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Conserved domains on  [gi|514164098|gb|EPG42785|]
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type I restriction enzyme, S subunit [Acinetobacter colistiniresistens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 1-176 6.74e-96

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoBI TRD1-CR1, S.EcoSanI TRD1-CR1, and S.EcoVR50I TRD1-CR1; Escherichia coli B S subunit (S.EcoBI) and Escherichia coli VR50 S subunit (S.EcoVR50I) recognize 5'... TGANNNNNNNNTGCT ... 3', while Escherichia coli Sanji S subunit (S.EcoSanI) recognizes 5'... TGANNNNNNCTTC ... 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: 341146 [Multi-domain]  Cd Length: 176  Bit Score: 282.49  E-value: 6.74e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   1 MEKVQLGTLVKITSGFAFKSNLFNTDKKGLPLIRIRDVVRGYSDTYYDGEYKAEYLIQKGDALIGMDGEFNLALWNSGKA 80
Cdd:cd17257    1 WEVVRLGDVADVQNGFPFKSKLFNDEGGGLPLIRIRDLKSGDTETYYTGEYDEKYLVKNGDILIGMDGDFNAAIWKGGDA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  81 LLNQRVCKIQSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQ 160
Cdd:cd17257   81 LLNQRVCRIRPKSEELDKRFLYYALPPPLKAIEDTTSSTTVKHLSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLI 160

                        170
                 ....*....|....*.
gi 514164098 161 QAIEKLDQLLQATFID 176
Cdd:cd17257  161 AKLEKLRDLLLPLLQS 176
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 188-324 4.94e-51

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 cd17288:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 163  Bit Score: 167.26  E-value: 4.94e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 188 WEVLKWRDALKIINGKNQKavLDQNGIFPICGSGGVMGYANEWLTPAKSVIIGRKGNINKPILMFENFWNVDTAFGLVPN 267
Cdd:cd17288    1 WEVKKLGDLLKIKNGKDYK--HLEDGNYPVYGSGGIMGYVNDYLYDGESVLIGRKGTIDKPLYVNGPFWTVDTMFYTEIK 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 514164098 268 KDVlNADYLFWFCHFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQ 324
Cdd:cd17288   79 KNN-DPKFLYYLLKTIDFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDK 134
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 304-349 8.52e-03

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 cd17287:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 184  Bit Score: 36.70  E-value: 8.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 514164098 304 NIDIPTPPLDKQLCFSNICD----QTRILKSKMELKDlNLFSSLQNQAFN 349
Cdd:cd17287  136 SIEIPVPPLDEQQKIAAFLSaidaKIDALEQKLELLQ-ELKKSLMQQLFT 184
 
Name Accession Description Interval E-value
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 1-176 6.74e-96

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoBI TRD1-CR1, S.EcoSanI TRD1-CR1, and S.EcoVR50I TRD1-CR1; Escherichia coli B S subunit (S.EcoBI) and Escherichia coli VR50 S subunit (S.EcoVR50I) recognize 5'... TGANNNNNNNNTGCT ... 3', while Escherichia coli Sanji S subunit (S.EcoSanI) recognizes 5'... TGANNNNNNCTTC ... 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: 341146 [Multi-domain]  Cd Length: 176  Bit Score: 282.49  E-value: 6.74e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   1 MEKVQLGTLVKITSGFAFKSNLFNTDKKGLPLIRIRDVVRGYSDTYYDGEYKAEYLIQKGDALIGMDGEFNLALWNSGKA 80
Cdd:cd17257    1 WEVVRLGDVADVQNGFPFKSKLFNDEGGGLPLIRIRDLKSGDTETYYTGEYDEKYLVKNGDILIGMDGDFNAAIWKGGDA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  81 LLNQRVCKIQSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQ 160
Cdd:cd17257   81 LLNQRVCRIRPKSEELDKRFLYYALPPPLKAIEDTTSSTTVKHLSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLI 160

                        170
                 ....*....|....*.
gi 514164098 161 QAIEKLDQLLQATFID 176
Cdd:cd17257  161 AKLEKLRDLLLPLLQS 176
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 188-324 4.94e-51

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Lactococcus lactis S subunit (S.LlaAI06ORF1089P) TRD1-CR1 and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) TRD2-CR2; The recognition sequences of Lactococcus lactis S subunit (S.LlaAI06ORF1089P) and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341177 [Multi-domain]  Cd Length: 163  Bit Score: 167.26  E-value: 4.94e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 188 WEVLKWRDALKIINGKNQKavLDQNGIFPICGSGGVMGYANEWLTPAKSVIIGRKGNINKPILMFENFWNVDTAFGLVPN 267
Cdd:cd17288    1 WEVKKLGDLLKIKNGKDYK--HLEDGNYPVYGSGGIMGYVNDYLYDGESVLIGRKGTIDKPLYVNGPFWTVDTMFYTEIK 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 514164098 268 KDVlNADYLFWFCHFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQ 324
Cdd:cd17288   79 KNN-DPKFLYYLLKTIDFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDK 134
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 1-165 1.15e-19

Type I restriction modification DNA specificity domain; This domain is also known as the target recognition domain (TRD). 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 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 subunit (this family), two modification (M) subunits and two restriction (R) subunits.


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 84.71  E-value: 1.15e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098    1 MEKVQLGTLVKITSGFAFKSNLFNtDKKGLPLIRIRDvvrgYSDTYYDG-EYKAEYLIQKGDALIGMDGEFNLALWNSGK 79
Cdd:pfam01420   4 WEVFKLGDVFEIKKGKTPKKKELK-NNGKYPYIRAGD----LNNVVKGGlGYIKKYILPKGDITISSRATIGYVFYRDKP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   80 ALLNQRVCKIQSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQAD---ELR 156
Cdd:pfam01420  79 YYTNQHIIVLIPKNNIKITEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDntiELE 158


                  ....*....
gi 514164098  157 QKRQQAIEK 165
Cdd:pfam01420 159 KGILNELER 167
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
100-172 1.69e-12

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 62.38  E-value: 1.69e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514164098 100 YLIRFlPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:COG0732    4 YYLRS-PSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDA 75
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 186-315 3.32e-11

Type I restriction modification DNA specificity domain; This domain is also known as the target recognition domain (TRD). 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 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 subunit (this family), two modification (M) subunits and two restriction (R) subunits.


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 61.22  E-value: 3.32e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  186 KGWEVLKWRDALKIINGKNQ-KAVLDQNGIFPICGSG-------GVMGYANEWLTPAKSVIIGRKGNINKPILMFENFWN 257
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPkKKELKNNGKYPYIRAGdlnnvvkGGLGYIKKYILPKGDITISSRATIGYVFYRDKPYYT 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  258 VDTAFGLVP-NKDVLNADYLFWFCHFFN-FEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:pfam01420  82 NQHIIVLIPkNNIKITEFLYLYLLLKLKkLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQ 141
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
285-352 2.27e-07

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 48.13  E-value: 2.27e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514164098 285 FEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQL----CFSNICDQTRILKSKMELKDlNLFSSLQNQAFNGTL 352
Cdd:COG0732   15 LRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKriveILDSLFDKIAALEKEIEKLK-ELRDALLPKLFTGEL 85
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
2-230 5.61e-07

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 51.04  E-value: 5.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   2 EKVQLGTLVKITSGFAFKSN---LFNTDKKgLPLIRIRDVVRGYSDT----YYDGEYKA--EYLIQKGDALIGMDGEF-- 70
Cdd:PRK09737  11 VTTHISEICSVIRGVKPPKGyatKSLTMGD-LPFIRTTDITNGAVDLttlpYCMDAPEDvsKYQLQDRDIVISSAGSIgf 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  71 -----NLALWNSGKALLNQRVCKIQSIDERldqnYLIRFLPKAL--KDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQR 143
Cdd:PRK09737  90 sflaqNPLPSNVVFASFAIRLKPVNYFSEY----FLKHFLESSDyrNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAEQK 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 144 RIASILD----QADELRQKRQQAIEKLDQLLQATFIDMFGDPV-------SNSKGWEVLKWRDALKIINGKNQKAVLDQN 212
Cdd:PRK09737 166 IIAEKLDtllaQVDSTKARLEQIPQILKRFRQAVLGAAVSGKLteewrwpDLPSTWSVHKYSELVDSRLGGMSSKANNFG 245

                        250
                 ....*....|....*...
gi 514164098 213 GIFPICGSGGVMGYANEW 230
Cdd:PRK09737 246 SATPYLRNINVRWGSFDL 263
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 304-349 8.52e-03

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) TRD2-CR2, and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) TRD2-CR2; The recognition sequences of Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341176 [Multi-domain]  Cd Length: 184  Bit Score: 36.70  E-value: 8.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 514164098 304 NIDIPTPPLDKQLCFSNICD----QTRILKSKMELKDlNLFSSLQNQAFN 349
Cdd:cd17287  136 SIEIPVPPLDEQQKIAAFLSaidaKIDALEQKLELLQ-ELKKSLMQQLFT 184
 
Name Accession Description Interval E-value
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 1-176 6.74e-96

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoBI TRD1-CR1, S.EcoSanI TRD1-CR1, and S.EcoVR50I TRD1-CR1; Escherichia coli B S subunit (S.EcoBI) and Escherichia coli VR50 S subunit (S.EcoVR50I) recognize 5'... TGANNNNNNNNTGCT ... 3', while Escherichia coli Sanji S subunit (S.EcoSanI) recognizes 5'... TGANNNNNNCTTC ... 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: 341146 [Multi-domain]  Cd Length: 176  Bit Score: 282.49  E-value: 6.74e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   1 MEKVQLGTLVKITSGFAFKSNLFNTDKKGLPLIRIRDVVRGYSDTYYDGEYKAEYLIQKGDALIGMDGEFNLALWNSGKA 80
Cdd:cd17257    1 WEVVRLGDVADVQNGFPFKSKLFNDEGGGLPLIRIRDLKSGDTETYYTGEYDEKYLVKNGDILIGMDGDFNAAIWKGGDA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  81 LLNQRVCKIQSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQ 160
Cdd:cd17257   81 LLNQRVCRIRPKSEELDKRFLYYALPPPLKAIEDTTSSTTVKHLSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLI 160

                        170
                 ....*....|....*.
gi 514164098 161 QAIEKLDQLLQATFID 176
Cdd:cd17257  161 AKLEKLRDLLLPLLQS 176
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 188-324 4.94e-51

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Lactococcus lactis S subunit (S.LlaAI06ORF1089P) TRD1-CR1 and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) TRD2-CR2; The recognition sequences of Lactococcus lactis S subunit (S.LlaAI06ORF1089P) and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341177 [Multi-domain]  Cd Length: 163  Bit Score: 167.26  E-value: 4.94e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 188 WEVLKWRDALKIINGKNQKavLDQNGIFPICGSGGVMGYANEWLTPAKSVIIGRKGNINKPILMFENFWNVDTAFGLVPN 267
Cdd:cd17288    1 WEVKKLGDLLKIKNGKDYK--HLEDGNYPVYGSGGIMGYVNDYLYDGESVLIGRKGTIDKPLYVNGPFWTVDTMFYTEIK 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 514164098 268 KDVlNADYLFWFCHFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQ 324
Cdd:cd17288   79 KNN-DPKFLYYLLKTIDFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDK 134
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 1-179 3.51e-38

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: 134.95  E-value: 3.51e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   1 MEKVQLGTLVKITSGFAFKSNLFNtdKKGLPLIRIRDVVRGYSDT-------YYDGEYKAEYLIQKGDALIGMDGE--FN 71
Cdd:cd17278    1 WEVVKLGDIADIQNGYAFKSSDFS--DEGIPVIRIGNIKNGGIDLddnskypEEPLEKYEKFLLKKGDILIAMTGGtvGK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  72 LALWNSG--KALLNQRVCKIQSIDErLDQNYLIRFL--PKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIAS 147
Cdd:cd17278   79 VAIVPEDdePALLNQRVGKFRPKDK-IDKEFLYYLLrsDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAE 157

                        170       180       190
                 ....*....|....*....|....*....|..
gi 514164098 148 ILDQADELRQKRQQAIEKLDQLLQATFIDMFG 179
Cdd:cd17278  158 ILDSLDAKIDKLEQKLEKLRDLLKPLLQSLFT 189
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 2-172 6.74e-37

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to TRD2-CR2's of StySKI, S.EcoAI, S.EcoJA17PI, and S.EcoJA23PI; Salmonella kaduna CDC-388 S subunit (StySKI) recognizes 5'... CGATNNNNNNNGTTA ... 3' while Escherichia coli Type-1 restriction enzyme EcoAI specificity protein (S.EcoAI), Escherichia coli UCD_JA17_pb S subunit (S.EcoJA17PI) and Escherichia coli UCD_JA23_pb S subunit (S.EcoJA23PI) recognize 5'... GAGNNNNNNNGTCA ... 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: 341148 [Multi-domain]  Cd Length: 189  Bit Score: 131.48  E-value: 6.74e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   2 EKVQLGTLVKITSGFAFKSNLFNTDkkGLPLIRIRDVVRGY----SDTYYDGEYKAE---YLIQKGDALIGMDGefnlAL 74
Cdd:cd17259    2 EWVKLGDVADILSGYAFKSSEFSES--GIRLLRGANVGVGEirwdDTVYLPEEYLEEyekYLLKEGDIVIALDR----PI 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  75 WNSGK-----------ALLNQRVCKIQSIDErLDQNYLIRFL--PKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAE 141
Cdd:cd17259   76 ISGGLkvaripksdlpALLVQRVARIRPKDE-LNSDFLYYLLqsDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEE 154

                        170       180       190
                 ....*....|....*....|....*....|.
gi 514164098 142 QRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17259  155 QKKIAEFLSSLDALIDLLEQKLEKLQQLKKG 185
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-178 4.98e-34

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.FclI TRD1-CR1; The recognition sequence of Flavobacterium columnare G4 S subunit (S.FclI) 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 contains TRD-CR-like sequence-recognition domains of type I DNA methyltransferases, such as putative Type I N6-adenine DNA methyltransferases from Microbacterium ketosireducens (M.Msp12510ORF408P) and Treponema primitia ZAS-2 (M.TprZAS2ORF3630P). It may also include various type II restriction enzymes and methyltransferases.


