SUPERFAMILY 1.75 HMM library and genome assignments server

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Duffy binding domain-like alignments

These alignments are sequences aligned to the 0052122 model.

Sophisticated options are available for refining alignments:


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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     
                                  |         |         |         |         |         |         |     
d2c6ja1          .......k-CNDKRKRGERDWDCPAEKDICISDRRYQLCMKELTNLVNNTRTHSHNDITFLKLNLKRKLMYDAAVEGDLLLKK
A0A024VEB1:9-406 tlggqctd---SKIKGNKYNRNTRKDCGACAPYRRLHLCHHNLESI--------DTDKIDNTHKLLLEVCMAAKYEGNSIKTY


                          80        90       100            110       120                          1
                           |         |         |              |         |                           
d2c6ja1          NN......YQYNKEFCKDIRWGLGDFGDIIMGTNMEGIGY.....SQVVENNLRSIFGTD...................EKAK
A0A024VEB1:9-406 YTeheytnPDTKSQLCTVLERSFADIGDIVRGRDLFHGNPqekekRDELESKLKKIFGKIyeglkttkgaqnyykddpkKNYY


                 30       140       150                    160       170       180       190       2
                  |         |         |                      |         |         |         |        
d2c6ja1          QDRKQWWNESKEHIWRAMMFSLRSRL.............KEKFVWICKKDVTLKVEPQIYRWIREWGRDYMSELPKEQGKLNE
A0A024VEB1:9-406 KLREDWWTVNRDQVWKALTCDVKGNKyfrgtcstgtatyEKCRCNDDQVPTYFDYVPQYLRWFEEWAEDFCRLRKHKLEDAIK


                 00           210                     220       230       240       250             
                  |             |                       |         |         |         |             
d2c6ja1          KCASK....LYYNNMAICM..............LPLCHDACKSYDQWITRKKKQWDVLSTKFSSVKKTQKIGTEN........
A0A024VEB1:9-406 KCRGDknekYCDLNRHDCVktirgdhdfveeddCIGCHFSCAGFVKWIDNQKLEFLKQKNKYADEMQKYTNGETRggggsgkk


                                          260       270                       280       290      
                                            |         |                         |         |      
d2c6ja1          .......................IATAYDILKQELNGFKE................ATFENEINKRDNLYNHLCPC--vv
A0A024VEB1:9-406 rvagksnydryeskfydklkknnYKNVEDFLKKLNNEAICqkrpeasgetadaadfTKIKTNETFSHTTYCKACPWC-..


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: 0052122 (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



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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)


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