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.


mu transposase, C-terminal domain alignments

These alignments are sequences aligned to the 0035462 model.

Sophisticated options are available for refining alignments:


Jump to [ Top of page · Refine alignments · Add alignments from genomes ]

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 
                 |         |         |         |         |         |         |         | 
d1bcoa1 TEEQKRMLLLPAEAVNVSRKGEFTLKVGGSLKGAKNVYYNMALMNAGVKKVVVRFDPQQLHSTVYCYTLDGRFICEAEC-l


Statistics on alignment.   Save alignment.

Jump to [ Top of page · Alignments · Add alignments from genomes ]

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: 0035462 (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   Lucilia cuprina - Australian sheep blowfly
NoYes   Microcoleus sp. PCC 7113
NoYes   Geitlerinema sp. PCC 7407
NoYes   Cyanothece sp. PCC 8802
NoYes   Rivularia sp. PCC 7116
NoYes   Anabaena variabilis ATCC 29413
NoYes   Nostoc sp. PCC 7107
NoYes   Nostoc punctiforme PCC 73102
NoYes   Nostoc sp. PCC 7120
NoYes   Microlunatus phosphovorus NM-1
NoYes   Actinoplanes sp. N902-109
NoYes   Gordonia polyisoprenivorans VH2
NoYes   [Cellvibrio] gilvus ATCC 13127
NoYes   Arthrobacter phenanthrenivorans Sphe3
NoYes   Arthrobacter sp. FB24
NoYes   Ethanoligenens harbinense YUAN-3
NoYes   Pelotomaculum thermopropionicum SI
NoYes   Syntrophobotulus glycolicus DSM 8271
NoYes   Desulfotomaculum acetoxidans DSM 771
NoYes   Desulfotomaculum ruminis DSM 2154
NoYes   Roseburia intestinalis
NoYes   Alkaliphilus metalliredigens QYMF
NoYes   Listeria innocua Clip11262
NoYes   Staphylococcus pseudintermedius HKU10-03
NoYes   Staphylococcus lugdunensis HKU09-01
NoYes   Staphylococcus haemolyticus JCSC1435
NoYes   Staphylococcus aureus subsp. aureus JH1
NoYes   Candidatus Cloacamonas acidaminovorans
NoYes   Ignavibacterium album JCM 16511
NoYes   Sulfurihydrogenibium sp. YO3AOP1
NoYes   Granulicella tundricola MP5ACTX9
NoYes   Candidatus Koribacter versatilis Ellin345
NoYes   Ilyobacter polytropus DSM 2926
NoYes   Syntrophus aciditrophicus SB
NoYes   Desulfobulbus propionicus DSM 2032
NoYes   Desulfatibacillum alkenivorans AK-01
NoYes   Desulfovibrio magneticus RS-1
NoYes   Desulfovibrio alaskensis G20
NoYes   Desulfovibrio africanus str. Walvis Bay
NoYes   Pelobacter propionicus DSM 2379
NoYes   Dechlorosoma suillum PS
NoYes   Pseudogulbenkiania sp. NH8B
NoYes   Laribacter hongkongensis HLHK9
NoYes   Neisseria meningitidis FAM18
NoYes   Rubrivivax gelatinosus IL144
NoYes   Burkholderia vietnamiensis G4
NoYes   Burkholderia glumae BGR1
NoYes   Polaromonas naphthalenivorans CJ2
NoYes   Acidovorax sp. JS42
NoYes   Acidovorax citrulli AAC00-1
NoYes   Bordetella petrii DSM 12804
NoYes   Sideroxydans lithotrophicus ES-1
NoYes   Caulobacter sp. K31
NoYes   Sphingobium sp. SYK-6
NoYes   Sphingobium japonicum UT26S
NoYes   Sphingomonas sp. MM-1
NoYes   Dinoroseobacter shibae DFL 12
NoYes   Jannaschia sp. CCS1
NoYes   Rhodobacter capsulatus SB 1003
NoYes   Rhodospirillum photometricum DSM 122
NoYes   Tistrella mobilis KA081020-065
NoYes   Magnetospirillum magneticum AMB-1
NoYes   Rhodospirillum centenum SW
