NCBI Conserved Domain Search

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: 183.47 E-value: 8.86e-57

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 188 KLSELCNLISGQHIDAKNYNNEQRGIGYLTGPSDFGVINPTVTKWTEHPKRTAIKGDILITVKGSGVGKVNImSAGELAI 267
Cdd:cd17496     2 KLGDIAEIIMGQSPKGESYNTEGIGIPLLNGPADFGDGYPIPKKWTTKPTKLCKKGDILFCVRGSTTGRLNI-ADDEYCI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 268 SRQLMAVRPTNAV-GDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQFNletvDLERIY 346
Cdd:cd17496    81 GRGVAAIRPKNGIdTEFLYYLLESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLD----EKIDKN 156

                         170
                  ....*....|....*....
gi 2294874845 347 TDKLSSLDELKKSILQKAF 365
Cdd:cd17496   157 KQEIEKLEELRDTLLPKLL 175

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: 123.80 E-value: 5.90e-34

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 188 KLSELCNLISGQHIDAKNYNNEQRGIGYLTGPSDFGVINPTVTKWTEHPKRTAIKGDILITVKGSgVGKVNImSAGELAI 267
Cdd:cd17245     2 KLGEVAEIIMGQSPPSSTYNEEGEGLPFLQGKADFGEIYPTPRVWCTKPTKIAEKGDILISVRAP-VGDVNI-ADEKCCI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 268 SRQLMAVRPTNAV-GDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQelvdRISQFnLETVDLERIY 346
Cdd:cd17245    80 GRGLAAIRANKDIdNLFLYYYLKYNKPELEKLGTGSTFKAINKKDLEELKIPLPPLEEQQ----KIAEI-LSTVDEAIEK 154

                         170       180
                  ....*....|....*....|
gi 2294874845 347 TDK-LSSLDELKKSILQKAF 365
Cdd:cd17245   155 TKAlIEKLDELKKGLMQELF 174

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: 107.77 E-value: 6.13e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 187 YKLSELCNLISGQHIDAKNYNNEQRGIGYLTGPSDFGVINPTVTKWTEHPKRTAIKGDILITVKGSgVGKVNIMSAgELA 266
Cdd:cd17498     1 VKLGEIAEITMGQSPKSEFYNEDGIGLPFLQGNRTFGDKYPYIDTYTTDIKKIAKKGDILMSVRAP-VGDLNIANK-DIC 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 267 ISRQLMAVRPTNAVGDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQFNletvDLERIY 346
Cdd:cd17498    79 IGRGLCSIRMKNGNNSFLYYLLKNNIKNLINKSSGTVFGSINKDDIENLEVDIPEDEEQKRIANILSKID----DKIEIN 154

                         170
                  ....*....|....*....
gi 2294874845 347 TDKLSSLDELKKSILQKAF 365
Cdd:cd17498   155 NQINKNLEELAQAIFKHWF 173

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: 105.61 E-value: 2.80e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  24 NISHGKIKEDdGPYPVFGAKGYIQNISFYQQENDYIAIIKDGAGIGRVSVHPAKSSVLATMQYLLPKEGFDLRFIKYFLE 103
Cdd:cd17266    14 SITASKISEE-GDYPVYGGNGIIGYTDEYNHEGEYILIGRVGALCGNVHYVEGKFWVTDNALVVTPKKENNIKFLYYLLK 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2294874845 104 SLDFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNARELFE 170
Cdd:cd17266    93 SLNLNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKELMQ 159

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: 99.55 E-value: 7.31e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 188 KLSELCNLISGQHIDAKNYNNEQRGIGYLTGPSDFGVINPTVTKWTEHPKRTAIKGDILITVKGSgVGKVNImSAGELAI 267
Cdd:cd17497     2 KLKYVADIIMGQSPPSSTYNTEGIGLPFLQGKAEFGKLYPTPRKWCSAPKKIAEKGDILLSVRAP-VGPTNI-ADQEYCI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 268 SRQLMAVRPTNAVG-DLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQfnletvDLERIy 346
Cdd:cd17497    80 GRGLAAIRPKKGLDkKYLLYYLKSIENELSSLGTGSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDE------LTAKI- 152

                         170
                  ....*....|....*..
gi 2294874845 347 tDKLSSLDELKKSILQK 363
Cdd:cd17497   153 -DQLIALLEKAIELLKE 168

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: 92.68 E-value: 2.67e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 188 KLSELCNLISGQHIDAKNYNNEQRGIGYLTGPSDFG--VINPTvTKWTEHPKRTAIKGDILITVKGSgVGKVNIMSAgEL 265
Cdd:cd17499     2 RLGDVAEIIMGQSPEGKSYNTNKEGLPFYQGKKEFGdkYIKEP-NTWTTSPTKIAEKNDILMSVRAP-VGDVNITTR-KI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 266 AISRQLMAVRPTNAVGD--LLYWFLSMQfDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQFNLETVDLE 343
Cdd:cd17499    79 CIGRGLAAIRAKKNIDKkyLFYFLLSNK-DYFKGKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAK 157

                         170
                  ....*....|....*...
gi 2294874845 344 RIYTDKLSSLDELKKSIL 361
Cdd:cd17499   158 NNIEEALANAQQLFKSIL 175

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: 81.03 E-value: 5.29e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  22 SSNISHGKIKEDDGPYpvFGAKGYIQNISFYQ-QENDyIAIIKDGAgIGRVSVHPaKSSVLATMQYL----LPKEGFDLR 96
Cdd:cd17246    33 SKNIKNGKIDFSDVKY--ISEEDHNEILKRSKlKKGD-ILFSIIGT-IGRVAIVP-EDLPANINQAValirPKKEKIDPK 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  97 FIKYFLESLDFEEY----RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNARELFESY 172
Cdd:cd17246   108 YLLYYLNSPIIQKQieknAVGGTQKNLSLGDLKNLKIPLPPLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDL 187


                  .
gi 2294874845 173 L 173
Cdd:cd17246   188 L 188

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: 81.02 E-value: 6.00e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  23 SNISHGKIKEDDgpyPVFGAKGYIQNISFYQ-QENDYI-----AIIKDGAGIGRV--SVHPAkssvlatmqyLL------ 88
Cdd:cd17259    34 ANVGVGEIRWDD---TVYLPEEYLEEYEKYLlKEGDIVialdrPIISGGLKVARIpkSDLPA----------LLvqrvar 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  89 --PKEGFDLRFIKYFLESLDFEEY----RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKteqnL 162
Cdd:cd17259   101 irPKDELNSDFLYYLLQSDFFLNYvepvLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQK----L 176

                         170
                  ....*....|...
gi 2294874845 163 KNARELFESYLQQ 175
Cdd:cd17259   177 EKLQQLKKGLMQS 189

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: 80.62 E-value: 6.05e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  54 QENDyIAIIKDGAGIGRVSVhpAKSSVLA-TMQYLLPKEG-FDLRFIKYFLESLDFEEY---RTGSTIPHIYFKDYKSAP 128
Cdd:cd17263    56 NEDD-ILIVRDGANAGEVGT--GLEGAIAsTLFKIIPDKNiIDKDYLYYFLKSKEIQLNiltKAGSTIPHVNKKDLENLK 132

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2294874845 129 FPLISVPEQKRIVAILDQAFADIEqaraKTEQNLKNARELFESYLQQVF 177
Cdd:cd17263   133 IPLPSLEEQKKIAEILDKLDALID----KLKELIEKLIELKKGLFQELL 177

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: 79.73 E-value: 1.47e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  21 GSSNISHGKIKEDDGPYPVFGAKGYIQNISFyqqENDyIAIIKDGaGIGRVSVHPAKSSVLATMQ--YLLPKEGFDLRFI 98
Cdd:cd16961    31 RISDINNGGIILTDEKITEEGAEKLKKKILP---KGD-ILISRSG-TIGKVAIVKENDKALLNQAviVIRPKDEVDSEFL 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2294874845  99 KYFLESLDFEEY---RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNAREL 168
Cdd:cd16961   106 YYFLKSPFGKKLiegSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDALIELLEQKLEKLEQLKQAL 178

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 83.01 E-value: 2.63e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  23 SNISHGKIKEDDGPYpvfgAKGYIQNISFYQQENDYIAIiKDGAGIGRV-SVH---PAKSSVLATMQYLLPKEGFDLRFI 98
Cdd:PRK09737   47 TDITNGAVDLTTLPY----CMDAPEDVSKYQLQDRDIVI-SSAGSIGFSfLAQnplPSNVVFASFAIRLKPVNYFSEYFL 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  99 KYFLESLD----FEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQN---LKNARE---- 167
Cdd:PRK09737  122 KHFLESSDyrnqLSLMSAGNAVQNINAQSLSTLTFPIPPIAEQKIIAEKLDTLLAQVDSTKARLEQIpqiLKRFRQavlg 201

