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At2g10285.1/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/At2g10285-1nb4_A.pir.txt

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

Assigned types to 116 residues in Sequence 2-10285, 15 remain unknown
Assigned types to 103 residues in Sequence 1nb4_A, 28 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 87  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 88  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 89  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 90  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 110  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 111  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 112  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 116  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 117  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 118  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 119  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 120  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 121  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 122  All residues are positively and negatively charged

Translated sequence file At2g10285-1nb4_A.pir.txt into sequence alignment.

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

>1NB4.pdb  Made from 8771 ATOM records in 1NB4.pdb
SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQK
KVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSK
FGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPE
KGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQR
VEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEAR
QAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAT
AACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPP
GDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETA
RHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGA
CYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTW
RHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGW
FVAGYSGGDIYHSLSRSMSYTWTGALITPCAAEESKLPINPLSNSLLRHH
NMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLS
IEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPI
DTTIMAKSEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQ
AVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIR
VEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGV
LTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAA
ALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYL
TRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILL
AQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINR
VASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKL
KLTPIPAASQLDLSGWFVAGYSGGDIYHSLS

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

Best alignment:
1NB4.pdb   452  YSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWR   501
                YSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWR
1nb4_A       1  YSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWR    50

1NB4.pdb   502  HRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWF   551
                HRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWF
1nb4_A      51  HRARSVRAKLLSQGGRAATCGRYXXXXAVRTKLKLTPIPAASQLDXXXXF   100

1NB4.pdb   552  VAGYSGGDIYHSLSRS   567
                VAGYSGGDIYHSLSR+
1nb4_A     101  VAXXXXXXXYHSLSRA   116

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

Highlighted IDENTICAL residue SER  453  index1  453  path    7  %Seq 100.00
Highlighted IDENTICAL residue LEU  457  index1  457  path   11  %Seq 100.00
Highlighted IDENTICAL residue PRO  460  index1  460  path   14  %Seq 100.00
Highlighted IDENTICAL residue ARG  465  index1  465  path   19  %Seq 100.00
Highlighted IDENTICAL residue ALA  471  index1  471  path   25  %Seq 100.00
Highlighted IDENTICAL residue LEU  474  index1  474  path   36  %Seq 100.00
Highlighted IDENTICAL residue GLY  480  index1  480  path   42  %Seq 100.00
Highlighted IDENTICAL residue PRO  496  index1  496  path   58  %Seq 100.00
Highlighted IDENTICAL residue ARG  508  index1  508  path   70  %Seq 100.00
Highlighted IDENTICAL residue LYS  510  index1  510  path   72  %Seq 100.00
Highlighted IDENTICAL residue LEU  545  index1  545  path  107  %Seq 100.00
Highlighted IDENTICAL residue ASP  546  index1  546  path  108  %Seq 100.00
Highlighted IDENTICAL residue PHE  551  index1  551  path  113  %Seq 100.00
Highlighted IDENTICAL residue ALA  553  index1  553  path  115  %Seq 100.00
Highlighted IDENTICAL residue HIS  562  index1  562  path  124  %Seq 100.00
Highlighted IDENTICAL residue SER  563  index1  563  path  125  %Seq 100.00
Highlighted IDENTICAL residue ARG  566  index1  566  path  128  %Seq 100.00
Highlighted 17 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10285-1nb4_A.pir.txt.1NB4.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10285-1nb4_A.pir.txt PIR amino_acid 1NB4.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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