NoYes   Azospirillum brasilense Sp245
NoYes   Acetobacter pasteurianus IFO 3283-01
NoYes   Xanthobacter autotrophicus Py2
NoYes   Rhizobium leguminosarum bv. viciae 3841
NoYes   Agrobacterium vitis S4
NoYes   Mesorhizobium sp. BNC1
NoYes   Mesorhizobium loti MAFF303099
NoYes   Nitrobacter hamburgensis X14
NoYes   Bartonella tribocorum CIP 105476
NoYes   Gallibacterium anatis UMN179
NoYes   Vibrio cholerae O395
NoYes   Shewanella oneidensis MR-1
NoYes   Pseudoalteromonas haloplanktis TAC125
NoYes   Rhodanobacter denitrificans
NoYes   Thioalkalivibrio sulfidophilus HL-EbGr7
NoYes   Thiocystis violascens DSM 198
NoYes   Escherichia blattae DSM 4481
NoYes   Shigella flexneri 5 str. 8401
NoYes   Citrobacter rodentium ICC168
NoYes   Pseudomonas sp. TKP
NoYes   Chamaesiphon minutus PCC 6605
NoYes   Crinalium epipsammum PCC 9333
NoYes   Oscillatoria acuminata PCC 6304
NoYes   Cyanothece sp. PCC 7822
NoYes   Cyanothece sp. PCC 7424
NoYes   Cyanothece sp. ATCC 51142
NoYes   Cyanothece sp. PCC 8801
NoYes   Stanieria cyanosphaera PCC 7437
NoYes   Calothrix parietina Calothrix sp. PCC 6303
NoYes   Anabaena cylindrica PCC 7122
NoYes   Streptomyces collinus Tu 365
NoYes   Propionibacterium acidipropionici ATCC 4875
NoYes   Sulfobacillus acidophilus TPY
NoYes   Bacillus cereus AH820
NoYes   Bacillus cereus E33L
NoYes   Staphylococcus pseudintermedius ED99
NoYes   Staphylococcus epidermidis ATCC 12228
NoYes   Staphylococcus aureus CA-347
NoYes   Staphylococcus aureus Bmb9393
NoYes   Staphylococcus aureus subsp. aureus Z172
NoYes   Staphylococcus aureus subsp. aureus 11819-97
NoYes   Staphylococcus aureus subsp. aureus T0131
NoYes   Staphylococcus aureus subsp. aureus TW20
NoYes   Staphylococcus aureus subsp. aureus 55/2053
NoYes   Staphylococcus aureus subsp. aureus TCH60
NoYes   Staphylococcus aureus subsp. aureus str. JKD6008
NoYes   Staphylococcus aureus subsp. aureus JH9
NoYes   Staphylococcus aureus subsp. aureus MRSA252
NoYes   Staphylococcus aureus subsp. aureus N315
NoYes   Fusobacterium nucleatum subsp. animalis 4_8
NoYes   Desulfovibrio hydrothermalis AM13 = DSM 14728
NoYes   Desulfovibrio vulgaris RCH1
NoYes   Desulfovibrio vulgaris str. 'Miyazaki F'
NoYes   Desulfovibrio vulgaris str. Hildenborough
NoYes   Desulfovibrio gigas DSM 1382 = ATCC 19364
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   Ralstonia solanacearum CMR15
NoYes   Burkholderia cenocepacia J2315
NoYes   Phaeobacter gallaeciensis DSM 26640
NoYes   Leisingera methylohalidivorans DSM 14336
NoYes   Rhodobacter sphaeroides ATCC 17025
NoYes   Acetobacter pasteurianus 386B
NoYes   Acetobacter pasteurianus IFO 3283-12
NoYes   Acetobacter pasteurianus IFO 3283-01-42C
NoYes   Acetobacter pasteurianus IFO 3283-32
NoYes   Acetobacter pasteurianus IFO 3283-26
NoYes   Acetobacter pasteurianus IFO 3283-22
NoYes   Acetobacter pasteurianus IFO 3283-07
NoYes   Acetobacter pasteurianus IFO 3283-03
NoYes   Sinorhizobium fredii USDA 257
NoYes   Sinorhizobium fredii HH103
NoYes   Bartonella vinsonii subsp. berkhoffii str. Winnie
NoYes   Bibersteinia trehalosi USDA-ARS-USMARC-192
NoYes   Aggregatibacter actinomycetemcomitans D11S-1
NoYes   Haemophilus somnus 2336
