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 Got here 4 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  VNALNSWKKTPLSLRSKRSQDRIRELFSQAESHFRNSMPSFAVSK   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

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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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