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Conserved domains on  [gi|30684984|ref|NP_196966|]
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domains rearranged methyltransferase 2 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Dcm super family cl43082
DNA-cytosine methylase [Replication, recombination and repair];
502-622 2.39e-12

DNA-cytosine methylase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0270:

Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 67.53  E-value: 2.39e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684984 502 INVLSLFTGIGGGEVALHrlQIKMKLVVSVEISkvnrnilKDFWE--QTNQTGELIEFSDIQHLTNDTIEglmekyGGFD 579
Cdd:COG0270   4 LTVIDLFAGAGGLSLGFE--KAGFEVVFAVEID-------PDACEtyRANFPEAKVIEGDIRDIDPEELI------PDVD 68

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 30684984 580 LVIGGSPCNN--LAGGNRvsrvGLEGDQSSLFFEYCRILEVVRAR 622
Cdd:COG0270  69 LLIGGPPCQPfsVAGKRK----GLEDPRGTLFFEFIRIVEELRPK 109
UBA_atDRM2_like cd14330
UBA domain found in Arabidopsis thaliana DNA (cytosine-5)-methyltransferase DRM2 (atDRM2) and ...
 195-233 1.15e-11

UBA domain found in Arabidopsis thaliana DNA (cytosine-5)-methyltransferase DRM2 (atDRM2) and similar proteins; atDRM2, also called protein domains rearranged methylase 2, is a homolog of the mammalian de novo methyltransferase DNMT3. It is the major de novo methyltransferase targeted to DNA by small interfering RNAs (siRNAs) in the RNA-directed DNA methylation (RdDM) pathway in Arabidopsis thaliana. atDRM2 is a part of the RdDM effector complex and plays a catalytic role in RdDM. It contains an N-terminal UBA domains and a C-terminal methyltransferase domain, both of which are required for normal RdDM.


:

Pssm-ID: 270515  Cd Length: 37  Bit Score: 59.38  E-value: 1.15e-11
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 30684984 195 GSKIRSLVKMGFSELEASLAVERCGEnvDIAELTDFLCA 233
Cdd:cd14330   1 EEKIKTLVSMGFSESDARRALERCGY--DVAAAADFLFS 37
 
Name Accession Description Interval E-value
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
502-622 2.39e-12

DNA-cytosine methylase [Replication, recombination and repair];


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 67.53  E-value: 2.39e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684984 502 INVLSLFTGIGGGEVALHrlQIKMKLVVSVEISkvnrnilKDFWE--QTNQTGELIEFSDIQHLTNDTIEglmekyGGFD 579
Cdd:COG0270   4 LTVIDLFAGAGGLSLGFE--KAGFEVVFAVEID-------PDACEtyRANFPEAKVIEGDIRDIDPEELI------PDVD 68

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 30684984 580 LVIGGSPCNN--LAGGNRvsrvGLEGDQSSLFFEYCRILEVVRAR 622
Cdd:COG0270  69 LLIGGPPCQPfsVAGKRK----GLEDPRGTLFFEFIRIVEELRPK 109
UBA_atDRM2_like cd14330
UBA domain found in Arabidopsis thaliana DNA (cytosine-5)-methyltransferase DRM2 (atDRM2) and ...
 195-233 1.15e-11

UBA domain found in Arabidopsis thaliana DNA (cytosine-5)-methyltransferase DRM2 (atDRM2) and similar proteins; atDRM2, also called protein domains rearranged methylase 2, is a homolog of the mammalian de novo methyltransferase DNMT3. It is the major de novo methyltransferase targeted to DNA by small interfering RNAs (siRNAs) in the RNA-directed DNA methylation (RdDM) pathway in Arabidopsis thaliana. atDRM2 is a part of the RdDM effector complex and plays a catalytic role in RdDM. It contains an N-terminal UBA domains and a C-terminal methyltransferase domain, both of which are required for normal RdDM.


