At2g07360.1/PDB N-terminus

&&&&&&&&&&&&&&&&&&&& 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 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 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 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 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/At2g07360-1-700-1gw5B.pir.txt

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Assigned types to 1196 residues in Sequence 2-07360, 13 remain unknown Assigned types to 466 residues in Sequence 1gw5B, 743 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 At2g07360-1-700-1gw5B.pir.txt into sequence alignment.

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>1GW5.pdb Made from 13211 ATOM records in 1GW5.pdb GMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKY VCKLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSEL IRLINNAIKNDLASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAG DTMDSVKQSAALCLLRLYRTSPDLVPMGDWTSRVVHLLNDQHLGVVTAAT SLITTLAQKNPEEFKTSVSLAVSRLSRIVTSASTDLQDYTYYFVPAPWLS VKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKVQHSNAKNA VLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLAS SEFSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAE MLSYLETADYSIREEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVS EEVWYRVIQIVINRDDVQGYAAKTVFEALQAPACHENLVKVGGYILGEFG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSKYFTTNKKGEIFELK AELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLV YLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKIT EYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLI ADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQ IFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLEL LPKDSDYYNMLLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQ EIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYATEVDVDF VRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFR KYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESF LEGFHDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLSXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIEPTLLDELICHIGS LASVYHKPPNAFVMIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVI HARQQVRSPVTNIARTSFFHVKRSNIWLAAVTKQNVNAAMVFEFLYKMCD VMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQG IKSQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKS YLSGMPECKFGMNDKIVIKIAIDDCTFHQCVRLSRSISFIPPDGEFELMR YRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPT PLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTN DKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIG RSGIYETRCMIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTV RDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVL NEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSL E

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Best alignment: 1GW5.pdb  595  EIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVS-SLFPDVVNC-MQTD   642 I EL A L ++K  +K+ V  V   + V   V  SL P ++    Q + 2-07360   109  SIHELAATL--DQKSSQKQLVNHVFPKLAVYNSVDPSLAPSLLMLNQQCE   156

1GW5.pdb  643  NLELKKLVYLYL   654 + + + VY YL 2-07360    157  DRNVLRYVYYYL   168

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Highlighted IDENTICAL residue ILE  15  index1  596  path  110  %Seq 100.00 Highlighted IDENTICAL residue GLU  17  index1  598  path  112  %Seq 100.00 Highlighted IDENTICAL residue LEU  18  index1  599  path  113  %Seq 100.00 Highlighted IDENTICAL residue ALA  20  index1  601  path  115  %Seq 100.00 Highlighted IDENTICAL residue LEU  22  index1  603  path  117  %Seq 100.00 Highlighted IDENTICAL residue LYS  31  index1  612  path  124  %Seq 100.00 Highlighted IDENTICAL residue VAL  34  index1  615  path  127  %Seq  50.00 Highlighted IDENTICAL residue LYS  35  index1  616  path  128  %Seq  50.00 Highlighted IDENTICAL residue ALA  40  index1  621  path  133  %Seq 100.00 Highlighted IDENTICAL residue VAL  47  index1  628  path  140  %Seq 100.00 Highlighted IDENTICAL residue GLN  59  index1  640  path  156  %Seq 100.00 Highlighted IDENTICAL residue VAL  69  index1  650  path  166  %Seq 100.00 Highlighted IDENTICAL residue TYR  70  index1  651  path  167  %Seq 100.00 Highlighted IDENTICAL residue TYR  72  index1  653  path  169  %Seq 100.00 Highlighted IDENTICAL residue LEU  73  index1  654  path  170  %Seq 100.00 Highlighted 15 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g07360-1-700-1gw5B.pir.txt.1GW5.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g07360-1-700-1gw5B.pir.txt PIR amino_acid 1GW5.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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