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At2g07360.1/PDB N-terminus

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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

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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g07360-1-700-1gw5B.pir.txt

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

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

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

>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

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

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

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

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

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

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.

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

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