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Conserved domains on  [gi|518505114|ref|WP_019675321|]
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SAM-dependent methyltransferase [Arsukibacterium perlucidum]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
OphMA_like cd19916
tetrapyrrole methylase family protein similar to Omphalotus olearius omphalotin ...
 4-240 1.04e-124

tetrapyrrole methylase family protein similar to Omphalotus olearius omphalotin methyltransferase (OphMA) and Dendrothele bispora dbOphMA; OphMA, is the precursor protein of the fungal cyclic peptide Omphalotin A. Omphalotin A is a potent nematicide, having 9 out of 12 of its residues methylated at the backbone amide. Omphalotin A derives from the C-terminus of OphMA (also known as OphA). OphMA catalyzes the automethylation of its own C-terminus using S-adenosyl methionine (SAM); this C terminus is subsequently released and macrocyclized by the protease OphP to give Omphalotin A.


:

Pssm-ID: 381179  Cd Length: 237  Bit Score: 354.09  E-value: 1.04e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114   4 GSLICVGTGIMLGAHLDPLSRNYIEQADVVFMLMADAMTEQWLLQMHPDVRSLQPYYHQAPSRQHSYQLMVEAMLAEVTA 83
Cdd:cd19916    1 GSLVVVGTGIKGIGHLTLEAESAIEQADKVFYLVADPLTEEWLRELNPNAEDLYDLYGEGKPRLDTYREMAERILEAVRA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114  84 GKKVVGAFYGHPAVFALVPHEAVRQARELGYYSKMLPGISAEDCLYADLGIDPGRYGCQLYECSQFMFYQRTIDTAAYLV 163
Cdd:cd19916   81 GKPVCAAFYGHPGVFVSPSHLAIRIARREGYRARMLPGISAEDCLFADLGIDPGRPGCQSYEATDFLLRRRPLDPSAHLI 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518505114 164 LWQLGIAGDRSLARFSTPSQYRQLLTDYLCQFYPPGHIITLYEAASLPTEQARIDSLPLNALASAAVSGKTTLVIPP 240
Cdd:cd19916  161 LWQVGVVGDLTFTRFGYDNRGLELLVEYLLKFYPPDHEVILYEAATYPGCEPRIERIPLSDLAEAELTGISTLYIPP 237
 
Name Accession Description Interval E-value
OphMA_like cd19916
tetrapyrrole methylase family protein similar to Omphalotus olearius omphalotin ...
 4-240 1.04e-124

tetrapyrrole methylase family protein similar to Omphalotus olearius omphalotin methyltransferase (OphMA) and Dendrothele bispora dbOphMA; OphMA, is the precursor protein of the fungal cyclic peptide Omphalotin A. Omphalotin A is a potent nematicide, having 9 out of 12 of its residues methylated at the backbone amide. Omphalotin A derives from the C-terminus of OphMA (also known as OphA). OphMA catalyzes the automethylation of its own C-terminus using S-adenosyl methionine (SAM); this C terminus is subsequently released and macrocyclized by the protease OphP to give Omphalotin A.


Pssm-ID: 381179  Cd Length: 237  Bit Score: 354.09  E-value: 1.04e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114   4 GSLICVGTGIMLGAHLDPLSRNYIEQADVVFMLMADAMTEQWLLQMHPDVRSLQPYYHQAPSRQHSYQLMVEAMLAEVTA 83
Cdd:cd19916    1 GSLVVVGTGIKGIGHLTLEAESAIEQADKVFYLVADPLTEEWLRELNPNAEDLYDLYGEGKPRLDTYREMAERILEAVRA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114  84 GKKVVGAFYGHPAVFALVPHEAVRQARELGYYSKMLPGISAEDCLYADLGIDPGRYGCQLYECSQFMFYQRTIDTAAYLV 163
Cdd:cd19916   81 GKPVCAAFYGHPGVFVSPSHLAIRIARREGYRARMLPGISAEDCLFADLGIDPGRPGCQSYEATDFLLRRRPLDPSAHLI 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518505114 164 LWQLGIAGDRSLARFSTPSQYRQLLTDYLCQFYPPGHIITLYEAASLPTEQARIDSLPLNALASAAVSGKTTLVIPP 240
Cdd:cd19916  161 LWQVGVVGDLTFTRFGYDNRGLELLVEYLLKFYPPDHEVILYEAATYPGCEPRIERIPLSDLAEAELTGISTLYIPP 237
TP_methylase pfam00590
Tetrapyrrole (Corrin/Porphyrin) Methylases; This family uses S-AdoMet in the methylation of ...
 6-220 2.10e-22

Tetrapyrrole (Corrin/Porphyrin) Methylases; This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function. This family includes the methylase Dipthine synthase.


