NCBI Conserved Domain Search

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: 345.24 E-value: 4.46e-120

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   9 SSIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGQGKTRGQVA 88
Cdd:cd17287     1 KKLGEIAKVSSGGTPSRSNPEYWNGGIPWVKTGEVNFNEITDTEEKITEEGLKNSSAKLFPKGTLLMAMYGQGKTRGRVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  89 KLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNA 168
Cdd:cd17287    81 ILGIEAATNQACAAILPNDGINPDFLFYYLQSSYEELRDLSNGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAK 160

                         170       180
                  ....*....|....*....|....
gi 2018995424 169 ISVTEKLLTNSQQQKKALMQQLLT 192
Cdd:cd17287   161 IDALEQKLELLQELKKSLMQQLFT 184

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: 250.04 E-value: 1.11e-82

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  11 IGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGQgkTRGQVAKL 90
Cdd:cd17515     3 LGDIGKWGSGGTPSRSNPEYYGGGIPWIKSGELNDGYITSTEEKITEEGLKNSSAKLFPKGSVLIAMYGA--TAGKVGIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  91 GIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAIS 170
Cdd:cd17515    81 GIDAATNQAICAILPNEEIDNEFLFYFLKSQKEYLISLGKGGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKLIE 160

                         170       180
                  ....*....|....*....|.
gi 2018995424 171 VTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17515   161 KLEKALEKLEELKKALMQKLL 181

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: 240.89 E-value: 6.05e-79

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   3 PKGWELSSIGKISDVSSGGTPSRNNEAYWNGN-IPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGQG 81
Cdd:cd17247     1 PEHWEVVRLGDVARVGNGSTPSRKNPDYWNGGtIPWVSSGEVNDNRITEADEFITELALKECSLPLVPPGSVLVAMIGQG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  82 KTRGQVAKLGIDASTNQACAAIVLHTGYEV-DFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAK 160
Cdd:cd17247    81 KTRGQAAILAIEATINQNLAAIRPNEERVLpEYLHYYLESQYDELRRIGSGGGQGALNCGILKAFPIPLPPLDEQREIVA 160

                         170       180       190
                  ....*....|....*....|....*....|
gi 2018995424 161 ILSTWDNAISVTEKLLTNSQQQKKALMQQL 190
Cdd:cd17247   161 ELEALLAKIDLLEEKIARLIELLKELRQAL 190

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: 234.30 E-value: 1.86e-76

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   6 WELSSIGKISDVSSGGTPSRNNEAYWNGN-IPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGQGKTR 84
Cdd:cd17294     1 WEWKTLGEIAKIFSGGTPSTSNPEYWDGGtIPWLSSGEVNFKEIYETEKRITEEGLKNSSAKWIPKNSVLIALAGQGKTR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  85 GQVAKLGIDASTNQACAAIVlhTGYEV---DFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKI 161
Cdd:cd17294    81 GTVAILKIPLTTNQSLAAIE--PDEEIansRFLYYNLSSRYEELRSLSGGGGRGGLNLKIIKSLPIPLPPLEEQKKIVAI 158

                         170       180       190
                  ....*....|....*....|....*....|
gi 2018995424 162 LSTWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17294   159 LDKFDALINDLKEGLPALLELRQKQYEYLR 188

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) TRD1-CR1, and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) TRD1-CR1; The recognition sequences of Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains TRD1-CR1. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341191 [Multi-domain] Cd Length: 186 Bit Score: 214.46 E-value: 1.03e-68

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  10 SIGKIS-DVSSGGTPSRNNEAYW-NGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGQGKTRGQV 87
Cdd:cd17500     1 KLEDICiKITSGGTPSRSNKEYYnGGNIPWLKTKELNFKRIYDTEEKITEEGLKNSSAKLIPENTVIIAMYGAGKTAGRV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  88 AKLGIDASTNQACAAIVLHTGY-EVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWD 166
Cdd:cd17500    81 AINKIPLTTNQACCNLIIDNKKaDYRFVYYSLKTQYEELVNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLD 160

                         170       180
                  ....*....|....*....|....*..
gi 2018995424 167 NAIsvtekllTNSQQQKKAL--MQQLL 191
Cdd:cd17500   161 DKI-------ELNNRQNETLeaMAETL 180

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: 198.15 E-value: 2.31e-62

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   7 ELSSIGKISD-VSSGGTPSRNNEAYWNGNIPWVTTAEV--QFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGqgkT 83
Cdd:cd17275     1 EQVKLGELCEkMKSGGTPSTSNKEYYGGDIPFVKISDMtkSGKYIYSTEKYITEEGLKNSSAWIVPKGTILYAMYA---S 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  84 RGQVAKLGIDASTNQACAAIVLHTGY-EVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKIL 162
Cdd:cd17275    78 VGKVAINKIDVATNQAILGIIPKDEKlDFEFLYYWLLSLKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIAEIL 157

                         170       180
                  ....*....|....*....|....*....
gi 2018995424 163 STWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17275   158 DKIDAEIDKLEEKIEKLRELKKGLLQKMF 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: 194.93 E-value: 5.03e-61

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   6 WELSSIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEV---QFKIIEDTVEKITEEGLANSSAKLFPAGTILMAmygqgk 82
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKNPEYWNGDIPWITPTDLtklKGKYISDTERKITELGLKNSSAKLLPAGSVLLS------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  83 TR---GQVAKLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIA 159
Cdd:cd17273    75 SRapiGYVAIATNPLATNQGFKSIIPNEEIDNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEIPLPPLEEQKKIA 154

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2018995424 160 KILSTWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17273   155 AILSKLDELIELLEKENEKLKELRDGLLPKLF 186

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio cholerae 1311-69 S subunit (S.Vch69ORF1407P) TRD2-CR2, and Methanococcoides methylutens MM1 S subunit (S.MmeMM1ORF456P) TRD2-CR2; The recognition sequences of Vibrio cholerae 1311-69 S subunit (S.Vch69ORF1407P) and Methanococcoides methylutens MM1 S subunit (S.MmeMM1ORF456P) 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: 341192 [Multi-domain] Cd Length: 191 Bit Score: 180.07 E-value: 2.90e-55

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   2 VPKGWELSSI-GKISDVSSGGTPSRNNEAYW-NGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYg 79
Cdd:cd17501     1 VPEGWEVGTIlDLCYKTQSGGTPSRKNPEYWdGGIIPWLKTGELRDNIILDTEEKITEEGLKNSSAKLFPKGTVLVAMY- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  80 qGKTRGQVAKLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPlteqkkiA 159
Cdd:cd17501    80 -GATAGKLGILAKEATTNQACCALIPKEEYSPFFLYLYLLNSRDYLANLASGSAQQNISQQIIKNTKVLIPP-------E 151

                         170       180
                  ....*....|....*....|....*.
gi 2018995424 160 KILSTWDNAISVT-EKLLTNSQQQKK 184
Cdd:cd17501   152 DLLEIFNKLVEPLfDKIINNLKENQK 177

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: 174.24 E-value: 2.20e-53

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 213 TLSMFCNIAKGKALSASDLEV-GDFPVIAGGKSSPYSHSDY-THENVVTVSASGAYAGYISYHNYKIWASDCSVVSAKAD 290
Cdd:cd17291     2 KLGEIAEIKKGKQITKKELIEnGKYPVIAGGIEPSGYHNEYnREGNTITISASGASAGYVNYWKEPFWASDCCYILSSKN 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2018995424 291 NLIDYF-YQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKL 358
Cdd:cd17291    82 ELVNKFlYYFLKNKQEEIYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFTELTAELPAEL 150

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Nitrosopumilus maritimus SCM1 S subunit (S2.NmaSCMORF606P) TRD2-CR2, Corynebacterium jeikeium K411 S subunit (S.CjeKORF1254P) TRD2-CR2 and Porphyromonas canoris COT-108 OH27; The recognition sequences of Nitrosopumilus maritimus SCM1 S subunit (S2.NmaSCMORF606P), Corynebacterium jeikeium K411 S subunit (S.CjeKORF1254P), and Porphyromonas canoris COT-108 OH2762 S subunit (S2.Pca2762ORF8685P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341160 [Multi-domain] Cd Length: 186 Bit Score: 174.38 E-value: 4.79e-53

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  16 DVSSGGTPSRNNEAYWNGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYG--QGKTRGQVAKLGID 93
Cdd:cd17271     7 GLSSGATPSRGNPEYFNGDIPWITSGELNYNYITDTNEKITEEAVKNTNLKIHPKGTFLIAITGleAAGTRGKCAITGIP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  94 ASTNQACAAIVLHTGYEVDFYYQFLIsQYENIREMANSGG--QQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISV 171
Cdd:cd17271    87 ATTNQSCMAFYPTKKLTTEFLFYWYK-KYGNYLGFKYAQGtkQQSYTADIVKKLPILLPTLKEQKKIANFLSDIDELIAT 165

                         170       180
                  ....*....|....*....|.
gi 2018995424 172 TEKLLTNSQQQKKALMQQLLT 192
Cdd:cd17271   166 LEKKIEKLKKIKKGLMQKLLT 186

