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  Home > SCOP hierarchy > S-adenosyl-L-methionine-dependent methyltransferases > Alignments


S-adenosyl-L-methionine-dependent methyltransferases alignments

These alignments are sequences aligned to the 0041444 model.

Sophisticated options are available for refining alignments:

Jump to [ Top of page · Refine alignments · Add alignments from genomes ]

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        80        
                     |         |         |         |         |         |         |         |        
d1nkva_ ...p-RIFTISESEHRIHNPFTEEKYATLGRVLRMKPGTRILDLGSGSGEMLCTWARDHGITGTGIDMSSLFTAQAKRRAEELGVSERVHFI
d5bp7b1 dipr--IFTITESAHRIHNPITPEKLTTLGAALRLEPGTRVLDLGSGSGEMLCTWARDHGIIGTGIDMSQLFTAQAKLRAEELGVADRVTFI


        90       100       110       120       130       140       150       160       170       180
         |         |         |         |         |         |         |         |         |         |
d1nkva_ HNDAAGYVANEKCDVAACVGATWIAGGFAGAEELLAQSLKPGGIMLIGEPYWRQLPATEEIAQACGVSSTSDFLTLPGLVGAFDDLGYDVVE
d5bp7b1 HGDASGYVSDDKAGVAACVGATWIGGGVAGTIELLARSLRPGGIILIGEPYWRQVPPTEDVARGCLANSTSDFLMLPELLASFGRLGYDVVE


