SUPERFAMILY 1.75 HMM library and genome assignments server

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Viral glycoprotein ectodomain-like alignments

These alignments are sequences aligned to the 0053782 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.

                                                                                                    
                                                                                                    
d2cmza1 ............................................................................................
d2guma1 anfyvcppptgatvvqfeqprrcptrpegqnytegiavvfkeniapykfkatmyykdvtvsqvwfghrysqfmgifedrapvpfeevidkin


                                                                                                    
                                                                                                    
d2cmza1 ............................................................................................
d2guma1 akgvcrstakyvrnnlettafhrddhetdmelkpanaatrtsrgwhttdlkynpsrveafhrygttvnciveevdarsvypydefvlatgdf


                                                                                        10        20
                                                                                         |         |
d2cmza1 ........................................................................KFTIVFPHNQKGNWKNVPSN
d2guma1 vymspfygyregshtehttyaadrfkqvdgfyardlttkaratapttrnllttpkftvawdwvpkrpsvctm--------------------


                30        40        50        60        70        80        90       100       110  
                 |         |         |         |         |         |         |         |         |  
d2cmza1 YHYCPSSSDLNWHNDLIGTAIQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGPKYITQSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQ
d2guma1 ------T-------------------------------------------------------------------------------------


             120       130       140       150       160       170       180       190       200    
               |         |         |         |         |         |         |         |         |    
d2cmza1 SCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFINGKCSNYICPTVHNSTTWHSDYKVKGLCDSNLISMDITFFSEDGELSSLGKEGTG
d2guma1 --------------------------------------------------------------------------------------------


           210       220       230       240       250       260       270       280       290      
             |         |         |         |         |         |         |         |         |      
d2cmza1 FRSNYFAYETGGKACKMQYCKHWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLP
d2guma1 --------------------------------------------------------------------------------------------


         300       310       320       330       340       350       360       370       380       3
           |         |         |         |         |         |         |         |         |        
d2cmza1 ISPVDLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLRTSSGYKFPLYMIG
d2guma1 --------------------------------------------------------------------------------------------


        90       400                                                                                
         |         |                                                                                
d2cmza1 HGMLDSDLHLSSKAQVFEHPH.......................................................................
d2guma1 ---------------------kwqevdemlrseyggsfrfssdaisttfttnlteyplsrvdlgdcigkdardamdrifarrynathikvgq


                                                                                                    
                                                                                                    
d2cmza1 ............................................................................................
d2guma1 pqyyqanggfliayqpllsntlaelyvrehlreqsrkppnptppppgasanasverikttssiefarlqftynhiqrhvndmlgrvaiawce


                                                                                                    
                                                                                                    
d2cmza1 ............................................................................................
d2guma1 lqnheltlwnearklnpnaiasvtvgrrvsarmlgdvmavstcvpvaadnvivqnsmrissrpgacysrplvsfryedqgplvegqlgenne


                                                                                                    
                                                                                                    
d2cmza1 ............................................................................................
d2guma1 lrltrdaiepctvghrryftfgggyvyfeeyayshqlsradittvstfidlnitmledhefvplevytrheikdsglldytevqrrnqlhdl


                   
                   
d2cmza1 ...........
d2guma1 rfadidtviha


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: 0053782 (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   Aedes aegypti 55 - Yellow fever mosquito
NoYes   Meloidogyne incognita - Southern root-knot nematode
NoYes   Caenorhabditis japonica
NoYes   Caenorhabditis brenneri
NoYes   Caenorhabditis remanei
NoYes   Loa loa v3.3 - Eye worm
NoYes   NCBI 2017_08 genome
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI viral sequences (Viral)
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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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