At2g07713.1/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/

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

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 Sequence 2 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/At2g07713-1jmu_G.pir.txt

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

Assigned types to 122 residues in Sequence 2-07713, 19 remain unknown Assigned types to 98 residues in Sequence 1jmu_G, 43 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

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

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 36 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 37 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 38 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 39 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 40 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 41 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 42 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 43 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 44 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 45 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 46 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 71 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 115 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 116 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 117 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 118 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 119 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 120 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 121 All residues are positively and negatively charged

Translated sequence file At2g07713-1jmu_G.pir.txt into sequence alignment.

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

>1JMU.pdb Made from 23268 ATOM records in 1JMU.pdb TINVTGDGNVFKPSAETSSTAVPSLSLSPGMLNPGGVPWIAIGDETSVTS PGALRRMTSKDIDEPLVVVTEHAIANFTKAEMALEFNREFLDKLRVLSVS PKYSDLLTYVDCYVGVSARQALNNFQKQVPVITPTRQTMYVDSIQAALKA LEKWEIDLRVAQTLLPTNVPIGEVSCPMQSVVKLLDDQLPDDSLIRRYPK EAAVALAKRNGGIQWMDVSEGTVMNEAVNAVAASALAPSASAPPLEEKSK LTEQAMDLVTAAEPEIIASLVPVPAPVFAIPPKPADYNVRTLKIDEATWL RMIPKTMGTLFQIQVTDNTGTNWHFNLRGGTRVVNLDQIAPMRFVLDLGG KSYKETSWDPNGKKVGFIVFQSKIPFELWTAASQIGQATVVNYVQLYAED SSFTAQSIIATTSLAYNYEPEQLNKTDPEMNYYLLATFIDSAAITPTNMT QPDVWDALLTMSPLSAGEVTVKGAVVSEVVPAELIGSYTPESLNASLPND AARCMIDRASKIAEAIKIDDDAGPDEYSPNSVPIQGQLAISQLETGYGVR IFNPKGILSKIASRAMQAFIGDPSTIITQAAPVLSDKNNWIALAQGVKTS LRTKSLSAGVKTAVSKLSSSESIQNWTQGFLDKVSTHFPAPTINVTGDGN VFKPSAETSSTAVPSLSLSPGMLNPGGVPWIAIGDETSVTSPGALRRMTS KDIDEPLVVVTEHAIANFTKAEMALEFNREFLDKLRVLSVSPKYSDLLTY VDCYVGVSARQALNNFQKQVPVITPTRQTMYVDSIQAALKALEKWEIDLR VAQTLLPTNVPIGEVSCPMQSVVKLLDDQLPDDSLIRRYPKEAAVALAKR NGGIQWMDVSEGTVMNEAVNAVAASALAPSASAPPLEEKSKLTEQAMDLV TAAEPEIIASLVPVPAPVFAIPPKPADYNVRTLKIDEATWLRMIPKTMGT LFQIQVTDNTGTNWHFNLRGGTRVVNLDQIAPMRFVLDLGGKSYKETSWD PNGKKVGFIVFQSKIPFELWTAASQIGQATVVNYVQLYAEDSSFTAQSII ATTSLAYNYEPEQLNKTDPEMNYYLLATFIDSAAITPTNMTQPDVWDALL TMSPLSAGEVTVKGAVVSEVVPAELIGSYTPESLNASLPNDAARCMIDRA SKIAEAIKIDDDAGPDEYSPNSVPIQGQLAISQLETGYGVRIFNPKGILS KIASRAMQAFIGDPSTIITQAAPVLSDKNNWIALAQGVKTSLRTKSLSAG VKTAVSKLSSSESIQNWTQGFLDKVSTHFPAPTINVTGDGNVFKPSAETS STAVPSLSLSPGMLNPGGVPWIAIGDETSVTSPGALRRMTSKDIDEPLVV VTEHAIANFTKAEMALEFNREFLDKLRVLSVSPKYSDLLTYVDCYVGVSA RQALNNFQKQVPVITPTRQTMYVDSIQAALKALEKWEIDLRVAQTLLPTN VPIGEVSCPMQSVVKLLDDQLPDDSLIRRYPKEAAVALAKRNGGIQWMDV SEGTVMNEAVNAVAASALAPSASAPPLEEKSKLTEQAMDLVTAAEPEIIA SLVPVPAPVFAIPPKPADYNVRTLKIDEATWLRMIPKTMGTLFQIQVTDN TGTNWHFNLRGGTRVVNLDQIAPMRFVLDLGGKSYKETSWDPNGKKVGFI VFQSKIPFELWTAASQIGQATVVNYVQLYAEDSSFTAQSIIATTSLAYNY EPEQLNKTDPEMNYYLLATFIDSAAITPTNMTQPDVWDALLTMSPLSAGE VTVKGAVVSEVVPAELIGSYTPESLNASLPNDAARCMIDRASKIAEAIKI DDDAGPDEYSPNSVPIQGQLAISQLETGYGVRIFNPKGILSKIASRAMQA FIGDPSTIITQAAPVLSDKNNWIALAQGVKTSLRTKSLSAGVKTAVSKLS SSESIQNWTQGFLDKVSTHFPAPMEVCLPNGHQIVDLINNAFEGRVSIYS AQEGWDKTISAQPDMMVCGGAVVCMHCLGVVGSLQRKLKHLPHHRCNQQI RHQDYVDVQFADRVTAHWKRGMLSFVCQMHAMMNDVSPEDLDRVRTEGGS LVELNWLQVDPNSMFRSIHSSWTDPLQVVDDLDTKLDQYWTALNLMIDSS DLVPNFMMRDPSHAFNGVRLEGDARQTQFSRTFDSRSSLEWGVMVYDYSE LEHDPSKGRAYRKELVTPARDFGHFGLSHYSRATTPILGKMPAVFSGMLT GNCKMYPFIKGTAKLKTVRKLVDSVNHAWGVEKIRYALGPGGMTGWYNRT MQQAPIVLTPAALTMFSDTTKFGDLDYPVMIGDPMILGMEVCLPNGHQIV DLINNAFEGRVSIYSAQEGWDKTISAQPDMMVCGGAVVCMHCLGVVGSLQ RKLKHLPHHRCNQQIRHQDYVDVQFADRVTAHWKRGMLSFVCQMHAMMND VSPEDLDRVRTEGGSLVELNWLQVDPNSMFRSIHSSWTDPLQVVDDLDTK LDQYWTALNLMIDSSDLVPNFMMRDPSHAFNGVRLEGDARQTQFSRTFDS RSSLEWGVMVYDYSELEHDPSKGRAYRKELVTPARDFGHFGLSHYSRATT PILGKMPAVFSGMLTGNCKMYPFIKGTAKLKTVRKLVDSVNHAWGVEKIR YALGPGGMTGWYNRTMQQAPIVLTPAALTMFSDTTKFGDLDYPVMIGDPM ILGMEVCLPNGHQIVDLINNAFEGRVSIYSAQEGWDKTISAQPDMMVCGG AVVCMHCLGVVGSLQRKLKHLPHHRCNQQIRHQDYVDVQFADRVTAHWKR GMLSFVCQMHAMMNDVSPEDLDRVRTEGGSLVELNWLQVDPNSMFRSIHS SWTDPLQVVDDLDTKLDQYWTALNLMIDSSDLVPNFMMRDPSHAFNGVRL EGDARQTQFSRTFDSRSSLEWGVMVYDYSELEHDPSKGRAYRKELVTPAR DFGHFGLSHYSRATTPILGKMPAVFSGMLTGNCKMYPFIKGTAKLKTVRK LVDSVNHAWGVEKIRYALGPGGMTGWYNRTMQQAPIVLTPAALTMFSDTT KFGDLDYPVMIGDPMILG

