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Output format



DESCRIPTION

Example of output is found below. The output is divided into the folowinng sections:
  • Query sequence: In this section the query sequence that you submitted are shown in fasta format.
  • Searching for template: The template for building the model is sought by iteratively building up a profile by aligning the query sequence to a nonredundant database of protein sequences and then searching a database of proteins with known structure (pdb) to find a suitable template for making a model.
  • Retrieving template: In this section the pdb entry name and the chain identifier are listed for the template that are used to construct the model.
  • Making profile-profile alignment: In this section the score fro the profile profile alignment (in bits) and the percentage sequence identity between query and template are shown together with the alignment in "Blast-like" format.
  • Modeling: By clicking on the link "model.pdb" you can download the coordinates in pdb format to your own computer.
  • PDB3D: If you have an java enabled browser the C-alpha trace of the model will be shown. You can rotate it by klicking on it with the left mouse button and holding it down while mooving the mouse. The right mouse button can be used to scale the model.



EXAMPLE OUTPUT


Query sequence:

>gi_140856_sp_P23840.1_DIND_ECOLI
MNEHHQPFEEIKLINANGAEQWSARQLGKLLGYSEYRHFIPVLTRAKEACENSGHTIDDH
FEEILDMVKIGSNAKRALKDIVLSRYACYLVVQNGDPAKPVIAAGQTYFAIQTRRQELAD
DEAFKQLREDEKRLFLRNELKEHNKQLVEAAQQAGVATATDFAIFQNHGYQGLYGGLDQK
AIHQRKGLKKNQKILDHMGSTELAANLFRATQTEEKLKRDGVNSKQQANTTHFDVGRKVR
QTIQELGGTMPEELPTPQVSIKQLENSVKITEKK

Searching for template ...

Round   0. Hits better than threshold: 0.000010:
	Found 0

Searching for template ...

Round   1. Hits better than threshold: 0.000010:
	Found 0

Searching for template ...

Round   2. Hits better than threshold: 0.000010:
	Found 0

Searching for template ...

Round   3. Hits better than threshold: 0.000010:
	Found 0

Searching for template ...

Round   4. Hits better than threshold: 0.000010:
	Found 0

Searching for template ...

Round   5. Hits better than threshold: 0.000010:
	Found 0

PDB Blast failed. Doing remote homology modeling
# Template found 1QAX.B 1QAX.B
qseqs: PVLTRAKEACENSGHTIDDHFEEILDMVKIGSNAKRALKDIVLSRYACYLVVQNGDPAK--PVIAAGQTYFAIQTRRQELADDEAFKQLREDEKRLFLRNELKEHNKQLVEAAQQAGVATATDFAIFQNHGY----------QGLYGGLD-----QKAIHQRKGLKKNQKILDHMGSTELAANL--FRATQTE
dresseqs: NTVNTMAEAVAPL---MEAITGGQVRLRILSNLADLRLARAQVRITPQQLETAEFSGEAVIEGILDAYAFAAVDPYRAATHNKGIMNGIDPLI--VATGNDWRAVEAGAHAYACRSGHYGSLTTWEKDNNGHLVGTLEMPMPVGLVGGATKTHPLAQLSLRILGVKTAQALAEIAVAVGLAQNLGAMRALATE
datomseqs: NTVNTMAEAVAPL---MEAITGGQVRLRILSNLADLRLARAQVRITPQQLETAEFSGEAVIEGILDAYAFAAVDPYRAATHNKGIMNGIDPLI--VATGNDWRAVEAGAHAYACRSGHYGSLTTWEKDNNGHLVGTLEMPMPVGLVGGATKTHPLAQLSLRILGVKTAQALAEIAVAVGLAQNLGAMRALATE
qname: gi_140856_
dname: 1QAX.B
zscore: 3.885038
Alignment_length: 193
Retrieving template ...

Entry: 1qax
Chain: B

Z-Score:       3.9

Query: 1   PVLTRAKEACENSGHTIDDHFEEILDMVKIGSNAKRALKDIVLSRYACYLVVQNGDPAK- 60  
Templ: 1   NTVNTMAEAVAPL---MEAITGGQVRLRILSNLADLRLARAQVRITPQQLETAEFSGEAV 60  

Query: 61  -PVIAAGQTYFAIQTRRQELADDEAFKQLREDEKRLFLRNELKEHNKQLVEAAQQAGVAT 120 
Templ: 61  IEGILDAYAFAAVDPYRAATHNKGIMNGIDPLI--VATGNDWRAVEAGAHAYACRSGHYG 120 

Query: 121 ATDFAIFQNHGY----------QGLYGGLD-----QKAIHQRKGLKKNQKILDHMGSTEL 180 
Templ: 121 SLTTWEKDNNGHLVGTLEMPMPVGLVGGATKTHPLAQLSLRILGVKTAQALAEIAVAVGL 180 

Query: 181 AANL--FRATQTE 193 
Templ: 181 AQNLGAMRALATE 193 

Modeling ...

A Z-score above 10 indicates a high reliability model

File with coordinates for model in pdb format:model.pdb

Coordinates are free for users


      
      
   

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PDB3D is a high speed 3D molecule rendering applet written by Scott Legrand at UCLA.

Controls:

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  2. Right Mouse Button: Scale molecule (left & right)



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