FANDOM


&&&&&&&&&&&&&&&&&&&& 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 = 1

Read 2 amino_acid sequences from FASTA Sequence file /usr/local/www/html/proteins/workspace/At2g02980-1e3b_A.pir.txt

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

Assigned types to 603 residues in Sequence P1;, 10 remain unknown
Assigned types to 378 residues in Sequence P1;, 235 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 195  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 196  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 197  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 294  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 295  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 296  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 339  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 400  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 409  All residues are positively and negatively charged

Translated sequence file At2g02980-1e3b_A.pir.txt into sequence alignment.

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

>1W3B.pdb  Made from 5568 ATOM records in 1W3B.pdb
GPMELAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLD
RSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDF
IDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGR
LEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP
NFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQ
GLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL
CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQ
QQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDGPMELAHREYQA
GDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQ
NPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALV
AAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAI
ETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNV
LKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRR
AIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSYRKAL
EVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNT
LKEMQD

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

Best alignment:
1W3B.pdb     2  PMELAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDR    51
                PMELAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDR
P1;          1  PMELAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDR    50

1W3B.pdb    52  SAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFI   101
                SAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFI
P1;         51  SAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFI   100

1W3B.pdb   102  DGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRL   151
                DGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRL
P1;        101  DGYINLAAALVAAGDMEGAVQAYVSALQYNXXXYCVRSDLGNLLKALGRL   150

1W3B.pdb   152  EEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPN   201
                EEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPN
P1;        151  EEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPN   200

1W3B.pdb   202  FLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQG   251
                FLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQG
P1;        201  FLDAYINLGNVLKEARIFDRAVAAYLRXXXLSPNHAVVHGNLACVYYEQG   250

1W3B.pdb   252  LIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC   301
                LIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC
P1;        251  LIDLAIDTYRRAIELQPHFPXAYCNLANALKEKGSVAEAEDCYNTALRLC   300

1W3B.pdb   302  PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQ   351
                PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQ
P1;        301  PTHADSLNNLANIKREQGNIEEAVRLYRKXLEVFPEFAXAHSNLASVLQQ   350

1W3B.pdb   352  QGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDG   389
                QGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD 
P1;        351  QGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD*   388

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

Highlighted IDENTICAL residue GLU   28  index1   16  path   76  %Seq 100.00
Highlighted IDENTICAL residue LEU   37  index1   25  path   85  %Seq 100.00
Highlighted IDENTICAL residue LEU   85  index1   73  path  135  %Seq 100.00
Highlighted IDENTICAL residue LEU   95  index1   83  path  145  %Seq 100.00
Highlighted IDENTICAL residue GLU   97  index1   85  path  147  %Seq 100.00
Highlighted IDENTICAL residue LEU  108  index1   96  path  158  %Seq 100.00
Highlighted IDENTICAL residue ASP  111  index1   99  path  162  %Seq 100.00
Highlighted IDENTICAL residue LEU  119  index1  107  path  170  %Seq 100.00
Highlighted IDENTICAL residue ASP  128  index1  116  path  179  %Seq 100.00
Highlighted IDENTICAL residue ALA  132  index1  120  path  183  %Seq 100.00
Highlighted IDENTICAL residue ARG  162  index1  150  path  213  %Seq 100.00
Highlighted IDENTICAL residue GLU  165  index1  153  path  216  %Seq 100.00
Highlighted IDENTICAL residue ALA  166  index1  154  path  217  %Seq 100.00
Highlighted IDENTICAL residue GLY  195  index1  183  path  247  %Seq 100.00
Highlighted IDENTICAL residue LEU  199  index1  187  path  251  %Seq 100.00
Highlighted IDENTICAL residue ALA  207  index1  195  path  259  %Seq 100.00
Highlighted IDENTICAL residue LEU  221  index1  209  path  274  %Seq 100.00
Highlighted IDENTICAL residue ASP  232  index1  220  path  285  %Seq 100.00
Highlighted IDENTICAL residue ALA  234  index1  222  path  287  %Seq 100.00
Highlighted IDENTICAL residue VAL  235  index1  223  path  288  %Seq 100.00
Highlighted IDENTICAL residue TYR  259  index1  247  path  312  %Seq 100.00
Highlighted IDENTICAL residue GLY  263  index1  251  path  316  %Seq 100.00
Highlighted IDENTICAL residue ARG  274  index1  262  path  327  %Seq 100.00
Highlighted IDENTICAL residue GLN  279  index1  267  path  334  %Seq 100.00
Highlighted IDENTICAL residue PRO  280  index1  268  path  335  %Seq 100.00
Highlighted IDENTICAL residue LEU  289  index1  277  path  344  %Seq 100.00
Highlighted IDENTICAL residue ASN  291  index1  279  path  346  %Seq 100.00
Highlighted IDENTICAL residue ALA  292  index1  280  path  347  %Seq 100.00
Highlighted IDENTICAL residue GLY  297  index1  285  path  352  %Seq 100.00
Highlighted IDENTICAL residue VAL  299  index1  287  path  354  %Seq 100.00
Highlighted IDENTICAL residue GLU  301  index1  289  path  356  %Seq 100.00
Highlighted IDENTICAL residue GLY  331  index1  319  path  388  %Seq 100.00
Highlighted IDENTICAL residue ASN  332  index1  320  path  389  %Seq 100.00
Highlighted IDENTICAL residue GLU  334  index1  322  path  391  %Seq 100.00
Highlighted IDENTICAL residue ALA  336  index1  324  path  393  %Seq 100.00
Highlighted IDENTICAL residue LYS  342  index1  330  path  399  %Seq 100.00
Highlighted IDENTICAL residue LEU  344  index1  332  path  401  %Seq 100.00
Highlighted IDENTICAL residue PRO  348  index1  336  path  405  %Seq 100.00
Highlighted IDENTICAL residue LEU  357  index1  345  path  414  %Seq 100.00
Highlighted IDENTICAL residue LEU  367  index1  355  path  424  %Seq 100.00
Highlighted IDENTICAL residue ALA  370  index1  358  path  427  %Seq 100.00
Highlighted IDENTICAL residue TYR  388  index1  376  path  445  %Seq 100.00
Highlighted IDENTICAL residue ASN  393  index1  381  path  450  %Seq 100.00
Highlighted IDENTICAL residue GLY   13  index1  389  path  613  %Seq 100.00
Highlighted 44 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02980-1e3b_A.pir.txt.1W3B.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02980-1e3b_A.pir.txt FASTA amino_acid 1W3B.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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