NCBI Conserved Domain Search

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: 205.36 E-value: 3.88e-65

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 229 WENKFIKDIFIFENNRRKPITSSLREK--GLYPYYGATGIIDYVKDYLFNnEERLLIGEDGAKWGQFET-SSFIANGQYW 305
Cdd:cd17262    1 WEVKKLGEVVENLDSKRIPLSSEERERrqGNYPYYGASGIVDYVDDYIFD-GEYVLIGEDGANLLSRGTpIAFYVSGKFW 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 306 VNNHAHVVKSND-HNLFFMNYYLNFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIE 384
Cdd:cd17262   80 VNNHAHVLKGKNgISTEFLYYYLNSIDISPYVTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELE 159

                        170
                 ....*....|...
gi 928790070 385 LLKERKKGLLQKM 397
Cdd:cd17262  160 KLIELKKALLQKL 172

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: 154.22 E-value: 3.97e-45

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGSGKTPkggSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDE-MKNSRTYYGDVLLNITGaSI 99
Cdd:cd17246    1 WEWVKLGEISSDITDGTHP---TPKYVESGIPFITSKNIKNGKIDFSDVKYISEEDHNEiLKRSKLKKGDILFSIIG-TI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 100 GRTAINSIVEThANLNQHVCIIRLKKEYYYN-FFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQK 178
Cdd:cd17246   77 GRVAIVPEDLP-ANINQAVALIRPKKEKIDPkYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPPL-EEQKR 154

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 928790070 179 IGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIFT 213
Cdd:cd17246  155 IAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLLT 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: 151.50 E-value: 3.45e-44

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  26 LGNLTTKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKNSRTYYGDVLLNITGaSIGRTAin 105
Cdd:cd17256    1 LGEIARVKGGGRLPKGESLSDGPTGVPYIRVTDIKNGGIDLDNLKYISPEIHEKIKRYTLSKGDILISIVG-TIGRVG-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 106 sIVETH---ANLNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKF 182
Cdd:cd17256   78 -IVPKEldgANLTENAARIRPKDSISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPL-EEQKRIVAI 155


                 ....*...
gi 928790070 183 FSKLDRQI 190
Cdd:cd17256  156 LDSLDAKI 163

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: 103.74 E-value: 3.42e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTtKIgsgktpKGG----SENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKNSRTYYGDVLLNITG 96
Cdd:cd17278    1 WEVVKLGDIA-DI------QNGyafkSSDFSDEGIPVIRIGNIKNGGIDLDDNSKYPEEPLEKYEKFLLKKGDILIAMTG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  97 ASIGRTAINSIVETHANLNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQ 176
Cdd:cd17278   74 GTVGKVAIVPEDDEPALLNQRVGKFRPKDKIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPL-EEQ 152

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 928790070 177 QKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIFT 213
Cdd:cd17278  153 KKIAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLFT 189

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: 103.61 E-value: 3.86e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLNLNDlVYISKDIDDEMKNSRTYYGDVLLNITGaSIGRTA 103
Cdd:cd16961    1 KKLGEIA-EIISGKTPSSSSEYWDNGIIPWIRISDINNGGIILTD-EKITEEGAEKLKKKILPKGDILISRSG-TIGKVA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 104 INSIVEThANLNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIfLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFF 183
Cdd:cd16961   78 IVKENDK-ALLNQAVIVIRPKDEVDSEFLYYFLKSPFGKKLI-EGSAGSTQPNLNKSDLKNLKIPLPPL-EEQKKIANIL 154


                 ....*..
gi 928790070 184 SKLDRQI 190
Cdd:cd16961  155 DKLDALI 161

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: 98.67 E-value: 1.23e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 232 KFIKDIFIFENNrrKPITSS-LREKGLYPYYGATGIIDYVKDYLfNNEERLLIGEDGAKWGqfetSSFIANGQYWVNNHA 310
Cdd:cd17266    1 VKLGELCKIKSG--KSITASkISEEGDYPVYGGNGIIGYTDEYN-HEGEYILIGRVGALCG----NVHYVEGKFWVTDNA 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 311 HVVKS-NDHNLFFMNYYLNFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKER 389
Cdd:cd17266   74 LVVTPkKENNIKFLYYLLKSLNLNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLIEL 153


                 ....*.
gi 928790070 390 KKGLLQ 395
Cdd:cd17266  154 KKELMQ 159

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: 96.79 E-value: 1.38e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTtKIGSGKTPKGGSENYTNKG-IPFLRSQNIRNgklnlNDLVYISKDIDDE-MKNSRTYY---GDVL--LN 93
Cdd:cd17294    1 WEWKTLGEIA-KIFSGGTPSTSNPEYWDGGtIPWLSSGEVNF-----KEIYETEKRITEEgLKNSSAKWipkNSVLiaLA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  94 ITGASIGRTAINSIVEThanLNQHVCIIRLKKEY------YYNFFGQY--LLSRKGkrkiflaqsGGSREGLNFKEIANL 165
Cdd:cd17294   75 GQGKTRGTVAILKIPLT---TNQSLAAIEPDEEIansrflYYNLSSRYeeLRSLSG---------GGGRGGLNLKIIKSL 142

                        170       180
                 ....*....|....*....|....*
gi 928790070 166 KIFTPTIfEEQQKIGKFFSKLDRQI 190
Cdd:cd17294  143 PIPLPPL-EEQKKIVAILDKFDALI 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: 92.19 E-value: 6.61e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTtKIGSGKTPKggSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKNSRTYYGDVLLNITgasig 100
Cdd:cd17259    1 WEWVKLGDVA-DILSGYAFK--SSEFSESGIRLLRGANVGVGEIRWDDTVYLPEEYLEEYEKYLLKEGDIVIALD----- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 101 RTAINS------IVETHAN--LNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTI 172
Cdd:cd17259   73 RPIISGglkvarIPKSDLPalLVQRVARIRPKDELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPL 152

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 928790070 173 fEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQK 210
Cdd:cd17259  153 -EEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKGLMQS 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: 88.75 E-value: 1.36e-20

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGSGKTPKggsENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKNSRTYYGDVLLNITGAS-- 98
Cdd:cd17517    1 WEVVKLGDLLEDPRYGTSKK---SSYDGSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKELEKYLLKKGDILFNRSNGSpe 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 -IGRTAI------NSIVETHanlnqhvCI-IRLKKEYYYN-FFGQYLLSRKGKRKIF-LAQSGGSREGLNFKEIANLKIF 168
Cdd:cd17517   78 lVGKCALvdeedePAIFASY-------LIrLRLDKKKILPeFLYYYLNSPLGRKQIEkIAKSAAGQANINQKDLKKLPIP 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 928790070 169 TPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKI 211
Cdd:cd17517  151 LPPL-EEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192

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: 82.22 E-value: 2.23e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGsGKT--PKGGSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKnsRTYYGDVLlnITGAS 98
Cdd:cd17252    1 WEWVRLGEIAEIIR-GVTykKSDASEEPSEGGIPVLRANNIQNGGLDFDDLVYVPKSKVKEEQ--KLKKGDIL--ICMSS 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 -----IGRTAINSiVETHANLNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTIf 173
Cdd:cd17252   76 gskelVGKAAFID-EDTDYTFGAFCGVIRPKKEIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPL- 153

                        170
                 ....*....|....*..
gi 928790070 174 EEQQKIGKFFSKLDRQI 190
Cdd:cd17252  154 AEQKRIVAKLDKLDALI 170

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: 79.01 E-value: 3.24e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKGGSENYTNKGIPFLRSqnirnGKLNlNDLVYISKD-IDDE-MKNSRTYY---GDVLLNITGAS 98
Cdd:cd17515    1 VKLGDIG-KWGSGGTPSRSNPEYYGGGIPWIKS-----GELN-DGYITSTEEkITEEgLKNSSAKLfpkGSVLIAMYGAT 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 IGRTAINSIvetHANLNQHVCIIRLKKEYYYNFFGQYLLSRKGKrkiFLAQS-GGSREGLNFKEIANLKIFTPTIfEEQQ 177
Cdd:cd17515   74 AGKVGILGI---DAATNQAICAILPNEEIDNEFLFYFLKSQKEY---LISLGkGGAQPNISQGIIKNIEIPLPPL-AEQK 146

