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 . Operon analysis showed that Syd protein may function as immunity protein in bacterial toxin systems .
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
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
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR009948
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 [PUBMED:7890670].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||internal side of plasma membrane (GO:0009898)|
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SUKH superfamily unites a diverse group of proteins including Smi1/Knr4, PGs2, Fbxo3, Skip16, Syd, herpesviral US22, IRS1 and TRS1, and their bacterial homologs .
The clan contains the following 7 members:SMI1_KNR4 SUKH-3 SUKH-4 SUKH_5 SUKH_6 Syd US22
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Curation and family details
|Seed source:||Pfam-B_19909 (release 10.0)|
|Author:||Vella Briffa B, Zhang D, Aravind L|
|Number in seed:||43|
|Number in full:||745|
|Average length of the domain:||173.90 aa|
|Average identity of full alignment:||60 %|
|Average coverage of the sequence by the domain:||95.43 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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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 seqence.
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