FANDOM


&&&&&&&&&&&&&&&&&&&& 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/At2g07724-1kyoD.pir.txt

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

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

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

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

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

>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

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

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

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

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.

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

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