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 928790070 178 KIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17515  147 RIVAKLDKLDKLIEKLEKALEKLEELKKALMQKLL 181

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: 78.36 E-value: 4.90e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  22 EEKKLGNLTTKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLnlndlvYIS---KDIDDE-MKNSRTYY---GDVLLNI 94
Cdd:cd17275    1 EQVKLGELCEKMKSGGTPSTSNKEYYGGDIPFVKISDMTKSGK------YIYsteKYITEEgLKNSSAWIvpkGTILYAM 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  95 tGASIGRTAINSI-VEThanlNQHVCIIRLKKEYYYNFFGQYLLSRKgKRKIFLAQSGGSREGLNFKEIANLKIFTPTIf 173
Cdd:cd17275   75 -YASVGKVAINKIdVAT----NQAILGIIPKDEKLDFEFLYYWLLSL-KNELKRLIRTGTQANLNAEIVKNLPIPLPPL- 147

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 928790070 174 EEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17275  148 EEQKKIAEILDKIDAEIDKLEEKIEKLRELKKGLLQKMF 186

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: 74.49 E-value: 7.38e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 232 KFIKDIFifENNRRKPITSS--LREKGLYPYY-GAT---GIIDYVKDYLFNnEERLLIGEDGAKWGQFetssFIANGQYW 305
Cdd:cd17255    1 KKLGDLF--EIGRGRVISKKyiSENPGDYPVYsSQTknnGIMGYINTYDFD-GEYITWTTDGANAGTV----FYRNGKFS 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 306 VNNHAHVVKSNDHNLF--FMNYYLNfKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRI 383
Cdd:cd17255   74 VTNVCGVLKVKNKNINnkFLYYALN-LIAKKYVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIAKL 152

                        170
                 ....*....|....
gi 928790070 384 ELLKERKKGLLQKM 397
Cdd:cd17255  153 KKLIELRKKQLEYY 166

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: 73.74 E-value: 2.09e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTKIGSGKTPKGGSENYTNKGIPFLRSqnirnGKLNLNDLVYISKDIDDEMKNS----RTY-YGDVLLNITGAS 98
Cdd:cd17280    1 WKISHLFGLIGSGTTPKSDNEDYYDGGIPWVTT-----GDLRDGIITETSKKITDKALDDysalKIYpAGSLVIAMYGAT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 IGRTainSIVETHANLNQHVCIirLKKEYYYN-FFGQYLLSRKgKRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQ 177
Cdd:cd17280   76 IGRL---GILGIDATTNQACCV--LSGSNKIDiKFLFYWLLAN-RDELISLASGGGQPNISQELIKSLRIPVPPL-EEQK 148

                        170
                 ....*....|...
gi 928790070 178 KIGKFfskLDRQI 190
Cdd:cd17280  149 QIAAF---LDKKT 158

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: 73.41 E-value: 3.28e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIgsgktpKGG---SENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKNSRTYYGDVLLNITG- 96
Cdd:cd17512    1 WEEIRLGDIIDYQ------KGYafkSKDYQDSGIRIVRVSDFTDDSIDINNLVYISEEKANKYKKYELKENDIIITTVGs 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  97 -----ASI-GRTAINSIVETHANLNQHVCIIRLKKEYYYNFFGQYLLsrkgKRKIF------LAQSGGSREGLNFKEIAN 164
Cdd:cd17512   75 wpsnpDSVvGKVVRVPKEADGALLNQNAVKIRPKKGILDQSFLFYNL----KSERFknyiesIARGNANQASITLGDIKK 150

                        170       180
                 ....*....|....*....|....*.
gi 928790070 165 LKIFTPTIfEEQQKIGKFFSKLDRQI 190
Cdd:cd17512  151 FKFLLPPL-EEQKKIASILSAYDDLI 175

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: 71.67 E-value: 1.03e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  37 KTPKGGSEnYTNKGIPFLRSQNIRNgklNLNDLVYISKDIDDEMKNSRTY-YGDVLLNITGAsIGRTAInsIVETHANLN 115
Cdd:cd17258    4 GPNKDPEL-FCNGNIKLVCIKNELI---NSLKVKIVEPDYKIGLKQSKIFkKGDVLITRHGT-IGRVSI--ILSEEACLS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 116 QHVCIIRLKKEYYYNFFGQYLLSRKgKRKIFLAQSGGSRE--GLNFKEIANLKIFTPTiFEEQQKIGKFFSKLDRQIELE 193
Cdd:cd17258   77 SHVAGFNSKEGISDNKFIKYLFNSK-KIKNRLMSYGASSTqpALNLSRLLKIKFPNPP-LEEQQKIGKILSTWDRAIELT 154

                        170
                 ....*....|....*....
gi 928790070 194 EQKLELLQQQKKGYMQKIF 212
Cdd:cd17258  155 EQKLELLQQQKKGLMQQLF 173

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

Pssm-ID: 341153 [Multi-domain] Cd Length: 184 Bit Score: 71.03 E-value: 1.70e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  43 SENYTNK------GIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKNSRTYYGDVLLNITGaSIGRTAINSIVETHAnLNQ 116
Cdd:cd17264   14 GKNYPSKsefvdeGIPFINAGHLEDGTIDLSNMNFISEEKYNSLGSGKLQKGDILYCLRG-SLGKCAIVDNYDEGA-IAS 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 928790070 117 HVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQI 190
Cdd:cd17264   92 SLVIIRPFAKVDVRYLYYYLNSPLGKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPL-EEQKRIVAKLDELDALI 164

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: 70.59 E-value: 3.10e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGSGKTpkgGSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKnsrtYY---GDVLLNITGA 97
Cdd:cd17521    1 WEVKKLGELSEKIQYGYT---ASAAYEDGGPRYLRITDIQDDGVLWDTVPYCSISEEDAEK----YLlkdGDILFARTGA 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  98 SIGRTAInsivetHANLNQHVC-----I-IRLKKEYYYN-FFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTP 170
Cdd:cd17521   74 TVGKSYL------YKEDDGKAVfasylIrFRPNKKKVLPkYLFYFTQSSLYWKQIKSISSGSAQPNINAEKLKSLKIPLP 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 928790070 171 TIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKI 211
Cdd:cd17521  148 PL-EEQKRIVAILDALDAKIDALEELLEKLEELLKELLQSL 187

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: 70.21 E-value: 3.43e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLNLNDlVYISKDiddEMKNSRTYY---GDVLLNITGASI- 99
Cdd:cd17287    1 KKLGEIA-KVSSGGTPSRSNPEYWNGGIPWVKTGEVNFNEITDTE-EKITEE---GLKNSSAKLfpkGTLLMAMYGQGKt 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 100 -GRTAINSIvetHANLNQHVCIIRLKKE-----YYYNFFGQYLLSRKgkrkifLAqSGGSREGLNFKEIANLKIFTPTIf 173
Cdd:cd17287   76 rGRVAILGI---EAATNQACAAILPNDGinpdfLFYYLQSSYEELRD------LS-NGGGQPNLNAGLIKSIEIPVPPL- 144

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 928790070 174 EEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIFT 213
Cdd:cd17287  145 DEQQKIAAFLSAIDAKIDALEQKLELLQELKKSLMQQLFT 184

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: 69.81 E-value: 5.46e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  20 EWEEKKLGNLTTkIGSGKT--PK-GGSENYTnkgiPFLRSQNIRNGKLNLNDLvyisKDID---DEMKNSRTYYGDVLLN 93
Cdd:cd17253    1 GWEWVRLGDVAE-VQSGITkgKKrRGGELEV----PYLRVANVQDGYLDLSEV----KEIEvteEELERYRLRKGDLLVT 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  94 ITGAS--IGRTAI--NSIVE-THANlnqHVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLA---QSGG--SregLNFKEIA 163
Cdd:cd17253   72 EGGDSdkLGRGAIwrGEIPPcLHQN---HLFRVRPKDDLLLPEFLSYWLNSAYGRGYFLRaakQTTNlaS---INSTKLK 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 928790070 164 NLKIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17253  146 ALPVPLPPL-EEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193

