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
=======================================================================