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: 172.00 E-value: 3.81e-52

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  10 SIGKISDVSSGGTPSRNN-EAYWNGN-IPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGQGKTRGQV 87
Cdd:cd17276     2 KIGDIAKTSSGGTPLRSNqEYYFNGGtIPWVKTTDLNNGVIYETEEKITEKALKETSCKLLPKGTVLVAMYGGFGQIGRT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  88 AKLGIDASTNQACAAIVLHtgyEVDFYYQFLISQYENIRE--MANSGGQQ---NLSGGIVKSIPVPVPPLTEQKKIAKIL 162
Cdd:cd17276    82 GLLGIPAAINQAICAILPN---EKKVNPEFLLRYLNFNRPywMRVAASSRkdpNITKDDVRNFPIPLPPLDEQRAIVEFL 158

                         170       180
                  ....*....|....*....|....*....
gi 2018995424 163 STWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17276   159 SDVDALIDSLEALIEKLRELKKGLMQQLL 187

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: 171.63 E-value: 4.00e-52

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  11 IGKISDVSSGGTPSRNNEAYW-NGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGqgkTRGQVAK 89
Cdd:cd17296     3 LGEICSIQSGGTPSRSKKEYWnNGTIPWVKISDCKNKYVDETEEFITEEGLNNSSAKLLKKGTILIAIFA---TIGKVGI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  90 LGIDASTNQACAAI-VLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNA 168
Cdd:cd17296    80 LKIEATTNQAIAGIkPKNKSINPKYLYYYLKSLYEKFLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKFEKL 159

                         170       180
                  ....*....|....*....|...
gi 2018995424 169 ISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17296   160 INKRQEGLQLLDELVKSLFEEMF 182

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: 170.71 E-value: 1.20e-51

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   9 SSIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMygqgktRG--- 85
Cdd:cd17249     1 VRLGDLGKFLSGGTPSKSNPEYWGGDIPWVSPKDMKSDYISDSEDHITELAVEESGTKLVPAGSVLIVV------RGmil 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  86 ----QVAKLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMAN--SGGQQNLSGGIVKSIPVPVPPLTEQKKIA 159
Cdd:cd17249    75 ahtfPVAITTRPVAFNQDIKALIPKEGIDPEFLLYALKANEDRILSLVDkaGHGTGSLDTDDLKNLPIPLPPLEEQRRIA 154

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2018995424 160 KILSTWDNAISVTEKLLTNSQQQKKALMQQL 190
Cdd:cd17249   155 AILDALDALIDLLERKLAKLEELLKALMQAL 185

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: 166.19 E-value: 7.71e-50

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   6 WELSSIGKIsdVSSGGTPSRNNEAYWNGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSA-KLFPAGTILMAMYGQgkTR 84
Cdd:cd17280     1 WKISHLFGL--IGSGTTPKSDNEDYYDGGIPWVTTGDLRDGIITETSKKITDKALDDYSAlKIYPAGSLVIAMYGA--TI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  85 GQVAKLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKIL-- 162
Cdd:cd17280    77 GRLGILGIDATTNQACCVLSGSNKIDIKFLFYWLLANRDELISLASGGGQPNISQELIKSLRIPVPPLEEQKQIAAFLdk 156

                         170       180
                  ....*....|....*....|....*.
gi 2018995424 163 --STWDNAISVTEKLLTNSQQQKKAL 186
Cdd:cd17280   157 ktAKIDSLIEKKERLIELLKERRQAL 182

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: 165.37 E-value: 1.23e-49

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  14 ISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAmygqgkTR---GQVAKL 90
Cdd:cd17285     7 VEKIVGGGTPSKSNPEYWNGDIPWASVKDLKGKYLTSTEDKITEEGLKNSSSNLIPKGTVIIA------TRmglGKVAIN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  91 GIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMAnsggqqnlSGGIVK--------SIPVPVPPLTEQKKIAKIL 162
Cdd:cd17285    81 KIDVAINQDLKALFPKDELDPEYLLYWFLSIEETIESLG--------TGTTVKgitledlkSLKIPLPPLEEQKRIVAIL 152

                         170       180
                  ....*....|....*....|....*....
gi 2018995424 163 STWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17285   153 DELDELIDKLEAKLEKLKQLKKGLMQSLL 181

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: 157.72 E-value: 1.11e-46

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  16 DVSSGGTPSRNNEAYWN-GNIPWVTTAEVQFKIIEDTVEKITEE-GLANSSAKLFPAGTILMAMYGQGKTRGQVAKLGID 93
Cdd:cd17514     9 EIINGGTPSRNEPEYWNnGDIPWLTSGETDDNFINNTSEKITTKnGLEDSSIRIVPKGTILIACTGQGYTRGQVAVLQID 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  94 ASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWD--NAISV 171
Cdd:cd17514    89 ASTNQAIAAIRCKENVNPKYLYYYLKTQKNNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNILETLEffEKDSL 168

                         170
                  ....*....|....
gi 2018995424 172 TEKLLTNSQQQKKA 185
Cdd:cd17514   169 RKIKETAQDINLMI 182

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: 155.77 E-value: 9.87e-46

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   3 PKGWELSSIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQ---FKIIEDTVEKITEEGLANSSAKLFPAGTILM---A 76
Cdd:cd17248     1 PAHWEVVPLTDVAKLESGHTPSRSRPEYWNGCIPWISLADVKqlrGDYIYETKEKISELGIANSSARLLPAGTVVLsrtA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  77 mygqgkTRGQVAKLGIDASTNQACAAIVlhTGYEVD---FYYQFLISQYENIREMANSGGQQnlsggI----VKSIPVPV 149
Cdd:cd17248    81 ------SVGKSAIMGRPMATSQDFANWV--CGPELDpeyLLYVLRAMKPEFERLAMGSTHKT-----IympdFKALRIAL 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2018995424 150 PPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLLTGKKRL 197
Cdd:cd17248   148 PPLEEQRKIVDRLEALDAKIDALERKLERLIELLKELRQALLTAAVTG 195

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: 150.30 E-value: 6.15e-44

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   7 ELSSIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEV--QFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGqgkTR 84
Cdd:cd17243     1 EVKSLSDVVDIIGGGTPKTSVPEYWNGDIPWFSVKDVnnDSRFVLDTEKKITELGLKNSSTKLLPKGTTIISARG---TV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  85 GQVAKLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILST 164
Cdd:cd17243    78 GKLALLGIPMAMNQSCYGLRGKDGLSNYFLYYLLKNLIEELKQKAHGSVFDTITRKTFDEIKVPLPPEELQKSFENIVSP 157

                         170       180
                  ....*....|....*....|....*....
gi 2018995424 165 WDnaisvtEKLLTNSQQQKK--ALMQQLL 191
Cdd:cd17243   158 LF------DKILNNLKENQTlaQLRDTLL 180

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: 150.36 E-value: 7.26e-44

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  10 SIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQFKIIEDT--VEKITEEGLANSSAKLFPAGTILMAmygqgkTR--- 84
Cdd:cd17513     2 KLGELGKFIGGGTPSTKNPEYWNGNIPWITSSDLSEDDIFKIniRKFITEEAIKNSATKIIPANSILIV------TRvgv 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  85 GQVAKLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIremansggQQNLSG----GI----VKSIPVPVPPLTEQK 156
Cdd:cd17513    76 GKVAINPFDICTSQDFTSLIPIKEVNPLFLAYLLYSLLQKL--------KSQLQGtsikGItkddLKNLKIPLPPLEEQQ 147

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2018995424 157 KIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17513   148 KIAAILSKLDKLIEAHEKKLEKLKQLKKGLMQKLF 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: 138.67 E-value: 2.02e-39

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  10 SIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGqgkTRGQVA- 88
Cdd:cd16961     2 KLGEIAEIISGKTPSSSSEYWDNGIIPWIRISDINNGGIILTDEKITEEGAEKLKKKILPKGDILISRSG---TIGKVAi 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  89 -KLGIDASTNQACAAIVLHTGYEVDFYYQFLIS-QYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWD 166
Cdd:cd16961    79 vKENDKALLNQAVIVIRPKDEVDSEFLYYFLKSpFGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLD 158

                         170       180
                  ....*....|....*....|
gi 2018995424 167 NAISVTEKLLTNSQQQKKAL 186
Cdd:cd16961   159 ALIELLEQKLEKLEQLKQAL 178

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: 134.54 E-value: 7.33e-38

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  10 SIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQ-FKIIEDTVEKITEEGLAnsSAKLFPAGTILMAMYGqgkTRGQVA 88
Cdd:cd17286     2 KLGDLGEIVTGNTPSTKNSEYYGGEILFVTPTDIDgNKYIYKTEKKLSEKGFK--KARILPKGSILVTCIG---SIGKNA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  89 KLGIDASTNQACAAIVLHTGYEVDF-YYQFLIsqyeNIREMANSGGQQNLSggIV-KS----IPVPVPPLTEQKKIAKIL 162
Cdd:cd17286    77 IATEDCATNQQINAIIPNKNYDPEFlYYALEN----WSKKIKSLAGKQAVP--IInKTefskIKILVPPLEEQQKIANFL 150

