G-protein--coupled Receptor (GCRDb) Email Fasta Search Server

Lee F. FrankKolakowski lfk at receptor.mgh.harvard.edu
Tue Apr 19 15:19:02 EST 1994


Dear Colleagues:

An email server has been created to perform fasta searches against the
G-protein--coupled Receptor database.

The GCRDb Email Fasta Search Server will search your input protein
sequence against the most current version of GCRDb (only those
sequences which are publicly available or that the owners of that data
have allowed me to place in the public portion of the database.  GCRDb
has been updated to use the nomenclature of IUPHAR (International
Union of Pharmacology) which is pending or approved has presented in
the 1994 Receptor and Ion Channel Nomenclature Supplement published by
Trends in Pharmacological Sciences and also conforms to that in the
new book "The G-protein Linked Receptor Facts Book" by S. Watson and
S. Arkinstall 1994 Academic Press. The classification data provided is
developed by Kolakowski and Rice (manuscript submitted) and Kolakowski
and Lynch (Manuscript submitted) and is based on parsimony and other
phylogenetic methods.

SEQUENCE DATA sent to this server does not get seen by human eyes
unless there is a problem with the processing. Under no circumstances
is data sent to this server retained for any longer that it takes to
do the search.

If you would like to donate or otherwise get a more complete analysis
of your protein, send email to lfk at receptor.mgh.harvard.edu

Please cite the use of this service in your publications as:
Kolakowski, L.F., (1994) GCRDb: A G-protein--coupled receptor database,
Receptors and Channels: The International Journal of Receptors, Channels and
Transporters, In press.

Copyright (c) 1990, 1991, 1992, 1993, 1994 by Lee F. Kolakowski, Jr.
All rights reserved.

TO GET HELP
+++++++++++
send an email address with the word "HELP" in the body or in the
Subject line.

TO USE EMAIL SEARCH SERVER
++++++++++++++++++++++++++
send just a single pearson format protein sequence.

Example:
==================================================
To: gcrdb at receptor.mgh.harvard.edu


> BOVOPS1
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIML
GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
GYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE
NHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNN
ESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV
TRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV
YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA
==================================================


And the result returned (edited for brevity) is:

Return-Path: <gcrdb>
Date: Sun, 17 Apr 94 16:48:41 EDT
From: gcrdb (G-Protein - Coupled Receptor Database Server)
To: lfk
Subject: Search Results - GCRDb Email Fasta Search Server
Content-Type: text
Content-Length: 29992

===================================================================
|  GGGGGG              CCCCCC         RRRRRRRR                    |
| G      G  Protein   C      Coupled  R       Receptor - DATABASE |
| G                   C               R       R                   |
| G   GGG             C               RRRRRRRR                    |
| G      G            C      C        R      R                    |
|  GGGGGG              CCCCCC         R       R                   |
|                                                                 |
| Including several other unknown seven transmenbrane segment     |
| containing proteins                                             |
===================================================================

Collected and Maintained by:
Lee F. Kolakowski, Jr (aka Frank)
Massachusetts General Hospital
Renal Unit
Charlestown Navy Yard / Building 149
13th Street
Boston, MA 02129
(617)-726-5666 (Voice)
(617)-726-5669 (Fax)
lfk at receptor.mgh.harvard.edu (main-email)
kolakowski at helix.mgh.harvard.edu (email)
lfk at eastman1.mit.edu (email)
	
Release 1.0  $Revision: 1.2 $

====N=O=T=I=C=E===T=O==A=L=L==U=S=E=R=S==========================
Copyright (c) 1990, 1991, 1992, 1993, 1994 by Lee F. Kolakowski, Jr.
All rights reserved.

The GCRDb Email Fasta Search Server will search your input protein
sequence against the most current version of GCRDb (only those
sequences which are publicly available or that the owners of that data
have allowed me to place in the public portion of the database.

DATA sent to this server does not get seen by human eyes unless there
is a problem with the processing.

Under no circumstances is data sent to this server retained for any
longer that it takes to do the search.

If you would like to donate or otherwise get a more complete analysis
of your protein, send email to lfk at receptor.mgh.harvard.edu

Please cite the use of this service in your publications as

Kolakowski, L.F., (1994) GCRDb: A G-protein--coupled receptor
database, Receptors and Channels: The International Journal of
Receptors, Channels and Transporters, In press.

