At2g07724.1/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/

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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/At2g07724-1kyoD.pir.txt

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Assigned types to 107 residues in Sequence 2-07724, 2 remain unknown Assigned types to 87 residues in Sequence 1kyoD, 22 remain unknown

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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

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Translated sequence file At2g07724-1kyoD.pir.txt into sequence alignment.

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>1KYO.pdb Made from 35248 ATOM records in 1KYO.pdb AEVTQLSNGIVVATEHNPAHTASVGVVFGSGAANENPYNNGVSNLWKNIF LSKENSAVAAKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQ KANLLSSSNFEATKKSVLKQVQDFEDNDHPNRVLEHLHSTAFQNTPLSLP TRGTLESLENLVVADLESFANNHFLNSNAVVVGTGNIKHEDLVNSIESKN LSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVEGEPVNSPNYFV AKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSGL WGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQL YESGNPVNDANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLW DQDIAIAGTGQIEGLLDYMRIRSDMSMMRWLTVSARDAPTKISTLAVKVH GGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGGTFKSTLDREY ITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLE VSGENVVEADLKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGD SVAAIGIPVNKASLAQYEVLANYLTSALSELSGLISSAKLDKFTDGGLFT LFVRDQDSAVVSSNIKKIVADLKKGKDLSPAINYTKLKNAVQNESVSSPI ELNFDAVKDFKLGKFNYVAVGDVSNLPYLDELMAFRKSNVYLSLVNSYII DSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIELAFSSVEHI MRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGV IIFTLTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGG FSVSNPTIQRFFALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDR IPMHSYFIFKDLVTVFLFMLILALFVFYSPNTLGHPDNYIPGNPLVTPAS IVPEWYLLPFYAILRSIPDKLLGVITMFAAILVLLVLPFTDRSVVRGNTF KVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYFAYFLIIVP VISTIENVLFYIGRVNKMTAAEHGLHAPAYAWSHNGPFETFDHASIRRGY QVYREVCAACHSLDRVAWRTLVGVSHTNEEVRNMAEEFEYDDEPDEQGNP KKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIVKARHGGCDYIFSL LTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTPATT SQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAG IKTRKFVFNPPKKSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSS AGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFI RHRTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVPIG EAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGDKVIVGDTD QLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEE FFHLQHYLDTATAPRLFDKLKQSFTSIARIGDYILKSPVLSKLCVPVANQ FINLAGYKKLGLKFDDLIAEENPIMQTALRRLPEDESYARAYRIIRAHQT ELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELDNIEVSKGPPS GKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQ FLYVLIPAGIYWYWWKNGNEYNEFLYSKAGREELERVNVSSLYKTFFKRN AVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKAKIEVKLQESG AGLVQPSQSLSLTCSVTGYSITSGYYWNWIRLFPGNKLEWVGYISNVGDN NYNPSLKDRLSITRDTSKNQFFLKLNSVTTEDTATYYCARSEYYSVTGYA MDYWGQGTTVTVSSAWRHPDIELTQTPVSLAASLGDRVTISCRASQDINN FLNWYQQKPDGTIKLLIYYTSRLHAGVPSRFSGSGSGTDYSLTISNLEPE DIATYFCQHHIKFPWTFGAGTKLEIKAEVTQLSNGIVVATEHNPAHTASV GVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVAAKEGLALSSNISRDF QSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLKQVQDF EDNDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHF LNSNAVVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRL RDDTLPKAWISLAVEGEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIK LLDNIQEYQLCDNFNHFSLSYKDSGLWGFSTATRNVTMIDDLIHFTLKQW NRLTISVTDTEVERAKSLLKLQLGQLYESGNPVNDANLLGAEVLIKGSKL SLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYMRIRSD MSMMRWLTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTN TRSALKLVRESELLGGTFKSTLDREYITLKATFLKDDLPYYVNALADVLY KTAFKPHELTESVLPAARYDYAVAEQCPVKSAEDQLYAITFRKGLGNPLL YDGVERVSLQDIKDFADKVYTKENLEVSGENVVEADLKRFVDESLLSTLP AGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVLANYL TSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKK GKDLSPAINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVS NLPYLDELMAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVI QIVTGIFMAMHYSSNIELAFSSVEHIMRDVHNGYILRYLHANGASFFFMV MFMHMAKGLYYGSYRSPRVTLWNVGVIIFTLTIATAFLGYCCVYGQMSHW GATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFFALHYLVPFIIAA MVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLILAL FVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGV ITMFAAILVLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGAC HVEVPYVLMGQIATFIYFAYFLIIVPVISTIENVLFYIGRVNKMTAAEHG LHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGV SHTNEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAA NQGALPPDLSLIVKARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYF PGGSIAMARVLFDDMVEYEDGTPATTSQMAKDVTTFLNWCAEPEHDERKR LGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFVFNPPKKSTYRTPNFDDV LKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLAMA KVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQT DADRVKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIR KGPAPLNLEIPAYEFDGDKVIVGDTDQLEDLREHFKNTEEGKALVHHYEE CAERVKIQQQQPGYADLEHKEDCVEEFFHLQHYLDTATAPRLFDKLKQSF TSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPI MQTALRRLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLP YILEAEAAAKEKDELDNIEVSKGPPSGKTYMGWWGHMGGPKQKGITSYAV SPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLIPAGIYWYWWKNGNEYNEF LYSKAGREELERVNVSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITS WYENHNKGKLWKDVKAKIEVKLQESGAGLVQPSQSLSLTCSVTGYSITSG YYWNWIRLFPGNKLEWVGYISNVGDNNYNPSLKDRLSITRDTSKNQFFLK LNSVTTEDTATYYCARSEYYSVTGYAMDYWGQGTTVTVSSAWRHPDIELT QTPVSLAASLGDRVTISCRASQDINNFLNWYQQKPDGTIKLLIYYTSRLH AGVPSRFSGSGSGTDYSLTISNLEPEDIATYFCQHHIKFPWTFGAGTKLE IKTEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQA EGYSYTDANIKKNVLWDENNMSEYLTNPKYIPGTKMAFGGLKKEKDRNDL ITYLKKACE

