SUPERFAMILY 1.75 HMM library and genome assignments server

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NE0471 N-terminal domain-like alignments

These alignments are sequences aligned to the 0051838 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    
                                             |         |         |         |         |         |    
d2auwa2                            y-FFPKLTAVEALAPYRLRTTWSTGEVLEVDVGDILRKIPDLAPILDPEAFARVHIAEWEGSVEW
gi|16330461|ref|NP_441189.1|:10-84 l----KAISVFPLDNFQLQIKLENGQELILDLQTIIETNDNYWRLKNPRYFRQAQIDPL-GGIAW


                                        70        80       
                                         |         |       
d2auwa2                            F.DTEFGRDNVYAWAKEQA--ge.
gi|16330461|ref|NP_441189.1|:10-84 PeGEDLSPTGLE---------rya


Statistics on alignment.   Save alignment.

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Refine alignments

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Members of the same: including
Include all superfamily members: , or just those assigned by the selected model:
Initial T99 seed sequence: NoYes

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Model: 0051838 (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   Synechocystis sp. PCC 6803
NoYes   Synechococcus sp. PCC 6312
NoYes   Synechococcus elongatus PCC 7942
NoYes   Trichodesmium erythraeum IMS101
NoYes   Microcystis aeruginosa NIES-843
NoYes   Nostoc sp. PCC 7107
NoYes   Eggerthella lenta DSM 2243
NoYes   Slackia heliotrinireducens DSM 20476
NoYes   Microlunatus phosphovorus NM-1
NoYes   Bifidobacterium dentium Bd1
NoYes   Bifidobacterium bifidum S17
NoYes   Caldilinea aerophila DSM 14535 = NBRC 104270
NoYes   Roseiflexus sp. RS-1
NoYes   Chloroflexus sp. Y-400-fl
NoYes   Chloroflexus aurantiacus J-10-fl
NoYes   Truepera radiovictrix DSM 17093
NoYes   Deinococcus proteolyticus MRP
NoYes   Selenomonas sputigena ATCC 35185
NoYes   Sulfobacillus acidophilus DSM 10332
NoYes   Desulfosporosinus orientis DSM 765
NoYes   Syntrophobotulus glycolicus DSM 8271
NoYes   Desulfitobacterium hafniense Y51
NoYes   Desulfotomaculum acetoxidans DSM 771
NoYes   Desulfotomaculum kuznetsovii DSM 6115
NoYes   Acetobacterium woodii DSM 1030
NoYes   Clostridium saccharolyticum WM1
NoYes   Eubacterium rectale M104/1
NoYes   Eubacterium rectale ATCC 33656
NoYes   Coprococcus sp. ART55/1
NoYes   Roseburia hominis A2-183
NoYes   Butyrivibrio fibrisolvens
NoYes   Syntrophothermus lipocalidus DSM 12680
NoYes   Syntrophomonas wolfei subsp. wolfei str. Goettingen
NoYes   Alkaliphilus metalliredigens QYMF
NoYes   Candidatus Arthromitus sp. SFB-mouse-Japan
NoYes   Clostridium novyi NT
NoYes   Clostridium ljungdahlii DSM 13528
NoYes   Caldicellulosiruptor obsidiansis OB47
NoYes   Caldicellulosiruptor kronotskyensis 2002
NoYes   Caldicellulosiruptor hydrothermalis 108
NoYes   Caldicellulosiruptor owensensis OL
NoYes   Caldicellulosiruptor lactoaceticus 6A
NoYes   Caldicellulosiruptor kristjanssonii 177R1B
NoYes   Caldicellulosiruptor saccharolyticus DSM 8903
NoYes   Caldicellulosiruptor bescii DSM 6725
NoYes   Thermoanaerobacterium thermosaccharolyticum DSM 571
NoYes   Moorella thermoacetica ATCC 39073
NoYes   Thermoanaerobacter mathranii subsp. mathranii str. A3
NoYes   Thermoanaerobacter pseudethanolicus ATCC 33223
NoYes   Thermoanaerobacter italicus Ab9
NoYes   Thermoanaerobacter wiegelii Rt8.B1
NoYes   Thermoanaerobacter brockii subsp. finnii Ako-1
NoYes   Pelodictyon phaeoclathratiforme BU-1
NoYes   Chlorobium chlorochromatii CaD3
NoYes   Chlorobium phaeobacteroides DSM 266
NoYes   Chlorobium limicola DSM 245
NoYes   Chlorobaculum parvum NCIB 8327
NoYes   Chlorobium tepidum TLS
NoYes   Chloroherpeton thalassium ATCC 35110
NoYes   Haliscomenobacter hydrossis DSM 1100
NoYes   Cyclobacterium marinum DSM 745
NoYes   Marivirga tractuosa DSM 4126
NoYes   Dyadobacter fermentans DSM 18053
NoYes   Spirosoma linguale DSM 74
NoYes   Parabacteroides distasonis ATCC 8503
NoYes   Fibrobacter succinogenes subsp. succinogenes S85
