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At2g04700.1/PDB

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

======================================================

Assigned types to 146 residues in Sequence 2-4700, 0 remain unknown
Assigned types to 110 residues in Sequence 1dj7A, 36 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

======================================================

Translated sequence file At2g04700-1dj7A.pir.txt into sequence alignment.

======================================================

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

======================================================

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

======================================================

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

===============================================================================

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.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@

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