                         170       180
                  ....*....|....*....|....*....
gi 2018995424 163 STWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17286   151 SKLDELIELQQQKIEKLEELKKGLLQKLF 179

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: 132.60 E-value: 4.45e-37

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  10 SIGKISDVSSGGTPSRNNEAYWNG-NIPWVTTAEV-QFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMygqgK-TRGQ 86
Cdd:cd17244     2 KLGDIFDIKIGKTPPRKEPEYWSGdNIPWVSISDMgKGKYISDTKEYITDEAVKKFNVKLVPKGTLLMSF----KlTIGR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  87 VAKLGIDASTNQACAAIVLHTGYeVD----FYY--QFLISQYENiremaNSGGQQNLSGGIVKSIPVPVPPLTEQKKIAK 160
Cdd:cd17244    78 VAIAGKDLYTNEAIAHFIPKDKK-IDteylYYYlkSFDYSSLGS-----TASKGKTLNSKKIKEIPIPLPPLEEQKRIAP 151

                         170       180
                  ....*....|....*....|....*....
gi 2018995424 161 ILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17244   152 ILDKIDALIDQLETLIELLDELLPKLMSG 180

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: 128.45 E-value: 1.41e-35

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  10 SIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQF---KIIEDTVEKITEEGLANSSAKLFPAGTILMAmygqgkTR-- 84
Cdd:cd17279     2 PLKRIFRIVNGSTPKSGEEDYWDGDIPWVTPADLSKldgKYISSSQRKITEAGLESCGTSLVPAGSIILS------TRap 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  85 -GQVAKLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIremaNSGGQ----QNLSGGIVKSIPVPVPPLTEQKKIA 159
Cdd:cd17279    76 iGYVAIATVELCTNQGCKALVPNSDVDSRFLYYLLLAAKEEL----NSLGRgttfLELSTDELANFKIPLPPLSEQRAIA 151

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2018995424 160 --------KIlstwDNAISVTEKLLTNSQQQKKAL 186
Cdd:cd17279   152 dfldretaKI----DALIAKKQQLIELLKEKRQAL 182

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: 121.01 E-value: 5.73e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 213 TLSMFCNIAKGKALSASDL-EVGDFPVIAG----GKsspysHSDYTHE-NVVTVSASGAYAGYISYHNYKIWASDCS-VV 285
Cdd:cd17266     2 KLGELCKIKSGKSITASKIsEEGDYPVYGGngiiGY-----TDEYNHEgEYILIGRVGALCGNVHYVEGKFWVTDNAlVV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 286 SAKADNLIDYFYQLLLSLqdKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEK 365
Cdd:cd17266    77 TPKKENNIKFLYYLLKSL--NLNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLIELK 154


                  ....*
gi 2018995424 366 KALMQ 370
Cdd:cd17266   155 KELMQ 159

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: 121.48 E-value: 8.58e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   6 WELSSIGKIS-DVSSGGTPSrnnEAYWNGNIPWVTTAEVQ-FKIIEDTVEKITEEGL--ANSSAKLFPaGTILMAMYGqg 81
Cdd:cd17246     1 WEWVKLGEISsDITDGTHPT---PKYVESGIPFITSKNIKnGKIDFSDVKYISEEDHneILKRSKLKK-GDILFSIIG-- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  82 kTRGQVA--KLGIDASTNQACAAIVLHTGYEVDFY-YQFLISQY--ENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQK 156
Cdd:cd17246    75 -TIGRVAivPEDLPANINQAVALIRPKKEKIDPKYlLYYLNSPIiqKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQK 153

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2018995424 157 KIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLLT 192
Cdd:cd17246   154 RIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLLT 189

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: 119.12 E-value: 5.77e-32

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  11 IGKISDVSSGGTPsR--NNEAYWNGN-IPWVTTAEV--QFKIIEDTVEKITEEGLANSsaKLFPAGTILMAMYGqgkTRG 85
Cdd:cd17283     3 LGDISEIVRGASP-RpiGDPITFDGDgIPWIKIGDVtkDGKYITKTKEKITEEGAKKS--RLVKPGDLILSNSM---SFG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  86 QVAKLGIDAstnqaCAaivlHTG----------YEVDFYYQFLISQYENIREMAN-SGGQQNLSGGIVKSIPVPVPPLTE 154
Cdd:cd17283    77 RPYILKIDG-----CI----HDGwlvfsdlkkkLDKDFLYYLLSSITVQLQFSAQaGGGTKNLNTDIVKNLKIPLPPLEE 147

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2018995424 155 QKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQ 188
Cdd:cd17283   148 QKRIAEILDSLDALIDALEEKLEKLEELKKGLMQ 181

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: 116.40 E-value: 5.17e-31

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  10 SIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEV-QFKIIEDTVEKITEEGLanSSAKLFPAGTILMAMYgqGKTRGQVA 88
Cdd:cd17293     2 KLGELGEVVTGNTPSKKNPEYYGGDIPFIKPDDLnNGGIILTSEEYLSEEGA--KKARIVPKGSILVTCI--GGSIGKVG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  89 KLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGgqqNLsgGIV-KS----IPVPVPPLTEQKKIAKILS 163
Cdd:cd17293    78 IADREVAFNQQINAIIPNKSVDPKFLYYQLLSSKFQLQAIASST---TL--PIInKSkfekIEIPLPPLEEQKRIVAKLD 152

                         170       180
                  ....*....|....*....|....*...
gi 2018995424 164 TWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17293   153 KLFALIDKLEESLEELDELLKSLFQSAF 180

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: 114.62 E-value: 2.77e-30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   3 PKGWELSSIGKISDVSsggTPSRNNEAYWNGNIPWVTTAEVQFKIIEDTVEK--ITEEGLANSSAKLFPAGTILMAMYGq 80
Cdd:cd17284     1 PEGWEVKRVGDVCDCI---VPGRDKPKSFDGNIPWITIEDIKGKYISSSKSGlgVSEEEIKEMNLKVIPKGSVIMSCVG- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  81 gkTRGQVAKLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAK 160
Cdd:cd17284    77 --DFGIVAIATNELVINQQLHAFVPSKKINPEYLMYLLSLQKKYMEKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAK 154

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2018995424 161 ILSTWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17284   155 ILDSIDKKIDLLIAKLEKLQQLKKGLMQQLF 185

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: 112.92 E-value: 1.01e-29

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   6 WELSSIGKISDVS---SGGTPsRNNEAYWNGNIPWVTTAEVQ--FKIIEDTVEKITEEGLANSsaKLFPAGTILM---Am 77
Cdd:cd17282     1 WEVKKLSDLGSLErgkFKHRP-RNDPRLYGGDYPFIQTGDVAraNGYITSYSQTLNEKGLAQS--KLFPKGTLCItiaA- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  78 ygqgkTRGQVAKLGIDAstnqaC------AAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPP 151
Cdd:cd17282    77 -----NIGDTAILGFDA-----CfpdsvvGFIPNEEKIDVEFLEYYLRTLKKELEAIAPQSAQKNINLEILRPLKIPVPP 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2018995424 152 LTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17282   147 LEEQKKIVEILDALDDLIDNLEKRIAKLEELKQSLLQEAF 186

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: 107.68 E-value: 1.36e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   5 GWELSSIGKISDVSSGGTPSRNNEAYW-NGNIPWvttaevqFK---------IIEDTVEKITEEGLANSsaKLFPAGTIL 74
Cdd:cd17281     1 GVEWKKLGEIFDIRNGYTPSKSNKEYWeNGTIPW-------FRmedirengrILSDSIQHITPSAVKGG--KLFPANSII 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  75 MAMYGqgkTRGQVAKLGIDASTNQACAAIVLHTGYE--VD----FYYQFLISqyENIREMANSGGQQNLSGGIVKSIPVP 148
Cdd:cd17281    72 LSTTA---TIGEHALITVDSLANQRFTNFSLKKSYKnkLDikflFYYFFVLG--EWCKKNINIGGFPSVDMNKLKKFKIP 146

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2018995424 149 VPPLTEQKKIAKILSTWDNAISVTEKLLTNS----QQQKKALMQQLLTGK 194
Cdd:cd17281   147 IPPLEEQEKIVEILDKFTKLTADLTAELPAElearKKQYEYYRDKLLSFE 196

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: 106.13 E-value: 3.55e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  14 ISDVSSGGTPSRNNEAYW-NGNIPWVTTAEVQ-FKIIEDTVEKITEEGLANSSAKLFPAGTILMAmyGQGKTRGQVAKLG 91
Cdd:cd17290     7 AKSIKTGTTPPSENEEYYdGGIIPWFTPGDFNgDLILSESKRKLSELAIEDGEARLFPKNSVLVV--GIGATIGKVGYSD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  92 IDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKIL----STWDN 167
Cdd:cd17290    85 KESSSNQQITGIIFNKDINPKFLFYWLSSSKEELENLANGATLPILNQEKLKNIKLPVPPLNEQQKIVEFLdkktAKIDA 164

