SUPERFAMILY 1.75 HMM library and genome assignments server

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Positive stranded ssRNA viruses alignments

These alignments are sequences aligned to the 0041857 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  
                                     |         |         |         |         |         |         |  
d1ohfc_                    .NIDNVTAAAQELGQSLDANVITFPTNVATMPEFRSWARGKLDIDQDSIGWYFKYLDPAGATESARAVGEYSK
ENSMUSP00000099810:575-736 s------------------------------------------------------------------------


                                 80        90       100       110       120       130       140     
                                  |         |         |         |         |         |         |     
d1ohfc_                    IPDGLVKFSVDAEIREIYNEECPTVSDASIPLDGAQWSLSIISYPMFRTAYFAVANVDNKEISLDVTNDLIVW
ENSMUSP00000099810:575-736 -------------------------------------------------------------------------


                             150       160       170       180       190       200       210       2
                               |         |         |         |         |         |         |        
d1ohfc_                    LNNLASWRDVVDSGQWFTFSDDPTWFVRIRVLHPTYDLPDPTEGLLRTVSDYRLTYKSITCEANMPTLVDQGF
ENSMUSP00000099810:575-736 --------------------------------------------------------------SSTVPATQQLF


                           20       230       240       250          260       270       280       2
                            |         |         |         |            |         |         |        
d1ohfc_                    WIGGHYALTPIATTQNAVEGSGFVHPFNVTRPGIAA...GVTLTWASMPPGGSAPSGDPAWIPDSTTQFQWRH
ENSMUSP00000099810:575-736 SQGSSFPPNP--RPAENFRNSGLTPPVTIVQPSSSAgqiLAQISRHSNPAQGSAPTWTSS----SRPGFAAQQ


                           90       300       310       320       330       340       350       360 
                            |         |         |         |         |         |         |         | 
d1ohfc_                    GGFDAPTGVITYTIPRGYTMQYFDTTTNEWNGFANPDDVVTFGQTGGAAGTNATITITAPTVTLTILATTTSA
ENSMUSP00000099810:575-736 VPT-----------------QATAKTRSSQFGVNNFQTSSSFSA---------MSLPGAPTASSGTAAYPALP


                                 370       380       390       400       410       420       430    
                                   |         |         |         |         |         |         |    
d1ohfc_                    ANVINFRNLDAETTAASNRSEVPLPPLTFGQTAPNNPKIEQTLVKDTLGSYLVHSKMRNPVFQLTPASSFGAI
ENSMUSP00000099810:575-736 NRGSNFP------------------------------------------------------------------


                              440       450       460       470       480       490       500       
                                |         |         |         |         |         |         |       
d1ohfc_                    SFTNPGFDRNLDLPGFGGIRDSLDVNMSTAVCHFRSLSKSCSIVTKTYQGWEGVTNVNTPFGQFAHSGLLKND
ENSMUSP00000099810:575-736 ------------------------------------------------------PETGQTTGQFQARTAE---


                           510       520       530       540       550       560       570       580
                             |         |         |         |         |         |         |         |
d1ohfc_                    EILCLADDLATRLTGVYGATDNFAAAVLAFAANMLTSVLKSEATTSVIKELGNQATGLANQGLARLPGLLASI
ENSMUSP00000099810:575-736 ------------------------------------------------------GVGVWPQWQGQQP------


                                  590       600            
                                    |         |            
d1ohfc_                    PGKIAARV------------rarrdrrraarm
ENSMUSP00000099810:575-736 --------------------............


