SUPERFAMILY 1.73 HMM library and genome assignments server

  Home > SCOP hierarchy > "Winged helix" DNA-binding domain > Alignments


"Winged helix" DNA-binding domain alignments

These alignments are sequences aligned to the 0043935 model.

Sophisticated options are available for refining alignments:

Jump to [ Top of page · Refine alignments · Add alignments from genomes ]

Alignments

The numbers along the top are the segment numbers of the HMM states, and each sequence is seperately aligned to the model.
The first sequence is the seed the model was built from.
Upper case letters are aligned, lower case letters are insertions, '-' signifies a deletion and '.' is nothing.

                10        20        30        40        50        60        70        80        90  
                 |         |         |         |         |         |         |         |         |  
d1tbxa_ STPFFYPEAIVLAYLYDNEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFAISLKTAIETYKQIKKRH


          
          
d1tbxa_ HH
Statistics on alignment.   Save alignment.

Jump to [ Top of page · Alignments · Add alignments from genomes ]

Refine alignments

Sophisticated options are available for refining alignments:

Add your sequences to the alignment:
Members of the same: including
Include all superfamily members: , or just those assigned by the selected model:
Initial T99 seed sequence: NoYes

You may enter many sequences at once using FASTA format:

Upload a multiple sequence FASTA file:




Model: 0043935 (list models)
Initial SAMT99 seed:
Alignment:



Display Options:
Output in FASTA-like format: NoYes
Output column indices: NoYes
Sequence index (number) on each line: NoYes

Max number of insertions shown: (0 does not show insertions)
Characters per line:
Character to show inserts:
Maximum number of sequences:
Exclude sequences shorter than: residues


Jump to [ Top of page · Alignments · Refine alignments ]

Add alignments from genomes

Select below additional genomes you would like to see alignments for, then click on 'Re-Submit'. The genome assignments will be added to this page.


Select to display   Genome
NoYes   Sulfolobus islandicus L.S.2.15
NoYes   NCBI viral sequences (Viral)
NoYes   PDB chains (SCOP 1.73) (PDB)
NoYes   UniProt 15.0 (UniProt)
NoYes   UniProt 15.0 viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


Jump to [ Top of page · Alignments · Refine alignments · Add alignments from genomes ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@mrc-lmb.cam.ac.uk or use the feedback form.

© Copyright 2001-2010 The Medical Research Council and the SUPERFAMILY authors; Derek Wilson, Martin Madera and Julian Gough.