At2g13440.1/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 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 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/At2g13440-1qo8A.pir.txt

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Assigned types to 723 residues in Sequence 2-13440, 71 remain unknown Assigned types to 456 residues in Sequence 1qo8A, 338 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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Translated sequence file At2g13440-1qo8A.pir.txt into sequence alignment.

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>1QO8.pdb Made from 8468 ATOM records in 1QO8.pdb TPDMGSFHADMGSCQSCHAKPIKVTDSETHENAQCKSCHGEYAELANDKL QFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFDIKPMPFSDAKKKKSW DDGWDQDKIQKAIAAGPSETTQVLVVGAGSAGFNASLAAKKAGANVILVD KAPFSGGNSMISAGGMNAVGTKQQTAHGVEDKVEWFIEDAMKGGRQQNDI KLVTILAEQSADGVQWLESLGANLDDLKRSGGARVDRTHRPHGGKSSGPE IIDTLRKAAKEQGIDTRLNSRVVKLVVNDDHSVVGAVVHGKHTGYYMIGA KSVVLATGGYGMNKEMIAYYRPTMKDMTSSNNITATGDGVLMAKEIGASM TDIDWVQAHPTVGKDSRILISETVRGVGAVMVNKDGNRFISELTTRDKAS DAILKQPGQFAWIIFDNQLYKKAKMVRGYDHLEMLYKGDTVEQLAKSTGM KVADLAKTVSDYNGYVASGKDTAFGRADMPLNMTQSPYYAVKVAPGIHHT MGGVAINTTASVLDLQSKPIDGLFAAGEVTGGVHGYNRLGGNAIADTVVF GRIAGDNAAKHALDTPDMGSFHADMGSCQSCHAKPIKVTDSETHENAQCK SCHGEYAELANDKLQFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFDI KPMPFSDAKKKKSWDDGWDQDKIQKAIAAGPSETTQVLVVGAGSAGFNAS LAAKKAGANVILVDKAPFSGGNSMISAGGMNAVGTKQQTAHGVEDKVEWF IEDAMKGGRQQNDIKLVTILAEQSADGVQWLESLGANLDDLKRSGGARVD RTHRPHGGKSSGPEIIDTLRKAAKEQGIDTRLNSRVVKLVVNDDHSVVGA VVHGKHTGYYMIGAKSVVLATGGYGMNKEMIAYYRPTMKDMTSSNNITAT GDGVLMAKEIGASMTDIDWVQAHPTVGKDSRILISETVRGVGAVMVNKDG NRFISELTTRDKASDAILKQPGQFAWIIFDNQLYKKAKMVRGYDHLEMLY KGDTVEQLAKSTGMKVADLAKTVSDYNGYVASGKDTAFGRADMPLNMTQS PYYAVKVAPGIHHTMGGVAINTTASVLDLQSKPIDGLFAAGEVTGGVHGY NRLGGNAIADTVVFGRIAGDNAAKHALD

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Best alignment: 1QO8.pdb  114  AAGPSETTQVLVVGAGSAGFNASLAAKKAGANVILV   149 A   T  V+VVGAG AG  A+LA+ + GA+ +L+ 2-13440    66  GATSDSTYDVIVVGAGHAGCEAALASARLGASTLLL   101

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Highlighted IDENTICAL residue ALA 116  index1  115  path   67  %Seq 100.00 Highlighted IDENTICAL residue THR 121  index1  120  path   72  %Seq 100.00 Highlighted IDENTICAL residue VAL 124  index1  123  path   75  %Seq 100.00 Highlighted IDENTICAL residue VAL 126  index1  125  path   77  %Seq 100.00 Highlighted IDENTICAL residue VAL 127  index1  126  path   78  %Seq 100.00 Highlighted IDENTICAL residue GLY 128  index1  127  path   79  %Seq 100.00 Highlighted IDENTICAL residue ALA 129  index1  128  path   80  %Seq 100.00 Highlighted IDENTICAL residue GLY 130  index1  129  path   81  %Seq 100.00 Highlighted IDENTICAL residue ALA 132  index1  131  path   83  %Seq 100.00 Highlighted IDENTICAL residue GLY 133  index1  132  path   84  %Seq 100.00 Highlighted IDENTICAL residue ALA 136  index1  135  path   87  %Seq 100.00 Highlighted IDENTICAL residue LEU 138  index1  137  path   89  %Seq 100.00 Highlighted IDENTICAL residue ALA 139  index1  138  path   90  %Seq 100.00 Highlighted IDENTICAL residue GLY 144  index1  143  path   95  %Seq 100.00 Highlighted IDENTICAL residue ALA 145  index1  144  path   96  %Seq 100.00 Highlighted IDENTICAL residue LEU 149  index1  148  path  100  %Seq 100.00 Highlighted 16 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13440-1qo8A.pir.txt.1QO8.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13440-1qo8A.pir.txt PIR amino_acid 1QO8.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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