SUPERFAMILY 1.75 HMM library and genome assignments server


Duffy binding domain-like alignments

These alignments are sequences aligned to the 0052122 model.

Sophisticated options are available for refining alignments:

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


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       100       110       120       130       140       150       160       170   
                |         |         |         |         |         |         |         |         |   

                 180       190       200       210       220       230       240       250       260
                   |         |         |         |         |         |         |         |         |

                    270       280       290      
                      |         |         |      

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: 0052122 (list models)
Initial SAMT99 seed:

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   Plasmodium falciparum 3D7
NoYes   Plasmodium vivax SaI-1 7.0
NoYes   Plasmodium knowlesi strain H
NoYes   Plasmodium yoelii ssp. yoelii 1
NoYes   Plasmodium chabaudi
NoYes   Plasmodium berghei ANKA
NoYes   Geobacillus sp. JF8
NoYes   Plasmodium falciparum HB3
NoYes   Plasmodium falciparum Dd2
NoYes   NCBI 2017_08 genome
NoYes   Protozoadb 2010_08 (Protozoadb)
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
NoYes   PDB chains (SCOP 1.75) (PDB)
NoYes   Protein Data Bank (all PDB sequenc)
NoYes   SCOP2 SCOPe CATH ECOD (all domain sequ)
NoYes   TargetDB (Targets)
NoYes   ALL (only advised for small superfamilies)

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