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

Best alignment: 1JMU.pdb   38  PWIAIGDETSVTSPGALRRMTSKDIDEPLVVVTEHAIANFTKAEMALEFN    87 P + + + S TS    + +   +++  L V   +   +FT+   A  F 2-07713     15  PAVPVSSKASSTSFIKTKALRISEVNRELSVPRVYREKSFTRRLNAPIFG    64

1JMU.pdb   88  REFLDK    93 F+DK 2-07713    65  SLFVDK    70

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

Highlighted IDENTICAL residue PRO  47  index1   38  path   15  %Seq  50.00 Highlighted IDENTICAL residue ILE  49  index1   40  path   17  %Seq 100.00 Highlighted IDENTICAL residue THR  55  index1   46  path   23  %Seq 100.00 Highlighted IDENTICAL residue THR  58  index1   49  path   26  %Seq 100.00 Highlighted IDENTICAL residue PRO  60  index1   51  path   28  %Seq 100.00 Highlighted IDENTICAL residue LEU  63  index1   54  path   31  %Seq 100.00 Highlighted IDENTICAL residue THR  67  index1   58  path   35  %Seq 100.00 Highlighted IDENTICAL residue LYS  69  index1   60  path   48  %Seq 100.00 Highlighted IDENTICAL residue ASP  70  index1   61  path   49  %Seq 100.00 Highlighted IDENTICAL residue VAL 101  index1   67  path   55  %Seq 100.00 Highlighted IDENTICAL residue THR 104  index1   70  path   58  %Seq 100.00 Highlighted IDENTICAL residue HIS 106  index1   72  path   60  %Seq 100.00 Highlighted IDENTICAL residue ALA 107  index1   73  path   61  %Seq 100.00 Highlighted IDENTICAL residue THR 112  index1   78  path   66  %Seq 100.00 Highlighted IDENTICAL residue LYS 113  index1   79  path   67  %Seq  50.00 Highlighted IDENTICAL residue ALA 114  index1   80  path   68  %Seq  50.00 Highlighted IDENTICAL residue GLU 115  index1   81  path   69  %Seq  50.00 Highlighted IDENTICAL residue MET 116  index1   82  path   70  %Seq  50.00 Highlighted IDENTICAL residue ALA 117  index1   83  path   72  %Seq 100.00 Highlighted IDENTICAL residue PHE 120  index1   86  path   75  %Seq 100.00 Highlighted IDENTICAL residue ASN 121  index1   87  path   76  %Seq 100.00 Highlighted 21 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g07713-1jmu_G.pir.txt.1JMU.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g07713-1jmu_G.pir.txt PIR amino_acid 1JMU.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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