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Conserved domains on  [gi|495644966|ref|WP_008369545|]
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MULTISPECIES: class I SAM-dependent methyltransferase [Coprococcus]

Protein Classification

tRNA (mnm(5)s(2)U34)-methyltransferase( domain architecture ID 10536603)

tRNA (mnm(5)s(2)U34)-methyltransferase catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34 to form mnm(5)s(2)U34

CATH:  2.20.25.110
EC:  2.1.1.61
Gene Ontology:  GO:0004808|GO:1904047|GO:0008033|GO:0032259|GO:0008757
PubMed:  12826405|12504684
SCOP:  3000118

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rRNA_methylase pfam06962
Putative rRNA methylase; This family contains a number of putative rRNA methylases. Note that ...
 47-182 2.66e-77

Putative rRNA methylase; This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins.


:

Pssm-ID: 429214  Cd Length: 137  Bit Score: 226.91  E-value: 2.66e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966   47 VYAFDVQEMAIAHTRERLEKANLSTRAKLIQDGHEKMQTYVKEEAKVIIFNFGYLPGGDHKIATRAATSLTAIESALNLL 126
Cdd:pfam06962   1 VYAFDIQEEALENTRERLEEEGLEERVELILDGHENLDEYVPGPVDAAMFNLGYLPGGDKSITTKPETTLKALEAALELL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 495644966  127 KKGGIINLCIYSGGDTGYEEKEAILNYLKTLDSKKWLVIVNSYFNRKNDPPLPVFI 182
Cdd:pfam06962  81 KPGGIISLVVYPGHPGGKEEKEAVLEYLSSLDQKKYNVLKYEFLNQPNNPPFLVLI 136
 
Name Accession Description Interval E-value
rRNA_methylase pfam06962
Putative rRNA methylase; This family contains a number of putative rRNA methylases. Note that ...
 47-182 2.66e-77

Putative rRNA methylase; This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins.


Pssm-ID: 429214  Cd Length: 137  Bit Score: 226.91  E-value: 2.66e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966   47 VYAFDVQEMAIAHTRERLEKANLSTRAKLIQDGHEKMQTYVKEEAKVIIFNFGYLPGGDHKIATRAATSLTAIESALNLL 126
Cdd:pfam06962   1 VYAFDIQEEALENTRERLEEEGLEERVELILDGHENLDEYVPGPVDAAMFNLGYLPGGDKSITTKPETTLKALEAALELL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 495644966  127 KKGGIINLCIYSGGDTGYEEKEAILNYLKTLDSKKWLVIVNSYFNRKNDPPLPVFI 182
Cdd:pfam06962  81 KPGGIISLVVYPGHPGGKEEKEAVLEYLSSLDQKKYNVLKYEFLNQPNNPPFLVLI 136
RmsH COG0275
16S rRNA C1402 N4-methylase RsmH [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 10-99 8.85e-09

16S rRNA C1402 N4-methylase RsmH [Translation, ribosomal structure and biogenesis]; 16S rRNA C1402 N4-methylase RsmH is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440044  Cd Length: 312  Bit Score: 53.52  E-value: 8.85e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966  10 HHI---LEEYIE-----EGDICIDATAGNGGDTEFLCQKVGETGNVYAFDVQEMAIAHTRERLekANLSTRAKLIQDGHE 81
Cdd:COG0275    6 YHIpvlLEEVLEalapkPGGVYVDGTLGGGGHSRAILERLGPGGRLIGIDRDPDAIAAAKERL--AEFGDRFTLVHGNFS 83

                         90       100
                 ....*....|....*....|..
gi 495644966  82 KMQTYVKEE--AKV--IIFNFG 99
Cdd:COG0275   84 ELDEVLAELgiEKVdgILLDLG 105
cbiT PRK00377
cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
 17-132 1.44e-04

cobalt-precorrin-6Y C(15)-methyltransferase; Provisional


Pssm-ID: 234740  Cd Length: 198  Bit Score: 40.94  E-value: 1.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966  17 IEEGDICIDATAGNGGDTEFLCQKVGETGNVYAFDVQEMAIAHTRERLEKANLSTRAKLIQDGHEKMQTYVKEEAKVIif 96
Cdd:PRK00377  38 LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNAEKFGVLNNIVLIKGEAPEILFTINEKFDRI-- 115

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 495644966  97 nfgYLPGGDHKIAtraatslTAIESALNLLKKGGII 132
Cdd:PRK00377 116 ---FIGGGSEKLK-------EIISASWEIIKKGGRI 141
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 24-132 1.78e-04

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 39.34  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966  24 IDATAGNGGDTEFLCQKVGetGNVYAFDVQEMAIAHTRERLEKANLSTRAKLIQDGhEKMQTYVKEEAKVIIFNFGYLPG 103
Cdd:cd02440    3 LDLGCGTGALALALASGPG--ARVTGVDISPVALELARKAAAALLADNVEVLKGDA-EELPPEADESFDVIISDPPLHHL 79

                         90       100
                 ....*....|....*....|....*....
gi 495644966 104 GDHKIAtraatsltAIESALNLLKKGGII 132
Cdd:cd02440   80 VEDLAR--------FLEEARRLLKPGGVL 100
 
Name Accession Description Interval E-value
rRNA_methylase pfam06962
Putative rRNA methylase; This family contains a number of putative rRNA methylases. Note that ...
 47-182 2.66e-77

Putative rRNA methylase; This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins.