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 168 ------LFESYLqqvFSQRGEGWGFYKLSELCNLISGQHIDAKNynNEQRGIGYLT------GPSDFGVINPTVTKWTEH 235
Cdd:PRK09737  202 aavsgkLTEEWR---WPDLPSTWSVHKYSELVDSRLGGMSSKAN--NFGSATPYLRninvrwGSFDLEDLQDILISDIER 276

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 236 PKRTAIKGDILITVKGS--GVGKVNIMSAGE---LAISRQLMAVRPT-NAVGDLLYWFL----SMQFDYFQsLANGAAIP 305
Cdd:PRK09737  277 RELKLKLGDVLFCRGNEplEVGRCAIWKEPQdipVIYQKALIRARVKdDIIPEYLVYNLkspdSRNISLSQ-LFTGTTQK 355

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2294874845 306 GISRHDVLDLKLSIPLSGDQQELVDRISQFNLETVDLERIYTDKLSSLDELKKSILQKAFSGELT 370
Cdd:PRK09737  356 HITGKALANYPIRVPPLEEQAEIVRRVEQLFAYADTIEKQVNNALARVNNLTQSILAKAFRGELT 420

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: 77.83 E-value: 3.46e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  34 DGPYPVFGAKGyiqnISFYQqeNDYIAiikDGAGI--GR---V-SVH--PAKSSVLATMQYLLPKEGFDLRFIKYFLESL 105
Cdd:cd17267    22 PGPYPVYGSNG----IVGYH--NEALV---KGPGIvvGRkgsIgKVHysEEDFWPIDTTLYVKDFKGNDPRFLYYLLKTL 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2294874845 106 DFEEYRTGSTIP-----HIYfkdykSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNARELFES 171
Cdd:cd17267    93 DLERLNSGSAVPglnrnDVY-----SLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADALLPK 158

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: 77.86 E-value: 5.16e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  35 GPYPVFGAKGYIQNISFYQQENDYIAIIKDGAGIGrvsvhpAKSSVLATMQY-----------LLPKEGFDLRFIKYFLE 103
Cdd:cd17262    30 GNYPYYGASGIVDYVDDYIFDGEYVLIGEDGANLL------SRGTPIAFYVSgkfwvnnhahvLKGKNGISTEFLYYYLN 103

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2294874845 104 SLDFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNARELFESY 172
Cdd:cd17262   104 SIDISPYVTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQKL 172

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: 76.39 E-value: 2.18e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  87 LLPKEGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKN 164
Cdd:cd17285    93 LFPKDELDPEYLLYWFLSIeeTIESLGTGTTVKGITLEDLKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEKLKQL 172


                  ....*....
gi 2294874845 165 ARELFESYL 173
Cdd:cd17285   173 KKGLMQSLL 181

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: 76.01 E-value: 3.13e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  23 SNISHGKIKEDDGPYPVFGAKGYIQNISFyqQENDyIAIIKDGAGIGRVSVHPAKSSVlatmqYLL--------PKEGFD 94
Cdd:cd17278    34 GNIKNGGIDLDDNSKYPEEPLEKYEKFLL--KKGD-ILIAMTGGTVGKVAIVPEDDEP-----ALLnqrvgkfrPKDKID 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  95 LRFIKYFLESLDFEEY----RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQAraktEQNLKNARELFE 170
Cdd:cd17278   106 KEFLYYLLRSDSFRNQikssATGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKL----EQKLEKLRDLLK 181


                  ....*...
gi 2294874845 171 SYLQQVFS 178
Cdd:cd17278   182 PLLQSLFT 189

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: 75.73 E-value: 3.39e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  89 PKEGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNAR 166
Cdd:cd17499    89 AKKNIDKKYLFYFLLSNkdYFKGKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNNIEEALANAQ 168


                  ....*..
gi 2294874845 167 ELFESYL 173
Cdd:cd17499   169 QLFKSIL 175

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: 75.36 E-value: 6.38e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  87 LLPKEGFDLRFIKYFLESLDFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQAraktEQNLKNAR 166
Cdd:cd17250    99 LIPNEGIDSEYLYYWLKKVDLYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKL----KQALEAAK 174

                          90
                  ....*....|.
gi 2294874845 167 ELFESYLQQVF 177
Cdd:cd17250   175 EQLKGLRQSLL 185

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: 73.40 E-value: 2.19e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  24 NISHGKI----KEDDGPYPVFGAKGYIQNISFYQQENDYIAIIKDGAGIGRVSVHPAKssvLATMQ--YLLP--KEGFDL 95
Cdd:cd17269     8 EIKTGKLdanaANENGKYPFFTCSKEPLRIDTYAFDEEAILIAGNGSGVGNVKYYNGK---FNAYQrtYVIHpfKEEIDP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  96 RFIKYFLESLdFEEYRT----GSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIeqarAKTEQNLKNARELFES 171
Cdd:cd17269    85 KFLYYYLKSY-FKKYIEknsvGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALT----AELPAELEARKKQYEY 159


                  ....*...
gi 2294874845 172 YLQQVFSQ 179
Cdd:cd17269   160 YRDALLSF 167

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: 73.62 E-value: 2.39e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  65 GAGIGrvsvhpaKSSVL----ATMQ---YLLPKEGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVP 135
Cdd:cd17515    71 GATAG-------KVGILgidaATNQaicAILPNEEIDNEFLFYFLKSQkeYLISLGKGGAQPNISQGIIKNIEIPLPPLA 143

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2294874845 136 EQKRIVAILDQAFADIEqaraKTEQNLKNARELFESYLQQVF 177
Cdd:cd17515   144 EQKRIVAKLDKLDKLIE----KLEKALEKLEELKKALMQKLL 181

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: 72.94 E-value: 2.87e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 188 KLSELCNLISGQHIDAKNYNNEQRGIGYLTGPSDF--GVINPTVtkWTEHPKRTAIKGDILITVKGSgVGKVNImSAGEL 265
Cdd:cd17494     2 KLGEIAEITMGQSPSSKNYNDNPNGLPLVQGNADIknGKVIPRI--WTSEITKTANKGDIILSVRAP-VGEVAK-TNFDA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 266 AISRQLMAVRPTNavgdLLYWFLSMQF--DYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQelvdRISQFnLETVDLE 343
Cdd:cd17494    78 CIGRGVCAIKGNE----FIFLYLYLLNieGYWSKISQGSTFESINSNDIKNLKISIPSLEEQQ----KIATF-LSTLDAE 148

                         170       180
                  ....*....|....*....|...
gi 2294874845 344 -RIYTDKLSSLDELKKSILQKAF 365
Cdd:cd17494   149 iTLLEKKLEKLKQLKKGLLQKLF 171

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Crinalium epipsammum S subunit (S.Cep9333ORF4827P) TRD2-CR2 and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) T; The recognition sequences for Crinalium epipsammum S subunit (S.Cep9333ORF4827P) and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) 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: 341186 [Multi-domain] Cd Length: 174 Bit Score: 72.88 E-value: 3.39e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 188 KLSELCNLISGQHIDAKNYNNEQRGIGYLTGPSDFGVINPTVTKWTEHPKRTAIKGDILITVKGSgVGKVNImSAGELAI 267
Cdd:cd17495     2 TLGDIANITMGQSPKGESYNEDGEGLPFYQGVTDFGFRFPTNRVYTTAPTRFAEAGDILFSVRAP-VGDINI-ANEKCCI 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2294874845 268 SRQLMAVRPTNAVGDLLYWFLSMQFDYFQSLANGAAIPG-ISRHDVLDLKLSIPLSGDQQELVDRISQFNLE 338
Cdd:cd17495    80 GRGLAAIRSKSGSQSFLFYQLKSLFKEFDIFNGEGTVFGsINKKDLENLPIIIPSDEIIEAFEKLVSPIDQK 151

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: 72.91 E-value: 3.73e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  54 QENDYIAIIKdGAGIGRVsvhpakssVLATMQYLL--------PKEGFDLRFIKYFLESLdFEEYR---TGSTIPHIYFK 122
Cdd:cd17496    55 KKGDILFCVR-GSTTGRL--------NIADDEYCIgrgvaairPKNGIDTEFLYYLLESN-LDYLLaaaTGSTFPNISRD 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2294874845 123 DYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKteqnLKNARELFESYLQQVF 177
Cdd:cd17496   125 DLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQE----IEKLEELRDTLLPKLL 175

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 68.93 E-value: 9.46e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  99 KYFLESLDFEEY----RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQAraktEQNLKNARELFESYLQ 174
Cdd:COG0732     3 KYYLRSPSFREYlrslATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAAL----EKEIEKLKELRDALLP 78


                  ....
gi 2294874845 175 QVFS 178
Cdd:COG0732    79 KLFT 82

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: 70.96 E-value: 1.36e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845   9 WRYGVLEDAVTkgssnISHGK-IKED-DGPYPVFGAKGYIQNIsfyqqeNDYIAiikDGA--GIGRvsvhpaKSSV---- 80
Cdd:cd17288     1 WEVKKLGDLLK-----IKNGKdYKHLeDGNYPVYGSGGIMGYV------NDYLY---DGEsvLIGR------KGTIdkpl 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  81 --------LATMQYLLPKEGFDLRFIKYFLESLDFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIE 152
Cdd:cd17288    61 yvngpfwtVDTMFYTEIKKNNDPKFLYYLLKTIDFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDA 140

