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At2g05620.1/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
Sequence 2
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/At2g05620-1h2vC.pir.txt

======================================================

Assigned types to 133 residues in Sequence 2-05620, 0 remain unknown
Assigned types to 71 residues in Sequence 1h2vC, 62 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

======================================================

Translated sequence file At2g05620-1h2vC.pir.txt into sequence alignment.

======================================================

>1H2V.pdb  Made from 6667 ATOM records in 1H2V.pdb
DHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARL
LPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLV
RFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLP
WVGKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEY
LDCLWAQIQKLKKDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTE
DSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENLHCIIKSHWKE
RKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIE
LCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRW
SWEDWSDCLSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCP
SNPTCIYKYGDESSNSLPGHSVALCLAVAFKSKATNDEIFSILKDVPNFN
PLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVLRVM
FEVWRNHPQMIAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEI
LHSTIRKMNKHVLKIQKELEEAKIERLQEKVESAQSEQKNLFLVIFQRFI
MILTEHLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENL
LFTAELDPHILAVFQQFCALQAEKLLKKSCTLYVGNLSFYTTEEQIYELF
SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI
IRTDWDAGFKEGRQY

======================================================

Best alignment:
1H2V.pdb   498  NFNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVL   547
                +FNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVL
1h2vC        4  SFNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVL    53

1H2V.pdb   548  RVMFEVWRNHPQMIAVLV   565
                RVMFEVWRNHPQMIAVLV
1h2vC       54  RVMFEVWRNHPQMIAVLV    71

======================================================

Highlighted IDENTICAL residue LEU  542  index1  502  path   69  %Seq 100.00
Highlighted IDENTICAL residue VAL  548  index1  508  path   75  %Seq 100.00
Highlighted IDENTICAL residue THR  550  index1  510  path   77  %Seq 100.00
Highlighted IDENTICAL residue LYS  557  index1  517  path   84  %Seq 100.00
Highlighted IDENTICAL residue PHE  559  index1  519  path   86  %Seq 100.00
Highlighted IDENTICAL residue ALA  565  index1  525  path   93  %Seq 100.00
Highlighted IDENTICAL residue ALA  567  index1  527  path   95  %Seq 100.00
Highlighted IDENTICAL residue VAL  572  index1  532  path  100  %Seq 100.00
Highlighted IDENTICAL residue SER  579  index1  539  path  107  %Seq 100.00
Highlighted IDENTICAL residue LEU  604  index1  564  path  132  %Seq 100.00
Highlighted 10 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g05620-1h2vC.pir.txt.1H2V.pdb.conservation.pml

===============================================================================

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g05620-1h2vC.pir.txt PIR amino_acid 1H2V.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@


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