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Methyl-coenzyme M reductase subunits alignments

These alignments are sequences aligned to the 0046473 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.

                                                                                                    
                                                                                                    
d1e6va2 ............................................................................................
d1e6ya2 aadifskfkkdmevkfaqefg.......................................................................
d1e6yb2 sdtvdiyddrgkllesnvdims......................................................................
d1mroc_ aqyypgttkvaqnrrnfcnpeyeleklreisdedvvkilghrapgeeypsvhppleemdepedairemvepidgakagdrvryiqftdsmyf


                                                                                                 10 
                                                                                                  | 
d1e6va2 .................................................................................LFMKALKEKFE
d1e6ya2 .................................................................................------SNKQT
d1e6yb2 .................................................................................-----------
d1mroc_ apaqpyvrsraylcryrgadagtlsgrqiietrerdlekiskelleteffdparsgvrgksvhghslrldedgmmfdmlrr-----------


               20        30        40        50          60        70        80        90       100 
                |         |         |         |           |         |         |         |         | 
d1e6va2 ESPEEKYTKFYIFGGWKQSERKKEFKEWADKIVEERGVPHYNPDI..GVPLGQRKLMSYQVSGTDVFVEGDDLTFVNNAAMQQMWDDIRRTV
d1e6ya2 GGDITDKTAKFLRLGPEQDPRKVEMIKAGKEIAEKRGIAFYNPMMhsGAPLGQRAITPYTISGTDIVCEPDDLHYVNNAAMQQMWDDIRRTC
d1e6yb2 ---------------------------------------------..-------------------------LAPTRNAAIQSIIMDTKRSV
d1mroc_ ---------------------------------------------..-------------------------------------------Q-


              110       120       130       140       150       160       170       180       190   
                |         |         |         |         |         |         |         |         |   
d1e6va2 IVGMDTAHRVLERRLGKEVTPETINEYMETLNHALPGGAVVQEHMVEIHPGLTWDCYAKIITGDLELADEIDDKFLIDIEKLFPEEQAEQLI
d1e6ya2 IVGLDMAHETLEKRLGKEVTPETINHYLEVLNHAMPGAAVVQEMMVETHPALVDDCYVKVFTGDDALADEIDKQFLIDINKEFSEEQAAQIK
d1e6yb2 AVNLAGIQG-----------------------------------------------------------------------------------
d1mroc_ --------------------------------------------------------------------------------------------


            200       210       220       230       240       250       260                         
              |         |         |         |         |         |         |                         
d1e6va2 KAIGNRTYQVCRMPTIVGHVCDGATMYRWAAMQIAMSFICAYKIAAGEAAVSDFAFASKHAEVINMGEMLPA....................
d1e6ya2 ASIGKTSWQAIHIPTIVSRTTDGAQTSRWAAMQIGMSFISAYAMCAGEAAVADLSFAAKHAALVSMGEMLPA....................
d1e6yb2 ------------------------------------------------------------------------alasgkmggkgrqilgrgln
d1mroc_ ------------------------------------------------------------------------iynkdtgrvemvknqigdel


                                                                                                    
                                                                                                    
d1e6va2 ............................................................................................
d1e6ya2 ............................................................................................
d1e6yb2 ydivgnadaiaenvkklvqvdegddtnvikvkggkslliqspksriiagadfmsattvgaaavtqtimdmfgtdpydapivksavwgsypqt
d1mroc_ depvdlgepldeetlmekttiyrvdgeayrddveaveimqrihvlrsqggfnl.......................................


                             
                             
d1e6va2 .....................
d1e6ya2 .....................
d1e6yb2 mdlmggqvqgilsipqnnegl
d1mroc_ .....................


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: 0046473 (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   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   Thermoplasmatales archaeon BRNA1
NoYes   Methanobacterium sp. AL-21
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   Methanomethylovorans hollandica DSM 15978
NoYes   Methanolobus psychrophilus R15
NoYes   Methanosarcina mazei Tuc01
NoYes   Methanoregula formicica Methanoregula formicicum SMSP
NoYes   Candidatus Methanomethylophilus alvus Mx1201
NoYes   Candidatus Methanomassiliicoccus intestinalis Issoire-Mx1
NoYes   Methanococcus maripaludis X1
NoYes   Methanococcus maripaludis C6
NoYes   Methanococcus maripaludis C7
NoYes   Methanococcus maripaludis S2
NoYes   Methanobacterium sp. SWAN-1
NoYes   Anaerobic methane oxidation (AOM) community from Eel River Basin sediment, California (meta-genome)
NoYes   Groundwater dechlorinating community (KB-1) from synthetic mineral medium in Toronto, ON, sample from Site contaminated with chlorinated ethenes
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP15 from Mushroom Spring (meta-genome)
NoYes   Human Gut Community Subject 7 (meta-genome)
NoYes   Human Gut Community Subject 8 (meta-genome)
NoYes   NCBI 2017_08 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 community from bioreactor at Alameda Naval Air Station, CA, contaminated with Chloroethene, Sample 196 (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Uniprot 2018_03 genome
NoYes   Wastewater Terephthalate-degrading communities from Bioreactor (meta-genome)
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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