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Conserved domains on  [gi|490688175|ref|WP_004552628|]
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N-6 DNA methylase [Burkholderia pseudomallei]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
292-545 2.47e-51

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


:

Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 180.00  E-value: 2.47e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 292 DSKGAAFEYFVR--ATLKGKKLGQYFTPRPLVRLMSAIVGQEKIVnallsgaaapKVLDPACGTGGFLVYlmgdslrvan 369
Cdd:COG0286    1 DVLGDAYEYLLRkfAEESGKKAGEFYTPREVVRLMVELLDPKPGE----------TVYDPACGSGGFLVE---------- 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 370 qklADRAInaatHRELVRKIRQQVFFGSDANEGVACAAKMNMIVAGDGHSNIQPENSLArtakNWNIQDSDCDFILTNPP 449
Cdd:COG0286   61 ---AAEYL----KEHGGDERKKLSLYGQEINPTTYRLAKMNLLLHGIGDPNIELGDTLS----NDGDELEKFDVVLANPP 129

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 450 FGTSESGALSDKDM-GQFEV---QTTKGQLLFLQKMVLSARRGGEICTVIDEGVLNTDTAAPIRKWLLSKAKLLAVVRLP 525
Cdd:COG0286  130 FGGKWKKEELKDDLlGRFGYglpPKSNADLLFLQHILSLLKPGGRAAVVLPDGVLFRGAEKEIRKKLLENDLLEAIIGLP 209

                        250       260
                 ....*....|....*....|
gi 490688175 526 DETFRPNKINVrsSVLYLQR 545
Cdd:COG0286  210 SNLFYNTGIPT--CILFLTK 227
COG2810 super family cl43716
Predicted type IV restriction endonuclease [Defense mechanisms];
3-111 1.01e-11

Predicted type IV restriction endonuclease [Defense mechanisms];


The actual alignment was detected with superfamily member COG2810:

Pssm-ID: 442059 [Multi-domain]  Cd Length: 340  Bit Score: 67.31  E-value: 1.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175   3 KSANETETVIKRILPYLQRRGYEI--ETDLHFEtaastpERYEAGFVDILVWPNdktypkGKPAFLIEAKRIAKKLSEQD 80
Cdd:COG2810   24 RSANEAATRQEFIDPLLEALGWDIdnPEEVIPE------ERVEGGRPDYALRLN------GKRKLFVEAKKPGVNLKDKP 91

                         90       100       110
                 ....*....|....*....|....*....|.
gi 490688175  81 KKQALSYARADGydVPFVVVCNGAEIRSYNA 111
Cdd:COG2810   92 ARQARSYAWSSG--VRWAILTNGREWRVYDA 120
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 646-831 1.11e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR) and similar domains; The restriction-modification (RM) system S subunit generally consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily represents a single TRD-CR unit; in addition to type I TRD-CR units, it includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P, as well as TRD-CR-like sequence-recognition domains of the M subunit of putative type I DNA methyltransferase such as M2.CinURNWORF2828P and M.Mae7806ORF3969P.


The actual alignment was detected with superfamily member cd17246:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 189  Bit Score: 64.47  E-value: 1.11e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 646 KTIKELNTIPTaRGTSPSaDSYVDaaDGYALVikSGSNIsRYGELIVDGD-YIEKSLFDEYVEKAHtqgrnfnlVRPGDV 724
Cdd:cd17246    4 VKLGEISSDIT-DGTHPT-PKYVE--SGIPFI--TSKNI-KNGKIDFSDVkYISEEDHNEILKRSK--------LKKGDI 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 725 LVSSTGdgTLGKCCVYRpstdpitgETVPYAAIAegHVAIIRVDPDVIWPEYLCDYLRVGFGAQQIERLYTGST-GMIEL 803
Cdd:cd17246   69 LFSIIG--TIGRVAIVP--------EDLPANINQ--AVALIRPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTqKNLSL 136

                        170       180
                 ....*....|....*....|....*...
gi 490688175 804 TPaaLDEVVVNLLSgIEEQKKYSEALRK 831
Cdd:cd17246  137 GD--LKNLKIPLPP-LEEQKRIAAILDS 161
YeeA super family cl26272
Type II restriction/modification system, endonuclease and methylase domains [Defense ...
 123-450 9.07e-05

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


The actual alignment was detected with superfamily member COG1002:

Pssm-ID: 440626 [Multi-domain]  Cd Length: 838  Bit Score: 46.24  E-value: 9.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 123 LSSKIPAKSQLKSVLKDFKTDPQAVRIELPGEDGPL----DGSSALPFRPSLPLRQLNALFSRCHDAIRKNEKDENHIFD 198
Cdd:COG1002   48 EAGIIQLDSLLKTSRLSKKTGVGFKTLTRLLNVAALlaitDLNLILLLKLLEALLKALLLAEEAAAALLLLTLALNDPDT 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 199 DFSKLLFLKLLEEKADTEEGFNLPYSYTFHELAALPDAKADQVQNAIMDMIKKIRTDKSYGDVLANpiHLKVAKTFLYLV 278
Cdd:COG1002  128 DALFELLAALLAEFREDFELLFAKFLPLNSSLLFELRLAFATLLILLLRLELEITLYVNTVLKDDN--GKRRTGLLDPLF 205

