SUPERFAMILY 1.75 HMM library and genome assignments server

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Family 10 polysaccharide lyase alignments

These alignments are sequences aligned to the 0038318 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  
                                                                                       |         |  
d1gxma_ .......................................................mtgrmltldgnpaan---------------WLNNART
d1r76a_ avigmneaasaltpsrvsslpdtqraawqeylarseaqlsrdkaslaaelapgqplppppaegkgadtmp------------LDKPAAWYTS


              30        40        50        60                                 70        80         
               |         |         |         |                                  |         |         
d1gxma_ KWSASRADVVLSYQQNNGGWPKNLDYNSVGNGGGGNES.........................GTIDNGATITEMVFLAEVYKSGGNT...K
d1r76a_ KAARHVADVIVSFQTPAGGWGKNQPRDGALRLPGQHYTgenvakvksgsndldaardrdwhyvGTIDNDATVTEIRFLAQVVSQLAPEeaaP


          90       100       110       120       130       140       150       160       170       1
           |         |         |         |         |         |         |         |         |        
d1gxma_ YRDAVRKAANFLVNSQYSTGALPQFYPLKGGYSDHATFNDNGMAYALTVLDFAANKRAPFDTDVFSDNDRTRFKTAVTKGTDYILKAQWKQN
d1r76a_ YRDAALKGIEYLLASQFPNGGWPQVWPLEGGYHDAITYNDDALVHVAELLSDIAAGRDGFG--FVPPAIRTRALEATNAAIHCIVETQVVQD


        80       190       200       210       220        230       240       250       260       27
         |         |         |         |         |          |         |         |         |         
d1gxma_ GVLTVWCAQHGALDYQPKKARAYELESLSGSESVGVLAFLMTQP.QTAEIEQAVRAGVAWFNSPRTYLEGYTYDSSLAATNPIVPRAGSKMW
d1r76a_ GKRLGWGQQHDALTLRPTSARNFEPAALSSTESARILLFLMEIEaPSDAVKQAIRGGVAWLNTSVIRDRAWVKS--DQGYQLVTEQGAKPLW


        0       280       290       300       310       320          
        |         |         |         |         |         |          
d1gxma_ YRFYDLNTNRGFFSDRDGSKFYDITQMSLERRTGYSWGGNYGTSIINFA------qkvgyl
d1r76a_ SRFYSLDGNKPVFGDRDKTIHDDVMGISQERRTGYAWYTTSPQKALSAFTKW---ekrs..