                         170       180
                  ....*....|....*....|...
gi 2294874845 153 QArAKTEQNLKNARELFESYLQQ 175
Cdd:cd17288   141 LI-ELQEKLLEKLKQYKLALMQE 162

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 68.16 E-value: 2.15e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 285 YWFLSMQF-DYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQFNLETVDLERiytdKLSSLDELKKSILQK 363
Cdd:COG0732     4 YYLRSPSFrEYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEK----EIEKLKELRDALLPK 79


                  ....*.
gi 2294874845 364 AFSGEL 369
Cdd:COG0732    80 LFTGEL 85

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: 69.47 E-value: 6.07e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILItVKGSGVGKVNIMSAgELAISRQLMAVRPTNAVGDL-LYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIP 320
Cdd:cd17513    64 ANSILI-VTRVGVGKVAINPF-DICTSQDFTSLIPIKEVNPLfLAYLLYSLLQKLKSQLQGTSIKGITKDDLKNLKIPLP 141

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2294874845 321 LSGDQQelvdRISQFnLETVDlERI--YTDKLSSLDELKKSILQKAF 365
Cdd:cd17513   142 PLEEQQ----KIAAI-LSKLD-KLIeaHEKKLEKLKQLKKGLMQKLF 182

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: 68.56 E-value: 1.05e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 187 YKLSELCNLISGQHIDAKNYNNEQRGIGYLTGPS-DFGVINPTVTKWT----EHPKRTAI-KGDILITVKGSgVGKVNIM 260
Cdd:cd16961     1 KKLGEIAEIISGKTPSSSSEYWDNGIIPWIRISDiNNGGIILTDEKITeegaEKLKKKILpKGDILISRSGT-IGKVAIV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 261 S-AGELAISRQLMAVRPTNAVGD--LLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQFNl 337
Cdd:cd16961    80 KeNDKALLNQAVIVIRPKDEVDSefLYYFLKSPFGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLD- 158

                         170       180
                  ....*....|....*....|...
gi 2294874845 338 etvDLERIYTDKLSSLDELKKSI 360
Cdd:cd16961   159 ---ALIELLEQKLEKLEQLKQAL 178

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: 68.68 E-value: 1.08e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  22 SSNISHGKIKEDDGPYpvfgakgyI-----QNISFYQ-QEND-YIAIikdgAG-IGRVSVHP------------AKssvl 81
Cdd:cd17256    31 VTDIKNGGIDLDNLKY--------IspeihEKIKRYTlSKGDiLISI----VGtIGRVGIVPkeldganltenaAR---- 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  82 atmqyLLPKEGFDLRFIKYFLESLDFEEY----RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAK 157
Cdd:cd17256    95 -----IRPKDSISPRYLYYYLRSPFGQSQieseTKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQ 169

                         170
                  ....*....|....*..
gi 2294874845 158 teqnLKNARELFESYLQ 174
Cdd:cd17256   170 ----LAKLEELKKALMQ 182

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: 66.74 E-value: 5.72e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  96 RFIKYFLESLDFEEY----RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNARELFES 171
Cdd:cd17521   107 KYLFYFTQSSLYWKQiksiSSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLKELLQS 186


                  .
gi 2294874845 172 Y 172
Cdd:cd17521   187 L 187

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: 66.03 E-value: 7.74e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  89 PKEGFDLRFIKYFLESLD--FEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNAR 166
Cdd:cd17497    88 PKKGLDKKYLLYYLKSIEneLSSLGTGSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDELTAKIDQLIALLEKAIELLK 167


                  ....*..
gi 2294874845 167 ELFESYL 173
Cdd:cd17497   168 EYRQAVL 174

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: 65.60 E-value: 1.38e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 187 YKLSELCNLISGQHIDAKNYNNEQR--GIGYLTgPSDFGviNPTVTKWTEHPKRTAI--KGDILITVKGSGVGKVNIMSA 262
Cdd:cd17263     1 VKLGEVCKFSKGKQPPISERFDEPKegSVRYIQ-IEDLR--NNNEKKYIENPKKSVIcnEDDILIVRDGANAGEVGTGLE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 263 GelAISRQLMAVRPTNAV--GDLLYWFLSMQFDYFQSLAN-GAAIPGISRHDVLDLKLSIPLSGDQQelvdRISQFnLET 339
Cdd:cd17263    78 G--AIASTLFKIIPDKNIidKDYLYYFLKSKEIQLNILTKaGSTIPHVNKKDLENLKIPLPSLEEQK----KIAEI-LDK 150

                         170       180
                  ....*....|....*....|....*...
gi 2294874845 340 VDlERIYT--DKLSSLDELKKSILQKAF 365
Cdd:cd17263   151 LD-ALIDKlkELIEKLIELKKGLFQELL 177

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: 65.63 E-value: 1.69e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  66 AGIGRVSVHPAKssvLATMQYL---LPKEGFDLRFIKYFL--ESLDFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRI 140
Cdd:cd17248    80 ASVGKSAIMGRP---MATSQDFanwVCGPELDPEYLLYVLraMKPEFERLAMGSTHKTIYMPDFKALRIALPPLEEQRKI 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2294874845 141 VAILDQAFADIEQARAKTEQNLKNARELFesylQQVFSQRGEG 183
Cdd:cd17248   157 VDRLEALDAKIDALERKLERLIELLKELR----QALLTAAVTG 195

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: 64.47 E-value: 2.25e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  18 VTKGSSnISHGKIKEDDGPYPVF-------GAKGYIqniSFYQQENDYIAIIKDGAGIGRVSVHPAKSSVLATMQYLLPK 90
Cdd:cd17255     9 IGRGRV-ISKKYISENPGDYPVYssqtknnGIMGYI---NTYDFDGEYITWTTDGANAGTVFYRNGKFSVTNVCGVLKVK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  91 EG-FDLRFIKYFLESLDFEeYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQafadIEQARAKTEQNLKNARELF 169
Cdd:cd17255    85 NKnINNKFLYYALNLIAKK-YVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDK----LDELINLLIAKLKKLIELR 159


                  ....*.
gi 2294874845 170 ESYLQQ 175
Cdd:cd17255   160 KKQLEY 165

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: 64.06 E-value: 5.11e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 237 KRTAIK-GDILITVKGSgVGKVNIMSAgELA---ISRQLMAVRPTNAV-GDLLYWFLSMQF--DYFQSLANGAAIPGISR 309
Cdd:cd17256    56 KRYTLSkGDILISIVGT-IGRVGIVPK-ELDganLTENAARIRPKDSIsPRYLYYYLRSPFgqSQIESETKGAAQPKLNL 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2294874845 310 HDVLDLKLSIPLSGDQQELVDRISQFNLETVDLERIYTDKLSSLDELKK 358
Cdd:cd17256   134 KRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKALMQ 182

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: 63.25 E-value: 6.64e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  87 LLPKEGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKteqnLKN 164
Cdd:cd17254    85 VVPDEEIDKDYLYYLLKALteEIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQ----LKK 160

                          90
                  ....*....|...
gi 2294874845 165 ARELFESYLQQVF 177
Cdd:cd17254   161 LEELRKALLQSLL 173

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: 62.91 E-value: 7.09e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  29 KIKEDDGPYPVFGA----KGYIqniSFYQQENDYIAIIKDGAGIGRVSVHPAK--SSVLATmqYLLPKEGFDLRFIKYFL 102
Cdd:cd17291    18 KELIENGKYPVIAGgiepSGYH---NEYNREGNTITISASGASAGYVNYWKEPfwASDCCY--ILSSKNELVNKFLYYFL 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2294874845 103 ESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLK 163
Cdd:cd17291    93 KNKqeEIYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFTELTAELPAELEARKK 155

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: 63.58 E-value: 7.46e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  66 AGIGRVSVhpAKSSVlATMQ---YLLPKEGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRI 140
Cdd:cd17273    77 APIGYVAI--ATNPL-ATNQgfkSIIPNEEIDNEFLYYLLKNNkpEIESLASGSTFKEISKSTFKKIEIPLPPLEEQKKI 153

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2294874845 141 VAILDQAFADIEQarakTEQNLKNARELFESYLQQVF 177
Cdd:cd17273   154 AAILSKLDELIEL----LEKENEKLKELRDGLLPKLF 186

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: 62.45 E-value: 1.18e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  89 PKEGFDLRFIKYFLESLDF----EEYRTGST----IPHIYFKDYKsapFPLISVPEQKRIVAILDQAFADIEQARAKTEQ 160
Cdd:cd17260    76 PKEGILPEFLYYLLRSPSFrkeaIKSMTGSSgrqrVPKDFLENYK---IPLPPLEEQKRIAAILDSLDAKIDALEAEIET 152

