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.


Transposase IS200-like alignments

These alignments are sequences aligned to the 0051712 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        9
                    |         |         |         |         |         |         |         |         
d2a6oa1 avl---YKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRIL
d2ec2d_ ...-MEYKSTRHAKYLCNYHFVWIPKYRRKVLTGEVAEYTKEVLRTIAEELGCEVLALEVMPDHIHLFVNCPPRYAPSYLANYFKGKSARLI
d2f5ga1 ..e---LKSTRHTKYLCNYHFVWIPKHRRNTLVNEIAEYTKEVLKSIAEELGCEIIALEVMPDHIHLFVNCPPRYAPSYLANYFKGKSARLI
d2fyxa1 ..m----KKGRGYVYKLEYHLIWATKYRHQVLVDEVADGLKDILRDIATQNGLELVALEVMPDYVHLLLGATPQHVIPDFVKALKGASARRM


        0         100       110       120       130      
        |           |         |         |         |      
d2a6oa1 RQEFNHLK..TKLPTLWTNSCFISTVGGAPLNVVKQYIENQQ-n.....
d2ec2d_ LKKFQELKk.STNGKLWTRSYFVSTSGNVSSETIKKYIEEQ--......
d2f5ga1 LKKFPQ--..LNKGKLWTRSYFVATAGNVSSEVIKKYIEEQ--wrkege
d2fyxa1 FSAFPHLKqpHWGGNLWNPSYCVLTVSEHTRAQIQQYIENQH-aa....


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: 0051712 (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   Apis mellifera 38.2d - Honey bee
NoYes   Halothece sp. PCC 7418
NoYes   Rivularia sp. PCC 7116
NoYes   'Nostoc azollae' 0708
NoYes   Nostoc sp. PCC 7120
NoYes   Nostoc sp. PCC 7524
NoYes   Anabaena sp. 90
NoYes   Slackia heliotrinireducens DSM 20476
NoYes   Frankia sp. EAN1pec
NoYes   Thermobifida fusca YX
NoYes   Streptosporangium roseum DSM 43021
NoYes   Streptomyces violaceusniger Tu 4113
NoYes   Mycobacterium vanbaalenii PYR-1
NoYes   Mycobacterium gilvum PYR-GCK
NoYes   Chloroflexus aggregans DSM 9485
NoYes   Truepera radiovictrix DSM 17093
NoYes   Deinococcus geothermalis DSM 11300
NoYes   Deinococcus radiodurans R1
NoYes   Meiothermus silvanus DSM 9946
NoYes   Finegoldia magna ATCC 29328
NoYes   Megamonas hypermegale
NoYes   Selenomonas sputigena ATCC 35185
NoYes   Natranaerobius thermophilus JW/NM-WN-LF
NoYes   Clostridium clariflavum DSM 19732
NoYes   Clostridium cellulolyticum H10
NoYes   Ruminococcus sp.
