At2g11910.1/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/

=
=========================================

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/At2g11910-1ux6A.pir.txt

=
=========================================

Assigned types to 168 residues in Sequence 2-11910, 17 remain unknown Assigned types to 91 residues in Sequence 1ux6A, 94 remain unknown

=
=========================================

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

=
=========================================

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 79 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 80 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 81 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 82 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 83 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 84 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 95 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 113 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 114 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 115 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 155 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 156 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 157 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 158 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 159 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 160 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 161 All residues are positively and negatively charged

Translated sequence file At2g11910-1ux6A.pir.txt into sequence alignment.

=
=========================================

>1UX6.pdb Made from 2667 ATOM records in 1UX6.pdb ALADNCPLEHNPDQLDSDSDRIGDTCDNNQDIDEDGHQNNLDNCPYVPNA NQADHDKDGKGDACDHDDDNDGIPDDKDNCRLVPNPDQKDSDGDGRGDAC KDDFDHDSVPDIDDICPENVDISETDFRRFQMIPLDPKGTSQNDPNWVVE LVQTVNSDPGLAVGYDEFNAVDFSGTFFINTERDDDYAGFVFGYQSSSRF YVVMWKQVTQSYWDTNPTRAQGYSGLSVKVVKSTTGPGEHLRNALWHTGN TPGQVRTLWHDPRHIGWKDFTAYRWRLSHRPKTGFIRVVMYEGKKIMADS GPIYDKTYAGGRLGLFVFSQEMVFFSDLKYECRDP

=
=========================================

Best alignment: 1UX6.pdb    8  LEHNPDQLDSDSDRIGDTCDNNQDIDEDGHQNNLDNCPYVPNANQADHDK    57 +E N D DSD D   +  D + D ++D +  +           +AD + 2-11910    66  IEENKDASDSDDDDDDEDADEDDDDEDDANDEDFSGGEGDEGEEEADPED   115

1UX6.pdb   58  D-GKGDACDHDDDNDGIPDDKDNCRLVPNPDQKDSDGD    94 D    G G   + DDD +G  DD+D        D  + D D 2-11910    116  DPVTNGGGGSDDEDDDDEEGDNDDEDEDNEDEEEDDDEEDDD   157

=
=========================================

Highlighted IDENTICAL residue GLU 821  index1    9  path   67  %Seq 100.00 Highlighted IDENTICAL residue ASN 823  index1   11  path   69  %Seq 100.00 Highlighted IDENTICAL residue ASP 825  index1   13  path   71  %Seq 100.00 Highlighted IDENTICAL residue ASP 828  index1   16  path   74  %Seq 100.00 Highlighted IDENTICAL residue SER 829  index1   17  path   75  %Seq 100.00 Highlighted IDENTICAL residue ASP 830  index1   18  path   76  %Seq 100.00 Highlighted IDENTICAL residue ASP 832  index1   20  path   78  %Seq 100.00 Highlighted IDENTICAL residue ARG 833  index1   21  path   85  %Seq 100.00 Highlighted IDENTICAL residue THR 837  index1   25  path   89  %Seq 100.00 Highlighted IDENTICAL residue ASP 839  index1   27  path   91  %Seq 100.00 Highlighted IDENTICAL residue ASN 840  index1   28  path   92  %Seq 100.00 Highlighted IDENTICAL residue ASN 841  index1   29  path   93  %Seq 100.00 Highlighted IDENTICAL residue ASP 847  index1   35  path  100  %Seq 100.00 Highlighted IDENTICAL residue VAL 859  index1   47  path  112  %Seq 100.00 Highlighted IDENTICAL residue ASN 861  index1   49  path  117  %Seq 100.00 Highlighted IDENTICAL residue ALA 865  index1   53  path  121  %Seq 100.00 Highlighted IDENTICAL residue LYS 869  index1   57  path  125  %Seq 100.00 Highlighted IDENTICAL residue ASP 870  index1   58  path  126  %Seq 100.00 Highlighted IDENTICAL residue LYS 872  index1   60  path  133  %Seq 100.00 Highlighted IDENTICAL residue ALA 875  index1   63  path  136  %Seq 100.00 Highlighted IDENTICAL residue CYS 876  index1   64  path  137  %Seq 100.00 Highlighted IDENTICAL residue HIS 878  index1   66  path  139  %Seq 100.00 Highlighted IDENTICAL residue ASP 887  index1   75  path  148  %Seq 100.00 Highlighted IDENTICAL residue ASP 890  index1   78  path  151  %Seq 100.00 Highlighted IDENTICAL residue CYS 892  index1   80  path  153  %Seq 100.00 Highlighted IDENTICAL residue VAL 895  index1   83  path  163  %Seq 100.00 Highlighted IDENTICAL residue GLN 900  index1   88  path  168  %Seq 100.00 Highlighted IDENTICAL residue ASP 904  index1   92  path  172  %Seq 100.00 Highlighted IDENTICAL residue ASP 906  index1   94  path  174  %Seq 100.00 Highlighted 29 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g11910-1ux6A.pir.txt.1UX6.pdb.conservation.pml

=
==================================================================

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g11910-1ux6A.pir.txt PIR amino_acid 1UX6.pdb _ 100.0 BLOSUM62.dat

completed successfully.

@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@