SUPERFAMILY 1.75 HMM library and genome assignments server

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Nucleic acid-binding proteins alignments

These alignments are sequences aligned to the 0052237 model.

Sophisticated options are available for refining alignments:

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


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   
                 |         |         |         |         |         |         |         |   

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: 0052237 (list models)
Initial SAMT99 seed:

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   Callithrix jacchus 76_3.2.1 - White-tufted-ear marmoset
NoYes   Mus musculus 76_38 - House mouse
NoYes   Myotis lucifugus 76_2.0 - Little brown bat
NoYes   Saccoglossus kowalevskii v3.0
NoYes   Ciona savignyi 76_2.0 - Pacific transparent sea squirt
NoYes   Capitella sp. I
NoYes   Caenorhabditis elegans 76_235 - Roundworm
NoYes   Caenorhabditis briggsae 2
NoYes   Sphaeroforma arctica JP610
NoYes   Saccharomyces bayanus MIT
NoYes   Dictyostelium discoideum
NoYes   Dictyostelium purpureum
NoYes   Picea abies - Norway spruce
NoYes   Carica papaya - Papaya
NoYes   Malus domestica v196 - Apple
NoYes   Musa balbisiana - Balbis banana
NoYes   Albugo laibachii 22
NoYes   Pythium iwayamai DAOM BR242034 22
NoYes   Pythium arrhenomanes ATCC 12531 22
NoYes   Pythium ultimum v1.7-2
NoYes   Pythium aphanidermatum DAOM BR444 22
NoYes   Pythium irregulare DAOM BR486 22
NoYes   Pythium vexans DAOM BR484 22
NoYes   Phytophthora ramorum 1.1 - Sudden oak death agent
NoYes   Phytophthora sojae 1.1
NoYes   Phytophthora infestans T30-4
NoYes   Phytophthora capsici
NoYes   Hyaloperonospora arabidopsidis 22
NoYes   Symbiodinium minutum clade B1 v1.2
NoYes   Caenorhabditis elegans WormBase WS218 - Roundworm
NoYes   Coccidioides immitis RMSCC 3703
NoYes   Saccharomyces cerevisiae FostersO
NoYes   Saccharomyces cerevisiae Y10
NoYes   Felis catus 69 - Domestic cat
NoYes   Myotis lucifugus 69_2.0 - Little brown bat
NoYes   Dasypus novemcinctus 69_2 - Nine-banded armadillo
NoYes   Ciona savignyi 69_2.0 - Pacific transparent sea squirt
NoYes   Caenorhabditis elegans 69_215 - Roundworm
NoYes   Lotus japonicus
NoYes   Malus x domestica - Apple
NoYes   Core Eukaryotic Genes 458 (CEGMA)
NoYes   NCBI 2017_08 genome
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 ]