               190       200       210       220       230       240         
                 |         |         |         |         |         |         
d1nkva_ MVLADQEGWDRYEAAKWLTMRRWLEANPDDDFAAEVRAELNIAPKRYVTYARECFGWGVFA----liar
d5bp7b1 MVLADQDGWDRYEAAKWLTMRRWLEANPDDELAKEVRAQLTSEPGRYASYTREYLGWGVFA----lmpr
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: 0041444 (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   Frankia alni ACN14a
NoYes   Streptosporangium roseum DSM 43021
NoYes   Streptomyces coelicolor A3(2)
NoYes   Streptomyces sp. PAMC26508
NoYes   Streptomyces flavogriseus ATCC 33331
NoYes   Streptomyces griseus subsp. griseus NBRC 13350
NoYes   Verrucosispora maris AB-18-032
NoYes   Micromonospora sp. L5
NoYes   Micromonospora aurantiaca ATCC 27029
NoYes   Actinoplanes sp. SE50/110
NoYes   Mycobacterium vanbaalenii PYR-1
NoYes   Chlorobium luteolum DSM 273
NoYes   Desulfurispirillum indicum S5
NoYes   Desulfobacca acetoxidans DSM 11109
NoYes   Syntrophus aciditrophicus SB
NoYes   Desulfomonile tiedjei DSM 6799
NoYes   Syntrophobacter fumaroxidans MPOB
NoYes   Desulfobulbus propionicus DSM 2032
NoYes   Desulfovibrio aespoeensis Aspo-2
NoYes   Desulfovibrio magneticus RS-1
NoYes   Desulfovibrio africanus str. Walvis Bay
NoYes   Geobacter daltonii FRC-32
NoYes   Geobacter uraniireducens Rf4
NoYes   Geobacter sulfurreducens KN400
NoYes   Geobacter metallireducens GS-15
NoYes   Pelobacter propionicus DSM 2379
NoYes   Pelobacter carbinolicus DSM 2380
NoYes   Anaeromyxobacter dehalogenans 2CP-1
NoYes   Dechloromonas aromatica RCB
NoYes   Thauera sp. MZ1T
NoYes   Azoarcus sp. BH72
NoYes   Rubrivivax gelatinosus IL144
NoYes   Rhodoferax ferrireducens T118
NoYes   Thiobacillus denitrificans ATCC 25259
NoYes   Rhodospirillum photometricum DSM 122
NoYes   Rhodospirillum centenum SW
NoYes   Rhodospirillum rubrum F11
NoYes   Azospirillum brasilense Sp245
NoYes   Polymorphum gilvum SL003B-26A1
NoYes   Tolumonas auensis DSM 9187
NoYes   Allochromatium vinosum DSM 180
NoYes   Nitrosococcus halophilus Nc4
NoYes   Proteus mirabilis HI4320
NoYes   Enterobacteriaceae bacterium strain FGI 57
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
NoYes   Klebsiella oxytoca E718
NoYes   Klebsiella variicola At-22
NoYes   Klebsiella pneumoniae NTUH-K2044
NoYes   Enterobacter aerogenes KCTC 2190
NoYes   Escherichia fergusonii ATCC 35469
NoYes   Escherichia coli 'BL21-Gold(DE3)pLysS AG'
NoYes   Enterobacter asburiae LF7a
NoYes   Enterobacter cloacae subsp. dissolvens SDM
NoYes   Citrobacter rodentium ICC168
NoYes   Azotobacter vinelandii DJ
NoYes   Methanocella arvoryzae MRE50
NoYes   Methanocella conradii HZ254
NoYes   Methanocella paludicola SANAE
NoYes   Methanosphaerula palustris E1-9c
NoYes   Nocardiopsis alba ATCC BAA-2165
NoYes   Streptomyces albus J1074
NoYes   Actinoplanes friuliensis DSM 7358
NoYes   Desulfovibrio vulgaris str. 'Miyazaki F'
NoYes   Geobacter sulfurreducens PCA
NoYes   Anaeromyxobacter sp. K
NoYes   Anaeromyxobacter dehalogenans 2CP-C
NoYes   Rhodospirillum rubrum ATCC 11170
NoYes   Rhodopseudomonas palustris TIE-1
NoYes   Rhodopseudomonas palustris CGA009
NoYes   Proteus mirabilis BB2000
NoYes   Morganella morganii subsp. morganii KT
NoYes   Raoultella ornithinolytica B6
NoYes   Salmonella bongori N268-08
NoYes   Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. 08-1736
NoYes   Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992
NoYes   Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633
NoYes   Salmonella enterica subsp. enterica Serovar Cubana str. CFSAN002050
NoYes   Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
NoYes   Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
NoYes   Salmonella enterica subsp. enterica serovar Newport str. USMARC-S3124.1
NoYes   Salmonella enterica subsp. enterica serovar Newport str. SL254
NoYes   Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str. CFSAN001921
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. U288
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. 798
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
NoYes   Salmonella enterica The genome of subsp. enterica serovar Typhimurium str. DT2
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
NoYes   Salmonella enterica subsp. enterica serovar Typhimurium Definitive Type 104
NoYes   Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12
NoYes   Salmonella enterica subsp. enterica serovar Typhi str. Ty21a
NoYes   Salmonella enterica subsp. enterica serovar Typhi str. CT18
NoYes   Salmonella enterica subsp. enterica serovar Typhi str. Ty2
NoYes   Salmonella enterica serovar Bovismorbificans genomics
NoYes   Salmonella enterica subsp. enterica serovar Bareilly str. CFSAN000189
NoYes   Salmonella enterica subsp. enterica serovar Agona str. 24249
NoYes   Salmonella enterica subsp. enterica serovar Agona str. SL483
NoYes   Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601
NoYes   Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
NoYes   Salmonella enterica subsp. enterica Serovar Heidelberg str. CFSAN002069
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. B182
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. 41578
NoYes   Salmonella enterica subsp. enterica serovar Heidelberg str. SL476
NoYes   Salmonella enterica subsp. enterica serovar Thompson str. RM6836
NoYes   Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
NoYes   Klebsiella oxytoca KCTC 1686
NoYes   Klebsiella pneumoniae JM45
NoYes   Klebsiella pneumoniae CG43
NoYes   Klebsiella pneumoniae KCTC 2242
NoYes   Klebsiella pneumoniae 342
NoYes   Klebsiella pneumoniae subsp. pneumoniae 1084
NoYes   Klebsiella pneumoniae subsp. pneumoniae HS11286
NoYes   Klebsiella pneumoniae subsp. pneumoniae MGH 78578
NoYes   Enterobacter aerogenes EA1509E
NoYes   Escherichia coli JJ1886
NoYes   Escherichia coli APEC O78
NoYes   Escherichia coli NA114
NoYes   Escherichia coli UMN026
NoYes   Escherichia coli S88
NoYes   Escherichia coli DH1
NoYes   Escherichia coli DH1
NoYes   Escherichia coli BL21(DE3)
NoYes   Escherichia coli BL21(DE3)
NoYes   Escherichia coli SE15
NoYes   Escherichia coli SE11
NoYes   Escherichia coli BW2952
NoYes   Escherichia coli str. K-12 substr. MG1655
NoYes   Escherichia coli str. K-12 substr. W3110
NoYes   Escherichia coli str. K-12 substr. DH10B
NoYes   Escherichia coli B str. REL606
NoYes   Enterobacter cloacae EcWSU1
NoYes   Enterobacter cloacae subsp. cloacae ENHKU01
NoYes   Enterobacter cloacae subsp. cloacae NCTC 9394
NoYes   Enterobacter cloacae subsp. cloacae ATCC 13047
NoYes   Azotobacter vinelandii CA6
NoYes   Azotobacter vinelandii CA
NoYes   Pseudomonas stutzeri RCH2
NoYes   2_050719S (meta-genome)
NoYes   4_050719Q (meta-genome)
NoYes   Atta cephalotes fungus garden (ACEF) (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Endophytic microbiome from Rice (meta-genome)
NoYes   Fungus garden combined (combined) (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   Hot spring microbial community from Yellowstone Hot Springs, sample YNP16 from Fairy Spring Red Layer (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 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   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   The Salmonella enterica Pan-genome (meta-genome)
NoYes   ALL (only advised for small superfamilies)


Jump to [ Top of page · Alignments · Refine alignments · Add alignments from genomes ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.