From lfk@ATHENA.MIT.EDU Thu Aug 16 18:52:35 1990 Received: from ATHENA.MIT.EDU by silver.ucs.indiana.edu (5.61+/9.2jsm) id AA13277; Thu, 16 Aug 90 18:52:29 -0500 Received: from E40-008-8.MIT.EDU by ATHENA.MIT.EDU with SMTP id AA02843; Thu, 16 Aug 90 19:48:48 EDT From: lfk@ATHENA.MIT.EDU Received: by E40-008-8.MIT.EDU (5.61/4.7) id AA01970; Thu, 16 Aug 90 19:16:04 -0400 Date: Thu, 16 Aug 90 19:16:04 -0400 Message-Id: <9008162316.AA01970@E40-008-8.MIT.EDU> To: gilbertd@silver.ucs.indiana.edu Subject: ProSearch Update -- New Version Status: R Note: You may have received two previous copies of this message. We have been having problems with our mailer, Also, I have fixed some small problems with the MSDOS batch files. Use This Version. If you have received this more than once, I apologize for stuffing your mailboxes Enclosed is a Unix style shar (shell archive) containing the new version of ProSearch. This version of ProSearch is necessary for a bug fix, and easier use of this software by none Unix systems. If you get ReadSeq (D. Gilbert), ProSearch can handle any sequence format ReadSeq knows about (many). The VMS command files require ReadSeq. Additionally, this release is covered by the Gnu Public License. This allows anyone the right to do what ever they want with the code, as long as it remains free. Finally, I am keeping a list of persons using ProSearch to make these kind of updates possible. If you do not wish to be on this list, send me mail. I hope two have three versions of this release available at the popular FTP sites: 1) Unix shar (enclosed) 2) UUencode Zoo archive (MSDOS, Unix, VMS) 3) DCL Shar (VMS specific) If in the future you wish to receive a specific format (other than shar) let me know. As usual please let me know of any bugs, or desired features. Frank Kolakowski ====================================================================== |lfk@athena.mit.edu || Lee F. Kolakowski | |lfk@eastman2.mit.edu || M.I.T. | |kolakowski@wccf.mit.edu || Dept of Chemistry | |lfk@mbio.med.upenn.edu || Room 18-506 | |lfk@hx.lcs.mit.edu || 77 Massachusetts Ave.| |AT&T: 1-617-253-1866 || Cambridge, MA 02139 | |--------------------------------------------------------------------| | #include | | One-Liner Here! | ====================================================================== #! /bin/sh # This is a shell archive. Remove anything before this line, then unpack # it by saving it into a file and typing "sh file". To overwrite existing # files, type "sh file -c". You can also feed this as standard input via # unshar, or by typing "sh 'COPYING' <<'END_OF_FILE' X GNU GENERAL PUBLIC LICENSE X Version 1, February 1989 X X Copyright (C) 1990 Lee F. Kolakowski X X Everyone is permitted to copy and distribute verbatim copies X of this license document, but changing it is not allowed. X X Preamble X X The license agreements of most software companies try to keep users Xat the mercy of those companies. By contrast, our General Public XLicense is intended to guarantee your freedom to share and change free Xsoftware--to make sure the software is free for all its users. The XGeneral Public License applies to the Free Software Foundation's Xsoftware and to any other program whose authors commit to using it. XYou can use it for your programs, too. X X When we speak of free software, we are referring to freedom, not Xprice. Specifically, the General Public License is designed to make Xsure that you have the freedom to give away or sell copies of free Xsoftware, that you receive source code or can get it if you want it, Xthat you can change the software or use pieces of it in new free Xprograms; and that you know you can do these things. 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BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY XFOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN XOTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES XPROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED XOR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF XMERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS XTO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE XPROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, XREPAIR OR CORRECTION. X X 10. 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It is safest to Xattach them to the start of each source file to most effectively convey Xthe exclusion of warranty; and each file should have at least the X"copyright" line and a pointer to where the full notice is found. X X X Copyright (C) 19yy X X This program is free software; you can redistribute it and/or modify X it under the terms of the GNU General Public License as published by X the Free Software Foundation; either version 1, or (at your option) X any later version. X X This program is distributed in the hope that it will be useful, X but WITHOUT ANY WARRANTY; without even the implied warranty of X MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X GNU General Public License for more details. X X You should have received a copy of the GNU General Public License X along with this program; if not, write to the Free Software X Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X XAlso add information on how to contact you by electronic and paper mail. X XIf the program is interactive, make it output a short notice like this Xwhen it starts in an interactive mode: X X Gnomovision version 69, Copyright (C) 19xx name of author X Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. X This is free software, and you are welcome to redistribute it X under certain conditions; type `show c' for details. X XThe hypothetical commands `show w' and `show c' should show the Xappropriate parts of the General Public License. Of course, the Xcommands you use may be called something other than `show w' and `show Xc'; they could even be mouse-clicks or menu items--whatever suits your Xprogram. X XYou should also get your employer (if you work as a programmer) or your Xschool, if any, to sign a "copyright disclaimer" for the program, if Xnecessary. Here a sample; alter the names: X X Yoyodyne, Inc., hereby disclaims all copyright interest in the X program `Gnomovision' (a program to direct compilers to make passes X at assemblers) written by James Hacker. X X , 1 April 1989 X Ty Coon, President of Vice X XThat's all there is to it! X END_OF_FILE if test 12437 -ne `wc -c <'COPYING'`; then echo shar: \"'COPYING'\" unpacked with wrong size! fi # end of 'COPYING' fi if test -f 'INSTALL.msdos' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'INSTALL.msdos'\" else echo shar: Extracting \"'INSTALL.msdos'\" \(981 characters\) sed "s/^X//" >'INSTALL.msdos' <<'END_OF_FILE' XINSTALLATION for MSDOS X X1) Get the datafile ProSite.doc from NETSERV@EMBL.BITNET X X This file must be mailed to you from the file X server. X X Send a Mail message to the above address X with a subject line that says: X X Subject: Get Prosite:Prosite.doc X X2) If you do not have a working version of Awk. FTP to X WSMR-SIMTEL20.ARMY.MIL X (26.2.0.74) X Simtel is a DEC-20 so use tenex mode for binaries. X mget PD1:GAWK*.