                         170
                  ....*....|....*....
gi 2018995424 168 AISVTEKLLTNSQQQKKAL 186
Cdd:cd17290   165 LIAKKEQLIELLKEYRQAL 183

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: 102.10 E-value: 9.40e-26

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  27 NEAYWNGNIPWVTtaeVQFKIIEDTVEKITEEGLANS--SAKLFPAGTILMAMYGqgkTRGQVAKLGI-DASTNQACAAI 103
Cdd:cd17258     9 PELFCNGNIKLVC---IKNELINSLKVKIVEPDYKIGlkQSKIFKKGDVLITRHG---TIGRVSIILSeEACLSSHVAGF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 104 VLHTGYE----VDFYYQFLISQYENIREMAnSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNS 179
Cdd:cd17258    83 NSKEGISdnkfIKYLFNSKKIKNRLMSYGA-SSTQPALNLSRLLKIKFPNPPLEEQQKIGKILSTWDRAIELTEQKLELL 161

                         170
                  ....*....|..
gi 2018995424 180 QQQKKALMQQLL 191
Cdd:cd17258   162 QQQKKGLMQQLF 173

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: 100.89 E-value: 2.31e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   3 PKGWELSSIGKISDVSSGGTPSRNNEaYWNGNIPWVTTAevqfkiiedTVEKITEEGLANSSAKLFPAGTILMAMYGqgk 82
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKEL-KNNGKYPYIRAG---------DLNNVVKGGLGYIKKYILPKGDITISSRA--- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  83 TRGQVAKLGIDASTNQACAAI-VLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKI 161
Cdd:pfam01420  68 TIGYVFYRDKPYYTNQHIIVLiPKNNIKITEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKI 147

                         170
                  ....*....|....*
gi 2018995424 162 LSTWDNAISVTEKLL 176
Cdd:pfam01420 148 LSQLDNTIELEKGIL 162

Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 Calditerrivibrio nitroreducens M.Cni19672ORF1405P TRD1-CR1 and RMtype11G Helicobacter cinaedi PAGU611 RM.Hci611ORFHP TRD1-CR1; The recognition sequence of Calditerrivibrio nitroreducens M.Cni19672ORF1405P is undetermined, and the predicted recognition sequence of RM.Hci611ORFHP is 5'... GAGNNNNNGT ... 3'. M.Cni19672ORF1405P is a putative type I N6-adenine DNA methyltransferase. RM.Hci611ORFHP is a type II subtype gamma (also called type IIG and type IIC) N6-adenine DNA methyltransferase. Both are DNA methyltransferase-specificity subunit fusion proteins, they each have a domain corresponding to a HsdM methylation (M) subunit followed by a C-terminal, TRD-CR-like domain for sequence-recognition, which corresponds to the HsdS specificty (S) subunit. The latter consists of two variable TRDs, and two CRs which separate the TRDs; the TRDs each bind to different specific sequences in the DNA. RM.Hci611ORFHP has an additional N-terminal HSDR_N domain. Restriction-modification (RM) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit, two modification (M) subunits, and two restriction (R) subunits.

Pssm-ID: 341166 [Multi-domain] Cd Length: 184 Bit Score: 100.17 E-value: 5.37e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   6 WELSSIGKISDVSSGGTPSRNNEAYW-NGNIPWVTTA--EVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGqgk 82
Cdd:cd17277     1 WPIVKLGEVCEIINGSTPSKKNEEYWnNGTIKWLTIPdiDERGLIISSTKQFITEKALEEKKVKLVPKNSVLLSCTA--- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2018995424  83 TRGQVAKLGIDASTNQACAAIVLHTGY---EVDFYYQFLISQyeNIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKI 158
Cdd:cd17277    78 TIGKVAIAKIELTTNQQINALICKDSKilpEYLFYALKHIKQ--VLERLTTNPGVKHVNLSMLSNLQIPLPPLEVQKKI 154

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: 99.89 E-value: 8.88e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   6 WELSSIGKISDVSSG-GTPSrnnEAYWNGNIPWVTTAEVQF-KIIEDTVEKITEEGLANSSAKLFPAGTILMAMygqgkT 83
Cdd:cd17259     1 WEWVKLGDVADILSGyAFKS---SEFSESGIRLLRGANVGVgEIRWDDTVYLPEEYLEEYEKYLLKEGDIVIAL-----D 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  84 R----GQ--VAKLGID---ASTNQACAAIVLHTGYEVDFYYQFLISQY--ENIREMANSGGQQNLSGGIVKSIPVPVPPL 152
Cdd:cd17259    73 RpiisGGlkVARIPKSdlpALLVQRVARIRPKDELNSDFLYYLLQSDFflNYVEPVLTGTDVPHISTKQIKNFKIPLPPL 152

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2018995424 153 TEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17259   153 EEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKGLMQS 189

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: 98.77 E-value: 2.16e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  11 IGKISDVSSGGTPSRNNEAYWNGNIPWVT-TAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGQgkTRGQVAK 89
Cdd:cd17516     3 IGDLGKVVTGKTPSTKNPEYFGGDIPFITpSDMKGGKYIIKTERRLSSKGLEKVKNKLIPANSICVTCIGS--DMGKVAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  90 LGIDASTNQACAAIVLHTG-YEVDFYYQFLISQYENIREMANSG-GQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDN 167
Cdd:cd17516    81 TKEPSVTNQQINSIIVNKNkFDPDFVYYLLKNNSKYLKSIAGGStATPIINKSTFSNIEIPLPPLPEQKKIAAILSSLDD 160

                         170       180
                  ....*....|....*....|...
gi 2018995424 168 AISVTEKLLTNSQQQKKALMQQL 190
Cdd:cd17516   161 KIENNRRINKTLEEMAQALFKEW 183

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: 94.88 E-value: 5.06e-23

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  71 GTILMAMygQGKTRGQVAKLGIDAST---NQACAAIVLHTGYEVDFYYQFLISQY--ENIREMANSGGQQNLSGGIVKSI 145
Cdd:cd17278    65 GDILIAM--TGGTVGKVAIVPEDDEPallNQRVGKFRPKDKIDKEFLYYLLRSDSfrNQIKSSATGTAQPNISPKDIESI 142

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2018995424 146 PVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLLT 192
Cdd:cd17278   143 KIPLPPLEEQKKIAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLFT 189

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: 92.59 E-value: 2.02e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 214 LSMFCNIAKGKALSASDLE--VGDFPV---------IAGgksspYSHSDYTHENVVTVSASGAYAGYISYHNYKIWAS-D 281
Cdd:cd17255     3 LGDLFEIGRGRVISKKYISenPGDYPVyssqtknngIMG-----YINTYDFDGEYITWTTDGANAGTVFYRNGKFSVTnV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 282 CSVVSAKADNLIDYFYQLLLSLqdKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACL 361
Cdd:cd17255    78 CGVLKVKNKNINNKFLYYALNL--IAKKYVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIAKLKKL 155

                         170
                  ....*....|.
gi 2018995424 362 RDEKKALMQQL 372
Cdd:cd17255   156 IELRKKQLEYY 166

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: 92.96 E-value: 2.55e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 287 AKADNLIDYFYQLLLS--LQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDE 364
Cdd:cd17259   103 PKDELNSDFLYYLLQSdfFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQL 182


                  ....*..
gi 2018995424 365 KKALMQQ 371
Cdd:cd17259   183 KKGLMQS 189

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

Pssm-ID: 341145 [Multi-domain] Cd Length: 182 Bit Score: 90.64 E-value: 1.88e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  11 IGKISDVSSGG-TPSRNNEAYWNGNIPWVTTAEVQF-KIIEDTVEKITEE---GLANSsaKLFP-------AGTIlmamy 78
Cdd:cd17256     1 LGEIARVKGGGrLPKGESLSDGPTGVPYIRVTDIKNgGIDLDNLKYISPEiheKIKRY--TLSKgdilisiVGTI----- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  79 gqgktrGQVAKLGID---ASTNQACAAIVLHTGYEVDFYYQFLISQY--ENIREMANSGGQQNLSGGIVKSIPVPVPPLT 153
Cdd:cd17256    74 ------GRVGIVPKEldgANLTENAARIRPKDSISPRYLYYYLRSPFgqSQIESETKGAAQPKLNLKRIRELPIPLPPLE 147

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2018995424 154 EQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQ 188
Cdd:cd17256   148 EQKRIVAILDSLDAKIDALEKQLAKLEELKKALMQ 182

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: 89.88 E-value: 4.14e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 287 AKADNLIDYFYQLLLS--LQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDE 364
Cdd:cd17278   100 PKDKIDKEFLYYLLRSdsFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKLEQKLEKLRDL 179

                          90
                  ....*....|
gi 2018995424 365 KKALMQQLLT 374
Cdd:cd17278   180 LKPLLQSLFT 189

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 85.88 E-value: 7.52e-21

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2018995424 302 SLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQLLTGKRRVK 380
Cdd:COG0732    10 SFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFTGELRVR 88

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 83.95 E-value: 4.87e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 116 QFLISQY--ENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLLTG 193
Cdd:COG0732     4 YYLRSPSfrEYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFTG 83


