At2g04700.1/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/At2g04700-1dj7A.pir.txt

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Assigned types to 146 residues in Sequence 2-4700, 0 remain unknown Assigned types to 110 residues in Sequence 1dj7A, 36 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 At2g04700-1dj7A.pir.txt into sequence alignment.

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>1DJ7.pdb Made from 1396 ATOM records in 1DJ7.pdb NNKTLAAMKNFAEQYAKRTDTYFCSDLSVTAVVIEGLARHKEELGSPLCP CRHYEDKEAEVKNTFWNCPCVPMRERKECHCMLFLTPDNDFAGDAQDIPM ETLEEVKASMNVGDRVRVTSSVVVYHHPEHKKTAFDLQGMEGEVAAVLTE WQGRPISANLPVLVKFEQRFKAHFRPDEVTLI

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Best alignment: 1DJ7.pdb    1  NNKTLAAMKNFAEQYAKRTDTYFCSDLSVTAVVIEGLARHKEELGSPLCP    50 + K++ M+ F+EQYA+R+ TYFC D  VT+VVI+GLA HK+  G+PLCP 2-4700     37  SEKSVEIMRKFSEQYARRSGTYFCVDKGVTSVVIKGLAEHKDSYGAPLCP    86

1DJ7.pdb   51  CRHYEDKEAEVKNTFWNCPCVPMRERKECHCMLFLTPDNDFAGDAQDIPM   100 CRHY+DK AEV  FWNCPCVPMRERKECHCMLFLTPDNDFAG  Q I  2-4700      87  CRHYDDKAAEVGQGFWNCPCVPMRERKECHCMLFLTPDNDFAGKDQTITS   136