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 279 RQLAAVSFTDSTTDSK-------GAAFEYfVRATLKGKKLGQYFTPRP----LVR-LMSAIVGQE----KIVNALLSGAA 342
Cdd:COG1002  206 YLFAFLDATDLSSDWTkinpdifGSMFEA-VLDPEERSKLGMHYTSVPnimkVVRpLFLDPLRAEweaaGAWEALLEKIE 284

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 343 AP-------------KVLDPACGTGGFLV--YLMgdsLRV----ANQKLADRAINAATHRELVRKIRQqvFFGSDANEgV 403
Cdd:COG1002  285 AErellnllkrlasiRVLDPACGSGNFLViaYKE---LKAiegeVLIRLEELDGLSQFHRKSTIIPNN--FYGIEINP-F 358

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490688175 404 ACA-AK---------MNMIVAGDGHS---------NIQPENSL---ARTAKNWN---IQDSDCDFILTNPPF 450
Cdd:COG1002  359 AAEiARlalwiaelqWNYRYRGQLAPflpllnddnNIECGNALrlrDGNAADWRfvcPETGGEDYIIGNPPF 430
 
Name Accession Description Interval E-value
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
292-545 2.47e-51

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


Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 180.00  E-value: 2.47e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 292 DSKGAAFEYFVR--ATLKGKKLGQYFTPRPLVRLMSAIVGQEKIVnallsgaaapKVLDPACGTGGFLVYlmgdslrvan 369
Cdd:COG0286    1 DVLGDAYEYLLRkfAEESGKKAGEFYTPREVVRLMVELLDPKPGE----------TVYDPACGSGGFLVE---------- 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 370 qklADRAInaatHRELVRKIRQQVFFGSDANEGVACAAKMNMIVAGDGHSNIQPENSLArtakNWNIQDSDCDFILTNPP 449
Cdd:COG0286   61 ---AAEYL----KEHGGDERKKLSLYGQEINPTTYRLAKMNLLLHGIGDPNIELGDTLS----NDGDELEKFDVVLANPP 129

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 450 FGTSESGALSDKDM-GQFEV---QTTKGQLLFLQKMVLSARRGGEICTVIDEGVLNTDTAAPIRKWLLSKAKLLAVVRLP 525
Cdd:COG0286  130 FGGKWKKEELKDDLlGRFGYglpPKSNADLLFLQHILSLLKPGGRAAVVLPDGVLFRGAEKEIRKKLLENDLLEAIIGLP 209

                        250       260
                 ....*....|....*....|
gi 490688175 526 DETFRPNKINVrsSVLYLQR 545
Cdd:COG0286  210 SNLFYNTGIPT--CILFLTK 227
N6_Mtase pfam02384
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ...
 292-591 5.32e-26

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: 109.33  E-value: 5.32e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175  292 DSKGAAFEYFVR--ATLKGKKLGQYFTPRPLVRLMSAIvgqekivnallsgaAAPK----VLDPACGTGGFLVylmgdsl 365
Cdd:pfam02384   3 DLFGDAYEYLLRkfAPNAGKSGGEFFTPREVSKLIVEL--------------LDPKpgesIYDPACGSGGFLI------- 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175  366 rvanqkLADRAINAATHrelvrKIRQQVFFGSDANEGVACAAKMNMIVAG--DGHSNIQPENSLartAKNWNIQDSDCDF 443
Cdd:pfam02384  62 ------QAEKFVKEHDG-----DTNDLSIYGQEKNPTTYRLARMNMILHGieYDDFHIRHGDTL---TSPKFEDDKKFDV 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175  444 ILTNPPFGTSESG--ALSD----KDMGQFeVQTTKGQLLFLQKMVLSARRGGEICTVIDEGVL---NTDTAapIRKWLLS 514
Cdd:pfam02384 128 VVANPPFSDKWDAndTLENdprfRPAYGV-APKSNADLAFLQHIIYYLAPGGRAAVVLPNGVLfrgGAEGK--IRKALVD 204

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490688175  515 KAKLLAVVRLPDETFRPNKINVrsSVLYLQRMTeeeeeiaDDIKYPVAFCDI-ETFGMDGAGDIARNFDLDTLIDSVG 591
Cdd:pfam02384 205 KDLVETVIALPPNLFYNTSIPT--CILFLTKNK-------AERKGKVLFIDAsNEFKKEGKLNILTDEHIEKIIDTFG 273
COG2810 COG2810
Predicted type IV restriction endonuclease [Defense mechanisms];
3-111 1.01e-11

Predicted type IV restriction endonuclease [Defense mechanisms];


Pssm-ID: 442059 [Multi-domain]  Cd Length: 340  Bit Score: 67.31  E-value: 1.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175   3 KSANETETVIKRILPYLQRRGYEI--ETDLHFEtaastpERYEAGFVDILVWPNdktypkGKPAFLIEAKRIAKKLSEQD 80
Cdd:COG2810   24 RSANEAATRQEFIDPLLEALGWDIdnPEEVIPE------ERVEGGRPDYALRLN------GKRKLFVEAKKPGVNLKDKP 91

                         90       100       110
                 ....*....|....*....|....*....|.
gi 490688175  81 KKQALSYARADGydVPFVVVCNGAEIRSYNA 111
Cdd:COG2810   92 ARQARSYAWSSG--VRWAILTNGREWRVYDA 120
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 646-831 1.11e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2; This model contains Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2 and similar TRD-CR's. S.SonII recognizes 5'... GTCANNNNNNRTCA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.SonII TRD1-CR1 does not belong to this subfamily.


