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
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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
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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.
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>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.
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