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.


FnI-like domain alignments

These alignments are sequences aligned to the 0046485 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             
                          |         |           |         |             
d1e88a3 ........y-GHCVTDSGVVYSVGMQWLKTQGN..KQMLCTCLGNGVSCQE-t...........
d1fbra2 ....nrcnd-----QDTRTSYRIGDTWSKKDNRg.NLLQCICTGNGRGEWKCerhts.......
d1qgba1 ......skp---GCYDNGKHYQINQQWERTYLG..NALVCTCYGGSRG----fnceskp.....
d1qgba2 eaeetcfdk------YTGNTYRVGDTYERPKDS..MIWDCTCIGAGRGRISCtianr.......
d1tpga2 syqvicrde------KTQMIYQQHQSWLRPVLRsnRVEYCWCNS--------graqchsvpvks


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: 0046485 (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   Homo sapiens 76_38 - Human
NoYes   Pan troglodytes 76_2.1.4 - Chimpanzee
NoYes   Gorilla gorilla 76_3.1 - Western gorilla
NoYes   Pongo abelii 76_2 - Sumatran orangutan
NoYes   Nomascus leucogenys 76_1.0 - Northern white-cheeked gibbon
NoYes   Papio anubis 76 - Olive baboon
NoYes   Macaca mulatta 76_1 - Rhesus monkey
NoYes   Callithrix jacchus 76_3.2.1 - White-tufted-ear marmoset
NoYes   Mus musculus 76_38 - House mouse
NoYes   Cavia porcellus 76_3 - Domestic guinea pig
NoYes   Sus scrofa 76_10.2 - Pig
NoYes   Bos taurus 76_3.1 - Cattle
NoYes   Ovis aries 76_3.1 - Sheep
NoYes   Ailuropoda melanoleuca 76_1 - Giant panda
NoYes   Equus caballus 76_2 - Horse
NoYes   Erinaceus europaeus 76 - Western European hedgehog
NoYes   Dasypus novemcinctus 76_2 - Nine-banded armadillo
NoYes   Choloepus hoffmanni 76_1 - Hoffmann's two-fingered sloth
NoYes   Macropus eugenii 76_1.0 - Tammar wallaby
NoYes   Latimeria chalumnae 76_1 - Coelacanth
NoYes   Homo sapiens 69_37 - Human
NoYes   Pan troglodytes 69_2.1.4 - Chimpanzee
NoYes   Gorilla gorilla 69_3.1 - Western gorilla
NoYes   Pongo abelii 69_2 - Sumatran orangutan
NoYes   Nomascus leucogenys 69_1.0 - Northern white-cheeked gibbon
NoYes   Macaca mulatta 69_1 - Rhesus monkey
NoYes   Callithrix jacchus 69_3.2.1 - White-tufted-ear marmoset
NoYes   Mus musculus 69_38 - House mouse
NoYes   Cavia porcellus 69_3 - Domestic guinea pig
NoYes   Sus scrofa 69_10.2 - Pig
NoYes   Bos taurus 69_3.1 - Cattle
NoYes   Ailuropoda melanoleuca 69_1 - Giant panda
NoYes   Equus caballus 69_2 - Horse
NoYes   Erinaceus europaeus 69 - Western European hedgehog
NoYes   Dasypus novemcinctus 69_2 - Nine-banded armadillo
NoYes   Choloepus hoffmanni 69_1 - Hoffmann's two-fingered sloth
NoYes   Macropus eugenii 69_1.0 - Tammar wallaby
NoYes   Latimeria chalumnae 69_1 - Coelacanth
NoYes   Homo sapiens 75_37 - Human
NoYes   Homo sapiens - Human
NoYes   Mus musculus 63_37 (longest transcript per gene) - House mouse
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   TargetDB (Targets)
NoYes   ALL (only advised for small superfamilies)


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