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.

Dhaf3308-like alignments

These alignments are sequences aligned to the 0054010 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  
                                     |         |         |         |         |         |         |  
d2h1qa1                    .MWEIYDAMINGIPEDFLVDELVCGTTHSVIRSGNGVGLGPNRPFETRMPMLTQNLLGLPLRVAAGCVKSWNY
ENSGGOP00000023867:107-175 n------------------------------------------------------------------------


                                 80        90       100       110       120       130       140     
                                  |         |         |         |         |         |         |     
d2h1qa1                    VEASIGLAAINAYYNNPQVAREHGVIFSDAKRVEDRMNDPFIMSQNEVKGKKVGVVGHFPHLESLLEPICDLS
ENSGGOP00000023867:107-175 -------------------------------------------------------------------------


                             150       160       170       180       190       200         210      
                               |         |         |         |         |         |           |      
d2h1qa1                    ILEWSPEEGDYPLPASEFILPECDYVYITCASVVDKTLPRLLELSRNARRITLVGPGTPLAPV..LFEHGLQE
ENSGGOP00000023867:107-175 -----------------------------GSTLLNHTSDRICDKS---CYAIMVGSTVTFIAGvyQVAMGFFQ


                            220       230       240       250    
                              |         |         |         |    
d2h1qa1                    LSGFMVKDNARAFRIVAGAEKVKIYSAGQKVT---ikk
ENSGGOP00000023867:107-175 VGFVSVYLSDALLSGFVTGASFTI-----------lts


