At2g10390.1/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/
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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
Sequence 2
Got here 3
Got here 4
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/At2g10390-1g3jA.pir.txt
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Assigned types to 194 residues in Sequence 2-10390, 11 remain unknown
Assigned types to 174 residues in Sequence 1g3jA, 31 remain unknown
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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
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Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 35 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 36 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 37 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 158 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 159 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 160 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 161 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 162 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 163 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 164 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 165 All residues are positively and negatively charged
Translated sequence file At2g10390-1g3jA.pir.txt into sequence alignment.
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>1G3J.pdb Made from 7531 ATOM records in 1G3J.pdb
HAVVNLINYQDDAELATRAIPELTKLLNDEDQVVVNKAAVMVHQLSKKEA
SRHAIMRSPQMVSAIVRTMQNTNDVETARCTAGTLHNLSHHREGLLAIFK
SGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLAGGLQKMV
ALLNKTNVKFLAITTDCLQILAYGNQESKLIILASGGPQALVNIMRTYTY
EKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLW
TLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYK
NKMMVCQVGGIEALVRTVLRAGDREDITEPAICALRHLTSRHQEAEMAQN
AVRLHYGLPVVVKLLHPPSHWPLIKATVGLIRNLALCPANHAPLREQGAI
PRLVQLLVRAHQDTQRRFVEGVRMEEIVEGCTGALHILARDVHNRIVIRG
LNTIPLFVQLLYSPIENIQRVAAGVLCELAQDKEAAEAIEAEGATAPLTE
LLHSRNEGVATYAAAVLFRMSEPQLNSGGGDELGANDELIRFKDEGEQEE
DLADVKSSLVNESHHREGLLAIFKSGGIPALVKMLGSPVDSVLFYAITTL
HNLLLHQEGAKMAVRLAGGLQKMVALLNKTNVKFLAITTDCLQILAYGNQ
ESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVE
AGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLL
GSDDINVVTCAAGILSNLTCNNYKNKMMVCQVGGIEALVRTVLRAGDRED
ITEPAICALRHLTSRHQEAEMAQNAVRLHYGLPVVVKLLHPPSHWPLIKA
TVGLIRNLALCPANHAPLREQGAIPRLVQLLVRAHQDTQRRTSMGQQFVE
GVRMEEIVEGCTGALHILARDVHNRIVIRGLNTIPLFVQLLYSPIENIQR
VAAGVLCELAQDKEAAEAIEAEGATAPLTELLHSRNEGVATYAAAVLFRM
SEPQLNSGGGDELGANDELIRFKDEDLADVKSSLVN
======================================================
Best alignment:
1G3J.pdb 1 HAVVNLINYQDDAELATRAIPE 22
 H++ IN Q ++A IPE
2-10390 9 HSITQPINTQ--RKIARLYIPE 28
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Highlighted IDENTICAL residue HIS 134 index1 1 path 9 %Seq 100.00
Highlighted IDENTICAL residue LEU 148 index1 15 path 21 %Seq 100.00
Highlighted 2 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10390-1g3jA.pir.txt.1G3J.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10390-1g3jA.pir.txt PIR amino_acid 1G3J.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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