Pssm-ID: 341135 [Multi-domain]  Cd Length: 189  Bit Score: 64.47  E-value: 1.11e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 646 KTIKELNTIPTaRGTSPSaDSYVDaaDGYALVikSGSNIsRYGELIVDGD-YIEKSLFDEYVEKAHtqgrnfnlVRPGDV 724
Cdd:cd17246    4 VKLGEISSDIT-DGTHPT-PKYVE--SGIPFI--TSKNI-KNGKIDFSDVkYISEEDHNEILKRSK--------LKKGDI 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 725 LVSSTGdgTLGKCCVYRpstdpitgETVPYAAIAegHVAIIRVDPDVIWPEYLCDYLRVGFGAQQIERLYTGST-GMIEL 803
Cdd:cd17246   69 LFSIIG--TIGRVAIVP--------EDLPANINQ--AVALIRPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTqKNLSL 136

                        170       180
                 ....*....|....*....|....*...
gi 490688175 804 TPaaLDEVVVNLLSgIEEQKKYSEALRK 831
Cdd:cd17246  137 GD--LKNLKIPLPP-LEEQKRIAAILDS 161
HSDR_N_2 pfam13588
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N ...
 45-118 2.12e-06

Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA.


Pssm-ID: 433331 [Multi-domain]  Cd Length: 110  Bit Score: 47.20  E-value: 2.12e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490688175   45 GFVDILVWPNDktypkGKPAFLIEAKRIAKKLSEQDKKQALSYARAdgYDVPFVVVCNGAEI----RSYNAKTGEPIQ 118
Cdd:pfam13588  37 KRADIVVYNKD-----GKPYILVECKAPSIKISQKVFDQLARYNSV--LGAPFLVVTNGLQHicfkVDYDKQQFEFLD 107
YeeA COG1002
Type II restriction/modification system, endonuclease and methylase domains [Defense ...
 123-450 9.07e-05

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


Pssm-ID: 440626 [Multi-domain]  Cd Length: 838  Bit Score: 46.24  E-value: 9.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 123 LSSKIPAKSQLKSVLKDFKTDPQAVRIELPGEDGPL----DGSSALPFRPSLPLRQLNALFSRCHDAIRKNEKDENHIFD 198
Cdd:COG1002   48 EAGIIQLDSLLKTSRLSKKTGVGFKTLTRLLNVAALlaitDLNLILLLKLLEALLKALLLAEEAAAALLLLTLALNDPDT 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 199 DFSKLLFLKLLEEKADTEEGFNLPYSYTFHELAALPDAKADQVQNAIMDMIKKIRTDKSYGDVLANpiHLKVAKTFLYLV 278
Cdd:COG1002  128 DALFELLAALLAEFREDFELLFAKFLPLNSSLLFELRLAFATLLILLLRLELEITLYVNTVLKDDN--GKRRTGLLDPLF 205

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 279 RQLAAVSFTDSTTDSK-------GAAFEYfVRATLKGKKLGQYFTPRP----LVR-LMSAIVGQE----KIVNALLSGAA 342
Cdd:COG1002  206 YLFAFLDATDLSSDWTkinpdifGSMFEA-VLDPEERSKLGMHYTSVPnimkVVRpLFLDPLRAEweaaGAWEALLEKIE 284

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 343 AP-------------KVLDPACGTGGFLV--YLMgdsLRV----ANQKLADRAINAATHRELVRKIRQqvFFGSDANEgV 403
Cdd:COG1002  285 AErellnllkrlasiRVLDPACGSGNFLViaYKE---LKAiegeVLIRLEELDGLSQFHRKSTIIPNN--FYGIEINP-F 358

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490688175 404 ACA-AK---------MNMIVAGDGHS---------NIQPENSL---ARTAKNWN---IQDSDCDFILTNPPF 450
Cdd:COG1002  359 AAEiARlalwiaelqWNYRYRGQLAPflpllnddnNIECGNALrlrDGNAADWRfvcPETGGEDYIIGNPPF 430
 
Name Accession Description Interval E-value
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
292-545 2.47e-51

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


Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 180.00  E-value: 2.47e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 292 DSKGAAFEYFVR--ATLKGKKLGQYFTPRPLVRLMSAIVGQEKIVnallsgaaapKVLDPACGTGGFLVYlmgdslrvan 369
Cdd:COG0286    1 DVLGDAYEYLLRkfAEESGKKAGEFYTPREVVRLMVELLDPKPGE----------TVYDPACGSGGFLVE---------- 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 370 qklADRAInaatHRELVRKIRQQVFFGSDANEGVACAAKMNMIVAGDGHSNIQPENSLArtakNWNIQDSDCDFILTNPP 449
Cdd:COG0286   61 ---AAEYL----KEHGGDERKKLSLYGQEINPTTYRLAKMNLLLHGIGDPNIELGDTLS----NDGDELEKFDVVLANPP 129

