At2g05590.2/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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g05590-2-1ei3_B.txt
======================================================
Assigned types to 303 residues in Sequence 2-05590-2, 24 remain unknown
Assigned types to 285 residues in Sequence 1ei3_B, 42 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
======================================================
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 195 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 196 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 197 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 198 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 199 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 200 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 201 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 202 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 203 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 204 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 205 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 206 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 216 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 217 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 218 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 219 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 271 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 278 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 279 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 280 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 281 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 282 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 283 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 284 All residues are positively and negatively charged
Translated sequence file At2g05590-2-1ei3_B.txt into sequence alignment.
======================================================
>1EI3.pdb Made from 1896 ATOM records in 1EI3.pdb
PICVDDDWGTKCPSCCRMQGIIDDTDQNYSQRIDNIRQQLADSQNKYKTS
NRVIVETINILKPGLEGAQQLDENYGHVSTELRRRIVTLKQRVATQVNRI
KALQNSIQEQVVEMKRLEVDIDIKIRACKGSCARSFDYQVDKEGYDNIQK
HLTQASSIDGGCKHPLDELGVLCPTGCELQTTLLKQEKTVKPVLRDLKDR
VAKFSDTSTTMYQYVNMIDNKLVKTQKQRKDNDIILSEYNTEMELHYNYI
KDNLDNNIPSSLRVLRAVIDSLHKKIQKLENAIATQTDYCRSPCVASCNI
PVVSGRECEDIYRKGGETSEMYIIQPDPFTTPYRVYCDMETDNGGWTLIQ
NRQDGSVNFGRAWDEYKRGFGNIAKSGGKKYCDTPGEYWLGNDKISQLTK
IGPTKVLIEMEDWNGDKVSALYGGFTIHNEGNKYQLSVSNYKGNAGNALM
EGASQLYGENRTMTIHNGMYFSTYDRDNDGWLTTDPRKQCSKEDGGGWWY
NRCHAANPNGRYYWGGTYSWDMAKHGTDDGIVWMNWKGSWYSMKKMSMKI
KPYFYIATRENCCILDERFGSYCPTTCGIADFFNKYRLTTDGELLEIEGL
LQQATNSTGSIEYLIQHIKTIYPSEKQTLPQSIEQLTQKSKKIIEEIIRY
ENTILAHENTIQQLTDMHIMNSNKITQLKQKIAQLESHCQEPCKDTAEIQ
ETTGRDCQDIANKGARKSGLYFIKPQKAKQSFLVYCEIDTYGNGWTVLQR
RLDGSEDFRRNWVQYKEGFGHLSPDDTTEFWLGNEKIHLITTQSTLPYAL
RIELEDWSGKKGTADYAVFKVGTEEDKYRLTYAYFIGGERGDAFDGFNFG
DDPSDKSYTYHNGMRFSTFDNDNDNFEGNCAEQDGSGWWMNRCHAGHLNG
PYYIGGVYSRDTGTNSYDNGIIWATWRDRWYSMKKTTMKIIPFNRLSIDG
QICVDDDWGTKCPSCCRMQGIIDDTDQNYSQRIDNIRQQLADSQNKYKTS
NRVIVETINILKPGLEGAQQLDENYGHVSTELRRRIVTLKQRVATQVNRI
KALQNSIQEQVVEMKRLEVDIDIKIRACKGSCARSFDYQVDKEGYDNIQK
HLTQGGCKHPLDELGVLCPTGCELQTTLLKQEKTVKPVLRDLKDRVAKFS
DTSTTMYQYVNMIDNKLVKTQKQRKDNDIILSEYNTEMELHYNYIKDNLD
NNIPSSLRVLRAVIDSLHKKIQKLENAIATQTDYCRSPCVASCNIPVVSG
RECEDIYRKGGETSEMYIIQPDPFTTPYRVYCDMETDNGGWTLIQNRQDG
SVNFGRAWDEYKRGFGNIAKSGGKKYCDTPGEYWLGNDKISQLTKIGPTK
VLIEMEDWNGDKVSALYGGFTIHNEGNKYQLSVSNYKGNAGNALMEGASQ
LYGENRTMTIHNGMYFSTYDRDNDGWLTTDPRKQCSKEDGGGWWYNRCHA
ANPNGRYYWGGTYSWDMAKHGTDDGIVWMNWKGSWYSMKKMSMKIKPYFY
IATRENCCILDERFGSYCPTTCGIADFFNKYRLTTDGELLEIEGLLQQAT
NSTGSIEYLIQHIKTIYPSEKQTLPQSIEQLTQKSKKIIEEIIRYENTIL
AHENTIQQLTDMHIMNSNKITQLKQKIAQLESHCQEPCKDTAEIQETTGR
DCQDIANKGARKSGLYFIKPQKAKQSFLVYCEIDTYGNGWTVLQRRLDGS
EDFRRNWVQYKEGFGHLSPDDTTEFWLGNEKIHLITTQSTLPYALRIELE
DWSGKKGTADYAVFKVGTEEDKYRLTYAYFIGGERGDAFDGFNFGDDPSD
KSYTYHNGMRFSTFDNDNDNFEGNCAEQDGSGWWMNRCHAGHLNGPYYIG
GVYSRDTGTNSYDNGIIWATWRDRWYSMKKTTMKIIPFNRLSIDGQ
======================================================
Best alignment:
1EI3.pdb 274 KKIQKLENAIATQTDYCRSPCVASCNIP 301
 K QKL N A SP ++ + P
2-05590-2 7 KVSQKLSNLFADSPSQSASPRYSNSDSP 34
======================================================
Highlighted IDENTICAL residue ALA 190 index1 282 path 15 %Seq 100.00
Highlighted IDENTICAL residue CYS 202 index1 294 path 27 %Seq 100.00
Highlighted 2 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g05590-2-1ei3_B.txt.1EI3.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g05590-2-1ei3_B.txt PIR amino_acid 1EI3.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@