Pssm-ID: 341143 [Multi-domain]  Cd Length: 173  Bit Score: 123.34  E-value: 4.98e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGFAFKsnlfNTD--KKGLPLIRIRDVVRGYSDT-YYDGEYKAEYLIQKGDALIGMDGEFNLALWNSGKA 80
Cdd:cd17254    1 VKLGDLATFINGRAFK----PSEwsDSGLPIIRIQNLNGGNAPFnYYSGLLDEKYYVEKGDLLFSWSASFGPFIWNGGKA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  81 LLNQRVCKIQsIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQ 160
Cdd:cd17254   77 ILNQHIFKVV-PDEEIDKDYLYYLLKALTEEIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALE 155

                        170
                 ....*....|....*...
gi 514164098 161 QAIEKLDQLLQATFIDMF 178
Cdd:cd17254  156 EQLKKLEELRKALLQSLL 173
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-172 1.10e-32

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.


Pssm-ID: 341131 [Multi-domain]  Cd Length: 178  Bit Score: 120.18  E-value: 1.10e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGFAFKSNLFNTDKKGLPLIRIRDVVRGYSD------TYYDGEYKAEYLIQKGDALIGMDGEF-NLALWN 76
Cdd:cd16961    1 KKLGEIAEIISGKTPSSSSEYWDNGIIPWIRISDINNGGIIltdekiTEEGAEKLKKKILPKGDILISRSGTIgKVAIVK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  77 -SGKALLNQRVCKIQSIDErLDQNYLIRFL--PKALKDIEDRTPfVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQAD 153
Cdd:cd16961   81 eNDKALLNQAVIVIRPKDE-VDSEFLYYFLksPFGKKLIEGSAG-STQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLD 158

                        170
                 ....*....|....*....
gi 514164098 154 ELRQKRQQAIEKLDQLLQA 172
Cdd:cd16961  159 ALIELLEQKLEKLEQLKQA 177
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 1-179 5.06e-31

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: 116.08  E-value: 5.06e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   1 MEKVQLGTLV-KITSGfafKSNLFNTDKKGLPLIRIRDVVRGYSDT----YYDGEYKAEYL----IQKGDALIGMDGEF- 70
Cdd:cd17246    1 WEWVKLGEISsDITDG---THPTPKYVESGIPFITSKNIKNGKIDFsdvkYISEEDHNEILkrskLKKGDILFSIIGTIg 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  71 NLALWNSG-KALLNQRVCKIQSIDERLDQNYLIRFL--PKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIAS 147
Cdd:cd17246   78 RVAIVPEDlPANINQAVALIRPKKEKIDPKYLLYYLnsPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQKRIAA 157

                        170       180       190
                 ....*....|....*....|....*....|..
gi 514164098 148 ILDQADELRQKRQQAIEKLDQLLQATFIDMFG 179
Cdd:cd17246  158 ILDSLDALIDKLEQKLEKLEDLKKGLMQDLLT 189
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 192-338 5.01e-26

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoAO83I TRD1-CR1 and S.AbaB8342I TRD2-CR2; Escherichia coli strain A0 34/86 S subunit (S.EcoAO83I) recognizes 5'... GGANNNNNNNNATGC ... 3, and Acinetobacter baumannii B8342 S subunit (S.AbaB8342I) recognizes 5'... TTCANNNNNNTCC ... 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.AbaB8342I-TRD1 recognizes TTCA/TGAA and S.AbaB8342I-TRD2 recognizes GGA/TCC. 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 Type IIG restriction enzyme/N6-adenine DNA methyltransferases from Thermus scotoductus RFL1 (RM.TstI) and Acinetobacter lwoffi Ks 4-8 (RM.AloI), as well as type I DNA methyltransferases such as Sideroxydans lithotrophicus ES-1 Type I N6-adenine DNA methyltransferase (M.SliESORF1090P). RM.TstI recognizes 5' ... CACNNNNNNTCC ... 3' and RM.AloI recognizes 5' ... GAACNNNNNNTCC ... 3'.


Pssm-ID: 341156 [Multi-domain]  Cd Length: 158  Bit Score: 101.71  E-value: 5.01e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 192 KWRDALKIINGKNQKAVLDQNGIFPICGSGGVMGYANEWLTPAKSVIIGRKGNINKPILMFENFWNVDTAFGLVPNKDVl 271
Cdd:cd17267    2 KLGDVIELQYGKDLPKSRRIPGPYPVYGSNGIVGYHNEALVKGPGIVVGRKGSIGKVHYSEEDFWPIDTTLYVKDFKGN- 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 514164098 272 NADYLFWFCHFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNicdqtrILKSKMELKDLN 338
Cdd:cd17267   81 DPRFLYYLLKTLDLERLNSGSAVPGLNRNDVYSLKVPLPPLEEQKAIAA------ILDALDDKIELN 141
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-178 4.21e-24

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) TRD1-CR1; Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) recognizes 5'... GAYNNNNNNNTCYC ... 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: 341152 [Multi-domain]  Cd Length: 177  Bit Score: 97.19  E-value: 4.21e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGFAF-KSNLFNTDKKG-LPLIRIRDVvRGYSDTYYDGEYKAEYLIQKGDALIGMDGEfnlalwNSGKAL 81
Cdd:cd17263    1 VKLGEVCKFSKGKQPpISERFDEPKEGsVRYIQIEDL-RNNNEKKYIENPKKSVICNEDDILIVRDGA------NAGEVG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  82 LNQR------VCKIQSIDERLDQNYLIRFLPKALKDIEDRTPF-VTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADE 154
Cdd:cd17263   74 TGLEgaiastLFKIIPDKNIIDKDYLYYFLKSKEIQLNILTKAgSTIPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDA 153

                        170       180
                 ....*....|....*....|....
gi 514164098 155 LRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17263  154 LIDKLKELIEKLIELKKGLFQELL 177
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-178 1.43e-21

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus licheniformis S subunit (S1.BliBORF2384P) TRD1-CR1 and Chlorobium tepidum TLS S subunit (S.CteTORF675P) TRD1-CR1; The recognition sequences for Bacillus licheniformis S subunit (S1.BliBORF2384P) and Chlorobium tepidum TLS S subunit (S.CteTORF675P) 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. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341187 [Multi-domain]  Cd Length: 175  Bit Score: 90.25  E-value: 1.43e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGFAFKSNLFNTDKKGLPLIRirdvvrGYSDtyYDGEY--KAEY------LIQKGDALIGMD----GEFN 71
Cdd:cd17496    1 VKLGDIAEIIMGQSPKGESYNTEGIGIPLLN------GPAD--FGDGYpiPKKWttkptkLCKKGDILFCVRgsttGRLN 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  72 LAlwnSGKALLNQRVCKIQSIDErLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQ 151
Cdd:cd17496   73 IA---DDEYCIGRGVAAIRPKNG-IDTEFLYYLLESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDP 148

                        170       180
                 ....*....|....*....|....*..
gi 514164098 152 ADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17496  149 LDEKIDKNKQEIEKLEELRDTLLPKLL 175
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 27-174 1.52e-21

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: 90.25  E-value: 1.52e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  27 KKGLPLIRIRDVVRGYSDTY--------YDGEYKAeYLIQKGDALIG--------------MDGefnlalwnsgkALLNQ 84
Cdd:cd17256   23 PTGVPYIRVTDIKNGGIDLDnlkyispeIHEKIKR-YTLSKGDILISivgtigrvgivpkeLDG-----------ANLTE 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  85 RVCKIqSIDERLDQNYLIRFL--PKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQA 162
Cdd:cd17256   91 NAARI-RPKDSISPRYLYYYLrsPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQ 169

                        170
                 ....*....|..
gi 514164098 163 IEKLDQLLQATF 174
Cdd:cd17256  170 LAKLEELKKALM 181
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-178 3.47e-21

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2 and Aminobacterium colombiense DSM 12261 S subunit (S.Aco12; The S.Aco12261I S subunit recognizes 5'... GCANNNNNNTGT ... 3', while the recognition sequence is undetermined for S.TteMORF1547P TRD2-CR2. 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. S.TteMORF1547P TRD1-CR1 and S.Aco12261I TRD2-CR2 do not belong to this family. This family may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341134 [Multi-domain]  Cd Length: 174  Bit Score: 89.13  E-value: 3.47e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGFAFKSNLFNTDKKGLPLirirdvvrgysdtyYDGeyKAEY----------------LIQKGDALIGMD 67
Cdd:cd17245    1 VKLGEVAEIIMGQSPPSSTYNEEGEGLPF--------------LQG--KADFgeiyptprvwctkptkIAEKGDILISVR 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  68 ---GEFNLAlwnsgkallNQRVC------KIqSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPP 138
Cdd:cd17245   65 apvGDVNIA---------DEKCCigrglaAI-RANKDIDNLFLYYYLKYNKPELEKLGTGSTFKAINKKDLEELKIPLPP 134

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 514164098 139 LAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17245  135 LEEQQKIAEILSTVDEAIEKTKALIEKLDELKKGLMQELF 174
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 88-178 7.92e-20

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Campylobacter species RM1670 S subunit (S.Csp16704I) TRD2-CR2, Aeromonas media WS S subunit (S.AmeWSORF2351P) TRD1-CR1, and Clos; Campylobacter species RM16704 S subunit (S.Csp16704I ) recognizes 5'... ACANNNNNNNNTCG ... 3', and the recognition sequences of Aeromonas media WS TRD1-CR1 S subunit (S.AmeWSORF2351P) and Clostridium carboxidivorans P7 S subunit (S.CcaPORF573P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341174 [Multi-domain]  Cd Length: 181  Bit Score: 85.63  E-value: 7.92e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  88 KIQSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLD 167
Cdd:cd17285   91 KALFPKDELDPEYLLYWFLSIEETIESLGTGTTVKGITLEDLKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEKLK 170

                         90
                 ....*....|.
gi 514164098 168 QLLQATFIDMF 178
Cdd:cd17285  171 QLKKGLMQSLL 181
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 1-165 1.15e-19

Type I restriction modification DNA specificity domain; This domain is also known as the target recognition domain (TRD). 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 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 subunit (this family), two modification (M) subunits and two restriction (R) subunits.


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 84.71  E-value: 1.15e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098    1 MEKVQLGTLVKITSGFAFKSNLFNtDKKGLPLIRIRDvvrgYSDTYYDG-EYKAEYLIQKGDALIGMDGEFNLALWNSGK 79
Cdd:pfam01420   4 WEVFKLGDVFEIKKGKTPKKKELK-NNGKYPYIRAGD----LNNVVKGGlGYIKKYILPKGDITISSRATIGYVFYRDKP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   80 ALLNQRVCKIQSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQAD---ELR 156
Cdd:pfam01420  79 YYTNQHIIVLIPKNNIKITEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDntiELE 158


                  ....*....
gi 514164098  157 QKRQQAIEK 165
Cdd:pfam01420 159 KGILNELER 167
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 56-178 1.93e-19

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to MjaXIP/S.MjaORF132P TRD1-CR1, S.Sau1132ORF3780P TRD1-CR1, S.Mca353ORF290P TRD1-CR1, and other TRD-CR's; The Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 3'. The recognition sequence of Methanococcus jannaschii S subunit (MjaXIP/S.MjaORF132P) 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.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG, and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. 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: 341196 [Multi-domain]  Cd Length: 181  Bit Score: 84.41  E-value: 1.93e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  56 LIQKGDALIGMDGEfnlalwNSGK-ALL------NQRVCKIqSIDERLDQNYLIRFLpKALKD--IEDRTPfVTVKHLSV 126
Cdd:cd17515   59 LFPKGSVLIAMYGA------TAGKvGILgidaatNQAICAI-LPNEEIDNEFLFYFL-KSQKEylISLGKG-GAQPNISQ 129

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 514164098 127 KDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17515  130 GIIKNIEIPLPPLAEQKRIVAKLDKLDKLIEKLEKALEKLEELKKALMQKLL 181
RMtype1_S_HpyCR35ORFAP-TRD1-CR1_like cd17519
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 6-164 3.11e-19

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) TRD1-CR1 and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190; The recognition sequences of Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341200 [Multi-domain]  Cd Length: 183  Bit Score: 83.90  E-value: 3.11e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   6 LGTLVKITSGFAFKSNLFNTdkKGLPLIRIRDVVRGYSDT-----YYDGEYK---AEYLIQKGDALIGMDGE--FNLALW 75
Cdd:cd17519    5 LGEVCKFQNGFAFKSSKYRE--SGFPIIRITNIQNGKIDTdnlkyFDLNDYKenlDKYIVRPGDIVIAMSGAttGKVGIN 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  76 NSGKAL-LNQRVCKIQSIDERLDQNYLIRFLpkALKDIEDR-TPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQAD 153
Cdd:cd17519   83 LTDQEFyLNQRVGKFIPNEEILNNRYLYHFL--LSKQNEKYiLAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILDKFR 160