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: 68.31 E-value: 1.93e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTKIGSGkTPKGGSENYTNKGIPFLRSQNIRNGKLNLNDlvyISKDIDDE-MKNSRTYY--GDVLLNITGASIG 100
Cdd:cd17513    1 VKLGELGKFIGGG-TPSTKNPEYWNGNIPWITSSDLSEDDIFKIN---IRKFITEEaIKNSATKIipANSILIVTRVGVG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 101 RTAINSI-VEThanlNQHVCIIRLKKEYYYNFFgQYLLSRKGKRKIFLAQsGGSREGLNFKEIANLKIFTPTIfEEQQKI 179
Cdd:cd17513   77 KVAINPFdICT----SQDFTSLIPIKEVNPLFL-AYLLYSLLQKLKSQLQ-GTSIKGITKDDLKNLKIPLPPL-EEQQKI 149

                        170       180       190
                 ....*....|....*....|....*....|...
gi 928790070 180 GKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17513  150 AAILSKLDKLIEAHEKKLEKLKQLKKGLMQKLF 182

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: 66.81 E-value: 5.45e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTKIGSGKTPKGGSENYTNKG-IPFLRSQNIRNGKLNLNDlVYISKDIDDEMKNSRTY-YGDVLLNITGASIGR 101
Cdd:cd17514    1 VKIQDIAFEIINGGTPSRNEPEYWNNGdIPWLTSGETDDNFINNTS-EKITTKNGLEDSSIRIVpKGTILIACTGQGYTR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 102 TAInSIVETHANLNQHVCIIRLKKEYYYNFFGQYLLSRKGkrKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGK 181
Cdd:cd17514   80 GQV-AVLQIDASTNQAIAAIRCKENVNPKYLYYYLKTQKN--NLRNLTSGVAQKNLNIEMLRNLQIPLPPK-EEQQKIVN 155


                 ....*.
gi 928790070 182 FFSKLD 187
Cdd:cd17514  156 ILETLE 161

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: 66.85 E-value: 6.05e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGSGKTPKGGSEnyTNKGIPFLRSQNI-RNGKLNLNDLVYISKdIDDEMKNSRTYYGDVLLNITGAS- 98
Cdd:cd17526    1 WEVVRLGDIILDIQSGFASGKQNE--DEDGVPQLRPHNItTDGELDLDKLIKIVP-SPKERKRYLLQKGDVLFNNTNSQe 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 -IGRTAINSIVETHANLNqHVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLA-------QSGGSREGLnfkeiANLKIFTP 170
Cdd:cd17526   78 lVGKTALFDGEEPYVFSN-HMTRIRVKKSKINPEFLARYLHLLWRSGYFKKlctnwvnQAGINSDTL-----ANLKIPLP 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 928790070 171 TIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17526  152 PL-PEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192

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: 66.37 E-value: 8.81e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNL-TTKIGSGKTPkggsENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMknsRTYYGDVLL---NITGASI 99
Cdd:cd17265    1 KKLKEIgEAIIGLTYSP----EDVSDEGTLVLRSSNIQNGKLDFDDNVYVNSKIPEKL---IVKEGDILIcvrNGSRALI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 100 GRTAInsIVETHANLN--QHVCIIRLKkeyYYNFFGQYLLSrkgkrKIFLAQSGgSREG-----LNFKEIANLKIFTPTI 172
Cdd:cd17265   74 GKNAL--IDKEAEGMTfgAFMTVFRSE---YNDYLFHLFNS-----DLFKKQIG-SFLTatinqITNGNLNNFKIPLPPL 142

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 928790070 173 fEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17265  143 -EEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKELMQQLI 181

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

Pssm-ID: 396139 [Multi-domain] Cd Length: 167 Bit Score: 65.07 E-value: 1.48e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  228 EWENKFIKDIFIFENNRRkPITSSLREKGLYPYYGAT-------GIIDYVKDYLFnNEERLLIGEdGAKWGQFetssFIA 300
Cdd:pfam01420   3 DWEVFKLGDVFEIKKGKT-PKKKELKNNGKYPYIRAGdlnnvvkGGLGYIKKYIL-PKGDITISS-RATIGYV----FYR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  301 NGQYWVNNHAHVVKSNDHNLFFMNYYL----NFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKm 376
Cdd:pfam01420  76 DKPYYTNQHIIVLIPKNNIKITEFLYLylllKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDNT- 154

                         170
                  ....*....|....*....
gi 928790070  377 nnqmnrIELLKERKKGLLQ 395
Cdd:pfam01420 155 ------IELEKGILNELER 167

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: 65.39 E-value: 2.10e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  25 KLGNLTTKIGSGKTPK-GGSENYTNKGIPFLRSQNIRNGKLNLNDLvYISkdiDDEMKNS--RTYYGD-VLLNITGAS-- 98
Cdd:cd17500    1 KLEDICIKITSGGTPSrSNKEYYNGGNIPWLKTKELNFKRIYDTEE-KIT---EEGLKNSsaKLIPENtVIIAMYGAGkt 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 IGRTAINSIVEThanLNQHVC--IIRLKK---EY-YYNFFGQY--LLSRKgkrkiflaqSGGSREGLNFKEIANLKIFTP 170
Cdd:cd17500   77 AGRVAINKIPLT---TNQACCnlIIDNKKadyRFvYYSLKTQYeeLVNLA---------SGAAQQNLNSKLIKNFEIPLP 144

                        170       180
                 ....*....|....*....|
gi 928790070 171 TIfEEQQKIGKFFSKLDRQI 190
Cdd:cd17500  145 PL-PEQKRIASILSSLDDKI 163

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: 64.47 E-value: 4.70e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  20 EWEEKKLGNLTtKIGSGKTPKGGSENY-TNKGIPFLRSqnirnGKLNLNDLVYISKDIDDE-MKNSRTYY---GDVLLNI 94
Cdd:cd17247    3 HWEVVRLGDVA-RVGNGSTPSRKNPDYwNGGTIPWVSS-----GEVNDNRITEADEFITELaLKECSLPLvppGSVLVAM 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  95 TGASI--GRTAINSIVETHanlNQHVCIIRLKKEY------YYNFFGQYLLSRKGKrkiflaqSGGSREGLNFKEIANLK 166
Cdd:cd17247   77 IGQGKtrGQAAILAIEATI---NQNLAAIRPNEERvlpeylHYYLESQYDELRRIG-------SGGGQGALNCGILKAFP 146

                        170       180
                 ....*....|....*....|....*
gi 928790070 167 IFTPTIfEEQQKIGKFFSKLDRQIE 191
Cdd:cd17247  147 IPLPPL-DEQREIVAELEALLAKID 170

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: 62.81 E-value: 1.64e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTtKIGSGKTPKGGSENYTNKGIPFlrsqnIRNGKLNLNDLVYIS---KDIDDE-MKNSRTYY---GDVLLN 93
Cdd:cd17273    1 WEVVKLGDVA-EIVGGGTPSTKNPEYWNGDIPW-----ITPTDLTKLKGKYISdteRKITELgLKNSSAKLlpaGSVLLS 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  94 iTGASIGRTAINSI-VEThanlNQ--HVCIIrlKKEYYYNFFGQYLLSRKgkrKIFLAQSGGSreglNFKEI-----ANL 165
Cdd:cd17273   75 -SRAPIGYVAIATNpLAT----NQgfKSIIP--NEEIDNEFLYYLLKNNK---PEIESLASGS----TFKEIskstfKKI 140

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 928790070 166 KIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17273  141 EIPLPPL-EEQKKIAAILSKLDELIELLEKENEKLKELRDGLLPKLF 186

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: 62.51 E-value: 1.74e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 312 VVKSNDHNLFFmnYYL---NFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKE 388
Cdd:cd17286   92 IPNKNYDPEFL--YYAlenWSKKIKSLAGKQAVPIINKTEFSKIKILVPPLEEQQKIANFLSKLDELIELQQQKIEKLEE 169

                         90
                 ....*....|
gi 928790070 389 RKKGLLQKMF 398
Cdd:cd17286  170 LKKGLLQKLF 179

