NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446947368|ref|WP_001024624|]
View 

site-specific DNA-methyltransferase [Helicobacter pylori]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
14-287 6.14e-58

DNA modification methylase [Replication, recombination and repair];


:

Pssm-ID: 440623  Cd Length: 236  Bit Score: 185.51  E-value: 6.14e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  14 MNEVPDNSVDLIITSPPYFNIKDYAKNGTQDlqhsaqhvedlGALEKYEDYLLGLLKVWLECYRALKPNGKLCINaplmp 93
Cdd:COG0863   11 LKELPDESVDLIVTDPPYNLGKKYGLGRREI-----------GNELSFEEYLEFLREWLAECYRVLKPGGSLYVN----- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  94 mlkkvLNTHYNRHIFDLHADIqhsilhdlnntlenkpKMFLLDVYIWKRANPTkrlmfgsyPYPRNFYAQNTIEFIGVFV 173
Cdd:COG0863   75 -----IGDRYISRLIAALRDA----------------GFKLRNEIIWRKPNGV--------PGPSKRRFRNSHEYILWFT 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368 174 KDGKPKQPTEEQKeqsqltQEEWVEFTKQIWEIPIPNKNDiaFGKHAALMPAELARRLIRLYSCVGDVVLDPFSGSGTTL 253
Cdd:COG0863  126 KGKKYTFNVDAVK------SIEDGRNPSDVWDIPGVTPKE--RKGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTL 197

                        250       260       270
                 ....*....|....*....|....*....|....
gi 446947368 254 REAKLLKRNFIGYELYENYKPLIEQKLGNLFDFE 287
Cdd:COG0863  198 VAAERLGRRFIGIEIDPEYVEVARRRLEEATGLE 231
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
14-287 6.14e-58

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 185.51  E-value: 6.14e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  14 MNEVPDNSVDLIITSPPYFNIKDYAKNGTQDlqhsaqhvedlGALEKYEDYLLGLLKVWLECYRALKPNGKLCINaplmp 93
Cdd:COG0863   11 LKELPDESVDLIVTDPPYNLGKKYGLGRREI-----------GNELSFEEYLEFLREWLAECYRVLKPGGSLYVN----- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  94 mlkkvLNTHYNRHIFDLHADIqhsilhdlnntlenkpKMFLLDVYIWKRANPTkrlmfgsyPYPRNFYAQNTIEFIGVFV 173
Cdd:COG0863   75 -----IGDRYISRLIAALRDA----------------GFKLRNEIIWRKPNGV--------PGPSKRRFRNSHEYILWFT 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368 174 KDGKPKQPTEEQKeqsqltQEEWVEFTKQIWEIPIPNKNDiaFGKHAALMPAELARRLIRLYSCVGDVVLDPFSGSGTTL 253
Cdd:COG0863  126 KGKKYTFNVDAVK------SIEDGRNPSDVWDIPGVTPKE--RKGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTL 197

                        250       260       270
                 ....*....|....*....|....*....|....
gi 446947368 254 REAKLLKRNFIGYELYENYKPLIEQKLGNLFDFE 287
Cdd:COG0863  198 VAAERLGRRFIGIEIDPEYVEVARRRLEEATGLE 231
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 22-278 2.14e-55

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: 178.36  E-value: 2.14e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368   22 VDLIITSPPYFNIKDYakngtqdlqhsaqhvEDLGALEKYEDYLLGLLKVWLECYRALKPNGKLCINAPlmpmlkkvlnT 101
Cdd:pfam01555   1 VDLIVTDPPYNLGKDY---------------GQWDDKDSIEEYLEWLEEWLKEVRRVLKPGGSIFINIG----------D 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  102 HYNRHIFDLHADIQHSilhdlnntlenkpkMFLLDVYIWKRANPtkrlmfgsYPYPRNFYAQNTIEFIGVFVKDGKP--- 178
Cdd:pfam01555  56 SNIKSLKALALEILGI--------------FKLLNDIIWRKPNG--------MPNSNGERFTPAHEYILWFSKTKKYktf 113

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  179 -----KQPTEEQKEQSQLTQEEWVEFTKQIWEIPI---PNKNDIAFGKHAALMPAELARRLIRLYSCVGDVVLDPFSGSG 250
Cdd:pfam01555 114 nydaiKVPYDEKDKLKKRGSEPNGKPIGDVWDFSRvqpSEKESGGNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSG 193

                         250       260
                  ....*....|....*....|....*...
gi 446947368  251 TTLREAKLLKRNFIGYELYENYKPLIEQ 278
Cdd:pfam01555 194 TTGAAAKELGRNFIGIEIEEEYVEIAKE 221
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
2-272 5.18e-15