* X X3) Place the two batch files (prosearc.bat and pros.bat) in your path. X Edit the line: X X set prolib=\mit\lfk\lib\prosite X X to reflect where the awk scripts, the regular expression file X and the prosite.doc file will be kept. Then replace all X occurances of 'awk' in the batch files with the path and name X of your implementation of the AWK language. X X4) If you get Readseq working on your system, uncomment the lines X in the scripts to use readseq. Readseq can be obtained from X iubio.bio.indiana.edu 129.79.1.101. This code requires an ANSI X C compiler. X END_OF_FILE if test 981 -ne `wc -c <'INSTALL.msdos'`; then echo shar: \"'INSTALL.msdos'\" unpacked with wrong size! fi # end of 'INSTALL.msdos' fi if test -f 'INSTALL.unix' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'INSTALL.unix'\" else echo shar: Extracting \"'INSTALL.unix'\" \(906 characters\) sed "s/^X//" >'INSTALL.unix' <<'END_OF_FILE' XINSTALLATION for UNIX X X1) Get the datafile ProSite.doc from NETSERV@EMBL.BITNET X X This file must be mailed to you from the file X server. X X Send a Mail message to the above address X with a subject line that says: X X Subject: Get Prosite:Prosite.doc X X2) If you do not have a working version of Awk. FTP to X PREP.AI.MIT.EDU (18.71.0.38) and X get the file pub/gnu/gawk* X X X3) Place the two scripts (prosearch and pros) in your path. Edit X the line: X X prolib='/mit/lfk/lib/prosite' X X to reflect where the awk scripts, the regular expression file X and the prosite.doc file will be kept. Then edit the next line: X X awk=gawk X X to reflect the path and name of your implementation of the AWK X language. X X4) If you get Readseq working on your system, uncomment the lines X in the scripts to use readseq. Readseq can be obtained from X iubio.bio.indiana.edu 129.79.1.101. This code requires an ANSI X C compiler. X END_OF_FILE if test 906 -ne `wc -c <'INSTALL.unix'`; then echo shar: \"'INSTALL.unix'\" unpacked with wrong size! fi # end of 'INSTALL.unix' fi if test -f 'INSTALL.vms' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'INSTALL.vms'\" else echo shar: Extracting \"'INSTALL.vms'\" \(1238 characters\) sed "s/^X//" >'INSTALL.vms' <<'END_OF_FILE' XINSTALLATION for VMS X X1) Get the datafile ProSite.doc from NETSERV@EMBL.BITNET X X This file must be mailed to you from the file X server. X X Send a Mail message to the above address X with a subject line that says: X X Subject: Get Prosite:Prosite.doc X X2) If you do not have a working version of Awk. FTP to X RML2.SRI.COM (128.18.22.20) and X get the file getting_gawk. There are instructions for X getting the backup save set containing the VMS implementation X of gawk. X X3) Place the two command files (prosearch.com and pros.com) in a directory. X Edit the lines X X $ prosearch_awk = "GCGMITPROSITE:prosite.awk" X $ prodoc_awk = "GCGMITPROSITE:prodoc.awk" X $ prosite_doc = "gengenbankdisk:[prosite]prosite.doc" X $ prosite_regex ="gengenbankdisk:[prosite]prosite.regex" X X to reflect where the awk scripts, the regular expression file X and the prosite.doc file will be kept. Then replace all X occurances of 'awk' in the command files with the path and name X of your implementation of the AWK language. X X4) You must get Readseq working on your system. Readseq can be X obtained from iubio.bio.indiana.edu 129.79.1.101. This code X requires an ANSI C compiler. X X5) I'd like to thank Anna Tomecka and Jasper Rees for writting the X VMS command files. X END_OF_FILE if test 1238 -ne `wc -c <'INSTALL.vms'`; then echo shar: \"'INSTALL.vms'\" unpacked with wrong size! fi # end of 'INSTALL.vms' fi if test -f 'MANIFEST' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'MANIFEST'\" else echo shar: Extracting \"'MANIFEST'\" \(717 characters\) sed "s/^X//" >'MANIFEST' <<'END_OF_FILE' XFile Description X==== ============ XCOPYING Gnu Public License XINSTALL.msdos Details for MSDOS XINSTALL.unix Details for UNIX XINSTALL.vms Details for VMS XMANIFEST this file Xprodoc.awk awk script for data formatting Xpros short output script Xpros.1 unformatted manual page Xpros.bat MSDOS batch file for short output Xpros.com VMS command file for short output Xpros.nro formatted manual page Xprosearc.bat MSDOS batch file for long output Xprosearch long output script Xprosearch.com VMS command file for long output Xprosearch.doc background and info Xprosite.awk awk script for search Xprosite.bug Details of a small bug Xprosite.regex regular expression data for search END_OF_FILE if test 717 -ne `wc -c <'MANIFEST'`; then echo shar: \"'MANIFEST'\" unpacked with wrong size! fi # end of 'MANIFEST' fi if test -f 'prodoc.awk' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'prodoc.awk'\" else echo shar: Extracting \"'prodoc.awk'\" \(1597 characters\) sed "s/^X//" >'prodoc.awk' <<'END_OF_FILE' X# prodoc.awk - release version 1.1 X# Copyright (C) 1990 Lee F. Kolakowski X# X# This program is free software; you can redistribute it and/or modify X# it under the terms of the GNU General Public License as published by X# the Free Software Foundation; either version 1, or (at your option) X# any later version. X# X# This program is distributed in the hope that it will be useful, X# but WITHOUT ANY WARRANTY; without even the implied warranty of X# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X# GNU General Public License for more details. X# X# You should have received a copy of the GNU General Public License X# along with this program; if not, write to the Free Software X# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X# X# X# Send bugs or improvements to X# lfk@athena.mit.edu X# X# August 13, 1990 X# usage: {ng}awk -f prodoc.awk X# this provides long output X# X# usage: {ng}awk -f prodoc.awk X# this provides short output X# XBEGIN { X printf("\n%s\t%12s\t%-20s\t%s\n", "Access#", "From->To", "Name", "Doc#") X printf("%s\t%12s\t%-20s\t%s\n", "_______", "________", "____________________", "_________") X n=1 X} X{ X if ($0 ~ /^PS/ && NF == 4) { X printf("%s\t%12s\t%-20s\t%s\n", $1, $2, $3, $4) X regex[NR] = "{"$4 X regex_num = NR X } X if ($0 ~ /^{PDOC/ && n < regex_num) { X for (i=n; i <= regex_num; i++) { X if ( regex[i] != regex_last ) { X regex_last = regex[i] X if ($0 ~ regex[i]) { X n = i X print $0 X while ( $0 !~ /{END}/) { X getline X print $0 X } X } X } X } X } X} END_OF_FILE if test 1597 -ne `wc -c <'prodoc.awk'`; then echo shar: \"'prodoc.awk'\" unpacked with wrong size! fi # end of 'prodoc.awk' fi if test -f 'pros' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'pros'\" else echo shar: Extracting \"'pros'\" \(1359 characters\) sed "s/^X//" >'pros' <<'END_OF_FILE' X#!