SUPERFAMILY 1.75 HMM library and genome assignments server

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Fic-like alignments

These alignments are sequences aligned to the 0052609 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        90
                   |         |         |         |         |         |         |         |         |
d2f6sa1 mh--LDRQSLEKAKHLIQSGLIDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNIAKGNFRFANCLYLDLILPRIESMPQNNFNQIVEKYV


               100       110       120       130       140       150       160       170         
                 |         |         |         |         |         |         |         |         
d2f6sa1 EMNIAHPFLEGNGRATRIWLDLLLKKELKKIVLWDRIDKAAYLSAMERSPVNDLEIKTLLKKHLSSNTNDPLTLIKGITQSYYYE--gl


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: 0052609 (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   Mycoplasma leachii 99/014/6
NoYes   Mycoplasma mycoides subsp. capri LC str. 95010
NoYes   Mycoplasma capricolum subsp. capricolum ATCC 27343
NoYes   Mycoplasma bovis HB0801
NoYes   Mycoplasma fermentans M64
NoYes   Finegoldia magna ATCC 29328
NoYes   Selenomonas ruminantium subsp. lactilytica TAM6421
NoYes   Ruminococcus bromii
NoYes   Ruminococcus albus 7
NoYes   butyrate-producing bacterium SS3/4
NoYes   Syntrophobotulus glycolicus DSM 8271
NoYes   Acetobacterium woodii DSM 1030
NoYes   Roseburia intestinalis
NoYes   Streptococcus pseudopneumoniae IS7493
NoYes   Streptococcus macedonicus ACA-DC 198
NoYes   butyrate-producing bacterium SSC/2
NoYes   Bacillus thuringiensis str. Al Hakam
NoYes   Pelodictyon phaeoclathratiforme BU-1
NoYes   Prevotella intermedia 17
NoYes   Prevotella denticola F0289
NoYes   Porphyromonas asaccharolytica DSM 20707
NoYes   Alistipes finegoldii DSM 17242
NoYes   Capnocytophaga ochracea DSM 7271
NoYes   Leptotrichia buccalis C-1013-b
NoYes   Campylobacter lari RM2100
NoYes   Helicobacter cetorum MIT 00-7128
NoYes   Helicobacter mustelae 12198
NoYes   Helicobacter acinonychis str. Sheeba
NoYes   Helicobacter pylori B38
NoYes   Desulfovibrio alaskensis G20
NoYes   Geobacter lovleyi SZ
NoYes   Neisseria meningitidis FAM18
NoYes   Taylorella asinigenitalis MCE3
NoYes   Aggregatibacter actinomycetemcomitans D7S-1
NoYes   Haemophilus influenzae PittEE
NoYes   Francisella philomiragia subsp. philomiragia ATCC 25017
NoYes   Mycoplasma leachii PG50
NoYes   Mycoplasma mycoides subsp. mycoides SC str. Gladysdale
NoYes   Mycoplasma mycoides subsp. mycoides SC str. PG1
NoYes   Mycoplasma bovis Hubei-1
NoYes   Mycoplasma bovis PG45
NoYes   Mycoplasma fermentans JER
NoYes   Mycoplasma fermentans PG18
NoYes   Ruminococcus champanellensis 18P13
NoYes   Roseburia intestinalis XB6B4
NoYes   Enterococcus mundtii QU 25
NoYes   Enterococcus faecium Aus0085
NoYes   Enterococcus faecium DO
NoYes   Lactococcus lactis subsp. lactis CV56
NoYes   Lactococcus lactis subsp. cremoris UC509.9
NoYes   Streptococcus constellatus subsp. pharyngis C1050
NoYes   Streptococcus constellatus subsp. pharyngis C818
NoYes   Streptococcus constellatus subsp. pharyngis C232
NoYes   Streptococcus intermedius B196
NoYes   Streptococcus anginosus C238
NoYes   Streptococcus mutans UA159
NoYes   Streptococcus suis T15
NoYes   Streptococcus suis SC070731
NoYes   Streptococcus suis S735
NoYes   Streptococcus suis ST3
NoYes   Streptococcus suis D9
NoYes   Streptococcus suis SS12
NoYes   Streptococcus suis ST1
NoYes   Streptococcus suis A7
NoYes   Streptococcus suis JS14
NoYes   Streptococcus suis GZ1
NoYes   Streptococcus suis 98HAH33
NoYes   Streptococcus suis 05ZYH33
NoYes   Bacillus thuringiensis HD-789
NoYes   Bacillus thuringiensis MC28
