At2g10285.1/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
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.
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