/bin/sh X# pros - release version 1.1 X# Copyright (C) 1990 Lee F. Kolakowski X# X# This program is free software; you can redistribute it and/or modify X# it under the terms of the GNU General Public License as published by X# the Free Software Foundation; either version 1, or (at your option) X# any later version. X# X# This program is distributed in the hope that it will be useful, X# but WITHOUT ANY WARRANTY; without even the implied warranty of X# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X# GNU General Public License for more details. X# X# You should have received a copy of the GNU General Public License X# along with this program; if not, write to the Free Software X# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X# X# X# Send bugs or improvements to X# lfk@athena.mit.edu X# X# August 13, 1990 X# X# usage: pros files... X# produces short output X# Xprolib='/mit/lfk/src/prosearch' Xawk=gawk Xecho 'Prosite Database -- Release 5.0 of April 1990 Copyright: Amos Bairoch' Xecho 'ProSearch Software -- Release 1.1 -- Copyright: Lee Kolakowski' Xfor file in $* ; do X echo "The following patterns are in < $file >:" X# readseq -f10 $file > /tmp/pros$$.tmp X# ${awk} -f ${prolib}/prosite.awk ${prolib}/prosite.regex /tmp/pros$$.tmp | X ${awk} -f ${prolib}/prosite.awk ${prolib}/prosite.regex $file | X ${awk} -f ${prolib}/prodoc.awk - Xdone X END_OF_FILE if test 1359 -ne `wc -c <'pros'`; then echo shar: \"'pros'\" unpacked with wrong size! fi chmod +x 'pros' # end of 'pros' fi if test -f 'pros.1' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'pros.1'\" else echo shar: Extracting \"'pros.1'\" \(647 characters\) sed "s/^X//" >'pros.1' <<'END_OF_FILE' X.TH PROS 1 "July 13, 1990" X.SH NAME Xpros \- search protein sequence for Prosite Patterns X.SH SYNOPSIS X.B pros Xfile ... X.br X.B prosearch Xfile ... X.br X.SH DESCRIPTION X.I Pros Xreads each X.I file Xin sequence and searchs for regular expression patterns described Xsites or structures in the Prosite Database. The output is displayed Xon the standard output. The output is a table of sites. Longer output Xis generated by prosearch, which also displays the relevant section Xfrom the Prosite database. X.SH "SEE ALSO" Xawk(1), gawk(1) X.br Xprosite.regex - the regular expression file X.br Xprosite.doc - the Prosite database (available from NETSERV@EMBL.BITNET) END_OF_FILE if test 647 -ne `wc -c <'pros.1'`; then echo shar: \"'pros.1'\" unpacked with wrong size! fi # end of 'pros.1' fi if test -f 'pros.bat' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'pros.bat'\" else echo shar: Extracting \"'pros.bat'\" \(1509 characters\) sed "s/^X//" >'pros.bat' <<'END_OF_FILE' XREM Note: If you uncomment the ReadSeq Lines replace RIGHT_CARET XREM with the proper redirection character Xecho off XREM pros.bat - release version 1.1 XREM Copyright (C) 1990 Lee F. Kolakowski XREM XREM This program is free software; you can redistribute it and/or modify XREM it under the terms of the GNU General Public License as published by XREM the Free Software Foundation; either version 1, or (at your option) XREM any later version. XREM XREM This program is distributed in the hope that it will be useful, XREM but WITHOUT ANY WARRANTY; without even the implied warranty of XREM MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the XREM GNU General Public License for more details. XREM XREM You should have received a copy of the GNU General Public License XREM along with this program; if not, write to the Free Software XREM Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. XREM XREM XREM Send bugs or improvements to XREM lfk@athena.mit.edu XREM XREM August 13, 1990 XREM XREM usage: pros files... XREM produces short output XREM Xset prolib=\usr\lib\prosite Xecho Prosite Database -- Release 5.0 of April 1990 Copyright: Amos Bairoch Xecho ProSearch Software -- Release 1.1 -- Copyright: Lee Kolakowski Xecho The following patterns are in [ %1 ]: XREM readseq -f10 %1 RIGHT_CARET pros$$.tmp XREM awk -f %prolib%\prosite.awk %prolib%\prosite.regex pros$$.tmp RIGHT_CARET pros$$2.tmp Xawk -f %prolib%\prosite.awk %prolib%\prosite.regex %1 > pros$$2.tmp Xawk -f %prolib%\prodoc.awk pros$$2.tmp Xdel pros$$*.tmp END_OF_FILE if test 1509 -ne `wc -c <'pros.bat'`; then echo shar: \"'pros.bat'\" unpacked with wrong size! fi # end of 'pros.bat' fi if test -f 'pros.com' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'pros.com'\" else echo shar: Extracting \"'pros.com'\" \(3913 characters\) sed "s/^X//" >'pros.com' <<'END_OF_FILE' X$! pros.com - release version 1.1 X$! Copyright (C) 1990 Lee F. Kolakowski X$! X$! This program is free software; you can redistribute it and/or modify X$! it under the terms of the GNU General Public License as published by X$! the Free Software Foundation; either version 1, or (at your option) X$! any later version. X$! X$! This program is distributed in the hope that it will be useful, X$! but WITHOUT ANY WARRANTY; without even the implied warranty of X$! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X$! GNU General Public License for more details. X$! X$! You should have received a copy of the GNU General Public License X$! along with this program; if not, write to the Free Software X$! Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X$! X$! X$! Send bugs or improvements to X$! lfk@athena.mit.edu X$! X$! August 13, 1990 X$! X$ ver=F$verify(0) X$ Start: X$ type sys$input XProSite Database Version 5.0 Copyright Amos Bairoch XProSearch Version 1.1 Copyright Lee F. Kolakowski X$ goto ProMatch X$! X$ ProMatch: X$!========== X$ prosearch_awk = "GCGMITPROSITE:prosite.awk" X$ prodoc_awk = "GCGMITPROSITE:prodoc.awk" X$ prosite_doc = "gengenbankdisk:[prosite]prosite.doc" X$ prosite_regex ="gengenbankdisk:[prosite]prosite.regex" X$ type sys$input X X Prosearch scans your protein sequence against the Prosite X database and records the list of matches as positions, X pattern names and accession numbers. Your file of protein X sequence can be in any format, it will be read into the correct X format by this procedure. X X$! X$ get_doc = 2 X$ count = 1 X$ Get_seq: X$ file = p'count' X$ if file.nes."" X$ then X$ if f$search("''file'").nes."" X$ then X$ write sys$output " Analyzing sequence ''file'" X$ else X$ write sys$output " file ''file' cannot be found, trying next file" X$ count = count + 1 X$ goto getseq X$ endif X$ else X$ if count.gt.1 then goto leave X$ Inquire file " Name of protein sequence file " X$ if file.eqs."" then goto get_seq X$ if f$search("''file'").eqs."" X$ then X$ write sys$output "" X$ write sys$output " your file ''file' was not found" X$ inquire retry " type 1 to continue, return to quit " X$ if retry .eqs. "1" X$ then X$ file="" X$ goto get_seq X$ else X$ goto leave X$ endif X$ endif X$ endif X$ X$Setup: X$ file = "''f$parse(file)'" X$ def_dir="''f$environment("DEFAULT")'" X$ staden_file = "''def_dir'"+"''F$parse(file,,,"NAME")'"+".STADENPRO" X$ temp_file = "''def_dir'"+"''F$parse(file,,,"NAME")'"+".temp_file" X$ outfile = "''def_dir'"+"''F$parse(file,,,"NAME")'"+".prosearch" X$ X$ write sys$output "" X$ write sys$output " Your output will be in ''outfile'" X$ if get_doc.eqs."1" .or. get_doc.eqs."2" then goto work_out X$Get_DOC: X$ write sys$output "" X$ write sys$output " Do you want to include documentation in ''outfile'" X$ inquire get_doc " Type 1 to include, 2 to exclude, QUIT to quit" X$ if get_doc.eqs."QUIT" then goto leave X$ if get_doc.eqs."1" .or. get_doc.eqs."2" then goto work_out X$ goto Get_doc X$ X$work_out: X$ write sys$output "" X$ write sys$output " Matching against prosite: please wait...." X$ write sys$output "" X$ X$TOSTADEN: X$ on control_y then goto leave X$ readseq -f13 'file' -o'staden_file' X$ X$ Prosearch: X$ gawk -f 'prosearch_awk' 'prosite_regex' 'staden_file' > 'temp_file' X$ if Get_doc.eqs."1" X$ then X$ gawk -f 'prodoc_awk' 'temp_file' 'prosite_doc' > 'outfile' X$ else X$ gawk -f 'prodoc_awk' 'temp_file' > 'outfile' X$ endif X$ X$check_count: X$ count= count+1 X$ goto get_seq X$Leave: X$ save_message = f$environment("MESSAGE") X$ set message/nofacility/noiden/noseverity/notext X$ dele/nolog/noconf *.stadenpro;* X$ dele/nolog/noconf *.temp_file;* X$ set message 'save_message' X END_OF_FILE if test 3913 -ne `wc -c <'pros.com'`; then echo shar: \"'pros.com'\" unpacked with wrong size! fi # end of 'pros.com' fi if test -f 'pros.nro' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'pros.nro'\" else echo shar: Extracting \"'pros.nro'\" \(833 characters\) sed "s/^X//" >'pros.nro' <<'END_OF_FILE' X X X XPROS(1) UNIX Programmer's Manual PROS(1) X X X XNAME X pros - search protein sequence for Prosite Patterns X XSYNOPSIS X pros file ... X prosearch file ... X XDESCRIPTION X _P_r_o_s reads each _f_i_l_e in sequence and searchs for regular X expression patterns described sites or structures in the X Prosite Database. The output is displayed on the standard X output. The output is a table of sites. Longer output is X generated by prosearch, which also displays the relevant X section from the Prosite database. X XSEE ALSO X awk(1), gawk(1) X prosite.regex - the regular expression file X prosite.doc - the Prosite database (available from X NETSERV@EMBL.BITNET) X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X XPrinted 7/13/90 July 13, 1990 1 X X X END_OF_FILE echo shar: 8 control characters may be missing from \"'pros.nro'\" if test 833 -ne `wc -c <'pros.nro'`; then echo shar: \"'pros.nro'\" unpacked with wrong size! fi # end of 'pros.nro' fi if test -f 'prosearc.bat' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'prosearc.bat'\" else echo shar: Extracting \"'prosearc.bat'\" \(1538 characters\) sed "s/^X//" >'prosearc.bat' <<'END_OF_FILE' XREM Note: If you uncomment the ReadSeq Lines replace RIGHT_CARET XREM with the proper redirection character Xecho off XREM prosearc.bat - release version 1.1 XREM Copyright (C) 1990 Lee F. Kolakowski XREM XREM This program is free software; you can redistribute it and/or modify XREM it under the terms of the GNU General Public License as published by XREM the Free Software Foundation; either version 1, or (at your option) XREM any later version. XREM XREM This program is distributed in the hope that it will be useful, XREM but WITHOUT ANY WARRANTY; without even the implied warranty of XREM MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the XREM GNU General Public License for more details. XREM XREM You should have received a copy of the GNU General Public License XREM along with this program; if not, write to the Free Software XREM Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. XREM XREM XREM Send bugs or improvements to XREM lfk@athena.mit.edu XREM XREM August 13, 1990 XREM XREM usage: prosearch files... XREM produces long output XREM Xset prolib=\usr\lib\prosite Xecho Prosite Database -- Release 5.0 of April 1990 Copyright: Amos Bairoch Xecho ProSearch Software -- Release 1.1 -- Copyright: Lee Kolakowski Xecho The following patterns are in [ %1 ]: XREM readseq -f10 %1 RIGHT_CARET pros$$.tmp XREM awk -f %prolib%\prosite.awk %prolib%\prosite.regex pros$$.tmp RIGHT_CARET pros$$2.tmp Xawk -f %prolib%\prosite.awk %prolib%\prosite.regex %1 > pros$$2.tmp Xawk -f %prolib%\prodoc.awk pros$$2.tmp %prolib%\prosite.doc Xdel pros$$*.tmp END_OF_FILE if test 1538 -ne `wc -c <'prosearc.bat'`; then echo shar: \"'prosearc.bat'\" unpacked with wrong size! fi # end of 'prosearc.bat' fi if test -f 'prosearch' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'prosearch'\" else echo shar: Extracting \"'prosearch'\" \(1387 characters\) sed "s/^X//" >'prosearch' <<'END_OF_FILE' X#!/bin/sh X# prosearch - release version 1.1 X# Copyright (C) 1990 Lee F. Kolakowski X# X# This program is free software; you can redistribute it and/or modify X# it under the terms of the GNU General Public License as published by X# the Free Software Foundation; either version 1, or (at your option) X# any later version. X# X# This program is distributed in the hope that it will be useful, X# but WITHOUT ANY WARRANTY; without even the implied warranty of X# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X# GNU General Public License for more details. X# X# You should have received a copy of the GNU General Public License X# along with this program; if not, write to the Free Software X# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X# X# X# Send bugs or improvements to X# lfk@athena.mit.edu X# X# August 13, 1990 X# X# usage: prosearch files... X# produces long output X# Xprolib='/mit/lfk/lib/prosite' Xawk=gawk Xecho 'Prosite Database -- Release 5.0 of April 1990 Copyright: Amos Bairoch' Xecho 'ProSearch Software -- Release 1.1 -- Copyright: Lee Kolakowski' Xfor file in $* ; do X echo "The following patterns are in < $file >:" X# readseq -f10 $file > /tmp/pros$$.tmp X# ${awk} -f ${prolib}/prosite.awk ${prolib}/prosite.regex /tmp/pros$$.tmp | X ${awk} -f ${prolib}/prosite.awk ${prolib}/prosite.regex $file | X ${awk} -f ${prolib}/prodoc.awk - ${prolib}/prosite.doc Xdone X END_OF_FILE if test 1387 -ne `wc -c <'prosearch'`; then echo shar: \"'prosearch'\" unpacked with wrong size! fi chmod +x 'prosearch' # end of 'prosearch' fi if test -f 'prosearch.com' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'prosearch.com'\" else echo shar: Extracting \"'prosearch.com'\" \(3917 characters\) sed "s/^X//" >'prosearch.com' <<'END_OF_FILE' X$! prosearch.com - release version 1.1 X$! Copyright (C) 1990 Lee F. Kolakowski X$! X$! This program is free software; you can redistribute it and/or modify X$! it under the terms of the GNU General Public License as published by X$! the Free Software Foundation; either version 1, or (at your option) X$! any later version. X$! X$! This program is distributed in the hope that it will be useful, X$! but WITHOUT ANY WARRANTY; without even the implied warranty of X$! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X$! GNU General Public License for more details. X$! X$! You should have received a copy of the GNU General Public License X$! along with this program; if not, write to the Free Software X$! Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X$! X$! X$! Send bugs or improvements to X$! lfk@athena.mit.edu X$! X$! August 13, 1990 X$! X$ ver=F$verify(0) X$ Start: X$ type sys$input XProSite Database Version 5.0 Copyright Amos Bairoch XProSearch Version 1.1 Copyright Lee F. Kolakowski X$ goto ProMatch X$! X$ ProMatch: X$!