At2g06555.1/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/At2g06555-2haqt_C.pir.txt

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Assigned types to 159 residues in Sequence 2-06555, 9 remain unknown Assigned types to 125 residues in Sequence 2aqt_C, 43 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 52 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 53 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 54 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 55 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 56 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 136 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 137 All residues are positively and negatively charged

Translated sequence file At2g06555-2haqt_C.pir.txt into sequence alignment.

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>2AQT.pdb Made from 3456 ATOM records in 2AQT.pdb ASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLHGFHIH ENPSCEPKEQEGQLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDLPALTV LHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGGGPRMA CGVIKASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLH GFHIHENPSCEPKEQEGQLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDL PALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGG GPRMACGVIKASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGL SEGLHGFHIHENPSCEPKEQEGQLTAGLGAGGHWDPKGAKQHGYPWQDDA HLGDLPALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPA PLGGGGPRMACGVIK

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Best alignment: 2AQT.pdb  128  IHTGGDNHSDHPAPLGGGGPRMACGVIKASIEV   160 +   + +SD        G    CGV+     V 2-06555    126  VFVSENEYSDFLLEASDVGKERRCGVLMLECRV   158

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Highlighted IDENTICAL residue SER 167  index1  136  path  143  %Seq 100.00 Highlighted IDENTICAL residue ASP 168  index1  137  path  144  %Seq 100.00 Highlighted IDENTICAL residue GLY 177  index1  146  path  153  %Seq 100.00 Highlighted IDENTICAL residue CYS 182  index1  151  path  158  %Seq 100.00 Highlighted IDENTICAL residue GLY 183  index1  152  path  159  %Seq 100.00 Highlighted IDENTICAL residue VAL 184  index1  153  path  160  %Seq 100.00 Highlighted IDENTICAL residue LYS 186  index1  155  path  162  %Seq  50.00 Highlighted IDENTICAL residue ALA  32  index1  156  path  163  %Seq  50.00 Highlighted IDENTICAL residue SER  33  index1  157  path  164  %Seq  50.00 Highlighted IDENTICAL residue ILE  34  index1  158  path  165  %Seq  50.00 Highlighted IDENTICAL residue GLU  35  index1  159  path  166  %Seq  50.00 Highlighted IDENTICAL residue VAL  36  index1  160  path  167  %Seq  50.00 Highlighted 12 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g06555-2haqt_C.pir.txt.2AQT.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g06555-2haqt_C.pir.txt PIR amino_acid 2AQT.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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