                  ....
gi 2018995424 194 KKRL 197
Cdd:COG0732    84 ELRV 87

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: 85.63 E-value: 1.07e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  73 ILMAMYGQgkTRGQV--AKLGIDASTnqACAAIVLHTGYEVDFYYQFLISQYENIREMANSG-GQQNLSGGIVKSIPVPV 149
Cdd:cd17263    60 ILIVRDGA--NAGEVgtGLEGAIAST--LFKIIPDKNIIDKDYLYYFLKSKEIQLNILTKAGsTIPHVNKKDLENLKIPL 135

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2018995424 150 PPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17263   136 PSLEEQKKIAEILDKLDALIDKLKELIEKLIELKKGLFQELL 177

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: 84.99 E-value: 1.95e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  11 IGKISDVSSG-GTPSRNnEAYWNGNIPWVT----TAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGQGKTRG 85
Cdd:cd17250     3 LGDVCDFKAGsGFPEKY-QGKEDGEYPFYKvgdmNNSGNEKYLSTAENYISEEIVKELKAKLFPKGTIIFAKIGEAIKLN 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  86 QVAKLGIDASTNQACAAIVLHTGyeVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTW 165
Cdd:cd17250    82 RRAILSKDSCIDNNVMGLIPNEG--IDSEYLYYWLKKVDLYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDEL 159

                         170       180
                  ....*....|....*....|....*.
gi 2018995424 166 DNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17250   160 FEKLDKLKQALEAAKEQLKGLRQSLL 185

Type I restriction modification DNA specificity domain; This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits.

Pssm-ID: 396139 [Multi-domain] Cd Length: 167 Bit Score: 84.71 E-value: 2.00e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 208 EWRNSTLSMFCNIAKGKALSASDL-EVGDFPVIAGG-------KSSPYSHSDYTHENVVTVSaSGAYAGYISYHNYKIWA 279
Cdd:pfam01420   3 DWEVFKLGDVFEIKKGKTPKKKELkNNGKYPYIRAGdlnnvvkGGLGYIKKYILPKGDITIS-SRATIGYVFYRDKPYYT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 280 SD-CSVVSAKADNLIDYF-YQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKK 357
Cdd:pfam01420  82 NQhIIVLIPKNNIKITEFlYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDNTIELEKGI 161


                  ..
gi 2018995424 358 LA 359
Cdd:pfam01420 162 LN 163

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: 84.11 E-value: 4.36e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 295 YFYQLLLS--LQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQL 372
Cdd:cd17246   108 YLLYYLNSpiIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDL 187


                  ..
gi 2018995424 373 LT 374
Cdd:cd17246   188 LT 189

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: 81.43 E-value: 4.65e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 113 FYYQFLISQY--ENIREMANS-GGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17517   112 FLYYYLNSPLgrKQIEKIAKSaAGQANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQS 191


                  .
gi 2018995424 190 L 190
Cdd:cd17517   192 L 192

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: 79.41 E-value: 1.30e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 102 AIVL--HTGYEVDFYYQFLISQyeNIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNS 179
Cdd:cd17266    73 ALVVtpKKENNIKFLYYLLKSL--NLNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKL 150


                  ....*....
gi 2018995424 180 QQQKKALMQ 188
Cdd:cd17266   151 IELKKELMQ 159

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: 79.47 E-value: 1.58e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 290 DNLIDYFYQLLLSLQDKIYSL-QSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKAL 368
Cdd:cd17263    93 IIDKDYLYYFLKSKEIQLNILtKAGSTIPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALIDKLKELIEKLIELKKGL 172


                  ....*
gi 2018995424 369 MQQLL 373
Cdd:cd17263   173 FQELL 177

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: 79.10 E-value: 1.75e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 291 NLIDYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQ 370
Cdd:cd17494    89 NEFIFLYLYLLNIEGYWSKISQGSTFESINSNDIKNLKISIPSLEEQQKIATFLSTLDAEITLLEKKLEKLKQLKKGLLQ 168


                  ...
gi 2018995424 371 QLL 373
Cdd:cd17494   169 KLF 171

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: 79.06 E-value: 2.86e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 112 DFYYQFLIS-QYEN-IREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17521   107 KYLFYFTQSsLYWKqIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLKELLQS 186


                  .
gi 2018995424 190 L 190
Cdd:cd17521   187 L 187

Type I restriction-modification system specificity (S) subunit 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 mostly 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: 341140 [Multi-domain] Cd Length: 185 Bit Score: 79.08 E-value: 2.89e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   6 WELSSIGKISDVSSGGTPSRNNEAYWNGNIPWVTTAEVQFKI-IEDTVEKITEEGLANSSAKLFPAGTILMAMYGqgkTR 84
Cdd:cd17251     1 WEVKTLKDFGKIITGKTPSTKNKEYYGGDIPFIKIPDMHGNVfITKTEDYLSEEGANSQKNKTLPKNSICVSCIA---TV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  85 GQVAKLGIDASTNQACAAIVLHTGYEVDFYYQFLISQYENIREMAnSGGQQ--NLSGGIVKSIPVPVPPLTEQKKIAKIL 162
Cdd:cd17251    78 GLVSITTEESQTNQQINSIIPKKENYRYYLYFALKSLKELLEALG-SGGSTtlNLNKGKFSKIKILLPSEDLLKKFHKIV 156

                         170       180
                  ....*....|....*....|..
gi 2018995424 163 StwdnaiSVTEKLLTNSQQQKK 184
Cdd:cd17251   157 S------PLFDKILNNQKENQK 172

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: 78.69 E-value: 3.58e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 281 DCSVVSAKADNLIDYFYQLLLS--LQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKL 358
Cdd:cd17256    91 NAARIRPKDSISPRYLYYYLRSpfGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQL 170

                          90
                  ....*....|..
gi 2018995424 359 ACLRDEKKALMQ 370
Cdd:cd17256   171 AKLEELKKALMQ 182

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: 76.67 E-value: 1.20e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 213 TLSMFCNIAKGKALSASDLEVGDFPVI-AGGKSspYSHSDYTHEN-VVTVSASGAYaG--YISYHNYkiWASDCS-VVSA 287
Cdd:cd17267     2 KLGDVIELQYGKDLPKSRRIPGPYPVYgSNGIV--GYHNEALVKGpGIVVGRKGSI-GkvHYSEEDF--WPIDTTlYVKD 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 288 KADNLIDYFYQLLLSLqdKIYSLQSGGAQP-----HIYpkdlnSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLR 362
Cdd:cd17267    77 FKGNDPRFLYYLLKTL--DLERLNSGSAVPglnrnDVY-----SLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLE 149


                  ....*....
gi 2018995424 363 DEKKALMQQ 371
Cdd:cd17267   150 ELADALLPK 158

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: 76.81 E-value: 1.43e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  66 KLFPAGTILMAMygqgktRGQVAKLGIdasTNQAC------AAIVLHTGYEVDFYYQFLISQYENIREManSGGQ--QNL 137
Cdd:cd17245    52 KIAEKGDILISV------RAPVGDVNI---ADEKCcigrglAAIRANKDIDNLFLYYYLKYNKPELEKL--GTGStfKAI 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2018995424 138 SGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17245   121 NKKDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKLDELKKGLMQELF 174

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: 76.81 E-value: 1.96e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 112 DFYYQFLISQY--ENIREMA--NSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALM 187
Cdd:cd17261   109 EYLALALNSPSarRQIESRAtgTAGSMPKISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLR 188


                  ...
gi 2018995424 188 QQL 190
Cdd:cd17261   189 QAL 191

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: 75.22 E-value: 5.44e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 284 VVSAKADNliDYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRD 363
Cdd:cd17286    92 IPNKNYDP--EFLYYALENWSKKIKSLAGKQAVPIINKTEFSKIKILVPPLEEQQKIANFLSKLDELIELQQQKIEKLEE 169

                          90
                  ....*....|
gi 2018995424 364 EKKALMQQLL 373
Cdd:cd17286   170 LKKGLLQKLF 179

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: 74.39 E-value: 9.13e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 103 IVLHTGYEVDFYYQFLISQYENIRE-----MANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLT 177
Cdd:cd17260    72 HVLRPKEGILPEFLYYLLRSPSFRKeaiksMTGSSGRQRVPKDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIE 151

                          90
                  ....*....|....
gi 2018995424 178 NSQQQKKALMQQLL 191
Cdd:cd17260   152 TLEELLDALLPKLL 165

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: 74.07 E-value: 1.33e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 101 AAIVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQ 180
Cdd:cd17496    85 AAIRPKNGIDTEFLYYLLESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLE 164

                          90
                  ....*....|.
gi 2018995424 181 QQKKALMQQLL 191
Cdd:cd17496   165 ELRDTLLPKLL 175

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: 73.65 E-value: 1.60e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 274 NYKIWasdcSVVSAKADNLiDYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEIST 353
Cdd:cd17254    79 NQHIF----KVVPDEEIDK-DYLYYLLKALTEEIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDA 153