                        170
                 ....*....|.
gi 514164098 154 ELRQKRQQAIE 164
Cdd:cd17519  161 ELTNELESELN 171
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 1-177 4.96e-19

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P/MjaXIIP) TRD1-CR1; The recognition sequence of Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P, also called MjaXIIP) 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: 341203 [Multi-domain]  Cd Length: 190  Bit Score: 83.74  E-value: 4.96e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   1 MEKVQLGT-LVKITSGFAFKSNlfnTDKKGLPLIRIR-------DVVR-GYSDTYYDGeyKAEYLIQKGDAL-------- 63
Cdd:cd17522    1 WKVVKLGDvLEEIRNGTTVKQN---KEGGGYPVTRIEtisngtiDLNRvGYAITNEEK--IEKYKLQKGDILfshinsie 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  64 -IGmdgefNLALWNS-------GKALLnqrvcKIQSIDERLDQNYLIRFL--PKALKDIEDRTpfvtvKH------LSVK 127
Cdd:cd17522   76 hIG-----KTAIYDGdpeplihGMNLL-----RLRPNKNIVDPKYLYYLLksDRFRNQFRSIA-----KKavnqasINQT 140

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 514164098 128 DINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDM 177
Cdd:cd17522  141 ELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEKLKELKKGLFQKL 190
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 1-175 6.27e-19

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoKI TRD1-CR1, S.StySPI TRD1-CR1, S.Ara36733II TRD1-CR1, and S.Eco3722I TRD1-CR1; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) and Escherichia coli NCM3722 S subunit (S.Eco3722I) recognize 5'... AACNNNNNNGTGC ... 3', Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3', and Actinomyces radicidentis S subunit (S.Ara36733II) recognizes 5'... CATCNNNNNNCTC ... 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 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 Treponema pedis T A4 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.TpeTA4ORF2695P. It may also include type I DNA methyltransferases.


Pssm-ID: 341141 [Multi-domain]  Cd Length: 189  Bit Score: 83.38  E-value: 6.27e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   1 MEKVQLGTLVKITSGFAFKSNLFNTDKK--GLPLIRIRDVVRG---YSDTYY--DGEYKAEYLIQKGDALIGMDgefnla 73
Cdd:cd17252    1 WEWVRLGEIAEIIRGVTYKKSDASEEPSegGIPVLRANNIQNGgldFDDLVYvpKSKVKEEQKLKKGDILICMS------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  74 lwNSGKALLNqRVCKIQSIDE----------R----LDQNYLIRFL--PKALKDIEDRTPFVTVKHLSVKDINNIQIPLP 137
Cdd:cd17252   75 --SGSKELVG-KAAFIDEDTDytfgafcgviRpkkeIDPRYLFYFLqsPSYREYIRSLASGTNINNLSNEHLENLKIPLP 151

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 514164098 138 PLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFI 175
Cdd:cd17252  152 PLAEQKRIVAKLDKLDALIDKLKQALEKLDELLKSLFQ 189
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 195-324 1.46e-17

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) TRD2-CR2; Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3'. The 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.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. 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: 341155 [Multi-domain]  Cd Length: 159  Bit Score: 78.64  E-value: 1.46e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 195 DALKIINGKN-QKAVLDQNGIFPICGSGGVMGYANEWLTPAKSVIIGRK----GNINkpiLMFENFWNVDTAFGLVPNKD 269
Cdd:cd17266    5 ELCKIKSGKSiTASKISEEGDYPVYGGNGIIGYTDEYNHEGEYILIGRVgalcGNVH---YVEGKFWVTDNALVVTPKKE 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 514164098 270 VlNADYLFWFCHFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQ 324
Cdd:cd17266   82 N-NIKFLYYLLKSLNLNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDS 135
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 2-172 2.23e-17

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: 79.12  E-value: 2.23e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   2 EKVQLGTLV-KITSGFAFKSNlfnTDKKGLPLIRIRDVVRGYSDTYYDGEY-------KAEYLIQKGDALigmdgeFNla 73
Cdd:cd17517    2 EVVKLGDLLeDPRYGTSKKSS---YDGSGTPVLRIPNIYDGGIDLDDLKKRvdlsekeLEKYLLKKGDIL------FN-- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  74 lWNSGKALLNQRVCKIQSIDE-----------RLDQN-----YLIRFL--PKALKDIEDR-TPFVTVKHLSVKDINNIQI 134
Cdd:cd17517   71 -RSNGSPELVGKCALVDEEDEpaifasylirlRLDKKkilpeFLYYYLnsPLGRKQIEKIaKSAAGQANINQKDLKKLPI 149

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 514164098 135 PLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17517  150 PLPPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKS 187
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 1-174 5.42e-17

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) TRD2-CR2; The recognition sequence of Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) 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: 341193 [Multi-domain]  Cd Length: 195  Bit Score: 78.03  E-value: 5.42e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   1 MEKVQLGTLVKITSGFAFKSNLFntDKKGLPLIRIRDVVRGYSDT----YYDGEYKAEY---LIQKGDALI--------- 64
Cdd:cd17512    1 WEEIRLGDIIDYQKGYAFKSKDY--QDSGIRIVRVSDFTDDSIDInnlvYISEEKANKYkkyELKENDIIIttvgswpsn 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  65 --GMDGEFNLALWNSGKALLNQRVCKIQSIDERLDQNYLIRFL-PKALKD-IEDRtpfvtVK------HLSVKDINNIQI 134
Cdd:cd17512   79 pdSVVGKVVRVPKEADGALLNQNAVKIRPKKGILDQSFLFYNLkSERFKNyIESI-----ARgnanqaSITLGDIKKFKF 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 514164098 135 PLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATF 174
Cdd:cd17512  154 LLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQALY 193
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 79-178 9.66e-17

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Methanococcus maripaludis C5 S subunit (S.MmaC5ORF1169P) TRD1-CR1, and Methanobacterium formicicum S subunit (S.Mfo3637ORF3708P); The recognition sequences of Methanococcus maripaludis C5 S subunit (S.MmaC5ORF1169P) and Methanobacterium formicicum S subunit (S.Mfo3637ORF3708P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341184 [Multi-domain]  Cd Length: 182  Bit Score: 77.25  E-value: 9.66e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  79 KALLNQRVCKIQSIDERLDQNYLIRFLpKALKD-IEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQ 157
Cdd:cd17296   83 EATTNQAIAGIKPKNKSINPKYLYYYL-KSLYEkFLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKFEKLIN 161

                         90       100
                 ....*....|....*....|.
gi 514164098 158 KRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17296  162 KRQEGLQLLDELVKSLFEEMF 182
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 75-178 1.64e-16

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S.MjaORF132P TRD1-CR1; The recognition sequence of Methanococcus jannaschii S subunit (MjaXIP/S.MjaORF132P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341164 [Multi-domain]  Cd Length: 186  Bit Score: 76.43  E-value: 1.64e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  75 WNSGKALLNQRVCKIQSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADE 154
Cdd:cd17275   83 INKIDVATNQAILGIIPKDEKLDFEFLYYWLLSLKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIAEILDKIDA 162

                         90       100
                 ....*....|....*....|....
gi 514164098 155 LRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17275  163 EIDKLEEKIEKLRELKKGLLQKMF 186
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 78-178 1.65e-16

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) TRD2-CR2 and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) TRD; The recognition sequences of Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341194 [Multi-domain]  Cd Length: 182  Bit Score: 76.40  E-value: 1.65e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  78 GK-ALLNQRVCKIQ-----SIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQ 151
Cdd:cd17513   76 GKvAINPFDICTSQdftslIPIKEVNPLFLAYLLYSLLQKLKSQLQGTSIKGITKDDLKNLKIPLPPLEEQQKIAAILSK 155

                         90       100
                 ....*....|....*....|....*..
gi 514164098 152 ADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17513  156 LDKLIEAHEKKLEKLKQLKKGLMQKLF 182
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 93-178 2.41e-16

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) TRD2-CR2 and Shewanella oneidensis MR-1 S subunit (S.SonIV) TRD1-CR1; Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) recognizes 5'... TACNNNNNNNRTRTC ... 3 while Shewanella oneidensis MR-1 S subunit (S.SonIV) recognizes 5'... TACNNNNNNGTNGT ... 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.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: 341139 [Multi-domain]  Cd Length: 185  Bit Score: 76.13  E-value: 2.41e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  93 DERLDQNYLIRFLPKAlkDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17250  102 NEGIDSEYLYYWLKKV--DLYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKG 179


                 ....*.
gi 514164098 173 TFIDMF 178
Cdd:cd17250  180 LRQSLL 185
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-174 6.06e-16

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) TRD1-CR1 and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) TR; The recognition sequences for Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) 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. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Helicobacter bizzozeronii CIII-1 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.HbiCORF8670P, and may also contain type I DNA methyltransferases.


Pssm-ID: 341190 [Multi-domain]  Cd Length: 175  Bit Score: 74.57  E-value: 6.06e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGFAFKSNLFNTDKKGLPlirirdvvrgysdtYYDG--EYKAEYLIQ-------------KGDALIGMD- 67
Cdd:cd17499    1 VRLGDVAEIIMGQSPEGKSYNTNKEGLP--------------FYQGkkEFGDKYIKEpntwttsptkiaeKNDILMSVRa 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  68 --GEFNLALWNS--GKALlnqrvCKIQSIdERLDQNYLIRFLpKALKD-IEDRTPFVTVKHLSVKDINNIQIPLPPLAEQ 142
Cdd:cd17499   67 pvGDVNITTRKIciGRGL-----AAIRAK-KNIDKKYLFYFL-LSNKDyFKGKSGGSTFKSINKNQIKNIKIPLPPLEEQ 139

                        170       180       190
                 ....*....|....*....|....*....|..
gi 514164098 143 RRIASILDQADELRQKRQQAIEKLDQLLQATF 174
Cdd:cd17499  140 KRIVSELDKLFKLIFEAKNNIEEALANAQQLF 171
RMtype1_S_Cje2232P-TRD2-CR2_like cd17526
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 2-178 8.67e-16

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: 74.55  E-value: 8.67e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   2 EKVQLGTLV-KITSGFAfkSNLFNTDKKGLPLIR----------IRDVVRGYsdtYYDGEYKAEYLIQKGDALigmdgeF 70
Cdd:cd17526    2 EVVRLGDIIlDIQSGFA--SGKQNEDEDGVPQLRphnittdgelDLDKLIKI---VPSPKERKRYLLQKGDVL------F 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  71 NLAlwNS----GK-ALLNQR---VC-----KIQSIDERLDQNYLIRFL-----PKALKDIEDRtpFVTVKHLSVKDINNI 132
Cdd:cd17526   71 NNT--NSqelvGKtALFDGEepyVFsnhmtRIRVKKSKINPEFLARYLhllwrSGYFKKLCTN--WVNQAGINSDTLANL 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 514164098 133 QIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17526  147 KIPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-174 3.69e-15

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) TRD2-CR2; Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3'. The 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.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. 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: 341155 [Multi-domain]  Cd Length: 159  Bit Score: 72.09  E-value: 3.69e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGfafksnlfntdkKGLPLIRIRDV----------VRGYSDTY-YDGEYkaeyliqkgdALIG------- 65
Cdd:cd17266    1 VKLGELCKIKSG------------KSITASKISEEgdypvyggngIIGYTDEYnHEGEY----------ILIGrvgalcg 58

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  66 ----MDGEFnlalWNSGKALlnqrVCKIqsiDERLDQNYLIRFLpKALKDIEDRT----PfvtvkHLSVKDINNIQIPLP 137
Cdd:cd17266   59 nvhyVEGKF----WVTDNAL----VVTP---KKENNIKFLYYLL-KSLNLNQYATgsaqP-----LITVSKLKKLKIPLP 121

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 514164098 138 PLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATF 174
Cdd:cd17266  122 PLEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKELM 158
RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like cd17289
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 1-178 7.09e-15

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus amyloliquefaciens JRS5 S subunit (S.BamJRS5ORF1993P) TRD1-CR1 and Bacillus pumilus Jo2 S subunit (S.BpuJo2I) TRD1-CR1; The recognition sequences of Bacillus amyloliquefaciens JRS5 S subunit (S.BamJRS5ORF1993P) and Bacillus pumilus Jo2 S subunit (S.BpuJo2I) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341178 [Multi-domain]  Cd Length: 191  Bit Score: 72.29  E-value: 7.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   1 MEKVQLGTLVKITSGfafkSNLFNTD--KKGLPLIRIRDVVRGY-----------SDTYYDgEYKAEYLI-QKGDALI-- 64
Cdd:cd17289    1 WEWKKLGDIAEITSS----KRIFKSEyvDSGIPFYRSKEIIELFngeeistelfiSEERYE-EIKSKYGVpKKGDILIts 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  65 ----------GMDGEF-----NLaLWnsgkallnqrvckIQSIdERLDQNYLIRFL--PKALKDIEDRTPFVTVKHLSVK 127
Cdd:cd17289   76 vgtigipylvKNDDPFyfkdgNL-TW-------------FKNI-KDINSKFLYYWFqsSIFKNQINSITIGSTQKALTIE 140

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 514164098 128 DINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17289  141 KLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEELAKTLFQYWF 191
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 90-178 7.49e-15

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoJA69PI TRD1-CR1, MjaXIP/S.MjaORF132P TRD2-CR2, and S.HspDL1ORF16625P TRD2-CR2; Escherichia coli UCD_JA69_pb S subunit (S.EcoJA69PI) recognizes 5'... CCANNNNNNNCTTC ... 3'. The recognition sequences of Methanococcus jannaschii MjaXIP/S.MjaORF132P TRD2-CR2 and Halobacterium species DL1 S subunit (S.HspDL1ORF16625P) 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. It also includes TRD-CR-like sequence-recognition domains of various putative type II restriction enzymes and methyltransferases and may also include type I DNA methyltransferases.


