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 0053980 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
                                                 |         |         |         |         |         |
d2guma1          ......................a-NFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTV
CJA00164:359-459 kitsttaprqnnesqpnqkkksn------------------------------------------------------------


                         70        80        90       100       110       120       130       140   
                          |         |         |         |         |         |         |         |   
d2guma1          SQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLK
CJA00164:359-459 -----------------------------------------------------------------------------------


                     150       160       170       180       190       200       210       220      
                       |         |         |         |         |         |         |         |      
d2guma1          YNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTTYAADRFKQVDGFYARDLTTKARA
CJA00164:359-459 -----------------------------------------------------------------------------------


                  230       240       250       260       270       280       290       300       31
                    |         |         |         |         |         |         |         |         
d2guma1          TAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARD
CJA00164:359-459 -----------------------------------------------------------------------------------


                 0       320       330       340       350       360       370       380       390  
                 |         |         |         |         |         |         |         |         |  
d2guma1          AMDRIFARRYNATHIKVGQPQYYQANGGFLIAYQPLLSNTLAELYVREHLREQSRKPPNPTPPPPGASANASVERIKTTSSIE
CJA00164:359-459 -----------------------------------------------------------------------------------


                      400       410       420       430       440        450       460       470    
                        |         |         |         |         |          |         |         |    
d2guma1          FARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTV.GRRVSARMLGDVMAVSTCVPVAADNVIVQ
CJA00164:359-459 -------------------EEIFNSVCKEQFAKTSLFETLLSIDPTAAVRSLLkRKDVSAKMIGESLLVSKCREVKPSTVHWN


                    480       490       500       510       520       530       540       550       
                      |         |         |         |         |         |         |         |       
d2guma1          NSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTV
CJA00164:359-459 RKVN-----NTCYD---------------------------------------------------------------------


                 560       570       580       590       600       610          
                   |         |         |         |         |         |          
d2guma1          STFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIH-a....
CJA00164:359-459 ----------------------------------------------------------lvpvt


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: 0053980 (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   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 ]