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: 62.33 E-value: 1.98e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  22 EEKKLGNLTtKIGSGKTPKggSENYTNKGIPFLRSQNIRNGKLNLNDLVYISK-DIDDEMKNSRTYYGDVLLNITGASIG 100
Cdd:cd17519    1 EYKTLGEVC-KFQNGFAFK--SSKYRESGFPIIRITNIQNGKIDTDNLKYFDLnDYKENLDKYIVRPGDIVIAMSGATTG 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 101 RTAINSiVETHANLNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLAqsGGSREGLNFKEIANLKIFTPTIfEEQQKIG 180
Cdd:cd17519   78 KVGINL-TDQEFYLNQRVGKFIPNEEILNNRYLYHFLLSKQNEKYILA--GGSQPNLSSEKLKKIKIPIPSL-EVQEEIV 153


                 ....*..
gi 928790070 181 KFFSKLD 187
Cdd:cd17519  154 SILDKFR 160

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: 61.71 E-value: 3.71e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKI--GSGKTPkggseNYTNKGIPFLRSQNIRNGKLNLNDLVYISKDiDDEMKNSRTYYGDVLLNITGAS 98
Cdd:cd17524    1 WEWVTIGDLVTSVqyGTSEKK-----SEDEGGYPVLRMGNIQDGGIDDDDLKYVDLD-EKEFEKYLLKKGDVLFNRTNSP 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 --IGRTAInsivethANLNQHVCI------IRLKKE----YYYNFfgqYLLSRKGKRKIF-LAQSGGSREGLNFKEIANL 165
Cdd:cd17524   75 elVGKTAI-------FRGDGPATFasylirIRLNEEkilpEYLNY---FLNSPYGRKQIKsVATQGVGQANINATKLKAI 144

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 928790070 166 KIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKI 211
Cdd:cd17524  145 PIPLPPL-EEQKEIVEKLDELDALIDRLEALLEEAEELLESLLQSL 189

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: 61.00 E-value: 4.48e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKggSENYTNKGIPFLRSQ---NIRNGKLNLNdlVYISK-----DIDDEMKNSRTYYGDVLLNIT 95
Cdd:cd17494    1 KKLGEIA-EITMGQSPS--SKNYNDNPNGLPLVQgnaDIKNGKVIPR--IWTSEitktaNKGDIILSVRAPVGEVAKTNF 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  96 GASIGRTainsivethanlnqhVCIIRLKK-EYYYnffgQYLLSRKGKRKIFlaQSGGSREGLNFKEIANLKIFTPTiFE 174
Cdd:cd17494   76 DACIGRG---------------VCAIKGNEfIFLY----LYLLNIEGYWSKI--SQGSTFESINSNDIKNLKISIPS-LE 133

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 928790070 175 EQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17494  134 EQQKIATFLSTLDAEITLLEKKLEKLKQLKKGLLQKLF 171

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 58.53 E-value: 5.12e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 928790070 321 FFMNYYLNFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:COG0732    4 YYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81

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: 61.12 E-value: 6.50e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTkIGSGKtpKGGSENYTNKGIPFLRSQNI---RNGKLNLNDLvYISKDIDDEMKNSrtyYG-----DVLL 92
Cdd:cd17289    1 WEWKKLGDIAE-ITSSK--RIFKSEYVDSGIPFYRSKEIielFNGEEISTEL-FISEERYEEIKSK---YGvpkkgDILI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  93 nitgASIGRTAINSIVETH-------ANLNQhvciIRLKKEYYYNFFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANL 165
Cdd:cd17289   74 ----TSVGTIGIPYLVKNDdpfyfkdGNLTW----FKNIKDINSKFLYYWFQSSIFKNQINSITIGSTQKALTIEKLKKT 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 928790070 166 KIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17289  146 KIPLPPL-EEQKKIVSILSALDEKIDLNKKQLQKLEELAKTLFQYWF 191

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: 60.18 E-value: 7.51e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 229 WENKFIKDIFIFENNRRKPITsslrEKGLYPYYGATGIIDYVKDYLFNnEERLLIGEDGakwgqfeT--SSFIANGQYWV 306
Cdd:cd17288    1 WEVKKLGDLLKIKNGKDYKHL----EDGNYPVYGSGGIMGYVNDYLYD-GESVLIGRKG-------TidKPLYVNGPFWT 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 307 NNHAHVVKSNDHNLF-FMNYYLNFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNK--MNNQMNR- 382
Cdd:cd17288   69 VDTMFYTEIKKNNDPkFLYYLLKTIDFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKdaLIELQEKl 148

                        170
                 ....*....|....*
gi 928790070 383 IELLKERKKGLLQKM 397
Cdd:cd17288  149 LEKLKQYKLALMQEL 163

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 63.36 E-value: 7.69e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  11 ELRFPGFEGEWEEKKLGNLTTKIGSGKTPKGgseNYTNKGIPFLRSQNIRNGKLNLNDLVYISKDiDDEMKNSRTYYGDV 90
Cdd:PRK09737 211 EWRWPDLPSTWSVHKYSELVDSRLGGMSSKA---NNFGSATPYLRNINVRWGSFDLEDLQDILIS-DIERRELKLKLGDV 286

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  91 LLNITGAS--IGRTAINSIVETHANLNQHVCI-IRLKKEYYYNFFgQYLLSRKGKRKIFLAQ--SGGSREGLNFKEIANL 165
Cdd:PRK09737 287 LFCRGNEPleVGRCAIWKEPQDIPVIYQKALIrARVKDDIIPEYL-VYNLKSPDSRNISLSQlfTGTTQKHITGKALANY 365

                        170
                 ....*....|....
gi 928790070 166 KIFTPTIfEEQQKI 179
Cdd:PRK09737 366 PIRVPPL-EEQAEI 378

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: 59.84 E-value: 1.09e-10

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 928790070 351 NINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17494  124 NLKISIPSLEEQQKIATFLSTLDAEITLLEKKLEKLKQLKKGLLQKLF 171

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: 60.15 E-value: 1.23e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 312 VVKSNDHNLFFMNYYLNF--KELRAFVAGNAPAklthanlcNINLKI--------PCLTEQDKVSALLKSIDNKMNNQMN 381
Cdd:cd17282   98 IPNEEKIDVEFLEYYLRTlkKELEAIAPQSAQK--------NINLEIlrplkipvPPLEEQKKIVEILDALDDLIDNLEK 169

                         90
                 ....*....|....*..
gi 928790070 382 RIELLKERKKGLLQKMF 398
Cdd:cd17282  170 RIAKLEELKQSLLQEAF 186

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: 59.86 E-value: 1.50e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGSGKTpkgGSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDiDDEMKNSRTYYGDVLL-NITGAS- 98
Cdd:cd17522    1 WKVVKLGDVLEEIRNGTT---VKQNKEGGGYPVTRIETISNGTIDLNRVGYAITN-EEKIEKYKLQKGDILFsHINSIEh 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 IGRTAI-NSIVET--H-ANLnqhvCIIRLKKEYYYNFFGQYLLSRKGKRKIF--LAQSGGSREGLNFKEIANLKIFTPTI 172
Cdd:cd17522   77 IGKTAIyDGDPEPliHgMNL----LRLRPNKNIVDPKYLYYLLKSDRFRNQFrsIAKKAVNQASINQTELKKIKIPLPPL 152

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 928790070 173 fEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKI 211
Cdd:cd17522  153 -EEQQKIASILEKLDKKIEKRKEKIEKLKELKKGLFQKL 190

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: 59.48 E-value: 2.38e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 312 VVKSNDHNLFFMNYYLNF--KELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKER 389
Cdd:cd17275   98 IPKDEKLDFEFLYYWLLSlkNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIAEILDKIDAEIDKLEEKIEKLREL 177


