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