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 450 FGTSESGALSDKDM-GQFEV---QTTKGQLLFLQKMVLSARRGGEICTVIDEGVLNTDTAAPIRKWLLSKAKLLAVVRLP 525
Cdd:COG0286  130 FGGKWKKEELKDDLlGRFGYglpPKSNADLLFLQHILSLLKPGGRAAVVLPDGVLFRGAEKEIRKKLLENDLLEAIIGLP 209

                        250       260
                 ....*....|....*....|
gi 490688175 526 DETFRPNKINVrsSVLYLQR 545
Cdd:COG0286  210 SNLFYNTGIPT--CILFLTK 227
N6_Mtase pfam02384
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ...
 292-591 5.32e-26

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: 109.33  E-value: 5.32e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175  292 DSKGAAFEYFVR--ATLKGKKLGQYFTPRPLVRLMSAIvgqekivnallsgaAAPK----VLDPACGTGGFLVylmgdsl 365
Cdd:pfam02384   3 DLFGDAYEYLLRkfAPNAGKSGGEFFTPREVSKLIVEL--------------LDPKpgesIYDPACGSGGFLI------- 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175  366 rvanqkLADRAINAATHrelvrKIRQQVFFGSDANEGVACAAKMNMIVAG--DGHSNIQPENSLartAKNWNIQDSDCDF 443
Cdd:pfam02384  62 ------QAEKFVKEHDG-----DTNDLSIYGQEKNPTTYRLARMNMILHGieYDDFHIRHGDTL---TSPKFEDDKKFDV 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175  444 ILTNPPFGTSESG--ALSD----KDMGQFeVQTTKGQLLFLQKMVLSARRGGEICTVIDEGVL---NTDTAapIRKWLLS 514
Cdd:pfam02384 128 VVANPPFSDKWDAndTLENdprfRPAYGV-APKSNADLAFLQHIIYYLAPGGRAAVVLPNGVLfrgGAEGK--IRKALVD 204

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490688175  515 KAKLLAVVRLPDETFRPNKINVrsSVLYLQRMTeeeeeiaDDIKYPVAFCDI-ETFGMDGAGDIARNFDLDTLIDSVG 591
Cdd:pfam02384 205 KDLVETVIALPPNLFYNTSIPT--CILFLTKNK-------AERKGKVLFIDAsNEFKKEGKLNILTDEHIEKIIDTFG 273
COG2810 COG2810
Predicted type IV restriction endonuclease [Defense mechanisms];
3-111 1.01e-11

Predicted type IV restriction endonuclease [Defense mechanisms];


Pssm-ID: 442059 [Multi-domain]  Cd Length: 340  Bit Score: 67.31  E-value: 1.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175   3 KSANETETVIKRILPYLQRRGYEI--ETDLHFEtaastpERYEAGFVDILVWPNdktypkGKPAFLIEAKRIAKKLSEQD 80
Cdd:COG2810   24 RSANEAATRQEFIDPLLEALGWDIdnPEEVIPE------ERVEGGRPDYALRLN------GKRKLFVEAKKPGVNLKDKP 91

                         90       100       110
                 ....*....|....*....|....*....|.
gi 490688175  81 KKQALSYARADGydVPFVVVCNGAEIRSYNA 111
Cdd:COG2810   92 ARQARSYAWSSG--VRWAILTNGREWRVYDA 120
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 646-831 1.11e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2; This model contains Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2 and similar TRD-CR's. S.SonII recognizes 5'... GTCANNNNNNRTCA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.SonII TRD1-CR1 does not belong to this subfamily.


Pssm-ID: 341135 [Multi-domain]  Cd Length: 189  Bit Score: 64.47  E-value: 1.11e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 646 KTIKELNTIPTaRGTSPSaDSYVDaaDGYALVikSGSNIsRYGELIVDGD-YIEKSLFDEYVEKAHtqgrnfnlVRPGDV 724
Cdd:cd17246    4 VKLGEISSDIT-DGTHPT-PKYVE--SGIPFI--TSKNI-KNGKIDFSDVkYISEEDHNEILKRSK--------LKKGDI 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 725 LVSSTGdgTLGKCCVYRpstdpitgETVPYAAIAegHVAIIRVDPDVIWPEYLCDYLRVGFGAQQIERLYTGST-GMIEL 803
Cdd:cd17246   69 LFSIIG--TIGRVAIVP--------EDLPANINQ--AVALIRPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTqKNLSL 136

                        170       180
                 ....*....|....*....|....*...
gi 490688175 804 TPaaLDEVVVNLLSgIEEQKKYSEALRK 831
Cdd:cd17246  137 GD--LKNLKIPLPP-LEEQKRIAAILDS 161
YtxK COG0827
Adenine-specific DNA N6-methylase [Replication, recombination and repair];
304-545 2.13e-09

Adenine-specific DNA N6-methylase [Replication, recombination and repair];