                 ....*....
gi 928790070 390 KKGLLQKMF 398
Cdd:cd17275  178 KKGLLQKMF 186

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: 58.14 E-value: 4.17e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070   20 EWEEKKLGNLTtKIGSGKTPKggSENYTNKG-IPFLRSqNIRNGkLNLNDLVYISKDIDDEmknsrtyyGDVLLnITGAS 98
Cdd:pfam01420   3 DWEVFKLGDVF-EIKKGKTPK--KKELKNNGkYPYIRA-GDLNN-VVKGGLGYIKKYILPK--------GDITI-SSRAT 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070   99 IGRTAINSIvetHANLNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLAQSGGsREGLNFKEIANLKIFTPtIFEEQQK 178
Cdd:pfam01420  69 IGYVFYRDK---PYYTNQHIIVLIPKNNIKITEFLYLYLLLKLKKLKSLKFGST-QPKLTKERLKEIKIPLP-PLEEQKK 143

                         170
                  ....*....|..
gi 928790070  179 IGKFFSKLDRQI 190
Cdd:pfam01420 144 IAKILSQLDNTI 155

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: 58.27 E-value: 4.49e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 314 KSNDHNLFFMNYYLNFKElraFVAGNapakltH-----ANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKE 388
Cdd:cd17274   90 KNNNVNLKFVYEALQTIK---YVPGD------HkrhwiSEYSKFKIPLPPLEEQNKIVRILDKFDELIAELEAKLELLKK 160

                         90
                 ....*....|.
gi 928790070 389 RKKGLLQKMFI 399
Cdd:cd17274  161 QKKYYLQKLFT 171

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: 57.13 E-value: 1.05e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTKIGsGKTPK--GGSENYTNKGIPFLRSQNIRNGklnlNDLVYIskdiDDEMKNSRTYYGDVLLNITGASIGR 101
Cdd:cd17263    1 VKLGEVCKFSK-GKQPPisERFDEPKEGSVRYIQIEDLRNN----NEKKYI----ENPKKSVICNEDDILIVRDGANAGE 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 102 --TAINSIVetHANLnqhVCIIRLKKEYYYNFFGQYLLSRKGKRKIfLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKI 179
Cdd:cd17263   72 vgTGLEGAI--ASTL---FKIIPDKNIIDKDYLYYFLKSKEIQLNI-LTKAGSTIPHVNKKDLENLKIPLPSL-EEQKKI 144

                        170       180       190
                 ....*....|....*....|....*....|...
gi 928790070 180 GKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17263  145 AEILDKLDALIDKLKELIEKLIELKKGLFQELL 177

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: 57.16 E-value: 1.13e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKGGSENYTNKGIPFLrsqnirNGKLNLNDL-----VYISKDIddemKNSRTyyGDVLLNITgAS 98
Cdd:cd17245    1 VKLGEVA-EIIMGQSPPSSTYNEEGEGLPFL------QGKADFGEIyptprVWCTKPT----KIAEK--GDILISVR-AP 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 IGRTAINsivethanlNQHVCI------IRLKKEYYYNFFGQYLlsrKGKRKIFLAQSGGSR-EGLNFKEIANLKIFTPt 171
Cdd:cd17245   67 VGDVNIA---------DEKCCIgrglaaIRANKDIDNLFLYYYL---KYNKPELEKLGTGSTfKAINKKDLEELKIPLP- 133

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 928790070 172 IFEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17245  134 PLEEQQKIAEILSTVDEAIEKTKALIEKLDELKKGLMQELF 174

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 54.29 E-value: 1.73e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 133 GQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:COG0732    3 KYYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPL-EEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81


                 ....*
gi 928790070 213 TQELR 217
Cdd:COG0732   82 TGELR 86

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: 56.51 E-value: 2.27e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  26 LGNLTTKIGSGKTPKGGSENYTNKGIPFLRSqnirnGKLNLNDLVYISKDIDDEM--KNSRTYY--GDVLLNITG----A 97
Cdd:cd17271    1 LGEVLKGLSSGATPSRGNPEYFNGDIPWITS-----GELNYNYITDTNEKITEEAvkNTNLKIHpkGTFLIAITGleaaG 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  98 SIGRTAINSIVEThanLNQHVCIIRLKKE-------YYYNFFGQYLLSRkgkrkifLAQsGGSREGLNFKEIANLKIFTP 170
Cdd:cd17271   76 TRGKCAITGIPAT---TNQSCMAFYPTKKltteflfYWYKKYGNYLGFK-------YAQ-GTKQQSYTADIVKKLPILLP 144

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 928790070 171 TIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIFT 213
Cdd:cd17271  145 TL-KEQKKIANFLSDIDELIATLEKKIEKLKKIKKGLMQKLLT 186

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) TRD2-CR2 and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) TRD; The recognition sequences of Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341194 [Multi-domain] Cd Length: 182 Bit Score: 55.99 E-value: 2.86e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 316 NDHNLFFMNYYLNFK--ELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGL 393
Cdd:cd17513   98 KEVNPLFLAYLLYSLlqKLKSQLQGTSIKGITKDDLKNLKIPLPPLEEQQKIAAILSKLDKLIEAHEKKLEKLKQLKKGL 177


                 ....*
gi 928790070 394 LQKMF 398
Cdd:cd17513  178 MQKLF 182

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: 54.43 E-value: 9.92e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 267 IDYVKDYLFNNEERLLIGEDGAKWGQFET--SSFIANgqywvnNHAHVV-KSNDHNLFFMNYYLNFKELRAF---VAGNA 340
Cdd:cd17263   46 IENPKKSVICNEDDILIVRDGANAGEVGTglEGAIAS------TLFKIIpDKNIIDKDYLYYFLKSKEIQLNiltKAGST 119

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 928790070 341 PAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17263  120 IPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALIDKLKELIEKLIELKKGLFQELL 177

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 56.81 E-value: 1.13e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  20 EWEEKKLGNLTTKIGSGKTPKGGSENYTNKG-IPFLRSQNIRNGKLNLNDLVYiSKDIDDEMKNSRTYYGDVLLNITGAS 98
Cdd:PRK09737   9 GWVTTHISEICSVIRGVKPPKGYATKSLTMGdLPFIRTTDITNGAVDLTTLPY-CMDAPEDVSKYQLQDRDIVISSAGSI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 IGRTAINSIVETHANLNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTIFEeqQK 178
Cdd:PRK09737  88 GFSFLAQNPLPSNVVFASFAIRLKPVNYFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAE--QK 165


                 ....*....
gi 928790070 179 IgkFFSKLD 187
Cdd:PRK09737 166 I--IAEKLD 172

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: 54.55 E-value: 1.27e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGSGkTPKGGSENytNKGIPFLRSQNI-RNGKLNLNDLVYISKDiDDEMKNSRTYYGDVLLNI--TGA 97
Cdd:cd17525    1 WEWVKLGDILSSTQLG-LVRSNSED--PNGYPYIKMGNIgRGGINLLKVETYVDAT-ELEVEKYLLEDGDLLFNTrnTLE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  98 SIGRTAINSIVETHANLNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKI-FLAQSGGSREGLNFKEIANLKIFTPTIfEEQ 176
Cdd:cd17525   77 LVGKVAIWRGELPKALFNNNILRIRFDDIVLPYFINYYLNSPDGKKQLeSIASGTTSVAAIYQKDLKKLKLPLPPL-DEQ 155

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 928790070 177 QKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKI 211
Cdd:cd17525  156 REIVSFLSELDAKIDQLEQKLEKLLQIKKALMQQL 190

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: 54.36 E-value: 1.40e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKigsgKTPKGGSENYTNKG-IPFLRSQNIRNGKlnlNDLVYISKDIDDEMKNSRTYYGDVLLNITGAsI 99
Cdd:cd17272    1 VEEKTLGDIAVD----GFQNGPAPNFDEKGeIPVITSKNISNGK---IDFEYVKYDFLSISKNRKINKGDILITMIGT-I 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 100 GRTAINSIVETHAnLNQHVCIIRLKKEY----YYNFFgqyLLSRKGKRKIFLAQSGgsREGLNFKEIANLKIFTPTIfEE 175
Cdd:cd17272   73 GETAIVKCLDPKF-YTLNLYLIRLKKEKllpsYLKYF---LDSEKFLNKSISATSG--QGYLKANQIDKLEIPLPPL-EE 145