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 73.22  E-value: 5.18e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368   2 NINKVFYH--SSTNMNEVPDNSVDLIITSPPYfNI-KDYAkngtqdlqhsaqhvedlGALEKY--EDYLLGLLKVWLECY 76
Cdd:PRK11524   6 NEAKTIIHgdALTELKKIPSESVDLIFADPPY-NIgKNFD-----------------GLIEAWkeDLFIDWLYEWIDECH 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  77 RALKPNGKLcinaplmpmlkKVLNTHYNRHIFDLHADIQHSILHDLnntlenkpkmflldVYIWKRANPTKRLMFGSYPY 156
Cdd:PRK11524  68 RVLKKQGTM-----------YIMNSTENMPFIDLYCRKLFTIKSRI--------------VWSYDSSGVQAKKYFGSMYE 122

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368 157 P-------RNFYAQNTiEFIGVFVKDGKPKQPTEEQKEQSQLTQEEWVefTKQIWEIPIPNKNDIAFGKHAALMPAELAR 229
Cdd:PRK11524 123 PilmmvkdAKNYTFNG-DAILVEAKTGAKRALIDYRKNPPQPYNTQKV--PGNVWDFPRVRYLMDEYENHPTQKPEALLK 199

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 446947368 230 RLIRLYSCVGDVVLDPFSGSGTTLREAKLLKRNFIGYELYENY 272
Cdd:PRK11524 200 RIILASSNPGDIVLDPFAGSFTTGAVAKASGRKFIGIEINSEY 242
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
14-287 6.14e-58

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 185.51  E-value: 6.14e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  14 MNEVPDNSVDLIITSPPYFNIKDYAKNGTQDlqhsaqhvedlGALEKYEDYLLGLLKVWLECYRALKPNGKLCINaplmp 93
Cdd:COG0863   11 LKELPDESVDLIVTDPPYNLGKKYGLGRREI-----------GNELSFEEYLEFLREWLAECYRVLKPGGSLYVN----- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  94 mlkkvLNTHYNRHIFDLHADIqhsilhdlnntlenkpKMFLLDVYIWKRANPTkrlmfgsyPYPRNFYAQNTIEFIGVFV 173
Cdd:COG0863   75 -----IGDRYISRLIAALRDA----------------GFKLRNEIIWRKPNGV--------PGPSKRRFRNSHEYILWFT 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368 174 KDGKPKQPTEEQKeqsqltQEEWVEFTKQIWEIPIPNKNDiaFGKHAALMPAELARRLIRLYSCVGDVVLDPFSGSGTTL 253
Cdd:COG0863  126 KGKKYTFNVDAVK------SIEDGRNPSDVWDIPGVTPKE--RKGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTL 197

                        250       260       270
                 ....*....|....*....|....*....|....
gi 446947368 254 REAKLLKRNFIGYELYENYKPLIEQKLGNLFDFE 287
Cdd:COG0863  198 VAAERLGRRFIGIEIDPEYVEVARRRLEEATGLE 231
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 22-278 2.14e-55

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: 178.36  E-value: 2.14e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368   22 VDLIITSPPYFNIKDYakngtqdlqhsaqhvEDLGALEKYEDYLLGLLKVWLECYRALKPNGKLCINAPlmpmlkkvlnT 101
Cdd:pfam01555   1 VDLIVTDPPYNLGKDY---------------GQWDDKDSIEEYLEWLEEWLKEVRRVLKPGGSIFINIG----------D 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  102 HYNRHIFDLHADIQHSilhdlnntlenkpkMFLLDVYIWKRANPtkrlmfgsYPYPRNFYAQNTIEFIGVFVKDGKP--- 178
Cdd:pfam01555  56 SNIKSLKALALEILGI--------------FKLLNDIIWRKPNG--------MPNSNGERFTPAHEYILWFSKTKKYktf 113

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  179 -----KQPTEEQKEQSQLTQEEWVEFTKQIWEIPI---PNKNDIAFGKHAALMPAELARRLIRLYSCVGDVVLDPFSGSG 250
Cdd:pfam01555 114 nydaiKVPYDEKDKLKKRGSEPNGKPIGDVWDFSRvqpSEKESGGNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSG 193

                         250       260
                  ....*....|....*....|....*...
gi 446947368  251 TTLREAKLLKRNFIGYELYENYKPLIEQ 278
Cdd:pfam01555 194 TTGAAAKELGRNFIGIEIEEEYVEIAKE 221
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
2-272 5.18e-15

