At2g01390.1/Structure

&&&&&&&&&&&&&&&&&&&& 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 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 Got here 3 Got here 4 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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