                        170
                 ....*....|..
gi 928790070 176 QQKIGKFFSKLD 187
Cdd:cd17272  146 QQRIVKILDKFD 157

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: 54.04 E-value: 1.42e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKdidDEMKNSRTYYGDVLLNITGASIGRTA 103
Cdd:cd17286    1 KKLGDLG-EIVTGNTPSTKNSEYYGGEILFVTPTDIDGNKYIYKTEKKLSE---KGFKKARILPKGSILVTCIGSIGKNA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 104 INSIVEThanLNQHVCIIRLKKEYYYNFFGqYLLSRKGKrKIFLAQSGGSREGLNFKEIANLKIFTPTiFEEQQKIGKFF 183
Cdd:cd17286   77 IATEDCA---TNQQINAIIPNKNYDPEFLY-YALENWSK-KIKSLAGKQAVPIINKTEFSKIKILVPP-LEEQQKIANFL 150

                        170       180
                 ....*....|....*....|....*....
gi 928790070 184 SKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17286  151 SKLDELIELQQQKIEKLEELKKGLLQKLF 179

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: 53.66 E-value: 1.75e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 312 VVKSNDHNlfFMNYYLNFKELRAFVAGNAPA---KLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKE 388
Cdd:cd17265   94 VFRSEYND--YLFHLFNSDLFKKQIGSFLTAtinQITNGNLNNFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIE 171

                         90
                 ....*....|
gi 928790070 389 RKKGLLQKMF 398
Cdd:cd17265  172 LKKELMQQLI 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: 52.46 E-value: 4.35e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIddeMKNSRTY-YGDVLLNITGASIGRT 102
Cdd:cd17293    1 VKLGELG-EVVTGNTPSKKNPEYYGGDIPFIKPDDLNNGGIILTSEEYLSEEG---AKKARIVpKGSILVTCIGGSIGKV 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 103 AINSI-VEThanlNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIflAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGK 181
Cdd:cd17293   77 GIADReVAF----NQQINAIIPNKSVDPKFLYYQLLSSKFQLQA--IASSTTLPIINKSKFEKIEIPLPPL-EEQKRIVA 149


                 ....*....
gi 928790070 182 FFSKLDRQI 190
Cdd:cd17293  150 KLDKLFALI 158

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: 52.59 E-value: 4.82e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTP-KGGSENYTNKG-IPFLRSQNIRNGKLNLNDlVYIS-KDIDDemkNSRTYY--GDVLLNITG-- 96
Cdd:cd17276    1 KKIGDIA-KTSSGGTPlRSNQEYYFNGGtIPWVKTTDLNNGVIYETE-EKITeKALKE---TSCKLLpkGTVLVAMYGgf 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  97 ASIGRTAINSIVethANLNQHVCIIRLKKEYYY-NFFGQYLLSRKGKRKIFlaqSGGSREGLNF--KEIANLKIFTPTIf 173
Cdd:cd17276   76 GQIGRTGLLGIP---AAINQAICAILPNEKKVNpEFLLRYLNFNRPYWMRV---AASSRKDPNItkDDVRNFPIPLPPL- 148

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 928790070 174 EEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17276  149 DEQRAIVEFLSDVDALIDSLEALIEKLRELKKGLMQQLL 187

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: 52.21 E-value: 5.55e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  19 GEWEEKKLGNLTTKIGSGKT-PKggsenyTNKG-IPFLRSQNIRNGKLNLNDL-VYISKDIDDEMkNSRTY-YGDVLLNI 94
Cdd:cd17284    2 EGWEVKRVGDVCDCIVPGRDkPK------SFDGnIPWITIEDIKGKYISSSKSgLGVSEEEIKEM-NLKVIpKGSVIMSC 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  95 TGaSIGRTAINS--IVethanLNQ--H--VCiirlkKEYYYNFFGQYLLSRKGKRKIFLAqSGGSREGLNFKEIANLKIF 168
Cdd:cd17284   75 VG-DFGIVAIATneLV-----INQqlHafVP-----SKKINPEYLMYLLSLQKKYMEKIA-TGTTIPYLNKTNCESIPIP 142

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 928790070 169 TPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17284  143 LPPI-EEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQQLF 185

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: 52.38 E-value: 5.73e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 234 IKDIFIFENNRRKPITSSLREKGLYPYYGATGIIDYVKDYLFNNEERLLIGEDGAKWgqFETSSFI-------------- 299
Cdd:cd16961    3 LGEIAEIISGKTPSSSSEYWDNGIIPWIRISDINNGGIILTDEKITEEGAEKLKKKI--LPKGDILisrsgtigkvaivk 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 300 ANGQYWVNNHAHVVKSNDH-NLFFMNYYLN---FKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNK 375
Cdd:cd16961   81 ENDKALLNQAVIVIRPKDEvDSEFLYYFLKspfGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDAL 160

                        170
                 ....*....|....*...
gi 928790070 376 MNNQMNRIELLKERKKGL 393
Cdd:cd16961  161 IELLEQKLEKLEQLKQAL 178

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: 52.10 E-value: 6.29e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  81 KNSR-TYYGDVLLNITgASIGRTAINSIvethanlnqHVCI-----------IRLKKEYYYnffgqYLLSRKGKRKIFLA 148
Cdd:cd17283   57 KKSRlVKPGDLILSNS-MSFGRPYILKI---------DGCIhdgwlvfsdlkKKLDKDFLY-----YLLSSITVQLQFSA 121

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 928790070 149 QSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQ 209
Cdd:cd17283  122 QAGGGTKNLNTDIVKNLKIPLPPL-EEQKRIAEILDSLDALIDALEEKLEKLEELKKGLMQ 181

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: 50.62 E-value: 1.40e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 928790070 348 NLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17292   99 NLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYLF 149

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: 50.96 E-value: 1.42e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTKIgSGKTPKGGSENYTNKGIPFLrsqnirNG-----KLNLNdlvyISKDIDDEMKNSRtyYGDVLLNITGAS 98
Cdd:cd17496    1 VKLGDIAEII-MGQSPKGESYNTEGIGIPLL------NGpadfgDGYPI----PKKWTTKPTKLCK--KGDILFCVRGST 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  99 IGRTAInsivethanLNQHVCI------IRLKKEYYYNFFGQYLLSrkgKRKIFLAQSGGSR-EGLNFKEIANLKIFTPT 171
Cdd:cd17496   68 TGRLNI---------ADDEYCIgrgvaaIRPKNGIDTEFLYYLLES---NLDYLLAAATGSTfPNISRDDLLNLKIPLPP 135

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 928790070 172 IfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17496  136 L-EEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTLLPKLL 175

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: 51.05 E-value: 1.46e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTKIGSGKTPKGGSENYTNKG-IPFLRSQNIRNGKLNLNDLVYISKD-IDDemKNSRTYYGDVLLNIT-GASIG 100
Cdd:cd17290    1 KKLKRLAKSIKTGTTPPSENEEYYDGGiIPWFTPGDFNGDLILSESKRKLSELaIED--GEARLFPKNSVLVVGiGATIG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 101 RTAinsIVETHANLNQHVCIIRLKKEyYYNFFGQYLLSrkGKRKIFLAQSGGSREG-LNFKEIANLKIFTPTIfEEQQKI 179
Cdd:cd17290   79 KVG---YSDKESSSNQQITGIIFNKD-INPKFLFYWLS--SSKEELENLANGATLPiLNQEKLKNIKLPVPPL-NEQQKI 151

                        170
                 ....*....|
gi 928790070 180 GKFfskLDRQ 189
Cdd:cd17290  152 VEF---LDKK 158

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: 50.96 E-value: 1.69e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 316 NDHNLFFMNYYL--NFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGL 393
Cdd:cd17496   91 NGIDTEFLYYLLesNLDYLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTL 170


                 ....*
gi 928790070 394 LQKMF 398
Cdd:cd17496  171 LPKLL 175

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: 50.97 E-value: 1.77e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 316 NDHNLFFMNYYLN----FKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKK 391
Cdd:cd17278  102 DKIDKEFLYYLLRsdsfRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKLEQKLEKLRDLLK 181


                 ....*...
gi 928790070 392 GLLQKMFI 399
Cdd:cd17278  182 PLLQSLFT 189

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) TRD2-CR2, and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) TRD2-CR2; The recognition sequences of Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341176 [Multi-domain] Cd Length: 184 Bit Score: 50.56 E-value: 2.06e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 315 SNDHNLFFMNYYLNFK--ELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKG 392
Cdd:cd17287   98 NDGINPDFLFYYLQSSyeELRDLSNGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAKIDALEQKLELLQELKKS 177


