patmatmotifs.output

emboss的linux版本的源代码

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: opsd_human.patmatmotifs</h3>
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<pre>
########################################
# Program: patmatmotifs
# Rundate: Sat 15 Jul 2006 12:00:00
# Commandline: patmatmotifs
#    -full
#    -sequence tsw:opsd_human
# Report_format: dbmotif
# Report_file: opsd_human.patmatmotifs
########################################

#=======================================
#
# Sequence: OPSD_HUMAN     from: 1   to: 348
# HitCount: 2
#
# Full: Yes
# Prune: Yes
# Data_file: ../prosextract-keep/PROSITE/prosite.lines
#
#=======================================

Length = 17
Start = position 123 of sequence
End = position 139 of sequence

Motif = G_PROTEIN_RECEP_F1_1

TLGGEIALWSLVVLAIERYVVVCKPMS
     |               |
   123               139

Length = 17
Start = position 290 of sequence
End = position 306 of sequence

Motif = OPSIN

PIFMTIPAFFAKSAAIYNPVIYIMMNK
     |               |
   290               306


#---------------------------------------
#
# Motif: G_PROTEIN_RECEP_F1_1
# Count: 1
# 
# *****************************************
# * G-protein coupled receptors signature *
# *****************************************


<font color=red>  [Part of this file has been deleted for brevity]</font>

# Count: 1
# 
# *************************************************
# * Visual pigments (opsins) retinal binding site *
# *************************************************
# 
# Visual pigments [1,2] are the light-absorbing  molecules that  mediate vision.
# They consist of  an apoprotein, opsin,  covalently  linked  to the chromophore
# cis-retinal.  Vision is  effected through  the absorption of a  photon by cis-
# retinal  which is isomerized to  trans-retinal.  This isomerization leads to a
# change  of conformation  of the protein. Opsins are integral membrane proteins
# with  seven transmembrane regions that belong to family 1 of G-protein coupled
# receptors (see &lt;PDOC00210&gt;).
# 
# In vertebrates four different pigments are generally found.   Rod cells, which
# mediate vision in dim light, contain the pigment rhodopsin.  Cone cells, which
# function in bright light, are responsible  for  color vision and contain three
# or more color pigments (for example, in mammals: red, blue and green).
# 
# In Drosophila, the  eye   is composed   of 800   facets  or   ommatidia.  Each
# ommatidium contains eight photoreceptor cells (R1-R8):  the R1 to R6 cells are
# outer cells,  R7  and R8 inner cells. Each of the three types of cells (R1-R6,
# R7 and R8) expresses a specific opsin.
# 
# Proteins evolutionary related to opsins include squid retinochrome, also known
# as retinal  photoisomerase, which converts various isomers of retinal into 11-
# cis retinal and mammalian retinal pigment  epithelium (RPE) RGR [3], a protein
# that may also act in retinal isomerization.
# 
# The attachment  site  for  retinal in the above proteins is a conserved lysine
# residue in  the  middle  of  the  seventh  transmembrane helix. The pattern we
# developed includes this residue.
# 
# -Consensus pattern: [LIVMWAC]-[PGAC]-x(3)-[SAC]-K-[STALIMR]-[GSACPNV]-[STACP]-
#                     x(2)-[DENF]-[AP]-x(2)-[IY]
#                     [K is the retinal binding site]
# -Sequences known to belong to this class detected by the pattern: ALL.
# -Other sequence(s) detected in SWISS-PROT: NONE.
# -Last update: July 1998 / Pattern and text revised.
# 
# [ 1] Applebury M.L., Hargrave P.A.
#      Vision Res. 26:1881-1895(1986).
# [ 2] Fryxell K.J., Meyerowitz E.M.
#      J. Mol. Evol. 33:367-378(1991).
# [ 3] Shen D., Jiang M., Hao W., Tao L., Salazar M., Fong H.K.W.
#      Biochemistry 33:13117-13125(1994).
# 
# ***************
# 
#
#---------------------------------------
</pre>
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