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4  structures 1411  species 0  interactions 3300  sequences 54  architectures

Family: Sedlin_N (PF04628)

Summary: Sedlin, N-terminal conserved region

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.

Sedlin, N-terminal conserved region Provide feedback

Mutations in this protein are associated with the X-linked spondyloepiphyseal dysplasia tarda syndrome ( OMIM:313400) [1]. This family represents an N-terminal conserved region.

Literature references

  1. Gedeon AK, Tiller GE, Le Merrer M, Heuertz S, Tranebjaerg L, Chitayat D, Robertson S, Glass IA, Savarirayan R, Cole WG, Rimoin DL, Kousseff BG, Ohashi H, Zabel B, Munnich A, Gecz J, Mulley JC; , Am J Hum Genet 2001;68:1386-1397.: The molecular basis of X-linked spondyloepiphyseal dysplasia tarda. PUBMED:11349230 EPMC:11349230


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006722

Trafficking protein particle complex subunit 2, also known as Sedlin, is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport [ PUBMED:20498720 ]. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400) [ PUBMED:11349230 ].

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
(23)
Full
(3300)
Representative proteomes UniProt
(5518)
RP15
(627)
RP35
(1508)
RP55
(2520)
RP75
(3418)
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
(23)
Full
(3300)
Representative proteomes UniProt
(5518)
RP15
(627)
RP35
(1508)
RP55
(2520)
RP75
(3418)
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
(23)
Full
(3300)
Representative proteomes UniProt
(5518)
RP15
(627)
RP35
(1508)
RP55
(2520)
RP75
(3418)
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_5308 (release 7.5)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W
Number in seed: 23
Number in full: 3300
Average length of the domain: 127.80 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 79.14 %

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 23.1 23.1
Trusted cut-off 23.1 23.1
Noise cut-off 22.9 23.0
Model length: 131
Family (HMM) version: 15
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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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 Sedlin_N domain has been found. There are 4 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
A0A0R0KH89 View 3D Structure Click here
A0A1D6EU63 View 3D Structure Click here
A0A1D6F4L4 View 3D Structure Click here
A0A1D6INY2 View 3D Structure Click here
A0A1D6IPQ7 View 3D Structure Click here
A0A1D8PMJ9 View 3D Structure Click here
A0A2R8S035 View 3D Structure Click here
A1Z8I0 View 3D Structure Click here
B2RYU6 View 3D Structure Click here
C0H4V0 View 3D Structure Click here
D3ZVF4 View 3D Structure Click here
F4HTY0 View 3D Structure Click here
G4SNB8 View 3D Structure Click here
I1KBQ5 View 3D Structure Click here
I1L653 View 3D Structure Click here
I1N439 View 3D Structure Click here
O02173 View 3D Structure Click here
O13732 View 3D Structure Click here
P0DI81 View 3D Structure Click here
P0DI82 View 3D Structure Click here
P32613 View 3D Structure Click here
P38334 View 3D Structure Click here
Q08CN0 View 3D Structure Click here
Q0JBY0 View 3D Structure Click here
Q4CQA9 View 3D Structure Click here
Q4CQS2 View 3D Structure Click here
Q54CU7 View 3D Structure Click here
Q54RV6 View 3D Structure Click here
Q5A920 View 3D Structure Click here
Q5BJL8 View 3D Structure Click here
Q651C7 View 3D Structure Click here
Q6K5Z3 View 3D Structure Click here
Q8IE05 View 3D Structure Click here
Q8R3W2 View 3D Structure Click here
Q9CQP2 View 3D Structure Click here
Q9JME7 View 3D Structure Click here
Q9SKS7 View 3D Structure Click here
Q9UL33 View 3D Structure Click here
Q9USZ5 View 3D Structure Click here
Q9VUZ1 View 3D Structure Click here