                 ....*.
gi 928790070 393 LLQKMF 398
Cdd:cd17287  178 LMQQLF 183

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: 50.48 E-value: 2.53e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 928790070 348 NLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17273  136 TFKKIEIPLPPLEEQKKIAAILSKLDELIELLEKENEKLKELRDGLLPKLF 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: 50.26 E-value: 3.11e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGSGKTPK-GGSENYTNKGIPFLRSQNIRNGKLnLNDLVYISkdiDDEMKNSRTYY---GDVLLNITG 96
Cdd:cd17501    5 WEVGTILDLCYKTQSGGTPSrKNPEYWDGGIIPWLKTGELRDNII-LDTEEKIT---EEGLKNSSAKLfpkGTVLVAMYG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  97 ASIGRTAINSIvetHANLNQHVCIIRLKKEYYYNFFGQYLLSrkgKRKIFLAQSGGS-REGLNFKEIANLKIFTPT---- 171
Cdd:cd17501   81 ATAGKLGILAK---EATTNQACCALIPKEEYSPFFLYLYLLN---SRDYLANLASGSaQQNISQQIIKNTKVLIPPedll 154


                 ....*...
gi 928790070 172 -IFEEQQK 178
Cdd:cd17501  155 eIFNKLVE 162

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: 49.67 E-value: 5.04e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  46 YTNKGIPFLRSQNIRNGKLNLNDL-VYISkdiDDEMKNSRTYY----GDVLLNITGASIGRTAInsIVETHANLNQHVCI 120
Cdd:cd17518   20 FTDEGIKLLNVTNIVNGSLDLDKTdRYIS---TEEYNGKYKHFlideGDILIASSGNSWGKVAI--VEKDHLPLMLNTST 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 928790070 121 IRLK---KEYYYNFFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQI 190
Cdd:cd17518   95 IRFKfidGLLDNNFLKYFLNSDYFKEQLDLLITGGAQPNFGPSHLKKIKIPLPPL-EEQKRIAEILDDADDAI 166

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: 49.43 E-value: 5.16e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLNlNDLVYISKDiddEMKNSRTYY---GDVLLnITGASIG 100
Cdd:cd17285    1 KKLGDLVEKIVGGGTPSKSNPEYWNGDIPWASVKDLKGKYLT-STEDKITEE---GLKNSSSNLipkGTVII-ATRMGLG 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 101 RTAINSIvetHANLNQHVCIIRLKKEYYYNFFGQYLLSrkgKRKIFLAQSGGSR-EGLNFKEIANLKIFTPTIfEEQQKI 179
Cdd:cd17285   76 KVAINKI---DVAINQDLKALFPKDELDPEYLLYWFLS---IEETIESLGTGTTvKGITLEDLKSLKIPLPPL-EEQKRI 148

                        170       180       190
                 ....*....|....*....|....*....|...
gi 928790070 180 GKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17285  149 VAILDELDELIDKLEAKLEKLKQLKKGLMQSLL 181

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli 541-15 S subunit (S.Eco15ORF14057P) TRD1-CR1 and Desulfotignum phosphitoxidans S subunit (S.Dph13687ORF2110P) TRD2-CR2; The recognition sequences of Escherichia coli 541-15 S subunit (S.Eco15ORF14057P) and Desulfotignum phosphitoxidans S subunit (S.Dph13687ORF2110P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341206 [Multi-domain] Cd Length: 190 Bit Score: 49.54 E-value: 5.77e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 307 NNHAHVVKSNDHNLFFMNYYLN----FKELRAFVAGNAP-AKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMN 381
Cdd:cd17525   95 NNILRIRFDDIVLPYFINYYLNspdgKKQLESIASGTTSvAAIYQKDLKKLKLPLPPLDEQREIVSFLSELDAKIDQLEQ 174

                         90
                 ....*....|....*.
gi 928790070 382 RIELLKERKKGLLQKM 397
Cdd:cd17525  175 KLEKLLQIKKALMQQL 190

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: 48.55 E-value: 6.60e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 234 IKDIFIFEnnRRKPITSSLREKGLYPYYGATGIIDYVKDYLFNNEErLLIGEDGAkWGQFetssFIANGQYWVNNHA-HV 312
Cdd:cd17267    3 LGDVIELQ--YGKDLPKSRRIPGPYPVYGSNGIVGYHNEALVKGPG-IVVGRKGS-IGKV----HYSEEDFWPIDTTlYV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 313 VKSNDHNLFFMNYYLNFKELRAFVAGNA-PAkLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKK 391
Cdd:cd17267   75 KDFKGNDPRFLYYLLKTLDLERLNSGSAvPG-LNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELAD 153


                 ....*
gi 928790070 392 GLLQK 396
Cdd:cd17267  154 ALLPK 158

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: 48.75 E-value: 8.72e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTkIGSGKTPKGGSENYTNKG-IPFLRSQNIRNGKLNLNDLvYISKDiddEMKNSRTYY---GDVLLNITgASI 99
Cdd:cd17296    1 KKLGEICS-IQSGGTPSRSKKEYWNNGtIPWVKISDCKNKYVDETEE-FITEE---GLNNSSAKLlkkGTILIAIF-ATI 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 100 GRTAINSIvetHANLNQHVCIIRLKKEYYYNFFGQYLLsrKGKRKIFLAQS-GGSREGLNFKEIANLKIFTPTIfEEQQK 178
Cdd:cd17296   75 GKVGILKI---EATTNQAIAGIKPKNKSINPKYLYYYL--KSLYEKFLSLGrGVAQNNINLSILKNLKIPLPPL-EEQQR 148

                        170
                 ....*....|..
gi 928790070 179 IGKFFSKLDRQI 190
Cdd:cd17296  149 IVAILDKFEKLI 160

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: 48.63 E-value: 1.33e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 308 NHAHVVKSNDHNL--FFMNYYLNFKELRAFVAGNApaKLThANLCNINLK--------IPCLTEQDKVSALLKSIDNKMN 377
Cdd:cd17253   96 NHLFRVRPKDDLLlpEFLSYWLNSAYGRGYFLRAA--KQT-TNLASINSTklkalpvpLPPLEEQRRIVERLDELLALID 172

                         90       100
                 ....*....|....*....|.
gi 928790070 378 NQMNRIELLKERKKGLLQKMF 398
Cdd:cd17253  173 ALEASLAKLEELLKALRQALL 193

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: 48.04 E-value: 1.81e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 321 FFMNYYLNFKELRAF--VAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17271  106 FLFYWYKKYGNYLGFkyAQGTKQQSYTADIVKKLPILLPTLKEQKKIANFLSDIDELIATLEKKIEKLKKIKKGLMQKLL 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: 47.92 E-value: 1.98e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 313 VKSNDHNLFFMNYYLNFKELRAFVAGNA-----PAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLK 387
Cdd:cd17522  101 PNKNIVDPKYLYYLLKSDRFRNQFRSIAkkavnQASINQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEKLK 180

                         90
                 ....*....|
gi 928790070 388 ERKKGLLQKM 397
Cdd:cd17522  181 ELKKGLFQKL 190

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: 47.14 E-value: 3.50e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 928790070 322 FMNYYL--NFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKM 397
Cdd:cd17247  113 YLHYYLesQYDELRRIGSGGGQGALNCGILKAFPIPLPPLDEQREIVAELEALLAKIDLLEEKIARLIELLKELRQAL 190

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: 46.76 E-value: 3.87e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 316 NDHNLFFMNYYLNFKE--LRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGL 393
Cdd:cd17245   90 KDIDNLFLYYYLKYNKpeLEKLGTGSTFKAINKKDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKLDELKKGL 169