========== X$ prosearch_awk = "GCGMITPROSITE:prosite.awk" X$ prodoc_awk = "GCGMITPROSITE:prodoc.awk" X$ prosite_doc = "gengenbankdisk:[prosite]prosite.doc" X$ prosite_regex ="gengenbankdisk:[prosite]prosite.regex" X$ type sys$input X X Prosearch scans your protein sequence against the Prosite X database and records the list of matches as positions, X pattern names and accession numbers. Your file of protein X sequence can be in any format, it will be read into the correct X format by this procedure. X X$! X$ get_doc = 1 X$ count = 1 X$ Get_seq: X$ file = p'count' X$ if file.nes."" X$ then X$ if f$search("''file'").nes."" X$ then X$ write sys$output " Analyzing sequence ''file'" X$ else X$ write sys$output " file ''file' cannot be found, trying next file" X$ count = count + 1 X$ goto getseq X$ endif X$ else X$ if count.gt.1 then goto leave X$ Inquire file " Name of protein sequence file " X$ if file.eqs."" then goto get_seq X$ if f$search("''file'").eqs."" X$ then X$ write sys$output "" X$ write sys$output " your file ''file' was not found" X$ inquire retry " type 1 to continue, return to quit " X$ if retry .eqs. "1" X$ then X$ file="" X$ goto get_seq X$ else X$ goto leave X$ endif X$ endif X$ endif X$ X$Setup: X$ file = "''f$parse(file)'" X$ def_dir="''f$environment("DEFAULT")'" X$ staden_file = "''def_dir'"+"''F$parse(file,,,"NAME")'"+".STADENPRO" X$ temp_file = "''def_dir'"+"''F$parse(file,,,"NAME")'"+".temp_file" X$ outfile = "''def_dir'"+"''F$parse(file,,,"NAME")'"+".prosearch" X$ X$ write sys$output "" X$ write sys$output " Your output will be in ''outfile'" X$ if get_doc.eqs."1" .or. get_doc.eqs."2" then goto work_out X$Get_DOC: X$ write sys$output "" X$ write sys$output " Do you want to include documentation in ''outfile'" X$ inquire get_doc " Type 1 to include, 2 to exclude, QUIT to quit" X$ if get_doc.eqs."QUIT" then goto leave X$ if get_doc.eqs."1" .or. get_doc.eqs."2" then goto work_out X$ goto Get_doc X$ X$work_out: X$ write sys$output "" X$ write sys$output " Matching against prosite: please wait...." X$ write sys$output "" X$ X$TOSTADEN: X$ on control_y then goto leave X$ readseq -f13 'file' -o'staden_file' X$ X$ Prosearch: X$ gawk -f 'prosearch_awk' 'prosite_regex' 'staden_file' > 'temp_file' X$ if Get_doc.eqs."1" X$ then X$ gawk -f 'prodoc_awk' 'temp_file' 'prosite_doc' > 'outfile' X$ else X$ gawk -f 'prodoc_awk' 'temp_file' > 'outfile' X$ endif X$ X$check_count: X$ count= count+1 X$ goto get_seq X$Leave: X$ save_message = f$environment("MESSAGE") X$ set message/nofacility/noiden/noseverity/notext X$ dele/nolog/noconf *.stadenpro;* X$ dele/nolog/noconf *.temp_file;* X$ set message 'save_message' END_OF_FILE if test 3917 -ne `wc -c <'prosearch.com'`; then echo shar: \"'prosearch.com'\" unpacked with wrong size! fi # end of 'prosearch.com' fi if test -f 'prosearch.doc' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'prosearch.doc'\" else echo shar: Extracting \"'prosearch.doc'\" \(4280 characters\) sed "s/^X//" >'prosearch.doc' <<'END_OF_FILE' XINTRODUCTION X X Over the past year or so Amos Bairoch (bairoch X@cgecmu51.BITNET) has released an number of versions of his Prosite Xdatabase. This is a database of patterns which have been associated Xwith particular enzymatic activities or structures. For example, the Xwell known pattern for N-link glycosylation Asn-Xxx-Ser/Thr. X X Amos has compiled a database that consists of references about Xeach pattern, validity of the patterns, occurrences, and a host of Xother details. This database is of general use, and has been used by XAmos in his PC/Gene Suite of programs for analysis of DNA and Protein Xsequences. X X I wanted to use this database on a Unix machine and be able to Xask the question, "Which of these patterns occur in sequence X?" X X This is the second release of Prosearch. It completely Xsupersedes the first version with one important bug fix, and support Xfor VMS, MS-DOS, and UNIX. Also, by using ReadSeq, a fine program Xfrom Don Gilbert , more protein Xdata formats are accessible. X XIMPLEMENTATION X X Most patterns can be expressed as regular expressions. For Xexample the pattern '^P' when used with the unix utility grep matches Xany line in the input that begins with a 'P'. X X I translated all but 1 of the 337 patterns in Prosite to Unix Xstyle regular expressions and wrote a simple searching program to Xsearch a protein sequence for their occurrence. The pattern I did not Xtranslate was the pattern PS0003 which is Tyrosine Sulfation. There is Xno clean pattern for this modification. X X The program is written in the Awk language, and runs on Xmachines which have either Nawk from AT&T, Gawk from the Free Software XFoundation, or one of several versions of Awk which run on MSDOS Xcompatibles. Read the approriate INSTALL file for details. X XINPUT FILES X X In put file are any protein sequence files in an unstructured Xformat. AWK will accept the input on any number of lines of any length X(I've tried proteins sequences up to 2500 amino acids on one line with Xno problem). Each ASCII character will be interpreted as an amino Xacid, and all letters must be capitalized. With 'readseq' any of a Xnumber of formats can be used. X XOUTPUT X X There are two possible forms of output. The "short" form is a Xtable of accession numbers, positions in the sequence and short names Xfor patterns. The "long" form is the same except that the relevant Xsections from the Prosite Database is also printed. X XHere is an example of the short output for Bovine Rhodopsin. X XProsite Database -- Release 5.0 of April 1990 Copyright: Amos Bairoch XProSearch Software -- Release 0.1beta -- Copyright: Lee Kolakowski XThe following patterns are in < test.ops >: X XAccess# From->To Name X_______ ________ ____ XPS00001 2->6 ASN_GLYCOSYLATION XPS00001 15->19 ASN_GLYCOSYLATION XPS00001 200->204 ASN_GLYCOSYLATION XPS00005 14->17 PKC_PHOSPHO_SITE XPS00005 229->232 PKC_PHOSPHO_SITE XPS00005 243->246 PKC_PHOSPHO_SITE XPS00006 22->26 CK2_PHOSPHO_SITE XPS00006 193->197 CK2_PHOSPHO_SITE XPS00006 198->202 CK2_PHOSPHO_SITE XPS00006 229->233 CK2_PHOSPHO_SITE XPS00006 338->342 CK2_PHOSPHO_SITE XPS00007 21->30 TYR_PHOSPHO_SITE XPS00008 89->95 MYRISTYL XPS00008 120->126 MYRISTYL XPS00008 156->162 MYRISTYL XPS00008 182->188 MYRISTYL XPS00013 157->168 PROKAR_LIPOPROTEIN XPS00237 68->85 G_PROTEIN_RECEPTOR XPS00238 296->314 OPSIN X XUSAGE X X This is described in the file pros.1, a printable version is Xin pros.nro. X X XBUGS X X Please send bug reports or improvements to me. X XNOTICES X X This code is covered by the Free Software Foundation's Gnu XPublic License. See the file COPYING for details. X X XFrank Kolakowski X X====================================================================== X|lfk@athena.mit.edu || Lee F. Kolakowski | X|lfk@eastman2.mit.edu || M.I.T. | X|kolakowski@wccf.mit.edu || Dept of Chemistry | X|lfk@mbio.med.upenn.edu || Room 18-506 | X|lfk@hx.lcs.mit.edu || 77 Massachusetts Ave.| X|AT&T: 1-617-253-1866 || Cambridge, MA 02139 | X====================================================================== X X X END_OF_FILE if test 4280 -ne `wc -c <'prosearch.doc'`; then echo shar: \"'prosearch.doc'\" unpacked with wrong size! fi # end of 'prosearch.doc' fi if test -f 'prosite.awk' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'prosite.awk'\" else echo shar: Extracting \"'prosite.awk'\" \(1761 characters\) sed "s/^X//" >'prosite.awk' <<'END_OF_FILE' X# prosite.awk - release version 1.1 X# Copyright (C) 1990 Lee F. Kolakowski X# X# This program is free software; you can redistribute it and/or modify X# it under the terms of the GNU General Public License as published by X# the Free Software Foundation; either version 1, or (at your option) X# any later version. X# X# This program is distributed in the hope that it will be useful, X# but WITHOUT ANY WARRANTY; without even the implied warranty of X# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the X# GNU General Public License for more details. X# X# You should have received a copy of the GNU General Public License X# along with this program; if not, write to the Free Software X# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. X# X# X# Send bugs or improvements to X# lfk@athena.mit.edu X# X# August 13, 1990 X# X# usage: {ng}awk -f prosite.awk prosite.regex filenames... X# produces unformatted