                          90
                  ....*....|...
gi 2294874845 161 NLKNARELFESYL 173
Cdd:cd17260   153 LEELLDALLPKLL 165

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: 61.78 E-value: 3.73e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 235 HPK------RTAikgdilitvkgsGVGKVNIMSAgELAISRQLMAVRPTNAVgD---LLYWFLSMQfDYFQSLANGAAIP 305
Cdd:cd17248    69 LPAgtvvlsRTA------------SVGKSAIMGR-PMATSQDFANWVCGPEL-DpeyLLYVLRAMK-PEFERLAMGSTHK 133

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2294874845 306 GISRHDVLDLKLSIPLSGDQQELVDRISQFNLETVDLERIYTDKLSSLDELKKSILQKAFSGE 368
Cdd:cd17248   134 TIYMPDFKALRIALPPLEEQRKIVDRLEALDAKIDALERKLERLIELLKELRQALLTAAVTGK 196

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: 61.42 E-value: 4.09e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  87 LLPKEGFDLRFIKYFLESLDFEEYR----TGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFAdieqARAKTEQNL 162
Cdd:cd17252   102 IRPKKEIDPRYLFYFLQSPSYREYIrslaSGTNINNLSNEHLENLKIPLPPLAEQKRIVAKLDKLDA----LIDKLKQAL 177

                          90
                  ....*....|..
gi 2294874845 163 KNARELFESYLQ 174
Cdd:cd17252   178 EKLDELLKSLFQ 189

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: 61.00 E-value: 5.64e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  90 KEGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNARE 167
Cdd:cd17257    93 SEELDKRFLYYALPPPlkAIEDTTSSTTVKHLSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLIAKLEKLRDLLLP 172


                  ....
gi 2294874845 168 LFES 171
Cdd:cd17257   173 LLQS 176

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: 60.45 E-value: 6.70e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845   8 DWRYGVLEDAVTKGSSNISHGKIKEDDGPYPVFGA-------KGYIQNISFYQQENDYIaIIKDGAGIGRVSVHPAKSSV 80
Cdd:pfam01420   3 DWEVFKLGDVFEIKKGKTPKKKELKNNGKYPYIRAgdlnnvvKGGLGYIKKYILPKGDI-TISSRATIGYVFYRDKPYYT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  81 LATMQYLLPK-EGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAK 157
Cdd:pfam01420  82 NQHIIVLIPKnNIKITEFLYLYLLLKlkKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDNTIELEKGI 161


                  ...
gi 2294874845 158 TEQ 160
Cdd:pfam01420 162 LNE 164

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: 60.55 E-value: 7.70e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  65 GAGIGRVSVhpAKSSVlATMQ---YLLPKEGFDLRFIKYFLESLDF--EEYRTGSTIPHIYFKDYKSAPFPLISVPEQKR 139
Cdd:cd17293    70 GGSIGKVGI--ADREV-AFNQqinAIIPNKSVDPKFLYYQLLSSKFqlQAIASSTTLPIINKSKFEKIEIPLPPLEEQKR 146

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2294874845 140 IVAILDQAFADIEQAraktEQNLKNARELFESYLQQVF 177
Cdd:cd17293   147 IVAKLDKLFALIDKL----EESLEELDELLKSLFQSAF 180

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: 60.35 E-value: 9.35e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  90 KEGFDLRFIKYFLESLDFEEY----RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNA 165
Cdd:cd17289   104 IKDINSKFLYYWFQSSIFKNQinsiTIGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEELA 183


                  ....*...
gi 2294874845 166 RELFESYL 173
Cdd:cd17289   184 KTLFQYWF 191

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: 59.09 E-value: 2.01e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  89 PKEGFDLRFIKYFLE--SLDFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNAR 166
Cdd:cd17245    88 ANKDIDNLFLYYYLKynKPELEKLGTGSTFKAINKKDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKLDELKK 167


                  ....*..
gi 2294874845 167 ELFESYL 173
Cdd:cd17245   168 GLMQELF 174

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: 58.69 E-value: 3.67e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 184 WGFYKLSELCNLIS-GQHiDAKNYNNEqrGIGYLTGPS------DFG----VINPTVTKWTehpKRTAI-KGDILITVKG 251
Cdd:cd17246     1 WEWVKLGEISSDITdGTH-PTPKYVES--GIPFITSKNikngkiDFSdvkyISEEDHNEIL---KRSKLkKGDILFSIIG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 252 SgVGKVNIMSAG-ELAISRQLMAVRPTNAVGD---LLYWFLSMQF-DYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQ 326
Cdd:cd17246    75 T-IGRVAIVPEDlPANINQAVALIRPKKEKIDpkyLLYYLNSPIIqKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQK 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2294874845 327 ELVDRISQFNletvDLERIYTDKLSSLDELKKSILQKAFS 366
Cdd:cd17246   154 RIAAILDSLD----ALIDKLEQKLEKLEDLKKGLMQDLLT 189

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: 57.37 E-value: 9.60e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2294874845  94 DLRFIKYFLESLDFEE----YRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNA 165
Cdd:cd17518   105 DNNFLKYFLNSDYFKEqldlLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEAALEALRKKKQAA 180

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: 57.44 E-value: 9.76e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILITVKGSGVGKVNIMSAgELAISRQLMAVRP-TNAVGDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIP 320
Cdd:cd17515    62 KGSVLIAMYGATAGKVGILGI-DAATNQAICAILPnEEIDNEFLFYFLKSQKEYLISLGKGGAQPNISQGIIKNIEIPLP 140

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2294874845 321 LSGDQQELVDRISQFNLETVDLERiytdKLSSLDELKKSILQKAF 365
Cdd:cd17515   141 PLAEQKRIVAKLDKLDKLIEKLEK----ALEKLEELKKALMQKLL 181

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: 56.73 E-value: 1.62e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 188 KLSELCNLISGQ---HIDAKNYNNEqrgIGYLTgPSDFG---VINPTVTKWTEHPK---RTAIKGDILITVKGSgVGKVN 258
Cdd:cd17286     2 KLGDLGEIVTGNtpsTKNSEYYGGE---ILFVT-PTDIDgnkYIYKTEKKLSEKGFkkaRILPKGSILVTCIGS-IGKNA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 259 IMSAgELAISRQLMAVRP-TNAVGDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQelvdRISQFnL 337
Cdd:cd17286    77 IATE-DCATNQQINAIIPnKNYDPEFLYYALENWSKKIKSLAGKQAVPIINKTEFSKIKILVPPLEEQQ----KIANF-L 150

                         170       180       190
                  ....*....|....*....|....*....|
gi 2294874845 338 ETVDlERIYT--DKLSSLDELKKSILQKAF 365
Cdd:cd17286   151 SKLD-ELIELqqQKIEKLEELKKGLLQKLF 179

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: 56.72 E-value: 1.75e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  96 RFIKYFLESLD----FEEYRTGST-IPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQnlknARELFE 170
Cdd:cd17253   111 EFLSYWLNSAYgrgyFLRAAKQTTnLASINSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEASLAK----LEELLK 186


                  ....*..
gi 2294874845 171 SYLQQVF 177
Cdd:cd17253   187 ALRQALL 193

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: 56.40 E-value: 2.02e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  65 GAGIGRVSVhpAKSSVlATMQYLL---PKEGF-DLRFIKYFLESLD--FEEYRTGSTIPHIYFKDYKSAPFPLISVPEQK 138
Cdd:cd17275    75 YASVGKVAI--NKIDV-ATNQAILgiiPKDEKlDFEFLYYWLLSLKneLKRLIRTGTQANLNAEIVKNLPIPLPPLEEQK 151

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2294874845 139 RIVAILDQAFADIEqaraKTEQNLKNARELFESYLQQVF 177
Cdd:cd17275   152 KIAEILDKIDAEID----KLEEKIEKLRELKKGLLQKMF 186

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: 54.86 E-value: 4.13e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  96 RFIKYFLESLDFEEyRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQnLKNARelfESYLQQ 175
Cdd:cd17292    73 KFLYYFYQIIKWKK-TEGSTIKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEK-LIALK---KGLMQY 147


                  ..
gi 2294874845 176 VF 177
Cdd:cd17292   148 LF 149

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: 55.54 E-value: 4.29e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  87 LLPKEGFDLRFIKYFLESldFEEY------RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKteq 160
Cdd:cd17249    96 LIPKEGIDPEFLLYALKA--NEDRilslvdKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERK--- 170

                          90
                  ....*....|....*.
gi 2294874845 161 nLKNARELFESYLQQV 176
Cdd:cd17249   171 -LAKLEELLKALMQAL 185

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: 55.60 E-value: 4.38e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  67 GIGRVSVHPAKssvLATMQ---YLLPKEGFDLRFIKYFLES-LDFEEYRT-GSTIPHIYFKDYKSAPFPLISVPEQKRIV 141
Cdd:cd17513    74 GVGKVAINPFD---ICTSQdftSLIPIKEVNPLFLAYLLYSlLQKLKSQLqGTSIKGITKDDLKNLKIPLPPLEEQQKIA 150