NoYes   butyrate-producing bacterium SS3/4
NoYes   Candidatus Desulforudis audaxviator MP104C
NoYes   Pelotomaculum thermopropionicum SI
NoYes   Desulfitobacterium hafniense Y51
NoYes   Desulfotomaculum reducens MI-1
NoYes   Desulfotomaculum acetoxidans DSM 771
NoYes   Desulfotomaculum kuznetsovii DSM 6115
NoYes   Clostridium difficile 630
NoYes   Filifactor alocis ATCC 35896
NoYes   Clostridium saccharolyticum WM1
NoYes   Eubacterium rectale M104/1
NoYes   Roseburia hominis A2-183
NoYes   Roseburia intestinalis
NoYes   Butyrivibrio proteoclasticus B316
NoYes   Clostridium tetani E88
NoYes   Caldicellulosiruptor obsidiansis OB47
NoYes   Caldicellulosiruptor owensensis OL
NoYes   Caldicellulosiruptor lactoaceticus 6A
NoYes   Caldicellulosiruptor kristjanssonii 177R1B
NoYes   Caldicellulosiruptor saccharolyticus DSM 8903
NoYes   Caldicellulosiruptor bescii DSM 6725
NoYes   Thermoanaerobacterium xylanolyticum LX-11
NoYes   Thermoanaerobacterium thermosaccharolyticum DSM 571
NoYes   Carboxydothermus hydrogenoformans Z-2901
NoYes   Ammonifex degensii KC4
NoYes   Thermoanaerobacter wiegelii Rt8.B1
NoYes   Acetohalobium arabaticum DSM 5501
NoYes   Halanaerobium praevalens DSM 2228
NoYes   Tetragenococcus halophilus NBRC 12172
NoYes   Lactobacillus kefiranofaciens ZW3
NoYes   Lactobacillus johnsonii FI9785
NoYes   Lactobacillus sanfranciscensis TMW 1.1304
NoYes   Lactobacillus ruminis ATCC 27782
NoYes   Lactobacillus fermentum IFO 3956
NoYes   Lactobacillus amylovorus GRL1118
NoYes   Lactobacillus reuteri DSM 20016
NoYes   Lactobacillus acidophilus 30SC
NoYes   Streptococcus pseudopneumoniae IS7493
NoYes   Streptococcus equi subsp. equi 4047
NoYes   Streptococcus mitis B6
NoYes   Streptococcus parasanguinis ATCC 15912
NoYes   Streptococcus suis P1/7
NoYes   Streptococcus salivarius 57.I
NoYes   Exiguobacterium sibiricum 255-15
NoYes   Kyrpidia tusciae DSM 2912
NoYes   Brevibacillus brevis NBRC 100599
NoYes   Salinibacter ruber M8
NoYes   Sphaerochaeta globus str. Buddy
NoYes   Calditerrivibrio nitroreducens DSM 19672
NoYes   Thermotoga sp. RQ2
NoYes   Thermotoga naphthophila RKU-10
NoYes   Thermotoga petrophila RKU-1
NoYes   Thermotoga maritima MSB8
NoYes   Desulfurobacterium thermolithotrophum DSM 11699
NoYes   Thermocrinis albus DSM 14484
NoYes   Sebaldella termitidis ATCC 33386
NoYes   Leptotrichia buccalis C-1013-b
NoYes   Acidithiobacillus caldus SM-1
NoYes   Helicobacter bizzozeronii CIII-1
NoYes   Helicobacter acinonychis str. Sheeba
NoYes   Desulfomonile tiedjei DSM 6799
NoYes   Desulfovibrio piezophilus
NoYes   Hippea maritima DSM 10411
NoYes   Rickettsia massiliae MTU5
NoYes   Vibrio cholerae O395
NoYes   Shewanella baltica OS185
NoYes   Shewanella woodyi ATCC 51908
NoYes   Marinobacter aquaeolei VT8
NoYes   Methylomonas methanica MC09
NoYes   Nitrosococcus watsonii C-113
NoYes   Nitrosococcus halophilus Nc4
NoYes   Nitrosococcus oceani ATCC 19707
NoYes   Photorhabdus luminescens subsp. laumondii TTO1
NoYes   Cronobacter sakazakii ES15
NoYes   Klebsiella oxytoca E718
NoYes   Enterobacter sp. R4-368
NoYes   Desulfurococcus kamchatkensis 1221n
NoYes   Metallosphaera sedula DSM 5348
NoYes   Sulfolobus tokodaii str. 7
NoYes   Sulfolobus solfataricus P2
NoYes   Vulcanisaeta moutnovskia 768-28
NoYes   halophilic archaeon DL31
NoYes   Methanocella conradii HZ254
NoYes   Methanosaeta concilii GP6
NoYes   Methanosarcina mazei Go1
NoYes   Archaeoglobus profundus DSM 5631
