At2g05590.1/PDB

&&&&&&&&&&&&&&&&&&&& BEGIN /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues &&&&&&&&&&&&&&&&&&&&
Successfully read 2 file paths from WYRM_file_paths.txt
generic_input /usr/local/www/html/proteins/workspace/
generic_output /usr/local/www/html/proteins/htdocs/results/
======================================================
Sequence file type = 3
Sequence type = 3
Got here 1
Got here 2
Got here 3
Sequence 1
Got here 3
Got here 4
Got here 3
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Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
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Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g05590-1-1deq_B.txt
======================================================
Assigned types to 263 residues in Sequence 2-05590-1, 17 remain unknown
Assigned types to 256 residues in Sequence 1deq_B, 24 remain unknown
======================================================
Successfully read 576 entries for residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
Read the residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
======================================================
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 195 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 196 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 197 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 198 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 199 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 200 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 201 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 202 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 203 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 204 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 205 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 206 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 214 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 215 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 216 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 217 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 269 All residues are positively and negatively charged
Translated sequence file At2g05590-1-1deq_B.txt into sequence alignment.
======================================================
>1DEQ.pdb Made from 3900 ATOM records in 1DEQ.pdb
NTKCPSGCRMKGLIDEVDQDFTSRINKLRDSLFNYQKNSKDSNTLTKNIV
ELMRGDFAKANNNDNTFKQINEDLRSRIEILRRKVIEQVQRINLLQKNVR
DQLVDMKRLEVDIDIKIRSCKGSCSRALEHKVDLEDYKNQQKQLEQVIAI
NLLPSRDIQYLPILKMSTITGPVPREFKSQKLQDTLVRQERPIRKSIEDL
RNTVDSVSRTSSSTFQYITLLKNMWKGRQNQVQDNENVVNEYSSHLEKHQ
LYIDETVKNNIPTKLRVLRSILENLRSKIQKLESDVSTQMEYCRTPCTVT
CNIPVVSGKECEKIIRNEGETSEMYLIQPEDSSKPYRVYCDMKTEKGGWT
VIQNRQDGSVDFGRKWDPYKQGFGNIATNAEGKKYCGVPGEYWLGNDRIS
QLTNMGPTKLLIEMEDWKGDKVTALYEGFTVQNEANKYQLSVSKYKGTAG
NALIEGASQLVGENRTMTIHNSMFFSTYDRDNDGWKTTDPRKQCSKEDGG
GWWYNRCHAANPNGRYYWGGAYTWDMAKHGTDDGVVWMNWQGSWYSMKKM
SKMIRPYFPEDFLNNYQTSVDKDLRTLEGILYQVENKTSEARELVKAIQI
SYNPDQPSKPNNIESATKNSKSMMEEIMKYETLISTHESTIRFLQEIYNS
NSQKIVNLRDKVVQLEANCQEPCQDTVKIHDVTGRDCQDVANKGAKESGL
YFIRPLKAKQQFLVYCEIDGSGNGWTVFQKRLDGSLDFKKNWIQYKEGFG
HLSPTGNTEFWLGNEKIHLISTQSTIPYVLRIQLEDWNGRTSTADYASFK
VTGENDKYRLTYAYFIGGDAGDAFDGYDFGDDSSDKFFTSHNGMQFSTWD
SDNDKYDGNCAEQDGSGWWMNKCHAGHLNGVYYQGGTYSKTSTPNGYDNG
IIWATWKSRWYSMKKTTMKIIPLNRLAIGENTKCPSGCRMKGLIDEVDQD
FTSRINKLRDSLFNYQKNSKDSNTLTKNIVELMRGDFAKANNNDNTFKQI
NEDLRSRIEILRRKVIEQVQRINLLQKNVRDQLVDMKRLEVDIDIKIRSC
KGSCSRALEHKVDLEDYKNQQKQLEQVIAINLLPSRDIQYLPILKMSTIT