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2294874845 142 AILDQafadIEQARAKTEQNLKNARELFESYLQQVF 177
Cdd:cd17513   151 AILSK----LDKLIEAHEKKLEKLKQLKKGLMQKLF 182

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: 55.30 E-value: 5.42e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  83 TMQYLLPKEGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKteq 160
Cdd:cd17284    93 QLHAFVPSKKINPEYLMYLLSLQkkYMEKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAK--- 169

                          90
                  ....*....|....*..
gi 2294874845 161 nLKNARELFESYLQQVF 177
Cdd:cd17284   170 -LEKLQQLKKGLMQQLF 185

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: 55.16 E-value: 5.57e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 238 RTAIKGDILITVKGSGVGKVNImsAG-ELAISRQLMAVRPTNAVGDL-LYWFLSMQFDYFQSLANGAAIPGISRHDVLDL 315
Cdd:cd17293    57 RIVPKGSILVTCIGGSIGKVGI--ADrEVAFNQQINAIIPNKSVDPKfLYYQLLSSKFQLQAIASSTTLPIINKSKFEKI 134

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2294874845 316 KLSIPLSGDQQELVDRISQFNLETVDLERIYTDKLSSLDELKKSIL 361
Cdd:cd17293   135 EIPLPPLEEQKRIVAKLDKLFALIDKLEESLEELDELLKSLFQSAF 180

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: 55.21 E-value: 6.18e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 184 WGFYKLSELCNLISGQHIDAKNYNNEqrGIGYLTgPSDF---GVINPTVTKWTEHPKRTAIK-----GDILITVKGSGVG 255
Cdd:cd17278     1 WEVVKLGDIADIQNGYAFKSSDFSDE--GIPVIR-IGNIkngGIDLDDNSKYPEEPLEKYEKfllkkGDILIAMTGGTVG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 256 KVNIMSAGEL-AISRQLMA-VRPTNAV-GDLLYWFLSMQF--DYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVD 330
Cdd:cd17278    78 KVAIVPEDDEpALLNQRVGkFRPKDKIdKEFLYYLLRSDSfrNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAE 157

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2294874845 331 RISQFnLETVDLERiytDKLSSLDELKKSILQKAFS 366
Cdd:cd17278   158 ILDSL-DAKIDKLE---QKLEKLRDLLKPLLQSLFT 189

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: 54.33 E-value: 8.77e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  50 SFYQQENDyIAIIKDGAgIGRVSVHPAKSSVLATMQYLL-PKEGF-DLRFIKYFLESLDFEE----YRTGSTIPHIYFKD 123
Cdd:cd17258    46 SKIFKKGD-VLITRHGT-IGRVSIILSEEACLSSHVAGFnSKEGIsDNKFIKYLFNSKKIKNrlmsYGASSTQPALNLSR 123

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2294874845 124 YKSAPFPLISVPEQKRIVAIL---DQAfadIEQarakTEQNLKNARELFESYLQQVF 177
Cdd:cd17258   124 LLKIKFPNPPLEEQQKIGKILstwDRA---IEL----TEQKLELLQQQKKGLMQQLF 173

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: 54.47 E-value: 9.20e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  89 PKEGFDLRFIKYFLESLDFEE----YRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKN 164
Cdd:cd17264    98 PFAKVDVRYLYYYLNSPLGKSqikkYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQALEKLEEL 177


                  ....*..
gi 2294874845 165 ARELFES 171
Cdd:cd17264   178 LQSLFQS 184

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: 54.08 E-value: 1.50e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  96 RFIKYFLESLDFEEY-----RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQafadIEQARAKTEQNLKNARELFE 170
Cdd:cd17517   111 EFLYYYLNSPLGRKQiekiaKSAAGQANINQKDLKKLPIPLPPLEEQKEIVEILES----LDSKIDLLEKKLEKLEQLFK 186


                  ....*.
gi 2294874845 171 SYLQQV 176
Cdd:cd17517   187 SLMQSL 192

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: 53.69 E-value: 2.03e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  94 DLRFIKYFLES----LDFEEYRTGS--TIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQarakTEQNLKNARE 167
Cdd:cd17261   107 LPEYLALALNSpsarRQIESRATGTagSMPKISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDR----LEAQLAAALQ 182


                  ....*....
gi 2294874845 168 LFESYLQQV 176
Cdd:cd17261   183 LLDRLRQAL 191

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: 52.92 E-value: 3.44e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 241 IKGDILITVKGSgVGKVNIM-SAGELAISRQLMAVRPTNAVGDL-LYWFLSMQFDY--FQSLANGAAIPGISRHDVLDLK 316
Cdd:cd17264    63 QKGDILYCLRGS-LGKCAIVdNYDEGAIASSLVIIRPFAKVDVRyLYYYLNSPLGKsqIKKYDNGSAQPNLSAKSLKKFL 141

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2294874845 317 LSIPLSGDQQELVDRISQFnLETVDLeriYTDKLSSLDELKKSILQK 363
Cdd:cd17264   142 IPLPPLEEQKRIVAKLDEL-DALIDK---LKQALEKLEELLQSLFQS 184

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: 52.83 E-value: 3.68e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  90 KEGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEqaraKTEQNLKNARE 167
Cdd:cd17282   101 EEKIDVEFLEYYLRTLkkELEAIAPQSAQKNINLEILRPLKIPVPPLEEQKKIVEILDALDDLID----NLEKRIAKLEE 176

                          90
                  ....*....|
gi 2294874845 168 LFESYLQQVF 177
Cdd:cd17282   177 LKQSLLQEAF 186

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: 52.79 E-value: 4.15e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 184 WGFYKLSELCNLISGQHIDAKN---YNNeqrGIGYLTgPSDfgvINPTVTKWTEHPKRTaikgdilITVKG---SG---- 253
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKNpeyWNG---DIPWIT-PTD---LTKLKGKYISDTERK-------ITELGlknSSakll 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 254 -VGKVnIMS--A--GELAISRQLMAvrpTN-----------AVGDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKL 317
Cdd:cd17273    67 pAGSV-LLSsrApiGYVAIATNPLA---TNqgfksiipneeIDNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEI 142

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2294874845 318 SIPLSGDQQELVDRISQFNLETVDLERiytdKLSSLDELKKSILQKAF 365
Cdd:cd17273   143 PLPPLEEQKKIAAILSKLDELIELLEK----ENEKLKELRDGLLPKLF 186

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: 52.70 E-value: 4.21e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  23 SNISHGKIKEDDGPYpvFGAKGYIQNISFYQQENDYIAIIKDGAGIGRVSVHPAKSSVLATMQY--LLPKEGF-DLRFIK 99
Cdd:cd17519    33 TNIQNGKIDTDNLKY--FDLNDYKENLDKYIVRPGDIVIAMSGATTGKVGINLTDQEFYLNQRVgkFIPNEEIlNNRYLY 110

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2294874845 100 YFLESLDFEEYRT-GSTIPHIYFKDYKSAPFPLISVPEQKRIVAILD 145
Cdd:cd17519   111 HFLLSKQNEKYILaGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILD 157

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: 51.74 E-value: 8.21e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILITVKgSGVGKVNIMSAgELAISRQLMAVRPTNAVGD-LLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIP 320
Cdd:cd17285    63 KGTVIIATR-MGLGKVAINKI-DVAINQDLKALFPKDELDPeYLLYWFLSIEETIESLGTGTTVKGITLEDLKSLKIPLP 140

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2294874845 321 LSGDQQELVDRISQFNLETVDLERIYTDKLSSLDELKKSIL 361
Cdd:cd17285   141 PLEEQKRIVAILDELDELIDKLEAKLEKLKQLKKGLMQSLL 181

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: 51.20 E-value: 9.27e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 182 EGWGFYKLSELCNLISGQHIDAKNYNNEQrGIGYLTGPsdfgvINPTVTKWTEHPKRTAI--KGDILITVKGSgVGKVNI 259
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPKKKELKNNG-KYPYIRAG-----DLNNVVKGGLGYIKKYIlpKGDITISSRAT-IGYVFY 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 260 MSAGELAiSRQLMAVRPTN--AVGDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQFnL 337
Cdd:pfam01420  75 RDKPYYT-NQHIIVLIPKNniKITEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQL-D 152


                  ....*..
gi 2294874845 338 ETVDLER 344
Cdd:pfam01420 153 NTIELEK 159

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: 51.38 E-value: 1.33e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILITvKGSG---VGkvniMSA------GELAISRQLMAVRPTN--AVGDLLYWFLSMQF--DYFQSLANGAA--IPG 306
Cdd:cd17261    63 PGDLLIS-RANTselVG----RAAlvdgdpDNLIYPDKLIRLRVNEelLLPEYLALALNSPSarRQIESRATGTAgsMPK 137

