View 3D Structure Click here
Q9VS60 View 3D Structure Click here
Q9XIG2 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;