Pssm-ID: 440589 [Multi-domain]  Cd Length: 327  Bit Score: 59.96  E-value: 2.13e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 304 ATLKGKK---LGQY-FTPRPLVRLMSAIVGQEKIVNALlsgaaapKVLDPACGTGGFLvylmgdsLRVANQkLADRaINA 379
Cdd:COG0827   80 ALLKGMKesvQPNHqMTPDAIGLLIGYLVEKFTKKEGL-------RILDPAVGTGNLL-------TTVLNQ-LKKK-VNA 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 380 athrelvrkirqqvfFGSDANEGVACAAKMNmivAGDGHSNIQ--PENSLartakNWNIQDSdCDFILTNPPFGtsesgA 457
Cdd:COG0827  144 ---------------YGVEVDDLLIRLAAVL---ANLQGHPVElfHQDAL-----QPLLIDP-VDVVISDLPVG-----Y 194

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 458 LSDKDMGQ-FEVQTTKGQ----LLFLQKMVLSARRGGEICTVIDEGVLNTDTAAPIRKWLLSKAKLLAVVRLPDETFRpn 532
Cdd:COG0827  195 YPNDERAKrFKLKADEGHsyahHLFIEQSLNYLKPGGYLFFLVPSNLFESDQAAQLREFLKEKAHIQGLIQLPESLFK-- 272

                        250
                 ....*....|...
gi 490688175 533 KINVRSSVLYLQR 545
Cdd:COG0827  273 NEAAAKSILILQK 285
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 696-824 6.42e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoJA65PI TRD1-CR1, S.Fco49512ORF2615P TRD1-CR1, and S.SonIV TRD2-CR2; Escherichia coli UCD_JA65_pb S subunit (S.EcoJA65PI) recognizes 5'... AGCANNNNNNTGA ... 3' while Shewanella oneidensis MR-1 S subunit (S.SonIV) recognizes 5'... TACNNNNNNGTNGT ... 3'. The recognition sequence of Flavobacterium columnare S subunit (S.Fco49512ORF2615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoJA65PI TRD1 recognizes AGCA/TGCT and S.EcoJA65PI TRD2 recognizes TCA/TGA; S.SonIV TRD1 recognizes TAC/GTA and S.SonIV TRD2 recognizes ACNAC/GTNGT. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341145 [Multi-domain]  Cd Length: 182  Bit Score: 56.35  E-value: 6.42e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 696 YIEKSLFDEYveKAHTqgrnfnlVRPGDVLVSSTGdgTLGKCCVYRPSTDPitgetvpyAAIAEgHVAIIRVDPDVIwPE 775
Cdd:cd17256   46 YISPEIHEKI--KRYT-------LSKGDILISIVG--TIGRVGIVPKELDG--------ANLTE-NAARIRPKDSIS-PR 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 490688175 776 YLCDYLRVGFGAQQIERLYTGSTgMIELTPAALDEVVVNLLSgIEEQKK 824
Cdd:cd17256  105 YLYYYLRSPFGQSQIESETKGAA-QPKLNLKRIRELPIPLPP-LEEQKR 151
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
 6-177 5.09e-08

Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];


Pssm-ID: 443272 [Multi-domain]  Cd Length: 806  Bit Score: 56.77  E-value: 5.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175   6 NETETVIKRILPYLQRRGYEIETDLHFET---------AASTPERYEAGFVDILVWpndktYPKGKPAFLIEAKRIAKKL 76
Cdd:COG4096    3 SEAETRKKLIDPALKEAGWDVDDQILREVrptagrnvvIGEWPTRGGKGYADYVLF-----GDDGKPLAVVEAKRTSKDV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175  77 SEqDKKQALSYAR---ADGYDVPFVVVCNGAEIRSYNAKTGEPIQwnGKLSSkIPAKSQLKSVLKDfktDPQAVRIELpg 153
Cdd:COG4096   78 SA-GLQQAKLYADgleKQYGQVPFIFATNGREIWFWDDRDPYPRE--REVDG-FPSPEELWELLKR---RKGTARKRL-- 148

                        170       180
                 ....*....|....*....|....*.
gi 490688175 154 edgpldgsSALPFRPSLPLR--QLNA 177
Cdd:COG4096  149 --------ATEPYNDGIALRyyQIEA 166
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 691-851 5.56e-08

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR),similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Salmonella enterica subsp. enterica serovar Potsdam S sub; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3' and Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 both recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2.It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341198 [Multi-domain]  Cd Length: 192  Bit Score: 53.70  E-value: 5.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 691 IVDGDYIEKSLFDEYVEKAHTQGRNfnLVRPGDVLV---SSTGDGtLGKCCVYRPSTDPitgetvpyaAIAEGHVAIIRV 767
Cdd:cd17517   36 IYDGGIDLDDLKKRVDLSEKELEKY--LLKKGDILFnrsNGSPEL-VGKCALVDEEDEP---------AIFASYLIRLRL 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 768 DPDVIWPEYLCDYLRVGFGAQQIERLYTGSTGMIELTPAALDEVVVNLLSgIEEQKKYSEALRKGEAQARSTSEQAAS-- 845
Cdd:cd17517  104 DKKKILPEFLYYYLNSPLGRKQIEKIAKSAAGQANINQKDLKKLPIPLPP-LEEQKEIVEILESLDSKIDLLEKKLEKle 182


                 ....*.
gi 490688175 846 EMSAAL 851
Cdd:cd17517  183 QLFKSL 188
HSDR_N_2 pfam13588
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N ...
 45-118 2.12e-06

Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA.