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2294874845 307 ISRHDVLDLKLSIPLSGDQQELVDRISQFNLETVDLERIYTDKLSSLDELKKSI 360
Cdd:cd17261   138 ISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191

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: 50.95 E-value: 1.82e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  87 LLPKEGFDLRFIKYFLESLdFEEYRT---GSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQafadIEQARAKTEQNLK 163
Cdd:cd17287    95 ILPNDGINPDFLFYYLQSS-YEELRDlsnGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSA----IDAKIDALEQKLE 169

                          90
                  ....*....|....*
gi 2294874845 164 NARELFESYLQQVFS 178
Cdd:cd17287   170 LLQELKKSLMQQLFT 184

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: 50.99 E-value: 1.87e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  90 KEGFDLRFIKYFLESLdFEEYRT---GSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNAR 166
Cdd:cd17247   106 EERVLPEYLHYYLESQ-YDELRRigsGGGQGALNCGILKAFPIPLPPLDEQREIVAELEALLAKIDLLEEKIARLIELLK 184


                  ..
gi 2294874845 167 EL 168
Cdd:cd17247   185 EL 186

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: 50.28 E-value: 3.00e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILITVKGSGVGKVNIMSAgELAISRQLMAVRPTNAV-GDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIP 320
Cdd:cd17290    65 KNSVLVVGIGATIGKVGYSDK-ESSSNQQITGIIFNKDInPKFLFYWLSSSKEELENLANGATLPILNQEKLKNIKLPVP 143

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2294874845 321 LSGDQQELVDRISQfnlETVDLERIyTDKLSSLDELKKSILQ 362
Cdd:cd17290   144 PLNEQQKIVEFLDK---KTAKIDAL-IAKKEQLIELLKEYRQ 181

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: 49.79 E-value: 3.99e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 188 KLSELCNLISGQHIDAKN---YNNeqrGIGYL-TGPSDFGVINPTVTKWTEhpkrTAIK---------GDILITVKGSGV 254
Cdd:cd17287     2 KLGEIAKVSSGGTPSRSNpeyWNG---GIPWVkTGEVNFNEITDTEEKITE----EGLKnssaklfpkGTLLMAMYGQGK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 255 --GKVNIMSAgELAISRQLMAVRPTNAV-GDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDR 331
Cdd:cd17287    75 trGRVAILGI-EAATNQACAAILPNDGInPDFLFYYLQSSYEELRDLSNGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAF 153

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2294874845 332 ISQFNLETVDLERiytdKLSSLDELKKSILQKAFS 366
Cdd:cd17287   154 LSAIDAKIDALEQ----KLELLQELKKSLMQQLFT 184

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: 48.98 E-value: 5.60e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 187 YKLSELCNLISGQHIDAKNYNNEqrG----------IGYltgpsdfgvinpTVTKWTEHPKrtaikgdILITVKGSGVGK 256
Cdd:cd17266     1 VKLGELCKIKSGKSITASKISEE--GdypvyggngiIGY------------TDEYNHEGEY-------ILIGRVGALCGN 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 257 VNImSAGELAISRQLMAVRP-TNAVGDLLYWFLSMqFDyFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQF 335
Cdd:cd17266    60 VHY-VEGKFWVTDNALVVTPkKENNIKFLYYLLKS-LN-LNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSL 136

                         170       180
                  ....*....|....*....|....*..
gi 2294874845 336 NLETVDLERiytdKLSSLDELKKSILQ 362
Cdd:cd17266   137 DAKIDLLEK----KLEKLIELKKELMQ 159

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: 49.14 E-value: 6.96e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILITVKGSgVGKV---NIMSAGELAISrqlmAVRPTNAVGDL--LYWFLSMQFDYFQSLANGAAIPGISRHDVLDLK 316
Cdd:cd17296    63 KGTILIAIFAT-IGKVgilKIEATTNQAIA----GIKPKNKSINPkyLYYYLKSLYEKFLSLGRGVAQNNINLSILKNLK 137

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2294874845 317 LSIPLSGDQQELVDRISQFNLETvdleRIYTDKLSSLDELKKSILQKAF 365
Cdd:cd17296   138 IPLPPLEEQQRIVAILDKFEKLI----NKRQEGLQLLDELVKSLFEEMF 182

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: 49.15 E-value: 7.30e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  97 FIKYFLESLDF----EEYRTGST-IPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQarakTEQNLKNARELFES 171
Cdd:cd17525   110 FINYYLNSPDGkkqlESIASGTTsVAAIYQKDLKKLKLPLPPLDEQREIVSFLSELDAKIDQ----LEQKLEKLLQIKKA 185


                  ....*
gi 2294874845 172 YLQQV 176
Cdd:cd17525   186 LMQQL 190

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: 48.27 E-value: 1.27e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  96 RFIKYFLESLDFEEYRT---GSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEqaraKTEQNLKNARELFESY 172
Cdd:cd17265   101 DYLFHLFNSDLFKKQIGsflTATINQITNGNLNNFKIPLPPLEEQEKIAEFLSSLDAKID----KLIKKIEKLIELKKEL 176


                  ....*
gi 2294874845 173 LQQVF 177
Cdd:cd17265   177 MQQLI 181

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: 48.35 E-value: 1.38e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2294874845 117 PHIYFKDYKSAPFPLISVPEQKRIVAILDqafaDIEQARAKTEQNLKNARELFESYLQQVF 177
Cdd:cd17276   131 PNITKDDVRNFPIPLPPLDEQRAIVEFLS----DVDALIDSLEALIEKLRELKKGLMQQLL 187

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: 48.28 E-value: 1.49e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 184 WGFYKLSELCNLISGQHIDAKNYNNEQR--------GIGYLTG------PSDFgvinptvtkWTEHPKRTAIKGDILI-- 247
Cdd:cd17259     1 WEWVKLGDVADILSGYAFKSSEFSESGIrllrganvGVGEIRWddtvylPEEY---------LEEYEKYLLKEGDIVIal 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 248 --TVKGSGVgKVNIMSAGEL-AISRQLMA-VRP-TNAVGDLLYWFLSMQF--DYFQSLANGAAIPGISRHDVLDLKLSIP 320
Cdd:cd17259    72 drPIISGGL-KVARIPKSDLpALLVQRVArIRPkDELNSDFLYYLLQSDFflNYVEPVLTGTDVPHISTKQIKNFKIPLP 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2294874845 321 LSGDQQELVDRISQFNLETVDLERiytdKLSSLDELKKSILQK 363
Cdd:cd17259   151 PLEEQKKIAEFLSSLDALIDLLEQ----KLEKLQQLKKGLMQS 189

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: 48.36 E-value: 1.55e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2294874845 125 KSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNARELFESYL 173
Cdd:cd17526   144 ANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192

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: 47.82 E-value: 1.94e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  96 RFIKYFLESLDF----EEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEqaraKTEQNLKNARELFES 171
Cdd:cd17268   107 KYLSYLLNSPAFqkqkRKLGTGTKVVHISASDLAKIKIPVPPLEEQERIVEILDKFDALIA----GLPAEIEARRKQYEY 182


                  ...
gi 2294874845 172 YLQ 174
Cdd:cd17268   183 YRD 185

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: 47.59 E-value: 2.49e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  87 LLPKEG-FDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLK 163
Cdd:cd17296    93 IKPKNKsINPKYLYYYLKSLyeKFLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKFEKLINKRQEGLQLLDE 172

                          90
                  ....*....|
gi 2294874845 164 NARELFESYL 173
Cdd:cd17296   173 LVKSLFEEMF 182

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: 47.47 E-value: 2.62e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  89 PKEGFDLRFIKYFLES----LDFEEYRTGST-------IphiyfkdyKSAPFPLISVPEQKRIVAILDQAFADIEQARAK 157
Cdd:cd17283    97 LKKKLDKDFLYYLLSSitvqLQFSAQAGGGTknlntdiV--------KNLKIPLPPLEEQKRIAEILDSLDALIDALEEK 168

                          90
                  ....*....|...
gi 2294874845 158 TEQNLKNARELFE 170
Cdd:cd17283   169 LEKLEELKKGLMQ 181

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: 47.54 E-value: 2.78e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  65 GAGIGRVSVhpakSSVLATM-Q---YLLPKEGFDLRFIKYFLESldFEEY----RTGSTIPHIYFKDYKSAPFPLISVPE 136
Cdd:cd17280    73 GATIGRLGI----LGIDATTnQaccVLSGSNKIDIKFLFYWLLA--NRDElislASGGGQPNISQELIKSLRIPVPPLEE 146

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2294874845 137 QKRIVAILDQAFADIEQARAKTEQNLKNARE 167
Cdd:cd17280   147 QKQIAAFLDKKTAKIDSLIEKKERLIELLKE 177

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: 47.15 E-value: 3.75e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2294874845 122 KDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKteqnLKNARELFESYLQQV 176
Cdd:cd17522   140 TELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEK----IEKLKELKKGLFQKL 190

