SUPERFAMILY 1.75 HMM library and genome assignments server

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Aerolisin/ETX pore-forming domain alignments

These alignments are sequences aligned to the 0042431 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      
                                           |         |         |         |         |         |      
d1prea2 ..........................IPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLAHYLGYAWVGGNHSQYVGEDMDVTRDGDGWV
d1uyja_ sydnvdtliekgryntkynylkrmek------------------------------------------------------------------


          70        80        90       100       110        120       130       140       150       
           |         |         |         |         |          |         |         |         |       
d1prea2 IRGNNDGGCDGYRCGDKTAIKVSNFAYNLDPDSFKHGDVTQSDRQLVKTV.VGWAVNDSDTPQSGYDVTLRYDTATNWSKTNTYGLSEKVTT
d1uyja_ ------YYPNAMAYFDKVTINPQGNDFYINNPKVELDGEPSMNYLEDVYVgKALLTNDTQQEQKLKSQSFTCKNTDTVTATTTHTVGTSIQA


        160       170       180       190          200       210       220       230       240      
          |         |         |         |            |         |         |         |         |      
d1prea2 KNKFKWPLVGETELSIEIAANQSWASQNGGSTTTSLSQSVR...PTVPARSKIPVKIELYKADISYPYEFKADVSYDLTLSGFLRWGGNAWY
d1uyja_ TAKFTVPFN---ETGVSLTTSYSFANTNTNTNSKEITHNVPsqdILVPANTTVEVIAYLKKVNVKGNVKL----------------------


         250       260       270       280       290       300       310       320       330       3
           |         |         |         |         |         |         |         |         |        
d1prea2 THPDNRPNWNHTFVIGPYKDKASSIRYQWDKRYIPGEVKWWDWNWTIQQNGLSTMQNNLARVLRPVRAGITGDFSAESQFAGNIEIGAPVPL
d1uyja_ --------------------------------------------------------------------------------------------


        40       350       360       370       380                                                  
         |         |         |         |         |                                                  
d1prea2 AADSKVRRARSVDGAGQGLRLEIPLDAQELSGLGFNNVSLSVTPAA--nq..........................................
d1uyja_ ------------------------------------------------vgqvsgsewgeipsylafprdgykfslsdtvnksdlnedgtini


                                                                 
                                                                 
d1prea2 .........................................................
d1uyja_ ngkgnysavmgdelivkvrnlntnnvqeyvipvdkkeksndsnivkyrslsikapgi


