At2g10965.1/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
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Sequence 1
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Sequence 2
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g10965-1e6yA.pir.txt
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Assigned types to 249 residues in Sequence 2-10965, 26 remain unknown
Assigned types to 213 residues in Sequence 1e6yA, 62 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 At2g10965-1e6yA.pir.txt into sequence alignment.
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>1E6Y.pdb Made from 18862 ATOM records in 1E6Y.pdb
AADIFSKFKKDMEVKFAQEFGSNKQTGGDITDKTAKFLRLGPEQDPRKVE
MIKAGKEIAEKRGIAFYNPMMHSGAPLGQRAITPYTISGTDIVCEPDDLH
YVNNAAMQQMWDDIRRTCIVGLDMAHETLEKRLGKEVTPETINHYLEVLN
HAMPGAAVVQEMMVETHPALVDDCYVKVFTGDDALADEIDKQFLIDINKE
FSEEQAAQIKASIGKTSWQAIHIPTIVSRTTDGAQTSRWAAMQIGMSFIS
AYAMCAGEAAVADLSFAAKAALVSMGEMLPARARGPNEPGGLSFGHLSDI
VQTSRVSEDPAKIALEVVGAGCMLYDQIWLGSYMSGGVGFTQYATAAYTD
DILDNNTYYDVDYINDKYNGAATVGKDNKVKASLEVVKDIATESTLYGIE
TYEKFPTALEDHFGGSQRATVLAAAAGVACSLATGNANAGLSGWYLSMYL
HKEAWGRLGFFFDLQDQGATNVLSYQGDEGLPDELRGPNYPNYAMNVGHQ
GGYAGIAQAAHSGRGDAFTVNPLLKVCFADDLLPFNFAEPRREFGRGAIR
EFVPAGERSLVIPASDTVDIYDDRGKLLESNVDIMSLAPTRNAAIQSIIM
DTKRSVAVNLAGIQGALASGKMGGKGRQILGRGLNYDIVGNADAIAENVK
KLVQVDEGDDTNVIKVKGGKSLLIQSPKSRIIAGADFMSATTVGAAAVTQ
TIMDMFGTDPYDAPIVKSAVWGSYPQTMDLMGGQVQGILSIPQNNEGLGF
SLRNIMANHVAAISNRNAMNASALSSIYEQSGIFEMGGAVGMFERHQLLG
LAYQGLNANNLLYDIVKENGKDGTIGTVIESVVRRAIEAGIISVDKTAPS
GYNFYKANDVPKWNACAAVGTLAATLVNCGAGRAAQNVSSTLLYFNDILE
KETGLPGCDYGKVEGTAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSRGFA
IPCVCAAVALDAGTQMFSIESTSGLIGDVFGAIPEFREPIKAVAGVAYER
QYYPGATSVAANRRKHMSGKLEKLREISDEDLTAVLGHRAPGSDYPSTHP
PLAEMGEPASTRENVAATPGAAAGDRVRYIQFADSMYNAPATPYFRSYFA
AINFRGVDPGTLSGRQIVEARERDMEQCAKVQMETEITDHALAGVRGATV
HGHSVRLQEDGVMFDMLDRRRLENGTIIMDKDQVAIPLDRKVDLGKPMSS
EEAAKRTTIYRVDNVAFRDDAEVVEWVHRIFDQRTKFGFQPKAADIFSKF
KKDMEVKFAQEFGSNKQTGGDITDKTAKFLRLGPEQDPRKVEMIKAGKEI
AEKRGIAFYNPMMHSGAPLGQRAITPYTISGTDIVCEPDDLHYVNNAAMQ
QMWDDIRRTCIVGLDMAHETLEKRLGKEVTPETINHYLEVLNHAMPGAAV
VQEMMVETHPALVDDCYVKVFTGDDALADEIDKQFLIDINKEFSEEQAAQ
IKASIGKTSWQAIHIPTIVSRTTDGAQTSRWAAMQIGMSFISAYAMCAGE
AAVADLSFAAKAALVSMGEMLPARARGPNEPGGLSFGHLSDIVQTSRVSE
DPAKIALEVVGAGCMLYDQIWLGSYMSGGVGFTQYATAAYTDDILDNNTY
YDVDYINDKYNGAATVGKDNKVKASLEVVKDIATESTLYGIETYEKFPTA
LEDHFGGSQRATVLAAAAGVACSLATGNANAGLSGWYLSMYLHKEAWGRL
GFFFDLQDQGATNVLSYQGDEGLPDELRGPNYPNYAMNVGHQGGYAGIAQ
AAHSGRGDAFTVNPLLKVCFADDLLPFNFAEPRREFGRGAIREFVPAGER
SLVIPASDTVDIYDDRGKLLESNVDIMSLAPTRNAAIQSIIMDTKRSVAV
NLAGIQGALASGKMGGKGRQILGRGLNYDIVGNADAIAENVKKLVQVDEG
DDTNVIKVKGGKSLLIQSPKSRIIAGADFMSATTVGAAAVTQTIMDMFGT
DPYDAPIVKSAVWGSYPQTMDLMGGQVQGILSIPQNNEGLGFSLRNIMAN
HVAAISNRNAMNASALSSIYEQSGIFEMGGAVGMFERHQLLGLAYQGLNA
NNLLYDIVKENGKDGTIGTVIESVVRRAIEAGIISVDKTAPSGYNFYKAN
DVPKWNACAAVGTLAATLVNCGAGRAAQNVSSTLLYFNDILEKETGLPGC
DYGKVEGTAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSRGFAIPCVCAAV
ALDAGTQMFSIESTSGLIGDVFGAIPEFREPIKAVAGVLAYERQYYPGAT
SVAANRRKHMSGKLEKLREISDEDLTAVLGHRAPGSDYPSTHPPLAEMGE
PASTRENVAATPGAAAGDRVRYIQFADSMYNAPATPYFRSYFAAINFRGV
DPGTLSGRQIVEARERDMEQCAKVQMETEITDHALAGVRGATVHGHSVRL
QEDGVMFDMLDRRRLENGTIIMDKDQVAIPLDRKVDLGKPMSSEEAAKRT
TIYRVDNVAFRDDAEVVEWVHRIFDQRTKFGFQPK
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Best alignment:
1E6Y.pdb 639 VGNADAIAENVKKL 652
 VG+A A E V KL
2-10965 141 VGSAAATVERVNKL 154
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Highlighted IDENTICAL residue ALA 2079 index1 642 path 146 %Seq 100.00
Highlighted 1 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10965-1e6yA.pir.txt.1E6Y.pdb.conservation.pml
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The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10965-1e6yA.pir.txt PIR amino_acid 1E6Y.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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