SUPERFAMILY 1.75 HMM library and genome assignments server

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Lipovitellin-phosvitin complex; beta-sheet shell regions alignments

These alignments are sequences aligned to the 0040643 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.

                                                                                                    
                                                                                                    
d1lsha2 ............................................................................................
d1lsha3 cryskavhvdtfnartmagvsadyfrinspsgplpravaakirgqgmgyasdivefglraeglqellyrgsqeqdaygtaldrqtllrsgqa
d1lshb_ skpkvvivlravradgkqqglqttlyygltsnglpkakivavelsdlsvwklcakfrlsahmkakaaigwgkncqqyramleas........


                                                                                                    
                                                                                                    
d1lsha2 ............................................................................................
d1lsha3 rshvssihdtlrklsdwksvpeerplasgyvkvhgqevvfaeldkkmmqrisqlwhsarshhaaaqeqigavvskleqgmdvlltkgyvvse
d1lshb_ ............................................................................................


                                                                                                    
                                                                                                    
d1lsha2 ............................................................................................
d1lsha3 vrymqpvcigipmdlnllvsgvttnranlsasfsslpadmkladllatnielrvaattsmsqhavaimglttdlakagmqthyktsaglgvn
d1lshb_ ............................................................................................


                                                                       10        20        30       
                                                                        |         |         |       
d1lsha2 .......................................................EFQPGKVYRYSYDAFSISGLPEPGVNRAGLSGEMKIE
d1lsha3 gkiemnaresnfkaslkpfqqktvvvlstmesivfvrdpsgsrilpvlppkmtld-------------------------------------
d1lshb_ .......................................................-------------------------------------


         40        50        60        70        80        90       100       110       120       13
          |         |         |         |         |         |         |         |         |         
d1lsha2 IHGHTHNQATLKITQVNLKYFLGPWPSDSFYPLTGGYDHFIQQLEVPVRFDYSAGRIGDIYAPPQVTDTAVNIVRGILNLFQLSLKKNQQTF
d1lsha3 --------------------------------------------------------------------------K-----------------
d1lshb_ -----------------T--------------------------------------------------------------------------


        0       140       150       160       170       180       190       200       210       220 
        |         |         |         |         |         |         |         |         |         | 
d1lsha2 ELQETGVEGICQTTYVVQEGYRTNEMAVVKTKDLNNCDHKVYKTMGTAYAERCPTCQKMNKNLRSTAVYNYAIFDEPSGYIIKSAHSEEIQQ
d1lsha3 --------------------------------------------------------------------------------------------
d1lshb_ --------------------------------------------------------------------------------------------


              230       240       250       260                                                     
                |         |         |         |                                                     
d1lsha2 LSVFDIKEGNVVIESRQKLILEGIQSAPAASQAASLQNRGGLMYKF-p............................................
d1lsha3 -----------------------------------------------glisqqqqqphhqqqphqhgqdqaraayqrpwashefspaeqkqi
d1lshb_ -----------------------------------------------gnlqshpaarvdikwgrlpsslqraknallengapviasklemei


                                                                                   
                                                                                   
d1lsha2 ...........................................................................
d1lsha3 hdimtarpvmrrkqscsksaalsskvcfsarlrnaafirnallykitgdyvskvyvqptsskaqitkvelelqag
d1lshb_ mpkanqkhqvsvilaamtprrmniivklpkvtyfqqgillpftf...............................


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: 0040643 (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   Danio rerio 58 (pseudogenes) - Zebrafish
NoYes   Sarcophilus harrisii 76_7.0 - Tasmanian devil
NoYes   Ornithorhynchus anatinus 76_5 - Platypus
NoYes   Saccoglossus kowalevskii v3.0
NoYes   Meleagris gallopavo 76_2 - Turkey
NoYes   Gallus gallus 76_4 - Chicken
NoYes   Anas platyrhynchos 76_1.0 - Mallard
NoYes   Taeniopygia guttata 76_3.2.4 - Zebra finch
NoYes   Ficedula albicollis 76_1.0 - Collared flycatcher
NoYes   Pelodiscus sinensis 76_1.0 - Chinese soft-shelled turtle
NoYes   Anolis carolinensis 76_2.0 - Green anole
NoYes   Xenopus laevis - African clawed frog
NoYes   Xenopus tropicalis 76_4.2 - Tropical clawed frog
NoYes   Latimeria chalumnae 76_1 - Coelacanth
NoYes   Lepisosteus oculatus 76 - Spotted gar
NoYes   Gadus morhua 76_1 - Atlantic cod
NoYes   Tetraodon nigroviridis 76_8 - Spotted green pufferfish
NoYes   Takifugu rubripes 76_4 - Torafugu
NoYes   Gasterosteus aculeatus 76_1 - Three-spined stickleback
NoYes   Oryzias latipes 76_1 - Japanese medaka
NoYes   Xiphophorus maculatus 76_4.4.2 - Southern platyfish
NoYes   Oreochromis niloticus 76_1.0 - Nile tilapia
NoYes   Astyanax mexicanus 76 - Mexican tetra
NoYes   Danio rerio 76_9 - Zebrafish
NoYes   Trichoplax adhaerens
NoYes   Xenopus (Silurana) tropicalis v7.1 (annotation v7.2) - Tropical clawed frog
NoYes   Sarcophilus harrisii 69_7.0 - Tasmanian devil
NoYes   Ornithorhynchus anatinus 69_5 - Platypus
NoYes   Meleagris gallopavo 69_2 - Turkey
NoYes   Gallus gallus 69_2 - Chicken
NoYes   Taeniopygia guttata 69_3.2.4 - Zebra finch
NoYes   Pelodiscus sinensis 69_1.0 - Chinese soft-shelled turtle
NoYes   Anolis carolinensis 69_2.0 - Green anole
NoYes   Xenopus tropicalis 69_4.2 - Tropical clawed frog
NoYes   Latimeria chalumnae 69_1 - Coelacanth
NoYes   Gadus morhua 69_1 - Atlantic cod
NoYes   Tetraodon nigroviridis 69_8 - Spotted green pufferfish
NoYes   Takifugu rubripes 69_4 - Torafugu
NoYes   Gasterosteus aculeatus 69_1 - Three-spined stickleback
NoYes   Oryzias latipes 69_1 - Japanese medaka
NoYes   Xiphophorus maculatus 69_4.4.2 - Southern platyfish
NoYes   Oreochromis niloticus 69_1.0 - Nile tilapia
NoYes   Danio rerio 69_9 - Zebrafish
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)


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