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21  structures 1410  species 0  interactions 3289  sequences 68  architectures

Family: Sybindin (PF04099)

Summary: Sybindin-like family

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.

Sybindin-like family Provide feedback

Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses [1].

Literature references

  1. Ethell IM, Hagihara K, Miura Y, Irie F, Yamaguchi Y; , J Cell Biol 2000;151:53-68.: Synbindin, A novel syndecan-2-binding protein in neuronal dendritic spines. PUBMED:11018053 EPMC:11018053


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007233

This entry includes a group of trafficking protein particle complex subunit (TRAPPC) proteins, such as TPPC1/4 from humans and Trs23/Bet5 from yeasts.

Budding yeast Trs23 and Bet5 are components of the TRAPP I, TRAPP II and TRAPP III. TRAPP complexes are guanine nucleotide exchange factors (GEF) for the GTPase Ypt1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. RAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation [ PUBMED:11239471 , PUBMED:20972447 , PUBMED:20375281 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 PF (CL0431), which has the following description:

The families here all show the Profilin-like fold, and represent both the Profilin (actin-binding protein) (55770) and the Roadblock/LC7 domain-type (103196) superfamilies.

The clan contains the following 21 members:

Clat_adaptor_s FNIP_N Fuz_longin_1 Fuz_longin_2 Fuz_longin_3 Intu_longin_1 Intu_longin_2 Intu_longin_3 LAMTOR5 Longin Longin_2 MAPKK1_Int Nyv1_N Profilin Robl_LC7 Sedlin_N SLM4 SRP-alpha_N SRX Sybindin uDENN

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
(11)
Full
(3289)
Representative proteomes UniProt
(5544)
RP15
(642)
RP35
(1512)
RP55
(2515)
RP75
(3404)
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
(11)
Full
(3289)
Representative proteomes UniProt
(5544)
RP15
(642)
RP35
(1512)
RP55
(2515)
RP75
(3404)
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
(11)
Full
(3289)
Representative proteomes UniProt
(5544)
RP15
(642)
RP35
(1512)
RP55
(2515)
RP75
(3404)
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_3240 (release 7.3);
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Finn RD
Number in seed: 11
Number in full: 3289
Average length of the domain: 144.40 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 82.33 %

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 143
Family (HMM) version: 14
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

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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Tree controls

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The tree shows the occurrence of this domain across different species. 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 Sybindin domain has been found. There are 21 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
A0A1D6KZ33 View 3D Structure Click here
A4I893 View 3D Structure Click here
A4IBH6 View 3D Structure Click here
B1GRL5 View 3D Structure Click here
B4FEQ9 View 3D Structure Click here
B6T5T0 View 3D Structure Click here
B9FRI7 View 3D Structure Click here
C6SXH4 View 3D Structure Click here
C6TMZ5 View 3D Structure Click here
C6TN24 View 3D Structure Click here
F1QJL7 View 3D Structure Click here
F1QNE7 View 3D Structure Click here
I1L708 View 3D Structure Click here
I1LLI8 View 3D Structure Click here
O43041 View 3D Structure Click here
O77358 View 3D Structure Click here
Q03630 View 3D Structure Click here
Q03784 View 3D Structure Click here
Q03784 View 3D Structure Click here
Q03784 View 3D Structure Click here
Q20100 View 3D Structure Click here
Q2KMM2 View 3D Structure Click here
Q4CTC4 View 3D Structure Click here
Q4CY94 View 3D Structure Click here
Q4DI27 View 3D Structure Click here
Q4DVQ7 View 3D Structure Click here
Q54UU1 View 3D Structure Click here
Q557G3 View 3D Structure Click here
Q59VY5 View 3D Structure Click here
Q5AEG6 View 3D Structure Click here
Q5NCF2 View 3D Structure Click here
Q5QNC8 View 3D Structure Click here
Q69BT7 View 3D Structure Click here
Q84NS9 View 3D Structure Click here
Q8IM42 View 3D Structure Click here
Q9ES56 View 3D Structure Click here
Q9LZ97 View 3D Structure Click here
Q9SYB8 View 3D Structure Click here
Q9UT70 View 3D Structure Click here
Q9VA95 View 3D Structure Click here
Q9VLI9 View 3D Structure Click here
Q9Y296 View 3D Structure Click here
Q9Y5R8 View 3D Structure Click here