FANDOM


&&&&&&&&&&&&&&&&&&&& 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 @@@@@@@@@@@@@@@@@@@@

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