SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


Agglutinin alignments

These alignments are sequences aligned to the 0047621 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.

                     10        20        30        40        50        60        70        80       
                      |         |         |         |         |         |         |         |       
d1jlxa1 ...a-GLPV.IMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKILDPLAQFEVEPSKTYDGLVHIKSRYTNKYLVRWSPNHYWITASANEPDE
d1jlxa2 wksiFQFPKgYVTFKGN-NGKYLGVIT--INQLPCLQFGYDNLNDPKVAHQMFV--TSNGTICIKSNYMNKFWRLSTDD--WILVDGNDPRE


         90       100       110       120        130       140       150    
          |         |         |         |          |         |         |    
d1jlxa1 NKSNWACTLFKPLYVEEGNMKKVRLLHVQLGHYTQNYTVGGS.FVSYLFAESSQIDTGSKDVFHVID.
d1jlxa2 --TNEAAALFRS---DVHDFNVISLLNMQKTWFIKRFTSGKPgFINCMNAATQNVDETAILEIIE--l


Statistics on alignment.   Save alignment.

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

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: 0047621 (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   Selaginella moellendorffii
NoYes   Pinus taeda - Loblolly pine
NoYes   Picea abies - Norway spruce
NoYes   Gossypium raimondii v221
NoYes   Carica papaya - Papaya
NoYes   Cucumis sativus v122 - Cucumber
NoYes   Fragaria vesca - Wild strawberry
NoYes   Malus domestica v196 - Apple
NoYes   Prunus persica v139 - Peach
NoYes   Linum usitatissimum v200 - Flax
NoYes   Vitis vinifera - Wine grape
NoYes   Actinidia chinensis Hongyang
NoYes   Aquilegia coerulea v195
NoYes   Triticum urartu 22
NoYes   Triticum aestivum 22 - Bread wheat
NoYes   Aegilops tauschii 22
NoYes   Brachypodium distachyon - Stiff brome
NoYes   Phyllostachys heterocyclavar. pubescens - Mosochiku
NoYes   Panicum virgatum v202 - Switchgrass
NoYes   Setaria italica v164 - Foxtail millet
NoYes   Zea mays subsp. mays - Maize
NoYes   Zea mays v181 - Maize
NoYes   Hordeum vulgare 22 - Domesticated barley
NoYes   Malus x domestica - Apple
NoYes   Ricinus communis - Castor bean
NoYes   NCBI 2017_08 genome
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   ALL (only advised for small superfamilies)


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