                          90       100
                  ....*....|....*....|
gi 2018995424 354 LEKKLACLRDEKKALMQQLL 373
Cdd:cd17254   154 LEEQLKKLEELRKALLQSLL 173

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: 73.62 E-value: 1.70e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 284 VVSAKADNLIDYFYQLLLSLqdKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRD 363
Cdd:cd17262    86 VLKGKNGISTEFLYYYLNSI--DISPYVTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIE 163


                  ....*....
gi 2018995424 364 EKKALMQQL 372
Cdd:cd17262   164 LKKALLQKL 172

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: 72.80 E-value: 4.03e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 213 TLSMFCNIAKGKALSAS--DLEVGDFPVIAGG----------------KSSPYSHSDYTHENVVTVSASGaYAGYISYH- 273
Cdd:cd16961     2 KLGEIAEIISGKTPSSSseYWDNGIIPWIRISdinnggiiltdekiteEGAEKLKKKILPKGDILISRSG-TIGKVAIVk 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 274 -NYKIWASDcSVVSAKADNLID---YFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADA 349
Cdd:cd16961    81 eNDKALLNQ-AVIVIRPKDEVDsefLYYFLKSPFGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDA 159

                         170
                  ....*....|....*....
gi 2018995424 350 EISTLEKKLACLRDEKKAL 368
Cdd:cd16961   160 LIELLEQKLEKLEQLKQAL 178

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: 71.88 E-value: 9.55e-15

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2018995424 319 IYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQL 372
Cdd:cd17525   137 IYQKDLKKLKLPLPPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKKALMQQL 190

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: 71.37 E-value: 1.15e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 285 VSAKADNLIDYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDE 364
Cdd:cd17496    87 IRPKNGIDTEFLYYLLESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEEL 166


                  ....*....
gi 2018995424 365 KKALMQQLL 373
Cdd:cd17496   167 RDTLLPKLL 175

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: 70.65 E-value: 1.25e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2018995424 295 YFYQLLlslqdkIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQLL 373
Cdd:cd17292    77 YFYQII------KWKKTEGSTIKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYLF 149

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: 70.54 E-value: 2.44e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 108 GYEVDFYYQFLisQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALM 187
Cdd:cd17262    92 GISTEFLYYYL--NSIDISPYVTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALL 169


                  ...
gi 2018995424 188 QQL 190
Cdd:cd17262   170 QKL 172

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: 70.67 E-value: 2.50e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   6 WELSSIGKISDVSSGGT--PSRNNEAYWNGNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPaGTILMAMyGQGkT 83
Cdd:cd17252     1 WEWVRLGEIAEIIRGVTykKSDASEEPSEGGIPVLRANNIQNGGLDFDDLVYVPKSKVKEEQKLKK-GDILICM-SSG-S 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  84 RGQVAKLG-IDASTNQA----CAAIVLHTGYEVDFYYQFLISQY--ENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQK 156
Cdd:cd17252    78 KELVGKAAfIDEDTDYTfgafCGVIRPKKEIDPRYLFYFLQSPSyrEYIRSLASGTNINNLSNEHLENLKIPLPPLAEQK 157

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2018995424 157 KIAKILSTWDNAISVTEKLLTNSQQQKKALMQ 188
Cdd:cd17252   158 RIVAKLDKLDALIDKLKQALEKLDELLKSLFQ 189

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: 69.81 E-value: 2.90e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 209 WRNSTLSMFCNIAKGKalSASDLEVGDFPVIAggksspyshsdythenvvtvsaSGAYAGYIS----------------- 271
Cdd:cd17288     1 WEVKKLGDLLKIKNGK--DYKHLEDGNYPVYG----------------------SGGIMGYVNdylydgesvligrkgti 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 272 ----YHNYKIWASD---CSVVsaKADNLIDYFYQLLLSLqdKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVL 344
Cdd:cd17288    57 dkplYVNGPFWTVDtmfYTEI--KKNNDPKFLYYLLKTI--DFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASIL 132

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2018995424 345 SAADAE---ISTLEKKLACLRDEKKALMQQL 372
Cdd:cd17288   133 DKLDAKdalIELQEKLLEKLKQYKLALMQEL 163

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: 70.18 E-value: 3.38e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 103 IVLHTGYEVDFYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQ 182
Cdd:cd17254    85 VVPDEEIDKDYLYYLLKALTEEIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLEEL 164


                  ....*....
gi 2018995424 183 KKALMQQLL 191
Cdd:cd17254   165 RKALLQSLL 173

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: 70.20 E-value: 3.83e-14

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2018995424 136 NLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17253   138 SINSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 72.99 E-value: 5.82e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424   2 VPKGWELSSIGKISDVSSGGTPSRNNEAYWN--GNIPWVTTAEVQFKIIEDTVEKITEEGLANSSAKLFPAGTILMAmyg 79
Cdd:PRK09737    6 LPEGWVTTHISEICSVIRGVKPPKGYATKSLtmGDLPFIRTTDITNGAVDLTTLPYCMDAPEDVSKYQLQDRDIVIS--- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  80 QGKTRGQVAKLGIDASTNQACAAIVLHTGYEVDFYYQFL-----ISQYEN-IREMANSGGQQNLSGGIVKSIPVPVPPLT 153
Cdd:PRK09737   83 SAGSIGFSFLAQNPLPSNVVFASFAIRLKPVNYFSEYFLkhfleSSDYRNqLSLMSAGNAVQNINAQSLSTLTFPIPPIA 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 154 EQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLLTGKKRLLDENGVRFSGE---WRNSTLSMFCNIAKGKALSASD 230
Cdd:PRK09737  163 EQKIIAEKLDTLLAQVDSTKARLEQIPQILKRFRQAVLGAAVSGKLTEEWRWPDLpstWSVHKYSELVDSRLGGMSSKAN 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 231 LEVGDFPVIaGGKSSPYSHSDYTHENVVTVSAS--------------GAYAGYISYHNYKIWAS--DCSVVSAKA----- 289
Cdd:PRK09737  243 NFGSATPYL-RNINVRWGSFDLEDLQDILISDIerrelklklgdvlfCRGNEPLEVGRCAIWKEpqDIPVIYQKAlirar 321

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2018995424 290 --DNLI----DYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKL 358
Cdd:PRK09737  322 vkDDIIpeylVYNLKSPDSRNISLSQLFTGTTQKHITGKALANYPIRVPPLEEQAEIVRRVEQLFAYADTIEKQV 396

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: 69.43 E-value: 5.90e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 294 DYFYQLLLSLQDKIYSLQSGGAQPhiypKDLNS-------IPLwvPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKK 366
Cdd:cd17283   104 DFLYYLLSSITVQLQFSAQAGGGT----KNLNTdivknlkIPL--PPLEEQKRIAEILDSLDALIDALEEKLEKLEELKK 177


                  ....
gi 2018995424 367 ALMQ 370
Cdd:cd17283   178 GLMQ 181

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: 69.42 E-value: 8.38e-14

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2018995424 125 IREMA-NSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQL 190
Cdd:cd17524   123 IKSVAtQGVGQANINATKLKAIPIPLPPLEEQKEIVEKLDELDALIDRLEALLEEAEELLESLLQSL 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: 68.59 E-value: 1.12e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 295 YFYQLLLSL--QDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQL 372
Cdd:cd17258    93 FIKYLFNSKkiKNRLMSYGASSTQPALNLSRLLKIKFPNPPLEEQQKIGKILSTWDRAIELTEQKLELLQQQKKGLMQQL 172


                  .
gi 2018995424 373 L 373
Cdd:cd17258   173 F 173

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: 68.80 E-value: 1.15e-13

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2018995424 143 KSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQL 190
Cdd:cd17525   143 KKLKLPLPPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKKALMQQL 190

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: 68.24 E-value: 1.60e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 283 SVVSAKADNL---IDYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLA 359
Cdd:cd17282    93 SVVGFIPNEEkidVEFLEYYLRTLKKELEAIAPQSAQKNINLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIA 172

                          90
                  ....*....|....
gi 2018995424 360 CLRDEKKALMQQLL 373
Cdd:cd17282   173 KLEELKQSLLQEAF 186

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: 67.52 E-value: 2.26e-13

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2018995424 145 IPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLLT 192
Cdd:cd17274   124 FKIPLPPLEEQNKIVRILDKFDELIAELEAKLELLKKQKKYYLQKLFT 171

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: 67.55 E-value: 2.41e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  85 GQVAKLGIDASTNQACAAIvlhTGYEVDFYYQFLISqYENIREMANSGGQ-QNLSGGIVKSIPVPVPPLTEQKKIAKILS 163
Cdd:cd17494    68 GEVAKTNFDACIGRGVCAI---KGNEFIFLYLYLLN-IEGYWSKISQGSTfESINSNDIKNLKISIPSLEEQQKIATFLS 143

                          90       100
                  ....*....|....*....|....*...
gi 2018995424 164 TWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17494   144 TLDAEITLLEKKLEKLKQLKKGLLQKLF 171