Pssm-ID: 270515  Cd Length: 37  Bit Score: 59.38  E-value: 1.15e-11
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 30684984 195 GSKIRSLVKMGFSELEASLAVERCGEnvDIAELTDFLCA 233
Cdd:cd14330   1 EEKIKTLVSMGFSESDARRALERCGY--DVAAAADFLFS 37
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 502-617 5.81e-10

Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.


Pssm-ID: 238192 [Multi-domain]  Cd Length: 275  Bit Score: 60.71  E-value: 5.81e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684984 502 INVLSLFTGIGGGEVALHrlQIKMKLVVSVEIskvNRNILKDFweQTNQTGELIEFsDIQHLTNDtieglmEKYGGFDLV 581
Cdd:cd00315   1 LRVIDLFAGIGGFRLGLE--KAGFEIVAANEI---DKSAAETY--EANFPNKLIEG-DITKIDEK------DFIPDIDLL 66

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 30684984 582 IGGSPCN--NLAGgnrvSRVGLEGDQSSLFFEYCRILE 617
Cdd:cd00315  67 TGGFPCQpfSIAG----KRKGFEDTRGTLFFEIIRILK 100
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 504-618 5.93e-10

DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273211 [Multi-domain]  Cd Length: 315  Bit Score: 60.80  E-value: 5.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684984   504 VLSLFTGIGGGEVALHrlQIKMKLVVSVEISKVNRNILKDFWeqtnqtGELIEFSDIQHLTNDTIeglmekyGGFDLVIG 583
Cdd:TIGR00675   1 FIDLFAGIGGIRLGFE--QAGFKCVFASEIDKYAQKTYEANF------GNKVPFGDITKISPSDI-------PDFDILLG 65

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 30684984   584 GSPCN--NLAGgnrvSRVGLEGDQSSLFFEYCRILEV 618
Cdd:TIGR00675  66 GFPCQpfSIAG----KRKGFEDTRGTLFFEIVRILKE 98
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
502-617 8.44e-09

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 57.32  E-value: 8.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684984   502 INVLSLFTGIGGGEVALHrlQIKMKLVVSVEISKVnrniLKDFWEQTNqtGELIEFsDIqhlTNDTIEglmeKYGGFDLV 581
Cdd:pfam00145   1 FKFIDLFAGIGGFRLGLE--QAGFECVAANEIDKS----AAKTYEANF--PKVPIG-DI---TLIDIK----DIPDIDIL 64

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 30684984   582 IGGSPCN--NLAGGNRvsrvGLEGDQSSLFFEYCRILE 617
Cdd:pfam00145  65 TGGFPCQdfSIAGKQK----GFEDTRGTLFFEIIRIIK 98
 
Name Accession Description Interval E-value
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
502-622 2.39e-12

DNA-cytosine methylase [Replication, recombination and repair];


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 67.53  E-value: 2.39e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684984 502 INVLSLFTGIGGGEVALHrlQIKMKLVVSVEISkvnrnilKDFWE--QTNQTGELIEFSDIQHLTNDTIEglmekyGGFD 579
Cdd:COG0270   4 LTVIDLFAGAGGLSLGFE--KAGFEVVFAVEID-------PDACEtyRANFPEAKVIEGDIRDIDPEELI------PDVD 68

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 30684984 580 LVIGGSPCNN--LAGGNRvsrvGLEGDQSSLFFEYCRILEVVRAR 622
Cdd:COG0270  69 LLIGGPPCQPfsVAGKRK----GLEDPRGTLFFEFIRIVEELRPK 109
UBA_atDRM2_like cd14330
UBA domain found in Arabidopsis thaliana DNA (cytosine-5)-methyltransferase DRM2 (atDRM2) and ...
 195-233 1.15e-11

UBA domain found in Arabidopsis thaliana DNA (cytosine-5)-methyltransferase DRM2 (atDRM2) and similar proteins; atDRM2, also called protein domains rearranged methylase 2, is a homolog of the mammalian de novo methyltransferase DNMT3. It is the major de novo methyltransferase targeted to DNA by small interfering RNAs (siRNAs) in the RNA-directed DNA methylation (RdDM) pathway in Arabidopsis thaliana. atDRM2 is a part of the RdDM effector complex and plays a catalytic role in RdDM. It contains an N-terminal UBA domains and a C-terminal methyltransferase domain, both of which are required for normal RdDM.


