Summary: Sec61beta family
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Sec61beta family Provide feedback
This family consists of homologues of Sec61beta - a component of the Sec61/SecYEG protein secretory system. The domain is found in eukaryotes and archaea and is possibly homologous to the bacterial SecG. It consists of a single putative transmembrane helix, preceded by a short stretch containing various charged residues; this arrangement may help determine orientation in the cell membrane [1].
Literature references
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Kinch LN, Saier MH Jr, Grishin NV; , Trends Biochem Sci 2002;27:170-171.: Sec61beta - a component of the archaeal protein secretory system. PUBMED:11943537 EPMC:11943537
External database links
Transporter classification: | 3.A.5 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR016482
This family includes preprotein translocase subunit SecG, protein transport protein Sec61 subunit beta and Sbh1.
A conserved heterotrimeric integral membrane protein complex--the Sec61 complex (eukaryotes) or SecY complex (prokaryotes)--forms a protein-conducting channel that allows polypeptides to be transferred across (or integrated into) the endoplasmic reticulum (eukaryotes) or across the cytoplasmic membrane (prokaryotes) [PUBMED:14661030, PUBMED:11597451]. This complex is itself a part of a larger translocase complex.
The alpha subunits (INTERPRO), called Sec61alpha in mammals, Sec61p in Saccharomyces cerevisiae (Baker's yeast), and SecY in prokaryotes, and the gamma subunits, called Sec61gamma in mammals, Sss1p in S. cerevisiae, and SecE in prokaryotes, show significant sequence conservation. Both subunits are required for cell viability in S. cerevisiae and Escherichia coli. The beta subunits, called Sec61beta in mammals, Sbh in S. cerevisiae, and SecG in archaea, are not essential for cell viability. They are similar in eukaryotes and archaea, but show no obvious homology to the corresponding SecG subunits in bacteria.
SecY forms the channel pore, and it is the cross-linking partner of polypeptide chains passing through the membrane [PUBMED:14661030]. SecY and SecE constitute the high-affinity SecA-binding site on the membrane [PUBMED:11597451]. The channel is a passive conduit for polypeptides. It must therefore associate with other components that provide a driving force. The partner proteins in bacteria and eukaryotes differ. In bacteria, the translocase complex comprises 7 proteins [PUBMED:14661030], including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF). The SecA ATPase interacts dynamically with the SecYEG integral membrane components to drive the transmembrane movement of newly synthesized preproteins [PUBMED:11597451]. In S. cerevisiae (and probably in all eukaryotes), the full translocase comprises another membrane protein subcomplex (the tetrameric Sec62/63p complex), and the lumenal protein BiP, a member of the Hsp70 family of ATPases. BiP promotes translocation by acting as a molecular ratchet, preventing the polypeptide chain from sliding back into the cytosol [PUBMED:14661030].
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 (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 (119) |
Full (1493) |
Representative proteomes | UniProt (2589) |
NCBI (2213) |
Meta (55) |
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RP15 (414) |
RP35 (888) |
RP55 (1291) |
RP75 (1623) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (119) |
Full (1493) |
Representative proteomes | UniProt (2589) |
NCBI (2213) |
Meta (55) |
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RP15 (414) |
RP35 (888) |
RP55 (1291) |
RP75 (1623) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | [1] |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Yeats C |
Number in seed: | 119 |
Number in full: | 1493 |
Average length of the domain: | 40.50 aa |
Average identity of full alignment: | 44 % |
Average coverage of the sequence by the domain: | 35.63 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 41 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 Sec61_beta domain has been found. There are 19 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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