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.
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