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: 67.56 E-value: 2.81e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  23 PSRNneAYWNGNIPWVTTAEVQ-FKIIEDTVEKITEEGLAN-SSAKLFPaGTILMAmygqgkTRGQVAKLGI-DASTNQA 99
Cdd:cd17264    18 PSKS--EFVDEGIPFINAGHLEdGTIDLSNMNFISEEKYNSlGSGKLQK-GDILYC------LRGSLGKCAIvDNYDEGA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 100 CAA----IVLHTGYEVDFYYQFLISQ--YENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILstwDNAISVTE 173
Cdd:cd17264    89 IASslviIRPFAKVDVRYLYYYLNSPlgKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKL---DELDALID 165

                         170
                  ....*....|....*...
gi 2018995424 174 KL---LTNSQQQKKALMQ 188
Cdd:cd17264   166 KLkqaLEKLEELLQSLFQ 183

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) TRD2-CR2; The recognition sequence of Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341193 [Multi-domain] Cd Length: 195 Bit Score: 67.63 E-value: 3.19e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2018995424 112 DFYYQFLISQYeniREMANsggQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17512   124 ERFKNYIESIA---RGNAN---QASITLGDIKKFKFLLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQALYQE 195

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: 65.98 E-value: 1.11e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 112 DFYYQFLISQ--YENIREMANSGGQQnLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17265   101 DYLFHLFNSDlfKKQIGSFLTATINQ-ITNGNLNNFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKELMQQ 179


                  ..
gi 2018995424 190 LL 191
Cdd:cd17265   180 LI 181

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: 65.03 E-value: 2.37e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  11 IGKISDVSSGGTPSRNNEAYW---NGNIPWVTTAEV--QFKIIEDTVEKITEegLANSSAKLFPAGTILMAMYGqgkTRG 85
Cdd:cd17270     3 LGEVAKFRRGSFPQPYGNSEWydgEGSMPFVQVADVgdNFKLVEKTKQKISK--LAQPKSVFVPKGTVIVTLQG---SIG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  86 QVAKLGIDASTNQAcaaIVLHTGYEVDF---YYQFLISQ-YENIREMAnsggqqnlSGGIVKSIP--------VPVPPLT 153
Cdd:cd17270    78 RVAITQYDAYVDRT---LLIFESYKINInkkFFAYQLKLkFEIEKEKA--------PGGTIKTITkeelskfeIPIPSLE 146

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2018995424 154 EQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQL 190
Cdd:cd17270   147 EQKEIVNILDKFDELITELQLRKKQLEYYKKALLSFM 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: 64.54 E-value: 3.06e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 290 DNLIDYFYQLLLSLQ-DKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKAL 368
Cdd:cd17284   101 KKINPEYLMYLLSLQkKYMEKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGL 180


                  ....*
gi 2018995424 369 MQQLL 373
Cdd:cd17284   181 MQQLF 185

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: 64.05 E-value: 4.41e-12

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2018995424 326 SIPLwvPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQLLT 374
Cdd:cd17274   125 KIPL--PPLEEQNKIVRILDKFDELIAELEAKLELLKKQKKYYLQKLFT 171

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: 63.66 E-value: 7.34e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 288 KADNLIDYFYQLLLSLQ--DKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEK 365
Cdd:cd17521   101 KKKVLPKYLFYFTQSSLywKQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELL 180


                  ....*..
gi 2018995424 366 KALMQQL 372
Cdd:cd17521   181 KELLQSL 187

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: 63.04 E-value: 1.26e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 281 DCSVVS----AKADNLIDYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEK 356
Cdd:cd17250    89 DSCIDNnvmgLIPNEGIDSEYLYYWLKKVDLYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQ 168

                          90
                  ....*....|....*..
gi 2018995424 357 KLACLRDEKKALMQQLL 373
Cdd:cd17250   169 ALEAAKEQLKGLRQSLL 185

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: 62.94 E-value: 1.29e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2018995424 113 FYYQFLISQYENIREMANSggQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQL 190
Cdd:cd17522   115 LKSDRFRNQFRSIAKKAVN--QASINQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEKLKELKKGLFQKL 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: 62.23 E-value: 1.41e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 113 FYYQFLISQYENIREmansggqQNLSGGIVKSI--------PVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKK 184
Cdd:cd17269    86 FLYYYLKSYFKKYIE-------KNSVGSSVPYIrlpmlenfKIPLPPLEEQKRIVRILDKFDALTAELPAELEARKKQYE 158


                  ....*...
gi 2018995424 185 ALMQQLLT 192
Cdd:cd17269   159 YYRDALLS 166

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: 61.40 E-value: 1.93e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 112 DFYYQFlisqYENIREMANSGGQ-QNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQL 190
Cdd:cd17292    73 KFLYYF----YQIIKWKKTEGSTiKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYL 148


                  .
gi 2018995424 191 L 191
Cdd:cd17292   149 F 149

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: 61.77 E-value: 2.53e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 285 VSAKADNLIDYFyqLLLSLQ---DKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACL 361
Cdd:cd17257    89 IRPKSEELDKRF--LYYALPpplKAIEDTTSSTTVKHLSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLIAKLEKL 166

                          90
                  ....*....|
gi 2018995424 362 RDEKKALMQQ 371
Cdd:cd17257   167 RDLLLPLLQS 176

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: 60.60 E-value: 5.17e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2018995424 113 FYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQK 183
Cdd:cd17291    87 FLYYFLKNKQEEIYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFTELTAELPAELEARKKQY 157

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: 59.02 E-value: 1.66e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 113 FYYQFLISQYENIREmanSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNA---ISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17288    86 LYYLLKTIDFKKYNE---ATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKdalIELQEKLLEKLKQYKLALMQE 162


                  .
gi 2018995424 190 L 190
Cdd:cd17288   163 L 163

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: 59.08 E-value: 2.13e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  95 STNQACAAIVLHTGYEVDFYYQFLISqyENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEK 174
Cdd:cd17255    73 SVTNVCGVLKVKNKNINNKFLYYALN--LIAKKYVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIA 150

                          90
                  ....*....|....*.
gi 2018995424 175 LLTNSQQQKKALMQQL 190
Cdd:cd17255   151 KLKKLIELRKKQLEYY 166

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: 59.49 E-value: 2.35e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 282 CSVVSAKADNLIDYFYQLLLS--LQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLA 359
Cdd:cd17252    99 CGVIRPKKEIDPRYLFYFLQSpsYREYIRSLASGTNINNLSNEHLENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQALE 178

                          90
                  ....*....|.
gi 2018995424 360 CLRDEKKALMQ 370
Cdd:cd17252   179 KLDELLKSLFQ 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: 58.53 E-value: 4.21e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2018995424 112 DFYYQFLISQY--ENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAIsvtEKLLTNSQQQKKAL 186
Cdd:cd17518   107 NFLKYFLNSDYfkEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAI---EAALEALRKKKQAA 180

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: 58.61 E-value: 4.29e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2018995424 137 LSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQ 188
Cdd:cd17268   134 ISASDLAKIKIPVPPLEEQERIVEILDKFDALIAGLPAEIEARRKQYEYYRD 185

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) TRD2-CR2 and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) TRD2-CR; Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) recognizes 5'... GAGNNNNNGTTY ... 3', and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) recognizes 5'... YTCANNNNNNGTTY ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Eco4255III-TRD1 recognizes GAG/CTC and S.EcoNIH1II-TRD1 recognizes YTCA/TGAR, while both S.EcoNIH1II-TRD2 and S.Eco4255III-TRD2 recognize RAAC/GTTY. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341154 [Multi-domain] Cd Length: 181 Bit Score: 58.28 E-value: 4.45e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 294 DYFYQLLLSlqdKIYSLQSG---GA---QphIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKA 367
Cdd:cd17265   101 DYLFHLFNS---DLFKKQIGsflTAtinQ--ITNGNLNNFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKE 175


                  ....*.
gi 2018995424 368 LMQQLL 373
Cdd:cd17265   176 LMQQLI 181

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: 57.93 E-value: 5.73e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 288 KADNLID--YFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEK 365
Cdd:cd17245    87 RANKDIDnlFLYYYLKYNKPELEKLGTGSTFKAINKKDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKLDELK 166


                  ....*...
gi 2018995424 366 KALMQQLL 373
Cdd:cd17245   167 KGLMQELF 174

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: 57.93 E-value: 6.52e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2018995424 316 QPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQL 372
Cdd:cd17522   134 QASINQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEKLKELKKGLFQKL 190

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: 57.65 E-value: 9.18e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 290 DNLIDYFYQLLLS--LQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKA 367
Cdd:cd17289   106 DINSKFLYYWFQSsiFKNQINSITIGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEELAKT 185


                  ....*.
gi 2018995424 368 LMQQLL 373
Cdd:cd17289   186 LFQYWF 191

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: 57.16 E-value: 1.32e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 295 YFYQLLLSL--QDKIYSL-QSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQ 371
Cdd:cd17517   112 FLYYYLNSPlgRKQIEKIaKSAAGQANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQS 191


                  .
gi 2018995424 372 L 372
Cdd:cd17517   192 L 192

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: 56.88 E-value: 1.46e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 112 DFYYQFLISQY--ENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17289   110 KFLYYWFQSSIfkNQINSITIGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEELAKTLFQY 189


