At2g13680.1/PDB N-terminus

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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

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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g13680-N-2ix0A.pir.txt

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Assigned types to 980 residues in Sequence 2-13680-N, 17 remain unknown
Assigned types to 233 residues in Sequence 2ixoA, 764 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 At2g13680-N-2ix0A.pir.txt into sequence alignment.

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>2IXO.pdb  Made from 5049 ATOM records in 2IXO.pdb
SLDRVDWPHATFSTPVKRIFDTQTTLDFQSSLAIHRIKYHLHKYTTLISH
CSDPDPHATASSIAMVNGLMGVLDKLAHLIDETPPLPGYGNLACREWHHK
LDERLPQWLQEMLPSEYHEVVPELQYYLGNSFGSSTRLDYGTGHELSFMA
TVAALDMLGMFPHHRGADVFLLFNKYYTIMRRLILTYTLEPAGLDDHFHL
VYILGSSQWQLLDAQAPLQPREILDKSLVREYKDTNFYCQGINFINEVKM
GPFEEHSPILYDIAVTVPRWSKVCKGLLKMYSVEVEKKFPVVQHFWFGTG
FFPWVNISLDRVDWPHATFSTPVKRIFDTQTTLDFQSSLAIHRIKYHLHK
YTTLISHCSDPDPHATASSIAMVNGLMGVLDKLAHLIDETPPLPGPRRYG
NLACREWHHKLDERLPQWLQEMLPSEYHEVVPELQYYLGNSFGSSTRLDY
GTGHELSFMATVAALDMLGMFPHHRGADVFLLFNKYYTIMRRLILTYTLE
PAGSGLDDHFHLVYILGSSQWQLLDAQAPLQPREILDKSLVREYKDTNFY
CQGINFINEVKMGPFEEHSPILYDIAVTVPRWSKVCKGLLKMYSVEVEKK
FPVVQHFWFGTGFFPWVNI

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Best alignment:
2IXO.pdb      1  SLDRVDWPHATF    12
                 +LD +DW  A F
2-13680-N   237  NLDLLDWLRAMF   248

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Highlighted IDENTICAL residue SER    2  index1    1  path  237  %Seq  50.00
Highlighted IDENTICAL residue LEU    3  index1    2  path  238  %Seq  50.00
Highlighted IDENTICAL residue ASP    4  index1    3  path  239  %Seq  50.00
Highlighted IDENTICAL residue ARG    5  index1    4  path  240  %Seq  50.00
Highlighted IDENTICAL residue VAL    6  index1    5  path  241  %Seq  50.00
Highlighted IDENTICAL residue ASP    7  index1    6  path  242  %Seq  50.00
Highlighted IDENTICAL residue TRP    8  index1    7  path  243  %Seq  50.00
Highlighted IDENTICAL residue PRO    9  index1    8  path  244  %Seq  50.00
Highlighted IDENTICAL residue HIS   10  index1    9  path  245  %Seq  50.00
Highlighted IDENTICAL residue ALA   11  index1   10  path  246  %Seq  50.00
Highlighted IDENTICAL residue THR   12  index1   11  path  247  %Seq  50.00
Highlighted IDENTICAL residue PHE   13  index1   12  path  248  %Seq  50.00
Highlighted 12 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13680-N-2ix0A.pir.txt.2IXO.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13680-N-2ix0A.pir.txt PIR amino_acid 2IXO.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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