Difference between revisions of "Homology modeling fallback data"

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−
==PHYLIP input data: Mbp1 orthologues==
+
==Target sequence==
  
−
  16  55
+
  >MBP1_CHAGL XP_001224558:33..108
−
MBP1_SACCERDFIHSTGNFAKAKTQRLHTATNSQTPLMLLHETVFGDVVFFSLQKTNKLSSLVK
+
  HVMRRREDNWINATHILKAAGFDKPARTRILERDVQKDVHEKIQGGYGKY
−
MBP1_CANGLKDFIHPTGNFAKAKMQRLHTAANANTPLMLLSETVFNDREFFSLQKTRKISELIS
+
  QGTWIPLEQGRALAQRNNIYDRLRPIF
−
MBP1_EREGOKEFLHPTGKFAKAKTGQHHTALNQATPLMLLQDTVFRDKKFFSTEKMHKINRLIE
 
−
MBP1_KLULAKDFIHPTGKFPKAKTQRHHTALNNVTPLIILKDTVFKDDQFYDLVKMRKLNQIID
 
−
MBP1_CANALTPFVTSEGKFPKAKIQRGNTIRNNNTPLMLLKESVLLNKKCIQMERTKLVDEISK
 
−
MBP1_DEBHATPFVTLEGKFPKAKVQHGNTIKNNRTPLMLLFDSILLNKKCITYFKVENKENIKE
 
−
MBP1_YARLITPFQCKNVGFDKPQVQSGHTATNMFTPLTILQDTLFGAKKVSMYFKLDLVDDVVE
 
−
MBP1_SCHPOVECFIKGVDFDKPQASSGHTSCNRLTPLMLLQSTIYGAMDCVQVRQMKDTLYIRK
 
−
MBP1_USTMATPCIINNVGLDKPQIETEHTAVNSNTALMSFTDPSLRSKRLVRANRLELVDKFVA
 
−
MBP1_ASPNITPFKIGTDGFDKPAVSAGNTALSIHTPLVLLLDTISGVFRLVQAHGLAAVKELAQ
 
−
MBP1_ASPTETPFKIEGDGFDKPAVSAGNTALSVHTPLVLLLDTVSGAFRLVSSYGAAAVKELAQ
 
−
MBP1_CRYNEVPAMIRGIGVHKSAISMGHSAGNYATPLILLSPSIRGNKGLVVSYGSEVLEDKIR
 
−
MBP1_GIBZESDMEVNNIGVDKGKESRSHTAVNGSTALMVLGGTIEGNRSIIATEASKMVSALKG
 
−
MBP1_NEUCRTGMEVNNVNIDKGRENRSHTAVNACTALMLLGCTLDGNRSIITLHSTQAVAALQA
 
−
  MBP1_MAGGRVEFEVNGVGVEKGKEQRCHTAVNTSTPLMILGNTMEGNRSIITLHSQQSVVALKG
 
−
  MBP1_ASPFUVSMEVNGVGVVKARERKRNNALNGATALQVLAPTIDRSV-LVSLHATEILAEVDR
 
  
−
==PHYLIP distance matrix: Mbp1 orthologues==
+
==FASTA formatted alignment==
  
−
    16
+
  >1MB1 sequence from coordinates 3..100
−
MBP1_SACCE  0.000000  0.340197  0.641436  0.698015  1.217853  1.575914
+
  NQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTR
−
  1.679015  1.734556  2.205033  2.021848  2.012439  2.665819  1.676493
+
  ILEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLF                   
−
  1.594736  1.572812  1.998416
+
  >MBP1_CHAGL XP_001224558:33..108
−
MBP1_CANGL  0.340197  0.000000  0.573520  0.606792  1.101098  1.571271
+
  ---------------------HVMRRREDNWINATHILKAAGFDKPARTR
−
  1.788034  2.092392  1.858878  2.098264  2.010324  2.531040  1.531216
+
  ILERDVQKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF
−
  1.410911  1.432764  2.300807
 