Pssm-ID: 433331 [Multi-domain]  Cd Length: 110  Bit Score: 47.20  E-value: 2.12e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490688175   45 GFVDILVWPNDktypkGKPAFLIEAKRIAKKLSEQDKKQALSYARAdgYDVPFVVVCNGAEI----RSYNAKTGEPIQ 118
Cdd:pfam13588  37 KRADIVVYNKD-----GKPYILVECKAPSIKISQKVFDQLARYNSV--LGAPFLVVTNGLQHicfkVDYDKQQFEFLD 107
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 718-857 4.87e-06

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Escherichia coli A58 S subunit (S.EcoEI) TRD2-CR2, and Aminomonas paucivorans S subunit (S.Apa12260I); Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3', Escherichia coli A58 S subunit (S.EcoEI) recognizes 5'... GAGNNNNNNNATGC ... 3', and Aminomonas paucivorans S subunit (S.Apa12260I) recognizes 5'... GCCNNNNNCTCC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 recognizes AAC/GTT and S.EcoKI-TRD2 recognizes GCAC/GTGC, S.EcoEI TRD1 recognizes GAG/CTC and S.EcoEI TRD2 recognizes GCAT/ATGC, and S.Apa12260I TRD1 recognizes GCC/GGC and S.Apa12260I TRD2 recognizes GGAG/CTCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341150 [Multi-domain]  Cd Length: 191  Bit Score: 47.92  E-value: 4.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 718 LVRPGDVLVSStGDGTL--GKCCVYRPSTDPItgetvpyaaiaeghvaI-------IRVDPDVIWPEYLCDYLRVGFGAQ 788
Cdd:cd17261   60 WLKPGDLLISR-ANTSElvGRAALVDGDPDNL----------------IypdklirLRVNEELLLPEYLALALNSPSARR 122

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 789 QIERLYTGSTG-MIELTPAALDEVVVNLLSgIEEQKKYSEALRKGEAQARSTsEQAASEMSAALDSFRSS 857
Cdd:cd17261  123 QIESRATGTAGsMPKISQSDLKSLPIPLPP-LAEQKRIVARVDELLALIDRL-EAQLAAALQLLDRLRQA 190
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 718-851 9.78e-06

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I), Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) TRD2-CR2, and Streptomyces species SirexAA-E S subu; Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I) recognizes 5'... CACNNNNNNNCTGG ... 3' and Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) recognizes 5'... RTCANNNNNNNNGTGG ... 3'. The recognition sequence of Streptomyces species SirexAA-E S subunit (S.SspAAEORF2129P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Eco2071ORF3585P TRD1 recognizes RTCA/TGAY and S.Eco2071ORF3585P TRD2 recognizes CCAC/GTGG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341142 [Multi-domain]  Cd Length: 193  Bit Score: 47.09  E-value: 9.78e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 718 LVRPGDVLVSSTGDGT-LGKCCVYRPSTDPItgetvpyaaIAEGHVAIIRVDPDVIWPEYLCDYLRVGFGAQQIERLYTG 796
Cdd:cd17253   62 RLRKGDLLVTEGGDSDkLGRGAIWRGEIPPC---------LHQNHLFRVRPKDDLLLPEFLSYWLNSAYGRGYFLRAAKQ 132

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490688175 797 STGMIELTPAALDEVVVNLLSgIEEQKKYSEALR-------KGEAQARSTSEQAASEMSAAL 851
Cdd:cd17253  133 TTNLASINSTKLKALPVPLPP-LEEQRRIVERLDellalidALEASLAKLEELLKALRQALL 193
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 719-839 1.43e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O69:H11 07-3763 S subunit (S.Eco3763I) TRD2-CR2; Escherichia coli O69:H11 07-3763 S subunit (S.Eco3763I) recognizes 5'... TACNNNNNNNRTRTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341153 [Multi-domain]  Cd Length: 184  Bit Score: 46.38  E-value: 1.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 719 VRPGDVLVssTGDGTLGKCCVYRPSTDpitgetvpyAAIAEGHVaIIRVDPDVIwPEYLCDYLRVGFGAQQIERLYTGS- 797
Cdd:cd17264   62 LQKGDILY--CLRGSLGKCAIVDNYDE---------GAIASSLV-IIRPFAKVD-VRYLYYYLNSPLGKSQIKKYDNGSa 128

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 490688175 798 ----------TGMIELTPAALDEVVVNLLSGI-EEQKKYSEALRKGEAQARST 839
Cdd:cd17264  129 qpnlsakslkKFLIPLPPLEEQKRIVAKLDELdALIDKLKQALEKLEELLQSL 181
YeeA COG1002
Type II restriction/modification system, endonuclease and methylase domains [Defense ...
 123-450 9.07e-05

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


Pssm-ID: 440626 [Multi-domain]  Cd Length: 838  Bit Score: 46.24  E-value: 9.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 123 LSSKIPAKSQLKSVLKDFKTDPQAVRIELPGEDGPL----DGSSALPFRPSLPLRQLNALFSRCHDAIRKNEKDENHIFD 198
Cdd:COG1002   48 EAGIIQLDSLLKTSRLSKKTGVGFKTLTRLLNVAALlaitDLNLILLLKLLEALLKALLLAEEAAAALLLLTLALNDPDT 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 199 DFSKLLFLKLLEEKADTEEGFNLPYSYTFHELAALPDAKADQVQNAIMDMIKKIRTDKSYGDVLANpiHLKVAKTFLYLV 278
Cdd:COG1002  128 DALFELLAALLAEFREDFELLFAKFLPLNSSLLFELRLAFATLLILLLRLELEITLYVNTVLKDDN--GKRRTGLLDPLF 205

