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0  structures 2  species 0  interactions 57  sequences 3  architectures

Family: PSGP (PF07276)

Summary: Apopolysialoglycoprotein (PSGP)

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.

Apopolysialoglycoprotein (PSGP) Provide feedback

This family represents a series of 13 reside repeats found in the apopolysialoglycoprotein of Oncorhynchus mykiss (Rainbow trout) and Oncorhynchus masou (Cherry salmon). Polysialoglycoprotein (PSGP) of unfertilised eggs of rainbow trout consists of tandem repeats of a glycotridecapeptide, Asp-Asp-Ala-Thr*-Ser*-Glu-Ala-Ala-Thr*-Gly-Pro-Ser- Gly (* denotes the attachment site of a polysialoglycan chain). In response to egg activation, PSGP is discharged by exocytosis into the space between the vitelline envelope and the plasma membrane, i.e. the perivitelline space, where the 200-kDa PSGP molecules undergo rapid and dramatic depolymerisation by proteolysis into glycotridecapeptides [1].

Literature references

  1. Sorimachi H, Emori Y, Kawasaki H, Kitajima K, Inoue S, Suzuki K, Inoue Y; , J Biol Chem 1988;263:17678-17684.: Molecular cloning and characterization of cDNAs coding for apo-polysialoglycoprotein of rainbow trout eggs. Multiple mRNA species transcribed from multiple genes contain diverged numbers of exact 39-base (13-amino acid) repeats. PUBMED:3182867 EPMC:3182867


This tab holds annotation information from the InterPro database.

InterPro entry IPR009900

This entry represents a series of 13 residue repeats found in the apopolysialoglycoprotein of Oncorhynchus mykiss (Rainbow trout) and Oncorhynchus masou (Cherry salmon). Polysialoglycoprotein (PSGP) of unfertilised eggs of rainbow trout consists of tandem repeats of a glycotridecapeptide, Asp-Asp-Ala-Thr*-Ser*-Glu-Ala-Ala-Thr*-Gly-Pro-Ser- Gly (* denotes the attachment site of a polysialoglycan chain). In response to egg activation, PSGP is discharged by exocytosis into the space between the vitelline envelope and the plasma membrane, i.e. the perivitelline space, where the 200 kDa PSGP molecules undergo rapid and dramatic depolymerisation by proteolysis into glycotridecapeptides [PUBMED:3182867].

Domain organisation

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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...

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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
(3)
Full
(57)
Representative proteomes UniProt
(131)
NCBI
(152)
Meta
(0)
RP15
(1)
RP35
(57)
RP55
(57)
RP75
(57)
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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
(3)
Full
(57)
Representative proteomes UniProt
(131)
NCBI
(152)
Meta
(0)
RP15
(1)
RP35
(57)
RP55
(57)
RP75
(57)
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
(3)
Full
(57)
Representative proteomes UniProt
(131)
NCBI
(152)
Meta
(0)
RP15
(1)
RP35
(57)
RP55
(57)
RP75
(57)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped 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: Pfam-B_17916 (release 10.0)
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Moxon SJ
Number in seed: 3
Number in full: 57
Average length of the domain: 12.00 aa
Average identity of full alignment: 99 %
Average coverage of the sequence by the domain: 57.27 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 17.4 17.4
Trusted cut-off 17.6 18.2
Noise cut-off 16.7 17.3
Model length: 13
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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