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: 0042431 (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   Ornithorhynchus anatinus 76_5 - Platypus
NoYes   Saccoglossus kowalevskii v3.0
NoYes   Petromyzon marinus 76_7.0 - Sea lamprey
NoYes   Gallus gallus 76_4 - Chicken
NoYes   Anas platyrhynchos 76_1.0 - Mallard
NoYes   Ficedula albicollis 76_1.0 - Collared flycatcher
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   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   Poecilia formosa 76 - Amazon molly
NoYes   Oreochromis niloticus 76_1.0 - Nile tilapia
NoYes   Astyanax mexicanus 76 - Mexican tetra
NoYes   Danio rerio 76_9 - Zebrafish
NoYes   Oikopleura dioica
NoYes   Adineta vaga
NoYes   Octopus bimaculoides 280
NoYes   Crassostrea gigas 22 - Pacific oyster
NoYes   Lottia gigantea - Owl limpet
NoYes   Helobdella robusta
NoYes   Capitella sp. I
NoYes   Danaus plexippus OGS1.0 - Monarch butterfly
NoYes   Bombyx mori - Domestic silkworm
NoYes   Apis mellifera 38.2d - Honey bee
NoYes   Strigamia maritima 22
NoYes   Ixodes scapularis - Black-legged tick
NoYes   Pristionchus pacificus
NoYes   Meloidogyne incognita - Southern root-knot nematode
NoYes   Meloidogyne hapla
NoYes   Onchocerca volvulus 22
NoYes   Brugia malayi WS250 - Agent of lymphatic filariasis
NoYes   Caenorhabditis japonica
NoYes   Caenorhabditis brenneri
NoYes   Caenorhabditis remanei
NoYes   Caenorhabditis elegans 76_235 - Roundworm
NoYes   Caenorhabditis briggsae 2
NoYes   Trichinella spiralis 22
NoYes   Hymenolepis microstoma
NoYes   Echinococcus multilocularis
NoYes   Echinococcus granulosus
NoYes   Taenia solium - Pork tapeworm
NoYes   Schistosoma mansoni
NoYes   Mnemiopsis leidyi - Sea walnut
NoYes   Acropora digitifera v1.0
NoYes   Nematostella vectensis 1.0 - Starlet sea anemone
NoYes   Hydra vulgaris
NoYes   Proterospongia sp. ATCC 50818
NoYes   Mortierella verticillata NRRL 6337
NoYes   Sphaerobolus stellatus v1.0
NoYes   Coprinopsis cinerea okayama7 130 v3
NoYes   Galerina marginata v1.0
NoYes   Hebeloma cylindrosporum h7 v2.0
NoYes   Laccaria bicolor S238N-H82
NoYes   Agaricus bisporus var. bisporus
NoYes   Schizophyllum commune
NoYes   Stereum hirsutum FP-91666 SS1 v1.0
NoYes   Heterobasidion annosum
NoYes   Gloeophyllum trabeumv1.0
NoYes   Fomitiporia mediterranea v1.0
NoYes   Tulasnella calospora AL13/4D v1.0
NoYes   Postia placenta
NoYes   Fomitopsis pinicolav1.0
NoYes   Fomitopsis pinicola FP-58527 SS1 v3.0
NoYes   Dichomitus squalens
NoYes   Trametes versicolor v1.0
NoYes   Magnaporthe poae ATCC 64411 22
NoYes   Podospora anserina
NoYes   Glomerella graminicola 22
NoYes   Botrytis cinerea B05.10
NoYes   Sclerotinia sclerotiorum
NoYes   Setosphaeria turcica v1.0
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   Alternaria brassicicola
NoYes   Trichophyton equinum CBS 127.97
NoYes   Trichophyton verrucosum HKI 0517
NoYes   Aspergillus brasiliensis v1.0
NoYes   Aspergillus carbonarius ITEM 5010
NoYes   Aspergillus tubingensis v1.0
NoYes   Aspergillus wentii v1.0
NoYes   Dictyostelium discoideum
NoYes   Selaginella moellendorffii
NoYes   Pinus taeda - Loblolly pine
NoYes   Picea abies - Norway spruce
NoYes   Gossypium raimondii v221
NoYes   Carica papaya - Papaya
NoYes   Cucumis sativus v122 - Cucumber
NoYes   Fragaria vesca - Wild strawberry
NoYes   Malus domestica v196 - Apple
NoYes   Linum usitatissimum v200 - Flax
NoYes   Vitis vinifera - Wine grape
NoYes   Actinidia chinensis Hongyang
NoYes   Aquilegia coerulea v195
NoYes   Triticum urartu 22
NoYes   Triticum aestivum 22 - Bread wheat
NoYes   Aegilops tauschii 22
NoYes   Brachypodium distachyon - Stiff brome
NoYes   Phyllostachys heterocyclavar. pubescens - Mosochiku
NoYes   Panicum virgatum v202 - Switchgrass
NoYes   Setaria italica v164 - Foxtail millet
NoYes   Zea mays subsp. mays - Maize
NoYes   Zea mays v181 - Maize
NoYes   Bigelowiella natans CCMP2755 22
