At2g02980.1/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 = 1

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

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Assigned types to 603 residues in Sequence P1;, 10 remain unknown Assigned types to 378 residues in Sequence P1;, 235 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 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.

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>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

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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

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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

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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.

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