At2g14910.2/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 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 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/At2g14910-2-1jadA.pir.txt

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Assigned types to 366 residues in Sequence 2-14910-2, 5 remain unknown Assigned types to 221 residues in Sequence 1jadA, 150 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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Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 219 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 220 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 221 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 222 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 223 All residues are positively and negatively charged

Translated sequence file At2g14910-2-1jadA.pir.txt into sequence alignment.

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>1JAD.pdb Made from 3894 ATOM records in 1JAD.pdb NKEVTQLPEPQTASLAELQQKLFLKLLKKQEKELKELERKGSKRREELLQ KYSVLFLEPVYPRGLDSQVVELKERLEELIHLGEEYHDGIRRRKEQHATE QTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVRSTSD KAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQE KEGQLQQEAVAEYEEKLKTLTVEVQEVKNYKEVFPNKEVTQLPEPQTASL AELQQKLFLKLLKKQEKELKELERKGSKRREELLQKYSVLFLEPVYPRGL DSQVVELKERLEELIHLGEEYHDGIRRRKEQHATEQTAKITELAREKQIA ELKALKESSESNIKDIKKKLEAKRLDRIQVRSTSDKAAQERLKKEINNSH IQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQEKEGQLQQEAVAEYEE KLKTLTVEVQEVKNYKEVFP

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Best alignment: 1JAD.pdb    6  QLPEPQTASLAELQQ-KLFLKLLKKQEKELKELERKGSKRREELLQKYSV    54 QLPEPQTASLAELQQ KLFLKLLKKQEKELKELERKGSKRREELLQKYSV 1jadA       1  QLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREELLQKYSV    50

1JAD.pdb   55  LFLEPVYPRGLDSQVVELKERLE-ELIHLGEEYHDGIRRRKEQHATEQTA   103 LFLEPVYPRGLDSQVVELKERLE ELIHLGEEYHDGIRRRKEQHATEQTA 1jadA      51  LFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQHATEQTA   100

1JAD.pdb  104  KITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQV--RSTSDK   151 KITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQV RSTSDK 1jadA     101  KITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMMXXXXXK   150

1JAD.pdb  152  AAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQEK   201 AAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQEK 1jadA     151  AAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQEK   200

1JAD.pdb  202  EGQLQQEAVAEYEEKLKTLTVEVQEV   227 EGQLQQEAVAEYEEKLKTLTVEVQE+ 1jadA     201  EGQLQQEAVAEYEEKLKTLTVEVQEM   226

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Highlighted IDENTICAL residue LEU  10  index1    7  path   64  %Seq 100.00 Highlighted IDENTICAL residue SER  17  index1   14  path   71  %Seq 100.00 Highlighted IDENTICAL residue LEU  30  index1   26  path   84  %Seq 100.00 Highlighted IDENTICAL residue GLU  35  index1   31  path   89  %Seq 100.00 Highlighted IDENTICAL residue LEU  61  index1   57  path  116  %Seq 100.00 Highlighted IDENTICAL residue LEU  76  index1   72  path  131  %Seq 100.00 Highlighted IDENTICAL residue GLU  78  index1   74  path  133  %Seq 100.00 Highlighted IDENTICAL residue LEU  80  index1   76  path  135  %Seq 100.00 Highlighted IDENTICAL residue GLY  88  index1   83  path  146  %Seq 100.00 Highlighted IDENTICAL residue ARG  97  index1   92  path  155  %Seq 100.00 Highlighted IDENTICAL residue THR 111  index1  106  path  177  %Seq 100.00 Highlighted IDENTICAL residue GLU 112  index1  107  path  178  %Seq 100.00 Highlighted IDENTICAL residue GLU 116  index1  111  path  182  %Seq 100.00 Highlighted IDENTICAL residue SER 131  index1  126  path  197  %Seq 100.00 Highlighted IDENTICAL residue LEU 145  index1  140  path  211  %Seq 100.00 Highlighted IDENTICAL residue ARG 147  index1  142  path  213  %Seq 100.00 Highlighted IDENTICAL residue ARG 163  index1  156  path  229  %Seq 100.00 Highlighted IDENTICAL residue LEU 164  index1  157  path  230  %Seq 100.00 Highlighted IDENTICAL residue LYS 181  index1  174  path  247  %Seq 100.00 Highlighted IDENTICAL residue LEU 202  index1  195  path  268  %Seq 100.00 Highlighted IDENTICAL residue ARG 203  index1  196  path  269  %Seq 100.00 Highlighted IDENTICAL residue GLU 207  index1  200  path  274  %Seq 100.00 Highlighted IDENTICAL residue LYS 208  index1  201  path  275  %Seq 100.00 Highlighted IDENTICAL residue LEU 212  index1  205  path  279  %Seq 100.00 Highlighted IDENTICAL residue ALA 216  index1  209  path  283  %Seq 100.00 Highlighted IDENTICAL residue GLU 219  index1  212  path  286  %Seq 100.00 Highlighted IDENTICAL residue GLU 222  index1  215  path  289  %Seq 100.00 Highlighted 27 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14910-2-1jadA.pir.txt.1JAD.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14910-2-1jadA.pir.txt PIR amino_acid 1JAD.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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