SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.


Restriction endonuclease-like alignments

These alignments are sequences aligned to the 0041285 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 
                  |         |         |         |         |         |         |         |         | 
d1na6a2 v-NHKYILPEDWHLRFPSGSEIIQYAASHYVKNSLDPDEQLLDRRRVEYDIFLLVEELHVLDIIRKGFGSVDEFIALANSVSNRRKSRAGKS


              100       110       120       130       140       150       160       170       180   
                |         |         |         |         |         |         |         |         |   
d1na6a2 LELHLEHLFIEHGLRHFATQAITEGNKKPDFLFPSAGAYHDTEFPVENLRMLAVKTTCKDRWRQILNEADKIHQVHLFTLQEGVSLAQYREM


            190       200       210       220 
              |         |         |         | 
d1na6a2 RESGVRLVVPSSLHKKYPEAVRAELMTLGAFIAELT-g


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: 0041285 (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   Rhodnius prolixus 22
NoYes   Acetobacterium woodii DSM 1030
NoYes   Eubacterium rectale ATCC 33656
NoYes   Bacteroides fragilis YCH46
NoYes   Treponema succinifaciens DSM 2489
NoYes   Geobacter lovleyi SZ
NoYes   Pseudogulbenkiania sp. NH8B
NoYes   Maricaulis maris MCS10
NoYes   Rhodobacter sphaeroides ATCC 17029
NoYes   Acidiphilium cryptum JF-5
NoYes   Halorhodospira halophila SL1
NoYes   Xenorhabdus nematophila ATCC 19061
NoYes   Edwardsiella ictaluri 93-146
NoYes   Rahnella aquatilis CIP 78.65 = ATCC 33071
NoYes   Serratia proteamaculans 568
NoYes   Erwinia pyrifoliae Ep1/96
NoYes   Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)
NoYes   Citrobacter koseri ATCC BAA-895
NoYes   Bifidobacterium longum NCC2705
NoYes   Bifidobacterium longum DJO10A
NoYes   Bifidobacterium longum subsp. longum KACC 91563
NoYes   Bifidobacterium longum subsp. longum BBMN68
NoYes   Thermobacillus composti KWC4
NoYes   Leptospirillum ferriphilum ML-04
NoYes   Desulfovibrio vulgaris RCH1
NoYes   Desulfovibrio vulgaris str. Hildenborough
NoYes   Neisseria meningitidis WUE 2594
NoYes   Neisseria meningitidis M04-240196
NoYes   Neisseria meningitidis M01-240149
NoYes   Neisseria meningitidis NZ-05/33
NoYes   Neisseria meningitidis 053442
NoYes   Neisseria meningitidis Z2491
NoYes   Neisseria meningitidis H44/76
NoYes   Neisseria meningitidis alpha710
NoYes   Neisseria meningitidis MC58
NoYes   Erwinia pyrifoliae DSM 12163
NoYes   Cronobacter sakazakii CMCC 45402
NoYes   Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- str. RSK2980
NoYes   Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. 41578
NoYes   Escherichia coli O7:K1 str. CE10
NoYes   Escherichia coli IAI39
NoYes   Activated sludge plasmid pool Visp-2009 (Newbler) (meta-genome)
NoYes   Air microbial communities Singapore indoor air filters 1 (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Fungus garden combined (combined) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden bottom (Fungus garden bottom) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP16 from Fairy Spring Red Layer (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP6 from White Creek Site 3 (meta-genome)
NoYes   Human Gut Community Subject 8 (meta-genome)
NoYes   Mountain Pine Beetle microbial communities from Grand Prairie, Alberta, sample from Hybrid pine (MPB hybrid beetle) (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2- (Oak Ridge 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   The Salmonella enterica Pan-genome (meta-genome)
NoYes   ALL (only advised for small superfamilies)


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