SUPERFAMILY 1.75 HMM library and genome assignments server

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DNA-binding domain of intron-encoded endonucleases alignments

These alignments are sequences aligned to the 0038860 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  
                           |         |         |         |         |         |         |         |  
d1i3ja_          k-FCKCGVRIQTSAYTCSKCRNRSGENNSFFNHKHSDITKSKISEKMKGKKPSNIKKISCDGVIFDCAADAARHFKISSGLVT
M199.2.1:399-443 q------VRKLVTEVMGNKLNRVRARYNKMYGKDASEEAAKWMREELD-----------------------------------


                       90         
                        |         
d1i3ja_          YRVKSDKWNWFYI-n..
M199.2.1:399-443 --------------kkd


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: 0038860 (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



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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   Conidiobolus coronatus NRRL28638 v1.0
NoYes   Fomitopsis pinicolav1.0
NoYes   Daldinia eschscholzii EC12 v1.0
NoYes   Podospora anserina
NoYes   Didymella exigua CBS 183.55 v1.0
NoYes   Leptosphaeria maculans 22
NoYes   Cochliobolus miyabeanus ATCC 44560 v1.0
NoYes   Cochliobolus victoriae FI3 v1.0
NoYes   Cochliobolus carbonum 26-R-13 v1.0
NoYes   Cochliobolus heterostrophus - Southern corn leaf blight pathogen
NoYes   Cochliobolus lunatus m118 v2.0
NoYes   Pyrenophora teres f. teres 22
NoYes   Tuber melanosporum Mel28 22
NoYes   Tuber melanosporum Vittad - Perigord truffle
NoYes   Catenaria anguillulae PL171 v1.0
NoYes   Chlamydomonas reinhardtii 4.0
NoYes   Porphyridium purpureum 02_2012
NoYes   Bigelowiella natans CCMP2755 22
NoYes   Cyanophora paradoxa
NoYes   Ectocarpus siliculosus
NoYes   Aureococcus anophagefferens
NoYes   Fragilariopsis cylindrus
NoYes   Symbiodinium minutum clade B1 v1.2
NoYes   Emiliania huxleyi CCMP1516
NoYes   Mycobacterium rhodesiae NBB3
NoYes   Beutenbergia cavernae DSM 12333
NoYes   Cellulomonas flavigena DSM 20109
NoYes   [Cellvibrio] gilvus ATCC 13127
NoYes   butyrate-producing bacterium SS3/4
NoYes   Tetragenococcus halophilus NBRC 12172
NoYes   Lactobacillus rhamnosus Lc 705
NoYes   Lactobacillus ruminis ATCC 27782
NoYes   Bacillus anthracis str. A0248
NoYes   Granulicella mallensis MP5ACTX8
NoYes   Gordonibacter pamelaeae 7-10-1-b
NoYes   Clostridium sp. SY8519
NoYes   Clostridium saccharobutylicum DSM 13864
NoYes   Lactobacillus rhamnosus LOCK908
NoYes   Lactobacillus rhamnosus GG
NoYes   Lactobacillus rhamnosus GG
NoYes   Lactobacillus amylovorus GRL 1112
NoYes   Streptococcus agalactiae 2603V/R
NoYes   Paenibacillus mucilaginosus K02
NoYes   Bacillus amyloliquefaciens subsp. plantarum UCMB5033
NoYes   Bacillus amyloliquefaciens XH7
NoYes   Bacillus amyloliquefaciens LL3
NoYes   Bacillus amyloliquefaciens TA208
NoYes   Bacillus amyloliquefaciens DSM 7
NoYes   Bacillus thuringiensis HD-771
NoYes   Bacillus cereus AH820
NoYes   Bacillus cereus E33L
NoYes   Bacillus anthracis str. H9401
NoYes   Bacillus anthracis str. CDC 684
NoYes   Bacillus anthracis str. Sterne
NoYes   Bacillus anthracis str. Ames
NoYes   Psychroflexus torquis ATCC 700755
NoYes   Neisseria meningitidis WUE 2594
NoYes   Neisseria meningitidis M04-240196
NoYes   Neisseria meningitidis M01-240149
NoYes   Neisseria meningitidis NZ-05/33
NoYes   Neisseria meningitidis Z2491
NoYes   Neisseria meningitidis H44/76
NoYes   Neisseria meningitidis MC58
NoYes   Activated sludge plasmid pool Morges-2009 (Newbler) (meta-genome)
NoYes   Atta cephalotes fungus garden (ACEF) (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dendroctonus ponderosae beetle community (MPB hybrid beetle) (Lodgepole pine) (meta-genome)
NoYes   Dendroctonus ponderosae fungus gallery (Hybrid pine) (MPB hybrid gallery) (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Fungus garden combined (combined) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 08(T) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 10(Z) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP5 from Bath Lake Vista Annex (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP9 from Dragon Spring, Norris Geyser Basin (meta-genome)
NoYes   Macropus eugenii forestomach microbiome from Canberra, Australia, sample Macropus_eugenii_combined (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Formaldehyde enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methane enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methanol enrichment (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   Sludge/US, Phrap Assembly (meta-genome)
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2+ (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Termite Protist Endosymbiont Community (meta-genome)
NoYes   Uniprot 2018_03 genome
NoYes   Wastewater Terephthalate-degrading communities from Bioreactor (meta-genome)
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
NoYes   NCBI viral sequences (Viral)
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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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