At2g10285.1/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 Sequence 2 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/At2g10285-1nb4_A.pir.txt

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Assigned types to 116 residues in Sequence 2-10285, 15 remain unknown Assigned types to 103 residues in Sequence 1nb4_A, 28 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 87 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 88 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 89 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 90 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 109 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 110 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 111 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 112 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 116 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 117 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 118 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 119 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 120 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 121 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 122 All residues are positively and negatively charged

Translated sequence file At2g10285-1nb4_A.pir.txt into sequence alignment.

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>1NB4.pdb Made from 8771 ATOM records in 1NB4.pdb SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQK KVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSK FGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPE KGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQR VEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEAR QAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAT AACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPP GDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETA RHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGA CYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTW RHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGW FVAGYSGGDIYHSLSRSMSYTWTGALITPCAAEESKLPINPLSNSLLRHH NMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLS IEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPI DTTIMAKSEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQ AVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIR VEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGV LTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAA ALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYL TRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILL AQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINR VASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKL KLTPIPAASQLDLSGWFVAGYSGGDIYHSLS

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Best alignment: 1NB4.pdb  452  YSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWR   501 YSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWR 1nb4_A      1  YSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWR    50

1NB4.pdb  502  HRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWF   551 HRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWF 1nb4_A     51  HRARSVRAKLLSQGGRAATCGRYXXXXAVRTKLKLTPIPAASQLDXXXXF   100

1NB4.pdb  552  VAGYSGGDIYHSLSRS   567 VAGYSGGDIYHSLSR+ 1nb4_A    101  VAXXXXXXXYHSLSRA   116

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Highlighted IDENTICAL residue SER 453  index1  453  path    7  %Seq 100.00 Highlighted IDENTICAL residue LEU 457  index1  457  path   11  %Seq 100.00 Highlighted IDENTICAL residue PRO 460  index1  460  path   14  %Seq 100.00 Highlighted IDENTICAL residue ARG 465  index1  465  path   19  %Seq 100.00 Highlighted IDENTICAL residue ALA 471  index1  471  path   25  %Seq 100.00 Highlighted IDENTICAL residue LEU 474  index1  474  path   36  %Seq 100.00 Highlighted IDENTICAL residue GLY 480  index1  480  path   42  %Seq 100.00 Highlighted IDENTICAL residue PRO 496  index1  496  path   58  %Seq 100.00 Highlighted IDENTICAL residue ARG 508  index1  508  path   70  %Seq 100.00 Highlighted IDENTICAL residue LYS 510  index1  510  path   72  %Seq 100.00 Highlighted IDENTICAL residue LEU 545  index1  545  path  107  %Seq 100.00 Highlighted IDENTICAL residue ASP 546  index1  546  path  108  %Seq 100.00 Highlighted IDENTICAL residue PHE 551  index1  551  path  113  %Seq 100.00 Highlighted IDENTICAL residue ALA 553  index1  553  path  115  %Seq 100.00 Highlighted IDENTICAL residue HIS 562  index1  562  path  124  %Seq 100.00 Highlighted IDENTICAL residue SER 563  index1  563  path  125  %Seq 100.00 Highlighted IDENTICAL residue ARG 566  index1  566  path  128  %Seq 100.00 Highlighted 17 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10285-1nb4_A.pir.txt.1NB4.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10285-1nb4_A.pir.txt PIR amino_acid 1NB4.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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