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At2g03360.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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
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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/At2g03360-1h1lB.pir.txt

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

Assigned types to 393 residues in Sequence 2-03360, 19 remain unknown
Assigned types to 207 residues in Sequence 1h1lB, 205 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 At2g03360-1h1lB.pir.txt into sequence alignment.

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

>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

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

Best alignment:
1H1L.pdb    80  ISHGPV    85
                ISHGP+
2-03360    175  ISHGPM   180

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

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.

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

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