−
MBP1_EREGO  0.641436  0.573520  0.000000  0.537044  1.273771  1.429173
 
−
  1.510184  1.805609  1.780957  1.919228  1.961973  2.827827  1.791314
 
−
  2.121850  1.882121  2.853653
 
−
MBP1_KLULA  0.698015  0.606792  0.537044  0.000000  1.191955  1.453182
 
−
  1.674717  2.266314  2.264786  2.478006  2.696935  3.451189  2.487955
 
−
  2.758670  2.041124  2.617325
 
−
MBP1_CANAL  1.217853  1.101098  1.273771  1.191955  0.000000  0.540067
 
−
  1.525822  1.826937  1.371732  1.702409  1.765129  1.921376  1.853606
 
−
  2.028292  1.834001  2.184056
 
−
MBP1_DEBHA  1.575914  1.571271  1.429173  1.453182  0.540067  0.000000
 
−
  1.366472  2.111250  1.907877  2.038152  1.842951  2.041502  2.818372
 
−
  2.349724  1.893817  3.091846
 
−
MBP1_YARLI  1.679015  1.788034  1.510184  1.674717  1.525822  1.366472
 
−
  0.000000  1.458949  1.099978  1.258665  1.245131  1.791822  1.892723
 
−
  1.798693  1.546586  2.470074
 
−
MBP1_SCHPO  1.734556  2.092392  1.805609  2.266314  1.826937  2.111250
 
−
  1.458949  0.000000  1.965611  1.650181  1.760901  1.882590  1.829431
 
−
  1.798599  1.652280  2.232678
 
−
MBP1_USTMA  2.205033  1.858878  1.780957  2.264786  1.371732  1.907877
 
−
  1.099978  1.965611  0.000000  1.361737  1.543623  1.598177  1.516216
 
−
  1.508336  1.687661  1.953468
 
−
MBP1_ASPNI  2.021848  2.098264  1.919228  2.478006  1.702409  2.038152
 
−
  1.258665  1.650181  1.361737  0.000000  0.183195  1.506196  2.082772
 
−
  1.858936  1.901732  2.043755
 
−
MBP1_ASPTE  2.012439  2.010324  1.961973  2.696935  1.765129  1.842951
 
−
  1.245131  1.760901  1.543623  0.183195  0.000000  1.320001  1.972475
 
−
  1.766234  1.810925  1.734993
 
−
MBP1_CRYNE  2.665819  2.531040  2.827827 3.451189  1.921376  2.041502
 
−
  1.791822  1.882590  1.598177  1.506196  1.320001  0.000000  1.606068
 
−
  1.876348 1.696345  1.378680
 
−
  MBP1_GIBZE  1.676493  1.531216  1.791314  2.487955  1.853606  2.818372
 
−
  1.892723 1.829431  1.516216  2.082772  1.972475  1.606068  0.000000
 
−
  0.497095  0.523613 1.052197
 
−
  MBP1_NEUCR  1.594736  1.410911  2.121850  2.758670  2.028292  2.349724
 
−
  1.798693  1.798599  1.508336  1.858936  1.766234  1.876348  0.497095
 
−
  0.000000  0.488870  1.020647
 
−
MBP1_MAGGR  1.572812  1.432764  1.882121  2.041124  1.834001  1.893817
 
−
  1.546586  1.652280  1.687661  1.901732  1.810925  1.696345  0.523613
 
−
  0.488870  0.000000  1.108262
 
−
MBP1_ASPFU  1.998416  2.300807  2.853653  2.617325  2.184056  3.091846
 
−
  2.470074  2.232678  1.953468  2.043755  1.734993  1.378680  1.052197
 
−
  1.020647  1.108262  0.000000
 
  
  
−
==PHYLIP input data: Mbp1 APSES domains==
 
  
−
16  84
+
==SwissModel response==
−
MBP1_SACCESIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDG
 
