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At2g14910.2/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
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Sequence 1
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Sequence 2
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g14910-2-1jadA.pir.txt

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

Assigned types to 366 residues in Sequence 2-14910-2, 5 remain unknown
Assigned types to 221 residues in Sequence 1jadA, 150 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

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

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.

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

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

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

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

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

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

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

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.

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


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