NoYes   Cyanophora paradoxa
NoYes   Pythium arrhenomanes ATCC 12531 22
NoYes   Calothrix sp. PCC 7507
NoYes   Frankia alni ACN14a
NoYes   Kitasatospora setae KM-6054
NoYes   Saccharopolyspora erythraea NRRL 2338
NoYes   Salinispora arenicola CNS-205
NoYes   Verrucosispora maris AB-18-032
NoYes   Clostridium novyi NT
NoYes   Lysinibacillus sphaericus C3-41
NoYes   Bacillus anthracis str. A0248
NoYes   Fibrella aestuarina
NoYes   Candidatus Solibacter usitatus Ellin6076
NoYes   Burkholderia glumae BGR1
NoYes   Aeromonas veronii B565
NoYes   Aeromonas salmonicida subsp. salmonicida A449
NoYes   Aeromonas hydrophila subsp. hydrophila ATCC 7966
NoYes   Vibrio harveyi ATCC BAA-1116
NoYes   Photobacterium profundum SS9
NoYes   Shewanella denitrificans OS217
NoYes   Shewanella baltica OS185
NoYes   Pseudoalteromonas sp. SM9913
NoYes   Hahella chejuensis KCTC 2396
NoYes   Marinomonas posidonica IVIA-Po-181
NoYes   Pectobacterium wasabiae WPP163
NoYes   Pseudomonas entomophila L48
NoYes   Francisella cf. novicida 3523
NoYes   Methanosarcina mazei Go1
NoYes   Methanosarcina barkeri str. Fusaro
NoYes   Halogeometricum borinquense DSM 11551
NoYes   Xenopus (Silurana) tropicalis v7.1 (annotation v7.2) - Tropical clawed frog
NoYes   Ascaris suum Victoria/Ghent - Pig roundworm
NoYes   Caenorhabditis elegans WormBase WS218 - Roundworm
NoYes   Hordeum vulgare 22 - Domesticated barley
NoYes   Prochlorococcus marinus str. MIT 9303
NoYes   Nocardiopsis alba ATCC BAA-2165
NoYes   Clostridium botulinum BKT015925
NoYes   Enterococcus mundtii QU 25
NoYes   Paenibacillus larvae subsp. larvae DSM 25430
NoYes   Bacillus thuringiensis HD-789
NoYes   Bacillus thuringiensis MC28
NoYes   Bacillus thuringiensis serovar finitimus YBT-020
NoYes   Bacillus thuringiensis serovar thuringiensis str. IS5056
NoYes   Bacillus cereus biovar anthracis str. CI
NoYes   Bacillus anthracis str. H9401
NoYes   Bacillus anthracis str. CDC 684
NoYes   Bacillus anthracis str. 'Ames Ancestor'
NoYes   Bacillus anthracis str. A2012
NoYes   Echinicola vietnamensis DSM 17526
NoYes   Aeromonas hydrophila ML09-119
NoYes   Vibrio nigripulchritudo VibrioScope
NoYes   Shewanella baltica BA175
NoYes   Shewanella baltica OS117
NoYes   Shewanella baltica OS195
NoYes   Shewanella baltica OS155
NoYes   Ornithorhynchus anatinus 69_5 - Platypus
NoYes   Petromyzon marinus 69_7.0 - Sea lamprey
NoYes   Xenopus tropicalis 69_4.2 - Tropical clawed frog
NoYes   Latimeria chalumnae 69_1 - Coelacanth
NoYes   Gadus morhua 69_1 - Atlantic cod
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   Caenorhabditis elegans 69_215 - Roundworm
NoYes   Loa loa v3.3 - Eye worm
NoYes   Wuchereria bancrofti v1.0 - Agent of lymphatic filariasis
NoYes   Brugia malayi v1.0 - Agent of lymphatic filariasis
NoYes   Moniliophthora perniciosa FA553
NoYes   Malus x domestica - Apple
NoYes   Ricinus communis - Castor bean
NoYes   Vibrio campbellii ATCC BAA-1116
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Endophytic microbiome from Rice (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #2 (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 03(I) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 09(Y) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP20 from Bath Lake Vista Annex - Purple-Sulfur Mats (meta-genome)
NoYes   Human Gut Community Subject 7 (meta-genome)
NoYes   Human Gut Community Subject 8 (meta-genome)
NoYes   Macropus eugenii forestomach microbiome from Canberra, Australia, sample Macropus_eugenii_combined (meta-genome)
NoYes   Marine anammox bioreactor enriched for Scalindua species (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 4 Nevada Test Site Crust CO2- (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2+ (Oak Ridge elevated CO2) (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 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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