SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.

Duffy binding domain-like alignments

These alignments are sequences aligned to the 0051624 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   
                                                        |         |         |         |         |   
d1zroa2                                  ....ck--HTTTLVKSVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKP
gi|296004911|ref|XP_001349207.2|:430-740 tttlvk---------SVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKP


                                              60        70        80        90       100       110  
                                               |         |         |         |         |         |  
d1zroa2                                  YKLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKE
gi|296004911|ref|XP_001349207.2|:430-740 YKLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKE


                                              120       130       140       150       160       170 
                                                |         |         |         |         |         | 
d1zroa2                                  VCKIINKTFADIRDIIGGTDYWNDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVI
gi|296004911|ref|XP_001349207.2|:430-740 VCKIINKTFADIRDIIGGTDYWNDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVI


                                               180       190       200       210       220       230
                                                 |         |         |         |         |         |
d1zroa2                                  KKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQDKTKMIETLKVECKEKP
gi|296004911|ref|XP_001349207.2|:430-740 KKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQDKTKMIETLKVECKEKP


                                                240       250       260       270       280       29
                                                  |         |         |         |         |         
d1zroa2                                  CEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYS
gi|296004911|ref|XP_001349207.2|:430-740 CEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYS


                                         0       300       310    
                                         |         |         |    
d1zroa2                                  EKCSNLNFEDEFKEELHSDYKNKCT
gi|296004911|ref|XP_001349207.2|:430-740 EKCSNLNFEDEFKEELHSDYKNKCT


Statistics on alignment.   Save alignment.

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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: 0051624 (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   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 ]