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/
======================================================
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
======================================================
Assigned types to 150 residues in Sequence 2-10070-150, 28 remain unknown
Assigned types to 125 residues in Sequence c1ub1a_, 53 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
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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
======================================================
Best alignment:
1UB1.pdb 5 PEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKL 38
 P A P+ R +R + P E WT L
2-10070-150 108 PVADVLPELREDSLRALNDVLQVPG-REAWTTVL 140
======================================================
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
===============================================================================
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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