NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2462968942|ref|WP_276129961|]
View 

class I SAM-dependent methyltransferase [Rubrobacter indicoceani]

Protein Classification

class I SAM-dependent methyltransferase( domain architecture ID 10789277)

class I SAM-dependent methyltransferase is an enzyme that uses S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyl transfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)

CATH:  2.20.25.110
EC:  2.1.1.-
Gene Ontology:  GO:0008168|GO:1904047
PubMed:  12826405
SCOP:  3000118

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 2-93 1.06e-09

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: 53.07  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462968942   2 RADLRELPVESESVDRLLCAGVIQHIAgrtNRERVAGEFHRVLKPGGSAVVFgycwgrsirrdkEGYFPNggayrfaftR 81
Cdd:COG2226    75 VGDAEDLPFPDGSFDLVISSFVLHHLP---DPERALAEIARVLKPGGRLVVV------------DFSPPD---------L 130

                          90
                  ....*....|..
gi 2462968942  82 REFASMLKRGGF 93
Cdd:COG2226   131 AELEELLAEAGF 142
 
Name Accession Description Interval E-value
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 2-93 1.06e-09

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: 53.07  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462968942   2 RADLRELPVESESVDRLLCAGVIQHIAgrtNRERVAGEFHRVLKPGGSAVVFgycwgrsirrdkEGYFPNggayrfaftR 81
Cdd:COG2226    75 VGDAEDLPFPDGSFDLVISSFVLHHLP---DPERALAEIARVLKPGGRLVVV------------DFSPPD---------L 130

                          90
                  ....*....|..
gi 2462968942  82 REFASMLKRGGF 93
Cdd:COG2226   131 AELEELLAEAGF 142
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 2-52 1.63e-09

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 51.51  E-value: 1.63e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462968942   2 RADLRELPVESESVDRLLCAGVIQHIAgrtNRERVAGEFHRVLKPGGSAVV 52
Cdd:pfam08241  47 VGDAEDLPFPDNSFDLVLSSEVLHHVE---DPERALREIARVLKPGGILII 94
PRK08317 PRK08317
hypothetical protein; Provisional
 2-58 8.56e-08

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 49.16  E-value: 8.56e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462968942   2 RADLRELPVESESVDRLLCAGVIQHIAgrtNRERVAGEFHRVLKPGGSAVVFGYCWG 58
Cdd:PRK08317   75 RGDADGLPFPDGSFDAVRSDRVLQHLE---DPARALAEIARVLRPGGRVVVLDTDWD 128
MenG_MenH_UbiE TIGR01934
ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of ...
 1-103 3.28e-05

ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of methyltransferases involved in the biosynthesis of menaquinone and ubiqinone. Some members such as the UbiE enzyme from E. coli are believed to act in both pathways, while others may act in only the menaquinone pathway. These methyltransferases are members of the UbiE/CoQ family of methyltransferases (pfam01209) which also contains ubiquinone methyltransferases and other methyltransferases. Members of this clade include a wide distribution of bacteria and eukaryotes, but no archaea. An outgroup for this clade is provided by the phosphatidylethanolamine methyltransferase (EC 2.1.1.17) from Rhodobacter sphaeroides. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]


Pssm-ID: 273884 [Multi-domain]  Cd Length: 223  Bit Score: 41.86  E-value: 3.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462968942   1 MRADLRELPVESESVDRLLCAGVIQHIagrTNRERVAGEFHRVLKPGGSAVVF------------GYCW---------GR 59
Cdd:TIGR01934  93 IQADAEALPFEDNSFDAVTIAFGLRNV---TDIQKALREMYRVLKPGGRLVILefskpanallkkFYKFylknvlpsiGG 169

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462968942  60 SIRRDKEGY---------FPNggayrfaftRREFASMLKRGGFG-----NLTLGGAVL 103
Cdd:TIGR01934 170 LISKNAEAYtylpesiraFPS---------QEELAAMLKEAGFEevryrSLTFGVAAI 218
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 3-52 9.26e-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: 36.64  E-value: 9.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462968942   3 ADLRELP-VESESVDRLLCAGVIQHIAGrtNRERVAGEFHRVLKPGGSAVV 52
Cdd:cd02440    54 GDAEELPpEADESFDVIISDPPLHHLVE--DLARFLEEARRLLKPGGVLVL 102
 