Pssm-ID: 341162 [Multi-domain]  Cd Length: 186  Bit Score: 72.05  E-value: 7.49e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  90 QSI--DERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLD 167
Cdd:cd17273   96 KSIipNEEIDNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEIPLPPLEEQKKIAAILSKLDELIELLEKENEKLK 175

                         90
                 ....*....|.
gi 514164098 168 QLLQATFIDMF 178
Cdd:cd17273  176 ELRDGLLPKLF 186
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 124-174 1.09e-14

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: 71.41  E-value: 1.09e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 514164098 124 LSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATF 174
Cdd:cd17264  132 LSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQSLF 182
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 56-172 1.12e-14

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2; The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 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 CD 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: 341136 [Multi-domain]  Cd Length: 190  Bit Score: 71.41  E-value: 1.12e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  56 LIQKGDALIGMDGEfnlalwnsGK-----ALL------NQRVCKIQSIDERLDQNYLIRFLPKA---LKDIEDRTpfvTV 121
Cdd:cd17247   66 LVPPGSVLVAMIGQ--------GKtrgqaAILaieatiNQNLAAIRPNEERVLPEYLHYYLESQydeLRRIGSGG---GQ 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 514164098 122 KHLSVKDINNIQIPLPPLAEQRRIASILD----QADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17247  135 GALNCGILKAFPIPLPPLDEQREIVAELEallaKIDLLEEKIARLIELLKELRQA 189
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-172 1.13e-14

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2; The recognition sequence is undetermined for Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P). 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 CD contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.TteMORF1547P TRD1-CR1 does not belong to this subfamily.


Pssm-ID: 341188 [Multi-domain]  Cd Length: 174  Bit Score: 71.04  E-value: 1.13e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGFAFKSNLFNTDKKGLPlirirdvvrgysdtYYDGeyKAEY----------------LIQKGDALIGMD 67
Cdd:cd17497    1 KKLKYVADIIMGQSPPSSTYNTEGIGLP--------------FLQG--KAEFgklyptprkwcsapkkIAEKGDILLSVR 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  68 ---GEFNLAlwnsgkallNQR------VCKIQSiDERLDQNYL---IRFLPKALKDIEDRTPFVTVkhlSVKDINNIQIP 135
Cdd:cd17497   65 apvGPTNIA---------DQEycigrgLAAIRP-KKGLDKKYLlyyLKSIENELSSLGTGSTFKAI---SKEDLENLLIP 131

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 514164098 136 LPPLAEQRRIASILDQA----DELRQKRQQAIEKLDQLLQA 172
Cdd:cd17497  132 LPPLAEQKRIAAFLDELtakiDQLIALLEKAIELLKEYRQA 172
RMtype1_S_PluTORF4319P-TRD2-CR2_like cd17269
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 77-174 2.52e-14

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Photorhabdus luminescens S subunit (S.PluTORF4319P) TRD2-CR2; The recognition sequence of Photorhabdus luminescens S subunit (S.PluTORF4319P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341158 [Multi-domain]  Cd Length: 168  Bit Score: 69.93  E-value: 2.52e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  77 SGKALLNQRVCKIQSIDERLDQNYLIRFLPKALKDIEDRTPF-VTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADEL 155
Cdd:cd17269   63 NGKFNAYQRTYVIHPFKEEIDPKFLYYYLKSYFKKYIEKNSVgSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDAL 142

                         90       100
                 ....*....|....*....|...
gi 514164098 156 RQKRQQAIE----KLDQLLQATF 174
Cdd:cd17269  143 TAELPAELEarkkQYEYYRDALL 165
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 131-178 4.03e-14

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) TRD1-CR1, Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) TRD1-CR1; The recognition sequences of Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) and Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) 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 superfamily 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: 341182 [Multi-domain]  Cd Length: 180  Bit Score: 69.79  E-value: 4.03e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 514164098 131 NIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17293  133 KIEIPLPPLEEQKRIVAKLDKLFALIDKLEESLEELDELLKSLFQSAF 180
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 93-176 1.05e-13

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acetobacter pasteurianus S subunit (S.Apa101655I) TRD2-CR2; The S. Apa101655I S subunit recognizes 5'... TTAGNNNNNNTTC... 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: 341133 [Multi-domain]  Cd Length: 180  Bit Score: 68.65  E-value: 1.05e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  93 DERLDQNYLIRFLP-KALKDIEDRTpfVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQ 171
Cdd:cd17244   98 DKKIDTEYLYYYLKsFDYSSLGSTA--SKGKTLNSKKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDELLP 175


                 ....*
gi 514164098 172 ATFID 176
Cdd:cd17244  176 KLMSG 180
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 2-172 3.92e-13

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: 67.18  E-value: 3.92e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   2 EKVQLGTLV-KITSGFAFKSNlfnTDKKGLPLIRIRDVVRGYsdtYYDGEYK---------AEYLIQKGDALI------- 64
Cdd:cd17261    2 EWVRLGDLIeGIRNGWSPKPP---DDETGWPVLKLSAVTSGK---FDPSENKylpeslepaSEYWLKPGDLLIsrantse 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  65 --GMDGEFNLalwNSGKALLNQRVCKIQSIDERLDQNYLIRFL--PKALKDIEDR---TPFVTVKhLSVKDINNIQIPLP 137
Cdd:cd17261   76 lvGRAALVDG---DPDNLIYPDKLIRLRVNEELLLPEYLALALnsPSARRQIESRatgTAGSMPK-ISQSDLKSLPIPLP 151

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 514164098 138 PLAEQRRIASILDQ----ADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17261  152 PLAEQKRIVARVDEllalIDRLEAQLAAALQLLDRLRQA 190
RMtype1_S_Asp27244ORF1181P-TRD1-CR1_like cd17518
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 27-173 5.39e-13

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter sp. S subunit (S.Asp27244ORF1181P) TRD1-CR1; The recognition sequence of Acinetobacter sp. S subunit (S.Asp27244ORF1181P) 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: 341199 [Multi-domain]  Cd Length: 180  Bit Score: 66.62  E-value: 5.39e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  27 KKGLPLIRIRDVVRGY----------SDTYYDGEYKaEYLIQKGDALIGMDGefnlALWN--------SGKALLNQRVCK 88
Cdd:cd17518   22 DEGIKLLNVTNIVNGSldldktdryiSTEEYNGKYK-HFLIDEGDILIASSG----NSWGkvaivekdHLPLMLNTSTIR 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  89 IQSIDERLDQNYLIRFLP----KALKDIEDRT---PFVTVKHLSvkdinNIQIPLPPLAEQRRIASILDQADelrQKRQQ 161
Cdd:cd17518   97 FKFIDGLLDNNFLKYFLNsdyfKEQLDLLITGgaqPNFGPSHLK-----KIKIPLPPLEEQKRIAEILDDAD---DAIEA 168

                        170
                 ....*....|..
gi 514164098 162 AIEKLDQLLQAT 173
Cdd:cd17518  169 ALEALRKKKQAA 180
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 56-172 6.38e-13

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) TRD2-CR2, and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) TRD2-CR2; The recognition sequences of Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341176 [Multi-domain]  Cd Length: 184  Bit Score: 66.36  E-value: 6.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  56 LIQKGDALIGMDGEfnlalwnsGK-----ALL------NQRVCKIQSIDeRLDQNYLIRFLPKALKDIEDRTPFVTVKHL 124
Cdd:cd17287   59 LFPKGTLLMAMYGQ--------GKtrgrvAILgieaatNQACAAILPND-GINPDFLFYYLQSSYEELRDLSNGGGQPNL 129

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 514164098 125 SVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17287  130 NAGLIKSIEIPVPPLDEQQKIAAFLSAIDAKIDALEQKLELLQELKKS 177
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 93-174 1.42e-12

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoR124I TRD2-CR2, S.Eco540I TRD2-CR2, S.Eco540AI TRD2-CR2, and S.Eco540ANI TRD2-CR2; Escherichia coli (R124) S subunit (S.EcoR124I), E. coli ST540 S subunit (S.Eco540I), E. coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540AN S subunit (S.Eco540ANI) recognize the sequence 5'... GAANNNNNNRTCG ... 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.EcoR124I -TRD1 recognizes GAA/TTC, and -TRD2 recognizes CGAY/RTCG. 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: 341138 [Multi-domain]  Cd Length: 185  Bit Score: 65.55  E-value: 1.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  93 DERLDQNYLIRFLpKALKDI---EDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQL 169
Cdd:cd17249   99 KEGIDPEFLLYAL-KANEDRilsLVDKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEEL 177


                 ....*
gi 514164098 170 LQATF 174
Cdd:cd17249  178 LKALM 182
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 2-178 1.66e-12

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: 65.57  E-value: 1.66e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   2 EKVQLGTLVKITSGFAfKSNLFNTDKKGLPLIRIRDVVRGY---SDTYY----DGEYKaEYLIQKGDALI--GmdGEFNL 72
Cdd:cd17253    3 EWVRLGDVAEVQSGIT-KGKKRRGGELEVPYLRVANVQDGYldlSEVKEievtEEELE-RYRLRKGDLLVteG--GDSDK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  73 ----ALWNSgkallnqrvckiqSIDERLDQNYLIRFLPKALKDIED------RTP-----FVTV-------KHLSVKDIN 130
Cdd:cd17253   79 lgrgAIWRG-------------EIPPCLHQNHLFRVRPKDDLLLPEflsywlNSAygrgyFLRAakqttnlASINSTKLK 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 514164098 131 NIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17253  146 ALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
100-172 1.69e-12

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 62.38  E-value: 1.69e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514164098 100 YLIRFlPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:COG0732    4 YYLRS-PSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDA 75
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 89-174 2.05e-12

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) TRD2-CR2 and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) T; The recognition sequences of Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341172 [Multi-domain]  Cd Length: 181  Bit Score: 64.81  E-value: 2.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  89 IQSIDERLDQNYLIRFL-PKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLD 167
Cdd:cd17283   94 FSDLKKKLDKDFLYYLLsSITVQLQFSAQAGGGTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLE 173


                 ....*..
gi 514164098 168 QLLQATF 174
Cdd:cd17283  174 ELKKGLM 180
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 99-178 2.19e-12

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli G4/9 S subunit (S.Eco16444ORF1681P) TRD1-CR1 and Zobellia galactanivorans DsiJT S subunit (S.ZgaJTORF2697P)TRD2; The recognition sequences of Escherichia coli G4/9 S subunit (S.Eco16444ORF1681P) and Zobellia galactanivorans DsiJT S subunit (S.ZgaJTORF2697P) 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 putative type II restriction enzymes and methyltransferases and may also include type I DNA methyltransferases.