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 279 RQLAAVSFTDSTTDSK-------GAAFEYfVRATLKGKKLGQYFTPRP----LVR-LMSAIVGQE----KIVNALLSGAA 342
Cdd:COG1002  206 YLFAFLDATDLSSDWTkinpdifGSMFEA-VLDPEERSKLGMHYTSVPnimkVVRpLFLDPLRAEweaaGAWEALLEKIE 284

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 343 AP-------------KVLDPACGTGGFLV--YLMgdsLRV----ANQKLADRAINAATHRELVRKIRQqvFFGSDANEgV 403
Cdd:COG1002  285 AErellnllkrlasiRVLDPACGSGNFLViaYKE---LKAiegeVLIRLEELDGLSQFHRKSTIIPNN--FYGIEINP-F 358

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490688175 404 ACA-AK---------MNMIVAGDGHS---------NIQPENSL---ARTAKNWN---IQDSDCDFILTNPPF 450
Cdd:COG1002  359 AAEiARlalwiaelqWNYRYRGQLAPflpllnddnNIECGNALrlrDGNAADWRfvcPETGGEDYIIGNPPF 430
RMtype1_S_HmoORF3075P-TRD1-CR1_like cd17520
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 678-843 9.55e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Heliobacterium modesticaldum Ice1 S subunit (S1.HmoORF3075P) TRD1-CR1; The recognition sequence of Heliobacterium modesticaldum Ice1 S subunit (S1.HmoORF3075P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This subfamily also includes the TRD-CR-like sequence-recognition domain of type I N6-adenine DNA methyltransferase (M) subunit of Clostridium intestinale URNW (M2.CinURNWORF2828P). The recognition sequence of M2.CinURNWORF2828P is undetermined. Type I methyltransferases included in this group include two domains: one for methylation, and another (TRD-CR-like) for sequence-recognition.


Pssm-ID: 341201 [Multi-domain]  Cd Length: 180  Bit Score: 43.98  E-value: 9.55e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 678 IKSGS----NISRygelIVDGDYIEKSLfdEYVEKAHTQGRNFNLvRPGDVLVSSTGdgTLGKCCVYRPSTDPItgetvp 753
Cdd:cd17520   20 IKPGSisvlNISN----IEDGEIDYSGM--DTIEEEERKVKRYEL-RDGDLVLSCRG--TAIKVAVFREQKKIV------ 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 754 yaaIAEGHVAIIRVDPDVIwPEYLCDYLRVGFGAQQIERLYTGSTGMiELTPAALDEVVVNLLSgIEEQKKYSEALRKGE 833
Cdd:cd17520   85 ---IASANIIVIRPNEKVL-SEYLKIFLESPVGTALIKSFQRGTTVM-NINHSDIAEMEIPLLP-LEEQKKIAEEYRKER 158

                        170
                 ....*....|
gi 490688175 834 AQARSTSEQA 843
Cdd:cd17520  159 SLYRETVRKA 168
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 665-829 1.09e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Lactobacillus delbrueckii subsp. bulgaricus S subunit (S2.LdeBORF1052P) TRD2-CR2; The recognition sequence of Lactobacillus delbrueckii subsp. bulgaricus S subunit (S2.LdeBORF1052P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341167 [Multi-domain]  Cd Length: 189  Bit Score: 44.04  E-value: 1.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 665 DSYVDaaDGYaLVIKSGsNISRYGELIVDGDYIEKSLFDEYvekahtqgRNFnLVRPGDVLVSSTGdGTLGKCCVYRPST 744
Cdd:cd17278   21 SDFSD--EGI-PVIRIG-NIKNGGIDLDDNSKYPEEPLEKY--------EKF-LLKKGDILIAMTG-GTVGKVAIVPEDD 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 745 DPItgetvpYaaiaegH---VAIIRVDpDVIWPEYLCDYLRVGFGAQQIERLYTG------STGMIEltpaaldEVVVNL 815
Cdd:cd17278   87 EPA------L------LnqrVGKFRPK-DKIDKEFLYYLLRSDSFRNQIKSSATGtaqpniSPKDIE-------SIKIPL 146

                        170
                 ....*....|....
gi 490688175 816 LSgIEEQKKYSEAL 829
Cdd:cd17278  147 PP-LEEQKKIAEIL 159
RMtype1_S_EcoUTORF5051P-TRD2-CR2_like cd17524
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 659-857 1.40e-04

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) TRD2-CR2 and Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) TRD2-CR2; Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) recognizes 5'... CCANNNNNNNCTTC ... 3' and the recognition sequence of Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341205 [Multi-domain]  Cd Length: 189  Bit Score: 43.61  E-value: 1.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 659 GTSPSADsyvDAADGYAlVIKSGsNIsRYGELIVDGD---YIEKSLFDEYvekahtqgrnfnLVRPGDVL---------V 726
Cdd:cd17524   16 GTSEKKS---EDEGGYP-VLRMG-NI-QDGGIDDDDLkyvDLDEKEFEKY------------LLKKGDVLfnrtnspelV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 727 sstgdgtlGKCCVYRPSTDPItgetvpYAaiaeGHVAIIRVDPDVIWPEYLCDYLRVGFGAQQIERLYTGSTGMIELTPA 806
Cdd:cd17524   78 --------GKTAIFRGDGPAT------FA----SYLIRIRLNEEKILPEYLNYFLNSPYGRKQIKSVATQGVGQANINAT 139

