At2g03360.1/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
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Got here 3
Got here 4
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Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g03360-1h1lB.pir.txt
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Assigned types to 393 residues in Sequence 2-03360, 19 remain unknown
Assigned types to 207 residues in Sequence 1h1lB, 205 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 At2g03360-1h1lB.pir.txt into sequence alignment.
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>1H1L.pdb Made from 15392 ATOM records in 1H1L.pdb
TNATGERNLALIQEVLEVFPETARKERRKHMMVSDPKMKSVGKCIISNRK
SQPGVMTVRGCAYAGSKGVVFGPIKDMAHISHGPVGCGQYSRAGRRNYYT
GVSGVDSFGTLNFTSDFQERDIVFGGDKKLSKLIEEMELLFPLTKGITIQ
SECPVGLIGDDISAVANASSKALDKPVIPVRCEGFRGVSQSLGHHIANDV
VRDWILNNREGQPFETTPYDVAIIGDYNIGGDAWASRILLEEMGLRVVAQ
WSGDGTLVEMENTPFVKLNLVHCYRSMNYIARHMEEKHQIPWMEYNFFGP
TKIAESLRKIADQFDDTIRANAEAVIARYEGQMAAIIAKYRPRLEGRKVL
LYMGGLRPRHVIGAYEDLGMEIIAAGYEFAHNDDYDRTLPDLKEGTLLFD
DASSYELEAFVKALKPDLIGSGIKEKYIFQKMGVPFRQMHSWDYSGPYHG
YDGFAIFARDMDMTLNNPAWNELTAPWLSQTIDKINSCYPLFEQDEYQEL
FRNKRQLEEAHDAQRVQEVFAWTTTAEYEALNFRREALTVDPAKACQPLG
AVLCSLGFANTLPYVHGSQGCVAYFRTYFNRHFKEPIACVSDSMTEDAAV
FGGNNNMNLGLQNASALYKPEIIAVSTTCMAEVIGDDLQAFIANAKKDGF
VDSSIAVPHAHTPSFIGSHVTGWDNMFEGFAKTFTADYQGQPGKLPKLNL
VTGFETYLGNFRVLKRMMEQMAVPCSLLSDPSEVLDTPADGHYRMYSGGT
TQQEMKEAPDAIDTLLLQPWQLLKSKKVVQEMWNQPATEVAIPLGLAATD
ELLMTVSQLSGKPIADALTLERGRLVDMMLDSHTWLHGKKFGLYGDPDFV
MGLTRFLLELGCEPTVILSHNANKRWQKAMNKMLDASPYGRDSEVFINCD
LWHFRSLMFTRQPDFMIGNSYGKFIQRDTLAKGKAFEVPLIRLGFPLFDR
HHLHRQTTWGYEGAMNIVTTLVNAVLEKLDSDTSQLGKTDYSFDLVRTNA
TGERNLALIQEVLEVFPETARKERRKHMMVSDPKMKSVGKCIISNRKSQP
GVMTVRGCAYAGSKGVVFGPIKDMAHISHGPVGCGQYSRAGRRNYYTGVS
GVDSFGTLNFTSDFQERDIVFGGDKKLSKLIEEMELLFPLTKGITIQSEC
PVGLIGDDISAVANASSKALDKPVIPVRCEGFRGVSQSLGHHIANDVVRD
WILNNREGQPFETTPYDVAIIGDYNIGGDAWASRILLEEMGLRVVAQWSG
DGTLVEMENTPFVKLNLVHCYRSMNYIARHMEEKHQIPWMEYNFFGPTKI
AESLRKIADQFDDTIRANAEAVIARYEGQMAAIIAKYRPRLEGRKVLLYM
GGLRPRHVIGAYEDLGMEIIAAGYEFAHNDDYDRTLPDLKEGTLLFDDAS
SYELEAFVKALKPDLIGSGIKEKYIFQKMGVPFRQMHSWDYSGPYHGYDG
FAIFARDMDMTLNNPAWNELTAPWLSQTIDKINSCYPLFEQDEYQELFRN
KRQLEEAHDAQRVQEVFAWTTTAEYEALNFRREALTVDPAKACQPLGAVL
CSLGFANTLPYVHGSQGCVAYFRTYFNRHFKEPIACVSDSMTEDAAVFGG
NNNMNLGLQNASALYKPEIIAVSTTCMAEVIGDDLQAFIANAKKDGFVDS
SIAVPHAHTPSFIGSHVTGWDNMFEGFAKTFTADYQGQPGKLPKLNLVTG
FETYLGNFRVLKRMMEQMAVPCSLLSDPSEVLDTPADGHYRMYSGGTTQQ
EMKEAPDAIDTLLLQPWQLLKSKKVVQEMWNQPATEVAIPLGLAATDELL
MTVSQLSGKPIADALTLERGRLVDMMLDSHTWLHGKKFGLYGDPDFVMGL
TRFLLELGCEPTVILSHNANKRWQKAMNKMLDASPYGRDSEVFINCDLWH
FRSLMFTRQPDFMIGNSYGKFIQRDTLAKGKAFEVPLIRLGFPLFDRHHL
HRQTTWGYEGAMNIVTTLVNAVLEKLDSDTSQLGKTDYSFDLVR
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Best alignment:
1H1L.pdb 80 ISHGPV 85
 ISHGP+
2-03360 175 ISHGPM 180
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Highlighted IDENTICAL residue ILE 80 index1 80 path 175 %Seq 50.00
Highlighted IDENTICAL residue SER 81 index1 81 path 176 %Seq 50.00
Highlighted IDENTICAL residue HIS 82 index1 82 path 177 %Seq 50.00
Highlighted IDENTICAL residue GLY 83 index1 83 path 178 %Seq 50.00
Highlighted IDENTICAL residue PRO 84 index1 84 path 179 %Seq 50.00
Highlighted IDENTICAL residue VAL 85 index1 85 path 180 %Seq 50.00
Highlighted 6 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03360-1h1lB.pir.txt.1H1L.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03360-1h1lB.pir.txt PIR amino_acid 1H1L.pdb B 100.0 BLOSUM62.dat 
completed successfully.
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