At2g01580.1/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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01580_2bs2_C.pir.txt
======================================================
Assigned types to 191 residues in Sequence 2-01580, 6 remain unknown
Assigned types to 180 residues in Sequence 2bs2_C, 21 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 41 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 173 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
Translated sequence file At2g01580_2bs2_C.pir.txt into sequence alignment.
======================================================
>2BS2.pdb Made from 18272 ATOM records in 2BS2.pdb
MKVQYCDSLVIGGGLAGLRAAVATQQKGLSTIVLSLIPVKRSHSAAAQGG
MQASLGNSKMSDGDNEDLHFMDTVKGSDWGCDQKVARMFVNTAPKAIREL
AAWGVPWTRIHKGDRMAIINAQKTTITEEDFRHGLIHSRDFGGTKKWRTC
YTADATGHTMLFAVANECLKLGVSIQDRKEAIALIHQDGKCYGAVVRDLV
TGDIIAYVAKGTLIATGGYGRIYKNTTNAVVCEGTGTAIALETGIAQLGN
MEAVQFHPTPLFPSGILLTEGCRGDGGILRDVDGHRFMPDYEPEKKELAS
RDVVSRRMIEHIRKGKGVQSPYGQHLWLDISILGRKHIETNLRDVQEICE
YFAGIDPAEKWAPVLPMQHYSMGGIRTDYRGEAKLKGLFSAGEAACWDMH
GFNRLGGNSVSEAVVAGMIVGEYFAEHCANTQVDLETKTLEKFVKGQEAY
MKSLVESKGTEDVFKIKNRMKDVMDDNVGIFRDGPHLEKAVKELEELYKK
SKNVGIKNKRLHANPELEEAYRVPMMLKVALCVAKGALDRTESRGAHNRE
DYPKRDDINWLNRTLASWPNPEQTLPTLEYEALDVNEMEIAPGYRGYGAK
GNYIENPLSVKRQEEIDKIQSELEAAGKDRHAIQEALMPYELPAKYKARN
ERLGDKMGRMLTIRVFKYDPQSAVSKPHFQEYKIEEAPSMTIFIVLNMIR
ETYDPDLNFDFVCRAGICGSCGMMINGRPSLACRTLTKDFEDGVITLLPL
PAFKLIKDLSVDTGNWFNGMSQRVESWIHAQKEHDISKLEERIEPEVAQE
VFELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRFMIDPHDERTDED
YYELIGDDDGVFGCMTLLACHDVCPKNLPLQSKIAYLRRKMVSVNMMTNE
SILESYSGVTPERKKSRMPAKLDWWQSATGLFLGLFMIGHMFFVSTILLG
DNVMLWVTKKFELDFIFEGGKPIVVSFLAAFVFAVFIAHAFLAMRKFPIN
YRQYLTFKTHKDLMRHGDTTLWWIQAMTGFAMFFLGSVHLYIMMTQPQTI
GPVSSSFRMVSEWMWPLYLVLLFAVELHGSVGLYRLAVKWGWFDGETPDK
TRANLKKLKTLMSAFLIVLGLLTFGAYVKKGLEQTDPNIDYKYFDYKRTH
EMKVQYCDSLVIGGGLAGLRAAVATQQKGLSTIVLSLIPVKRSHSAAAQG
GMQASLGNSKMSDGDNEDLHFMDTVKGSDWGCDQKVARMFVNTAPKAIRE
LAAWGVPWTRIHKGDRMAIINAQKTTITEEDFRHGLIHSRDFGGTKKWRT
CYTADATGHTMLFAVANECLKLGVSIQDRKEAIALIHQDGKCYGAVVRDL
VTGDIIAYVAKGTLIATGGYGRIYKNTTNAVVCEGTGTAIALETGIAQLG
NMEAVQFHPTPLFPSGILLTEGCRGDGGILRDVDGHRFMPDYEPEKKELA
SRDVVSRRMIEHIRKGKGVQSPYGQHLWLDISILGRKHIETNLRDVQEIC
EYFAGIDPAEKWAPVLPMQHYSMGGIRTDYRGEAKLKGLFSAGEAACWDM
HGFNRLGGNSVSEAVVAGMIVGEYFAEHCANTQVDLETKTLEKFVKGQEA
YMKSLVESKGTEDVFKIKNRMKDVMDDNVGIFRDGPHLEKAVKELEELYK
KSKNVGIKNKRLHANPELEEAYRVPMMLKVALCVAKGALDRTESRGAHNR
EDYPKRDDINWLNRTLASWPNPEQTLPTLEYEALDVNEMEIAPGYRGYGA
KGNYIENPLSVKRQEEIDKIQSELEAAGKDRHAIQEALMPYELPAKYKAR
NERLGDKMGRMLTIRVFKYDPQSAVSKPHFQEYKIEEAPSMTIFIVLNMI
RETYDPDLNFDFVCRAGICGSCGMMINGRPSLACRTLTKDFEDGVITLLP
LPAFKLIKDLSVDTGNWFNGMSQRVESWIHAQKEHDISKLEERIEPEVAQ
EVFELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRFMIDPHDERTDE
DYYELIGDDDGVFGCMTLLACHDVCPKNLPLQSKIAYLRRKMVSVNMMTN
ESILESYSGVTPERKKSRMPAKLDWWQSATGLFLGLFMIGHMFFVSTILL
GDNVMLWVTKKFELDFIFEGGKPIVVSFLAAFVFAVFIAHAFLAMRKFPI
NYRQYLTFKTHKDLMRHGDTTLWWIQAMTGFAMFFLGSVHLYIMMTQPQT
IGPVSSSFRMVSEWMWPLYLVLLFAVELHGSVGLYRLAVKWGWFDGETPD
KTRANLKKLKTLMSAFLIVLGLLTFGAYVKKGLEQTDPNIDYKYFDYKRT
HE
======================================================
Best alignment:
2BS2.pdb 453 SLVESKGTEDVFKIKNRMKDVM 474
 +L+ SK T++VFK N +DV+
2-01580 103 NLLNSKETDEVFK-ANINRDVL 123
======================================================
Highlighted IDENTICAL residue LEU 454 index1 454 path 105 %Seq 100.00
Highlighted IDENTICAL residue LYS 458 index1 458 path 109 %Seq 100.00
Highlighted 2 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01580_2bs2_C.pir.txt.2BS2.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01580_2bs2_C.pir.txt PIR amino_acid 2BS2.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@