Pssm-ID: 429214  Cd Length: 137  Bit Score: 226.91  E-value: 2.66e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966   47 VYAFDVQEMAIAHTRERLEKANLSTRAKLIQDGHEKMQTYVKEEAKVIIFNFGYLPGGDHKIATRAATSLTAIESALNLL 126
Cdd:pfam06962   1 VYAFDIQEEALENTRERLEEEGLEERVELILDGHENLDEYVPGPVDAAMFNLGYLPGGDKSITTKPETTLKALEAALELL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 495644966  127 KKGGIINLCIYSGGDTGYEEKEAILNYLKTLDSKKWLVIVNSYFNRKNDPPLPVFI 182
Cdd:pfam06962  81 KPGGIISLVVYPGHPGGKEEKEAVLEYLSSLDQKKYNVLKYEFLNQPNNPPFLVLI 136
RmsH COG0275
16S rRNA C1402 N4-methylase RsmH [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 10-99 8.85e-09

16S rRNA C1402 N4-methylase RsmH [Translation, ribosomal structure and biogenesis]; 16S rRNA C1402 N4-methylase RsmH is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440044  Cd Length: 312  Bit Score: 53.52  E-value: 8.85e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966  10 HHI---LEEYIE-----EGDICIDATAGNGGDTEFLCQKVGETGNVYAFDVQEMAIAHTRERLekANLSTRAKLIQDGHE 81
Cdd:COG0275    6 YHIpvlLEEVLEalapkPGGVYVDGTLGGGGHSRAILERLGPGGRLIGIDRDPDAIAAAKERL--AEFGDRFTLVHGNFS 83

                         90       100
                 ....*....|....*....|..
gi 495644966  82 KMQTYVKEE--AKV--IIFNFG 99
Cdd:COG0275   84 ELDEVLAELgiEKVdgILLDLG 105
cbiT PRK00377
cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
 17-132 1.44e-04

cobalt-precorrin-6Y C(15)-methyltransferase; Provisional


Pssm-ID: 234740  Cd Length: 198  Bit Score: 40.94  E-value: 1.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966  17 IEEGDICIDATAGNGGDTEFLCQKVGETGNVYAFDVQEMAIAHTRERLEKANLSTRAKLIQDGHEKMQTYVKEEAKVIif 96
Cdd:PRK00377  38 LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNAEKFGVLNNIVLIKGEAPEILFTINEKFDRI-- 115

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 495644966  97 nfgYLPGGDHKIAtraatslTAIESALNLLKKGGII 132
Cdd:PRK00377 116 ---FIGGGSEKLK-------EIISASWEIIKKGGRI 141
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 17-132 1.50e-04

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 40.09  E-value: 1.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966   17 IEEGDICIDATAGNGGDTEFLCQKVGETGNVYAFDVQEMAIAHTRERLEKANLStRAKLIQDGHEKMQTYVKEEAKVIIF 96
Cdd:pfam13847   1 IDKGMRVLDLGCGTGHLSFELAEELGPNAEVVGIDISEEAIEKARENAQKLGFD-NVEFEQGDIEELPELLEDDKFDVVI 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 495644966   97 NFGYLPGGDHKIATraatsltaIESALNLLKKGGII 132
Cdd:pfam13847  80 SNCVLNHIPDPDKV--------LQEILRVLKPGGRL 107
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 28-130 1.54e-04

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 39.08  E-value: 1.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966   28 AGNGGDTEFLCQKVGetGNVYAFDVQEMAIAHTRERLEKANLstRAKLIQDGHEKMQTyvkEEAK----VIIFNFGYLPG 103
Cdd:pfam13649   6 CGTGRLTLALARRGG--ARVTGVDLSPEMLERARERAAEAGL--NVEFVQGDAEDLPF---PDGSfdlvVSSGVLHHLPD 78

                          90       100
                  ....*....|....*....|....*..
gi 495644966  104 GDHKiatraatslTAIESALNLLKKGG 130
Cdd:pfam13649  79 PDLE---------AALREIARVLKPGG 96
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 24-132 1.78e-04