table for prodoc.awk X# X{ X if ( FILENAME ~ /prosite\.reg/ ) { X accession[NR] = $1 ; X regex[NR] = $2; X name[NR] = $3; X doc[NR] = $4; X regex_num = NR; X } X else { X if (FILENAME != lastfile) { X while ( getline < FILENAME > 0 ) { X input = input$0 X } X $0 = input X n = length($0) X for (i = 1; i <= regex_num ; i++ ) { X if (match($0, regex[i])) { X printf("%s\t%d->%d\t%s\t%s\n", accession[i], RSTART, RSTART+RLENGTH, name[i], doc[i]); X offset = RSTART+1 X seq_rem = n-offset X new = substr($0, offset, seq_rem) X while (match(new,regex[i])) { X printf("%s\t%d->%d\t%s\t%s\n", accession[i], offset+RSTART-1, offset+RSTART+RLENGTH-1, name[i], doc[i]); X offset += RSTART+1 X seq_rem = n-offset X new = substr($0, offset, seq_rem) X } X lastfile= FILENAME X } X } X } X } X} X X X END_OF_FILE if test 1761 -ne `wc -c <'prosite.awk'`; then echo shar: \"'prosite.awk'\" unpacked with wrong size! fi # end of 'prosite.awk' fi if test -f 'prosite.bug' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'prosite.bug'\" else echo shar: Extracting \"'prosite.bug'\" \(343 characters\) sed "s/^X//" >'prosite.bug' <<'END_OF_FILE' XThe following is a note about an error in ProSite.doc. Please correct Xyour version X X Date: Fri, 27 Jul 90 22:23 N X From: Amos Bairoch X Subject: Re: PS number ambiguities in ProSite.doc X X The cross referenence for engrailed should be PS00033. X sorry abou that and thanks for pointing it to me. X X Amos X END_OF_FILE if test 343 -ne `wc -c <'prosite.bug'`; then echo shar: \"'prosite.bug'\" unpacked with wrong size! fi # end of 'prosite.bug' fi if test -f 'prosite.regex' -a "${1}" != "-c" ; then echo shar: Will not clobber existing file \"'prosite.regex'\" else echo shar: Extracting \"'prosite.regex'\" \(19585 characters\) sed "s/^X//" >'prosite.regex' <<'END_OF_FILE' XPS00001 N[^P][ST][^P] ASN_GLYCOSYLATION PDOC00001 XPS00002 SG.G GLYCOSAMINOGLYCAN PDOC00002 XPS00004 [RK][RK].[ST] CAMP_PHOSPHO_SITE PDOC00004 XPS00005 [ST].[RK] PKC_PHOSPHO_SITE PDOC00005 XPS00006 [ST]..[DE] CK2_PHOSPHO_SITE PDOC00006 XPS00007 [RK]...[DE]...Y TYR_PHOSPHO_SITE PDOC00007 XPS00007 [RK]...[DE]..Y TYR_PHOSPHO_SITE PDOC00007 XPS00007 [RK]..[DE]...Y TYR_PHOSPHO_SITE PDOC00007 XPS00007 [RK]..[DE]..Y TYR_PHOSPHO_SITE PDOC00007 XPS00008 G[^EDKRHPYFW]..[STAGCN][^P] MYRISTYL PDOC00008 XPS00009 .G[RK][RK] AMIDATION PDOC00009 XPS00010 C.[DN]....[FY].C.C ASX_HYDROXYL PDOC00010 XPS00011 ............E...E.C......[DEN].[LIVMFY].........[FYW] GLU_CARBOXYLATION PDOC00011 XPS00012 [LI]G[LIVMFYA]DS[LI]...[DE] PHOSPHOPANTETHEINE PDOC00012 XPS00013 [^DERK][^DERK][^DERK][^DERK][^DERK][^DERK][^DERK][LIVSTAG][LIVSTAG][AG]C PROKAR_LIPOPROTEIN PDOC00013 XPS00014 [RKH][DEN]EL$ ER_TARGET PDOC00014 XPS00015 [RKTA]KK[RQNTSG]K NUCLEAR PDOC00015 XPS00016 RGD RGD PDOC00016 XPS00017 [AG]....GK[ST] ATP_A PDOC00017 XPS00018 D.[DNS][^ILVFYW][DENSTG][DNQGHKR][^GP][LIVMC][DENQSTAGC]..[DE][LIVMFYW] EF_HAND PDOC00018 XPS00019 Q[RK]KTFT.W.N ACTININ_1 PDOC00019 XPS00020 A.....I.K[LIVM][LIVM]D..D[LIVM] ACTININ_2 PDOC00019 XPS00021 [FY]CRNPD KRINGLE PDOC00020 XPS00022 C.C.....G..C EGF PDOC00021 XPS00023 C..PF.[FYW].......C..........WC....[ND][FYW].....[FYW].[FYW]C FIBRONECTIN_2 PDOC00022 XPS00023 C..PF.[FYW].......C..........WC....[ND][FYW]...[FYW].[FYW]C FIBRONECTIN_2 PDOC00022 XPS00023 C..PF.[FYW].......C........WC....[ND][FYW].....[FYW].[FYW]C FIBRONECTIN_2 PDOC00022 XPS00023 C..PF.[FYW].......C........WC....[ND][FYW]...[FYW].[FYW]C FIBRONECTIN_2 PDOC00022 XPS00024 [LI]...W...[PE]..[LIVMFY][DE]A[AV][LIVMFY] HEMOPEXIN PDOC00023 XPS00024 [LI]...W..[PE]..[LIVMFY][DE]A[AV][LIVMFY] HEMOPEXIN PDOC00023 XPS00025 R..CG[FY]...[ST]...C....C TREFOIL PDOC00024 XPS00026 CG.......C....CCS..G.CG....[FYW]C CHITIN_BINDING PDOC00025 XPS00027 [LIVMF].....[LIVM]....[IV][RKQ].W........[RK] HOMEOBOX PDOC00027 XPS00028 C....C............H.....H ZINC_FINGER_C2H2 PDOC00028 XPS00028 C....C............H...H ZINC_FINGER_C2H2 PDOC00028 XPS00028 C..C............H.....H ZINC_FINGER_C2H2 PDOC00028 XPS00028 C..C............H...H ZINC_FINGER_C2H2 PDOC00028 XPS00029 L......L......L......L LEUCINE_ZIPPER PDOC00029 XPS00030 [RK]G[^EDKRHPCG][AGCI][FY][LIVA].[FY] RNP_1 PDOC00030 XPS00031 C..C.[DE].....H[FY]....C..CK.FF.R STEROID_FINGER PDOC00031 XPS00032 [LIVM][FY]PWM ANTENNAPEDIA PDOC00032 XPS00033 LMAQGLYN ENGRAILED PDOC00033 XPS00034 RPC...........CVS PAIRED_BOX PDOC00034 XPS00035 RRIKLG POU PDOC00035 XPS00036 [RK][RK].[RKS]N..[STA][STA].[RK].R.[RK] FOS_JUN_BASIC PDOC00036 XPS00037 W[ST]..ED..[LIV] MYB_1 PDOC00037 XPS00038 K[LIVMA].[IT]L..[TA]...[LIVMA]..[LIVM] HELIX_LOOP_HELIX PDOC00038 XPS00039 [LIVM][LIVM]DEAD.[LIVM][LIVM] ATP_HELICASE_1 PDOC00039 XPS00040 Y[LIVM]HRIGR ATP_HELICASE_2 PDOC00039 XPS00041 [LIV]..[LIV]....G[IFY].....F...[FY].......P HTH_ARAC_FAMILY PDOC00040 XPS00042 [ST]R.[DE]I...[LIV]G.[ST].ET HTH_CRP_FAMILY PDOC00041 XPS00043 E..[LIVM]...F.VSR..[LIVM]R.A[LIVM] HTH_GNTR_FAMILY PDOC00042 XPS00044 [LIVF]..[STAV][STA].....[STA][PQHR]..[LIVM][STA]..[LIVF]..[LIVF][RKEQ]..[LIVFY] HTH_LYSR_FAMILY PDOC00043 XPS00045 GF..............NP.T HISTONE_LIKE PDOC00044 XPS00046 AGL.FPV HISTONE_H2A PDOC00045 XPS00047 GAKRH HISTONE_H4 PDOC00046 XPS00048 [AV]RYR...[ST].S.S PROTAMINE_P1 PDOC00047 XPS00049 A[LIV][LIV][LIV].........[DN]G....[FY]..N..V[LIV] RIBOSOMAL_L14 PDOC00048 XPS00050 [RK][RK][AM][IVY][IV][RKT]L RIBOSOMAL_L23 PDOC00049 XPS00051 R[FY]N..RR.WRR RIBOSOMAL_L39 PDOC00050 XPS00052 L....[LIVM]......GKK.....I[LIVMF] RIBOSOMAL_RS7 PDOC00051 XPS00053 G..[LIV][LIV][ST]T..G[LIV]M....AR RIBOSOMAL_S8 PDOC00052 XPS00054 [DN]VTP.P.[DN] RIBOSOMAL_S11 PDOC00053 XPS00055 [RK].PNSA.R RIBOSOMAL_S12 PDOC00054 XPS00056 GD.[LIV].[LIV]...RP[LIV]..T RIBOSOMAL_S17 PDOC00055 XPS00057 AIK.AR...[LF]LP RIBOSOMAL_S18 PDOC00056 XPS00058 LGFRGEAL DNA_MISMATCH_REPAIR PDOC00057 XPS00059 GHE..G.....G..V ADH_ZINC PDOC00058 XPS00060 G..H..AH..G.....PHG ADH_IRON PDOC00059 XPS00061 Y[STAGC][STAGC][STAGC]K.[AG][LIVMAG]..[LIVMF] ADH_INSECT_TYPE PDOC00060 XPS00062 G....[LIVM]G[LIVM]SNF ALDOKETO_REDUCTASE_1 PDOC00061 XPS00063 Q.....[LIVM][AP]KS....R...N ALDOKETO_REDUCTASE_2 PDOC00061 XPS00064 [LIVM]G[EQ]HG[DN][ST] L_LDH PDOC00062 XPS00065 LIN..RG.V.D GLC_2_HYDROXYACID_DH PDOC00063 XPS00066 [RKH]......D.MG.N.[LIVM] HMG_COA_REDUCTASE_1 PDOC00064 XPS00067 GF[LIVM].NR[LIVM] 3HCDH PDOC00065 XPS00068 [LIVM]T[TR]LD..R[STA] MDH PDOC00066 XPS00069 DHYLGKE G6P_DEHYDROGENASE PDOC00067 XPS00070 [AG].F...GQ.C.A ALDEHYDE_DEHYDROGEN PDOC00068 XPS00071 ASCTT GAPDH PDOC00069 XPS00072 G..[FYW][LIV][LIV]NG.K.[FYW]ITN ACYL_COA_DH_1 PDOC00070 XPS00073 Q..GG.G[FY]..[DE].P ACYL_COA_DH_2 PDOC00070 XPS00074 [LIV]..GG[STAG]K[STAG]....[DN] GLU_DEHYDROGENASE PDOC00071 XPS00075 [LIF]G....[LIVMF]PW DHFR PDOC00072 XPS00076 GG.C[LIV]..GC[LIV]P PYRIDINE_REDOX PDOC00073 XPS00077 W.HH[LM] COX1 PDOC00074 XPS00078 C[SA]..CG..H COX2 PDOC00075 XPS00079 G.[FYW].[LIVMFYW].[CST]........G[LM]...[LIVMFYW] MULTICOPPER_OXIDASE1 PDOC00076 XPS00080 HCH...H...G[LM] MULTICOPPER_OXIDASE2 PDOC00076 XPS00081 HP[LIV].KL[LIV]..H LIPOXYGENASE PDOC00077 XPS00082 H........Y...P.G...E EXTRADIOL_DIOXYGENAS PDOC00078 XPS00083 G.[LIVM]....G..[LIVM]....[LIVM][DE].......G.[FY] INTRADIOL_DIOXYGENAS PDOC00079 XPS00084 HHM..F.C CU2_MONOOXYGENASE_1 PDOC00080 XPS00085 H.F....HTH..G CU2_MONOOXYGENASE_2 PDOC00080 XPS00086 F[SGN].[GD].