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.


Hypothetical protein MTH538 alignments

These alignments are sequences aligned to the 0037026 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 
                  |         |         |         |         |         |         |         |         | 
d1eiwa_ v-TAEIRLYITEGEVEDYRVFLERLEQSGLEWRPATPEDADAVIVLAGLWGTRRDEILGAVDLARKSSKPIITVRPYGLENVPPELEAVSSE


              100       110 
                |         | 
d1eiwa_ VVGWNPHCIRDALEDALDVI


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: 0037026 (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   Cyanophora paradoxa
NoYes   Synechococcus sp. PCC 6312
NoYes   Mycoplasma capricolum subsp. capricolum ATCC 27343
NoYes   Actinosynnema mirum DSM 43827
NoYes   Micromonospora sp. L5
NoYes   Actinoplanes sp. N902-109
NoYes   Rhodococcus jostii RHA1
NoYes   Mycobacterium rhodesiae NBB3
NoYes   Corynebacterium efficiens YS-314
NoYes   Kytococcus sedentarius DSM 20547
NoYes   Beutenbergia cavernae DSM 12333
NoYes   Clostridium thermocellum ATCC 27405
NoYes   Clostridium saccharolyticum WM1
NoYes   Syntrophothermus lipocalidus DSM 12680
NoYes   Candidatus Arthromitus sp. SFB-mouse-Japan
NoYes   Clostridium beijerinckii NCIMB 8052
NoYes   Carnobacterium sp. 17-4
NoYes   Leuconostoc kimchii IMSNU 11154
NoYes   Streptococcus equi subsp. equi 4047
NoYes   Paenibacillus terrae HPL-003
NoYes   Paenibacillus mucilaginosus 3016
NoYes   Chlorobium limicola DSM 245
NoYes   Chlorobaculum parvum NCIB 8327
NoYes   Chloroherpeton thalassium ATCC 35110
NoYes   Flexibacter litoralis DSM 6794
NoYes   Prevotella denticola F0289
NoYes   Porphyromonas gingivalis ATCC 33277
NoYes   Fretibacterium fastidiosum
NoYes   Turneriella parva DSM 21527
NoYes   Thermodesulfobacterium sp. OPB45
NoYes   Candidatus Koribacter versatilis Ellin345
NoYes   Bdellovibrio bacteriovorus HD100
NoYes   Syntrophus aciditrophicus SB
NoYes   Desulfobacterium autotrophicum HRM2
NoYes   Pelobacter carbinolicus DSM 2380
NoYes   Anaeromyxobacter dehalogenans 2CP-1
NoYes   Stigmatella aurantiaca DW4/3-1
NoYes   Pandoraea sp. RB-44
NoYes   Rubrivivax gelatinosus IL144
NoYes   Burkholderia gladioli BSR3
NoYes   Alicycliphilus denitrificans K601
NoYes   Polaromonas sp. JS666
NoYes   Rhodoferax ferrireducens T118
NoYes   Acidovorax ebreus TPSY
NoYes   Acidovorax sp. KKS102
NoYes   Acidovorax sp. JS42
NoYes   Herminiimonas arsenicoxydans
NoYes   Janthinobacterium sp. Marseille
NoYes   Nitrosomonas europaea ATCC 19718
NoYes   Gallionella capsiferriformans ES-2
NoYes   Magnetococcus marinus MC-1
NoYes   Tistrella mobilis KA081020-065
NoYes   Methylobacterium chloromethanicum CM4
NoYes   Sinorhizobium medicae WSM419
NoYes   Rhizobium etli CIAT 652
NoYes   Agrobacterium sp. H13-3
NoYes   Beijerinckia indica subsp. indica ATCC 9039
NoYes   Pelagibacterium halotolerans B2
NoYes   Hyphomicrobium denitrificans ATCC 51888
NoYes   Actinobacillus pleuropneumoniae serovar 5b str. L20
NoYes   Vibrio fischeri MJ11
NoYes   Vibrio cholerae O395
NoYes   Shewanella sediminis HAW-EB3
NoYes   Shewanella denitrificans OS217
NoYes   Shewanella pealeana ATCC 700345
NoYes   Shewanella baltica OS185
NoYes   Rhodanobacter denitrificans
NoYes   Xanthomonas campestris pv. campestris str. B100
NoYes   Dickeya zeae Ech1591
NoYes   Pseudomonas sp. UW4
NoYes   Psychrobacter sp. G
NoYes   Thiomicrospira crunogena XCL-2
NoYes   Methanosaeta harundinacea 6Ac
NoYes   Archaeoglobus profundus DSM 5631
NoYes   Methanobacterium sp. AL-21
NoYes   Natrialba magadii ATCC 43099
NoYes   Halorubrum lacusprofundi ATCC 49239
NoYes   Methanothermobacter marburgensis str. Marburg
NoYes   Methanothermobacter thermautotrophicus str. Delta H
NoYes   Methanosphaera stadtmanae DSM 3091
NoYes   Methanobrevibacter sp. AbM4
NoYes   Methanobrevibacter ruminantium M1
NoYes   Methanobrevibacter smithii ATCC 35061
NoYes   Complete genome sequence of Methanobacterium sp. Mb1
NoYes   Cyanothece sp. PCC 7424
NoYes   Streptomyces albus J1074
NoYes   Corynebacterium diphtheriae HC03
NoYes   Desulfitobacterium hafniense DCB-2
NoYes   Clostridium botulinum F str. 230613
NoYes   Clostridium botulinum F str. Langeland
NoYes   Enterococcus faecium DO
NoYes   Clostridium botulinum B str. Eklund 17B
NoYes   Paenibacillus mucilaginosus KNP414
NoYes   Paenibacillus mucilaginosus K02
NoYes   Listeria monocytogenes EGD sequence
NoYes   Listeria monocytogenes SLCC5850
NoYes   Listeria monocytogenes 10403S
NoYes   Bacillus cereus AH187
NoYes   Psychroflexus torquis ATCC 700755
NoYes   Helicobacter cetorum MIT 99-5656
NoYes   Desulfovibrio gigas DSM 1382 = ATCC 19364
NoYes   Burkholderia ambifaria MC40-6
NoYes   Sulfuricella denitrificans skB26
NoYes   Rhodobacter sphaeroides ATCC 17025
NoYes   Rhodopseudomonas palustris DX-1
NoYes   Bradyrhizobium sp. BTAi1
NoYes   Aggregatibacter actinomycetemcomitans ANH9381
NoYes   Aggregatibacter actinomycetemcomitans D11S-1
NoYes   Aeromonas hydrophila ML09-119
NoYes   Vibrio cholerae O395
NoYes   Shewanella baltica OS223
NoYes   Shewanella sp. MR-7
NoYes   Glaciecola psychrophila 170
NoYes   Serratia plymuthica 4Rx13
NoYes   Serratia marcescens FGI94
NoYes   Serratia marcescens WW4
NoYes   Pseudomonas monteilii SB3101
NoYes   Pseudomonas monteilii SB3078
NoYes   Pseudomonas putida W619
NoYes   Pseudomonas fluorescens R124
NoYes   Natrinema pellirubrum DSM 15624
NoYes   Halorhabdus tiamatea SARL4B
NoYes   Methanobacterium sp. SWAN-1
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   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   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 bottom (Fungus garden bottom) (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 04(N) (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   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 YNP7 from Chocolate Pots (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 Formaldehyde 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   NCBI 2017_08 genome
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (meta-genome)
NoYes   Sludge/US, Phrap Assembly (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 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   Termite Protist Endosymbiont Community (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)


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