At2g01390.1/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/At2g01390_1w3b_A.pir.txt
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Assigned types to 577 residues in Sequence 2-01390, 4 remain unknown
Assigned types to 383 residues in Sequence 1w3b_A, 198 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 296 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 297 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 488 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 526 All residues are positively and negatively charged
Translated sequence file At2g01390_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 69 AYSNLGNVYKERGQLQEAIEHYRHALRLKPDFID--GYINLAAALVAAGD 116
 Y+ + +++ E G++Q + H ++ K ID Y +L + ++GD
2-01390 124 TYTTMLDIFGEAGRIQSMYSVF-HLMKEKGVLIDTVTYTSLIHWVSSSGD 172
1W3B.pdb 117 MEGAVQAYVSALQYNPDLYCVR-SDLGNLLKALGRLEEAKACYLKAIETQ 165
 ++GA++ + + V + +L A GR+EEA Y + + ++
2-01390 173 VDGAMRLWEEMRDNGCEPTVVSYTAYMKMLFADGRVEEATEVYKEMLRSR 222
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Highlighted IDENTICAL residue ALA 81 index1 69 path 124 %Seq 50.00
Highlighted IDENTICAL residue ARG 92 index1 80 path 135 %Seq 100.00
Highlighted IDENTICAL residue GLY 93 index1 81 path 136 %Seq 100.00
Highlighted IDENTICAL residue ASP 111 index1 99 path 153 %Seq 50.00
Highlighted IDENTICAL residue LEU 119 index1 107 path 163 %Seq 100.00
Highlighted IDENTICAL residue GLU 130 index1 118 path 174 %Seq 100.00
Highlighted IDENTICAL residue PRO 144 index1 132 path 188 %Seq 50.00
Highlighted IDENTICAL residue GLY 161 index1 149 path 206 %Seq 100.00
Highlighted IDENTICAL residue GLU 165 index1 153 path 210 %Seq 100.00
Highlighted IDENTICAL residue ALA 166 index1 154 path 211 %Seq 100.00
Highlighted IDENTICAL residue ALA 168 index1 156 path 213 %Seq 100.00
Highlighted IDENTICAL residue TYR 170 index1 158 path 215 %Seq 100.00
Highlighted IDENTICAL residue ILE 174 index1 162 path 219 %Seq 100.00
Highlighted IDENTICAL residue GLU 175 index1 163 path 220 %Seq 100.00
Highlighted 14 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01390_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 At2g01390_1w3b_A.pir.txt PIR amino_acid 1W3B.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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