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Best alignment: 1KYO.pdb 1992  GYISNVGDNNYNPSLKDRLSITRDTSKNQFFLKL  2025 G+ +N     NP +  +       S+N F  K+ 2-07724     19  GFCANERTKCLNPKMPSKSMFGGSVSENLFLSKI    52

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Highlighted IDENTICAL residue GLY  50  index1 1992  path   19  %Seq 100.00 Highlighted IDENTICAL residue ASN  54  index1 1996  path   23  %Seq 100.00 Highlighted IDENTICAL residue LEU  64  index1 2006  path   33  %Seq 100.00 Highlighted IDENTICAL residue ARG  67  index1 2009  path   36  %Seq  50.00 Highlighted IDENTICAL residue LEU  68  index1 2010  path   37  %Seq  50.00 Highlighted IDENTICAL residue SER  69  index1 2011  path   38  %Seq  50.00 Highlighted IDENTICAL residue ILE  70  index1 2012  path   41  %Seq 100.00 Highlighted IDENTICAL residue THR  74  index1 2016  path   45  %Seq 100.00 Highlighted IDENTICAL residue GLN  78  index1 2020  path   49  %Seq  50.00 Highlighted IDENTICAL residue PHE  79  index1 2021  path   50  %Seq  50.00 Highlighted IDENTICAL residue PHE  80  index1 2022  path   51  %Seq  50.00 Highlighted IDENTICAL residue LEU  81  index1 2023  path   52  %Seq  50.00 Highlighted IDENTICAL residue LYS  82  index1 2024  path   53  %Seq  50.00 Highlighted IDENTICAL residue LEU  83  index1 2025  path   54  %Seq  50.00 Highlighted 14 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g07724-1kyoD.pir.txt.1KYO.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g07724-1kyoD.pir.txt PIR amino_acid 1KYO.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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