At2g13550.1/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 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/At2g13550-1bfp_.pir.txt

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Assigned types to 181 residues in Sequence 2-13550, 8 remain unknown Assigned types to 158 residues in Sequence 1bfp_, 31 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 46 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 47 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 59 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 60 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

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 100 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 101 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 102 All residues are positively and negatively charged

Translated sequence file At2g13550-1bfp_.pir.txt into sequence alignment.

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>1BFP.pdb Made from 1765 ATOM records in 1BFP.pdb MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTT GKLPVPWPTLVTTFVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDD GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYIM ADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLST QSALSKDPNEKRDHMVLLEFVTAAGI

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Best alignment: 1BFP.pdb  173  VQLADHYQQNTPIGDGPVLLPDNHY   197 + L  +Q NT  G  P   P++H+ 2-13550    13  MHLPTQFQPNTRTGRQPKSPPNSHH    37

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Highlighted IDENTICAL residue LEU 178  index1  175  path   15  %Seq 100.00 Highlighted IDENTICAL residue ASP 180  index1  177  path   17  %Seq 100.00 Highlighted IDENTICAL residue TYR 182  index1  179  path   19  %Seq 100.00 Highlighted IDENTICAL residue GLN 183  index1  180  path   20  %Seq  50.00 Highlighted IDENTICAL residue GLY 189  index1  186  path   26  %Seq  50.00 Highlighted IDENTICAL residue ASP 190  index1  187  path   27  %Seq 100.00 Highlighted IDENTICAL residue PRO 192  index1  189  path   29  %Seq 100.00 Highlighted 7 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13550-1bfp_.pir.txt.1BFP.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13550-1bfp_.pir.txt PIR amino_acid 1BFP.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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