1DJ7.pdb  101  ETLEEVKASM   110 + ++E A+M 2-4700    137  DEIKETTANM   146

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Highlighted IDENTICAL residue LYS   9  index1    3  path   39  %Seq 100.00 Highlighted IDENTICAL residue MET  14  index1    8  path   44  %Seq 100.00 Highlighted IDENTICAL residue PHE  17  index1   11  path   47  %Seq 100.00 Highlighted IDENTICAL residue GLU  19  index1   13  path   49  %Seq 100.00 Highlighted IDENTICAL residue GLN  20  index1   14  path   50  %Seq 100.00 Highlighted IDENTICAL residue TYR  21  index1   15  path   51  %Seq 100.00 Highlighted IDENTICAL residue ALA  22  index1   16  path   52  %Seq 100.00 Highlighted IDENTICAL residue ARG  24  index1   18  path   54  %Seq 100.00 Highlighted IDENTICAL residue THR  27  index1   21  path   57  %Seq 100.00 Highlighted IDENTICAL residue TYR  28  index1   22  path   58  %Seq 100.00 Highlighted IDENTICAL residue PHE  29  index1   23  path   59  %Seq 100.00 Highlighted IDENTICAL residue CYS  30  index1   24  path   60  %Seq 100.00 Highlighted IDENTICAL residue ASP  32  index1   26  path   62  %Seq 100.00 Highlighted IDENTICAL residue VAL  35  index1   29  path   65  %Seq 100.00 Highlighted IDENTICAL residue THR  36  index1   30  path   66  %Seq 100.00 Highlighted IDENTICAL residue VAL  38  index1   32  path   68  %Seq 100.00 Highlighted IDENTICAL residue VAL  39  index1   33  path   69  %Seq 100.00 Highlighted IDENTICAL residue ILE  40  index1   34  path   70  %Seq 100.00 Highlighted IDENTICAL residue GLY  42  index1   36  path   72  %Seq 100.00 Highlighted IDENTICAL residue LEU  43  index1   37  path   73  %Seq 100.00 Highlighted IDENTICAL residue ALA  44  index1   38  path   74  %Seq 100.00 Highlighted IDENTICAL residue HIS  46  index1   40  path   76  %Seq 100.00 Highlighted IDENTICAL residue LYS  47  index1   41  path   77  %Seq 100.00 Highlighted IDENTICAL residue GLY  51  index1   45  path   81  %Seq 100.00 Highlighted IDENTICAL residue PRO  53  index1   47  path   83  %Seq 100.00 Highlighted IDENTICAL residue LEU  54  index1   48  path   84  %Seq 100.00 Highlighted IDENTICAL residue CYS  55  index1   49  path   85  %Seq 100.00 Highlighted IDENTICAL residue PRO  56  index1   50  path   86  %Seq 100.00 Highlighted IDENTICAL residue CYS  57  index1   51  path   87  %Seq 100.00 Highlighted IDENTICAL residue ARG  58  index1   52  path   88  %Seq 100.00 Highlighted IDENTICAL residue HIS  59  index1   53  path   89  %Seq 100.00 Highlighted IDENTICAL residue TYR  60  index1   54  path   90  %Seq 100.00 Highlighted IDENTICAL residue ASP  62  index1   56  path   92  %Seq 100.00 Highlighted IDENTICAL residue LYS  63  index1   57  path   93  %Seq 100.00 Highlighted IDENTICAL residue ALA  65  index1   59  path   95  %Seq 100.00 Highlighted IDENTICAL residue GLU  66  index1   60  path   96  %Seq 100.00 Highlighted IDENTICAL residue VAL  67  index1   61  path   97  %Seq 100.00 Highlighted IDENTICAL residue PHE  71  index1   65  path  101  %Seq 100.00 Highlighted IDENTICAL residue TRP  72  index1   66  path  102  %Seq 100.00 Highlighted IDENTICAL residue ASN  73  index1   67  path  103  %Seq 100.00 Highlighted IDENTICAL residue CYS  74  index1   68  path  104  %Seq 100.00 Highlighted IDENTICAL residue PRO  75  index1   69  path  105  %Seq 100.00 Highlighted IDENTICAL residue CYS  76  index1   70  path  106  %Seq 100.00 Highlighted IDENTICAL residue VAL  77  index1   71  path  107  %Seq 100.00 Highlighted IDENTICAL residue PRO  78  index1   72  path  108  %Seq 100.00 Highlighted IDENTICAL residue MET  79  index1   73  path  109  %Seq 100.00 Highlighted IDENTICAL residue ARG  80  index1   74  path  110  %Seq 100.00 Highlighted IDENTICAL residue GLU  81  index1   75  path  111  %Seq 100.00 Highlighted IDENTICAL residue ARG  82  index1   76  path  112  %Seq 100.00 Highlighted IDENTICAL residue LYS  83  index1   77  path  113  %Seq 100.00 Highlighted IDENTICAL residue GLU  84  index1   78  path  114  %Seq 100.00 Highlighted IDENTICAL residue CYS  85  index1   79  path  115  %Seq 100.00 Highlighted IDENTICAL residue HIS  86  index1   80  path  116  %Seq 100.00 Highlighted IDENTICAL residue CYS  87  index1   81  path  117  %Seq 100.00 Highlighted IDENTICAL residue MET  88  index1   82  path  118  %Seq 100.00 Highlighted IDENTICAL residue LEU  89  index1   83  path  119  %Seq 100.00 Highlighted IDENTICAL residue PHE  90  index1   84  path  120  %Seq 100.00 Highlighted IDENTICAL residue LEU  91  index1   85  path  121  %Seq 100.00 Highlighted IDENTICAL residue THR  92  index1   86  path  122  %Seq 100.00 Highlighted IDENTICAL residue PRO  93  index1   87  path  123  %Seq 100.00 Highlighted IDENTICAL residue ASP  94  index1   88  path  124  %Seq 100.00 Highlighted IDENTICAL residue ASN  95  index1   89  path  125  %Seq 100.00 Highlighted IDENTICAL residue ASP  96  index1   90  path  126  %Seq 100.00 Highlighted IDENTICAL residue PHE  97  index1   91  path  127  %Seq 100.00 Highlighted IDENTICAL residue ALA  98  index1   92  path  128  %Seq 100.00 Highlighted IDENTICAL residue GLY  99  index1   93  path  129  %Seq 100.00 Highlighted IDENTICAL residue GLN 102  index1   96  path  132  %Seq 100.00 Highlighted IDENTICAL residue ILE 104  index1   98  path  134  %Seq 100.00 Highlighted IDENTICAL residue GLU 111  index1  105  path  141  %Seq 100.00 Highlighted IDENTICAL residue ALA 114  index1  108  path  144  %Seq 100.00 Highlighted IDENTICAL residue MET   1  index1  110  path  146  %Seq 100.00 Highlighted 71 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04700-1dj7A.pir.txt.1DJ7.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04700-1dj7A.pir.txt PIR amino_acid 1DJ7.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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