NoYes   Mannheimia haemolytica USMARC_2286
NoYes   Mannheimia haemolytica M42548
NoYes   Mannheimia haemolytica D174
NoYes   Mannheimia haemolytica D171
NoYes   Mannheimia haemolytica D153
NoYes   Mannheimia haemolytica USDA-ARS-USMARC-183
NoYes   Mannheimia haemolytica USDA-ARS-USMARC-185
NoYes   Haemophilus parasuis ZJ0906
NoYes   Haemophilus influenzae F3047
NoYes   Haemophilus influenzae F3031
NoYes   Haemophilus influenzae Rd KW20
NoYes   Vibrio cholerae O395
NoYes   Shewanella sp. W3-18-1
NoYes   Shewanella putrefaciens 200
NoYes   Alteromonas macleodii str. 'English Channel 673'
NoYes   Thalassolituus oleivorans MIL-1
NoYes   Yersinia pseudotuberculosis YPIII
NoYes   Shigella sonnei 53G
NoYes   Shigella flexneri 2002017
NoYes   Shigella flexneri 2a str. 2457T
NoYes   Shigella flexneri 2a str. 301
NoYes   Salmonella bongori N268-08
NoYes   Escherichia coli E24377A
NoYes   Escherichia coli LY180
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli KO11FL
NoYes   Escherichia coli W
NoYes   Escherichia coli W
NoYes   Escherichia coli SE11
NoYes   Escherichia coli O127:H6 str. E2348/69
NoYes   Escherichia coli O157:H7 str. Sakai
NoYes   Escherichia coli BW2952
NoYes   Pseudomonas denitrificans ATCC 13867
NoYes   Pseudomonas putida ND6
NoYes   Pseudomonas aeruginosa LES431
NoYes   Pseudomonas aeruginosa NCGM2.S1
NoYes   Pseudomonas aeruginosa LESB58
NoYes   Pseudomonas aeruginosa PA7
NoYes   4_050719Q (meta-genome)
NoYes   Activated sludge plasmid pool Morges-2009 (Newbler) (meta-genome)
NoYes   Activated sludge plasmid pool Visp-2009 (Newbler) (meta-genome)
NoYes   Air microbial communities Singapore indoor air filters 1 (meta-genome)
NoYes   Air microbial communities Singapore indoor air filters 2 (meta-genome)
NoYes   Atta cephalotes fungus garden (ACEF) (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Crater Hills (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dendroctonus ponderosae beetle community (MPB hybrid beetle) (Lodgepole pine) (meta-genome)
NoYes   Dendroctonus ponderosae fungus gallery (Hybrid pine) (MPB hybrid gallery) (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (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   Freshwater propionate enrichment of Brocadia fulgida (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 02(H) (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   Hindgut microbiome of Nasutitermes sp. (Costa Rica) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP17 from Obsidian Pool Prime (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methylamine enrichment (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   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (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 3 Nevada Test Site Creosote CO2+ (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   STRING v9.0.5 (STRING)
NoYes   Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)
NoYes   Switchgrass soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Rhizosphere soil sample from switchgrass (Panicum virg (meta-genome)
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)


Jump to [ Top of page · Alignments · Refine alignments · Add alignments from genomes ]