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At2g09900.1/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
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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/At2g09900-1q4kB.pir.txt

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

Assigned types to 175 residues in Sequence 2-09900, 5 remain unknown
Assigned types to 48 residues in Sequence 1q4kB, 132 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 At2g09900-1q4kB.pir.txt into sequence alignment.

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

>1Q4K.pdb  Made from 5483 ATOM records in 1Q4K.pdb
DCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDK
YGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPN
SLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSA
IILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEY
GCCKELASRLRYARTMVDKLLSSRCHLSDMLQQLHSVNASKPSERGLVRQ
EEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYND
GDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANI
TPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLM
AAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSCHLS
DMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGY
QLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKK
ITLLKYFRNYMSEHLLKAGDELARLPYLRTWFRTRSAIILHLSNGSVQIN
FFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYA
RTMVDKLLSSMQSPLMQSPLMQSPL

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

Best alignment:
1Q4K.pdb     1  DCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYS    48
                DC L D LQ L          + L  ++  + PA       + WV+YS
2-09900    120  DCILDDKLQSL----LHSALNQTLEHRKGKKTPATHSTSHSTTWVEYS   163

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

Highlighted IDENTICAL residue ASP  371  index1    1  path  120  %Seq 100.00
Highlighted IDENTICAL residue CYS  372  index1    2  path  121  %Seq 100.00
Highlighted IDENTICAL residue LEU  374  index1    4  path  123  %Seq 100.00
Highlighted IDENTICAL residue ASP  376  index1    6  path  125  %Seq 100.00
Highlighted IDENTICAL residue LEU  378  index1    8  path  127  %Seq 100.00
Highlighted IDENTICAL residue GLN  379  index1    9  path  128  %Seq 100.00
Highlighted IDENTICAL residue LEU  381  index1   11  path  130  %Seq 100.00
Highlighted IDENTICAL residue ALA  386  index1   16  path  131  %Seq  50.00
Highlighted IDENTICAL residue SER  387  index1   17  path  132  %Seq 100.00
Highlighted IDENTICAL residue LYS  388  index1   18  path  133  %Seq 100.00
Highlighted IDENTICAL residue LEU  394  index1   24  path  144  %Seq 100.00
Highlighted IDENTICAL residue PRO  403  index1   33  path  153  %Seq 100.00
Highlighted IDENTICAL residue ALA  404  index1   34  path  154  %Seq 100.00
Highlighted IDENTICAL residue TRP  414  index1   44  path  164  %Seq 100.00
Highlighted IDENTICAL residue VAL  415  index1   45  path  165  %Seq 100.00
Highlighted IDENTICAL residue TYR  417  index1   47  path  167  %Seq 100.00
Highlighted IDENTICAL residue SER  418  index1   48  path  168  %Seq 100.00
Highlighted 17 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g09900-1q4kB.pir.txt.1Q4K.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g09900-1q4kB.pir.txt PIR amino_acid 1Q4K.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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