−
MBP1_CANGLSIMKRKNDGWVNATHILKAANFAKAKRTRILEKEVLKEMHEKVQGGFGKYQGTWVPLNIAINLAEKFDVYQDLKPLFDFSEENG
 
−
MBP1_EREGOSIMKRKADDWVNATHILKAAKFAKAKRTRILEKEVIKDTHEKVQGGFGKYQGTWVPLDIARRLAQKFEVLEELRPLFDFTRRDG
 
−
MBP1_KLULASIMKRKADNWVNATHILKAAKFPKAKRTRILEKEVITDTHEKVQGGFGKYQGTWIPLELASKLAEKFEVLDELKPLFDFTQQEG
 
−
MBP1_CANALPIMRRKKDSWINATHILKIAKFPKAKRTRILEKDVQTGIHEKVQGGYGKYQGTYVPLDLGAAIARNFGVYDVLKPIFEFQYIEG
 
−
MBP1_DEBHAPIMRRKLDSWINATHILKIAKFPKAKRTRILEKDVQTGVHEKVQGGYGKYQGTYVPLDLGADIAKNFGVFDSLRPIFEFTYVEG
 
−
MBP1_YARLIAVMRRKSDGWVNATHILKVAGFDKPQRTRILEKEVQKGVHEKVQGGYGKYQGTWVPLERAREIATLYDVDSHLAPIFNYDDEDG
 
−
MBP1_SCHPOSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSLDIDEG
 
−
MBP1_USTMAAVMRRRSDDWLNATQILKVVGLDKPQRTRVLEREIQKGIHEKVQGGYGKYQGTWIPLDVAIELAERYNIQGLLQPITSYVPS--
 
−
MBP1_ASPNISVMRRRSDDWINATHILKVAGFDKPARTRILEREVQKGVHEKVQGGYGKYQGTWIPLQEGRQLAERNNILDKLLPIFDYVA--G
 
−
MBP1_ASPTESVMRRRADDWINATHILKVAGFDKPARTRILEREVQKGVHEKVQGGYGKYQGTWIPLPEGRLLAERNNIIDKLRPIFDYVA--G
 
−
MBP1_CRYNESVMRRASDSWVNATQILKVAGVHKSARTKILEKEVLNGIHEKIQGGYGKYQGTWVPLDRGRDLAEQYGVGSYLSSVFDFVPSAS
 
−
MBP1_GIBZEAVMRRRNDSWLNATQILKVAGVDKGKRTKILEKEIQTGEHEKVQGGYGKYQGTWIKFERGLQVCRQYGVEELLRPLLTYDMGQD
 
−
MBP1_NEUCRAVMRRQKDGWVNATQILKVANIDKGRRTKILEKEIQIGEHEKVQGGYGKYQGTWIPFERGLEVCRQYGVEELLSKLLTHNRGQE
 
−
MBP1_MAGGRAVMKRIGDSKLNATQILKVAGVEKGKRTKILEKEIQTGEHEKVQGGYGKYQGTWIKYERALEVCRQYGVEELLRPLLEYNRNPD
 
−
MBP1_ASPFUAVMKRRSDSWLNATQILKVAGVVKARRTKTLEKEIAAGEHEKVQGGYGKYQGTWVNYQRGVELCREYHVEELLRPLLEYDMGPN
 
  
−
==PHYLIP distance matrix: Mbp1 APSES domains==
+
Four e-mails are sent by SwissModel after submission of the modeling request. Two of the received files are ''welcome'' and ''help'' messages. Two other e-mail messages conatin the program output and the model.
  
−
    16
+
:*[[Assignment_5_SwissModel_Results| SwissModel '''Program Output''']]
−
MBP1_SACCE  0.000000  0.170047  0.205399  0.247219  0.487569  0.524603
+
:*[[Assignment_5_SwissModel_Model| SwissModel attached '''Model Coordinates''']]
−
  0.579198  0.798266  0.690172  0.527376  0.544473  0.657178  0.895524
 