Pssm-ID: 341171 [Multi-domain]  Cd Length: 186  Bit Score: 64.77  E-value: 2.19e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  99 NYLIRFLPKALKDIedrTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17282  110 EYYLRTLKKELEAI---APQSAQKNINLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIAKLEELKQSLLQEAF 186
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 124-178 2.76e-12

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Lactococcus lactis S subunit (S.LlaAI06ORF1089P) TRD1-CR1 and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) TRD2-CR2; The recognition sequences of Lactococcus lactis S subunit (S.LlaAI06ORF1089P) and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341177 [Multi-domain]  Cd Length: 163  Bit Score: 64.03  E-value: 2.76e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 514164098 124 LSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17288  107 LTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDALIELQEKLLEKLKQYKLALMQ 161
RMtype1_S_Ara36733I_TRD1-CR1_like cd17268
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 120-168 5.09e-12

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: 64.00  E-value: 5.09e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 514164098 120 TVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQ 168
Cdd:cd17268  130 KVVHISASDLAKIKIPVPPLEEQERIVEILDKFDALIAGLPAEIEARRK 178
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 129-178 8.50e-12

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoEI TRD1-CR1, S.EcoJA17PI TRD1-CR1, S.EcoJA23PI TRD1-CR1, and S.StyLTIII TRD1-CR1; Escherichia coli A58 S subunit (S.EcoEI) recognizes 5'... GAGNNNNNNNATGC ... 3', Escherichia coli UCD_JA17_pb S subunit (S.EcoJA17PI) and Escherichia coli UCD_JA23_pb S subunit (S.EcoJA23PI) recognize 5'... GAGNNNNNNNGTCA ... 3', and Salmonella typhimurium LT7 S subunit (S.StyLTIII) recognizes 5'... GAGNNNNNNRTAYG ... 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.EcoEI TRD1 and S.StyLTIII TRD1 recognize GAG/CTC, S.EcoEI TRD2 recognizes GCAT/ATGC, and S.StyLTIII TRD2 recognizes CRTAY/RTAYG. 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 methyltransferas RM.PpiI and Porphyromonas macacae COT-192 OH2631 RM.Pma2631ORF8845P, as well as type I DNA methyltransferases such as Chlorobium limicola M.Cli245ORF128P. RM.PpiI recognizes the sequence 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341149 [Multi-domain]  Cd Length: 165  Bit Score: 62.84  E-value: 8.50e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 514164098 129 INNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17260  116 LENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 56-178 1.20e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1 and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) TRD2-CR; The recognition sequences of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341183 [Multi-domain]  Cd Length: 188  Bit Score: 62.89  E-value: 1.20e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  56 LIQKGDALIGMDGefnlalwnSGK-----ALL------NQRVCKIQSIDERLDQNYLIRFLP------KALKDIEDRTpf 118
Cdd:cd17294   63 WIPKNSVLIALAG--------QGKtrgtvAILkiplttNQSLAAIEPDEEIANSRFLYYNLSsryeelRSLSGGGGRG-- 132

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 119 vtvkHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17294  133 ----GLNLKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLPALLELRQKQYEYLR 188
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 41-177 1.96e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) TRD2-CR2 and Moraxella catarrhalis S subunit (S.Mca353ORF290P) TRD2; Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) recognizes 5'... GCANNNNNNTGT ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 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: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 61.68  E-value: 1.96e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  41 GYSDTY-YDGEYkaeyliqkgdALIGMDGE------FNLALWNSGKALLNQRVCKIQSIDerldqNYLIRFLPKALKDIe 113
Cdd:cd17262   42 DYVDDYiFDGEY----------VLIGEDGAnllsrgTPIAFYVSGKFWVNNHAHVLKGKN-----GISTEFLYYYLNSI- 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 514164098 114 DRTPFVT---VKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDM 177
Cdd:cd17262  106 DISPYVTgaaQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQKL 172
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-178 2.00e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) TRD1-CR1; The S.Aco12261I S subunit recognizes 5'... GCANNNNNNTGT ... 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. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.Aco12261I TRD2-CR2 does not belong to this subfamily.


Pssm-ID: 341189 [Multi-domain]  Cd Length: 173  Bit Score: 61.93  E-value: 2.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGFAFKSNLFNTDKKGLPLIRIRdvvRGYSDTY-----YDGEYKAeyLIQKGDALIGMD---GEFNLAlw 75
Cdd:cd17498    1 VKLGEIAEITMGQSPKSEFYNEDGIGLPFLQGN---RTFGDKYpyidtYTTDIKK--IAKKGDILMSVRapvGDLNIA-- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  76 nsgkallNQRVC---KIQSIDERLDQN----YLIRFLPKALKDIEDRTPFVTVkhlSVKDINNIQIPLPPLAEQRRIASI 148
Cdd:cd17498   74 -------NKDICigrGLCSIRMKNGNNsflyYLLKNNIKNLINKSSGTVFGSI---NKDDIENLEVDIPEDEEQKRIANI 143

                        170       180       190
                 ....*....|....*....|....*....|
gi 514164098 149 LDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17498  144 LSKIDDKIEINNQINKNLEELAQAIFKHWF 173
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 186-315 3.32e-11

Type I restriction modification DNA specificity domain; This domain is also known as the target recognition domain (TRD). 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 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 subunit (this family), two modification (M) subunits and two restriction (R) subunits.


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 61.22  E-value: 3.32e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  186 KGWEVLKWRDALKIINGKNQ-KAVLDQNGIFPICGSG-------GVMGYANEWLTPAKSVIIGRKGNINKPILMFENFWN 257
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPkKKELKNNGKYPYIRAGdlnnvvkGGLGYIKKYILPKGDITISSRATIGYVFYRDKPYYT 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  258 VDTAFGLVP-NKDVLNADYLFWFCHFFN-FEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:pfam01420  82 NQHIIVLIPkNNIKITEFLYLYLLLKLKkLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQ 141
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 120-178 5.40e-11

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: 59.86  E-value: 5.40e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 514164098 120 TVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17292   91 TIKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYLF 149
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 120-178 2.70e-10

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) TRD2-CR2 and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) TRD2-CR; Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) recognizes 5'... GAGNNNNNGTTY ... 3', and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) recognizes 5'... YTCANNNNNNGTTY ... 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.Eco4255III-TRD1 recognizes GAG/CTC and S.EcoNIH1II-TRD1 recognizes YTCA/TGAR, while both S.EcoNIH1II-TRD2 and S.Eco4255III-TRD2 recognize RAAC/GTTY. 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: 341154 [Multi-domain]  Cd Length: 181  Bit Score: 58.67  E-value: 2.70e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 514164098 120 TVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17265  123 TINQITNGNLNNFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKELMQQLI 181
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 121-165 3.68e-10

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.MgeORF438P TRD1-CR1 and TRD2-CR2, and to Escherichia coli G5 S subunit (S.Eco16445ORF5013P ) TRD2-CR2 and Acetobacter pasteuri; The recognition sequences of Mycoplasma genitalium G-37 S subunit (S.MgeORF438P), Escherichia coli G5 S subunit (S.Eco16445ORF5013P), and Acetobacter pasteurianus IFO 3283-01 S subunit (S2.Apa3283ORF14230P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341180 [Multi-domain]  Cd Length: 161  Bit Score: 57.91  E-value: 3.68e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 514164098 121 VKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEK 165
Cdd:cd17291  108 QPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFTELTAELPAELEA 152
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 59-173 3.86e-10

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S.Sau1132ORF3780P TRD1-CR1, and S.Mca353ORF290P TRD1-CR1; The Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 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.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG, and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. 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: 341165 [Multi-domain]  Cd Length: 187  Bit Score: 58.37  E-value: 3.86e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  59 KGDALIGMDGEFN-------LALwnsgKALLNQRVCKIQSIDERLDQNYLIRFL----PK-------ALKDiedrtPfvt 120
Cdd:cd17276   64 KGTVLVAMYGGFGqigrtglLGI----PAAINQAICAILPNEKKVNPEFLLRYLnfnrPYwmrvaasSRKD-----P--- 131

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 514164098 121 vkHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQAT 173
Cdd:cd17276  132 --NITKDDVRNFPIPLPPLDEQRAIVEFLSDVDALIDSLEALIEKLRELKKGL 182
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 128-174 3.97e-10

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoAO83I TRD1-CR1 and S.AbaB8342I TRD2-CR2; Escherichia coli strain A0 34/86 S subunit (S.EcoAO83I) recognizes 5'... GGANNNNNNNNATGC ... 3, and Acinetobacter baumannii B8342 S subunit (S.AbaB8342I) recognizes 5'... TTCANNNNNNTCC ... 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.AbaB8342I-TRD1 recognizes TTCA/TGAA and S.AbaB8342I-TRD2 recognizes GGA/TCC. 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 Type IIG restriction enzyme/N6-adenine DNA methyltransferases from Thermus scotoductus RFL1 (RM.TstI) and Acinetobacter lwoffi Ks 4-8 (RM.AloI), as well as type I DNA methyltransferases such as Sideroxydans lithotrophicus ES-1 Type I N6-adenine DNA methyltransferase (M.SliESORF1090P). RM.TstI recognizes 5' ... CACNNNNNNTCC ... 3' and RM.AloI recognizes 5' ... GAACNNNNNNTCC ... 3'.


Pssm-ID: 341156 [Multi-domain]  Cd Length: 158  Bit Score: 57.80  E-value: 3.97e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 514164098 128 DINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATF 174
Cdd:cd17267  110 DVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADALL 156
RMtype1_M_Cni19672ORF1405P_RMtype11G_Hci611ORFHP_T cd17277
Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 ...
 4-174 4.86e-10

Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 Calditerrivibrio nitroreducens M.Cni19672ORF1405P TRD1-CR1 and RMtype11G Helicobacter cinaedi PAGU611 RM.Hci611ORFHP TRD1-CR1; The recognition sequence of Calditerrivibrio nitroreducens M.Cni19672ORF1405P is undetermined, and the predicted recognition sequence of RM.Hci611ORFHP is 5'... GAGNNNNNGT ... 3'. M.Cni19672ORF1405P is a putative type I N6-adenine DNA methyltransferase. RM.Hci611ORFHP is a type II subtype gamma (also called type IIG and type IIC) N6-adenine DNA methyltransferase. Both are DNA methyltransferase-specificity subunit fusion proteins, they each have a domain corresponding to a HsdM methylation (M) subunit followed by a C-terminal, TRD-CR-like domain for sequence-recognition, which corresponds to the HsdS specificty (S) subunit. The latter consists of two variable TRDs, and two CRs which separate the TRDs; the TRDs each bind to different specific sequences in the DNA. RM.Hci611ORFHP has an additional N-terminal HSDR_N domain. Restriction-modification (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, two modification (M) subunits, and two restriction (R) subunits.


Pssm-ID: 341166 [Multi-domain]  Cd Length: 184  Bit Score: 58.19  E-value: 4.86e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   4 VQLGTLVKITSGFA-FKSNLFNTDKKGLPLIRIRDVVRGYSDTYYDGEYKAE--------YLIQKGDALIGMDGEFNLAL 74
Cdd:cd17277    4 VKLGEVCEIINGSTpSKKNEEYWNNGTIKWLTIPDIDERGLIISSTKQFITEkaleekkvKLVPKNSVLLSCTATIGKVA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  75 WNSGKALLNQRVCKIQSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADE 154
Cdd:cd17277   84 IAKIELTTNQQINALICKDSKILPEYLFYALKHIKQVLERLTTNPGVKHVNLSMLSNLQIPLPPLEVQKKIVAEIEKVEK 163

                        170       180
                 ....*....|....*....|
gi 514164098 155 LRQKRQQAIEKLDQLLQATF 174
Cdd:cd17277  164 VIQGLRQKIDEYQPLINAIL 183
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 100-172 7.82e-10

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) TRD2-CR2 and Shewanella xiamenensis BC01 S subunit (S.SxiBC01OR; The recognition sequences of Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) and Shewanella xiamenensis BC01 S subunit (S.SxiBC01ORF77P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341173 [Multi-domain]  Cd Length: 185  Bit Score: 57.61  E-value: 7.82e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514164098 100 YLIRFLPKALKDIEDRTpfvTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17284  110 YLLSLQKKYMEKIATGT---TIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKG 179
RMtype1_S_Eco2747II-TRD2-CR2-like cd17272
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 2-159 7.96e-10

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Eco2747II TRD2-CR2 and S.Eco2747AII TRD2-CR2; Escherichia coli ST2747 S subunit (S.Eco2747II) and Escherichia coli ST2747A s SUBUNIT (S.Eco2747AII) recognize 5'... GAANNNNNNNTAAA ... 3'. Generally 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. 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 mainly 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: 341161 [Multi-domain]  Cd Length: 189  Bit Score: 57.44  E-value: 7.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   2 EKVQLGTLVkiTSGFAFkSNLFNTDKKGL-PLIRIRDVVRGYSDTYYDGEYKAEYL----IQKGDALIGMDGE----FNL 72
Cdd:cd17272    2 EEKTLGDIA--VDGFQN-GPAPNFDEKGEiPVITSKNISNGKIDFEYVKYDFLSISknrkINKGDILITMIGTigetAIV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  73 ALWNSGKALLNQRVCKIQSidERLDQNYLIRFL--PKALKDIEDRTpfVTVKHLSVKDINNIQIPLPPLAEQRRIASILD 150
Cdd:cd17272   79 KCLDPKFYTLNLYLIRLKK--EKLLPSYLKYFLdsEKFLNKSISAT--SGQGYLKANQIDKLEIPLPPLEEQQRIVKILD 154

                        170       180
                 ....*....|....*....|...
gi 514164098 151 QAD--------------ELRQKR 159
Cdd:cd17272  155 KFDtlcnditeglpaeiEARQKQ 177
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 97-177 1.48e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Flavobacterium columnare S subunit (S.Fco49512ORF2615P) TRD2-CR2; 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. 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: 341144 [Multi-domain]  Cd Length: 166  Bit Score: 56.38  E-value: 1.48e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  97 DQNYLIRFLPKALKDIE-DRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFI 175
Cdd:cd17255   85 NKNINNKFLYYALNLIAkKYVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIAKLKKLIELRKKQLE 164


                 ..
gi 514164098 176 DM 177
Cdd:cd17255  165 YY 166
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 120-172 2.13e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Burkholderia multivorans CF2 S subunit (S.BmuCF2ORF3362P) TRD1-CR1 and and Halomonas campaniensis LS21 S subunit (S.HcaLS21ORF99; The recognition sequences of Burkholderia multivorans CF2 S subunit (S.BmuCF2ORF3362P) and Halomonas campaniensis LS21 S subunit (S.HcaLS21ORF9970P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341168 [Multi-domain]  Cd Length: 184  Bit Score: 56.41  E-value: 2.13e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 514164098 120 TVKHLSVKDINNIQIPLPPLAEQRRIASILDQA----DELRQKRQQAIEKLDQLLQA 172
Cdd:cd17279  125 TFLELSTDELANFKIPLPPLSEQRAIADFLDREtakiDALIAKKQQLIELLKEKRQA 181
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 128-174 3.29e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Actinosynnema mirum DSM 43827 S subunit (S. AmiI) TRD2-CR2; The S. AmiI S subunit recognizes 5'... CAGNNNNNNNTCGA ... 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. AmiI -TRD1 recognizes CAG/CTG, and TRD2 recognizes TCGA. 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: 341137 [Multi-domain]  Cd Length: 196  Bit Score: 56.00  E-value: 3.29e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 514164098 128 DINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATF 174
Cdd:cd17248  139 DFKALRIALPPLEEQRKIVDRLEALDAKIDALERKLERLIELLKELR 185
RMtype1_S_MmaGORF2198P_TRD1-CR1_like cd17500
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 83-174 3.72e-09

