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1  structure 208  species 0  interactions 278  sequences 15  architectures

Family: Sec39 (PF08314)

Summary: Secretory pathway protein Sec39

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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.

Secretory pathway protein Sec39 Provide feedback

Mnaimneh et al [1] identified Sec39p as a protein involved in ER-Golgi transport in a large scale promoter shut down analysis of essential yeast genes. Kraynack et al. (2005) [2] showed that Sec39p (Dsl3p) is required for Golgi-ER retrograde transport and is part of a very stable protein complex that also includes Dsl1p (in mammals ZW10), Tip20p (Rint-1) and the ER localized Q-SNARE proteins Ufe1p (syntaxin-18), Sec20p and Use1p. This was confirmed in a genome-wide analysis of protein complexes by Gavin et al (2006) [3].

Literature references

  1. Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, Morris Q, Grigull J, Mitsakakis N, Roberts CJ, Greenblatt JF, Boone C, Kaiser CA, Andrews BJ, Hughes T, Cell. 2004;118:31-44.: Exploration of essential gene functions via titratable promoter alleles. PUBMED:15242642 EPMC:15242642

  2. Kraynack BA, Chan A, Rosenthal E, Essid M, Umansky B, Waters MG, Schmitt HD; , Mol Biol Cell 2005;16:3963-3977.: Dsl1p, Tip20p, and the Novel Dsl3(Sec39) Protein Are Required for the Stability of the Q/t-SNARE Complex at the Endoplasmic Reticulum in Yeast. PUBMED:15958492 EPMC:15958492

  3. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, C, Nature. 2006;440:631-636.: Proteome survey reveals modularity of the yeast cell machinery. PUBMED:16429126 EPMC:16429126

  4. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK; , Nature 2003;425:686-691.: Global analysis of protein localization in budding yeast. PUBMED:14562095 EPMC:14562095


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013244

Sec39 was originally identified as a protein involved in ER-Golgi transport in a large scale promoter shut down analysis of essential yeast genes [PUBMED:15242642]. A subsequent study found that Sec39p (Dsl3p) is required for Golgi-ER retrograde transport and is part of a very stable protein complex that also includes Dsl1p (in mammals ZW10), Tip20p (Rint-1) and the ER localized Q-SNARE proteins Ufe1p (syntaxin-18), Sec20p and Use1p [PUBMED:15242642]. This was confirmed in a genome-wide analysis of protein complexes [PUBMED:16429126].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

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(20)
Full
(278)
Representative proteomes NCBI
(289)
Meta
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RP15
(59)
RP35
(107)
RP55
(161)
RP75
(202)
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Format an alignment

  Seed
(20)
Full
(278)
Representative proteomes NCBI
(289)
Meta
(0)
RP15
(59)
RP35
(107)
RP55
(161)
RP75
(202)
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
(20)
Full
(278)
Representative proteomes NCBI
(289)
Meta
(0)
RP15
(59)
RP35
(107)
RP55
(161)
RP75
(202)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: manual
Previous IDs: none
Type: Domain
Author: Mistry J, Wood V, Schmitt HD
Number in seed: 20
Number in full: 278
Average length of the domain: 559.60 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 47.25 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 18.5 18.5
Trusted cut-off 19.2 18.6
Noise cut-off 17.7 18.3
Model length: 715
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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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 Sec39 domain has been found. There are 1 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 seqence.

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