Name Accession Description Interval E-value
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 2-93 1.06e-09

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: 53.07  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462968942   2 RADLRELPVESESVDRLLCAGVIQHIAgrtNRERVAGEFHRVLKPGGSAVVFgycwgrsirrdkEGYFPNggayrfaftR 81
Cdd:COG2226    75 VGDAEDLPFPDGSFDLVISSFVLHHLP---DPERALAEIARVLKPGGRLVVV------------DFSPPD---------L 130

                          90
                  ....*....|..
gi 2462968942  82 REFASMLKRGGF 93
Cdd:COG2226   131 AELEELLAEAGF 142
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 2-52 1.63e-09

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 51.51  E-value: 1.63e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462968942   2 RADLRELPVESESVDRLLCAGVIQHIAgrtNRERVAGEFHRVLKPGGSAVV 52
Cdd:pfam08241  47 VGDAEDLPFPDNSFDLVLSSEVLHHVE---DPERALREIARVLKPGGILII 94
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 2-48 1.92e-09

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 51.03  E-value: 1.92e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2462968942   2 RADLRELPVESESVDRLLCAGVIQHIAgRTNRERVAGEFHRVLKPGG 48
Cdd:pfam13649  51 QGDAEDLPFPDGSFDLVVSSGVLHHLP-DPDLEAALREIARVLKPGG 96
COG4627 COG4627
Predicted SAM-depedendent methyltransferase [General function prediction only];
3-108 5.87e-08

Predicted SAM-depedendent methyltransferase [General function prediction only];


Pssm-ID: 443666 [Multi-domain]  Cd Length: 161  Bit Score: 48.71  E-value: 5.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462968942   3 ADLRE-LPVESESVDRLLCAGVIQHIaGRTNRERVAGEFHRVLKPGG---------SAVVFGY-CWGRSIRRDKEGYFPN 71
Cdd:COG4627    34 GDLTDpLPFPDNSVDAIYSSHVLEHL-DYEEAPLALKECYRVLKPGGilrivvpdlEHVARLYlAEYDAALDVAELRLAG 112

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2462968942  72 GGAYRFAFTRREFASMLKRGGFGNLTLGGAVLLPRLG 108
Cdd:COG4627   113 PIDPLGIILGERLAGLAARHSVLFRTGFTRLALTARR 149
PRK08317 PRK08317
hypothetical protein; Provisional
 2-58 8.56e-08

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 49.16  E-value: 8.56e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462968942   2 RADLRELPVESESVDRLLCAGVIQHIAgrtNRERVAGEFHRVLKPGGSAVVFGYCWG 58
Cdd:PRK08317   75 RGDADGLPFPDGSFDAVRSDRVLQHLE---DPARALAEIARVLRPGGRVVVLDTDWD 128
arsM PRK11873
arsenite methyltransferase;
4-98 1.82e-07

arsenite methyltransferase;


Pssm-ID: 237007 [Multi-domain]  Cd Length: 272  Bit Score: 48.41  E-value: 1.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462968942   4 DLRELPVESESVDRLLCAGVIqHIAGrtNRERVAGEFHRVLKPGG----SAVVFGYCWGRSIRRDKEGYfpnGGAYRFAF 79
Cdd:PRK11873  136 EIEALPVADNSVDVIISNCVI-NLSP--DKERVFKEAFRVLKPGGrfaiSDVVLRGELPEEIRNDAELY---AGCVAGAL 209

                          90
                  ....*....|....*....
gi 2462968942  80 TRREFASMLKRGGFGNLTL 98
Cdd:PRK11873  210 QEEEYLAMLAEAGFVDITI 228
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 3-52 1.47e-06

2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis


Pssm-ID: 441829 [Multi-domain]  Cd Length: 126  Bit Score: 44.24  E-value: 1.47e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2462968942   3 ADLRELPVESESVDRLLCAGVIQHIagrTNRERVAGEFHRVLKPGGSAVV 52
Cdd:COG2227    76 GDLEDLPLEDGSFDLVICSEVLEHL---PDPAALLRELARLLKPGGLLLL 122
COG4976 COG4976
Predicted methyltransferase, contains TPR repeat [General function prediction only];
2-93 1.09e-05

