{PDOC00612}
{PS00755; SECY_1}
{PS00756; SECY_2}
{BEGIN}
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* Protein secY signatures *
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The eubacterial secY protein [1] plays an important role in protein export. It
interacts with the signal sequences of  secretory proteins as well as with two
other  components of the protein translocation system: secA and secE.  SecY is
an integral  plasma membrane protein  of  419 to 492  amino acid residues that
apparently  contains ten  transmembrane  segments.  Such  a structure probably
confers to secY a 'translocator' function, providing a channel for periplasmic
and outer-membrane precursor proteins.

Homologs of  secY  are  found in archaebacteria [2].  SecY  is also encoded in
the chloroplast  genome  of  some algae [3]  where  it  could be involved in a
prokaryotic-like protein  export  system  across  the  two  membranes  of  the
chloroplast endoplasmic reticulum (CER) which  is  present in  chromophyte and
cryptophyte algae.

In eukaryotes,  the  evolutionary related protein sec61-alpha plays a role  in
protein translocation  through  the  endoplasmic  reticulum;  it  is part of a
trimeric complex that also consist of sec61-beta and gamma [4].

We have  developed  two   signature patterns  for  secY  proteins.  The  first
corresponds to   the second  transmembrane region, which is the most conserved
section of  these proteins. The second spans the C-terminal part of the fourth
transmembrane region,   a short intracellular loop, and the N-terminal part of
the fifth transmembrane region.

-Consensus pattern: [GSTL]-[LIVMFK]-[LIVMFCA]-x-[LIVMF]-[GSAN]-[LIVM]-x-P-
                    [LIVMFYN]-[LIVMFY]-x-[AS]-[GSTQD]-[LIVMFAT](3)-[EQ]-
                    [LIVMFA](2)
-Sequences known to belong to this class detected by the pattern: ALL,  except
 for 2 sequences.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Consensus pattern: [LIVMFYW](2)-x-[DE]-x-[LIVM]-[STDNQ]-x(2,3)-[GK]-[LIVMF]-
                    [GST]-[NST]-G-x-[GST]-[LIV]-[LIVFP]
-Sequences known to belong to this class detected by the pattern: ALL,  except
 for 2 sequences.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: December 2004 / Pattern and text revised.

[ 1] Ito K.
     "SecY and integral membrane components of the Escherichia coli protein
     translocation system."
     Mol. Microbiol. 6:2423-2428(1992).
     PubMed=1406280
[ 2] Auer J., Spicker G., Boeck A.
     "Presence of a gene in the archaebacterium Methanococcus vannielii
     homologous to secY of eubacteria."
     Biochimie 73:683-688(1991).
     PubMed=1764515
[ 3] Douglas S.E.
     "A secY homologue is found in the plastid genome of Cryptomonas phi."
     FEBS Lett. 298:93-96(1992).
     PubMed=1544427
[ 4] Hartmann E., Sommer T., Prehn S., Goerlich D., Jentsch S., Rapoport T.A.
     "Evolutionary conservation of components of the protein translocation
     complex."
     Nature 367:654-657(1994).
     PubMed=8107851; DOI=10.1038/367654a0

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