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) TRD1-CR1, and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) TRD1-CR1; The recognition sequences of Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) 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 TRD1-CR1. 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: 341191 [Multi-domain]  Cd Length: 186  Bit Score: 55.76  E-value: 3.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  83 NQRVCKIQSIDERLDQNYLIRFLPKALKDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQA 162
Cdd:cd17500   90 NQACCNLIIDNKKADYRFVYYSLKTQYEELVNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLDDKIELNNRQ 169

                         90
                 ....*....|..
gi 514164098 163 IEKLDQLLQATF 174
Cdd:cd17500  170 NETLEAMAETLF 181
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 195-324 3.72e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.MgeORF438P TRD1-CR1 and TRD2-CR2, and to Escherichia coli G5 S subunit (S.Eco16445ORF5013P ) TRD2-CR2 and Acetobacter pasteuri; The recognition sequences of Mycoplasma genitalium G-37 S subunit (S.MgeORF438P), Escherichia coli G5 S subunit (S.Eco16445ORF5013P), and Acetobacter pasteurianus IFO 3283-01 S subunit (S2.Apa3283ORF14230P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341180 [Multi-domain]  Cd Length: 161  Bit Score: 55.21  E-value: 3.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 195 DALKIINGKNQ-KAVLDQNGIFPICgSGGV--MGYANEWLTPAKSVIIGRKGN----INkpiLMFENFWNVDTAFGLVPN 267
Cdd:cd17291    5 EIAEIKKGKQItKKELIENGKYPVI-AGGIepSGYHNEYNREGNTITISASGAsagyVN---YWKEPFWASDCCYILSSK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514164098 268 KDVLNaDYLFwfcHFFNFEQ-----LNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQ 324
Cdd:cd17291   81 NELVN-KFLY---YFLKNKQeeiysLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDK 138
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 262-315 4.21e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) TRD2-CR2 and Shewanella oneidensis MR-1 S subunit (S.SonIV) TRD1-CR1; Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) recognizes 5'... TACNNNNNNNRTRTC ... 3 while Shewanella oneidensis MR-1 S subunit (S.SonIV) recognizes 5'... TACNNNNNNGTNGT ... 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.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: 341139 [Multi-domain]  Cd Length: 185  Bit Score: 55.33  E-value: 4.21e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 514164098 262 FGLVPNkDVLNADYLFWFCHFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:cd17250   97 MGLIPN-EGIDSEYLYYWLKKVDLYKYSQATTVPSIRKSTLESIPIPLPPLEEQ 149
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 131-174 4.78e-09

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) TRD2-CR2, Escherichia coli E24377A S subunit (S.EcoE24377ORF286P) TRD1-CR1 and Pseudoalteromonas species P1-1; Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) recognizes 5'... TCTANNNNNNRTTC ... 3', and the recognition sequences of Escherichia coli E24377A S subunit (S.EcoE24377ORF286P) and Pseudoalteromonas species P1-13-1a S subunit (S.Psp1bORF2093P) are undetermined. 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. For example, Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) TRD1 recognizes TCTA/TAGA, and -TRD2 recognizes GAAY/RTTC. 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. In addition, this family includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P.


Pssm-ID: 341202 [Multi-domain]  Cd Length: 187  Bit Score: 55.18  E-value: 4.78e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 514164098 131 NIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATF 174
Cdd:cd17521  141 SLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLKELL 184
RMtype1_S_EcoUTORF5051P-TRD2-CR2_like cd17524
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 131-172 1.72e-08

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: 53.62  E-value: 1.72e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 514164098 131 NIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17524  143 AIPIPLPPLEEQKEIVEKLDELDALIDRLEALLEEAEELLES 184
RMtype1_S_Eco15ORF14057P-TRD1-CR1_like cd17525
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 2-172 4.94e-08

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli 541-15 S subunit (S.Eco15ORF14057P) TRD1-CR1 and Desulfotignum phosphitoxidans S subunit (S.Dph13687ORF2110P) TRD2-CR2; The recognition sequences of Escherichia coli 541-15 S subunit (S.Eco15ORF14057P) and Desulfotignum phosphitoxidans S subunit (S.Dph13687ORF2110P) 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. 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: 341206 [Multi-domain]  Cd Length: 190  Bit Score: 52.23  E-value: 4.94e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   2 EKVQLGTLVKITS-GFAFKSNLFNTdkkGLPLIRIRDVVRGYSDTYYDGEY-------KAEYLIQKGDALigmdgeFN-- 71
Cdd:cd17525    2 EWVKLGDILSSTQlGLVRSNSEDPN---GYPYIKMGNIGRGGINLLKVETYvdateleVEKYLLEDGDLL------FNtr 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  72 --------LALW--NSGKALLNQRVCKIQSIDERLDQ--NYLIRfLPKALKDIEDRTPFVTvkhlSV-----KDINNIQI 134
Cdd:cd17525   73 ntlelvgkVAIWrgELPKALFNNNILRIRFDDIVLPYfiNYYLN-SPDGKKQLESIASGTT----SVaaiyqKDLKKLKL 147

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 514164098 135 PLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17525  148 PLPPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKKA 185
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 264-348 1.30e-07

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) TRD1-CR1, Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) TRD1-CR1; The recognition sequences of Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) and Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) 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 superfamily 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: 341182 [Multi-domain]  Cd Length: 180  Bit Score: 50.92  E-value: 1.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 264 LVPNKDVlNADYLFWFChFFNFEQLNKTV---TIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQTRILKSKME---LKDL 337
Cdd:cd17293   92 IIPNKSV-DPKFLYYQL-LSSKFQLQAIAsstTLPIINKSKFEKIEIPLPPLEEQKRIVAKLDKLFALIDKLEeslEELD 169

                         90
                 ....*....|.
gi 514164098 338 NLFSSLQNQAF 348
Cdd:cd17293  170 ELLKSLFQSAF 180
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 198-315 1.83e-07

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.


Pssm-ID: 341131 [Multi-domain]  Cd Length: 178  Bit Score: 50.46  E-value: 1.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 198 KIINGKNQKAVLD--QNGIFPICGSGGVMG----------------YANEWLTPAKSVIIGRKGNINKPILM--FENFWN 257
Cdd:cd16961    8 EIISGKTPSSSSEywDNGIIPWIRISDINNggiiltdekiteegaeKLKKKILPKGDILISRSGTIGKVAIVkeNDKALL 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 514164098 258 VDTAFGLVPNKDVlNADYLFWFC---HFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:cd16961   88 NQAVIVIRPKDEV-DSEFLYYFLkspFGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQ 147
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 260-315 1.84e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) TRD1-CR1; Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) recognizes 5'... GAYNNNNNNNTCYC ... 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: 341152 [Multi-domain]  Cd Length: 177  Bit Score: 50.58  E-value: 1.84e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 514164098 260 TAFGLVPNKDVLNADYLFWFC---HFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:cd17263   83 TLFKIIPDKNIIDKDYLYYFLkskEIQLNILTKAGSTIPHVNKKDLENLKIPLPSLEEQ 141
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
285-352 2.27e-07

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 48.13  E-value: 2.27e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514164098 285 FEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQL----CFSNICDQTRILKSKMELKDlNLFSSLQNQAFNGTL 352
Cdd:COG0732   15 LRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKriveILDSLFDKIAALEKEIEKLK-ELRDALLPKLFTGEL 85
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 127-178 3.91e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) TRD2-CR2 and Lactobacillus amylovorus GRL 1112 S subunit (S1.L; The recognition sequences of Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) and Lactobacillus amylovorus GRL 1112 S subunit (S1.LamGRLORF5415P) 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. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341185 [Multi-domain]  Cd Length: 171  Bit Score: 49.44  E-value: 3.91e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 514164098 127 KDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17494  120 NDIKNLKISIPSLEEQQKIATFLSTLDAEITLLEKKLEKLKQLKKGLLQKLF 171
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 110-172 4.68e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Algibacter lectus S subunit (S.AleSS8ORF2795P) TRD1-CR1 and Vibrio parahaemolyticus O1:K33 CDC_K4557 S subunit (S.Vpa4557ORF2259; The recognition sequences of Algibacter lectus S subunit (S.AleSS8ORF2795P) and Vibrio parahaemolyticus O1:K33 CDC_K4557 S subunit (S.Vpa4557ORF22590P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341179 [Multi-domain]  Cd Length: 184  Bit Score: 49.51  E-value: 4.68e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 514164098 110 KDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQA----DELRQKRQQAIEKLDQLLQA 172
Cdd:cd17290  116 EELENLANGATLPILNQEKLKNIKLPVPPLNEQQKIVEFLDKKtakiDALIAKKEQLIELLKEYRQA 182
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 131-178 5.32e-07

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) TRD1-CR1, and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) TRD2-CR2; The recognition sequences of Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341175 [Multi-domain]  Cd Length: 179  Bit Score: 49.03  E-value: 5.32e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 514164098 131 NIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17286  132 KIKILVPPLEEQQKIANFLSKLDELIELQQQKIEKLEELKKGLLQKLF 179
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
2-230 5.61e-07

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 51.04  E-value: 5.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098   2 EKVQLGTLVKITSGFAFKSN---LFNTDKKgLPLIRIRDVVRGYSDT----YYDGEYKA--EYLIQKGDALIGMDGEF-- 70
Cdd:PRK09737  11 VTTHISEICSVIRGVKPPKGyatKSLTMGD-LPFIRTTDITNGAVDLttlpYCMDAPEDvsKYQLQDRDIVISSAGSIgf 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  71 -----NLALWNSGKALLNQRVCKIQSIDERldqnYLIRFLPKAL--KDIEDRTPFVTVKHLSVKDINNIQIPLPPLAEQR 143
Cdd:PRK09737  90 sflaqNPLPSNVVFASFAIRLKPVNYFSEY----FLKHFLESSDyrNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAEQK 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 144 RIASILD----QADELRQKRQQAIEKLDQLLQATFIDMFGDPV-------SNSKGWEVLKWRDALKIINGKNQKAVLDQN 212
Cdd:PRK09737 166 IIAEKLDtllaQVDSTKARLEQIPQILKRFRQAVLGAAVSGKLteewrwpDLPSTWSVHKYSELVDSRLGGMSSKANNFG 245

                        250
                 ....*....|....*...
gi 514164098 213 GIFPICGSGGVMGYANEW 230
Cdd:PRK09737 246 SATPYLRNINVRWGSFDL 263
RMtype1_S_Eco540ANI-TRD1-CR1_like cd17274
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 97-172 1.09e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Eco540ANI TRD1-CR1, S.Eco2747AII TRD1-CR1, S.Eco540AI TRD1-CR1, S.Eco2747II TRD1-CR1, and S.Eco540I TRD1-CR1; Escherichia coli ST540AN S subunit (S.Eco540ANI ), Escherichia coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540 S subunit (S.Eco540I) recognize 5'... GAANNNNNNRTCG ... 3'. Escherichia coli ST2747A S subunit (S.Eco2747AII) and Escherichia coli ST2747 S subunit (S.Eco2747II) recognize 5'... GAANNNNNNNTAAA ... 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: 341163  Cd Length: 171  Bit Score: 48.26  E-value: 1.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  97 DQNYLIRFLPKALKDIEdrtpFVTVKH----LSVkdINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQA 172
Cdd:cd17274   91 NNNVNLKFVYEALQTIK----YVPGDHkrhwISE--YSKFKIPLPPLEEQNKIVRILDKFDELIAELEAKLELLKKQKKY 164
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 50-178 1.17e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2, Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1, and re; The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 3'. The recognition sequence of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) 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 CD contains both TRD1-CR1 and TRD2-CR2. It also includes the TRD-CR-like domains of putative type II restriction enzymes and methyltransferases, such as Helicobacter cinaedi PAGU611 Hci611ORFHP which may recognize 5'... GAGNNNNNGT ... 3', and type I N6-adenine DNA methyltransferases, such as Calditerrivibrio nitroreducens M.Cni19672ORF1405P whose recognition sequence is undetermined.


