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 0051623 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 
                                                    |            |          |         |           | 
d1zroa1 ..................................n-EVLSNCREKRK..GM.KWDCKKKND.RSNYVCIPDRRIQLCIVNLAII..KTYTK.
d1zroa2 ckhtttlvksvlngndntikekrehidlddfskfg------CDKNSVdtNTkVWECKKPYKlSTKDVCVPPRRQELCLGNIDRI..YDKNL.
d2c6ja1 ..................................k------CNDKRKrgER.DWDCPAEK-.---DICISDRRYQLCMKELTNLvnN-TRTh
d4nuua1 ..................................n-TVMKNCNYKRKrrER.DWDCNTKK-.---DVCIPDRRYQLCMKELTNLv.NNTDTn


                         60        70        80        90       100       110       120       130   
                          |         |         |         |         |         |         |         |   
d1zroa1 .........ETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFLDYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHGEISEHKIKNFR
d1zroa2 .........LMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDYWNDLSNRKLVGKINTNSNYVHR--NKQNDKLFR
d2c6ja1 shnditflkLNLKRKLMYDAAVEGDLLLKKNNYQYNKEFCKDIRWGLGDFGDIIMGTNMEGIGYSQVVENNLRSIFGTDE------KAKQDR
d4nuua1 fhrditfrkLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVVENNLRSIFGTDE------KAQQRR


            140       150             160          170       180       190          200        210  
              |         |               |            |         |         |            |          |  
d1zroa1 KKWWNEFREKLWEAMLSEHK....NNIN..NCKNIPQE...ELQITQWIKEWHGEFLLERDNRAKLPKSKCKNN...ALYEAC.EKECIDPC
d1zroa2 DEWWKVIKKDVWNVISWVFK....DKTV..CKEDDIEN...IPQFFRWFSEWGDDYCQDKTKMIETLKVECKEK...----PCeDDNCKRKC
d2c6ja1 KQWWNESKEHIWRAMMFSLRsrlkEKFV..WICKKDVTlkvEPQIYRWIREWGRDYMSELPKEQGKLNEKCASKlyyNNMAICmLPLCHDAC
d4nuua1 KQWWNESKAQIWTAMMYSVKkrlkGNFIwiCKLNVAVNi..EPQIYRWIREWGRDYVSELPTEVQKLKEKCDGKinyTDKKVCkVPPCQNAC


             220       230       240                 250        260       270         
               |         |         |                   |          |         |         
d1zroa1 MKYRDWIIRSKFEWHTLSKEYETQKVPKE..........NAENYLIKISENKN.DAKVSLLLNNCDAEYSKYC-d...
d1zroa2 NSYKEWISKKKEEYNKQAKQYQEYQKGNNykmysefksiKPEVYLKKYSEKCSnLNFEDEFKEELHSDYKNKC-t...
d2c6ja1 KSYDQWITRKKKQWDVLSTKFSSVKKTQKigtenia...TAYDILKQELNGFK.EATFENEINKRDNLYNHLC-pcvv
d4nuua1 KSYDQWITRKKNQWDVLSNKFISVKNAEKvqtagiv...TPYDILKQELDEFN.EVAFENEINKRDGAYIELC-vcs.


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: 0051623 (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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