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 39.34  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966  24 IDATAGNGGDTEFLCQKVGetGNVYAFDVQEMAIAHTRERLEKANLSTRAKLIQDGhEKMQTYVKEEAKVIIFNFGYLPG 103
Cdd:cd02440    3 LDLGCGTGALALALASGPG--ARVTGVDISPVALELARKAAAALLADNVEVLKGDA-EELPPEADESFDVIISDPPLHHL 79

                         90       100
                 ....*....|....*....|....*....
gi 495644966 104 GDHKIAtraatsltAIESALNLLKKGGII 132
Cdd:cd02440   80 VEDLAR--------FLEEARRLLKPGGVL 100
Methyltransf_5 pfam01795
MraW methylase family; Members of this family are probably SAM dependent methyltransferases ...
 10-99 5.98e-04

MraW methylase family; Members of this family are probably SAM dependent methyltransferases based on Swiss:P18595. This family appears to be related to pfam01596.


Pssm-ID: 396387  Cd Length: 309  Bit Score: 39.24  E-value: 5.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966   10 HHI---LEEYIE-----EGDICIDATAGNGGDTEFLCQKVGEtGNVYAFDVQEMAIAHTRERLEKanLSTRAKLIQDGHE 81
Cdd:pfam01795   3 HHIpvlLQETVDllnpkPDGVYIDCTLGGGGHSEAILEQLPE-LRLIGIDRDPQAIARAKERLKP--FEDRVTLVHGNFR 79

                          90       100
                  ....*....|....*....|..
gi 495644966   82 KMQTYVKE----EAKVIIFNFG 99
Cdd:pfam01795  80 FFKEALAElgvtKVDGILLDLG 101
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 10-155 2.11e-03

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.


Pssm-ID: 426399  Cd Length: 179  Bit Score: 37.18  E-value: 2.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966   10 HHILEEY--IEEGDICIDATAGNGGDTEFLCQKvgETGNVYAFDVQEMaiahtreRLEKANLSTRAKLIQ------DGHE 81
Cdd:pfam01728  10 LEIDEKFglLKPGKTVLDLGAAPGGWSQVALQR--GAGKVVGVDLGPM-------QLWKPRNDPGVTFIQgdirdpETLD 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 495644966   82 KMQTYVKEEAKVII----FNFGYLPGGDHkiATRAATSLTAIESALNLLKKGGIINLCIYSGgdtgyEEKEAILNYLK 155
Cdd:pfam01728  81 LLEELLGRKVDLVLsdgsPFISGNKVLDH--LRSLDLVKAALEVALELLRKGGNFVCKVFQG-----EDFSELLYLLK 151
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 29-138 2.91e-03

SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only];


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 37.20  E-value: 2.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966  29 GNGGDTEFLCQKVGETgnVYAFDVQEMAIAHTRERLEKANLStRAKLIQDGHEKMQTYVKEEAKVIIFnFGYLpggdHKI 108
Cdd:COG0500   36 GTGRNLLALAARFGGR--VIGIDLSPEAIALARARAAKAGLG-NVEFLVADLAELDPLPAESFDLVVA-FGVL----HHL 107

                         90       100       110
                 ....*....|....*....|....*....|
gi 495644966 109 ATRAATSLtaIESALNLLKKGGIINLCIYS 138
Cdd:COG0500  108 PPEEREAL--LRELARALKPGGVLLLSASD 135
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 17-146 6.01e-03

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 36.77  E-value: 6.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966  17 IEEGDICIDATAGNGGDTEFLCQKVGETGNVYAFDVQEMAIAHTRERLEKANLSTRAKLIQDGhEKMQTYVKEEAKVIIF 96
Cdd:PRK14903 235 LEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADA-ERLTEYVQDTFDRILV 313

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495644966  97 NfgyLPGGDHKIATR----------------AATSLTAIESALNLLKKGGIInlcIYSGGDTGYEE 146
Cdd:PRK14903 314 D---APCTSLGTARNhpevlrrvnkedfkklSEIQLRIVSQAWKLLEKGGIL---LYSTCTVTKEE 373
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 20-77 7.98e-03

bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE;


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 35.90  E-value: 7.98e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 495644966  20 GDICIDATAGNGGDTEFLCQKVGETGNVYAFDV-QEM-AIAhtRERLEKANLSTRAKLIQ 77
Cdd:PRK00216  52 GDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFsEGMlAVG--REKLRDLGLSGNVEFVQ 109
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 17-77 8.30e-03

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 34.97  E-value: 8.30e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495644966  17 IEEGDICIDATAGNGGDTEFLCQKVGEtgnVYAFDVQEMAIAHTRERLEKANLstRAKLIQ 77
Cdd:COG2226   20 LRPGARVLDLGCGTGRLALALAERGAR---VTGVDISPEMLELARERAAEAGL--NVEFVV 75
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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