Pssm-ID: 270515  Cd Length: 37  Bit Score: 59.38  E-value: 1.15e-11
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 30684984 195 GSKIRSLVKMGFSELEASLAVERCGEnvDIAELTDFLCA 233
Cdd:cd14330   1 EEKIKTLVSMGFSESDARRALERCGY--DVAAAADFLFS 37
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 502-617 5.81e-10

Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.


Pssm-ID: 238192 [Multi-domain]  Cd Length: 275  Bit Score: 60.71  E-value: 5.81e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684984 502 INVLSLFTGIGGGEVALHrlQIKMKLVVSVEIskvNRNILKDFweQTNQTGELIEFsDIQHLTNDtieglmEKYGGFDLV 581
Cdd:cd00315   1 LRVIDLFAGIGGFRLGLE--KAGFEIVAANEI---DKSAAETY--EANFPNKLIEG-DITKIDEK------DFIPDIDLL 66

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 30684984 582 IGGSPCN--NLAGgnrvSRVGLEGDQSSLFFEYCRILE 617
Cdd:cd00315  67 TGGFPCQpfSIAG----KRKGFEDTRGTLFFEIIRILK 100
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 504-618 5.93e-10

DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273211 [Multi-domain]  Cd Length: 315  Bit Score: 60.80  E-value: 5.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684984   504 VLSLFTGIGGGEVALHrlQIKMKLVVSVEISKVNRNILKDFWeqtnqtGELIEFSDIQHLTNDTIeglmekyGGFDLVIG 583
Cdd:TIGR00675   1 FIDLFAGIGGIRLGFE--QAGFKCVFASEIDKYAQKTYEANF------GNKVPFGDITKISPSDI-------PDFDILLG 65

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 30684984   584 GSPCN--NLAGgnrvSRVGLEGDQSSLFFEYCRILEV 618
Cdd:TIGR00675  66 GFPCQpfSIAG----KRKGFEDTRGTLFFEIVRILKE 98
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
502-617 8.44e-09

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 57.32  E-value: 8.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684984   502 INVLSLFTGIGGGEVALHrlQIKMKLVVSVEISKVnrniLKDFWEQTNqtGELIEFsDIqhlTNDTIEglmeKYGGFDLV 581
Cdd:pfam00145   1 FKFIDLFAGIGGFRLGLE--QAGFECVAANEIDKS----AAKTYEANF--PKVPIG-DI---TLIDIK----DIPDIDIL 64

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 30684984   582 IGGSPCN--NLAGGNRvsrvGLEGDQSSLFFEYCRILE 617
Cdd:pfam00145  65 TGGFPCQdfSIAGKQK----GFEDTRGTLFFEIIRIIK 98
UBA1_NUB1_like cd14291
UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also called ...
 194-225 8.02e-03

UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also called negative regulator of ubiquitin-like proteins 1, renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) which may function in the regulation of cell cycle progression. NUB1 contains three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. This model corresponds to UBA1 domain.


Pssm-ID: 270477 [Multi-domain]  Cd Length: 36  Bit Score: 34.35  E-value: 8.02e-03
                        10        20        30
                ....*....|....*....|....*....|..
gi 30684984 194 NGSKIRSLVKMGFSELEASLAVERCGENVDIA 225
Cdd:cd14291   1 DEDKLQQLMEMGFSEAEARLALRACNGNVERA 32
 
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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