[RHP].C[LIVFA][GD] CYTOCHROME_P450 PDOC00081 XPS00087 [RH][GA][IF]H[LIV]H..G SOD_CU_ZN_1 PDOC00082 XPS00088 D.WEH[STA][FY][FY] SOD_MN PDOC00083 XPS00089 G..NS...A.MP RIBORED_SMALL PDOC00084 XPS00090 [LIVM]...[STANQ][ET]C.....GDD NITROGENASE_1 PDOC00085 XPS00091 M.L.PC....Q THYMIDYLATE_SYNTHASE PDOC00086 XPS00092 [LIVMA][LIVMFYA].[DN]PP[FY] N6_MTASE PDOC00087 XPS00093 [LIVM]TSPP[FY] N4_MTASE PDOC00088 XPS00094 [DN].[LIV]..G.PC..[FW]S C5_MTASE_1 PDOC00089 XPS00095 [RKQ]..GN[STA][LIV]...[LIV]...[LIV]...[LIV] C5_MTASE_2 PDOC00089 XPS00096 TTTTHKTL SER_HYDROXYMETHYLTRF PDOC00090 XPS00097 F.[EK].STRT CARBAMOYLTRANSFERASE PDOC00091 XPS00098 C[SAG]S[SAG][ILVMFY][RKQ][SAG][ILVM]......I THIOLASE_1 PDOC00092 XPS00099 [AG][LIVM].[STA].C.G.G.[AG] THIOLASE_2 PDOC00092 XPS00100 HH.VCD CAT PDOC00093 XPS00101 IGAGS[LIVM]V CYSE_LACA_NODL PDOC00094 XPS00102 GT.NMK PHOSPHORYLASE PDOC00095 XPS00103 [LIVMFYWC][LIVM][LIVM][LIVM][DE][DE].[LIVM]..[GC].[STA] PUR_PYR_PR_TRANSFER PDOC00096 XPS00104 C..KT[FYW]P.[FYW][FYW] EPSP_SYNTHASE PDOC00097 XPS00105 S[FY][SA]K...LY ASP_AMINOTRANSFERASE PDOC00098 XPS00106 GR.NLIGEH.DY GALACTOKINASE PDOC00099 XPS00107 [LIV]G.G.[FY][SG].[LIV] PROTEIN_KINASE_ATP PDOC00100 XPS00108 [LIVMFYC].[HY].D[LIVMFY]K..N[LIMVFC][LIMVFC][LIMVFC] PROTEIN_KINASE_ST PDOC00100 XPS00109 [LIVMFYC].[HY].D[LIVMFY][RA]..N[LIMVFC][LIMVFC][LIMVFC] PROTEIN_KINASE_TYR PDOC00100 XPS00110 II.KIEN PYRUVATE_KINASE PDOC00101 XPS00111 WNGP.G.FE PGLYCERATE_KINASE PDOC00102 XPS00112 LTCPSN CREATINE_KINASE PDOC00103 XPS00113 DG[FY]PR.[LIVM].Q ADENYLATE_KINASE PDOC00104 XPS00114 DLHA.QIQGFFD[LIVM]P[LIVM]D PRPP_SYNTHETASE PDOC00105 XPS00115 Y[ST]P[ST]SP[STANK] RNA_POL_II_REPEAT PDOC00106 XPS00116 [YA].DTDS[LIVM] DNA_POLYMERASE_B PDOC00107 XPS00117 G....HPH.Q GAL-P-UDP-TRANSFER PDOC00108 XPS00118 CC..H..C PA2_HIS PDOC00109 XPS00119 [LIVM]C[^LIVMFYWPCST]CD.....C PA2_ASP PDOC00109 XPS00120 [LIV].[LIVFY][LIV]G[HY]S.G LIPASE_SER PDOC00110 XPS00121 Y..YY.C.C COLIPASE PDOC00111 XPS00122 P.....[LIVFA]G.SAG CARBOXYLESTERASE_B PDOC00112 XPS00123 V.DS..[STG]AT ALKALINE_PHOSPHATASE PDOC00113 XPS00124 GKLR[LIV]LYE FBPASE PDOC00114 XPS00125 RGNHE SER_THR_PHOSPHATASE PDOC00115 XPS00126 HD[LIVMFY].H.[AG]..N.[LIVMFY] PDEASE PDOC00116 XPS00127 CK..NTF RNASE_PANCREATIC PDOC00118 XPS00128 C...C..[LF]...[DEN][LI].....C LACTALBUMIN_LYSOZYME PDOC00119 XPS00129 WIDMN SUCRASE PDOC00120 XPS00130 WA..GVLLLN U_DNA_GLYCOSYLASE PDOC00121 XPS00131 GESYAG CARBOXYPEPTIDASE_SER PDOC00122 XPS00132 [LIVMFY]H[SAG].E.[LIVM][STAG]......[LIVMFY] CARBOXYPEPTIDASE_ZN1 PDOC00123 XPS00133 H[SAG]...[LIVM]..[LIVMFYW]P[FYW] CARBOXYPEPTIDASE_ZN2 PDOC00123 XPS00134 [LIVM][ST]A[STAG]HC TRYPSIN_HIS PDOC00124 XPS00135 GDSGG TRYPSIN_SER PDOC00124 XPS00136 [SAIV].[LIVM][LIVM]D[DSTA]G[LIVMFC]...[DNH] SUBTILISIN_ASP PDOC00125 XPS00137 HGT..[STA]G.[LIVMA] SUBTILISIN_HIS PDOC00125 XPS00138 GTS.[SA].P..[STAV][AG] SUBTILISIN_SER PDOC00125 XPS00139 Q...[GE].CW..[STAG] THIOL_PROTEASE PDOC00126 XPS00140 N.CG...[LIVM][LIVM]H UCH PDOC00127 XPS00141 [LIVFA]DTG[STA][STAN] EUK_ASP_PROTEASE PDOC00128 XPS00142 [TAIV]..HE[LIVMFYW][^DEHKRP]H.[LIVMFYWQ] ZINC_PROTEASE PDOC00129 XPS00143 GL.H..EHM IDE_PTR PDOC00130 XPS00144 [STAG]TGGTIA[STAG] ASN_GLN_ASE PDOC00132 XPS00145 MVCHHLD UREASE PDOC00133 XPS00146 F.[LIVMFY].S..K....[AG].[LIVM]L BETA_LACTAMASE_A PDOC00134 XPS00147 LGGDHS ARGINASE_1 PDOC00135 XPS00148 SGNLHG ARGINASE_2 PDOC00135 XPS00149 GKWHLG SULFATASE PDOC00117 XPS00150 SVDYE[LIVM].G[RK] ACYLPHOSPHATASE_1 PDOC00136 XPS00151 GTV.GQ.QGP ACYLPHOSPHATASE_2 PDOC00136 XPS00152 P[SAP][IV][DN]...S.S ATPASE_ALPHA_BETA PDOC00137 XPS00153 IT.E..E...GA.A ATPASE_GAMMA PDOC00138 XPS00154 DKTGT[LIVM]T ATPASE_E1_E2 PDOC00139 XPS00155 GGYSQG CUTINASE PDOC00140 XPS00156 F.D.KF.DI..T OMPDECASE PDOC00141 XPS00157 G.DF.K.DE RUBISCO_LARGE PDOC00142 XPS00158 EG.LLKPN ALDOLASE PDOC00143 XPS00159 LEVTLR ALDOLASE_KDPG_KHG_1 PDOC00144 XPS00160 FK.FPAE ALDOLASE_KDPG_KHG_2 PDOC00144 XPS00161 KKCGHM ISOCITRATE_LYASE PDOC00145 XPS00162 Q.H.HWG CARBONIC_ANHYDRASE PDOC00146 XPS00163 GS..M..K.N FUMARATE_LYASES PDOC00147 XPS00164 DDLTV[STA]NP ENOLASE PDOC00148 XPS00165 K........S[IF]K.RG DEHYDRATASE_SER_THR PDOC00149 XPS00166 G.ALGGG ENOYL_COA_HYDRATASE PDOC00150 XPS00167 G...[LIVM]ELG..[FY][ST]DP[LIVM]A[DE]G TRP_SYNTHASE_ALPHA PDOC00151 XPS00168 L.H.G[STA]HK.N TRP_SYNTHASE_BETA PDOC00152 XPS00169 D.[LIVM][LIVM]VKP D_ALA_DEHYDRATASE PDOC00153 XPS00170 PG...MAN.GP PPIASE PDOC00154 XPS00171 AYEP.W TPI PDOC00155 XPS00172 [LI]EPKP..P XYLOSE_ISOMERASE_1 PDOC00156 XPS00173 FHD.D[LIV].P XYLOSE_ISOMERASE_2 PDOC00156 XPS00174 [FY]DQWGVELGK P_GLUCOSE_ISOMERASE PDOC00157 XPS00175 [LIVM].RHG[EQ]...N PG_MUTASE PDOC00158 XPS00176 E........SK..Y[LIM] TOPOISOMERASE_I_EUK PDOC00159 XPS00177 [LIVM].EGDSA.[STAG] TOPOISOMERASE_II PDOC00160 XPS00178 P..[STAN]..[LIVMFYP][HT][LIVMFYA]G[HNTG][LIVMFYSTA] AA_TRNA_LIGASE_HIGH PDOC00161 XPS00178 P[STAN]..[LIVMFYP][HT][LIVMFYA]G[HNTG][LIVMFYSTA] AA_TRNA_LIGASE_HIGH PDOC00161 XPS00179 [AG].G[LIVMF][DE]R[LIVM].[LMA][LIVMF] AA_TRNA_LIGASE_ATP PDOC00161 XPS00180 [FYW]DGSS GLNA_1 PDOC00162 XPS00181 NG[SA]G.H...S GLNA_ATP PDOC00162 XPS00182 K[LIVM].....[LIVM]D[RK][DN][LI]Y GLNA_ADENYLATION PDOC00162 XPS00183 [FY]HP........[LIV]C[LIV].[LIV][LIV].....P UBIQUITIN_CONJUGAT PDOC00163 XPS00183 [FY]HP.......[LIV]C[LIV].[LIV][LIV].....P UBIQUITIN_CONJUGAT PDOC00163 XPS00184 RFGDPETQ GARS PDOC00164 XPS00185 [RK].[STA]..S.CY[SL] IPNS_1 PDOC00165 XPS00186 [LIVM][LIVM].CG[STA]..[STAG]..T.[DNG] IPNS_2 PDOC00165 XPS00187 P....[LIVMF].[LIVMF].GD..[LIVMF].[LIVMF]...[DE] TPP_ENZYMES PDOC00166 XPS00188 [LIVM].[AV]MKM...[LIVM] BIOTIN PDOC00167 XPS00189 G..[LIVF]...[DEQN].[LIVF]..[LIVF]...K[STAV][STAVQN]..[LIVF] LIPOYL PDOC00168 XPS00190 C[^CPWHF][^CPWR]CH[^CFWY] CYTOCHROME_C PDOC00169 XPS00191 F[LIV]..HPGG CYTOCHROME_B5 PDOC00170 XPS00192 [DEQ]...G[FYW].[LIVM]R..H CYTOCHROME_B_HEME PDOC00171 XPS00193 PEW[FY][LFY][LFY] CYTOCHROME_B_QO PDOC00171 XPS00194 [TA].WC[AG][PH]C THIOREDOXIN PDOC00172 XPS00195 C.[FY]C..[TA][KQ].[LI] GLUTAREDOXIN PDOC00173 XPS00196 Y.[VFY].C..P.H COPPER_BLUE PDOC00174 XPS00196 Y.[VFY].C..PH COPPER_BLUE PDOC00174 XPS00196 Y.[VFY].C.P.H COPPER_BLUE PDOC00174 XPS00196 Y.[VFY].C.PH COPPER_BLUE PDOC00174 XPS00196 Y[VFY].C..P.H COPPER_BLUE PDOC00174 XPS00196 Y[VFY].C..PH COPPER_BLUE PDOC00174 XPS00196 Y[VFY].C.P.H COPPER_BLUE PDOC00174 XPS00196 Y[VFY].C.PH COPPER_BLUE PDOC00174 XPS00197 C..[STA]..C[STA][^P]C 2FE2S_FERREDOXIN PDOC00175 XPS00197 C.[STA]..C[STA][^P]C 2FE2S_FERREDOXIN PDOC00175 XPS00198 C..C..C...C[PEG] 4FE4S_FERREDOXIN PDOC00176 XPS00199 CTHLGCV RIESKE_1 PDOC00177 XPS00200 CPCHGS RIESKE_2 PDOC00177 XPS00201 [FY].[ST].TG.T...A..I FLAVODOXIN PDOC00178 XPS00202 W.CP.C[AG] RUBREDOXIN PDOC00179 XPS00203 C...C.C..C.C..C METALLOTHIONEIN_CL1 PDOC00180 XPS00204 DPH..DF[LI]E FERRITIN PDOC00181 XPS00205 Y.[VA]VA[VA][VA][RK] TRANSFERRIN_1 PDOC00182 XPS00206 Y.GA..CL.[DE] TRANSFERRIN_2 PDOC00182 XPS00207 LLC.[DN].....V.....C..A....H.V..R TRANSFERRIN_3 PDOC00182 XPS00208 [SN]P.L..HA...F PLANT_GLOBIN PDOC00183 XPS00209 Y[FYW].ED[LIVM]..N......H...P HEMOCYANIN_1 PDOC00184 XPS00210 T..RDP.F[FYW] HEMOCYANIN_2 PDOC00184 XPS00211 [LVF]SGG...[RK][LIVMA].[LIVMF][AG] ATP_BIND_TRANSPORT PDOC00185 XPS00212 [FY]......CC.......C[LFY]......[LIVMFYW] ALBUMIN PDOC00186 XPS00213 [DENST]...[LIVFY].G.W[FYWRH].[LIVM] LIPOCALIN PDOC00187 XPS00214 G.