At2g10070.1/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/At2g10070-1-c1ub1a_.pir.txt

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Assigned types to 150 residues in Sequence 2-10070-150, 28 remain unknown Assigned types to 125 residues in Sequence c1ub1a_, 53 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 At2g10070-1-c1ub1a_.pir.txt into sequence alignment.

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Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HE2 in residue GLU 77

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HD2 in residue ASP 91

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HD2 in residue ASP 97

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HD2 in residue ASP 98

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HE2 in residue GLU 103

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HD2 in residue ASP 122

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HE2 in residue GLU 138

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HE2 in residue GLU 144

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HD2 in residue ASP 148

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HD2 in residue ASP 152

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HD2 in residue ASP 155

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HD2 in residue ASP 157

Error in function WYRM_assign_PDB_Atom_type Unable to assign atom HE2 in residue GLU 170

>1UB1.pdb Made from 1969 ATOM records in 1UB1.pdb APAVPEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKY DVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTVTGRGSPSRREQ RPPKKAKSPKSPGSGRGRGRPKGSG

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Best alignment: 1UB1.pdb       5  PEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKL    38 P A  P+ R   +R    +   P   E WT  L 2-10070-150   108  PVADVLPELREDSLRALNDVLQVPG-REAWTTVL   140

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Highlighted IDENTICAL residue PRO  76  index1    5  path  136  %Seq  50.00 Highlighted IDENTICAL residue GLU  77  index1    6  path  137  %Seq  50.00 Highlighted IDENTICAL residue ALA  78  index1    7  path  138  %Seq  50.00 Highlighted IDENTICAL residue SER  79  index1    8  path  139  %Seq  50.00 Highlighted IDENTICAL residue ALA  80  index1    9  path  140  %Seq  50.00 Highlighted IDENTICAL residue SER  81  index1   10  path  141  %Seq  50.00 Highlighted IDENTICAL residue PRO  82  index1   11  path  142  %Seq  50.00 Highlighted IDENTICAL residue LYS  83  index1   12  path  143  %Seq  50.00 Highlighted IDENTICAL residue GLN  84  index1   13  path  144  %Seq  50.00 Highlighted IDENTICAL residue ARG  85  index1   14  path  145  %Seq  50.00 Highlighted IDENTICAL residue ARG  86  index1   15  path  146  %Seq  50.00 Highlighted IDENTICAL residue SER  87  index1   16  path  147  %Seq  50.00 Highlighted IDENTICAL residue ILE  88  index1   17  path  148  %Seq  50.00 Highlighted IDENTICAL residue ILE  89  index1   18  path  149  %Seq  50.00 Highlighted IDENTICAL residue ARG  90  index1   19  path  150  %Seq  50.00 Highlighted IDENTICAL residue ASP  91  index1   20  path  151  %Seq  50.00 Highlighted IDENTICAL residue ARG  92  index1   21  path  152  %Seq  50.00 Highlighted IDENTICAL residue GLY  93  index1   22  path  153  %Seq  50.00 Highlighted IDENTICAL residue PRO  94  index1   23  path  154  %Seq  50.00 Highlighted IDENTICAL residue MET  95  index1   24  path  155  %Seq  50.00 Highlighted IDENTICAL residue TYR  96  index1   25  path  156  %Seq  50.00 Highlighted IDENTICAL residue ASP  97  index1   26  path  157  %Seq  50.00 Highlighted IDENTICAL residue ASP  98  index1   27  path  158  %Seq  50.00 Highlighted IDENTICAL residue PRO  99  index1   28  path  159  %Seq  50.00 Highlighted IDENTICAL residue THR 100  index1   29  path  160  %Seq  50.00 Highlighted IDENTICAL residue PRO 102  index1   31  path  161  %Seq  50.00 Highlighted IDENTICAL residue GLU 103  index1   32  path  162  %Seq  50.00 Highlighted IDENTICAL residue GLY 104  index1   33  path  163  %Seq  50.00 Highlighted IDENTICAL residue TRP 105  index1   34  path  164  %Seq  50.00 Highlighted IDENTICAL residue THR 106  index1   35  path  165  %Seq  50.00 Highlighted IDENTICAL residue ARG 107  index1   36  path  166  %Seq  50.00 Highlighted IDENTICAL residue LYS 108  index1   37  path  167  %Seq  50.00 Highlighted IDENTICAL residue LEU 109  index1   38  path  168  %Seq  50.00 Highlighted 33 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10070-1-c1ub1a_.pir.txt.1UB1.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10070-1-c1ub1a_.pir.txt PIR amino_acid 1UB1.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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