At2g09865.1/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 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 Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g09865-1jas_A.pir.txt

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Assigned types to 339 residues in Sequence 2-09865, 17 remain unknown Assigned types to 108 residues in Sequence 1jas_A, 248 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 261 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 262 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 263 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 264 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 265 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 266 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 281 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 282 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 283 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 297 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 310 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 311 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 312 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 313 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 314 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 315 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 316 All residues are positively and negatively charged

Translated sequence file At2g09865-1jas_A.pir.txt into sequence alignment.

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>1JAS.pdb Made from 2391 ATOM records in 1JAS.pdb MSTPARRRLMRDFKRLQEDPPVGVSGAPSENNIMQWNAVIFGPEGTPFED GTFKLVIEFSEEYPNKPPTVRFLSKMFHPNVYADGSICLDILQNRWSPTY DVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWN DS

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Best alignment: 1JAS.pdb  133  NKREYEKRVSAIV   145 KR+ KRV +++ 2-09865   192  RKRKKSKRVGSLL   204

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Highlighted IDENTICAL residue ASN 133  index1  133  path  192  %Seq  50.00 Highlighted IDENTICAL residue LYS 134  index1  134  path  193  %Seq  50.00 Highlighted IDENTICAL residue ARG 135  index1  135  path  194  %Seq  50.00 Highlighted IDENTICAL residue GLU 136  index1  136  path  195  %Seq  50.00 Highlighted IDENTICAL residue TYR 137  index1  137  path  196  %Seq  50.00 Highlighted IDENTICAL residue GLU 138  index1  138  path  197  %Seq  50.00 Highlighted IDENTICAL residue LYS 139  index1  139  path  198  %Seq  50.00 Highlighted IDENTICAL residue ARG 140  index1  140  path  199  %Seq  50.00 Highlighted IDENTICAL residue VAL 141  index1  141  path  200  %Seq  50.00 Highlighted IDENTICAL residue SER 142  index1  142  path  201  %Seq  50.00 Highlighted IDENTICAL residue ALA 143  index1  143  path  202  %Seq  50.00 Highlighted IDENTICAL residue ILE 144  index1  144  path  203  %Seq  50.00 Highlighted IDENTICAL residue VAL 145  index1  145  path  204  %Seq  50.00 Highlighted 13 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g09865-1jas_A.pir.txt.1JAS.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g09865-1jas_A.pir.txt PIR amino_acid 1JAS.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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