SUPERFAMILY 1.75 HMM library and genome assignments server

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AF1862-like alignments

These alignments are sequences aligned to the 0054365 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 
                                      |         |         |         |         |         |         | 
d2oeba1                    di--REIEQERASFAFKVVSDIKDKYSQNKKVQGKYSSYAEKAPTIILNNGLGATLAFFLSKLEKPIDDVDYK
WP_012302891.1.36146:1-113 ..-MQTRNQEYAAKIFEQVMQVRDELG--KDGSNNYGSLAHRLPVFVRTAGLAQALAFVEARDGA--------


                                  80        90       100       110       120       130       140    
                                   |         |         |         |         |         |         |    
d2oeba1                    SINPESFGNAENIAYAFLYKHLSTWLAEGNGKDSAFSGLTNGEDPLKYIMEKTAIDVAISTEEALSILNWIKK
WP_012302891.1.36146:1-113 -------------AGRKLLRDIAAVVNE--------------EELLARSRTAELPEYMLLTRNVLAALAWYKR


                              150   
                                |   
d2oeba1                    FAKAMLE-e
WP_012302891.1.36146:1-113 FAQSVL--g


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: 0054365 (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   Thermobaculum terrenum ATCC BAA-798
NoYes   Rubrobacter xylanophilus DSM 9941
NoYes   Thermobifida fusca YX
NoYes   Caldilinea aerophila DSM 14535 = NBRC 104270
NoYes   Anaerolinea thermophila UNI-1
NoYes   Thermomicrobium roseum DSM 5159
NoYes   Herpetosiphon aurantiacus DSM 785
NoYes   Truepera radiovictrix DSM 17093
NoYes   Deinococcus geothermalis DSM 11300
NoYes   Marinithermus hydrothermalis DSM 14884
NoYes   Meiothermus silvanus DSM 9946
NoYes   Meiothermus ruber DSM 1279
NoYes   Thermus sp. CCB_US3_UF1
NoYes   Thermus thermophilus HB27
NoYes   Candidatus Desulforudis audaxviator MP104C
NoYes   Pelotomaculum thermopropionicum SI
NoYes   Syntrophobotulus glycolicus DSM 8271
NoYes   Desulfotomaculum acetoxidans DSM 771
NoYes   Desulfotomaculum kuznetsovii DSM 6115
NoYes   Syntrophothermus lipocalidus DSM 12680
NoYes   Clostridium botulinum A str. ATCC 3502
NoYes   Caldicellulosiruptor obsidiansis OB47
NoYes   Caldicellulosiruptor kronotskyensis 2002
NoYes   Thermoanaerobacterium thermosaccharolyticum DSM 571
NoYes   Thermoanaerobacter tengcongensis MB4
NoYes   Thermoanaerobacter mathranii subsp. mathranii str. A3
NoYes   Thermoanaerobacter italicus Ab9
NoYes   Halothermothrix orenii H 168
NoYes   Kyrpidia tusciae DSM 2912
NoYes   Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
NoYes   Paenibacillus terrae HPL-003
NoYes   Geobacillus thermoglucosidasius C56-YS93
NoYes   Geobacillus sp. GHH01
NoYes   Geobacillus sp. WCH70
NoYes   Bacillus halodurans C-125
NoYes   Chloroherpeton thalassium ATCC 35110
NoYes   Haliscomenobacter hydrossis DSM 1100
NoYes   Flexibacter litoralis DSM 6794
NoYes   Porphyromonas gingivalis ATCC 33277
NoYes   Isosphaera pallida ATCC 43644
NoYes   Fretibacterium fastidiosum
NoYes   Anaerobaculum mobile DSM 13181
NoYes   Treponema azotonutricium ZAS-9
NoYes   Thermodesulfatator indicus DSM 15286
NoYes   Flexistipes sinusarabici DSM 4947
NoYes   Marinitoga piezophila KA3
NoYes   Mesotoga prima MesG1.Ag.4.2
NoYes   Fervidobacterium pennivorans DSM 9078
NoYes   Thermosipho melanesiensis BI429
NoYes   Thermosipho africanus TCF52B
NoYes   Thermotoga thermarum DSM 5069
NoYes   Thermotoga sp. RQ2
NoYes   Sulfurihydrogenibium sp. YO3AOP1
NoYes   Thermocrinis albus DSM 14484
NoYes   Aquifex aeolicus VF5
NoYes   Candidatus Chloracidobacterium thermophilum B
NoYes   Syntrophus aciditrophicus SB
NoYes   Haliangium ochraceum DSM 14365
NoYes   Sorangium cellulosum 'So ce 56'
NoYes   Myxococcus xanthus DK 1622
NoYes   Myxococcus fulvus HW-1
NoYes   Candidatus Accumulibacter phosphatis clade IIA str. UW-1
NoYes   Rhodospirillum centenum SW
NoYes   Azospirillum lipoferum 4B
NoYes   Teredinibacter turnerae T7901
NoYes   Marinomonas sp. MWYL1
NoYes   Marinomonas mediterranea MMB-1
NoYes   Thioalkalivibrio sulfidophilus HL-EbGr7
NoYes   Halorhodospira halophila SL1
NoYes   Allochromatium vinosum DSM 180
NoYes   Candidatus Korarchaeum cryptofilum OPF8
NoYes   Acidilobus saccharovorans 345-15
