At2g01860.1/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 = 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 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 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/At2g01860_1w3b_A.pir.txt

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Assigned types to 486 residues in Sequence 2-01860, 11 remain unknown Assigned types to 370 residues in Sequence 1w3b_A, 127 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 157 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 193 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 230 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 251 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 252 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 253 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 254 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 255 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 264 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 442 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 478 All residues are positively and negatively charged

Translated sequence file At2g01860_1w3b_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  104  YINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEE   153 Y+ +  +    D    V A +  L+   DL   + D  +++K   +L E 2-01860    294  YVKMILEIAKNPDKYHLVVALLEELKKREDLKLSQQDCTSIMKICVKLGE   343

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Highlighted IDENTICAL residue ALA 125  index1  113  path  312  %Seq 100.00 Highlighted IDENTICAL residue GLN 134  index1  122  path  321  %Seq 100.00 Highlighted IDENTICAL residue ALA 135  index1  123  path  322  %Seq 100.00 Highlighted IDENTICAL residue ASP 145  index1  133  path  332  %Seq  50.00 Highlighted IDENTICAL residue LEU 146  index1  134  path  333  %Seq  50.00 Highlighted IDENTICAL residue GLU 164  index1  152  path  351  %Seq 100.00 Highlighted 6 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01860_1w3b_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 At2g01860_1w3b_A.pir.txt PIR amino_acid 1W3B.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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