Pssm-ID: 425769 [Multi-domain]  Cd Length: 209  Bit Score: 91.64  E-value: 2.10e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114    6 LICVGTGIMLGAHLDPLSRNYIEQADVVFMlmADAMTEQWLLQmHPDVRSLQPYYHQAPSRQHSYQLMVEAMLAEVTAGK 85
Cdd:pfam00590   2 LYLVGVGPGDPDLLTLRALRALKEADVVLG--DDSRALEILLD-LLPEDLYFPMTEDKEPLEEAYEEIAEALAAALRAGK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114   86 KVVGAFYGHPAVFALVPHEaVRQARELGYYSKMLPGISAEDCLYADLGIDPGRYGCQLyecsqFMFYQRTIDTAAYLVLW 165
Cdd:pfam00590  79 DVARLVSGDPLVYGTGSYL-VEALRAAGIDVEVVPGVSSAQAAAARLGIPLTEGGEVL-----SVLFLPGLARIELRLLE 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 518505114  166 QLGIAGDrSLARFSTPSQYRQLLTDyLCQFYPPGHIITLYEAASLPTEQARIDSL 220
Cdd:pfam00590 153 ALLANGD-TVVLLYGPRRLAELAEL-LLELYPDTTPVAVVERAGTPDEKVVRGTL 205
 
Name Accession Description Interval E-value
OphMA_like cd19916
tetrapyrrole methylase family protein similar to Omphalotus olearius omphalotin ...
 4-240 1.04e-124

tetrapyrrole methylase family protein similar to Omphalotus olearius omphalotin methyltransferase (OphMA) and Dendrothele bispora dbOphMA; OphMA, is the precursor protein of the fungal cyclic peptide Omphalotin A. Omphalotin A is a potent nematicide, having 9 out of 12 of its residues methylated at the backbone amide. Omphalotin A derives from the C-terminus of OphMA (also known as OphA). OphMA catalyzes the automethylation of its own C-terminus using S-adenosyl methionine (SAM); this C terminus is subsequently released and macrocyclized by the protease OphP to give Omphalotin A.


Pssm-ID: 381179  Cd Length: 237  Bit Score: 354.09  E-value: 1.04e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114   4 GSLICVGTGIMLGAHLDPLSRNYIEQADVVFMLMADAMTEQWLLQMHPDVRSLQPYYHQAPSRQHSYQLMVEAMLAEVTA 83
Cdd:cd19916    1 GSLVVVGTGIKGIGHLTLEAESAIEQADKVFYLVADPLTEEWLRELNPNAEDLYDLYGEGKPRLDTYREMAERILEAVRA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114  84 GKKVVGAFYGHPAVFALVPHEAVRQARELGYYSKMLPGISAEDCLYADLGIDPGRYGCQLYECSQFMFYQRTIDTAAYLV 163
Cdd:cd19916   81 GKPVCAAFYGHPGVFVSPSHLAIRIARREGYRARMLPGISAEDCLFADLGIDPGRPGCQSYEATDFLLRRRPLDPSAHLI 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518505114 164 LWQLGIAGDRSLARFSTPSQYRQLLTDYLCQFYPPGHIITLYEAASLPTEQARIDSLPLNALASAAVSGKTTLVIPP 240
Cdd:cd19916  161 LWQVGVVGDLTFTRFGYDNRGLELLVEYLLKFYPPDHEVILYEAATYPGCEPRIERIPLSDLAEAELTGISTLYIPP 237
TP_methylase pfam00590
Tetrapyrrole (Corrin/Porphyrin) Methylases; This family uses S-AdoMet in the methylation of ...
 6-220 2.10e-22

Tetrapyrrole (Corrin/Porphyrin) Methylases; This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function. This family includes the methylase Dipthine synthase.


Pssm-ID: 425769 [Multi-domain]  Cd Length: 209  Bit Score: 91.64  E-value: 2.10e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114    6 LICVGTGIMLGAHLDPLSRNYIEQADVVFMlmADAMTEQWLLQmHPDVRSLQPYYHQAPSRQHSYQLMVEAMLAEVTAGK 85
Cdd:pfam00590   2 LYLVGVGPGDPDLLTLRALRALKEADVVLG--DDSRALEILLD-LLPEDLYFPMTEDKEPLEEAYEEIAEALAAALRAGK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114   86 KVVGAFYGHPAVFALVPHEaVRQARELGYYSKMLPGISAEDCLYADLGIDPGRYGCQLyecsqFMFYQRTIDTAAYLVLW 165
Cdd:pfam00590  79 DVARLVSGDPLVYGTGSYL-VEALRAAGIDVEVVPGVSSAQAAAARLGIPLTEGGEVL-----SVLFLPGLARIELRLLE 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 518505114  166 QLGIAGDrSLARFSTPSQYRQLLTDyLCQFYPPGHIITLYEAASLPTEQARIDSL 220
Cdd:pfam00590 153 ALLANGD-TVVLLYGPRRLAELAEL-LLELYPDTTPVAVVERAGTPDEKVVRGTL 205
TP_methylase cd09815
S-AdoMet-dependent tetrapyrrole methylases; This superfamily uses S-AdoMet ...
 9-239 5.97e-19

S-AdoMet-dependent tetrapyrrole methylases; This superfamily uses S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. Most members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis. There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. The enzymes involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Most of the enzymes are shared by both pathways and a few enzymes are pathway-specific. Diphthine synthase and ribosomal RNA small subunit methyltransferase I (RsmI) are two superfamily members that are not involved in cobalamin biosynthesis. Diphthine synthase participates in the posttranslational modification of a specific histidine residue in elongation factor 2 (EF-2) of eukaryotes and archaea to diphthamide. RsmI catalyzes the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. Other superfamily members not involved in cobalamin biosynthesis include the N-terminal tetrapyrrole methylase domain of Bacillus subtilis YabN whose specific function is unknown, and Omphalotus olearius omphalotin methyltransferase which catalyzes the automethylation of its own C-terminus; this C terminus is subsequently released and macrocyclized to give Omphalotin A, a potent nematicide.


Pssm-ID: 381167 [Multi-domain]  Cd Length: 219  Bit Score: 82.83  E-value: 5.97e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114   9 VGTG------IMLGAHldplsrNYIEQADVVFMLMADAMTEQWLLQMHpDVRSLQPYYhqaPSRQHSYQLMVEAMLAEVT 82
Cdd:cd09815    1 VGVGpgdpdlLTLRAL------EILRAADVVVAEDKDSKLLSLVLRAI-LKDGKRIYD---LHDPNVEEEMAELLLEEAR 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114  83 AGKKVVGAFYGHPAVFalVPHEAVRQ-ARELGYYSKMLPGISAEDCLYADLGIDPGRyGCQLYECSqfmfyqrTIDTAAY 161
Cdd:cd09815   71 QGKDVAFLSPGDPGVA--GTGAELVErAEREGVEVKVIPGVSAADAAAAALGIDLGE-SFLFVTAS-------DLLENPR 140

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 518505114 162 LVLWQLGIAGDRSLARFSTPSQYRQLLTDYLCQFYPPGHIITLYEAASLPTEQARIDSL-PLNALASAAVSGKTTLVIP 239
Cdd:cd09815  141 LLVLKALAKERRHLVLFLDGHRFLKALERLLKELGEDDTPVVLVANAGSEGEVIRTGTVkELRAERTERGKPLTTILVG 219
YabN_N_like cd11723
N-terminal S-AdoMet-dependent tetrapyrrole methylase domain of Bacillus subtilis YabN and ...
 44-240 2.96e-10

N-terminal S-AdoMet-dependent tetrapyrrole methylase domain of Bacillus subtilis YabN and similar domains; This family includes the S-AdoMet (S-adenosyl-L-methionine or SAM)-dependent tetrapyrrole methylase (TP-methylase) domain of Bacillus subtilis YabN, and similar domains. YabN is a fusion of an N-terminal TP-methylase and a C-terminal MazG-type nucleotide pyrophosphohydrolase domain. MazG-like NTP-PPases have been implicated in house-cleaning functions such as degrading abnormal (d)NTPs. TP-methylases use S-AdoMet in the methylation of diverse substrates. Most TP-methylase family members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis, other members like diphthine synthase and ribosomal RNA small subunit methyltransferase I (RsmI) act on other substrates. The specific function of YabN's TP-methylase domain is not known.


Pssm-ID: 381177  Cd Length: 218  Bit Score: 58.65  E-value: 2.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114  44 QWLLQMHPDVRSLQPYYHQAPSRQHSYQLMVEAMLAEVtAGKKVVGAFYGHPAVF-ALVphEAVRQARELGYYSKMLPGI 122
Cdd:cd11723   39 EELKEEGIEFESFDDLYEEAEDFEEVYEAIAERLLEAA-EHGDVVYAVPGHPLVAeRTV--QLLLERAEEGIEVEIIPGV 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518505114 123 SAEDCLYADLGIDPGRyGCQLYECSQFMFYQRTIDTAayLVLWQLG---IAGDRSLArfstpsqyrqlltdyLCQFYPPG 199
Cdd:cd11723  116 SFLDAALAALGIDPIE-GLQILDALDLDAEDLDPRLP--LLITQVYnrlVASDVKLT---------------LMEVYPDE 177

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 518505114 200 HIITLYEAASLPTEqaRIDSLPLNALA-SAAVSGKTTLVIPP 240
Cdd:cd11723  178 HEVTVVRAAGLGDE--KVEEVPLYELDrQEDIDHLTSLYVPP 217
 
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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