At2g02540.1/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 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 Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02540-1wh5_A.pir.txt

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Assigned types to 310 residues in Sequence 2-02540, 0 remain unknown Assigned types to 78 residues in Sequence 1wh5_A, 232 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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Translated sequence file At2g02540-1wh5_A.pir.txt into sequence alignment.

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>1WH5.pdb Made from 1242 ATOM records in 1WH5.pdb GSSGSSGSSAEAGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEV IQRFCQETGVPRQVLKVWLHNNKHSGPSSG

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Best alignment: 1WH5.pdb   13  GGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPR    62 G  +KR RTKFT EQKE+M++ AER+GW+IQRQ++ V+Q+ CQE G+ R 2-02540    218  GHNQKKRFRTKFTQEQKEKMISFAERVGWKIQRQEESVVQQLCQEIGIRR   267

1WH5.pdb   63  QVLKVWLHNNKHS    75 +VLKVW+HNNK + 2-02540   268  RVLKVWMHNNKQN   280

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Highlighted IDENTICAL residue GLY  13  index1   13  path  218  %Seq 100.00 Highlighted IDENTICAL residue LYS  18  index1   18  path  223  %Seq 100.00 Highlighted IDENTICAL residue ARG  19  index1   19  path  224  %Seq 100.00 Highlighted IDENTICAL residue ARG  21  index1   21  path  226  %Seq 100.00 Highlighted IDENTICAL residue THR  22  index1   22  path  227  %Seq 100.00 Highlighted IDENTICAL residue LYS  23  index1   23  path  228  %Seq 100.00 Highlighted IDENTICAL residue PHE  24  index1   24  path  229  %Seq 100.00 Highlighted IDENTICAL residue THR  25  index1   25  path  230  %Seq 100.00 Highlighted IDENTICAL residue GLU  27  index1   27  path  232  %Seq 100.00 Highlighted IDENTICAL residue GLN  28  index1   28  path  233  %Seq 100.00 Highlighted IDENTICAL residue LYS  29  index1   29  path  234  %Seq 100.00 Highlighted IDENTICAL residue GLU  30  index1   30  path  235  %Seq 100.00 Highlighted IDENTICAL residue MET  32  index1   32  path  237  %Seq 100.00 Highlighted IDENTICAL residue ALA  36  index1   36  path  241  %Seq 100.00 Highlighted IDENTICAL residue GLU  37  index1   37  path  242  %Seq 100.00 Highlighted IDENTICAL residue ARG  38  index1   38  path  243  %Seq 100.00 Highlighted IDENTICAL residue GLY  40  index1   40  path  245  %Seq 100.00 Highlighted IDENTICAL residue TRP  41  index1   41  path  246  %Seq 100.00 Highlighted IDENTICAL residue ILE  43  index1   43  path  248  %Seq 100.00 Highlighted IDENTICAL residue GLN  44  index1   44  path  249  %Seq 100.00 Highlighted IDENTICAL residue ARG  45  index1   45  path  250  %Seq 100.00 Highlighted IDENTICAL residue GLN  46  index1   46  path  251  %Seq 100.00 Highlighted IDENTICAL residue VAL  50  index1   50  path  255  %Seq 100.00 Highlighted IDENTICAL residue GLN  52  index1   52  path  257  %Seq 100.00 Highlighted IDENTICAL residue CYS  55  index1   55  path  260  %Seq 100.00 Highlighted IDENTICAL residue GLN  56  index1   56  path  261  %Seq 100.00 Highlighted IDENTICAL residue GLU  57  index1   57  path  262  %Seq 100.00 Highlighted IDENTICAL residue GLY  59  index1   59  path  264  %Seq 100.00 Highlighted IDENTICAL residue ARG  62  index1   62  path  267  %Seq 100.00 Highlighted IDENTICAL residue VAL  64  index1   64  path  269  %Seq 100.00 Highlighted IDENTICAL residue LEU  65  index1   65  path  270  %Seq 100.00 Highlighted IDENTICAL residue LYS  66  index1   66  path  271  %Seq 100.00 Highlighted IDENTICAL residue VAL  67  index1   67  path  272  %Seq 100.00 Highlighted IDENTICAL residue TRP  68  index1   68  path  273  %Seq 100.00 Highlighted IDENTICAL residue HIS  70  index1   70  path  275  %Seq 100.00 Highlighted IDENTICAL residue ASN  71  index1   71  path  276  %Seq 100.00 Highlighted IDENTICAL residue ASN  72  index1   72  path  277  %Seq 100.00 Highlighted IDENTICAL residue LYS  73  index1   73  path  278  %Seq 100.00 Highlighted 38 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02540-1wh5_A.pir.txt.1WH5.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02540-1wh5_A.pir.txt PIR amino_acid 1WH5.pdb A 100.0 BLOSUM62.dat

completed successfully.

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