Predicted methyltransferase, contains TPR repeat [General function prediction only];


Pssm-ID: 444001 [Multi-domain]  Cd Length: 181  Bit Score: 42.68  E-value: 1.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462968942   2 RADLRELPVESESVDRLLCAGVIQHIAgrtNRERVAGEFHRVLKPGGsAVVFgycwgrSIRR-DKEGyfpnggayRFAFT 80
Cdd:COG4976    95 VADLADLAEPDGRFDLIVAADVLTYLG---DLAAVFAGVARALKPGG-LFIF------SVEDaDGSG--------RYAHS 156

                          90
                  ....*....|...
gi 2462968942  81 RREFASMLKRGGF 93
Cdd:COG4976   157 LDYVRDLLAAAGF 169
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 2-52 1.28e-05

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 42.22  E-value: 1.28e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462968942   2 RADLRELPVEsESVDRLLCAGVIQHIaGRTNRERVAGEFHRVLKPGGSAVV 52
Cdd:COG2230   107 LADYRDLPAD-GQFDAIVSIGMFEHV-GPENYPAYFAKVARLLKPGGRLLL 155
MenG_MenH_UbiE TIGR01934
ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of ...
 1-103 3.28e-05

ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of methyltransferases involved in the biosynthesis of menaquinone and ubiqinone. Some members such as the UbiE enzyme from E. coli are believed to act in both pathways, while others may act in only the menaquinone pathway. These methyltransferases are members of the UbiE/CoQ family of methyltransferases (pfam01209) which also contains ubiquinone methyltransferases and other methyltransferases. Members of this clade include a wide distribution of bacteria and eukaryotes, but no archaea. An outgroup for this clade is provided by the phosphatidylethanolamine methyltransferase (EC 2.1.1.17) from Rhodobacter sphaeroides. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]


Pssm-ID: 273884 [Multi-domain]  Cd Length: 223  Bit Score: 41.86  E-value: 3.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462968942   1 MRADLRELPVESESVDRLLCAGVIQHIagrTNRERVAGEFHRVLKPGGSAVVF------------GYCW---------GR 59
Cdd:TIGR01934  93 IQADAEALPFEDNSFDAVTIAFGLRNV---TDIQKALREMYRVLKPGGRLVILefskpanallkkFYKFylknvlpsiGG 169

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462968942  60 SIRRDKEGY---------FPNggayrfaftRREFASMLKRGGFG-----NLTLGGAVL 103
Cdd:TIGR01934 170 LISKNAEAYtylpesiraFPS---------QEELAAMLKEAGFEevryrSLTFGVAAI 218
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 1-99 1.10e-04

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


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 40.14  E-value: 1.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462968942   1 MRADLRELPVESESVDRLLcagviqhIA-G-R--TNRERVAGEFHRVLKPGGSAVV----------FGYCW--------- 57
Cdd:PRK00216  108 VQGDAEALPFPDNSFDAVT-------IAfGlRnvPDIDKALREMYRVLKPGGRLVIlefskptnppLKKAYdfylfkvlp 180

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462968942  58 --GRSIRRDKEGY---------FPNGgayrfaftrREFASMLKRGGFG-----NLTLG 99
Cdd:PRK00216  181 liGKLISKNAEAYsylaesiraFPDQ---------EELAAMLEEAGFErvryrNLTGG 229
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 3-52 9.26e-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: 36.64  E-value: 9.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462968942   3 ADLRELP-VESESVDRLLCAGVIQHIAGrtNRERVAGEFHRVLKPGGSAVV 52
Cdd:cd02440    54 GDAEELPpEADESFDVIISDPPLHHLVE--DLARFLEEARRLLKPGGVLVL 102
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 1-52 4.23e-03

tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440663 [Multi-domain]  Cd Length: 172  Bit Score: 35.31  E-value: 4.23e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462968942   1 MRADLRELPVESESVDRLLCA---GVIQHIAGRTNR---ERVAGEFHRVLKPGGSAVV 52
Cdd:COG1041    79 IRGDARDLPLADESVDAIVTDppyGRSSKISGEELLelyEKALEEAARVLKPGGRVVI 136
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH