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Conserved domains on  [gi|818550162|gb|KKS01719|]
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MAG: methylase N-4/N-6 domain protein [Candidatus Yanofskybacteria bacterium GW2011_GWA2_41_22]

Protein Classification

DNA-methyltransferase( domain architecture ID 10002921)

DNA methyltransferase catalyzes specific methylation on cytosine or adenine on both strands and protects the DNA from cleavage by endonuclease; belongs to the class I SAM-dependent methyltransferase superfamily

CATH:  2.20.25.110
SCOP:  3000118

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
27-210 1.04e-51

DNA modification methylase [Replication, recombination and repair];


:

Pssm-ID: 440623  Cd Length: 236  Bit Score: 166.64  E-value: 1.04e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  27 ALQNGYSHHN----DCMPHDEYVKWQRDCLTEMMRIIPEDGAIFYNHKWRVQGGLLQDRQDIvsDFPVRQIIIW-KRKGG 101
Cdd:COG0863   29 NLGKKYGLGRreigNELSFEEYLEFLREWLAECYRVLKPGGSLYVNIGDRYISRLIAALRDA--GFKLRNEIIWrKPNGV 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162 102 LNFNAGYFLPTYEVIYLIAKPKF----KLSTKANAHG----DVWDFTQEMNNE---HPAAFPVNLIDRIVSATDAK--IV 168
Cdd:COG0863  107 PGPSKRRFRNSHEYILWFTKGKKytfnVDAVKSIEDGrnpsDVWDIPGVTPKErkgHPTQKPVELLERLILASSNPgdIV 186

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 818550162 169 LDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARKRIKQHQ 210
Cdd:COG0863  187 LDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVARRRLEEAT 228
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
27-210 1.04e-51

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 166.64  E-value: 1.04e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  27 ALQNGYSHHN----DCMPHDEYVKWQRDCLTEMMRIIPEDGAIFYNHKWRVQGGLLQDRQDIvsDFPVRQIIIW-KRKGG 101
Cdd:COG0863   29 NLGKKYGLGRreigNELSFEEYLEFLREWLAECYRVLKPGGSLYVNIGDRYISRLIAALRDA--GFKLRNEIIWrKPNGV 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162 102 LNFNAGYFLPTYEVIYLIAKPKF----KLSTKANAHG----DVWDFTQEMNNE---HPAAFPVNLIDRIVSATDAK--IV 168
Cdd:COG0863  107 PGPSKRRFRNSHEYILWFTKGKKytfnVDAVKSIEDGrnpsDVWDIPGVTPKErkgHPTQKPVELLERLILASSNPgdIV 186

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 818550162 169 LDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARKRIKQHQ 210
Cdd:COG0863  187 LDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVARRRLEEAT 228
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 28-204 5.95e-36

DNA methylase; Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases.


Pssm-ID: 396230 [Multi-domain]  Cd Length: 221  Bit Score: 125.98  E-value: 5.95e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162   28 LQNGYSHHNDCMPHDEYVKWQRDCLTEMMRIIPEDGAIFYNHKWRVQGGLLQDRQDIVSDFPVRQIIIWKRKGGL-NFNA 106
Cdd:pfam01555  12 LGKDYGQWDDKDSIEEYLEWLEEWLKEVRRVLKPGGSIFINIGDSNIKSLKALALEILGIFKLLNDIIWRKPNGMpNSNG 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  107 GYFLPTYEVIYLIAKPKFKLSTKANA----------------------HGDVWDFTQEMNNE--------HPAAFPVNLI 156
Cdd:pfam01555  92 ERFTPAHEYILWFSKTKKYKTFNYDAikvpydekdklkkrgsepngkpIGDVWDFSRVQPSEkesggngkHPTQKPEALL 171

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 818550162  157 DRIV--SATDAKIVLDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARK 204
Cdd:pfam01555 172 ERLIlaSTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVEIAKE 221
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
37-215 2.63e-13

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 67.05  E-value: 2.63e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  37 DCMPHDEYVKWQRDCLTEMMRIIPEDGAIFynhkwrvqggLLQDRQDI-VSDFPVRQI------IIWKRKGGLNFNAGYF 109
Cdd:PRK11524  48 EAWKEDLFIDWLYEWIDECHRVLKKQGTMY----------IMNSTENMpFIDLYCRKLftiksrIVWSYDSSGVQAKKYF 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162 110 LPTYEVIYLIAKPK---------FKLSTKANAH--------------------GDVWDFTQ------EMNNeHPAAFPVN 154
Cdd:PRK11524 118 GSMYEPILMMVKDAknytfngdaILVEAKTGAKralidyrknppqpyntqkvpGNVWDFPRvrylmdEYEN-HPTQKPEA 196

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818550162 155 LIDRIV--SATDAKIVLDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARKRIK--QHQAQVKL 215
Cdd:PRK11524 197 LLKRIIlaSSNPGDIVLDPFAGSFTTGAVAKASGRKFIGIEINSEYIKMGLRRLDvaSHYSAEEL 261
XPF_nuclease_Mms4 cd20085
XPF-like nuclease domain of Saccharomyces cerevisiae crossover junction endonuclease Mms4 and ...
 50-131 6.23e-03

XPF-like nuclease domain of Saccharomyces cerevisiae crossover junction endonuclease Mms4 and similar proteins; Budding yeast Mms4, also known as Eme1 in other organisms, is a putative transcriptional (co)activator that protects Saccharomyces cerevisiae cells from endogenous and environmental DNA damage. It interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, D-loops, replication forks with regressed leading strands and nicked Holliday junctions. The nuclease domain of Mms4 lacks the catalytic motif.


