Summary: Syd protein (SUKH-2)
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Syd protein (SUKH-2) Provide feedback
This family contains a number of bacterial Syd proteins approximately 180 residues long. It has been suggested that Syd is loosely associated with the cytoplasmic surface of the cytoplasmic membrane, and that interaction with SecY may be involved in this membrane association [1]. Operon analysis showed that Syd protein may function as immunity protein in bacterial toxin systems [2].
Literature references
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Shimoike T, Taura T, Kihara A, Yoshihisa T, Akiyama Y, Cannon K, Ito K; , J Biol Chem 1995;270:5519-5526.: Product of a new gene, syd, functionally interacts with SecY when overproduced in Escherichia coli. PUBMED:7890670 EPMC:7890670
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Zhang D, Iyer LM, Aravind L;, Nucleic Acids Res. 2011;39:4532-4552.: A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. PUBMED:21306995 EPMC:21306995
This tab holds annotation information from the InterPro database.
InterPro entry IPR009948
This family contains the Syd protein that has been implicated in the Sec-dependent transport of polypeptides across the inner membrane in bacteria. Syd has been shown to bind the SecY subunit of membrane-embedded SecYEG heterotrimer (also known as core translocon or SecY complex) which is a conserved protein-conducting channel essential for the biogenesis of most of the secretory and integral membrane proteins [PUBMED:19139097]. The SecY-binding site of Syd is a conserved concave and electronegative groove that forms interactions with the electropositive loops of the SecY subunit [PUBMED:9645430]. Syd is also known to verify the proper assembly of the SecY complex in the membrane by interfering with protein translocation only when the channel displays abnormal SecY-SecE associations [PUBMED:21632250].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | cytoplasmic side of plasma membrane (GO:0009898) |
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 SUKH (CL0526), which has the following description:
SUKH superfamily unites a diverse group of proteins including Smi1/Knr4, PGs2, Fbxo3, Skip16, Syd, herpesviral US22, IRS1 and TRS1, and their bacterial homologs [1].
The clan contains the following 7 members:
SMI1_KNR4 SUKH-3 SUKH-4 SUKH_5 SUKH_6 Syd US22Alignments
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 (43) |
Full (345) |
Representative proteomes | UniProt (2813) |
NCBI (4157) |
Meta (25) |
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RP15 (26) |
RP35 (116) |
RP55 (311) |
RP75 (755) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (43) |
Full (345) |
Representative proteomes | UniProt (2813) |
NCBI (4157) |
Meta (25) |
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RP15 (26) |
RP35 (116) |
RP55 (311) |
RP75 (755) |
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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
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Curation
Seed source: | Pfam-B_19909 (release 10.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Vella Briffa B |
Number in seed: | 43 |
Number in full: | 345 |
Average length of the domain: | 169.50 aa |
Average identity of full alignment: | 36 % |
Average coverage of the sequence by the domain: | 92.66 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 175 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
SydStructures
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 Syd domain has been found. There are 2 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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