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: 46.92 E-value: 3.75e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 186 FYKLSELCNLISGQHIDAKNYNNEQRGIGYLTGPSDFGVINPTV-----TKWTEHPKRTAIK-GDILITVKGSGVGKVNI 259
Cdd:cd17519     2 YKTLGEVCKFQNGFAFKSSKYRESGFPIIRITNIQNGKIDTDNLkyfdlNDYKENLDKYIVRpGDIVIAMSGATTGKVGI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 260 MSAG-ELAISRQLMAVRPTNAVGD--LLYWFLSMQFDYFQSLANGAaIPGISRHDVLDLKLSIPLSGDQQELVDRISQFN 336
Cdd:cd17519    82 NLTDqEFYLNQRVGKFIPNEEILNnrYLYHFLLSKQNEKYILAGGS-QPNLSSEKLKKIKIPIPSLEVQEEIVSILDKFR 160


                  ....*...
gi 2294874845 337 LETVDLER 344
Cdd:cd17519   161 ELTNELES 168

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: 46.24 E-value: 3.80e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 284 LYWFLSmQFDyFQSLANGAAIPGISRHDVLDLKLSIPlSGDQQElvdRISQFnLETVDlERIYT--DKLSSLDELKKSIL 361
Cdd:cd17267    85 LYYLLK-TLD-LERLNSGSAVPGLNRNDVYSLKVPLP-PLEEQK---AIAAI-LDALD-DKIELnrRQNQTLEELADALL 156


                  ..
gi 2294874845 362 QK 363
Cdd:cd17267   157 PK 158

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: 46.75 E-value: 3.90e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  97 FIKYFLESLDFEEY----RTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEqaraKTEQNLKNARELFESY 172
Cdd:cd17494    91 FIFLYLYLLNIEGYwskiSQGSTFESINSNDIKNLKISIPSLEEQQKIATFLSTLDAEIT----LLEKKLEKLKQLKKGL 166


                  ....*
gi 2294874845 173 LQQVF 177
Cdd:cd17494   167 LQKLF 171

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: 46.40 E-value: 5.72e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 238 RTAIKGDILITVKGSG--VGKVNIMSAgELAISRQLMAVRPTNAVGDL-LYWFLSMQFDYFQSLANGAAIPGISRHDVLD 314
Cdd:cd17514    61 RIVPKGTILIACTGQGytRGQVAVLQI-DASTNQAIAAIRCKENVNPKyLYYYLKTQKNNLRNLTSGVAQKNLNIEMLRN 139

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2294874845 315 LKLSIPLSGDQQELVDRISQfnletvdLERIYTDKLSSLDELKKSILQKAF 365
Cdd:cd17514   140 LQIPLPPKEEQQKIVNILET-------LEFFEKDSLRKIKETAQDINLMIN 183

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: 46.05 E-value: 6.59e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILITVKGSgVGKVNIMSAgELAISRQLMAVRPTNAV-GDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIP 320
Cdd:cd17284    67 KGSVIMSCVGD-FGIVAIATN-ELVINQQLHAFVPSKKInPEYLMYLLSLQKKYMEKIATGTTIPYLNKTNCESIPIPLP 144

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2294874845 321 LSGDQQELVDRISQFnLETVDLeriYTDKLSSLDELKKSILQKAF 365
Cdd:cd17284   145 PIEEQNKIAKILDSI-DKKIDL---LIAKLEKLQQLKKGLMQQLF 185

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: 45.94 E-value: 7.80e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  90 KEGFDLRFIKYFLESldfeEY-----------RTGSTIPHIyfkdyKSAPFPLISVPEQKRIVAILDQAFADIEQARAKT 158
Cdd:cd17294   103 EEIANSRFLYYNLSS----RYeelrslsggggRGGLNLKII-----KSLPIPLPPLEEQKKIVAILDKFDALINDLKEGL 173

                          90
                  ....*....|....*
gi 2294874845 159 EQNLKNARELFESYL 173
Cdd:cd17294   174 PALLELRQKQYEYLR 188

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: 45.94 E-value: 8.33e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 184 WGFYKLSELCNLISGQHIDAKN---YNNEQrgIGYL-TGPSDFGVINPTV------------TKWtehpkrtAIKGDILI 247
Cdd:cd17294     1 WEWKTLGEIAKIFSGGTPSTSNpeyWDGGT--IPWLsSGEVNFKEIYETEkriteeglknssAKW-------IPKNSVLI 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 248 TVKGSG--VGKVNIMSAgELAISRQLMAVRP--TNAVGDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSG 323
Cdd:cd17294    72 ALAGQGktRGTVAILKI-PLTTNQSLAAIEPdeEIANSRFLYYNLSSRYEELRSLSGGGGRGGLNLKIIKSLPIPLPPLE 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2294874845 324 DQQELVDRISQFNLETVDLERiytdKLSSLDELKKSILQK 363
Cdd:cd17294   151 EQKKIVAILDKFDALINDLKE----GLPALLELRQKQYEY 186

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: 45.66 E-value: 9.28e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  65 GAGIGRVSVhpAKSSVLATMQY--LLPKEGFDLRFIKYFLESL--DFEEYRTGSTIPHIYFKDYKSAPFPLISVPEQKRI 140
Cdd:cd17290    74 GATIGKVGY--SDKESSSNQQItgIIFNKDINPKFLFYWLSSSkeELENLANGATLPILNQEKLKNIKLPVPPLNEQQKI 151

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2294874845 141 VAILDQAFADIEQARAKTEQNLKNARELFESY 172
Cdd:cd17290   152 VEFLDKKTAKIDALIAKKEQLIELLKEYRQAL 183

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: 45.92 E-value: 9.68e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2294874845 125 KSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQnlknARELFESYLQQV 176
Cdd:cd17524   142 KAIPIPLPPLEEQKEIVEKLDELDALIDRLEALLEE----AEELLESLLQSL 189

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: 45.16 E-value: 1.45e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  87 LLPKEG-FDLRFIKYFLESLDFEEYRTGS---------TIphiyfkdyKSAPFPLISVPEQKRIVAILDQAFADIEQARA 156
Cdd:cd17244    94 FIPKDKkIDTEYLYYYLKSFDYSSLGSTAskgktlnskKI--------KEIPIPLPPLEEQKRIAPILDKIDALIDQLET 165

                          90
                  ....*....|...
gi 2294874845 157 KTEQNLKNARELF 169
Cdd:cd17244   166 LIELLDELLPKLM 178

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: 44.86 E-value: 1.91e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  66 AGIGRVSVHPAKssvLATMQ---YLLPKEGFDLRFIKYFLESLDFE--EYRTGSTIPHIYFKDYKSAPFPLISVPEQKRI 140
Cdd:cd17279    74 APIGYVAIATVE---LCTNQgckALVPNSDVDSRFLYYLLLAAKEElnSLGRGTTFLELSTDELANFKIPLPPLSEQRAI 150

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2294874845 141 VAILDQAFADIEQARAKTEQNLKNARELFES 171
Cdd:cd17279   151 ADFLDRETAKIDALIAKKQQLIELLKEKRQA 181

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: 43.35 E-value: 7.99e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  90 KEGFDLRFIKYFLESLDfEEYR---TGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNAR 166
Cdd:cd17281   104 KNKLDIKFLFYYFFVLG-EWCKkniNIGGFPSVDMNKLKKFKIPIPPLEEQEKIVEILDKFTKLTADLTAELPAELEARK 182

                          90
                  ....*....|..
gi 2294874845 167 ELFESYLQQVFS 178
Cdd:cd17281   183 KQYEYYRDKLLS 194

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: 42.39 E-value: 1.09e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 237 KRTAIKGDILITVKGSgVGKVNIMSAGELAISRQLMAVRPTNAVGDLLYWFLSMQFDYFQ----SLANGAAIPGISRHDV 312
Cdd:cd17258    46 SKIFKKGDVLITRHGT-IGRVSIILSEEACLSSHVAGFNSKEGISDNKFIKYLFNSKKIKnrlmSYGASSTQPALNLSRL 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2294874845 313 LDLKLSIPLSGDQQelvdRISQFnLETVDLE-RIYTDKLSSLDELKKSILQKAF 365
Cdd:cd17258   125 LKIKFPNPPLEEQQ----KIGKI-LSTWDRAiELTEQKLELLQQQKKGLMQQLF 173

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: 42.43 E-value: 1.28e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 283 LLYWFLSMQfDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQFNLETVDLERiytdKLSSLDELKKSILQ 362
Cdd:cd17282   109 LEYYLRTLK-KELEAIAPQSAQKNINLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEK----RIAKLEELKQSLLQ 183


                  ...
gi 2294874845 363 KAF 365
Cdd:cd17282   184 EAF 186

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: 42.52 E-value: 1.41e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILIT---VKGSGVGKVNIMSA--GELAISRQLMAVRPTNAVGD---LLYWFLSMQF-DYFQSLANGAAI-PGISRHD 311
Cdd:cd17517    64 KGDILFNrsnGSPELVGKCALVDEedEPAIFASYLIRLRLDKKKILpefLYYYLNSPLGrKQIEKIAKSAAGqANINQKD 143