Pssm-ID: 341195 [Multi-domain]  Cd Length: 183  Bit Score: 48.32  E-value: 1.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  50 EYKAEYLIQKGDALIGMDGEfnlalwnsGKALLNQRVCKI-----QSI-----DERLDQNYLIRFLPKALKDIEDRTPFV 119
Cdd:cd17514   56 EDSSIRIVPKGTILIACTGQ--------GYTRGQVAVLQIdastnQAIaaircKENVNPKYLYYYLKTQKNNLRNLTSGV 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 514164098 120 TVKHLSVKDINNIQIPLPPLAEQRRIASILdqaDELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17514  128 AQKNLNIEMLRNLQIPLPPKEEQQKIVNIL---ETLEFFEKDSLRKIKETAQDINLMIN 183
RMtype1_S_Sba223ORF3470P-TRD1-CR1_like cd17270
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 89-171 1.30e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Sba223ORF3470P TRD1-CR1; The recognition sequence of Shewanella baltica OS223 S subunit (S.Sba223ORF3470P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341159 [Multi-domain]  Cd Length: 183  Bit Score: 48.08  E-value: 1.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  89 IQSIDERLDQNYLIRFLpKALKDIEDRT-PFVTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKL- 166
Cdd:cd17270   95 FESYKININKKFFAYQL-KLKFEIEKEKaPGGTIKTITKEELSKFEIPIPSLEEQKEIVNILDKFDELITELQLRKKQLe 173


                 ....*...
gi 514164098 167 ---DQLLQ 171
Cdd:cd17270  174 yykKALLS 181
RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like cd17258
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 43-168 1.87e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Sau13435ORF2165P TRD1-CR1 and S.SauL3067ORFAP TRD1-CR1; Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) recognizes 5'... TCTANNNNNNRTTC ... 3'; the recognition sequence of Staphylococcus aureus 3067 S.Sau3067ORFAP S subunit is as yet 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.Sau13435ORF2165P TRD1 recognizes TCTA/TAGA, and S.Sau13435ORF2165P TRD2 recognizes GAAY/RTTC. 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 mostly TRD1-CR1. 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: 341147 [Multi-domain]  Cd Length: 173  Bit Score: 47.40  E-value: 1.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  43 SDTYYDGEYKAEYLIQKGDALIGMDGEFNL-ALWNSGKALLNQRVCKIQSIDERLDQNYlIRFL---PKALKDIEDRTPF 118
Cdd:cd17258   35 VEPDYKIGLKQSKIFKKGDVLITRHGTIGRvSIILSEEACLSSHVAGFNSKEGISDNKF-IKYLfnsKKIKNRLMSYGAS 113

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 514164098 119 VTVKHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQ 168
Cdd:cd17258  114 STQPALNLSRLLKIKFPNPPLEEQQKIGKILSTWDRAIELTEQKLELLQQ 163
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 188-343 2.29e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) TRD2-CR2 and Moraxella catarrhalis S subunit (S.Mca353ORF290P) TRD2; Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) recognizes 5'... GCANNNNNNTGT ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 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: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 47.04  E-value: 2.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 188 WEVLKWRDALKIINGK----NQKAVLDQNGIFPICGSGGVMGYANEWLTPAKSVIIGRKG-NI---NKPILMFEN--FWn 257
Cdd:cd17262    1 WEVKKLGEVVENLDSKriplSSEERERRQGNYPYYGASGIVDYVDDYIFDGEYVLIGEDGaNLlsrGTPIAFYVSgkFW- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 258 vdtafglVPN-------KDVLNADYLFWFCHFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICD------- 323
Cdd:cd17262   80 -------VNNhahvlkgKNGISTEFLYYYLNSIDISPYVTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDkldalid 152

                        170       180
                 ....*....|....*....|.
gi 514164098 324 -QTRILKSKMELKDlNLFSSL 343
Cdd:cd17262  153 lLEEELEKLIELKK-ALLQKL 172
RMtype1_S_PluTORF4319P-TRD2-CR2_like cd17269
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 264-315 3.26e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Photorhabdus luminescens S subunit (S.PluTORF4319P) TRD2-CR2; The recognition sequence of Photorhabdus luminescens S subunit (S.PluTORF4319P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341158 [Multi-domain]  Cd Length: 168  Bit Score: 46.82  E-value: 3.26e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 514164098 264 LVPNKDVLNADYLFWF--CHFFNFEQLN-KTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:cd17269   75 IHPFKEEIDPKFLYYYlkSYFKKYIEKNsVGSSVPYIRLPMLENFKIPLPPLEEQ 129
RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like cd17280
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter ...
 124-172 4.37e-06

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter species EN3 S subunit (S.MspEN3ORF6650P) TRD1-CR1, Methanothermobacter marburgensis str. Marburg S subunit (S.Mma2133ORF14720P) TRD2-CR2 and Nostoc species NIES; The recognition sequences of Marinobacter species EN3 S subunit (S.MspEN3ORF6650P), Methanothermobacter marburgensis str. Marburg S subunit (S.Mma2133ORF14720P), and Nostoc species NIES-3756 S subunit (S.Nsp3756ORF27100P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341169 [Multi-domain]  Cd Length: 187  Bit Score: 46.77  E-value: 4.37e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 514164098 124 LSVKDINNIQIPLPPLAEQRRIASILDQA----DELRQKRQQAIEKLDQLLQA 172
Cdd:cd17280  129 ISQELIKSLRIPVPPLEEQKQIAAFLDKKtakiDSLIEKKERLIELLKERRQA 181
RMtype1_S_NmaSCMORF606P_TRD2-CR2_like cd17271
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 124-178 2.14e-05

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Nitrosopumilus maritimus SCM1 S subunit (S2.NmaSCMORF606P) TRD2-CR2, Corynebacterium jeikeium K411 S subunit (S.CjeKORF1254P) TRD2-CR2 and Porphyromonas canoris COT-108 OH27; The recognition sequences of Nitrosopumilus maritimus SCM1 S subunit (S2.NmaSCMORF606P), Corynebacterium jeikeium K411 S subunit (S.CjeKORF1254P), and Porphyromonas canoris COT-108 OH2762 S subunit (S2.Pca2762ORF8685P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341160 [Multi-domain]  Cd Length: 186  Bit Score: 44.57  E-value: 2.14e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 514164098 124 LSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQLLQATFIDMF 178
Cdd:cd17271  131 YTADIVKKLPILLPTLKEQKKIANFLSDIDELIATLEKKIEKLKKIKKGLMQKLL 185
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 75-174 2.80e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.HinAWORF1578P TRD2-CR2; Haemophilus influenzae RdAW S subunit (S.HinAWORF1578P) recognizes 5'... CTANNNNNGTTY ... 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: 341197 [Multi-domain]  Cd Length: 184  Bit Score: 44.08  E-value: 2.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  75 WNSGKALLNQRVC----KIQSI---DERLDQN---YLIRFLPKALKDIE---DRTPFVTVKHLSvkdinNIQIPLPPLAE 141
Cdd:cd17516   73 SDMGKVAITKEPSvtnqQINSIivnKNKFDPDfvyYLLKNNSKYLKSIAggsTATPIINKSTFS-----NIEIPLPPLPE 147

                         90       100       110
                 ....*....|....*....|....*....|...
gi 514164098 142 QRRIASILDQADELRQKRQQAIEKLDQLLQATF 174
Cdd:cd17516  148 QKKIAAILSSLDDKIENNRRINKTLEEMAQALF 180
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 266-335 2.85e-05

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: 43.69  E-value: 2.85e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514164098 266 PNKDVLNaDYLFWFCHFFNFEQLNKTvTIPSLTKSDLLNIDIPTPPLDKQL----CFSN----ICDQTRILKSKMELK 335
Cdd:cd17292   66 DESKVLN-KFLYYFYQIIKWKKTEGS-TIKRLYNDNLLNTKIPVPSLDEQRkiaeFLSLldalIALLQKKLEKLIALK 141
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 268-335 3.49e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) TRD1-CR1 and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) TR; The recognition sequences for Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) 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. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Helicobacter bizzozeronii CIII-1 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.HbiCORF8670P, and may also contain type I DNA methyltransferases.


Pssm-ID: 341190 [Multi-domain]  Cd Length: 175  Bit Score: 43.76  E-value: 3.49e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 268 KDVLNADYLFWFC--HFFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQtrILKSKMELK 335
Cdd:cd17499   90 KKNIDKKYLFYFLlsNKDYFKGKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSELDK--LFKLIFEAK 157
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 249-348 3.78e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli G4/9 S subunit (S.Eco16444ORF1681P) TRD1-CR1 and Zobellia galactanivorans DsiJT S subunit (S.ZgaJTORF2697P)TRD2; The recognition sequences of Escherichia coli G4/9 S subunit (S.Eco16444ORF1681P) and Zobellia galactanivorans DsiJT S subunit (S.ZgaJTORF2697P) 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 putative type II restriction enzymes and methyltransferases and may also include type I DNA methyltransferases.


Pssm-ID: 341171 [Multi-domain]  Cd Length: 186  Bit Score: 43.97  E-value: 3.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 249 ILMFenfwnvDTAF-----GLVPNKDVLNADYLFWFCHFF--NFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNI 321
Cdd:cd17282   83 ILGF------DACFpdsvvGFIPNEEKIDVEFLEYYLRTLkkELEAIAPQSAQKNINLEILRPLKIPVPPLEEQKKIVEI 156

                         90       100       110
                 ....*....|....*....|....*....|
gi 514164098 322 CDQ--TRILKSKMELKDLN-LFSSLQNQAF 348
Cdd:cd17282  157 LDAldDLIDNLEKRIAKLEeLKQSLLQEAF 186
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 259-340 4.35e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoKI TRD1-CR1, S.StySPI TRD1-CR1, S.Ara36733II TRD1-CR1, and S.Eco3722I TRD1-CR1; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) and Escherichia coli NCM3722 S subunit (S.Eco3722I) recognize 5'... AACNNNNNNGTGC ... 3', Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3', and Actinomyces radicidentis S subunit (S.Ara36733II) recognizes 5'... CATCNNNNNNCTC ... 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 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 Treponema pedis T A4 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.TpeTA4ORF2695P. It may also include type I DNA methyltransferases.


Pssm-ID: 341141 [Multi-domain]  Cd Length: 189  Bit Score: 43.70  E-value: 4.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 259 DTAFG-----LVPNKDVlNADYLFWFC---HFFNF-EQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQ--TRI 327
Cdd:cd17252   92 DYTFGafcgvIRPKKEI-DPRYLFYFLqspSYREYiRSLASGTNINNLSNEHLENLKIPLPPLAEQKRIVAKLDKldALI 170

                         90
                 ....*....|...
gi 514164098 328 LKSKMELKDLNLF 340
Cdd:cd17252  171 DKLKQALEKLDEL 183
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 264-347 4.83e-05

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: 43.68  E-value: 4.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 264 LVPNKDVLNADYLFwfcHFFNFEQLNK--------TVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQtrILKSKMELK 335
Cdd:cd17517  101 LRLDKKKILPEFLY---YYLNSPLGRKqiekiaksAAGQANINQKDLKKLPIPLPPLEEQKEIVEILES--LDSKIDLLE 175

                         90
                 ....*....|....*..
gi 514164098 336 D-----LNLFSSLQNQA 347
Cdd:cd17517  176 KkleklEQLFKSLMQSL 192
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 263-338 4.85e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acetobacter pasteurianus S subunit (S.Apa101655I) TRD2-CR2; The S. Apa101655I S subunit recognizes 5'... TTAGNNNNNNTTC... 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: 341133 [Multi-domain]  Cd Length: 180  Bit Score: 43.62  E-value: 4.85e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514164098 263 GLVPNKDVLNADYLFWFCHFFNFEQLNKTVTIPSLTKSDLL-NIDIPTPPLDKQLCFSNICDQ--TRILKSKMELKDLN 338
Cdd:cd17244   93 HFIPKDKKIDTEYLYYYLKSFDYSSLGSTASKGKTLNSKKIkEIPIPLPPLEEQKRIAPILDKidALIDQLETLIELLD 171
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 266-348 5.69e-05

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: 43.23  E-value: 5.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 266 PNKDVLNADYLFWFchfFN-------FEQLNKTVT-IPSLTKSDLLNIDIPTPPLDKQLCFSNICDQTRILKSKME---L 334
Cdd:cd17253  103 PKDDLLLPEFLSYW---LNsaygrgyFLRAAKQTTnLASINSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEaslA 179

                         90
                 ....*....|....
gi 514164098 335 KDLNLFSSLQNQAF 348
Cdd:cd17253  180 KLEELLKALRQALL 193
RMtype1_S_HpyCR35ORFAP-TRD1-CR1_like cd17519
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 262-333 9.22e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) TRD1-CR1 and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190; The recognition sequences of Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341200 [Multi-domain]  Cd Length: 183  Bit Score: 42.68  E-value: 9.22e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 514164098 262 FGLVPNKDVLNADYLFwfcHFF----NFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQTRILKSKME 333
Cdd:cd17519   95 GKFIPNEEILNNRYLY---HFLlskqNEKYILAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILDKFRELTNELE 167
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 272-348 1.50e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) TRD2-CR2 and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) TRD2-CR; Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) recognizes 5'... GAGNNNNNGTTY ... 3', and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) recognizes 5'... YTCANNNNNNGTTY ... 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.Eco4255III-TRD1 recognizes GAG/CTC and S.EcoNIH1II-TRD1 recognizes YTCA/TGAR, while both S.EcoNIH1II-TRD2 and S.Eco4255III-TRD2 recognize RAAC/GTTY. 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: 341154 [Multi-domain]  Cd Length: 181  Bit Score: 42.10  E-value: 1.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 272 NADYLFWFCH---FFNFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQ----LCFSNICDQTRILKSKMELKdLNLFSSLQ 344
Cdd:cd17265   99 YNDYLFHLFNsdlFKKQIGSFLTATINQITNGNLNNFKIPLPPLEEQekiaEFLSSLDAKIDKLIKKIEKL-IELKKELM 177


                 ....
gi 514164098 345 NQAF 348
Cdd:cd17265  178 QQLI 181
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
119-209 1.78e-04

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 43.33  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 119 VTVKHLSVKDINNIQIPLPPLAEQ----RRIASILDQADELRQKRQQAIEKLDQLLQATFIDMFgdpvsnsKGWEVLKWR 194
Cdd:PRK09737 352 TTQKHITGKALANYPIRVPPLEEQaeivRRVEQLFAYADTIEKQVNNALARVNNLTQSILAKAF-------RGELTAQWR 424

