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Conserved domains on  [gi|2539766982|ref|WP_295976109|]
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N-6 DNA methylase [uncultured Aggregatibacter sp.]

Protein Classification

N-6 DNA methylase family protein( domain architecture ID 1006218)

N-6 DNA methylase family protein might be a component of a type I or type IC restriction system and protect the host DNA from digestion via sequence-specific methylation

CATH:  1.20.1260.30
EC:  2.1.1.-
Gene Ontology:  GO:0008168|GO:0003677
PubMed:  35205080
SCOP:  4003146

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HsdM super family cl33828
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
18-141 1.41e-06

Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];


The actual alignment was detected with superfamily member COG0286:

Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 47.10  E-value: 1.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539766982  18 EVFTPSPIVKKMLDLLDKGnysPKTTFFDPSCGNGNFLAEILRRklakVREEYdGNEPAEWliydcasSVYGVDIQLDNV 97
Cdd:COG0286    24 EFYTPREVVRLMVELLDPK---PGETVYDPACGSGGFLVEAAEY----LKEHG-GDERKKL-------SLYGQEINPTTY 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2539766982  98 EECRQRLFdicyreltgilgvnpvpfvgvLQNVFKQNIVLGDTL 141
Cdd:COG0286    89 RLAKMNLL---------------------LHGIGDPNIELGDTL 111
 
Name Accession Description Interval E-value
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
18-141 1.41e-06

Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];


Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 47.10  E-value: 1.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539766982  18 EVFTPSPIVKKMLDLLDKGnysPKTTFFDPSCGNGNFLAEILRRklakVREEYdGNEPAEWliydcasSVYGVDIQLDNV 97
Cdd:COG0286    24 EFYTPREVVRLMVELLDPK---PGETVYDPACGSGGFLVEAAEY----LKEHG-GDERKKL-------SLYGQEINPTTY 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2539766982  98 EECRQRLFdicyreltgilgvnpvpfvgvLQNVFKQNIVLGDTL 141
Cdd:COG0286    89 RLAKMNLL---------------------LHGIGDPNIELGDTL 111
MmeI_Mtase pfam20473
MmeI, DNA-methyltransferase domain; Type IIL Restriction-Modification Enzyme MmeI is a large ...
 27-61 3.35e-04

MmeI, DNA-methyltransferase domain; Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919). The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove. This domain corresponds to the DNA-methyltransferase. Structurally, it consists of a twisted beta-sheet flanked by alpha-helices on both sides.


Pssm-ID: 466622 [Multi-domain]  Cd Length: 258  Bit Score: 40.14  E-value: 3.35e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2539766982  27 KKMLDLLDKgnySPKTTFFDPSCGNGNFL-----------AEILRR 61
Cdd:pfam20473   9 RKLLNLRKR---LAKIRVFDPACGSGNFLviaykelraleAEILRR 51
 
Name Accession Description Interval E-value
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
18-141 1.41e-06

Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];


Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 47.10  E-value: 1.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539766982  18 EVFTPSPIVKKMLDLLDKGnysPKTTFFDPSCGNGNFLAEILRRklakVREEYdGNEPAEWliydcasSVYGVDIQLDNV 97
Cdd:COG0286    24 EFYTPREVVRLMVELLDPK---PGETVYDPACGSGGFLVEAAEY----LKEHG-GDERKKL-------SLYGQEINPTTY 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2539766982  98 EECRQRLFdicyreltgilgvnpvpfvgvLQNVFKQNIVLGDTL 141
Cdd:COG0286    89 RLAKMNLL---------------------LHGIGDPNIELGDTL 111
MmeI_Mtase pfam20473
MmeI, DNA-methyltransferase domain; Type IIL Restriction-Modification Enzyme MmeI is a large ...
 27-61 3.35e-04

MmeI, DNA-methyltransferase domain; Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919). The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove. This domain corresponds to the DNA-methyltransferase. Structurally, it consists of a twisted beta-sheet flanked by alpha-helices on both sides.


Pssm-ID: 466622 [Multi-domain]  Cd Length: 258  Bit Score: 40.14  E-value: 3.35e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2539766982  27 KKMLDLLDKgnySPKTTFFDPSCGNGNFL-----------AEILRR 61
Cdd:pfam20473   9 RKLLNLRKR---LAKIRVFDPACGSGNFLviaykelraleAEILRR 51
N6_Mtase pfam02384
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ...
 18-92 3.37e-04

N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.


Pssm-ID: 426749 [Multi-domain]  Cd Length: 310  Bit Score: 40.38  E-value: 3.37e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2539766982  18 EVFTPSPIVKKMLDLLDKgnySPKTTFFDPSCGNGNFLAEIlrrklAKVREEYDGNEPAEwliydcasSVYGVDI 92
Cdd:pfam02384  26 EFFTPREVSKLIVELLDP---KPGESIYDPACGSGGFLIQA-----EKFVKEHDGDTNDL--------SIYGQEK 84
YeeA COG1002
Type II restriction/modification system, endonuclease and methylase domains [Defense ...
 4-105 1.53e-03

Type II restriction/modification system, endonuclease and methylase domains [Defense mechanisms];


Pssm-ID: 440626 [Multi-domain]  Cd Length: 838  Bit Score: 38.92  E-value: 1.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539766982   4 EKIIKSKQRVK--AFaevFTPSPIVKKML-------------------DLLDKGNYSPK----------TTFFDPSCGNG 52
Cdd:COG1002   233 EAVLDPEERSKlgMH---YTSVPNIMKVVrplfldplraeweaagaweALLEKIEAEREllnllkrlasIRVLDPACGSG 309

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2539766982  53 NFL-----------AEILRRklakvREEYDGNEPAEW---LIYDCassVYGVDIQlDN-VEECRQRLF 105
Cdd:COG1002   310 NFLviaykelkaieGEVLIR-----LEELDGLSQFHRkstIIPNN---FYGIEIN-PFaAEIARLALW 368
 
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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