Pssm-ID: 410860  Cd Length: 220  Bit Score: 36.41  E-value: 6.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  50 DCLTEMMRIIPEDgaiFYNHKWRVQ-GGLLQDR--QDIVSDFPVRQIIIWKRKggL----NFNAGYFLPTYEVI------ 116
Cdd:cd20085   13 ESTPEMIVDIPSS---LLSSSLGSQlEELLKPLgvEHSTWDSPVPNIIRWRRK--VtaeyDDELDHWEPIPERIeeekhv 87

                         90
                 ....*....|....*..
gi 818550162 117 --YLIAKPKFKLSTKAN 131
Cdd:cd20085   88 llYLTAKEFVELALGGN 104
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
27-210 1.04e-51

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 166.64  E-value: 1.04e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  27 ALQNGYSHHN----DCMPHDEYVKWQRDCLTEMMRIIPEDGAIFYNHKWRVQGGLLQDRQDIvsDFPVRQIIIW-KRKGG 101
Cdd:COG0863   29 NLGKKYGLGRreigNELSFEEYLEFLREWLAECYRVLKPGGSLYVNIGDRYISRLIAALRDA--GFKLRNEIIWrKPNGV 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162 102 LNFNAGYFLPTYEVIYLIAKPKF----KLSTKANAHG----DVWDFTQEMNNE---HPAAFPVNLIDRIVSATDAK--IV 168
Cdd:COG0863  107 PGPSKRRFRNSHEYILWFTKGKKytfnVDAVKSIEDGrnpsDVWDIPGVTPKErkgHPTQKPVELLERLILASSNPgdIV 186

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 818550162 169 LDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARKRIKQHQ 210
Cdd:COG0863  187 LDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVARRRLEEAT 228
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 28-204 5.95e-36

DNA methylase; Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases.


Pssm-ID: 396230 [Multi-domain]  Cd Length: 221  Bit Score: 125.98  E-value: 5.95e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162   28 LQNGYSHHNDCMPHDEYVKWQRDCLTEMMRIIPEDGAIFYNHKWRVQGGLLQDRQDIVSDFPVRQIIIWKRKGGL-NFNA 106
Cdd:pfam01555  12 LGKDYGQWDDKDSIEEYLEWLEEWLKEVRRVLKPGGSIFINIGDSNIKSLKALALEILGIFKLLNDIIWRKPNGMpNSNG 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  107 GYFLPTYEVIYLIAKPKFKLSTKANA----------------------HGDVWDFTQEMNNE--------HPAAFPVNLI 156
Cdd:pfam01555  92 ERFTPAHEYILWFSKTKKYKTFNYDAikvpydekdklkkrgsepngkpIGDVWDFSRVQPSEkesggngkHPTQKPEALL 171

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 818550162  157 DRIV--SATDAKIVLDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARK 204
Cdd:pfam01555 172 ERLIlaSTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVEIAKE 221
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
37-215 2.63e-13

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 67.05  E-value: 2.63e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  37 DCMPHDEYVKWQRDCLTEMMRIIPEDGAIFynhkwrvqggLLQDRQDI-VSDFPVRQI------IIWKRKGGLNFNAGYF 109
Cdd:PRK11524  48 EAWKEDLFIDWLYEWIDECHRVLKKQGTMY----------IMNSTENMpFIDLYCRKLftiksrIVWSYDSSGVQAKKYF 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162 110 LPTYEVIYLIAKPK---------FKLSTKANAH--------------------GDVWDFTQ------EMNNeHPAAFPVN 154
Cdd:PRK11524 118 GSMYEPILMMVKDAknytfngdaILVEAKTGAKralidyrknppqpyntqkvpGNVWDFPRvrylmdEYEN-HPTQKPEA 196

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818550162 155 LIDRIV--SATDAKIVLDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARKRIK--QHQAQVKL 215
Cdd:PRK11524 197 LLKRIIlaSSNPGDIVLDPFAGSFTTGAVAKASGRKFIGIEINSEYIKMGLRRLDvaSHYSAEEL 261
PRK13699 PRK13699
putative methylase; Provisional
 42-210 4.71e-11

putative methylase; Provisional


Pssm-ID: 184255  Cd Length: 227  Bit Score: 60.23  E-value: 4.71e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  42 DEYVKWQRDCLTEMMRIIPEDGAIFYNHKWrvqggllqDRQDivsdfpvRQIIIWKRKG-----GLNFN------AGYFL 110
Cdd:PRK13699  45 DKTDEWLQPACNEMYRVLKKDALMVSFYGW--------NRVD-------RFMAAWKNAGfsvvgHLVFTknytskAAYVG 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162 111 PTYEVIYLIAKPKFKLStkANAHGDVWDFTQEMNNEHPAAFPV-NLIDRIVSATD-AKIVLDPFMGSGTTAISALNFKRD 188
Cdd:PRK13699 110 YRHECAYILAKGRPALP--QNPLPDVLGWKYSGNRHHPTEKPVtSLQPLIESFTHpNAIVLDPFAGSGSTCVAALQSGRR 187