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2294874845 312 VLDLKLSIPLSGDQQELVDRISQFnLETVDLERiytDKLSSLDELKKSILQKA 364
Cdd:cd17517   144 LKKLPIPLPPLEEQKEIVEILESL-DSKIDLLE---KKLEKLEQLFKSLMQSL 192

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: 42.16 E-value: 1.55e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 254 VGKVNImSAGELAISRQLMAVRPTNAV-GDLLYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQelvdRI 332
Cdd:cd17279    76 IGYVAI-ATVELCTNQGCKALVPNSDVdSRFLYYLLLAAKEELNSLGRGTTFLELSTDELANFKIPLPPLSEQR----AI 150

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2294874845 333 SQF-NLETVDLERIYTDK---LSSLDELKKSI 360
Cdd:cd17279   151 ADFlDRETAKIDALIAKKqqlIELLKEKRQAL 182

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: 41.32 E-value: 2.29e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  76 AKSSvlaTMQYLLPKEG-FDLRFIKYFLESLDFEeyrTGSTIPHiYFKDYKSAPFPLISVPEQKRIVAILDQafadIEQA 154
Cdd:cd17274    79 VKSS---AMKILTPKNNnVNLKFVYEALQTIKYV---PGDHKRH-WISEYSKFKIPLPPLEEQNKIVRILDK----FDEL 147

                          90       100
                  ....*....|....*....|....
gi 2294874845 155 RAKTEQNLKNARELFESYLQQVFS 178
Cdd:cd17274   148 IAELEAKLELLKKQKKYYLQKLFT 171

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: 40.15 E-value: 7.35e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 271 LMAVRPTNAVGD---LLYWFLS-MQFDYFQSLANGAA-IPGISRHDVLDLKLSIPLSGDQQELVDRISQFNLETVDLERI 345
Cdd:cd17253    98 LFRVRPKDDLLLpefLSYWLNSaYGRGYFLRAAKQTTnLASINSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEAS 177

                          90
                  ....*....|....*.
gi 2294874845 346 YTDKLSSLDELKKSIL 361
Cdd:cd17253   178 LAKLEELLKALRQALL 193

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: 40.00 E-value: 8.98e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  90 KEGFDLRFIKYFLESLdFE---EYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIE--QARAKTEQNLKN 164
Cdd:cd17270    99 KININKKFFAYQLKLK-FEiekEKAPGGTIKTITKEELSKFEIPIPSLEEQKEIVNILDKFDELITelQLRKKQLEYYKK 177


                  .
gi 2294874845 165 A 165
Cdd:cd17270   178 A 178

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: 39.84 E-value: 9.15e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILITVKGSgVGKVNIMSaGELAISRQLMAVRPTNAVGD---LLYWFLSMQfDYFQSLANGAAIPGISRHDVLDLKLS 318
Cdd:cd17275    67 KGTILYAMYAS-VGKVAINK-IDVATNQAILGIIPKDEKLDfefLYYWLLSLK-NELKRLIRTGTQANLNAEIVKNLPIP 143

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2294874845 319 IPLSGDQQelvdRISQFnLETVDLE-RIYTDKLSSLDELKKSILQKAF 365
Cdd:cd17275   144 LPPLEEQK----KIAEI-LDKIDAEiDKLEEKIEKLRELKKGLLQKMF 186

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: 39.93 E-value: 1.01e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 271 LMAVRPTNAV-GDLLYWFLsMQFDyFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQFNLETVDLERIYTDK 349
Cdd:cd17250    96 VMGLIPNEGIdSEYLYYWL-KKVD-LYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQALEAA 173

                          90
                  ....*....|..
gi 2294874845 350 LSSLDELKKSIL 361
Cdd:cd17250   174 KEQLKGLRQSLL 185

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: 39.14 E-value: 1.50e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2294874845 125 KSAPFPLISVPEQKRIVAILDQAFADIEQARAKTEQNLKNARELFESY 172
Cdd:cd17523   143 KSLPIPLPPLKEQKKIVARVEELFALIDQLESSLDLAQQLQNKLAQSI 190

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: 38.34 E-value: 2.38e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 245 ILITVKGSGVGKVNIMSaGELAISRQLMAVRPTNAVGDL--LYWFLSMQF-DYFQSLANGAAIPGISRHDVLDLKLSIPL 321
Cdd:cd17269    47 ILIAGNGSGVGNVKYYN-GKFNAYQRTYVIHPFKEEIDPkfLYYYLKSYFkKYIEKNSVGSSVPYIRLPMLENFKIPLPP 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2294874845 322 SGDQQELVDRISQFNLETVDLERiytdKLSSLDELKKSILQKAFS 366
Cdd:cd17269   126 LEEQKRIVRILDKFDALTAELPA----ELEARKKQYEYYRDALLS 166

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: 38.30 E-value: 3.49e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  90 KEGFDLRFIKYFLESLDFE---EYRTGSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQAFADIEQARaKTEQNLKNAR 166
Cdd:cd17516    98 KNKFDPDFVYYLLKNNSKYlksIAGGSTATPIINKSTFSNIEIPLPPLPEQKKIAAILSSLDDKIENNR-RINKTLEEMA 176


                  ..
gi 2294874845 167 EL 168
Cdd:cd17516   177 QA 178

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: 38.18 E-value: 3.69e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845   9 WRYGVLEDAVTKGSSNISHGKIKEDdGPYPVFGAK----GYI--QNISFYQQENDYIAIIKDG-------AGIGRVS-VH 74
Cdd:cd17272     1 VEEKTLGDIAVDGFQNGPAPNFDEK-GEIPVITSKnisnGKIdfEYVKYDFLSISKNRKINKGdilitmiGTIGETAiVK 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2294874845  75 PAKSSVLATMQYL--LPKEGFDLRFIKYFLESLDFEEYRTGSTIPHIYFK--DYKSAPFPLISVPEQKRIVAILD 145
Cdd:cd17272    80 CLDPKFYTLNLYLirLKKEKLLPSYLKYFLDSEKFLNKSISATSGQGYLKanQIDKLEIPLPPLEEQQRIVKILD 154

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: 37.86 E-value: 3.93e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845  87 LLPKEGFDLRFIKYFLESLdFEEYRT---GSTIPHIYFKDYKSAPFPLISVPEQKRIVAILDQafadIEQARAKTEQNLK 163
Cdd:cd17286    91 IIPNKNYDPEFLYYALENW-SKKIKSlagKQAVPIINKTEFSKIKILVPPLEEQQKIANFLSK----LDELIELQQQKIE 165

                          90
                  ....*....|....
gi 2294874845 164 NARELFESYLQQVF 177
Cdd:cd17286   166 KLEELKKGLLQKLF 179

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Arthrobacter chlorophenolicus A6 S subunit (S.AchA6I) TRD2-CR2; The S.AchA6I S subunit recognizes 5'... TGAANNNNNTCG ... 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.AchA6I-TRD1 recognizes TGAA/TTCA, and TRD2 recognizes CGA/TCG. 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: 341132 [Multi-domain] Cd Length: 182 Bit Score: 37.05 E-value: 7.14e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 242 KGDILITVKGSgVGKVNIMsAGELAISRQLMAVRPTNAVGDL-LYWFLSMQFDYFQSLANGAAIPGISRHDVLDLKLSIP 320
Cdd:cd17243    66 KGTTIISARGT-VGKLALL-GIPMAMNQSCYGLRGKDGLSNYfLYYLLKNLIEELKQKAHGSVFDTITRKTFDEIKVPLP 143

                          90
                  ....*....|....*
gi 2294874845 321 LSGDQQELVDRISQF 335
Cdd:cd17243   144 PEELQKSFENIVSPL 158

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: 37.14 E-value: 8.48e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 187 YKLSELCNLI-SGQHIDAKNYNNEQRGIGYLTgPSDF--GVINPTVTKWT-----EHPK-RTAIKGDILITVKGSGVGKV 257
Cdd:cd17280     1 WKISHLFGLIgSGTTPKSDNEDYYDGGIPWVT-TGDLrdGIITETSKKITdkaldDYSAlKIYPAGSLVIAMYGATIGRL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2294874845 258 NIMSAGelAISRQLMAVRPTNAVGD---LLYWFLSMQfDYFQSLANGAAIPGISRHDVLDLKLSIPLSGDQQELVDRISQ 334
Cdd:cd17280    80 GILGID--ATTNQACCVLSGSNKIDikfLFYWLLANR-DELISLASGGGQPNISQELIKSLRIPVPPLEEQKQIAAFLDK 156

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2294874845 335 FnletvdLERIytDKLSS--------LDELKKSILQKA 364
Cdd:cd17280   157 K------TAKI--DSLIEkkerlielLKERRQALISEA 186