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/
======================================================
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
======================================================
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.
======================================================
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
======================================================
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
======================================================
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
===============================================================================
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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