[FYW].[LIVM]....N[FY][DE] FABP PDOC00188 XPS00215 P.[DE].[IVA][RK].[LR][LIVMFY] MITOCH_CARRIER PDOC00189 XPS00216 [LIVMST][DE].[LIVMFA]GR[RK].....G SUGAR_TRANSPORT_1 PDOC00190 XPS00216 [LIVMST][DE].[LIVMFA]GR[RK]....G SUGAR_TRANSPORT_1 PDOC00190 XPS00217 [LIVMF].G[LIVMFA]..G........[LY]..[EQ]......[RK] SUGAR_TRANSPORT_2 PDOC00190 XPS00218 A.GG.IGTGL AMINO_ACID_PERMEASE PDOC00191 XPS00219 FGGL[LIVM]RD[LIVM][RK]RRYP ANION_EXCHANGER_1 PDOC00192 XPS00220 FLISLIFIYETF.KL ANION_EXCHANGER_2 PDOC00192 XPS00221 SG.H.NPAVT MIP_NO26_GLPF PDOC00193 XPS00222 GCGCC..C IGF_BINDING PDOC00194 XPS00223 [TG][STV]........[LIVMF]..R...[DEQNH].......[IFY].......[LIVMF]...[LIVMF]...........[LIVMF]..[LIVMF] ANNEXIN PDOC00195 XPS00224 FLAQQES CLATHRIN_LIGHT_CHAIN PDOC00196 XPS00225 [LIVMFYWA].[^DEHKRSTP][FY][DEQHKY]...[FY].G....[LIVMFCST] CRYSTALLIN_BETAGAMMA PDOC00197 XPS00226 I.[TA]Y[RK].[LM]L[DE] IF PDOC00198 XPS00227 [AG]GGTG[SA]G TUBULIN PDOC00199 XPS00228 ^MR[DE]I TUBULIN_B_AUTOREG PDOC00200 XPS00229 GS..N..H.PGGG MAP2_TAU PDOC00201 XPS00230 Y.Y[DE]..[DE][RK] MAP1B_NEURAXIN PDOC00202 XPS00231 CDYNRD F_ACTIN_CAPPING_BETA PDOC00203 XPS00232 [LIV].[LIV].D.ND[NH].P CADHERIN PDOC00205 XPS00233 G......Y.A.E.GY CUTICLE_LARVAL PDOC00206 XPS00234 SLVGIE GAS_VESICLE_A PDOC00207 XPS00235 FL..T...R...A..Q...L..F GAS_VESICLE_C PDOC00208 XPS00236 C.[LIVM].[LIVM]..[FY]P.D...C NEUROTR_ION_CHANNEL PDOC00209 XPS00237 [LMR][RKHQN]...[NT][LIVMFYW][LIVMFYW][LIV].[SNH][LIV]...[DEG][LIVMFYWA] G_PROTEIN_RECEPTOR PDOC00210 XPS00238 K.....[DN]P.[IV]Y......[FY] OPSIN PDOC00211 XPS00239 D[LIV]Y...YYR RECEPTOR_TYR_KIN_II PDOC00212 XPS00240 C...G.P.P...W..C RECEPTOR_TYR_KIN_III PDOC00213 XPS00241 C[FR]........[STVN]C.W RECEPTOR_CYTOKINES PDOC00214 XPS00241 C[FR].......[STVN]C.W RECEPTOR_CYTOKINES PDOC00214 XPS00242 [FYW][RK].GFF.R INTEGRIN_ALPHA PDOC00215 XPS00243 C.[GNQ]...G.C.C..C.C INTEGRIN_BETA PDOC00216 XPS00243 C.[GNQ].G.C.C..C.C INTEGRIN_BETA PDOC00216 XPS00244 N....P.H..[SAG]...........[SAG].H[SAG][SAG] REACTION_CENTER PDOC00217 XPS00245 APH.CH PHYTOCHROME PDOC00218 XPS00246 QECKCHG INT1 PDOC00219 XPS00247 G.L.[STAG]......[DE]C.F.E HBGF_FGF PDOC00220 XPS00248 C........GC[RK]GID..HWNS.C NGF PDOC00221 XPS00249 CV...RC.GCCN PDGF PDOC00222 XPS00250 [LIVM]..P..[FY]....C.G.C TGF_BETA PDOC00223 XPS00251 Y..YSQV.F TNF PDOC00224 XPS00252 [FY]L.......[CY]AW INTERFERON_ALPHABETA PDOC00225 XPS00253 F.S...P..[FY][LI].T INTERLEUKIN_1 PDOC00226 XPS00254 C.........C......GL..[FY]...L INTERLEUKIN_6 PDOC00227 XPS00255 CFLKRLL INTERLEUKIN_7 PDOC00228 XPS00256 [EQ][LV][NT]F[ST]..W AKH PDOC00229 XPS00257 WA.G[SH][LF]M BOMBESIN PDOC00230 XPS00258 C[STAGDN][STAGDN]..TC[LIVMA]...[LFY]...[LFY] CALCITONIN PDOC00231 XPS00258 C[STAGDN][STAGDN].TC[LIVMA]...[LFY]...[LFY] CALCITONIN PDOC00231 XPS00259 Y.[GD][WH]M[DR]F GASTRIN PDOC00232 XPS00259 Y[GD][WH]M[DR]F GASTRIN PDOC00232 XPS00260 [YH][STA][DEQN][AG].[FY]..[DEQNST].............[LIV] GLUCAGON PDOC00233 XPS00261 C[SA]G.C.[ST] GLYCOPROTEIN_HORMONE PDOC00234 XPS00262 CC...C....[LIMF]...C INSULIN PDOC00235 XPS00263 CFG...DRIG..S..GC NATRIURETIC_PEPTIDE PDOC00236 XPS00264 C[IFY][IFY].NCP.G NEUROHYPOPHYS_HORM PDOC00237 XPS00265 N..TR.RY PANCREATIC_HORMONE PDOC00238 XPS00266 C.[ST]..[LIVMFY].[LIVMSTA]P.....[TAV].......[LIVMFY]......[LIVMFY]..[STA]W SOMATOTROPIN_1 PDOC00239 XPS00267 F[IVFY]G[LM]M[G$] TACHYKININ PDOC00240 XPS00268 W..[KN]..K[KE][LI]E[RKN] CECROPIN PDOC00241 XPS00268 W[KN]..K[KE][LI]E[RKN] CECROPIN PDOC00241 XPS00269 C.......G.C.........CC DEFENSIN PDOC00242 XPS00270 C.C....D..C..[FY]C ENDOTHELIN PDOC00243 XPS00271 CC.....R..[FY]..C THIONIN PDOC00244 XPS00272 CP........[LIVYST].CC SNAKE_TOXIN PDOC00245 XPS00272 CP......[LIVYST].CC SNAKE_TOXIN PDOC00245 XPS00273 CC..CC.PAC.GC ENTEROTOXIN_H_STABLE PDOC00246 XPS00274 T..NW..TNT AEROLYSIN PDOC00247 XPS00275 [LIV]....EA.R[FY][RKQ].[LIV] SHIGA_RICIN PDOC00248 XPS00276 T..W.P[LIVMFY][LIVMFY][LIVMFY]..E CHANNEL_COLICIN PDOC00249 XPS00277 YGG[LIV]T....N STAPH_STREP_TOX_1 PDOC00250 XPS00278 K..[LIV]....[LIV]D...R..L.....[LIV]Y STAPH_STREP_TOX_2 PDOC00250 XPS00279 Y......[FY]GTH[FY] MAC_PERFORIN PDOC00251 XPS00280 F...GC......[FY].....C BPTI_KUNITZ PDOC00252 XPS00281 C.[SAD][STA]C..C BOWMAN_BIRK PDOC00253 XPS00282 C.......C......Y...C...C KAZAL PDOC00254 XPS00282 C.......C......Y...C..C KAZAL PDOC00254 XPS00283 [LIVM].D..G..[LIVM].....Y.[LIVM] SOYBEAN_KUNITZ PDOC00255 XPS00284 [LIVMF].[LIVMFA][DNQ][RKHQ][PS]F[LIVMFY][LIVMFY].[LIVMF] SERPIN PDOC00256 XPS00285 [FYW]PE[LIV][LIV]...[STAV]..A POTATO_INHIBITOR PDOC00257 XPS00286 CP.....CK....C...C.C SQUASH_INHIBITOR PDOC00258 XPS00287 Q[LIVT]V[SAG]G..[LIVMFY].[LIVMFY].[LIVMFY] CYSTATIN PDOC00259 XPS00288 C.C.P.HP TIMP PDOC00260 XPS00289 H.C.[ST]W.S PENTRAXIN PDOC00261 XPS00290 [FY].C.[VA].H IG_MHC PDOC00262 XPS00291 GG.WGQ PRION PDOC00263 XPS00292 R..[LIV]..[FYW][LIV]........[LIV].....[FYW]......D[RK] CYCLIN PDOC00264 XPS00293 S[LIVM]SKI[LIVM][RK]C PCNA PDOC00265 XPS00294 C[^DENQ][LIVM].$ FARNESYLATION PDOC00266 XPS00295 N...K.VKKIK ARRESTIN PDOC00267 XPS00296 AA.EE....GGG CHAPERONIN PDOC00268 XPS00297 [IV]DLGTT.S HSP70_1 PDOC00269 XPS00298 NKEIFL HSP90 PDOC00270 XPS00299 VLRLRGG UBIQUITIN PDOC00271 XPS00300 PI.[FY][LIVM]G.G SRP54 PDOC00272 XPS00301 D....E...[GC].T[IV] EFACTOR_GTP PDOC00273 XPS00302 TGKHGH IF4D_HYPUSINE PDOC00274 XPS00303 LD...[DN]....[FY][EQ].[FY] S100_CABP PDOC00275 XPS00304 GSVGGE SASP PDOC00276 XPS00305 NG.[DE][DE]..C[ST] 11S_SEED_STORAGE PDOC00284 XPS00306 CL[LV]A.A[LV]A CASEIN_ALPHA_BETA PDOC00277 XPS00307 H[LIV]GI[DN][LIV].[ST][LIV].S..T LECTIN_LEGUME_BETA PDOC00278 XPS00308 P[EQ][FYW]V.[LIV]G.[ST] LECTIN_LEGUME_ALPHA PDOC00278 XPS00309 WG.E.RE LECTIN_GALACTOSIDE PDOC00279 XPS00310 [STA]C[LIVM][LIVMFYW]A.[LIVMFYW]...[LIVMFYW]...Y LAMP_1 PDOC00280 XPS00311 G.K..HAGY LAMP_2 PDOC00280 XPS00312 II..VMAG GLYCOPHORIN_A PDOC00281 XPS00313 GQD.VK.....K SVP PDOC00282 XPS00314 AGYGST.T ICE_NUCLEATION PDOC00283 XPS00315 SSSSSSSED[DE]G DEHYDRIN PDOC00285 XPS00316 G.C.TGDC.G...C THAUMATIN PDOC00286 XPS00317 C.[^C][DN]..C.....CC 4_DISULFIDE_CORE PDOC00026 XPS00318 [LIVM]G.[LIVM]GG[AG]T HMG_COA_REDUCTASE_2 PDOC00064 XPS00319 GVEFVCCP A4_EXTRA PDOC00204 XPS00320 NGYENPTYK A4_INTRA PDOC00204 XPS00321 ALKFYASVR RECA PDOC00131 XPS00322 KAPRKQL HISTONE_H3 PDOC00287 XPS00323 M[LIV]G[RKHNQ]KLGEF RIBOSOMAL_S19 PDOC00288 XPS00324 KFGG[ST]S ASPARTOKINASE PDOC00289 XPS00325 ^M[DE]AIKKKM TROPOMYOSIN_MUSCLE PDOC00290 XPS00326 LKEAE.RAE TROPOMYOSIN PDOC00290 XPS00327 [FYW]..LD[LIVM].AK..[FYW] BACTERIAL_OPSIN PDOC00291 XPS00328 HRHRGH..[DE][DE][DE][DE][DE][DE][DE] HCP PDOC00292 XPS00329 DLGGGTFD HSP70_2 PDOC00269 XPS00330 D.[LI]....G.D.[LI].GG...D HEMOLYSIN_CALCIUM PDOC00293 XPS00331 F.DD..GTA.V..AGLL MALIC_ENZYMES PDOC00294 XPS00332 [STAG]G[PAG]H[FY][DN]P SOD_CU_ZN_2 PDOC00082 XPS00333 EG[LIVM][LIVM][LIVM]K...[GC] DNA_LIGASE PDOC00295 XPS00334 W..[LI][SAG].....R........[YW]...[LIM] MYB_2 PDOC00037 XPS00335 VSE.Q..H..G PARATHYROID PDOC00296 XPS00336 FELGS[LIVM]SKTF BETA_LACTAMASE_C PDOC00134 XPS00337 P.STFKI BETA_LACTAMASE_D PDOC00134 XPS00338 C[LIVMFY]..D[LIVMFYST].....[LIVMFY]..[LIVMFY]..C SOMATOTROPIN_2 PDOC00239 END_OF_FILE if test 19585 -ne `wc -c <'prosite.regex'`; then echo shar: \"'prosite.regex'\" unpacked with wrong size! fi # end of 'prosite.regex' fi echo shar: End of shell archive. exit 0