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 490688175 807 ALDEVVVNLLSgIEEQKKYSEALRKGEAQARsTSEQAASEMSAALDSFRSS 857
Cdd:cd17524  140 KLKAIPIPLPP-LEEQKEIVEKLDELDALID-RLEALLEEAEELLESLLQS 188
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 696-740 2.40e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to the S subunit TRD2-CR2 regions of Lactococcus lactis subsp. cremoris A17 (S.LlaA17I), Haemophilus influenzae Rd (S.HindORF215P) ; Lactococcus lactis subsp. cremoris A17 S subunit (S.LlaA17I) recognizes 5'... CAANNNNNNNNTAYG... 3', while the recognition sequences of Clostridium species ASF502 S subunit (S.Csp502ORF478P) and Haemophilus influenzae Rd S subunit (S.HindORF215P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Porphyromonas species COT-108 OH1349 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.Psp1349ORF730P) of unknown recognition sequence. It may also include type I DNA methyltransferases.


Pssm-ID: 341181 [Multi-domain]  Cd Length: 149  Bit Score: 42.14  E-value: 2.40e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 490688175 696 YIEKSLFDEYVEKahtqgrnFNLVRPGDVLVSSTgdGTLGKCCVY 740
Cdd:cd17292   13 YISRELFEEYKSK-------YSYPKKGDILISAS--GTIGRTVIY 48
RMtype1_S_Ara36733I_TRD1-CR1_like cd17268
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 686-831 4.11e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Ara36733I TRD1-CR1 AND S.Ara36733I TRD2-CR2; Actinomyces radicidentis S subunit (S.Ara36733I) recognizes 5'... CGAGNNNNNCTG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341157 [Multi-domain]  Cd Length: 185  Bit Score: 42.05  E-value: 4.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 686 RYGELIVD-GDYIEKSL-F--DEYVEKAHTqgrnfnlVRPGDVLVSSTG----DgtLGKCCVYrpstdpiTGEtvpYAAI 757
Cdd:cd17268   32 HYGEIYTKyGIYTTKTKsFisEELAKKLRK-------AKPGDLLIAGTGetieD--IGKAVAW-------LGD---EEVA 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490688175 758 AEGHVAIIRVDPDviwPEYLCDYLRVGFGAQQIERLYTGSTgMIELTPAALDEVVVNLLSgIEEQKKYSEALRK 831
Cdd:cd17268   93 AGGDIIIFRHSQN---PKYLSYLLNSPAFQKQKRKLGTGTK-VVHISASDLAKIKIPVPP-LEEQERIVEILDK 161
UPF0020 pfam01170
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated ...
 347-458 2.34e-03

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: 40.03  E-value: 2.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175  347 LDPACGTGGFLVY--LMGdsLRVANQKLADRAInaathrelvrkirqQVFFGSDANEGVACAAKMNMIVAGDGHSnIQpe 424
Cdd:pfam01170  33 LDPMCGSGTILIEaaLMG--ANIAPGKFDARVR--------------APLYGSDIDRRMVQGARLNAENAGVGDL-IE-- 93

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 490688175  425 nslartAKNWNIQD-----SDCDFILTNPPFG--TSESGAL 458
Cdd:pfam01170  94 ------FVQADAADlplleGSVDVIVTNPPYGirLGSKGAL 128
RMtype1_S_Cje2232P-TRD2-CR2_like cd17526
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 683-844 3.69e-03

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) TRD2-CR2 and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) TRD1-CR1; The recognition sequences of Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. Also included in this subfamily is the C-terminal TRD-CR-like sequence-recognition domain of Microcystis aeruginosa putative type I N6-adenine DNA methyltransferase M subunit (M.Mae7806ORF3969P). The recognition sequence of M.Mae7806ORF3969P is undetermined.


Pssm-ID: 341207 [Multi-domain]  Cd Length: 192  Bit Score: 39.50  E-value: 3.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 683 NISRYGELIVDGDYIEKSLFDEyvekahtqgRNFNLVRPGDVLVSSTGDGTL-GKCCVYRpstdpitgETVPYAAiaEGH 761
Cdd:cd17526   36 NITTDGELDLDKLIKIVPSPKE---------RKRYLLQKGDVLFNNTNSQELvGKTALFD--------GEEPYVF--SNH 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490688175 762 VAIIRVDPDVIWPEYLCDYLRVGFGAQQIERLYT---GSTGmIELtpaaldEVVVNL---LSGIEEQKKYSEALRKGEAQ 835
Cdd:cd17526   97 MTRIRVKKSKINPEFLARYLHLLWRSGYFKKLCTnwvNQAG-INS------DTLANLkipLPPLPEQKRIAEILDQIDRL 169


                 ....*....
gi 490688175 836 ARSTSEQAA 844
Cdd:cd17526  170 AKALRAEAE 178
 
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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