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At2g05590.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
Got here 3
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Got here 3
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Got here 3
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Got here 3
Got here 4
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.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@


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