NoYes   Bacillus thuringiensis Bt407
NoYes   Bacillus cereus F837/76
NoYes   Prevotella sp. oral taxon 299 str. F0039
NoYes   Prevotella dentalis DSM 3688
NoYes   Porphyromonas gingivalis TDC60
NoYes   Helicobacter pylori BM012S
NoYes   Helicobacter pylori BM012A
NoYes   Helicobacter pylori SouthAfrica20
NoYes   Helicobacter pylori UM298
NoYes   Helicobacter pylori UM066
NoYes   Helicobacter pylori UM037
NoYes   Helicobacter pylori UM299
NoYes   Helicobacter pylori UM032
NoYes   Helicobacter pylori OK310
NoYes   Helicobacter pylori OK113
NoYes   Helicobacter pylori Rif2
NoYes   Helicobacter pylori Rif1
NoYes   Helicobacter pylori PeCan18
NoYes   Helicobacter pylori Shi169
NoYes   Helicobacter pylori Shi112
NoYes   Helicobacter pylori Shi417
NoYes   Helicobacter pylori XZ274
NoYes   Helicobacter pylori Aklavik86
NoYes   Helicobacter pylori SNT49
NoYes   Helicobacter pylori Puno135
NoYes   Helicobacter pylori Puno120
NoYes   Helicobacter pylori ELS37
NoYes   Helicobacter pylori SouthAfrica7
NoYes   Helicobacter pylori India7
NoYes   Helicobacter pylori Lithuania75
NoYes   Helicobacter pylori 2017
NoYes   Helicobacter pylori 2018
NoYes   Helicobacter pylori 908
NoYes   Helicobacter pylori F57
NoYes   Helicobacter pylori F30
NoYes   Helicobacter pylori F16
NoYes   Helicobacter pylori Cuz20
NoYes   Helicobacter pylori PeCan4
NoYes   Helicobacter pylori SJM180
NoYes   Helicobacter pylori B8
NoYes   Helicobacter pylori 52
NoYes   Helicobacter pylori v225d
NoYes   Helicobacter pylori 83
NoYes   Helicobacter pylori 35A
NoYes   Helicobacter pylori P12
NoYes   Helicobacter pylori G27
NoYes   Helicobacter pylori Shi470
NoYes   Helicobacter pylori HPAG1
NoYes   Helicobacter pylori 51
NoYes   Helicobacter pylori F32
NoYes   Helicobacter pylori J99
NoYes   Helicobacter pylori 26695
NoYes   Helicobacter pylori 26695
NoYes   Neisseria meningitidis WUE 2594
NoYes   Neisseria meningitidis G2136
NoYes   Neisseria meningitidis M04-240196
NoYes   Neisseria meningitidis M01-240149
NoYes   Neisseria meningitidis NZ-05/33
NoYes   Neisseria meningitidis M01-240355
NoYes   Neisseria meningitidis 8013
NoYes   Neisseria meningitidis 053442
NoYes   Neisseria meningitidis Z2491
NoYes   Neisseria meningitidis H44/76
NoYes   Neisseria meningitidis alpha710
NoYes   Neisseria meningitidis MC58
NoYes   Taylorella asinigenitalis 14/45
NoYes   Nitrosomonas sp. AL212
NoYes   Aggregatibacter actinomycetemcomitans ANH9381
NoYes   Aggregatibacter actinomycetemcomitans D11S-1
NoYes   Haemophilus somnus 2336
NoYes   Haemophilus influenzae KR494
NoYes   Haemophilus influenzae 10810
NoYes   Haemophilus influenzae R2866
NoYes   Haemophilus influenzae R2846
NoYes   Haemophilus influenzae Rd KW20
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #1 (meta-genome)
NoYes   Groundwater dechlorinating community (KB-1) from synthetic mineral medium in Toronto, ON, sample from Site contaminated with chlorinated ethenes
NoYes   Hindgut microbiome of Nasutitermes sp. (Costa Rica) (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   Mouse Gut Community lean3 (meta-genome)
NoYes   Mouse Gut Community ob1 (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (meta-genome)
NoYes   Sludge/Australian, Phrap Assembly (meta-genome)
NoYes   Soil microbial community from bioreactor at Alameda Naval Air Station, CA, contaminated with Chloroethene, Sample 196 (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)
NoYes   Termite Protist Endosymbiont Community (meta-genome)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
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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