GPVPREFKSQKLQDTLVRQERPIRKSIEDLRNTVDSVSRTSSSTFQYITL
LKNMWKGRQNQVQDNENVVNEYSSHLEKHQLYIDETVKNNIPTKLRVLRS
ILENLRSKIQKLESDVSTQMEYCRTPCTVTCNIPVVSGKECEKIIRNEGE
TSEMYLIQPEDSSKPYRVYCDMKTEKGGWTVIQNRQDGSVDFGRKWDPYK
QGFGNIATNAEGKKYCGVPGEYWLGNDRISQLTNMGPTKLLIEMEDWKGD
KVTALYEGFTVQNEANKYQLSVSKYKGTAGNALIEGASQLVGENRTMTIH
NSMFFSTYDRDNDGWKTTDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGG
AYTWDMAKHGTDDGVVWMNWQGSWYSMKKMSKMIRPYFPEDFLNNYQTSV
DKDLRTLEGILYQVENKTSEARELVKAIQISYNPDQPSKPNNIESATKNS
KSMMEEIMKYETLISTHESTIRFLQEIYNSNSQKIVNLRDKVVQLEANCQ
EPCQDTVKIHDVTGRDCQDVANKGAKESGLYFIRPLKAKQQFLVYCEIDG
SGNGWTVFQKRLDGSLDFKKNWIQYKEGFGHLSPTGNTEFWLGNEKIHLI
STQSTIPYVLRIQLEDWNGRTSTADYASFKVTGENDKYRLTYAYFIGGDA
GDAFDGYDFGDDSSDKFFTSHNGMQFSTWDSDNDKYDGNCAEQDGSGWWM
NKCHAGHLNGVYYQGGTYSKTSTPNGYDNGIIWATWKSRWYSMKKTTMKI
IPLNRLAIGEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
NTKCPSGCRMKGLIDEVDQDFTSRINKLRDSLFNYQKNSKDSNTLTKNIV
ELMRGDFAKANNNDNTFKQINEDLRSRIEILRRKVIEQVQRINLLQKNVR
DQLVDMKRLEVDIDIKIRSCKGSCSRALEHKVDLEDYKNQQKQLEQVIAI
NLLPSRDIQYLPILKMSTITGPVPREFKSQKLQDTLVRQERPIRKSIEDL
RNTVDSVSRTSSSTFQYITLLKNMWKGRQNQVQDNENVVNEYSSHLEKHQ
LYIDETVKNNIPTKLRVLRSILENLRSKIQKLESDVSTQMEYCRTPCTVT
CNIPVVSGKECEKIIRNEGETSEMYLIQPEDSSKPYRVYCDMKTEKGGWT
VIQNRQDGSVDFGRKWDPYKQGFGNIATNAEGKKYCGVPGEYWLGNDRIS
QLTNMGPTKLLIEMEDWKGDKVTALYEGFTVQNEANKYQLSVSKYKGTAG
NALIEGASQLVGENRTMTIHNSMFFSTYDRDNDGWKTTDPRKQCSKEDGG
GWWYNRCHAANPNGRYYWGGAYTWDMAKHGTDDGVVWMNWQGSWYSMKKM
SKMIRPYFPEDFLNNYQTSVDKDLRTLEGILYQVENKTSEARELVKAIQI
SYNPDQPSKPNNIESATKNSKSMMEEIMKYETLISTHESTIRFLQEIYNS
NSQKIVNLRDKVVQLEANCQEPCQDTVKIHDVTGRDCQDVANKGAKESGL
YFIRPLKAKQQFLVYCEIDGSGNGWTVFQKRLDGSLDFKKNWIQYKEGFG
HLSPTGNTEFWLGNEKIHLISTQSTIPYVLRIQLEDWNGRTSTADYASFK
VTGENDKYRLTYAYFIGGDAGDAFDGYDFGDDSSDKFFTSHNGMQFSTWD
SDNDKYDGNCAEQDGSGWWMNKCHAGHLNGVYYQGGTYSKTSTPNGYDNG
IIWATWKSRWYSMKKTTMKIIPLNRLAIGENTKCPSGCRMKGLIDEVDQD
FTSRINKLRDSLFNYQKNSKDSNTLTKNIVELMRGDFAKANNNDNTFKQI
NEDLRSRIEILRRKVIEQVQRINLLQKNVRDQLVDMKRLEVDIDIKIRSC
KGSCSRALEHKVDLEDYKNQQKQLEQVIAINLLPSRDIQYLPILKMSTIT
GPVPREFKSQKLQDTLVRQERPIRKSIEDLRNTVDSVSRTSSSTFQYITL
LKNMWKGRQNQVQDNENVVNEYSSHLEKHQLYIDETVKNNIPTKLRVLRS
ILENLRSKIQKLESDVSTQMEYCRTPCTVTCNIPVVSGKECEKIIRNEGE
TSEMYLIQPEDSSKPYRVYCDMKTEKGGWTVIQNRQDGSVDFGRKWDPYK
QGFGNIATNAEGKKYCGVPGEYWLGNDRISQLTNMGPTKLLIEMEDWKGD
KVTALYEGFTVQNEANKYQLSVSKYKGTAGNALIEGASQLVGENRTMTIH
NSMFFSTYDRDNDGWKTTDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGG
AYTWDMAKHGTDDGVVWMNWQGSWYSMKKMSKMIRPYFPEDFLNNYQTSV
DKDLRTLEGILYQVENKTSEARELVKAIQISYNPDQPSKPNNIESATKNS
KSMMEEIMKYETLISTHESTIRFLQEIYNSNSQKIVNLRDKVVQLEANCQ
EPCQDTVKIHDVTGRDCQDVANKGAKESGLYFIRPLKAKQQFLVYCEIDG
SGNGWTVFQKRLDGSLDFKKNWIQYKEGFGHLSPTGNTEFWLGNEKIHLI
STQSTIPYVLRIQLEDWNGRTSTADYASFKVTGENDKYRLTYAYFIGGDA
GDAFDGYDFGDDSSDKFFTSHNGMQFSTWDSDNDKYDGNCAEQDGSGWWM
NKCHAGHLNGVYYQGGTYSKTSTPNGYDNGIIWATWKSRWYSMKKTTMKI
IPLNRLAIGEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
======================================================
Best alignment:
1DEQ.pdb 926 LAIGENTKCPSGCRMKGLIDEVDQDFTSRINKLRD 960
 ++IGE+ C R+ ++E D+ + K+R+
2-05590-1 95 ISIGEDKDC--ELRVSAKVEESGNDYFDGVKKMRE 127
======================================================
Highlighted IDENTICAL residue LEU 57 index1 943 path 110 %Seq 100.00
Highlighted IDENTICAL residue ASP 59 index1 945 path 112 %Seq 100.00
Highlighted 2 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g05590-1-1deq_B.txt.1DEQ.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g05590-1-1deq_B.txt PIR amino_acid 1DEQ.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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