SUPERFAMILY 1.75 HMM library and genome assignments server

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Variant surface glycoprotein (N-terminal domain) alignments

These alignments are sequences aligned to the 0053532 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        80        90 
                  |         |         |         |         |         |         |         |         | 
d1vsga_ .AAEKGFKQAFWQPLCQVSEELDDQPKGALFTLQAAASKIQKMRDAALRASIYAEINHGTNRAKAAVIVANHYAMKADSGLEALKQTLSSQE
d2vsga_ t--HFGVKYELWQPECELTAELRKTAGVAKMKVNSDLNSFKTLELTKMKLLTFAAKFPESKEALTLRALEAALNTDLRALRDNI-ANGIDRA
d5ly9b_ .AERTGLKATAWKPLCKLTTELSKVSGEMLNEGQEVISNIQKIKAAEYKVSIYLAKNPETQALQQLTLLRGYFARKTNGGLESYKTMGLATQ


              100       110       120       130       140       150         160       170        180
                |         |         |         |         |         |           |         |          |
d1vsga_ VTATATASYLKGRIDEYLNLLLQTKESGTSGCMMDTSGTNTVTKAGGTIGGVPCKLQLSPI..QPKRPAATYLGKAGYVGLT.RQADAANNF
d2vsga_ VRATAYASEAAGALFSGIQTLHDAT-DGTTYCLSASGQGSN---GNAAMASQGCKPLALPEllTEDSYNTDVISDKGFPKIS.PLTNAQGQ-
d5ly9b_ IRSARAAAYLKGSIDEFLNLLESLKGGSENKCLVTTNADTAATRRETKLDDQECALSMPET..KPEAATRTELTQTGYPNLQhGGGGTANTF


                 190       200          210       220       230       240        250            260 
                   |         |            |         |         |         |          |              | 
d1vsga_ H..DNDAECRLASGHNTNGLGKSG...QLSAAVTMAAGYVTVANSQTAVTVQALDALQEASGAAHQ.PWIDAWKAKKALTGAE.....TAEF
d2vsga_ -..GKSGECGLFQAASGAQATNTGvqfSGGSRINLGLGAIV-ASAAQQPTRPDLSDFSGTARNQADtLYGKAHASITELLQLAqgpkpGQTE
d5ly9b_ QptTSTGTCKLLSGHSTNGYPTTS...ALDTTAKVLAGYMTIPNTQVEATLANMQAMGNGHKATAP.AWHEAWEARNREAKAK.....DLAY


              270       280       290          300       310       320        330       340       35
                |         |         |            |         |         |          |         |         
d1vsga_ RNETAGIAGKTGVTKLVEEALLKKKDSEAS...EIQTELKKYFSGHENEQWTAIEKLISEQPVAQNL.VGDNQPTKLGELEGNAKLTTILAY
d2vsga_ VETMKLLAQKTAALDSIKFQLAASTGKKTSdykEDENLKTEYFGK-TESNIEALWNKVKEEKVKGADpEDPSKESKISDLNTEEQLQRVLDY
d5ly9b_ TNETGNLDTQPTLKALVKTLLLPKDNTEHN...AEATKLEALFGGLAADKTKTYLDMVDAEIIPAGI.AGRTTEAPLGKIHDTVELGDILSN


        0       360                
        |         |                
d1vsga_ Y------------rmetagkfevlt..
d2vsga_ Y------------ava...........
d5ly9b_ Y------------emiaaqnvvtlkkn


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

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FASTA format:

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Model: 0053532 (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   Octopus bimaculoides 280
NoYes   Lodderomyces elongisporus NRRL YB-4239
NoYes   Trypanosoma vivax
NoYes   Trypanosoma congolense 2.4
NoYes   Trypanosoma brucei gambiense v4.1
NoYes   Trypanosoma brucei TREU927 v4.1
NoYes   Trypanosoma brucei Lister 427 v4.1
NoYes   NCBI 2017_08 genome
NoYes   Protozoadb 2010_08 (Protozoadb)
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
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 ]