patmatmotifs.txt

emboss的linux版本的源代码

FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -> R (IN ADRP).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (IN ADRP).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38892 MW;  07443BEA CRC32;
     MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
     VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
     GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
     EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
     ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
     YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//

Output file format

   The output is a standard EMBOSS report file.

   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, regions, seqtable, simple, srs, table, tagseq

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default patmatmotifs writes a 'dbmotif' report file.

  Output files for usage example

  File: opsd_human.patmatmotifs

########################################
# 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 *
# *****************************************


  [Part of this file has been deleted for brevity]

# 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 chromophor
e
# 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 protein
s
# with  seven transmembrane regions that belong to family 1 of G-protein couple
d
# receptors (see <PDOC00210>).
#
# In vertebrates four different pigments are generally found.   Rod cells, whic
h
# mediate vision in dim light, contain the pigment rhodopsin.  Cone cells, whic
h
# function in bright light, are responsible  for  color vision and contain thre
e
# or more color pigments (for example, in mammals: red, blue and green).
#
# In Drosophila, the  eye   is composed   of 800   facets  or   ommatidia.  Eac
h
# ommatidium contains eight photoreceptor cells (R1-R8):  the R1 to R6 cells ar
e
# 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 know
n
# as retinal  photoisomerase, which converts various isomers of retinal into 11
-
# cis retinal and mammalian retinal pigment  epithelium (RPE) RGR [3], a protei
n
# that may also act in retinal isomerization.
#
# The attachment  site  for  retinal in the above proteins is a conserved lysin
e
# residue in  the  middle  of  the  seventh  transmembrane helix. The pattern w
e
# 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).
#
# ***************
#
#
#---------------------------------------

Data files

   Data and documentation from PROSITE files is automatically read. This
   has been generated and formatted by running prosextract before running
   patmatmotifs.

Notes

   Program is only useful when prosextract is used beforehand.

References

   If you want to refer to PROSITE in a publication you can do so by
   citing:

   Bairoch A., Bucher P., Hofmann K. The PROSITE datatase, its status in
   1997. Nucleic Acids Res. 24:217-221(1997).

   Other references:

    1. Bairoch, A., Bucher P. (1994) PROSITE: recent developments.
       Nucleic Acids Research, Vol 22, No.17 3583-3589.
    2. Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in
       proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
    3. Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd
       Edition.
    4. Doolittle R.F. (In) Of URFs and ORFs: a primer on how to analyze
       derived amino acid sequences., University Science Books, Mill
       Valley, California, (1986).
    5. Lesk A.M. (In) Computational Molecular Biology, Lesk A.M., Ed.,
       pp17-26, Oxford University Press, Oxford (1988).

Warnings

   Your EMBOSS administrator must have set up the local EMBOSS PROSITE
   database using the utility 'prosextract' before this program will run.

Diagnostic Error Messages

   The error message:

"Either EMBOSS_DATA undefined or PROSEXTRACT needs running"

   indicates that your local EMBOSS administrator has not yet correctly
   set up the local EMBOSS PROSITE database using the utility
   'prosextract'.

Exit status

   It always exits with status 0

Known bugs

   None.

See also

    Program name                         Description
   antigenic      Finds antigenic sites in proteins
   digest         Protein proteolytic enzyme or reagent cleavage digest
   epestfind      Finds PEST motifs as potential proteolytic cleavage sites
   fuzzpro        Protein pattern search
   fuzztran       Protein pattern search after translation
   helixturnhelix Report nucleic acid binding motifs
   oddcomp        Find protein sequence regions with a biased composition
   patmatdb       Search a protein sequence with a motif
   pepcoil        Predicts coiled coil regions
   preg           Regular expression search of a protein sequence
   pscan          Scans proteins using PRINTS
   sigcleave      Reports protein signal cleavage sites

Author(s)

   Sinead O'Leary (current e-mail address unknown)
   while she was at:
   HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

History

   Completed May 13 1999.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None