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: 0041857 (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   Tarsius syrichta 76_1
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   Otolemur garnettii 76_3 - Small-eared galago
NoYes   Rattus norvegicus 76_5.0 - Norway rat
NoYes   Mus musculus 76_38 - House mouse
NoYes   Dipodomys ordii 76_1 - Ord's kangaroo rat
NoYes   Ictidomys tridecemlineatus 76_2 - Thirteen-lined ground squirrel
NoYes   Heterocephalus glaber v1.7-2 - Naked mole-rat
NoYes   Cavia porcellus 76_3 - Domestic guinea pig
NoYes   Oryctolagus cuniculus 76_2 - Rabbit
NoYes   Ochotona princeps 76 - American pika
NoYes   Tupaia belangeri 76 - Northern tree shrew
NoYes   Sus scrofa 76_10.2 - Pig
NoYes   Bos taurus 76_3.1 - Cattle
NoYes   Ovis aries 76_3.1 - Sheep
NoYes   Vicugna pacos 76_1 - Alpaca
NoYes   Mustela putorius furo 76_1.0 - Domestic ferret
NoYes   Ailuropoda melanoleuca 76_1 - Giant panda
NoYes   Canis familiaris 76_3.1 - Dog
NoYes   Felis catus 76_6.2 - Domestic cat
NoYes   Equus caballus 76_2 - Horse
NoYes   Myotis lucifugus 76_2.0 - Little brown bat
NoYes   Pteropus vampyrus 76_1 - Large flying fox
NoYes   Sorex araneus 76_1 - European shrew
NoYes   Loxodonta africana 76_3 - African savanna elephant
NoYes   Choloepus hoffmanni 76_1 - Hoffmann's two-fingered sloth
NoYes   Gallus gallus 76_4 - Chicken
NoYes   Tetraodon nigroviridis 76_8 - Spotted green pufferfish
NoYes   Takifugu rubripes 76_4 - Torafugu
NoYes   Neurospora tetrasperma
NoYes   Neurospora discreta FGSC 8579
NoYes   Neurospora crassa OR74A
NoYes   Aspergillus fumigatus Af293
NoYes   Neosartorya fischeri NRRL 181
NoYes   Schizosaccharomyces pombe - Fission yeast
NoYes   Thellungiella halophila v173
NoYes   Brassica rapa Chiifu-401 1.2 - Field mustard
NoYes   Capsella rubella v183
NoYes   Arabidopsis lyrata - Lyrate rockcress
NoYes   Arabidopsis thaliana 10 - Thale cress
NoYes   Cryptosporidium parvum Iowa II
NoYes   Bacillus halodurans C-125
NoYes   Bacillus cereus 03BB102
NoYes   Bacillus anthracis str. A0248
NoYes   Rhodopirellula baltica SH 1
NoYes   Candidatus Solibacter usitatus Ellin6076
NoYes   Desulfotalea psychrophila LSv54
NoYes   Cupriavidus metallidurans CH34
NoYes   Burkholderia cenocepacia HI2424
NoYes   Xanthomonas axonopodis pv. citri str. 306
NoYes   Xanthomonas oryzae pv. oryzae PXO99A
NoYes   Xanthomonas campestris pv. campestris str. B100
NoYes   Azotobacter vinelandii DJ
NoYes   Cryptococcus neoformans var. grubii H99
NoYes   Cryptococcus neoformans B-3501A
NoYes   Cryptococcus neoformans JEC21
NoYes   Aspergillus fumigatus A1163
NoYes   Schizosaccharomyces pombe 972h-
NoYes   Lactobacillus acidophilus La-14
NoYes   Lactobacillus acidophilus NCFM
NoYes   Bacillus toyonensis BCT-7112
NoYes   Bacillus thuringiensis HD-771
NoYes   Bacillus thuringiensis HD-789
NoYes   Bacillus thuringiensis serovar konkukian str. 97-27
NoYes   Bacillus cereus biovar anthracis str. CI
NoYes   Bacillus cereus AH820
NoYes   Bacillus cereus G9842
NoYes   Bacillus cereus Q1
NoYes   Bacillus cereus F837/76
NoYes   Bacillus cereus E33L
NoYes   Bacillus anthracis str. H9401
NoYes   Bacillus anthracis str. CDC 684
NoYes   Bacillus anthracis str. 'Ames Ancestor'
NoYes   Bacillus anthracis str. Sterne
NoYes   Bacillus anthracis str. Ames
NoYes   Desulfovibrio vulgaris RCH1
NoYes   Desulfovibrio vulgaris str. Hildenborough
NoYes   Burkholderia cenocepacia MC0-3
NoYes   Burkholderia cenocepacia AU 1054
NoYes   Xanthomonas citri subsp. citri Aw12879
NoYes   Xanthomonas campestris pv. vesicatoria str. 85-10
NoYes   Xanthomonas axonopodis pv. citrumelo F1
NoYes   Xanthomonas oryzae pv. oryzae MAFF 311018
NoYes   Xanthomonas oryzae pv. oryzae KACC 10331
NoYes   Xanthomonas campestris pv. raphani 756C
NoYes   Xanthomonas campestris pv. campestris str. 8004
NoYes   Xanthomonas campestris pv. campestris str. ATCC 33913
NoYes   Escherichia coli str. 'clone D i2'
NoYes   Escherichia coli str. 'clone D i14'
NoYes   Escherichia coli ABU 83972
NoYes   Escherichia coli IAI39
NoYes   Escherichia coli SMS-3-5
NoYes   Escherichia coli CFT073
NoYes   Azotobacter vinelandii CA6
NoYes   Azotobacter vinelandii CA
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   Otolemur garnettii 69_3 - Small-eared galago
NoYes   Tarsius syrichta 69_1
NoYes   Rattus norvegicus 69_3.4 - Norway rat
NoYes   Mus musculus 69_38 - House mouse
NoYes   Dipodomys ordii 69_1 - Ord's kangaroo rat
NoYes   Ictidomys tridecemlineatus 69_2 - Thirteen-lined ground squirrel
NoYes   Cavia porcellus 69_3 - Domestic guinea pig
NoYes   Oryctolagus cuniculus 69_2 - Rabbit
NoYes   Ochotona princeps 69 - American pika
NoYes   Tupaia belangeri 69 - Northern tree shrew
NoYes   Sus scrofa 69_10.2 - Pig
NoYes   Bos taurus 69_3.1 - Cattle
NoYes   Vicugna pacos 69_1 - Alpaca
NoYes   Mustela putorius furo 69_1.0 - Domestic ferret
NoYes   Ailuropoda melanoleuca 69_1 - Giant panda
NoYes   Canis familiaris 69_3.1 - Dog
NoYes   Felis catus 69 - Domestic cat
NoYes   Equus caballus 69_2 - Horse
NoYes   Myotis lucifugus 69_2.0 - Little brown bat
NoYes   Pteropus vampyrus 69_1 - Large flying fox
NoYes   Sorex araneus 69_1 - European shrew
NoYes   Loxodonta africana 69_3 - African savanna elephant
NoYes   Choloepus hoffmanni 69_1 - Hoffmann's two-fingered sloth
NoYes   Gallus gallus 69_2 - Chicken
NoYes   Tetraodon nigroviridis 69_8 - Spotted green pufferfish
NoYes   Takifugu rubripes 69_4 - Torafugu
NoYes   Arabidopsis thaliana 10 - Thale cress
NoYes   Homo sapiens 75_37 - Human
NoYes   Homo sapiens - Human
NoYes   Mus musculus 63_37 (longest transcript per gene) - House mouse
NoYes   Activated sludge plasmid pool Morges-2009 (Newbler) (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Protozoadb 2010_08 (Protozoadb)
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 1 Maryland Estuary CO2- (Maryland Estuary ambient) (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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