Your fasta search of the protein portion of GCRDb was run with the
following parameters:

$ fasta -b50 -d10 -Q -a -f -o -w 68 your_input DATABASE 1

if errors occurred during the search, they will appear here:

==========

The following sequence was searched:


>BOVOPS1, 348 bases, 3B660FD5 checksum.
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIML
GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
GYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE
NHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNN
ESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV
TRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV
YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

 >BOVOPS1, 348 bases, 3B660FD5 checksum. : 348 aa
 vs  library
 searching /u/gcrdb/TOTPEP library
LOCUS         ACCESSION  LEN  LIGAND           ABBREV     GRP
 BOVOPS1      K00506     348  OPSIN            OPS        A-3  1865  1865  1865
 BOVOPSA      M21606     343  OPSIN            OPS        A-3  1840  1840  1840
 SHPOPSD      PIR_A30407 348  OPSIN            OPS        A-3  1808  1808  1808
 CFOPSIN      X71380     348  OPSIN            OPS        A-3  1795  1795  1795
 MUSOPS       M55171     348  OPSIN            OPS        A-3  1786  1786  1786
 HUMOPS       K02281     348  OPSIN            OPS        A-3  1784  1784  1784
 CRURHOD      X61084     348  OPSIN            OPS        A-3  1781  1781  1781
 CHKRDPSN     D00702     351  OPSIN            OPS        A-3  1682  1682  1687
 AOIRHODOPS   L31503     352  OPSIN            OPS        A-3  1642  1642  1654
 S118599      S49004     354  OPSIN            OPS        A-3  1638  1638  1649
 XELOPSIN     L04692     354  OPSIN            OPS        A-3  1630  1630  1643
 XELRHODOP    L07770     354  OPSIN            OPS        A-3  1626  1626  1639
 LARRHODA     M63632     353  OPSIN            OPS        A-3  1636  1636  1638
 S62229       S62229     354  OPSIN            OPS        A-3  1633  1633  1636
 ZEFUVPIGX    L11014     354  OPSIN            OPS        A-3  1588  1588  1603
 CRAROD       L11863     354  OPSIN            OPS        A-3  1573  1573  1588
 PMRO         X62405     352  OPSIN            OPS        A-3  1530  1530  1537
 CHKPRA1A     M88178     355  OPSIN            OPSx       A-3  1463  1463  1463
 CHKGSCOB     M92038     355  OPSIN            OPSc       A-3  1463  1463  1463
 GECP467A     M92035     355  OPSIN            OPSx       A-3  1436  1436  1436
 CRAGRN       L11865     349  OPSIN            OPSc       A-3  1390  1390  1407

 BOVOPS1      K00506     348  OPSIN            OPS        A-3  1865  1865  1865
 100.0% identity in 348 aa overlap

               10        20        30        40        50        60        
BOVOPS MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKL
       X:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
       MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKL
               10        20        30        40        50        60        

       70        80        90       100       110       120       130      
BOVOPS RTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERY
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
       RTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERY
       70        80        90       100       110       120       130      

        140       150       160       170       180       190       200    
BOVOPS VVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
       VVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFV
        140       150       160       170       180       190       200    

          210       220       230       240       250       260       270  
BOVOPS IYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
       IYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVA
          210       220       230       240       250       260       270  

            280       290       300       310       320       330       340
BOVOPS FYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKT
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
       FYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKT
            280       290       300       310       320       330       340

               
BOVOPS ETSQVAPA
       :::::::X
       ETSQVAPA
               


-- 
Frank Kolakowski

=======================================================================
O Email: lfk at receptor.mgh.harvard.edu                                 O
O        kolakowski at helix.mgh.harvard.edu                             O
O        lfk at eastman1.mit.edu                                         O
O US Mail: Lee F. Kolakowski        Renal Unit, 8th Flr.              O
O Massachusetts General Hospital    Charlestown Navy Yard             O
O 149 13th Street                   FAX       :  1-617-726-5669       O
O Charlestown, MA 02129             Phone AT&T:  1-617-726-5666       O
=======================================================================
O     The home of the G-Protein-Coupled Receptor Database (GCRDb)     O
=======================================================================



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