NoYes   Turneriella parva DSM 21527
NoYes   Brachyspira intermedia PWS/A
NoYes   Brachyspira hyodysenteriae WA1
NoYes   Spirochaeta smaragdinae DSM 11293
NoYes   Treponema primitia ZAS-2
NoYes   Thermodesulfatator indicus DSM 15286
NoYes   Mesotoga prima MesG1.Ag.4.2
NoYes   Candidatus Methylomirabilis oxyfera
NoYes   Acidithiobacillus ferrivorans SS3
NoYes   Acidithiobacillus caldus SM-1
NoYes   Acidithiobacillus ferrooxidans ATCC 53993
NoYes   uncultured Sulfuricurvum sp. RIFRC-1
NoYes   Desulfomonile tiedjei DSM 6799
NoYes   Desulfobacterium autotrophicum HRM2
NoYes   Desulfococcus oleovorans Hxd3
NoYes   Desulfomicrobium baculatum DSM 4028
NoYes   Desulfovibrio magneticus RS-1
NoYes   Desulfovibrio salexigens DSM 2638
NoYes   Geobacter sp. M21
NoYes   Geobacter uraniireducens Rf4
NoYes   Geobacter lovleyi SZ
NoYes   Geobacter bemidjiensis Bem
NoYes   Geobacter metallireducens GS-15
NoYes   Corallococcus coralloides DSM 2259
NoYes   Aromatoleum aromaticum EbN1
NoYes   Pseudogulbenkiania sp. NH8B
NoYes   Laribacter hongkongensis HLHK9
NoYes   Candidatus Accumulibacter phosphatis clade IIA str. UW-1
NoYes   Verminephrobacter eiseniae EF01-2
NoYes   Herbaspirillum seropedicae SmR1
NoYes   Nitrosomonas europaea ATCC 19718
NoYes   Gallionella capsiferriformans ES-2
NoYes   Magnetococcus marinus MC-1
NoYes   Caulobacter sp. K31
NoYes   Magnetospirillum magneticum AMB-1
NoYes   Rhodospirillum rubrum F11
NoYes   Azospirillum lipoferum 4B
NoYes   Azospirillum sp. B510
NoYes   Acidiphilium cryptum JF-5
NoYes   Rickettsia felis URRWXCal2
NoYes   Methylobacterium sp. 4-46
NoYes   Methylobacterium populi BJ001
NoYes   Genome sequence of Rhizobium sp. strain IRBG74
NoYes   Rhodopseudomonas palustris BisA53
NoYes   Aeromonas veronii B565
NoYes   Aeromonas salmonicida subsp. salmonicida A449
NoYes   Aeromonas hydrophila subsp. hydrophila ATCC 7966
NoYes   Aliivibrio salmonicida LFI1238
NoYes   Vibrio cholerae O395
NoYes   Shewanella woodyi ATCC 51908
NoYes   Marinobacter hydrocarbonoclasticus ATCC 49840
NoYes   Marinobacter aquaeolei VT8
NoYes   Alteromonas macleodii str. 'Deep ecotype'
NoYes   Marinomonas sp. MWYL1
NoYes   Methylomicrobium alcaliphilum
NoYes   Halothiobacillus neapolitanus c2
NoYes   Allochromatium vinosum DSM 180
NoYes   Thiocystis violascens DSM 198
NoYes   Nitrosococcus halophilus Nc4
NoYes   Photorhabdus luminescens subsp. laumondii TTO1
NoYes   Edwardsiella ictaluri 93-146
NoYes   Edwardsiella tarda EIB202
NoYes   Dickeya zeae Ech1591
NoYes   Azotobacter vinelandii DJ
NoYes   Pseudomonas brassicacearum subsp. brassicacearum NFM421
NoYes   Thioalkalimicrobium cyclicum ALM1
NoYes   Synechocystis sp. PCC 6803 substr. PCC-P
NoYes   Synechocystis sp. PCC 6803 substr. PCC-N
NoYes   Synechocystis sp. PCC 6803 substr. GT-I
NoYes   Synechocystis sp. PCC 6803
NoYes   Dactylococcopsis salina PCC 8305
NoYes   Synechococcus elongatus PCC 6301
NoYes   Crinalium epipsammum PCC 9333
NoYes   Oscillatoria nigro-viridis PCC 7112
NoYes   Oscillatoria acuminata PCC 6304
NoYes   Cyanothece sp. PCC 7822
NoYes   Cyanothece sp. PCC 7425
NoYes   Cyanothece sp. PCC 7424
NoYes   Cyanobacterium stanieri PCC 7202
NoYes   Gordonibacter pamelaeae 7-10-1-b
NoYes   Bifidobacterium longum subsp. infantis 157F
NoYes   Bifidobacterium bifidum PRL2010
NoYes   Bifidobacterium bifidum BGN4
NoYes   Thermus oshimai JL-2
NoYes   Faecalibacterium prausnitzii L2-6
NoYes   Ruminococcus champanellensis 18P13
NoYes   Sulfobacillus acidophilus TPY
NoYes   Desulfosporosinus meridiei DSM 13257
NoYes   Desulfitobacterium dichloroeliminans LMG P-21439
NoYes   Desulfitobacterium hafniense DCB-2
NoYes   Desulfotomaculum gibsoniae DSM 7213
NoYes   Candidatus Arthromitus sp. SFB-rat-Yit
NoYes   Candidatus Arthromitus sp. SFB-mouse-Yit
NoYes   Clostridium autoethanogenum DSM 10061
NoYes   Clostridium tetani genome 12124569
NoYes   Echinicola vietnamensis DSM 17526
NoYes   Fibrobacter succinogenes subsp. succinogenes S85
NoYes   Acidithiobacillus ferrooxidans ATCC 23270
NoYes   Desulfobacula toluolica Tol2