                        170       180
                 ....*....|....*....|..
gi 818550162 189 YIGIDISPEYCEMARKRIKQHQ 210
Cdd:PRK13699 188 YIGIELLEQYHRAGQQRLAAVQ 209
Mod COG2189
Adenine specific DNA methylase Mod [Replication, recombination and repair];
134-207 2.65e-09

Adenine specific DNA methylase Mod [Replication, recombination and repair];


Pssm-ID: 441792 [Multi-domain]  Cd Length: 491  Bit Score: 56.32  E-value: 2.65e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162 134 GDVWD---FTQEMNNEHPAAF---------PVNLIDRIVSATDAK--IVLDPFMGSGTTAISAL------NFKRDYIGID 193
Cdd:COG2189  276 TTIWDdigTNQNGTKELKELFggkvfdtpkPEKLLKRIIEIATNPgdLVLDFFAGSGTTAHAVMklnaedGGNRRFILVQ 355

                         90
                 ....*....|....*
gi 818550162 194 IsPEYC-EMARKRIK 207
Cdd:COG2189  356 L-GEYAdTVTKERLR 369
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 147-207 8.41e-09

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: 53.03  E-value: 8.41e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818550162 147 HPAAFP-------VNLidriVSATDAKIVLDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARKRIK 207
Cdd:COG1041    6 YPGSLDprlaralVNL----AGAKEGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPKMVEGARENLE 69
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 168-215 8.19e-05

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 40.24  E-value: 8.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 818550162  168 VLDpfMGSGT---TAISALNFKRDYIGIDISPEYCEMARKRIKQHQAQVKL 215
Cdd:pfam13649   1 VLD--LGCGTgrlTLALARRGGARVTGVDLSPEMLERARERAAEAGLNVEF 49
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 155-215 9.90e-04

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: 38.05  E-value: 9.90e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818550162 155 LIDRIVSATDAKiVLDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARKRIKQHQAQVKL 215
Cdd:COG2226   14 LLAALGLRPGAR-VLDLGCGTGRLALALAERGARVTGVDISPEMLELARERAAEAGLNVEF 73
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 154-215 1.08e-03

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


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 38.74  E-value: 1.08e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818550162 154 NLIDRIVSATDAKIVLDpfMGSGT---TAISALNFKRDYIGIDISPEYCEMARKRI-KQHQAQVKL 215
Cdd:COG0500   16 ALLALLERLPKGGRVLD--LGCGTgrnLLALAARFGGRVIGIDLSPEAIALARARAaKAGLGNVEF 79
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 143-213 4.40e-03

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: 36.15  E-value: 4.40e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818550162 143 MNNEHPAAFPVNLIDRIVS--ATDAKIVLDPFMGSGTTAISALNFKRDYIGIDISPEYCEMARKRIKQHQAQV 213
Cdd:COG2227    1 MSDPDARDFWDRRLAALLArlLPAGGRVLDVGCGTGRLALALARRGADVTGVDISPEALEIARERAAELNVDF 73
XPF_nuclease_Mms4 cd20085
XPF-like nuclease domain of Saccharomyces cerevisiae crossover junction endonuclease Mms4 and ...
 50-131 6.23e-03

XPF-like nuclease domain of Saccharomyces cerevisiae crossover junction endonuclease Mms4 and similar proteins; Budding yeast Mms4, also known as Eme1 in other organisms, is a putative transcriptional (co)activator that protects Saccharomyces cerevisiae cells from endogenous and environmental DNA damage. It interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, D-loops, replication forks with regressed leading strands and nicked Holliday junctions. The nuclease domain of Mms4 lacks the catalytic motif.


Pssm-ID: 410860  Cd Length: 220  Bit Score: 36.41  E-value: 6.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818550162  50 DCLTEMMRIIPEDgaiFYNHKWRVQ-GGLLQDR--QDIVSDFPVRQIIIWKRKggL----NFNAGYFLPTYEVI------ 116
Cdd:cd20085   13 ESTPEMIVDIPSS---LLSSSLGSQlEELLKPLgvEHSTWDSPVPNIIRWRRK--VtaeyDDELDHWEPIPERIeeekhv 87

                         90
                 ....*....|....*..
gi 818550162 117 --YLIAKPKFKLSTKAN 131
Cdd:cd20085   88 llYLTAKEFVELALGGN 104
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 163-209 9.98e-03

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 35.47  E-value: 9.98e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 818550162  163 TDAKIVLDPFMGSGTTAISA---LNFKRDYIGIDISPEYCEMARKRIKQH 209
Cdd:pfam13847   2 DKGMRVLDLGCGTGHLSFELaeeLGPNAEVVGIDISEEAIEKARENAQKL 51
 
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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