At2g01870.1/Structure

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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
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Got here 3
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Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01870_1irjA.pir.txt
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Assigned types to 157 residues in Sequence 2-01870, 5 remain unknown
Assigned types to 80 residues in Sequence 1irjA, 82 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 37 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 38 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 39 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 40 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 41 All residues are positively and negatively charged
Translated sequence file At2g01870_1irjA.pir.txt into sequence alignment.
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>1IRJ.pdb Made from 5587 ATOM records in 1IRJ.pdb
TCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKK
ENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLCKMSQLERNIETIIN
TFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLD
TNADKQLSFEEFIMLMARLKMSQLERNIETIINTFHQYSVKLGHPDTLNQ
GEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMA
RLMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKE
NKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLKMSQLERNIETIINTF
HQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTN
ADKQLSFEEFIMLMARLCKMSQLERNIETIINTFHQYSVKLGHPDTLNQG
EFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMAR
LCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKK
ENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLTCKMSQLERNIETII
NTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDL
DTNADKQLSFEEFIMLMARL
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Best alignment:
1IRJ.pdb 31 LNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEE 77
 +++ + +E +++ Q + ++ ++I D+ + + FEE
2-01870 42 IDRDKAREALKQLDQQIESQADEKPRIINKTSSDVVRTNNDPIMFEE 88
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Highlighted IDENTICAL residue GLU 39 index1 38 path 54 %Seq 100.00
Highlighted IDENTICAL residue GLN 46 index1 45 path 61 %Seq 100.00
Highlighted IDENTICAL residue ILE 59 index1 58 path 74 %Seq 100.00
Highlighted IDENTICAL residue ASP 65 index1 64 path 80 %Seq 100.00
Highlighted IDENTICAL residue PHE 76 index1 75 path 91 %Seq 100.00
Highlighted IDENTICAL residue GLU 77 index1 76 path 92 %Seq 100.00
Highlighted IDENTICAL residue GLU 78 index1 77 path 93 %Seq 100.00
Highlighted 7 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01870_1irjA.pir.txt.1IRJ.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01870_1irjA.pir.txt PIR amino_acid 1IRJ.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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