NoYes   Desulfovibrio gigas DSM 1382 = ATCC 19364
NoYes   Geobacter sp. M18
NoYes   Myxococcus stipitatus DSM 14675
NoYes   Candidatus Symbiobacter mobilis Comamonadaceae bacterium CR
NoYes   Alicycliphilus denitrificans BC
NoYes   Sulfuricella denitrificans skB26
NoYes   Rhodospirillum rubrum ATCC 11170
NoYes   Rhizobium tropici CIAT 899
NoYes   Rhodopseudomonas palustris BisB5
NoYes   Rhodopseudomonas palustris BisB18
NoYes   Aeromonas hydrophila ML09-119
NoYes   Vibrio cholerae LMA3984-4
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   Thioflavicoccus mobilis 8321
NoYes   Legionella pneumophila subsp. pneumophila
NoYes   Dickeya dadantii Ech586
NoYes   Dickeya dadantii 3937
NoYes   Azotobacter vinelandii CA6
NoYes   Azotobacter vinelandii CA
NoYes   Pseudomonas syringae pv. phaseolicola 1448A
NoYes   Pseudomonas syringae pv. syringae B728a
NoYes   Pseudomonas putida NBRC 14164
NoYes   Pseudomonas putida DOT-T1E
NoYes   Pseudomonas fluorescens F113
NoYes   Pseudomonas fluorescens Pf0-1
NoYes   2_050719S (meta-genome)
NoYes   3_050719R (meta-genome)
NoYes   4_050719Q (meta-genome)
NoYes   4_Deep_abyss (meta-genome)
NoYes   5_050719P (meta-genome)
NoYes   5_Below_upper_mesopelagic (meta-genome)
NoYes   Activated sludge plasmid pool Morges-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   Bath Hot Springs, planktonic community (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dendroctonus ponderosae beetle community (MPB hybrid beetle) (Lodgepole pine) (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (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 #1 (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 bottom (Fungus garden bottom) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Groundwater dechlorinating community (KB-1) from synthetic mineral medium in Toronto, ON, sample from Site contaminated with chlorinated ethenes
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 05(O) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 07(S) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 08(T) (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 YNP11 from Octopus Springs (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP12 from Calcite Springs, Tower Falls Region (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 YNP16 from Fairy Spring Red Layer (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 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   Hot spring microbial community from Yellowstone Hot Springs, sample YNP7 from Chocolate Pots (meta-genome)
NoYes   Human Gut Community Subject 7 (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   Maize rhizosphere soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Soil sample from rhizosphere of corn (Zea mays))< (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 Formaldehyde enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Formate enrichment (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   Methylotrophic community from Lake Washington sediment Methylamine enrichment (meta-genome)
NoYes   Miscanthus field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing Miscanthu (meta-genome)
NoYes   Mouse Gut Community lean2 (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   Olavius algarvensis endosymbiont metagenome Delta1 (meta-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   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 3 Nevada Test Site Creosote CO2+ (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 elevated 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   Switchgrass soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Rhizosphere soil sample from switchgrass (Panicum virg (meta-genome)
NoYes   Termite Protist Endosymbiont Community (meta-genome)
NoYes   Uniprot 2018_03 genome
NoYes   Uranium Contaminated Groundwater FW106 (meta-genome)
NoYes   Wastewater Terephthalate-degrading communities from Bioreactor (meta-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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