At2g01190.1/Structure

&&&&&&&&&&&&&&&&&&&& 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 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 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 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 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/At2g01190_2cu1_A.pir.txt

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Assigned types to 720 residues in Sequence 2-01190, 2 remain unknown Assigned types to 96 residues in Sequence 2cu1_A, 626 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 98 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 99 All residues are positively and negatively charged

Translated sequence file At2g01190_2cu1_A.pir.txt into sequence alignment.

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>2CU1.pdb Made from 1612 ATOM records in 2CU1.pdb GSSGSSGDVRVKFEHRGEKRILQFPRPVKLEDLRSKAKIAFGQSMDLHYT NNELVIPLTTQDDLDKAVELLDRSIHMKSLKILLVINGSTQATNLEPSGP SSG

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Best alignment: 2CU1.pdb   17  GEKRILQFPRPVKLEDL--RSKAKIAFGQSMDLHY--TNNEL--VIPLTT    60 G+ RI+  R   L  L  R    +  G+S  L Y   + +L  +I +TT 2-01190    99  GDTRIVVVDRNSSLPSLIARLSNTLLDGRSFTLKYQLPSEDLDSLISVTT   148

2CU1.pdb   61  QDDLDKAVELLDRSI    75 +DLD +E  DR+I 2-01190   149  DEDLDNMIEEYDRTI   163

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Highlighted IDENTICAL residue GLY  17  index1   17  path  101  %Seq 100.00 Highlighted IDENTICAL residue ARG  20  index1   20  path  104  %Seq 100.00 Highlighted IDENTICAL residue ILE  21  index1   21  path  105  %Seq 100.00 Highlighted IDENTICAL residue ARG  26  index1   26  path  110  %Seq 100.00 Highlighted IDENTICAL residue LEU  30  index1   30  path  114  %Seq 100.00 Highlighted IDENTICAL residue LEU  33  index1   33  path  117  %Seq 100.00 Highlighted IDENTICAL residue ALA  40  index1   40  path  126  %Seq  50.00 Highlighted IDENTICAL residue PHE  41  index1   41  path  127  %Seq  50.00 Highlighted IDENTICAL residue GLY  42  index1   42  path  128  %Seq 100.00 Highlighted IDENTICAL residue SER  44  index1   44  path  130  %Seq 100.00 Highlighted IDENTICAL residue LEU  47  index1   47  path  133  %Seq 100.00 Highlighted IDENTICAL residue TYR  49  index1   49  path  135  %Seq 100.00 Highlighted IDENTICAL residue THR  50  index1   50  path  138  %Seq  50.00 Highlighted IDENTICAL residue LEU  54  index1   54  path  142  %Seq 100.00 Highlighted IDENTICAL residue ILE  56  index1   56  path  146  %Seq 100.00 Highlighted IDENTICAL residue THR  59  index1   59  path  149  %Seq 100.00 Highlighted IDENTICAL residue THR  60  index1   60  path  150  %Seq 100.00 Highlighted IDENTICAL residue ASP  63  index1   63  path  153  %Seq 100.00 Highlighted IDENTICAL residue LEU  64  index1   64  path  154  %Seq 100.00 Highlighted IDENTICAL residue ASP  65  index1   65  path  155  %Seq 100.00 Highlighted IDENTICAL residue GLU  69  index1   69  path  159  %Seq 100.00 Highlighted IDENTICAL residue ASP  72  index1   72  path  162  %Seq 100.00 Highlighted IDENTICAL residue ARG  73  index1   73  path  163  %Seq 100.00 Highlighted IDENTICAL residue SER  74  index1   74  path  164  %Seq  50.00 Highlighted IDENTICAL residue ILE  75  index1   75  path  165  %Seq  50.00 Highlighted 25 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01190_2cu1_A.pir.txt.2CU1.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01190_2cu1_A.pir.txt PIR amino_acid 2CU1.pdb A 100.0 BLOSUM62.dat

completed successfully.

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