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: 0038318 (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   Pan troglodytes 76_2.1.4 - Chimpanzee
NoYes   Ochotona princeps 76 - American pika
NoYes   Ailuropoda melanoleuca 76_1 - Giant panda
NoYes   Equus caballus 76_2 - Horse
NoYes   Myotis lucifugus 76_2.0 - Little brown bat
NoYes   Sorex araneus 76_1 - European shrew
NoYes   Procavia capensis 76_1 - Cape rock hyrax
NoYes   Macropus eugenii 76_1.0 - Tammar wallaby
NoYes   Ornithorhynchus anatinus 76_5 - Platypus
NoYes   Saccoglossus kowalevskii v3.0
NoYes   Petromyzon marinus 76_7.0 - Sea lamprey
NoYes   Taeniopygia guttata 76_3.2.4 - Zebra finch
NoYes   Latimeria chalumnae 76_1 - Coelacanth
NoYes   Tetraodon nigroviridis 76_8 - Spotted green pufferfish
NoYes   Takifugu rubripes 76_4 - Torafugu
NoYes   Oreochromis niloticus 76_1.0 - Nile tilapia
NoYes   Crassostrea gigas 22 - Pacific oyster
NoYes   Lottia gigantea - Owl limpet
NoYes   Capitella sp. I
NoYes   Danaus plexippus OGS1.0 - Monarch butterfly
NoYes   Daphnia pulex - Common water flea
NoYes   Tetranychus urticae - Two-spotted spider mite
NoYes   Pristionchus pacificus
NoYes   Meloidogyne incognita - Southern root-knot nematode
NoYes   Caenorhabditis elegans 76_235 - Roundworm
NoYes   Caenorhabditis briggsae 2
NoYes   Hydra vulgaris
NoYes   Apiospora montagnei NRRL 25634 v1.0
NoYes   Aspergillus fumigatus Af293
NoYes   Aspergillus flavus NRRL3357
NoYes   Pinus taeda - Loblolly pine
NoYes   Gossypium raimondii v221
NoYes   Citrus clementina v165
NoYes   Citrus sinensis v154 - Sweet orange
NoYes   Phaseolus vulgaris v186 - String bean
NoYes   Malus domestica v196 - Apple
NoYes   Prunus persica v139 - Peach
NoYes   Vitis vinifera - Wine grape
NoYes   Solanum lycopersicum v.2.3 - Tomato
NoYes   Triticum aestivum 22 - Bread wheat
NoYes   Panicum virgatum v202 - Switchgrass
NoYes   Phytophthora sojae 1.1
NoYes   Guillardia theta CCMP2712 v1.0
NoYes   Halothece sp. PCC 7418
NoYes   Rubrobacter xylanophilus DSM 9941
NoYes   Thermomonospora curvata DSM 43183
NoYes   Kribbella flavida DSM 17836
NoYes   Salinispora tropica CNB-440
NoYes   Clostridium cellulolyticum H10
NoYes   Ruminococcus albus 7
NoYes   Clostridium lentocellum DSM 5427
NoYes   Clostridium sp. BNL1100
NoYes   Clostridium cellulovorans 743B
NoYes   Paenibacillus mucilaginosus 3016
NoYes   Paenibacillus polymyxa M1
NoYes   Bacillus thuringiensis str. Al Hakam
NoYes   Bacillus cereus 03BB102
NoYes   Bacillus anthracis str. A0248
NoYes   Bacillus clausii KSM-K16
NoYes   Gemmatimonas aurantiaca T-27
NoYes   Melioribacter roseus P3M
NoYes   Haliscomenobacter hydrossis DSM 1100
NoYes   Niastella koreensis GR20-10
NoYes   Chitinophaga pinensis DSM 2588
NoYes   Cyclobacterium marinum DSM 745
NoYes   Leadbetterella byssophila DSM 17132
NoYes   Prevotella ruminicola 23
NoYes   Bacteroides salanitronis DSM 18170
NoYes   Bacteroides vulgatus ATCC 8482
NoYes   Bacteroides thetaiotaomicron VPI-5482
NoYes   Pedobacter heparinus DSM 2366
NoYes   Sphingobacterium sp. 21
NoYes   Flavobacteriaceae bacterium 3519-10
NoYes   Flavobacterium branchiophilum FL-15
NoYes   Flavobacterium johnsoniae UW101
NoYes   Fibrobacter succinogenes subsp. succinogenes S85
NoYes   Planctomyces brasiliensis DSM 5305
NoYes   Planctomyces limnophilus DSM 3776
NoYes   Rhodopirellula baltica SH 1
NoYes   Pirellula staleyi DSM 6068
NoYes   Opitutus terrae PB90-1
NoYes   Dictyoglomus turgidum DSM 6724
NoYes   Candidatus Solibacter usitatus Ellin6076
NoYes   Granulicella tundricola MP5ACTX9
NoYes   Granulicella mallensis MP5ACTX8
NoYes   Geobacter sp. M21
NoYes   Geobacter bemidjiensis Bem
NoYes   Pelobacter carbinolicus DSM 2380
NoYes   Stigmatella aurantiaca DW4/3-1
NoYes   Corallococcus coralloides DSM 2259
NoYes   Variovorax paradoxus S110
NoYes   Asticcacaulis excentricus CB 48
NoYes   Brevundimonas subvibrioides ATCC 15264
NoYes   Caulobacter sp. K31
NoYes   Caulobacter crescentus NA1000
NoYes   Phenylobacterium zucineum HLK1
NoYes   Hirschia baltica ATCC 49814
NoYes   Magnetospirillum magneticum AMB-1
NoYes   Mesorhizobium opportunistum WSM2075
NoYes   Saccharophagus degradans 2-40