−
  0.862050  0.905898  0.907783
 
−
MBP1_CANGL  0.170047  0.000000  0.279198  0.319549  0.559059  0.573474
 
−
  0.519177  0.789154  0.733572  0.615596  0.625874  0.665870  0.899041
 
−
  0.880370  0.935112  0.883959
 
−
MBP1_EREGO  0.205399  0.279198  0.000000  0.182532  0.544175  0.510304
 
−
  0.585979  0.846715  0.738784  0.557436  0.539410  0.674472  0.880525
 
−
  0.873348  0.850046  0.864623
 
−
MBP1_KLULA  0.247219  0.319549  0.182532  0.000000  0.467085  0.453277
 
−
  0.638363  0.813078  0.772358  0.567769  0.575968  0.690719  0.852917
 
−
  0.882337  0.830886  0.904034
 
−
MBP1_CANAL  0.487569  0.559059  0.544175  0.467085  0.000000  0.120290
 
−
  0.589271  0.686670  0.799405  0.647996  0.639552  0.681593  0.746085
 
−
  0.792284  0.817362  0.869237
 
−
MBP1_DEBHA  0.524603  0.573474  0.510304  0.453277  0.120290  0.000000
 
−
  0.555420  0.667709  0.800353  0.592738  0.583278  0.641173  0.744716
 
−
  0.811525  0.809515  0.839041
 
−
MBP1_YARLI  0.579198  0.519177  0.585979  0.638363  0.589271  0.555420
 
−
  0.000000  0.473875  0.462053  0.388599  0.421408  0.503568  0.581799
 
−
  0.593335  0.676734  0.691392
 
−
MBP1_SCHPO  0.798266  0.789154  0.846715  0.813078  0.686670  0.667709
 
−
  0.473875  0.000000  0.532761  0.545135  0.573415  0.643554  0.593169
 
−
  0.603559  0.762385  0.624657
 
−
MBP1_USTMA  0.690172  0.733572  0.738784  0.772358  0.799405  0.800353
 
−
  0.462053  0.532761  0.000000  0.346127  0.383120  0.560953  0.597524
 
−
  0.682290  0.675589  0.672514
 
−
MBP1_ASPNI  0.527376  0.615596  0.557436  0.567769  0.647996  0.592738
 
−
  0.388599  0.545135  0.346127  0.000000  0.064477  0.503545  0.673114
 
−
  0.778854  0.845557  0.762898
 
−
MBP1_ASPTE  0.544473  0.625874  0.539410  0.575968  0.639552  0.583278
 
−
  0.421408  0.573415  0.383120  0.064477  0.000000  0.534114  0.699665
 
−
  0.812899  0.847328  0.802412
 
−
MBP1_CRYNE  0.657178  0.665870  0.674472  0.690719  0.681593  0.641173
 
−
  0.503568  0.643554  0.560953  0.503545  0.534114  0.000000  0.650085
 
−
  0.653523  0.713330  0.695510
 
−
MBP1_GIBZE  0.895524  0.899041  0.880525  0.852917  0.746085  0.744716
 
−
  0.581799  0.593169  0.597524  0.673114  0.699665  0.650085  0.000000
 
−
  0.227631  0.185991  0.289073
 
−
MBP1_NEUCR  0.862050  0.880370  0.873348  0.882337  0.792284  0.811525
 
−
  0.593335  0.603559  0.682290  0.778854  0.812899  0.653523  0.227631
 
−
  0.000000  0.330632  0.480412
 
−
MBP1_MAGGR  0.905898  0.935112  0.850046  0.830886  0.817362  0.809515
 
−
  0.676734  0.762385  0.675589  0.845557  0.847328  0.713330  0.185991
 
−
  0.330632  0.000000  0.316199
 
−
MBP1_ASPFU  0.907783  0.883959  0.864623  0.904034  0.869237  0.839041
 
−
  0.691392  0.624657  0.672514  0.762898  0.802412  0.695510  0.289073
 
−
  0.480412  0.316199  0.000000
 
  
−
[end]
+
 
 +
==LGA superposition==
 +
 
 +
The resulting output produced by the LGA server for the 1DUX_ABC and 1MB1 superposition consists of two parts: the superposition report explains which residues were matched and what their RMSD after superposition was. The coordinates contain the rotated coordinates of the entire 1DUX file superimposed on 1MB1. In order to use this for as RasMol, the following manual edits were performed.
 +
:#LGA created several <code>END  </code> records in the middle of the file. These prevent the following lines to be read in. They were simply deleted. Since the protein chans of the Mbp1 and Elk-1 domains are closely superimposed, RasMol tries to draw multiple bonds between  the residues that have close contacts. This was addressed by bracketing the chains in <code>MODEL</code> and <code>ENDMDEL</code>, which prevents bonds between being drawn.
 +
 
 +
:*[[Assignment_5_LGA_Results| '''LGA superposition report''']]
 +
:*[[Assignment_5_1DUX_1MB1| '''1DUX_1MB1 Coordinates''']]
 +
 
 +
==Protein-DNA complex model==
 +
 
 +
The DNA coordinates (chain A and B) from the LGA superimposed coordinate file were copied, and pasted into the SwissModel coordinate file, thus generating a homology model of a Protein / DNA complex.
 +
 
 +
:*[[Assignment_5_Model_DNA| '''Model/DNA complex Coordinates''']]

Revision as of 04:55, 31 October 2007

 

Please remember: if you use information from this page as a fallback for technical problems with the assignment, you must document this in your submission. State what you tried, what didn't work and only then use the data from here.

   


Target sequence

>MBP1_CHAGL XP_001224558:33..108
HVMRRREDNWINATHILKAAGFDKPARTRILERDVQKDVHEKIQGGYGKY
QGTWIPLEQGRALAQRNNIYDRLRPIF

FASTA formatted alignment

>1MB1 sequence from coordinates 3..100
NQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTR
ILEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLF                     
>MBP1_CHAGL XP_001224558:33..108
---------------------HVMRRREDNWINATHILKAAGFDKPARTR
ILERDVQKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF


SwissModel response

Four e-mails are sent by SwissModel after submission of the modeling request. Two of the received files are welcome and help messages. Two other e-mail messages conatin the program output and the model.


LGA superposition

The resulting output produced by the LGA server for the 1DUX_ABC and 1MB1 superposition consists of two parts: the superposition report explains which residues were matched and what their RMSD after superposition was. The coordinates contain the rotated coordinates of the entire 1DUX file superimposed on 1MB1. In order to use this for as RasMol, the following manual edits were performed.

  1. LGA created several END records in the middle of the file. These prevent the following lines to be read in. They were simply deleted. Since the protein chans of the Mbp1 and Elk-1 domains are closely superimposed, RasMol tries to draw multiple bonds between the residues that have close contacts. This was addressed by bracketing the chains in MODEL and ENDMDEL, which prevents bonds between being drawn.

Protein-DNA complex model

The DNA coordinates (chain A and B) from the LGA superimposed coordinate file were copied, and pasted into the SwissModel coordinate file, thus generating a homology model of a Protein / DNA complex.

Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=Homology_modeling_fallback_data&oldid=3458"