At2g03540.1/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
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Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g03540-1ji6A.pir.txt
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Assigned types to 166 residues in Sequence 2-03540, 2 remain unknown
Assigned types to 102 residues in Sequence 1ji6A, 66 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 At2g03540-1ji6A.pir.txt into sequence alignment.
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>1JI6.pdb Made from 4750 ATOM records in 1JI6.pdb
DAVGTGISVVGQILGVVGVPFAGALTSFYQSFLNTIWPSDADPWKAFMAQ
VEVLIDKKIEEYAKSKALAELQGLQNNFEDYVNALNSWKKTPLSLRSKRS
QDRIRELFSQAESHFRNSMPSFAVSKFEVLFLPTYAQAANTHLLLLKDAQ
VFGEEWGYSSEDVAEFYHRQLKLTQQYTDHCVNWYNVGLNGLRGSTYDAW
VKFNRFRREMTLTVLDLIVLFPFYDIRLYSKGVKTELTRDIFTDPIFSLN
TLQEYGPTFLSIENSIRKPHLFDYLQGIEFHTRLQPGYFGKDSFNYWSGN
YVETRPSIGSSKTITSPFYGDKSTEPVQKLSFDGQKVYRTIANTDVAAWP
NGKVYLGVTKVDFSQYDDQKNETSTQTYDSKRNNGHVSAQDSIDQLPPET
TDEPLEKAYSHQLNYAECFLMQDRRGTIPFFTWTHRSVDFFNTIDAEKIT
QLPVVKAYALSSGASIIEGPGFTGGNLLFLKESSNSIAKFKVTLNSAALL
QRYRVRIRYASTTNLRLFVQNSNNDFLVIYINKTMNKDDDLTYQTFDLAT
TNSNMGFSGDKNELIIGAESFVSNEKIYIDKIEFIPVQL
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Best alignment:
1JI6.pdb 82 VNALNSWKKTPLSLRSKRSQDRIRELF----SQAESHFRNSMPSFAVSK 126
 V+ L S ++ R+ R+ ++ R L+ ESH N F K
2-03540 26 VDCLRSMEEMLALKRNSRTNEQDRVLWKGKNGHLESHTHNGEQGFLAQK 74
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Highlighted IDENTICAL residue VAL 145 index1 82 path 26 %Seq 50.00
Highlighted IDENTICAL residue ASN 146 index1 83 path 27 %Seq 50.00
Highlighted IDENTICAL residue ALA 147 index1 84 path 28 %Seq 50.00
Highlighted IDENTICAL residue LEU 148 index1 85 path 29 %Seq 50.00
Highlighted IDENTICAL residue ASN 149 index1 86 path 30 %Seq 50.00
Highlighted IDENTICAL residue SER 150 index1 87 path 31 %Seq 50.00
Highlighted IDENTICAL residue TRP 151 index1 88 path 32 %Seq 50.00
Highlighted IDENTICAL residue LYS 152 index1 89 path 33 %Seq 50.00
Highlighted IDENTICAL residue LYS 153 index1 90 path 34 %Seq 50.00
Highlighted IDENTICAL residue THR 154 index1 91 path 35 %Seq 50.00
Highlighted IDENTICAL residue PRO 155 index1 92 path 36 %Seq 50.00
Highlighted IDENTICAL residue LEU 156 index1 93 path 37 %Seq 50.00
Highlighted IDENTICAL residue SER 157 index1 94 path 38 %Seq 50.00
Highlighted IDENTICAL residue LEU 158 index1 95 path 39 %Seq 50.00
Highlighted IDENTICAL residue ARG 159 index1 96 path 40 %Seq 50.00
Highlighted IDENTICAL residue SER 160 index1 97 path 41 %Seq 50.00
Highlighted IDENTICAL residue LYS 161 index1 98 path 42 %Seq 50.00
Highlighted IDENTICAL residue ARG 162 index1 99 path 43 %Seq 50.00
Highlighted IDENTICAL residue SER 163 index1 100 path 44 %Seq 50.00
Highlighted IDENTICAL residue GLN 164 index1 101 path 45 %Seq 50.00
Highlighted IDENTICAL residue ASP 165 index1 102 path 46 %Seq 50.00
Highlighted IDENTICAL residue ARG 166 index1 103 path 47 %Seq 50.00
Highlighted IDENTICAL residue ILE 167 index1 104 path 48 %Seq 50.00
Highlighted IDENTICAL residue ARG 168 index1 105 path 49 %Seq 50.00
Highlighted IDENTICAL residue GLU 169 index1 106 path 50 %Seq 50.00
Highlighted IDENTICAL residue LEU 170 index1 107 path 51 %Seq 50.00
Highlighted IDENTICAL residue PHE 171 index1 108 path 52 %Seq 50.00
Highlighted IDENTICAL residue SER 172 index1 109 path 57 %Seq 50.00
Highlighted IDENTICAL residue GLN 173 index1 110 path 58 %Seq 50.00
Highlighted IDENTICAL residue ALA 174 index1 111 path 59 %Seq 50.00
Highlighted IDENTICAL residue GLU 175 index1 112 path 60 %Seq 50.00
Highlighted IDENTICAL residue SER 176 index1 113 path 61 %Seq 50.00
Highlighted IDENTICAL residue HIS 177 index1 114 path 62 %Seq 50.00
Highlighted 33 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03540-1ji6A.pir.txt.1JI6.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03540-1ji6A.pir.txt PIR amino_acid 1JI6.pdb A 100.0 BLOSUM62.dat 
completed successfully.
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