At2g01180.1/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/At2g01180_2a96_A.pir.txt

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Assigned types to 302 residues in Sequence 2-01180-1, 0 remain unknown Assigned types to 161 residues in Sequence 2a96_A, 141 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 At2g01180_2a96_A.pir.txt into sequence alignment.

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>2A96.pdb Made from 6960 ATOM records in 2A96.pdb QPFHSPEESVNSQFYLPPPPGNDDPAFRYDKEAYFKGYAIKGSPRWKQAA EDADISVENIARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAK KYYMRTRPFVLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQAR PERAQELARRGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQ KSLAKVREELNDKNNLLMQPFHSPEESVNSQFYLPPPPGNDDPAFRYDKE AYFKGYAIKGSPRWKQAAEDADISVENIARIFSPVVGAKISPKDTPETWN MLQNLLKVGGYYATASAKKYYMRTRPFVLFNHSTCRPEDENTLRKDGSYP SGHTAYSTLLALVLSQARPERAQELARRGWEFGQSRVICGAHWQSDVDAG RYVGAVEFARLQTIPAFQKSLAKVREELNDKNNLLSQPFHSPEESVNSQF YLPPPPGNDDPAFRYDKEAYFKGYAIKGSPRWKQAAEDADISVENIARIF SPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAKKYYMRTRPFVLFNH STCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQARPERAQELARRGWEF GQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREELNDKN NLLMQPFHSPEESVNSQFYLPPPPGNDDPAFRYDKEAYFKGYAIKGSPRW KQAAEDADISVENIARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYAT ASAKKYYMRTRPFVLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVL SQARPERAQELARRGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTI PAFQKSLAKVREELNDKNNLLS

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Best alignment: 2A96.pdb  278  IARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAKKYYMRTRPF   327 IARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAKKYYMRTRPF 2a96_A      1  IARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYATASAKKYYMRTRPF    50

2A96.pdb  328  VLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQARPERAQELAR   377 VLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQARPERAQELAR 2a96_A     51  VLFNHSTCRPEDENTLRKDGSYPSGHTAYSTLLALVLSQARPERAQELAR   100

2A96.pdb  378  RGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREE   427 RGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREE 2a96_A    101  RGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREE   150

2A96.pdb  428  LNDKNNLLSQ   437 LNDKNNLLS+ 2a96_A    151  LNDKNNLLSK   160

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Highlighted IDENTICAL residue ILE  86  index1  281  path   81  %Seq 100.00 Highlighted IDENTICAL residue LYS  94  index1  289  path   89  %Seq 100.00 Highlighted IDENTICAL residue THR 119  index1  314  path  114  %Seq 100.00 Highlighted IDENTICAL residue SER 121  index1  316  path  116  %Seq 100.00 Highlighted IDENTICAL residue LYS 123  index1  318  path  118  %Seq 100.00 Highlighted IDENTICAL residue ARG 128  index1  323  path  123  %Seq 100.00 Highlighted IDENTICAL residue ARG 130  index1  325  path  125  %Seq 100.00 Highlighted IDENTICAL residue PRO 131  index1  326  path  126  %Seq 100.00 Highlighted IDENTICAL residue CYS 140  index1  335  path  148  %Seq 100.00 Highlighted IDENTICAL residue SER 153  index1  348  path  161  %Seq 100.00 Highlighted IDENTICAL residue PRO 155  index1  350  path  163  %Seq 100.00 Highlighted IDENTICAL residue SER 156  index1  351  path  164  %Seq 100.00 Highlighted IDENTICAL residue GLY 157  index1  352  path  165  %Seq 100.00 Highlighted IDENTICAL residue HIS 158  index1  353  path  166  %Seq 100.00 Highlighted IDENTICAL residue THR 159  index1  354  path  167  %Seq 100.00 Highlighted IDENTICAL residue SER 162  index1  357  path  170  %Seq 100.00 Highlighted IDENTICAL residue LEU 169  index1  364  path  177  %Seq 100.00 Highlighted IDENTICAL residue SER 170  index1  365  path  178  %Seq 100.00 Highlighted IDENTICAL residue GLY 188  index1  383  path  211  %Seq 100.00 Highlighted IDENTICAL residue SER 190  index1  385  path  213  %Seq 100.00 Highlighted IDENTICAL residue ARG 191  index1  386  path  214  %Seq 100.00 Highlighted IDENTICAL residue VAL 192  index1  387  path  215  %Seq 100.00 Highlighted IDENTICAL residue HIS 197  index1  392  path  220  %Seq 100.00 Highlighted IDENTICAL residue ASP 201  index1  396  path  224  %Seq 100.00 Highlighted IDENTICAL residue VAL 202  index1  397  path  225  %Seq 100.00 Highlighted IDENTICAL residue ALA 204  index1  399  path  227  %Seq 100.00 Highlighted IDENTICAL residue GLY 205  index1  400  path  228  %Seq 100.00 Highlighted IDENTICAL residue GLY 209  index1  404  path  232  %Seq 100.00 Highlighted IDENTICAL residue ALA 214  index1  409  path  237  %Seq 100.00 Highlighted 29 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01180_2a96_A.pir.txt.2A96.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01180_2a96_A.pir.txt PIR amino_acid 2A96.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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