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: 0054010 (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   Trichodesmium erythraeum IMS101
NoYes   Cyanothece sp. PCC 8802
NoYes   Rivularia sp. PCC 7116
NoYes   Cryptobacterium curtum DSM 15641
NoYes   Eggerthella lenta DSM 2243
NoYes   Slackia heliotrinireducens DSM 20476
NoYes   Atopobium parvulum DSM 20469
NoYes   Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111
NoYes   Streptomyces sp. PAMC26508
NoYes   Streptomyces flavogriseus ATCC 33331
NoYes   Streptomyces scabiei 87.22
NoYes   Actinosynnema mirum DSM 43827
NoYes   Saccharopolyspora erythraea NRRL 2338
NoYes   Kribbella flavida DSM 17836
NoYes   Propionibacterium propionicum F0230a
NoYes   Tsukamurella paurometabola DSM 20162
NoYes   Gordonia bronchialis DSM 43247
NoYes   Rhodococcus opacus B4
NoYes   Actinomyces sp. F0330
NoYes   Natranaerobius thermophilus JW/NM-WN-LF
NoYes   Symbiobacterium thermophilum IAM 14863
NoYes   Ethanoligenens harbinense YUAN-3
NoYes   Oscillibacter valericigenes Sjm18-20
NoYes   Desulfosporosinus orientis DSM 765
NoYes   Syntrophobotulus glycolicus DSM 8271
NoYes   Desulfitobacterium hafniense Y51
NoYes   Desulfitobacterium dehalogenans ATCC 51507
NoYes   Desulfotomaculum acetoxidans DSM 771
NoYes   Desulfotomaculum ruminis DSM 2154
NoYes   Acetobacterium woodii DSM 1030
NoYes   Clostridium difficile 630
NoYes   Clostridium saccharolyticum WM1
NoYes   Syntrophomonas wolfei subsp. wolfei str. Goettingen
NoYes   Alkaliphilus oremlandii OhILAs
NoYes   Clostridium ljungdahlii DSM 13528
NoYes   Clostridium botulinum A str. ATCC 3502
NoYes   Thermodesulfobium narugense DSM 14796
NoYes   Moorella thermoacetica ATCC 39073
NoYes   Acetohalobium arabaticum DSM 5501
NoYes   Thermanaerovibrio acidaminovorans DSM 6589
NoYes   Anaerobaculum mobile DSM 13181
NoYes   Spirochaeta smaragdinae DSM 11293
NoYes   Sphaerochaeta pleomorpha str. Grapes
NoYes   Treponema azotonutricium ZAS-9
NoYes   Treponema primitia ZAS-2
NoYes   Thermodesulfatator indicus DSM 15286
NoYes   Thermodesulfobacterium sp. OPB45
NoYes   Calditerrivibrio nitroreducens DSM 19672
NoYes   Deferribacter desulfuricans SSM1
NoYes   Marinitoga piezophila KA3
NoYes   Petrotoga mobilis SJ95
NoYes   Kosmotoga olearia TBF 19.5.1
NoYes   Thermosipho melanesiensis BI429
NoYes   Thermosipho africanus TCF52B
NoYes   Caldisericum exile AZM16c01
NoYes   Sulfurospirillum barnesii SES-3
NoYes   Campylobacter curvus 525.92
NoYes   Wolinella succinogenes DSM 1740
NoYes   Desulfarculus baarsii DSM 2075
NoYes   Syntrophus aciditrophicus SB
NoYes   Desulfomonile tiedjei DSM 6799
NoYes   Syntrophobacter fumaroxidans MPOB
NoYes   Desulfotalea psychrophila LSv54
NoYes   Desulfatibacillum alkenivorans AK-01
NoYes   Desulfobacterium autotrophicum HRM2
NoYes   Desulfococcus oleovorans Hxd3
NoYes   Desulfohalobium retbaense DSM 5692
NoYes   Desulfovibrio piezophilus
NoYes   Desulfovibrio magneticus RS-1
NoYes   Desulfovibrio alaskensis G20
NoYes   Desulfovibrio salexigens DSM 2638
NoYes   Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774
NoYes   Desulfovibrio africanus str. Walvis Bay
NoYes   Hippea maritima DSM 10411
NoYes   Pelobacter propionicus DSM 2379
NoYes   Pelobacter carbinolicus DSM 2380
NoYes   Thauera sp. MZ1T
NoYes   Azoarcus sp. KH32C
NoYes   Alicycliphilus denitrificans K601
NoYes   Magnetococcus marinus MC-1
NoYes   Paracoccus denitrificans PD1222
NoYes   Rhodospirillum photometricum DSM 122
NoYes   Magnetospirillum magneticum AMB-1
NoYes   Azospirillum lipoferum 4B
NoYes   Azospirillum sp. B510
NoYes   Azospirillum brasilense Sp245
NoYes   Teredinibacter turnerae T7901
NoYes   Methylomonas methanica MC09
NoYes   Methylococcus capsulatus str. Bath
NoYes   Allochromatium vinosum DSM 180
NoYes   Serratia sp. ATCC 39006
NoYes   Azotobacter vinelandii DJ
NoYes   Pseudomonas stutzeri A1501
NoYes   Acidilobus saccharovorans 345-15
NoYes   Pyrolobus fumarii 1A
NoYes   Hyperthermus butylicus DSM 5456
NoYes   Ignicoccus hospitalis KIN4/I
NoYes   Staphylothermus hellenicus DSM 12710
NoYes   Staphylothermus marinus F1
NoYes   Metallosphaera cuprina Ar-4
NoYes   Metallosphaera sedula DSM 5348
NoYes   Acidianus hospitalis W1
NoYes   Sulfolobus tokodaii str. 7
NoYes   Sulfolobus islandicus Y.N.15.51
NoYes   Sulfolobus solfataricus P2
NoYes   Sulfolobus acidocaldarius DSM 639
NoYes   Thermofilum pendens Hrk 5
NoYes   Vulcanisaeta moutnovskia 768-28
NoYes   Vulcanisaeta distributa DSM 14429
NoYes   Caldivirga maquilingensis IC-167
NoYes   Pyrobaculum arsenaticum DSM 13514
NoYes   Pyrobaculum oguniense TE7
NoYes   Thermoproteus neutrophilus V24Sta
NoYes   Pyrobaculum islandicum DSM 4184
NoYes   Thermoproteus tenax Kra 1
NoYes   Methanosaeta harundinacea 6Ac
NoYes   Methanosaeta concilii GP6
NoYes   Methanosarcina acetivorans C2A
NoYes   Methanosarcina mazei Go1
NoYes   Methanosarcina barkeri str. Fusaro
NoYes   Methanohalophilus mahii DSM 5219
NoYes   Methanoregula boonei 6A8
NoYes   Methanospirillum hungatei JF-1
NoYes   Methanocorpusculum labreanum Z
