At2g01400.1/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
Got here 4
Got here 3
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01400_1u00_A.pir.txt
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Assigned types to 146 residues in Sequence 2-01400, 26 remain unknown
Assigned types to 123 residues in Sequence 1u00_A, 49 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
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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 38 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 39 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 40 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 41 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 71 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 72 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 73 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 74 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 75 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 76 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 77 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 78 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 79 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 80 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 113 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 114 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 115 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 116 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 117 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 118 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 119 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 120 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 121 All residues are positively and negatively charged
Translated sequence file At2g01400_1u00_A.pir.txt into sequence alignment.
======================================================
>1U00.pdb Made from 1738 ATOM records in 1U00.pdb
MDVIPLSLGLETMGGLVEKVIPRNTTIPVARAQDFTTFKDGQTAMSIHVM
QGERELVQDCRSLARFALRGIPALPAGGAHIRVTFQVDADGLLSVTAMEK
STGVEASIQVKPSYGLTDSEIASMIKDSMSYAEQDVKARMLAEQKVEAAR
VLESLHGALAADAALLSAAERQVIDDAAAHLSEVAQGDDVDAIEQAIKNV
DKQTQDFAARRMDQSVRRALKGHSVDEELPPVKIHC
======================================================
Best alignment:
1U00.pdb 213 DQSVRRALKGHSVDEELPP 231
 +Q + + L+ V LPP
2-01400 118 NQKIEKELEKEEVFPLLPP 136
======================================================
Highlighted IDENTICAL residue ARG 605 index1 217 path 148 %Seq 100.00
Highlighted IDENTICAL residue LYS 609 index1 221 path 152 %Seq 100.00
Highlighted IDENTICAL residue VAL 613 index1 225 path 156 %Seq 100.00
Highlighted IDENTICAL residue GLU 615 index1 227 path 158 %Seq 50.00
Highlighted IDENTICAL residue GLU 98 index1 228 path 159 %Seq 50.00
Highlighted IDENTICAL residue LEU 99 index1 229 path 160 %Seq 50.00
Highlighted IDENTICAL residue PRO 100 index1 230 path 161 %Seq 50.00
Highlighted IDENTICAL residue PRO 101 index1 231 path 162 %Seq 50.00
Highlighted 8 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01400_1u00_A.pir.txt.1U00.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01400_1u00_A.pir.txt PIR amino_acid 1U00.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@