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 73.22  E-value: 5.18e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368   2 NINKVFYH--SSTNMNEVPDNSVDLIITSPPYfNI-KDYAkngtqdlqhsaqhvedlGALEKY--EDYLLGLLKVWLECY 76
Cdd:PRK11524   6 NEAKTIIHgdALTELKKIPSESVDLIFADPPY-NIgKNFD-----------------GLIEAWkeDLFIDWLYEWIDECH 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  77 RALKPNGKLcinaplmpmlkKVLNTHYNRHIFDLHADIQHSILHDLnntlenkpkmflldVYIWKRANPTKRLMFGSYPY 156
Cdd:PRK11524  68 RVLKKQGTM-----------YIMNSTENMPFIDLYCRKLFTIKSRI--------------VWSYDSSGVQAKKYFGSMYE 122

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368 157 P-------RNFYAQNTiEFIGVFVKDGKPKQPTEEQKEQSQLTQEEWVefTKQIWEIPIPNKNDIAFGKHAALMPAELAR 229
Cdd:PRK11524 123 PilmmvkdAKNYTFNG-DAILVEAKTGAKRALIDYRKNPPQPYNTQKV--PGNVWDFPRVRYLMDEYENHPTQKPEALLK 199

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 446947368 230 RLIRLYSCVGDVVLDPFSGSGTTLREAKLLKRNFIGYELYENY 272
Cdd:PRK11524 200 RIILASSNPGDIVLDPFAGSFTTGAVAKASGRKFIGIEINSEY 242
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 216-271 3.91e-10

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: 57.65  E-value: 3.91e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446947368 216 FGKHAALMPAELARRLIRLYSCV-GDVVLDPFSGSGTTLREAKLLKRNFIGYELYEN 271
Cdd:COG1041    3 YFFYPGSLDPRLARALVNLAGAKeGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPK 59
Mod COG2189
Adenine specific DNA methylase Mod [Replication, recombination and repair];
224-270 1.41e-06

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


Pssm-ID: 441792 [Multi-domain]  Cd Length: 491  Bit Score: 49.00  E-value: 1.41e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446947368 224 PAELARRLIRLYSCVGDVVLDPFSGSGTT------LREAKLLKRNFIGYELYE 270
Cdd:COG2189  306 PEKLLKRIIEIATNPGDLVLDFFAGSGTTahavmkLNAEDGGNRRFILVQLGE 358
PRK13699 PRK13699
putative methylase; Provisional
 219-280 6.83e-06

putative methylase; Provisional


Pssm-ID: 184255  Cd Length: 227  Bit Score: 45.98  E-value: 6.83e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446947368 219 HAALMPAELARRLIRLYSCVGDVVLDPFSGSGTTLREAKLLKRNFIGYELYENYKPLIEQKL 280
Cdd:PRK13699 144 HPTEKPVTSLQPLIESFTHPNAIVLDPFAGSGSTCVAALQSGRRYIGIELLEQYHRAGQQRL 205
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 16-87 3.17e-04

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 41.28  E-value: 3.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446947368  16 EVPDNSVDLIITSPPYFNIKDYAKNgtQDLQHSAQHVEDLGALEKyedyllgllkvWLE-CYRALKPNGKLCI 87
Cdd:COG4123  103 ELPPGSFDLVVSNPPYFKAGSGRKS--PDEARAIARHEDALTLED-----------LIRaAARLLKPGGRFAL 162
UPF0020 pfam01170
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated ...
 216-262 8.85e-04

Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains.


Pssm-ID: 395932 [Multi-domain]  Cd Length: 184  Bit Score: 39.26  E-value: 8.85e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446947368  216 FGKHAALMPAeLARRLIRLYSC-VGDVVLDPFSGSGTTLREAKLLKRN 262
Cdd:pfam01170   6 FNGPAPLKET-LAAAMVNLAGWkPGDPLLDPMCGSGTILIEAALMGAN 52
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 18-87 1.48e-03

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


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 37.26  E-value: 1.48e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368   18 PDNSVDLIItsppyfnikdyakngtqdLQHSAQHVEDLgalekyedyllglLKVWLECYRALKPNGKLCI 87
Cdd:pfam08241  56 PDNSFDLVL------------------SSEVLHHVEDP-------------ERALREIARVLKPGGILII 94
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 18-99 9.41e-03

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: 35.74  E-value: 9.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446947368  18 PDNSVDLIITSppyfnikdyakngtqdlqHSAQHVEDLgalekyedyllglLKVWLECYRALKPNGKLCI---NAPLMPM 94
Cdd:COG2226   84 PDGSFDLVISS------------------FVLHHLPDP-------------ERALAEIARVLKPGGRLVVvdfSPPDLAE 132


                 ....*
gi 446947368  95 LKKVL 99
Cdd:COG2226  133 LEELL 137
 
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