                  ..
gi 2018995424 190 LL 191
Cdd:cd17289   190 WF 191

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: 55.61 E-value: 3.72e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2018995424 137 LSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17257   124 LSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLIAKLEKLRDLLLPLLQS 176

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: 54.71 E-value: 4.62e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2018995424 144 SIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17267   113 SLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADALLPK 158

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: 55.45 E-value: 4.84e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 288 KADNliDYFYQLLLSL--QDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEIstlEKKLACLRDEK 365
Cdd:cd17518   103 LLDN--NFLKYFLNSDyfKEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAI---EAALEALRKKK 177


                  ...
gi 2018995424 366 KAL 368
Cdd:cd17518   178 QAA 180

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: 55.24 E-value: 5.54e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 279 ASDCSVVSAKADNLIDYFYQLLLSL--QDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEK 356
Cdd:cd17264    90 ASSLVIIRPFAKVDVRYLYYYLNSPlgKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQ 169

                          90
                  ....*....|....
gi 2018995424 357 KLACLRDEKKALMQ 370
Cdd:cd17264   170 ALEKLEELLQSLFQ 183

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: 53.99 E-value: 1.37e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2018995424 318 HIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQ 370
Cdd:cd17268   133 HISASDLAKIKIPVPPLEEQERIVEILDKFDALIAGLPAEIEARRKQYEYYRD 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: 53.37 E-value: 1.78e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 212 STLSMFCNIAKGKaLSASD-LEVGDFPVIAGGKSsPYSHSDYTH-ENVVTVSASGAYAGYISYHN---------YKIwas 280
Cdd:cd17269     1 KTLGEVAEIKTGK-LDANAaNENGKYPFFTCSKE-PLRIDTYAFdEEAILIAGNGSGVGNVKYYNgkfnayqrtYVI--- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 281 dcsvVSAKADNLIDYFYQLLLSLQDKIYSLQS-GGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLA 359
Cdd:cd17269    76 ----HPFKEEIDPKFLYYYLKSYFKKYIEKNSvGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAELPAELE 151

                         170
                  ....*....|....*
gi 2018995424 360 CLRDEKKALMQQLLT 374
Cdd:cd17269   152 ARKKQYEYYRDALLS 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: 53.32 E-value: 2.51e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 283 SVVSAKADNLIDYFYQLLLSLQDKIYSLQSGG-AQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACL 361
Cdd:cd17516    93 SIIVNKNKFDPDFVYYLLKNNSKYLKSIAGGStATPIINKSTFSNIEIPLPPLPEQKKIAAILSSLDDKIENNRRINKTL 172

                          90
                  ....*....|.
gi 2018995424 362 RDEKKALMQQL 372
Cdd:cd17516   173 EEMAQALFKEW 183

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: 53.36 E-value: 2.70e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2018995424 143 KSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQLL 191
Cdd:cd17526   144 ANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192

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: 51.71 E-value: 9.11e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2018995424 324 LNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQLL 373
Cdd:cd17253   144 LKALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) TRD2-CR2; The recognition sequence of Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341193 [Multi-domain] Cd Length: 195 Bit Score: 51.45 E-value: 1.45e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 285 VSAKADNLI-DYFYQLLLSL--QDKIYSLQSGGA-QPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLAC 360
Cdd:cd17512   105 IRPKKGILDqSFLFYNLKSErfKNYIESIARGNAnQASITLGDIKKFKFLLPPLEEQKKIASILSAYDDLIENNEKRIKL 184

                          90
                  ....*....|.
gi 2018995424 361 LRDEKKALMQQ 371
Cdd:cd17512   185 LEQMKQALYQE 195

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: 49.36 E-value: 4.83e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2018995424 321 PKD-LNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQLL 373
Cdd:cd17260   112 PKDfLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165

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: 49.74 E-value: 4.95e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  13 KISDVSSGG---TPSRNNEAywNGNIPWVTTAEVqfKIIEDTVEKITEEGLANSSAKLFPAGTILMAMYGqgkTRGQVAk 89
Cdd:cd17272     5 TLGDIAVDGfqnGPAPNFDE--KGEIPVITSKNI--SNGKIDFEYVKYDFLSISKNRKINKGDILITMIG---TIGETA- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424  90 lGIDASTNQACA---AIVLHTGYEVD--FYYQFLISQYENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILST 164
Cdd:cd17272    77 -IVKCLDPKFYTlnlYLIRLKKEKLLpsYLKYFLDSEKFLNKSISATSGQGYLKANQIDKLEIPLPPLEEQQRIVKILDK 155


                  ..
gi 2018995424 165 WD 166
Cdd:cd17272   156 FD 157

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: 48.74 E-value: 1.09e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2018995424 322 KDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQLL 373
Cdd:cd17526   141 DTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192

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: 46.52 E-value: 4.20e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 282 CSVVSAKADNliDYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACL 361
Cdd:cd17498    84 CSIRMKNGNN--SFLYYLLKNNIKNLINKSSGTVFGSINKDDIENLEVDIPEDEEQKRIANILSKIDDKIEINNQINKNL 161

                          90
                  ....*....|
gi 2018995424 362 RDEKKALMQQ 371
Cdd:cd17498   162 EELAQAIFKH 171

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: 46.30 E-value: 5.06e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2018995424 295 YFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQLL 373
Cdd:cd17293   102 FLYYQLLSSKFQLQAIASSTTLPIINKSKFEKIEIPLPPLEEQKRIVAKLDKLFALIDKLEESLEELDELLKSLFQSAF 180

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: 46.76 E-value: 5.45e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2018995424 314 GAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQL 372
Cdd:cd17261   133 GSMPKISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191

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: 46.53 E-value: 5.60e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2018995424 295 YFYQLLLSLQDKIYSLqSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKL 358
Cdd:cd17519   108 YLYHFLLSKQNEKYIL-AGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILDKFRELTNELESEL 170

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: 45.68 E-value: 7.83e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 101 AAIVLHTGYEVDFYYQFLISQYENIREManSGGQQNLS--GGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTN 178
Cdd:cd17499    85 AAIRAKKNIDKKYLFYFLLSNKDYFKGK--SGGSTFKSinKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNNIEE 162

                          90
                  ....*....|...
gi 2018995424 179 SQQQKKALMQQLL 191
Cdd:cd17499   163 ALANAQQLFKSIL 175

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: 45.76 E-value: 9.23e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2018995424 113 FYYQFLISQyENIREMANSGGQQNLSGGIVKSIPVPVPPLTEQKKIAKIL-STWDNAISVTEKLLTNSQQQKK 184
Cdd:cd17519   108 YLYHFLLSK-QNEKYILAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILdKFRELTNELESELNLRLKQYEY 179

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: 45.53 E-value: 1.19e-05

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 2018995424 321 PKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQL 372
Cdd:cd17524   138 ATKLKAIPIPLPPLEEQKEIVEKLDELDALIDRLEALLEEAEELLESLLQSL 189

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: 42.92 E-value: 8.87e-05

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 285 VSAKADNLIDYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDE 364
Cdd:cd17497    86 IRPKKGLDKKYLLYYLKSIENELSSLGTGSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDELTAKIDQLIALLEKAIEL 165


                  ....*....
gi 2018995424 365 KKALMQQLL 373
Cdd:cd17497   166 LKEYRQAVL 174

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: 42.15 E-value: 1.53e-04

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                  ....*....|....*....|....*....|....*....|....*....|...
gi 2018995424 138 SGGIVKSIPVPVPPLTEQKKIA----KILSTWDNAISVTEKLLTNSQQQKKAL 186
Cdd:cd17497   121 SKEDLENLLIPLPPLAEQKRIAafldELTAKIDQLIALLEKAIELLKEYRQAV 173

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: 41.83 E-value: 1.71e-04

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 294 DYFYQLLLSLQDKIYSLQSGGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLaclrDEKKALMQQLL 373
Cdd:cd17499    96 KYLFYFLLSNKDYFKGKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNNI----EEALANAQQLF 171

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: 41.13 E-value: 3.34e-04

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                  ....*....|....*....|....*....|....*....|....*....
gi 2018995424 141 IVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQQ 189
Cdd:cd17498   123 DIENLEVDIPEDEEQKRIANILSKIDDKIEINNQINKNLEELAQAIFKH 171

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: 7.84e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018995424 313 GGAQPHIYPKDLNSIPLWVPCVKEQQKIAAVLSAADAEISTLEKKLACLRDEKKALMQQL 372
Cdd:cd17270   124 GGTIKTITKEELSKFEIPIPSLEEQKEIVNILDKFDELITELQLRKKQLEYYKKALLSFM 183

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: 39.53 E-value: 1.21e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2018995424 131 SGGQQNLSGGIVKSIPVPVPPLTEQKKIAKILSTWDNAISVTEKLLTNSQQQKKALMQ 188
Cdd:cd17523   131 SAGQKTVNQGHIKSLPIPLPPLKEQKKIVARVEELFALIDQLESSLDLAQQLQNKLAQ 188