                         90
                 ....*....|....*.
gi 514164098 195 -DALKIINGKNQKAVL 209
Cdd:PRK09737 425 aENPSLISGENSAAAL 440
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 268-336 1.97e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to TRD2-CR2's of StySKI, S.EcoAI, S.EcoJA17PI, and S.EcoJA23PI; Salmonella kaduna CDC-388 S subunit (StySKI) recognizes 5'... CGATNNNNNNNGTTA ... 3' while Escherichia coli Type-1 restriction enzyme EcoAI specificity protein (S.EcoAI), Escherichia coli UCD_JA17_pb S subunit (S.EcoJA17PI) and Escherichia coli UCD_JA23_pb S subunit (S.EcoJA23PI) recognize 5'... GAGNNNNNNNGTCA ... 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: 341148 [Multi-domain]  Cd Length: 189  Bit Score: 41.73  E-value: 1.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 268 KDVLNADYLF-WFC--HFFNFEQLNKTVT-IPSLTKSDLLNIDIPTPPLDKQLCFSNICDQ--------TRILKSKMELK 335
Cdd:cd17259  104 KDELNSDFLYyLLQsdFFLNYVEPVLTGTdVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSldalidllEQKLEKLQQLK 183


                 .
gi 514164098 336 D 336
Cdd:cd17259  184 K 184
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 233-348 2.22e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) TRD2-CR2 and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) TRD; The recognition sequences of Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341194 [Multi-domain]  Cd Length: 182  Bit Score: 41.35  E-value: 2.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 233 PAKSVIIG-RKGnINKPILMfenfwNVDTAF-----GLVPNKDVlNADYLFWFCHFF--NFEQLNKTVTIPSLTKSDLLN 304
Cdd:cd17513   63 PANSILIVtRVG-VGKVAIN-----PFDICTsqdftSLIPIKEV-NPLFLAYLLYSLlqKLKSQLQGTSIKGITKDDLKN 135

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 514164098 305 IDIPTPPLDKQLCFSNICDQT--RILKSKMELKDLN-LFSSLQNQAF 348
Cdd:cd17513  136 LKIPLPPLEEQQKIAAILSKLdkLIEAHEKKLEKLKqLKKGLMQKLF 182
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 262-315 2.27e-04

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S.MjaORF132P TRD1-CR1; The recognition sequence of Methanococcus jannaschii S subunit (MjaXIP/S.MjaORF132P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341164 [Multi-domain]  Cd Length: 186  Bit Score: 41.38  E-value: 2.27e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 514164098 262 FGLVPNKDVLNADYL-FWFCHFFN-FEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:cd17275   95 LGIIPKDEKLDFEFLyYWLLSLKNeLKRLIRTGTQANLNAEIVKNLPIPLPPLEEQ 150
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 263-348 2.93e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) TRD2-CR2 and Shewanella xiamenensis BC01 S subunit (S.SxiBC01OR; The recognition sequences of Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) and Shewanella xiamenensis BC01 S subunit (S.SxiBC01ORF77P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341173 [Multi-domain]  Cd Length: 185  Bit Score: 41.04  E-value: 2.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 263 GLVPNKDvLNADYLFWFCHFFN--FEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQTRILKSKME---LKDL 337
Cdd:cd17284   96 AFVPSKK-INPEYLMYLLSLQKkyMEKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIaklEKLQ 174

                         90
                 ....*....|.
gi 514164098 338 NLFSSLQNQAF 348
Cdd:cd17284  175 QLKKGLMQQLF 185
RMtype1_S_HpyAXIII_TRD1-CR1_like cd17281
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 125-155 3.72e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) TRD1-CR1, Neisseria meningitidis 510612 S subunit ; Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) recognizes 5'... CTANNNNNNNNTGT ... 3', and the recognition sequences of Neisseria meningitidis 510612 S subunit (S.Nme510612ORF1157P) and Streptococcus mitis SVGS_061 S subunit (S2.Smi61ORF7905P) 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. For example, Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) TRD1 recognizes CTA/TAG, and TRD2 recognizes ACA/TGT. 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: 341170  Cd Length: 196  Bit Score: 41.04  E-value: 3.72e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 514164098 125 SVKDINNIQIPLPPLAEQRRIASILDQADEL 155
Cdd:cd17281  136 DMNKLKKFKIPIPPLEEQEKIVEILDKFTKL 166
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 268-339 4.09e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus licheniformis S subunit (S1.BliBORF2384P) TRD1-CR1 and Chlorobium tepidum TLS S subunit (S.CteTORF675P) TRD1-CR1; The recognition sequences for Bacillus licheniformis S subunit (S1.BliBORF2384P) and Chlorobium tepidum TLS S subunit (S.CteTORF675P) 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. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341187 [Multi-domain]  Cd Length: 175  Bit Score: 40.56  E-value: 4.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 268 KDVLNADYL-FWFCHFFN-FEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQ--------TRILKSKMELKDL 337
Cdd:cd17496   90 KNGIDTEFLyYLLESNLDyLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPldekidknKQEIEKLEELRDT 169


                 ..
gi 514164098 338 NL 339
Cdd:cd17496  170 LL 171
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 266-315 4.20e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2 and Aminobacterium colombiense DSM 12261 S subunit (S.Aco12; The S.Aco12261I S subunit recognizes 5'... GCANNNNNNTGT ... 3', while the recognition sequence is undetermined for S.TteMORF1547P TRD2-CR2. 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. S.TteMORF1547P TRD1-CR1 and S.Aco12261I TRD2-CR2 do not belong to this family. This family may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341134 [Multi-domain]  Cd Length: 174  Bit Score: 40.60  E-value: 4.20e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 514164098 266 PNKDVlNADYLFWFCHFFN--FEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:cd17245   88 ANKDI-DNLFLYYYLKYNKpeLEKLGTGSTFKAINKKDLEELKIPLPPLEEQ 138
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 264-315 5.25e-04

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P/MjaXIIP) TRD1-CR1; The recognition sequence of Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P, also called MjaXIIP) 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: 341203 [Multi-domain]  Cd Length: 190  Bit Score: 40.60  E-value: 5.25e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 514164098 264 LVPNKDVLNADYLFWFCHFFNF-EQL----NKTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:cd17522   99 LRPNKNIVDPKYLYYLLKSDRFrNQFrsiaKKAVNQASINQTELKKIKIPLPPLEEQ 155
RMtype1_S_StySPI-TRD2-CR2_like cd17523
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Salmonella ...
 94-172 6.36e-04

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) TRD2-CR2; 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.StySPI-TRD1 recognizes AAC/GTT 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341204 [Multi-domain]  Cd Length: 190  Bit Score: 40.30  E-value: 6.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098  94 ERLDQNYLIRFL--PKALKDIEDRtpFVTV---KHLSVKDINNIQIPLPPLAEQRRIASILDQADELRQKRQQAIEKLDQ 168
Cdd:cd17523  104 EKIDPEFLSYIFnsPLIRRKIERN--FVTSagqKTVNQGHIKSLPIPLPPLKEQKKIVARVEELFALIDQLESSLDLAQQ 181


                 ....
gi 514164098 169 LLQA 172
Cdd:cd17523  182 LQNK 185
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 258-338 2.29e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoR124I TRD2-CR2, S.Eco540I TRD2-CR2, S.Eco540AI TRD2-CR2, and S.Eco540ANI TRD2-CR2; Escherichia coli (R124) S subunit (S.EcoR124I), E. coli ST540 S subunit (S.Eco540I), E. coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540AN S subunit (S.Eco540ANI) recognize the sequence 5'... GAANNNNNNRTCG ... 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.EcoR124I -TRD1 recognizes GAA/TTC, and -TRD2 recognizes CGAY/RTCG. 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: 341138 [Multi-domain]  Cd Length: 185  Bit Score: 38.59  E-value: 2.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 258 VDTAF-----GLVPNKDVlNADYLFWFCHFFNFEQLNKTVTIPSLTKS----DLLNIDIPTPPLDKQlcfSNIcdqTRIL 328
Cdd:cd17249   85 RPVAFnqdikALIPKEGI-DPEFLLYALKANEDRILSLVDKAGHGTGSldtdDLKNLPIPLPPLEEQ---RRI---AAIL 157

                         90
                 ....*....|
gi 514164098 329 KSKMELKDLN 338
Cdd:cd17249  158 DALDALIDLL 167
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 268-315 2.93e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2; The recognition sequence is undetermined for Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P). 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 CD contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.TteMORF1547P TRD1-CR1 does not belong to this subfamily.


Pssm-ID: 341188 [Multi-domain]  Cd Length: 174  Bit Score: 37.91  E-value: 2.93e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 514164098 268 KDVLNADYLFWFCHFFN--FEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQ 315
Cdd:cd17497   89 KKGLDKKYLLYYLKSIEneLSSLGTGSTFKAISKEDLENLLIPLPPLAEQ 138
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 263-324 3.83e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1 and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) TRD2-CR; The recognition sequences of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341183 [Multi-domain]  Cd Length: 188  Bit Score: 37.85  E-value: 3.83e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 514164098 263 GLVPNKDVLNADYLFWFCHFfNFEQLNKTVTIP---SLTKSDLLNIDIPTPPLDKQLCFSNICDQ 324
Cdd:cd17294   98 AIEPDEEIANSRFLYYNLSS-RYEELRSLSGGGgrgGLNLKIIKSLPIPLPPLEEQKKIVAILDK 161
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 265-338 4.22e-03

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: 37.86  E-value: 4.22e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514164098 265 VPNKDVLNADYLFWF-CHFFNFEQLN---KTVTIPSLTKSDLLNIDIPTPPLDKQlcfSNICDqtrILKSKMELKDLN 338
Cdd:cd17256   95 IRPKDSISPRYLYYYlRSPFGQSQIEsetKGAAQPKLNLKRIRELPIPLPPLEEQ---KRIVA---ILDSLDAKIDAL 166
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 249-334 4.51e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2; The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 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 CD 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: 341136 [Multi-domain]  Cd Length: 190  Bit Score: 37.89  E-value: 4.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 249 ILMFENFWNVDTAFgLVPNKDVLNADYLFWFCHFfNFEQL-------NKtvtiPSLTKSDLLNIDIPTPPLDKQLcfsNI 321
Cdd:cd17247   88 ILAIEATINQNLAA-IRPNEERVLPEYLHYYLES-QYDELrrigsggGQ----GALNCGILKAFPIPLPPLDEQR---EI 158

                         90
                 ....*....|...
gi 514164098 322 CDQTRILKSKMEL 334
Cdd:cd17247  159 VAELEALLAKIDL 171
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 304-349 8.52e-03

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) TRD2-CR2, and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) TRD2-CR2; The recognition sequences of Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341176 [Multi-domain]  Cd Length: 184  Bit Score: 36.70  E-value: 8.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 514164098 304 NIDIPTPPLDKQLCFSNICD----QTRILKSKMELKDlNLFSSLQNQAFN 349
Cdd:cd17287  136 SIEIPVPPLDEQQKIAAFLSaidaKIDALEQKLELLQ-ELKKSLMQQLFT 184
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 263-348 8.79e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to MjaXIP/S.MjaORF132P TRD1-CR1, S.Sau1132ORF3780P TRD1-CR1, S.Mca353ORF290P TRD1-CR1, and other TRD-CR's; The Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 3'. The recognition sequence of Methanococcus jannaschii S subunit (MjaXIP/S.MjaORF132P) 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.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG, and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. 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: 341196 [Multi-domain]  Cd Length: 181  Bit Score: 36.64  E-value: 8.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 263 GLVPNKDVLNaDYLFWFCHFF--NFEQLNKTVTIPSLTKSDLLNIDIPTPPLDKQLCFSNICDQ--TRILKSKMELKDLN 338
Cdd:cd17515   92 AILPNEEIDN-EFLFYFLKSQkeYLISLGKGGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKldKLIEKLEKALEKLE 170

                         90
                 ....*....|.
gi 514164098 339 -LFSSLQNQAF 348
Cdd:cd17515  171 eLKKALMQKLL 181
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 231-315 9.09e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Campylobacter species RM1670 S subunit (S.Csp16704I) TRD2-CR2, Aeromonas media WS S subunit (S.AmeWSORF2351P) TRD1-CR1, and Clos; Campylobacter species RM16704 S subunit (S.Csp16704I ) recognizes 5'... ACANNNNNNNNTCG ... 3', and the recognition sequences of Aeromonas media WS TRD1-CR1 S subunit (S.AmeWSORF2351P) and Clostridium carboxidivorans P7 S subunit (S.CcaPORF573P) 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341174 [Multi-domain]  Cd Length: 181  Bit Score: 36.71  E-value: 9.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514164098 231 LTPAKSVIIG-R----KGNINKpilmfenfwnVDTAF-----GLVPnKDVLNADYLF-WFCHFFN-FEQLNKTVTIPSLT 298
Cdd:cd17285   60 LIPKGTVIIAtRmglgKVAINK----------IDVAInqdlkALFP-KDELDPEYLLyWFLSIEEtIESLGTGTTVKGIT 128

                         90
                 ....*....|....*..
gi 514164098 299 KSDLLNIDIPTPPLDKQ 315
Cdd:cd17285  129 LEDLKSLKIPLPPLEEQ 145
 
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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