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
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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/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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