NoYes   Fervidicoccus fontis Kam940
NoYes   Pyrolobus fumarii 1A
NoYes   Hyperthermus butylicus DSM 5456
NoYes   Ignicoccus hospitalis KIN4/I
NoYes   Desulfurococcus kamchatkensis 1221n
NoYes   Sulfolobus tokodaii str. 7
NoYes   Sulfolobus solfataricus P2
NoYes   Thermofilum sp. 1910b
NoYes   Thermofilum pendens Hrk 5
NoYes   Vulcanisaeta moutnovskia 768-28
NoYes   Vulcanisaeta distributa DSM 14429
NoYes   Caldivirga maquilingensis IC-167
NoYes   Pyrobaculum sp. 1860
NoYes   Pyrobaculum calidifontis JCM 11548
NoYes   Pyrobaculum arsenaticum DSM 13514
NoYes   Pyrobaculum oguniense TE7
NoYes   Thermoproteus neutrophilus V24Sta
NoYes   Methanosaeta harundinacea 6Ac
NoYes   Methanosaeta thermophila PT
NoYes   Archaeoglobus fulgidus DSM 4304
NoYes   Pyrococcus yayanosii CH1
NoYes   Pyrococcus furiosus COM1
NoYes   Methanococcus voltae A3
NoYes   Methanococcus vannielii SB
NoYes   Thermus thermophilus HB8
NoYes   Clostridium botulinum H04402 065
NoYes   Clostridium botulinum F str. 230613
NoYes   Clostridium botulinum F str. Langeland
NoYes   Clostridium botulinum Ba4 str. 657
NoYes   Clostridium botulinum A str. Hall
NoYes   Clostridium botulinum A str. ATCC 19397
NoYes   Thermoanaerobacterium thermosaccharolyticum M0795
NoYes   Alicyclobacillus acidocaldarius subsp. acidocaldarius Tc-4-1
NoYes   Paenibacillus larvae subsp. larvae DSM 25430
NoYes   Geobacillus sp. Y412MC52
NoYes   Geobacillus sp. Y412MC61
NoYes   Porphyromonas gingivalis TDC60
NoYes   Porphyromonas gingivalis W83
NoYes   Desulfovibrio hydrothermalis AM13 = DSM 14728
NoYes   Myxococcus stipitatus DSM 14675
NoYes   Candidatus Symbiobacter mobilis Comamonadaceae bacterium CR
NoYes   Shewanella putrefaciens 200
NoYes   Thioalkalivibrio nitratireducens DSM 14787
NoYes   Thioflavicoccus mobilis 8321
NoYes   Sulfolobus islandicus LAL14/1
NoYes   Sulfolobus islandicus REY15A
NoYes   Sulfolobus islandicus HVE10/4
NoYes   Sulfolobus islandicus Y.G.57.14
NoYes   Sulfolobus islandicus L.S.2.15
NoYes   Sulfolobus islandicus M.16.27
NoYes   Sulfolobus islandicus M.14.25
NoYes   Sulfolobus islandicus M.16.4
NoYes   Sulfolobus islandicus L.D.8.5
NoYes   Sulfolobus solfataricus 98/2
NoYes   Pyrococcus furiosus DSM 3638
NoYes   1_050719N (meta-genome)
NoYes   2_050719S (meta-genome)
NoYes   3_050719R (meta-genome)
NoYes   4_050719Q (meta-genome)
NoYes   5_050719P (meta-genome)
NoYes   6_Upper_euphotic (meta-genome)
NoYes   Activated sludge plasmid pool Morges-2009 (Newbler) (meta-genome)
NoYes   Bath Hot Springs, filamentous community (meta-genome)
NoYes   Bath Hot Springs, planktonic community (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   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 05(O) (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 YNP1 from Alice Springs, Crater Hills (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP10 from Narrow Gauge (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 YNP13 from Bechler Spring (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 YNP16 from Fairy Spring Red Layer (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 YNP20 from Bath Lake Vista Annex - Purple-Sulfur Mats (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP3 from Monarch Geyser, Norris Geyser Basin (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   Hot spring microbial community from Yellowstone Hot Springs, sample YNP7 from Chocolate Pots (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP9 from Dragon Spring, Norris Geyser Basin (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   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 Methane enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methanol enrichment (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (meta-genome)
NoYes   Sludge/US, Jazz Assembly (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 community from bioreactor at Alameda Naval Air Station, CA, contaminated with Chloroethene, Sample 196 (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   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   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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