NoYes   Methanoplanus petrolearius DSM 11571
NoYes   Methanoculleus bourgensis MS2
NoYes   Methanoculleus marisnigri JR1
NoYes   Methanopyrus kandleri AV19
NoYes   Archaeoglobus profundus DSM 5631
NoYes   Thermococcus sp. 4557
NoYes   Thermococcus onnurineus NA1
NoYes   Thermococcus kodakarensis KOD1
NoYes   Thermococcus gammatolerans EJ3
NoYes   Thermococcus sibiricus MM 739
NoYes   Thermococcus barophilus MP
NoYes   Pyrococcus sp. ST04
NoYes   Pyrococcus yayanosii CH1
NoYes   Pyrococcus horikoshii OT3
NoYes   Pyrococcus abyssi GE5
NoYes   Methanotorris igneus Kol 5
NoYes   Methanocaldococcus sp. FS406-22
NoYes   Methanocaldococcus fervens AG86
NoYes   Methanocaldococcus vulcanius M7
NoYes   methanocaldococcus infernus ME
NoYes   Methanocaldococcus jannaschii DSM 2661
NoYes   Methanothermococcus okinawensis IH1
NoYes   Methanococcus aeolicus Nankai-3
NoYes   Methanococcus maripaludis C5
NoYes   Methanococcus voltae A3
NoYes   Methanococcus vannielii SB
NoYes   Methanothermus fervidus DSM 2088
NoYes   Methanothermobacter marburgensis str. Marburg
NoYes   Methanothermobacter thermautotrophicus str. Delta H
NoYes   Complete genome sequence of Methanobacterium sp. Mb1
NoYes   Aciduliprofundum sp. MAR08-339
NoYes   Cyanothece sp. ATCC 51142
NoYes   Cyanothece sp. PCC 8801
NoYes   Pleurocapsa minor Pleurocapsa sp. PCC 7327
NoYes   Calothrix parietina Calothrix sp. PCC 6303
NoYes   Gordonibacter pamelaeae 7-10-1-b
NoYes   Adlercreutzia equolifaciens DSM 19450
NoYes   Nocardiopsis alba ATCC BAA-2165
NoYes   Streptomyces rapamycinicus NRRL 5491
NoYes   Streptomyces davawensis JCM 4913
NoYes   Streptomyces venezuelae ATCC 10712
NoYes   Actinomyces odontolyticus ATCC 17982
NoYes   Actinomyces viscosus C505
NoYes   Clostridium acidurici 9a
NoYes   Desulfosporosinus meridiei DSM 13257
NoYes   Desulfitobacterium hafniense DCB-2
NoYes   Desulfotomaculum gibsoniae DSM 7213
NoYes   Clostridium difficile BI1
NoYes   Clostridium difficile R20291
NoYes   Clostridium difficile CD196
NoYes   Clostridium autoethanogenum DSM 10061
NoYes   Clostridium botulinum E3 str. Alaska E43
NoYes   Clostridium botulinum A3 str. Loch Maree
NoYes   Clostridium botulinum A str. Hall
NoYes   Clostridium botulinum A str. ATCC 19397
NoYes   Thermoanaerobacterium saccharolyticum JW/SL-YS485
NoYes   Thermacetogenium phaeum DSM 12270
NoYes   Halobacteroides halobius DSM 5150
NoYes   Clostridium botulinum B str. Eklund 17B
NoYes   Desulfobacula toluolica Tol2
NoYes   Desulfovibrio hydrothermalis AM13 = DSM 14728
NoYes   Desulfovibrio gigas DSM 1382 = ATCC 19364
NoYes   Desulfovibrio desulfuricans ND132
NoYes   Candidatus Symbiobacter mobilis Comamonadaceae bacterium CR
NoYes   Rhodopseudomonas palustris CGA009
NoYes   Azotobacter vinelandii CA6
NoYes   Azotobacter vinelandii CA
NoYes   Pseudomonas stutzeri DSM 4166
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   Sulfolobus acidocaldarius SUSAZ
NoYes   Sulfolobus acidocaldarius Ron12/I
NoYes   Sulfolobus acidocaldarius N8
NoYes   Methanosarcina mazei Tuc01
NoYes   Methanoregula formicica Methanoregula formicicum SMSP
NoYes   Thermococcus sp. AM4
NoYes   Thermococcus sp. CL1
NoYes   Thermococcus litoralis DSM 5473
NoYes   Pyrococcus sp. NA2
NoYes   Natronobacterium gregoryi SP2
NoYes   Methanococcus maripaludis X1
NoYes   Methanococcus maripaludis C6
NoYes   Methanococcus maripaludis C7
NoYes   Methanococcus maripaludis S2
NoYes   Methanobacterium sp. SWAN-1
NoYes   1_050719N (meta-genome)
NoYes   2_050719S (meta-genome)
NoYes   4_050719Q (meta-genome)
NoYes   5_050719P (meta-genome)
NoYes   7_Oxygen_minimum_layer (meta-genome)
NoYes   Anaerobic methane oxidation (AOM) community from Eel River Basin sediment, California (meta-genome)
NoYes   Bath Hot Springs, filamentous community (meta-genome)
NoYes   Bath Hot Springs, planktonic community (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 #1 (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 04(N) (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   Hot Spring microbial communities from Yellowstone Obsidian Hot Spring, Sample 10594 (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 YNP12 from Calcite Springs, Tower Falls Region (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 YNP2 from Nymph Lake 10 (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 YNP9 from Dragon Spring, Norris Geyser Basin (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 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   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   Olavius algarvensis endosymbiont metagenome Delta1 (meta-genome)
NoYes   Olavius algarvensis endosymbiont metagenome Gamma3 (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   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 5 Oak Ridge CO2+ (Oak Ridge elevated CO2) (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   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   ALL (only advised for small superfamilies)


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