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At2g05590.2/PDB

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&&&&&&&&&&&&&&&&&&&& 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
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Got here 3
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Got here 3
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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 @@@@@@@@@@@@@@@@@@@@


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