NoYes   Thermococcus sibiricus MM 739
NoYes   Pyrococcus yayanosii CH1
NoYes   Thermoplasma volcanium GSS1
NoYes   Thermoplasma acidophilum DSM 1728
NoYes   Natrialba magadii ATCC 43099
NoYes   Halorubrum lacusprofundi ATCC 49239
NoYes   Halogeometricum borinquense DSM 11551
NoYes   Haloferax mediterranei ATCC 33500
NoYes   Haloferax volcanii DS2
NoYes   Halomicrobium mukohataei DSM 12286
NoYes   Natronomonas pharaonis DSM 2160
NoYes   Haloarcula hispanica ATCC 33960
NoYes   Haloarcula marismortui ATCC 43049
NoYes   Halobacterium salinarum R1
NoYes   Halobacterium sp. NRC-1
NoYes   Methanocaldococcus sp. FS406-22
NoYes   Chroococcidiopsis thermalis PCC 7203
NoYes   Crinalium epipsammum PCC 9333
NoYes   Oscillatoria nigro-viridis PCC 7112
NoYes   Arthrospira platensis NIES-39
NoYes   Cyanothece sp. PCC 7822
NoYes   Cyanothece sp. PCC 7424
NoYes   Cyanothece sp. PCC 8801
NoYes   Cyanobacterium aponinum PCC 10605
NoYes   Cyanobacterium stanieri PCC 7202
NoYes   Stanieria cyanosphaera PCC 7437
NoYes   Frankia sp. CcI3
NoYes   Streptomyces albus J1074
NoYes   Mycobacterium canettii CIPT 140070017
NoYes   Clostridium acidurici 9a
NoYes   Desulfitobacterium hafniense DCB-2
NoYes   Desulfotomaculum gibsoniae DSM 7213
NoYes   Clostridium perfringens SM101
NoYes   Clostridium perfringens str. 13
NoYes   Clostridium pasteurianum BC1
NoYes   Clostridium botulinum Ba4 str. 657
NoYes   Clostridium botulinum A3 str. Loch Maree
NoYes   Thermoanaerobacterium saccharolyticum JW/SL-YS485
NoYes   Thermoanaerobacterium thermosaccharolyticum M0795
NoYes   Thermacetogenium phaeum DSM 12270
NoYes   Enterococcus mundtii QU 25
NoYes   Lactobacillus johnsonii N6.2
NoYes   Lactobacillus johnsonii DPC 6026
NoYes   Lactobacillus johnsonii NCC 533
NoYes   Lactobacillus salivarius UCC118
NoYes   Lactobacillus fermentum F-6
NoYes   Lactobacillus amylovorus GRL 1112
NoYes   Lactobacillus reuteri TD1
NoYes   Lactobacillus reuteri I5007
NoYes   Lactobacillus reuteri JCM 1112
NoYes   Lactobacillus reuteri SD2112
NoYes   Lactobacillus helveticus H10
NoYes   Lactobacillus delbrueckii subsp. bulgaricus ND02
NoYes   Streptococcus equi subsp. zooepidemicus ATCC 35246
NoYes   Streptococcus equi subsp. zooepidemicus MGCS10565
NoYes   Streptococcus iniae SF1
NoYes   Streptococcus parasanguinis FW213
NoYes   Streptococcus suis S735
NoYes   Streptococcus suis SS12
NoYes   Streptococcus suis D12
NoYes   Streptococcus suis ST1
NoYes   Streptococcus suis A7
NoYes   Streptococcus suis JS14
NoYes   Streptococcus suis BM407
NoYes   Streptococcus suis SC84
NoYes   Streptococcus suis GZ1
NoYes   Streptococcus suis 98HAH33
NoYes   Streptococcus suis 05ZYH33
NoYes   Streptococcus salivarius CCHSS3
NoYes   Streptococcus salivarius JIM8777
NoYes   Exiguobacterium antarcticum B7
NoYes   Paenibacillus sp. Y412MC10
NoYes   Paenibacillus larvae subsp. larvae DSM 25430
NoYes   Geobacillus sp. C56-T3
NoYes   Amphibacillus xylanus NBRC 15112
NoYes   Bacillus thuringiensis YBT-1518
NoYes   Bacillus thuringiensis serovar finitimus YBT-020
NoYes   Bacillus thuringiensis serovar thuringiensis str. IS5056
NoYes   Bacillus cereus FRI-35
NoYes   Bacillus cereus G9842
NoYes   Bacillus cereus Q1
NoYes   Bacillus cereus ATCC 14579
NoYes   Staphylococcus pasteuri SP1
NoYes   Salinibacter ruber DSM 13855
NoYes   Thermotoga maritima MSB8
NoYes   Fusobacterium nucleatum subsp. animalis 4_8