NoYes   Teredinibacter turnerae T7901
NoYes   Cellvibrio japonicus Ueda107
NoYes   Marinomonas mediterranea MMB-1
NoYes   Pseudoxanthomonas suwonensis 11-1
NoYes   Xanthomonas campestris pv. campestris str. B100
NoYes   Dickeya zeae Ech1591
NoYes   Methanocella paludicola SANAE
NoYes   Methanosarcina mazei Go1
NoYes   Methanopyrus kandleri AV19
NoYes   Thermococcus kodakarensis KOD1
NoYes   Thermococcus barophilus MP
NoYes   Caenorhabditis elegans WormBase WS218 - Roundworm
NoYes   Aspergillus fumigatus A1163
NoYes   Cyanothece sp. ATCC 51142
NoYes   Amycolatopsis orientalis HCCB10007
NoYes   Thermacetogenium phaeum DSM 12270
NoYes   Paenibacillus mucilaginosus KNP414
NoYes   Paenibacillus mucilaginosus K02
NoYes   Paenibacillus polymyxa CR1
NoYes   Paenibacillus polymyxa SC2
NoYes   Paenibacillus polymyxa E681
NoYes   Bacillus thuringiensis serovar konkukian str. 97-27
NoYes   Bacillus cereus biovar anthracis str. CI
NoYes   Bacillus cereus AH820
NoYes   Bacillus cereus Q1
NoYes   Bacillus cereus F837/76
NoYes   Bacillus cereus E33L
NoYes   Bacillus anthracis str. H9401
NoYes   Bacillus anthracis str. CDC 684
NoYes   Bacillus anthracis str. 'Ames Ancestor'
NoYes   Bacillus anthracis str. Sterne
NoYes   Bacillus anthracis str. Ames
NoYes   Echinicola vietnamensis DSM 17526
NoYes   Bacteroides xylanisolvens XB1A
NoYes   Fibrobacter succinogenes subsp. succinogenes S85
NoYes   Singulisphaera acidiphila DSM 18658
NoYes   Sorangium cellulosum So0157-2
NoYes   Myxococcus stipitatus DSM 14675
NoYes   Variovorax paradoxus EPS
NoYes   Caulobacter crescentus CB15
NoYes   Simiduia agarivorans SA1 = DSM 21679
NoYes   Xanthomonas campestris pv. raphani 756C
NoYes   Xanthomonas campestris pv. campestris str. 8004
NoYes   Xanthomonas campestris pv. campestris str. ATCC 33913
NoYes   Methanolobus psychrophilus R15
NoYes   Methanosarcina mazei Tuc01
NoYes   Methanobacterium sp. SWAN-1
NoYes   Pan troglodytes 69_2.1.4 - Chimpanzee
NoYes   Ochotona princeps 69 - American pika
NoYes   Ailuropoda melanoleuca 69_1 - Giant panda
NoYes   Equus caballus 69_2 - Horse
NoYes   Myotis lucifugus 69_2.0 - Little brown bat
NoYes   Sorex araneus 69_1 - European shrew
NoYes   Procavia capensis 69_1 - Cape rock hyrax
NoYes   Macropus eugenii 69_1.0 - Tammar wallaby
NoYes   Ornithorhynchus anatinus 69_5 - Platypus
NoYes   Petromyzon marinus 69_7.0 - Sea lamprey
NoYes   Taeniopygia guttata 69_3.2.4 - Zebra finch
NoYes   Latimeria chalumnae 69_1 - Coelacanth
NoYes   Tetraodon nigroviridis 69_8 - Spotted green pufferfish
NoYes   Takifugu rubripes 69_4 - Torafugu
NoYes   Oreochromis niloticus 69_1.0 - Nile tilapia
NoYes   Caenorhabditis elegans 69_215 - Roundworm
NoYes   Lotus japonicus
NoYes   Malus x domestica - Apple
NoYes   Ricinus communis - Castor bean
NoYes   Nicotiana benthamiana 0.4.4
NoYes   Solanum pimpinellifolium A-1.0 - Currant tomato
NoYes   Solanum lycopersicum v2.3 - Tomato
NoYes   1_050719N (meta-genome)
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   7_Oxygen_minimum_layer (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   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (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 01(G) (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   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 YNP15 from Mushroom Spring (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 YNP20 from Bath Lake Vista Annex - Purple-Sulfur Mats (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   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   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   Miscanthus rhizosphere soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Rhizosphere soil sample of Miscanthus x giga (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (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   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   STRING v9.0.5 (STRING)
NoYes   Switchgrass field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing switchgr (meta-genome)
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   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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