At2g13720.1/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 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 Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g13720-1bgw_.pir.txt

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Assigned types to 223 residues in Sequence 2-13720, 4 remain unknown Assigned types to 203 residues in Sequence 1bgw_, 24 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 58 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 109 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 126 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 127 All residues are positively and negatively charged

Translated sequence file At2g13720-1bgw_.pir.txt into sequence alignment.

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Error in function WYRM_assign_PDB_Atom_type Unable to assign atom H in residue PRO 1072

>1BGW.pdb Made from 6832 ATOM records in 1BGW.pdb RKSRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDY YGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRY GHLMIMTDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSI TKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFS NLDRHLKIFHSLQGLFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKS ELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAF GTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEW YLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHP WFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLL LGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLI SPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQ WEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPY YGSPNDEIAEELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLL KLSAKDIWNTDLKAFEVGYQEFLQRDAEAR

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Best alignment: 1BGW.pdb  104  MIMTDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKP   153 MIMTDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKP 1bgw_       1  MIMTDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKP    50

1BGW.pdb  154  TKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLD   203 TKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLD 1bgw_      51  XKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEXREYFSNLD   100

1BGW.pdb  204  RHLKIFHSLQ   213 RHLKIFHSLQ 1bgw_     101  RHLKIFHSXXGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIP   150

1BGW.pdb  213  -GLFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKV   254 LFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKV 1bgw_     151  ISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKV   200

1BGW.pdb  255  AQLAPYV   261 AQLAPYV 1bgw_     201  AQLAPYV   207

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Highlighted IDENTICAL residue GLY 532  index1  113  path   12  %Seq 100.00 Highlighted IDENTICAL residue SER 533  index1  114  path   13  %Seq 100.00 Highlighted IDENTICAL residue PHE 556  index1  137  path   41  %Seq 100.00 Highlighted IDENTICAL residue THR 562  index1  143  path   47  %Seq 100.00 Highlighted IDENTICAL residue PRO 563  index1  144  path   48  %Seq 100.00 Highlighted IDENTICAL residue LYS 566  index1  147  path   51  %Seq 100.00 Highlighted IDENTICAL residue VAL 567  index1  148  path   52  %Seq 100.00 Highlighted IDENTICAL residue SER 568  index1  149  path   53  %Seq 100.00 Highlighted IDENTICAL residue PHE 579  index1  160  path   64  %Seq 100.00 Highlighted IDENTICAL residue TRP 598  index1  179  path   93  %Seq 100.00 Highlighted IDENTICAL residue LYS 601  index1  182  path   96  %Seq 100.00 Highlighted IDENTICAL residue TYR 603  index1  184  path   98  %Seq 100.00 Highlighted IDENTICAL residue LYS 604  index1  185  path   99  %Seq 100.00 Highlighted IDENTICAL residue GLY 605  index1  186  path  100  %Seq 100.00 Highlighted IDENTICAL residue GLU 613  index1  194  path  108  %Seq 100.00 Highlighted IDENTICAL residue SER 619  index1  200  path  114  %Seq 100.00 Highlighted IDENTICAL residue ASN 620  index1  201  path  115  %Seq 100.00 Highlighted IDENTICAL residue ASP 622  index1  203  path  117  %Seq 100.00 Highlighted IDENTICAL residue PHE 628  index1  209  path  123  %Seq 100.00 Highlighted IDENTICAL residue LEU 683  index1  215  path  178  %Seq 100.00 Highlighted IDENTICAL residue ASN 689  index1  221  path  184  %Seq 100.00 Highlighted IDENTICAL residue ARG 691  index1  223  path  186  %Seq 100.00 Highlighted IDENTICAL residue ASN 695  index1  227  path  190  %Seq 100.00 Highlighted IDENTICAL residue LYS 701  index1  233  path  199  %Seq 100.00 Highlighted IDENTICAL residue LYS 706  index1  238  path  204  %Seq 100.00 Highlighted IDENTICAL residue LYS 713  index1  245  path  211  %Seq 100.00 Highlighted IDENTICAL residue LYS 714  index1  246  path  212  %Seq 100.00 Highlighted IDENTICAL residue LYS 717  index1  249  path  215  %Seq 100.00 Highlighted 28 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13720-1bgw_.pir.txt.1BGW.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13720-1bgw_.pir.txt PIR amino_acid 1BGW.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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