SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.


L domain-like alignments

These alignments are sequences aligned to the 0046297 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
                   |         |         |         |         |         |         |         |         |
d1dcea3 rv--LHLAHKDLTVLCHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDGVANLPRLQELLLCNNRLQQSAAIQPLVSCP


               100       110       120        
                 |         |         |        
d1dcea3 RLVLLNLQGNSLCQEEGIQERLAEMLPSVS----silt


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: 0046297 (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   Rattus norvegicus 58 (pseudogenes) - Norway rat
NoYes   Homo sapiens 76_38 - Human
NoYes   Pan troglodytes 76_2.1.4 - Chimpanzee
NoYes   Macaca mulatta 76_1 - Rhesus monkey
NoYes   Rattus norvegicus 76_5.0 - Norway rat
NoYes   Ictidomys tridecemlineatus 76_2 - Thirteen-lined ground squirrel
NoYes   Equus caballus 76_2 - Horse
NoYes   Sorex araneus 76_1 - European shrew
NoYes   Echinops telfairi 76 - Small Madagascar hedgehog
NoYes   Anolis carolinensis 76_2.0 - Green anole
NoYes   Homo sapiens 69_37 - Human
NoYes   Pan troglodytes 69_2.1.4 - Chimpanzee
NoYes   Macaca mulatta 69_1 - Rhesus monkey
NoYes   Rattus norvegicus 69_3.4 - Norway rat
NoYes   Ictidomys tridecemlineatus 69_2 - Thirteen-lined ground squirrel
NoYes   Equus caballus 69_2 - Horse
NoYes   Sorex araneus 69_1 - European shrew
NoYes   Echinops telfairi 69 - Small Madagascar hedgehog
NoYes   Dasypus novemcinctus 69_2 - Nine-banded armadillo
NoYes   Anolis carolinensis 69_2.0 - Green anole
NoYes   Homo sapiens 75_37 - Human
NoYes   Homo sapiens - Human
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 ]