NoYes   Helicobacter pylori BM012S
NoYes   Helicobacter pylori BM012A
NoYes   Helicobacter pylori HUP-B14
NoYes   Helicobacter pylori PeCan18
NoYes   Helicobacter pylori Shi112
NoYes   Helicobacter pylori Cuz20
NoYes   Helicobacter pylori PeCan4
NoYes   Candidatus Symbiobacter mobilis Comamonadaceae bacterium CR
NoYes   Nitrosomonas sp. AL212
NoYes   Vibrio alginolyticus NBRC 15630 = ATCC 17749
NoYes   Vibrio cholerae M66-2
NoYes   Vibrio cholerae O395
NoYes   Vibrio cholerae IEC224
NoYes   Vibrio cholerae O1 str. 2010EL-1786
NoYes   Vibrio cholerae MJ-1236
NoYes   Vibrio cholerae O1 biovar El Tor str. N16961
NoYes   Shewanella baltica BA175
NoYes   Klebsiella oxytoca KCTC 1686
NoYes   Sulfolobus islandicus LAL14/1
NoYes   Sulfolobus islandicus HVE10/4
NoYes   Sulfolobus islandicus M.16.27
NoYes   Sulfolobus islandicus M.14.25
NoYes   Sulfolobus islandicus M.16.4
NoYes   Sulfolobus solfataricus 98/2
NoYes   Methanomethylovorans hollandica DSM 15978
NoYes   Methanolobus psychrophilus R15
NoYes   Methanosarcina mazei Tuc01
NoYes   Archaeoglobus sulfaticallidus PM70-1
NoYes   Ferroplasma acidarmanus fer1
NoYes   Natrinema pellirubrum DSM 15624
NoYes   Halorhabdus tiamatea SARL4B
NoYes   Natronomonas moolapensis 8.8.11
NoYes   Haloarcula hispanica N601
NoYes   3_050719R (meta-genome)
NoYes   4_050719Q (meta-genome)
NoYes   4_Deep_abyss (meta-genome)
NoYes   5_050719P (meta-genome)
NoYes   Activated sludge plasmid pool Visp-2009 (Newbler) (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   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #3 (meta-genome)
NoYes   Hindgut microbiome of Nasutitermes sp. (Costa Rica) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP8 from OSP Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP11 from Octopus Springs (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP14 from OSP Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP15 from Mushroom Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP17 from Obsidian Pool Prime (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP18 from Washburn Springs #1 (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP19 from Cistern Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP2 from Nymph Lake 10 (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP20 from Bath Lake Vista Annex - Purple-Sulfur Mats (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP4 from Joseph's Coat Springs (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 YNP6 from White Creek Site 3 (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   Maize field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing corn (Zea may (meta-genome)
NoYes   Marine anammox bioreactor enriched for Scalindua species (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (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   Mouse Gut Community lean3 (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Nymph Lake Bulk Water (meta-genome)
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   Sludge/Australian, Phrap Assembly (meta-genome)
NoYes   Sludge/US, Jazz Assembly (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 1 Maryland Estuary CO2- (Maryland Estuary ambient) (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 ambient) (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   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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