SUPERFAMILY 1.75 HMM library and genome assignments server

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Methenyltetrahydromethanopterin cyclohydrolase alignments

These alignments are sequences aligned to the 0042849 model.

Sophisticated options are available for refining alignments:

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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  
                 |         |         |         |         |         |         |         |         |  

             100       110       120       130       140       150       160       170       180    
               |         |         |         |         |         |         |         |         |    

           190       200       210       220       230       240       250       260       270      
             |         |         |         |         |         |         |         |         |      

         280       290       300       310       
           |         |         |         |       

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: 0042849 (list models)
Initial SAMT99 seed:

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   Caldilinea aerophila DSM 14535 = NBRC 104270
NoYes   Desulfosporosinus acidiphilus SJ4
NoYes   Desulfosporosinus orientis DSM 765
NoYes   Halothermothrix orenii H 168
NoYes   Halanaerobium hydrogeniformans
NoYes   Isosphaera pallida ATCC 43644
NoYes   Planctomyces brasiliensis DSM 5305
NoYes   Planctomyces limnophilus DSM 3776
NoYes   Rhodopirellula baltica SH 1
NoYes   Pirellula staleyi DSM 6068
NoYes   Anaerobaculum mobile DSM 13181
NoYes   Spirochaeta smaragdinae DSM 11293
NoYes   Candidatus Methylomirabilis oxyfera
NoYes   Azoarcus sp. KH32C
NoYes   Methylibium petroleiphilum PM1
NoYes   Rubrivivax gelatinosus IL144
NoYes   Leptothrix cholodnii SP-6
NoYes   Burkholderia phymatum STM815
NoYes   Burkholderia xenovorans LB400
NoYes   Burkholderia sp. RPE64
NoYes   Burkholderia sp. CCGE1002
NoYes   Variovorax paradoxus S110
NoYes   Methylotenera versatilis 301
NoYes   Methylotenera mobilis JLW8
NoYes   Methylovorus sp. MP688
NoYes   Methylovorus glucosetrophus SIP3-4
NoYes   Methylobacillus flagellatus KT
NoYes   Azospirillum lipoferum 4B
NoYes   Azospirillum brasilense Sp245
NoYes   Granulibacter bethesdensis CGDNIH1
NoYes   Starkeya novella DSM 506
NoYes   Xanthobacter autotrophicus Py2
NoYes   Methylobacterium chloromethanicum CM4
NoYes   Methylobacterium extorquens AM1
NoYes   Methylobacterium sp. 4-46
NoYes   Methylobacterium populi BJ001
NoYes   Methylobacterium nodulans ORS 2060
NoYes   Methylobacterium radiotolerans JCM 2831
NoYes   Mesorhizobium ciceri biovar biserrulae WSM1271
NoYes   Methylocella silvestris BL2
NoYes   Hyphomicrobium sp. MC1
NoYes   Hyphomicrobium denitrificans ATCC 51888
NoYes   Methylocystis sp. SC2
NoYes   Methylomicrobium alcaliphilum
NoYes   Methylomonas methanica MC09
NoYes   Methylococcus capsulatus str. Bath
NoYes   Nitrosococcus halophilus Nc4
NoYes   Methylophaga sp. JAM1
NoYes   halophilic archaeon DL31
NoYes   Methanocella arvoryzae MRE50
NoYes   Methanocella conradii HZ254
NoYes   Methanocella paludicola SANAE
NoYes   Methanosaeta harundinacea 6Ac
NoYes   Methanosaeta thermophila PT
NoYes   Methanosaeta concilii GP6
NoYes   Methanosalsum zhilinae DSM 4017
NoYes   Methanohalobium evestigatum Z-7303
NoYes   Methanococcoides burtonii DSM 6242
NoYes   Methanosarcina acetivorans C2A
NoYes   Methanosarcina mazei Go1
NoYes   Methanosarcina barkeri str. Fusaro
NoYes   Methanohalophilus mahii DSM 5219
NoYes   Methanosphaerula palustris E1-9c
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   Ferroglobus placidus DSM 10642
NoYes   Archaeoglobus profundus DSM 5631
NoYes   Archaeoglobus veneficus SNP6
NoYes   Archaeoglobus fulgidus DSM 4304
NoYes   Salinarchaeum sp. Harcht-Bsk1
NoYes   Halopiger xanaduensis SH-6
NoYes   Methanobacterium sp. AL-21
NoYes   Haloterrigena turkmenica DSM 5511
NoYes   Natrinema sp. J7-2
NoYes   Natrialba magadii ATCC 43099
NoYes   Halorubrum lacusprofundi ATCC 49239
NoYes   Haloquadratum walsbyi DSM 16790
NoYes   Halogeometricum borinquense DSM 11551
NoYes   Haloferax mediterranei ATCC 33500
NoYes   Haloferax volcanii DS2
NoYes   Halomicrobium mukohataei DSM 12286
NoYes   Halorhabdus utahensis DSM 12940
NoYes   Natronomonas pharaonis DSM 2160
NoYes   Haloarcula hispanica ATCC 33960
NoYes   Haloarcula marismortui ATCC 43049
NoYes   Halalkalicoccus jeotgali B3
NoYes   Halobacterium salinarum R1
NoYes   Halobacterium sp. NRC-1
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   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   Desulfosporosinus meridiei DSM 13257
NoYes   Clostridium botulinum E3 str. Alaska E43
NoYes   Singulisphaera acidiphila DSM 18658
NoYes   Burkholderia phenoliruptrix BR3459a
NoYes   Burkholderia sp. YI23
NoYes   Burkholderia sp. CCGE1003
NoYes   Burkholderia sp. CCGE1001
NoYes   Variovorax paradoxus B4
NoYes   Methylobacterium extorquens DM4
NoYes   Methylobacterium extorquens PA1
NoYes   Hyphomicrobium nitrativorans NL23
NoYes   Hyphomicrobium denitrificans 1NES1
NoYes   Methylophaga sp. JAM7
NoYes   Methanomethylovorans hollandica DSM 15978
NoYes   Methanolobus psychrophilus R15
NoYes   Methanosarcina mazei Tuc01
NoYes   Methanoregula formicica Methanoregula formicicum SMSP
NoYes   Archaeoglobus sulfaticallidus PM70-1
NoYes   Halovivax ruber XH-70
NoYes   Natrinema pellirubrum DSM 15624
NoYes   Natronococcus occultus SP4
NoYes   Natronobacterium gregoryi SP2
NoYes   Haloquadratum walsbyi C23
NoYes   Halorhabdus tiamatea SARL4B
NoYes   Natronomonas moolapensis 8.8.11
NoYes   Haloarcula hispanica N601
NoYes   Methanococcus maripaludis X1
NoYes   Methanococcus maripaludis C6
NoYes   Methanococcus maripaludis C7
NoYes   Methanococcus maripaludis S2
NoYes   Methanobacterium sp. SWAN-1
NoYes   Ricinus communis - Castor bean
NoYes   Anaerobic methane oxidation (AOM) community from Eel River Basin sediment, California (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 03(I) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 08(T) (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 YNP19 from Cistern Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP4 from Joseph's Coat Springs (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   Methylotrophic community from Lake Washington sediment Methylamine enrichment (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   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 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 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   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   ALL (only advised for small superfamilies)

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