                 ....*
gi 928790070 394 LQKMF 398
Cdd:cd17245  170 MQELF 174

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: 46.84 E-value: 4.25e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTkIGSGKTPKGGSENYTNKGIPFLRsqnirnGKLNLNDLVYISKDIDDEMKNSRTYYGDVLLNITgASIGRTA 103
Cdd:cd17499    1 VRLGDVAE-IIMGQSPEGKSYNTNKEGLPFYQ------GKKEFGDKYIKEPNTWTTSPTKIAEKNDILMSVR-APVGDVN 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 104 INsivethanlNQHVCI------IRLKKEYYYNFFGQYLLSRKgkrKIFLAQSGGS-REGLNFKEIANLKIFTPTIfEEQ 176
Cdd:cd17499   73 IT---------TRKICIgrglaaIRAKKNIDKKYLFYFLLSNK---DYFKGKSGGStFKSINKNQIKNIKIPLPPL-EEQ 139

                        170
                 ....*....|....
gi 928790070 177 QKIGKFFSKLDRQI 190
Cdd:cd17499  140 KRIVSELDKLFKLI 153

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: 46.16 E-value: 6.67e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 316 NDHNLFFMNY--YLNFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGL 393
Cdd:cd17270  100 ININKKFFAYqlKLKFEIEKEKAPGGTIKTITKEELSKFEIPIPSLEEQKEIVNILDKFDELITELQLRKKQLEYYKKAL 179


                 ....
gi 928790070 394 LQKM 397
Cdd:cd17270  180 LSFM 183

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: 46.33 E-value: 6.97e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 928790070 322 FMNYYL--NFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17294  110 FLYYNLssRYEELRSLSGGGGRGGLNLKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLPALLELRQKQYEYLR 188

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: 45.99 E-value: 7.84e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 313 VKSNDHNLFFMNYYLNFKELRAFVAGNApaKLThANLCNINLK--------IPCLTEQDKVSALLKSIDNKMNNQMNRIE 384
Cdd:cd17517  103 LDKKKILPEFLYYYLNSPLGRKQIEKIA--KSA-AGQANINQKdlkklpipLPPLEEQKEIVEILESLDSKIDLLEKKLE 179

                         90
                 ....*....|...
gi 928790070 385 LLKERKKGLLQKM 397
Cdd:cd17517  180 KLEQLFKSLMQSL 192

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

Pssm-ID: 341150 [Multi-domain] Cd Length: 191 Bit Score: 45.99 E-value: 8.52e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGSGKTPKGGSEnytNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDemknsRTYY----GDVLlnITG 96
Cdd:cd17261    1 WEWVRLGDLIEGIRNGWSPKPPDD---ETGWPVLKLSAVTSGKFDPSENKYLPESLEP-----ASEYwlkpGDLL--ISR 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  97 AS----IGRTAInsivethANLNQHVCI-------IRLKKEYYY-NFFGQYLLSRKGKRKIFLAQSG--GSREGLNFKEI 162
Cdd:cd17261   71 ANtselVGRAAL-------VDGDPDNLIypdklirLRVNEELLLpEYLALALNSPSARRQIESRATGtaGSMPKISQSDL 143

                        170       180
                 ....*....|....*....|....*...
gi 928790070 163 ANLKIFTPTIfEEQQKIGKFFSKLDRQI 190
Cdd:cd17261  144 KSLPIPLPPL-AEQKRIVARVDELLALI 170

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: 45.71 E-value: 1.04e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 314 KSNDHNLFFMNYYLN---FK-ELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKER 389
Cdd:cd17289  103 NIKDINSKFLYYWFQssiFKnQINSITIGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEEL 182


                 ....*....
gi 928790070 390 KKGLLQKMF 398
Cdd:cd17289  183 AKTLFQYWF 191

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: 45.55 E-value: 1.31e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 928790070 348 NLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKM 397
Cdd:cd17521  138 KLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLKELLQSL 187

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: 45.09 E-value: 1.35e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 296 SSFIANGQYWVNNHAHVVKSND--HNLFFMNYYLNFKE-----LRAFVAGNAPAkLTHANLCNINLKIPCLTEQDKVSAL 368
Cdd:cd17258   65 VSIILSEEACLSSHVAGFNSKEgiSDNKFIKYLFNSKKiknrlMSYGASSTQPA-LNLSRLLKIKFPNPPLEEQQKIGKI 143

                         90       100       110
                 ....*....|....*....|....*....|
gi 928790070 369 LKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17258  144 LSTWDRAIELTEQKLELLQQQKKGLMQQLF 173

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: 45.20 E-value: 1.71e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 928790070 349 LCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQK 396
Cdd:cd17259  142 IKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKGLMQS 189

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: 44.75 E-value: 2.19e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTkIGSGKTPKGGSENYTNKGIPFlrsqnirngklnlndlvyIS-KDiddeMKnsRTYYGDVLLNITGASIGRT 102
Cdd:cd17249    1 VRLGDLGK-FLSGGTPSKSNPEYWGGDIPW------------------VSpKD----MK--SDYISDSEDHITELAVEES 55

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 103 AIN----------------------SIVETHANLNQHVCIIRLKKEYYYNFFGQYLlsrKGKRKIFLAQ---SGGSREGL 157
Cdd:cd17249   56 GTKlvpagsvlivvrgmilahtfpvAITTRPVAFNQDIKALIPKEGIDPEFLLYAL---KANEDRILSLvdkAGHGTGSL 132

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 928790070 158 NFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKI 211
Cdd:cd17249  133 DTDDLKNLPIPLPPL-EEQRRIAAILDALDALIDLLERKLAKLEELLKALMQAL 185

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.HinAWORF1578P TRD2-CR2; Haemophilus influenzae RdAW S subunit (S.HinAWORF1578P) recognizes 5'... CTANNNNNGTTY ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341197 [Multi-domain] Cd Length: 184 Bit Score: 44.46 E-value: 2.89e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 312 VVKSNDHNLFFMNYYL--NFKELRAFvAGNAPAK--LTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLK 387
Cdd:cd17516   95 IVNKNKFDPDFVYYLLknNSKYLKSI-AGGSTATpiINKSTFSNIEIPLPPLPEQKKIAAILSSLDDKIENNRRINKTLE 173

                         90
                 ....*....|.
gi 928790070 388 ERKKGLLQKMF 398
Cdd:cd17516  174 EMAQALFKEWF 184

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: 43.69 E-value: 5.36e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLNLNDLVYISKDIDDEMKNSRTYYGDVLLNITGASIGRTA 103
Cdd:cd17516    1 VKIGDLG-KVVTGKTPSTKNPEYFGGDIPFITPSDMKGGKYIIKTERRLSSKGLEKVKNKLIPANSICVTCIGSDMGKVA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 104 INSiVETHANlnQHV-CIIRLKKEYYYNFFgqYLLSRKGKRKIFLAQSGGSR-EGLNFKEIANLKIFTPTIfEEQQKIGK 181
Cdd:cd17516   80 ITK-EPSVTN--QQInSIIVNKNKFDPDFV--YYLLKNNSKYLKSIAGGSTAtPIINKSTFSNIEIPLPPL-PEQKKIAA 153


                 ....*....
gi 928790070 182 FFSKLDRQI 190
Cdd:cd17516  154 ILSSLDDKI 162

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: 42.06 E-value: 1.51e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  44 ENYTNKGIPFLRSQNIRNGKLNLNdlvYISKDIDDEmknsrtYY---GDVL------LnitGASI--GRTAInsivetha 112
Cdd:cd17254   18 SEWSDSGLPIIRIQNLNGGNAPFN---YYSGLLDEK------YYvekGDLLfswsasF---GPFIwnGGKAI-------- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 113 nLNQHVCIIRLKKEYYYNFFGQYLLSRKGKrkiFLAQSGGS------REGLNfkeiaNLKIFTPTIfEEQQKIGKFFSKL 186
Cdd:cd17254   78 -LNQHIFKVVPDEEIDKDYLYYLLKALTEE---IESQAHGStmvhitKGDLE-----NIKVPLPPL-EEQKRIAAILDEL 147

                        170       180
                 ....*....|....*....|....*.
gi 928790070 187 DRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17254  148 DALIDALEEQLKKLEELRKALLQSLL 173

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: 42.04 E-value: 1.54e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 928790070 351 NINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17515  134 NIEIPLPPLAEQKRIVAKLDKLDKLIEKLEKALEKLEELKKALMQKLL 181

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: 42.08 E-value: 1.74e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 928790070 351 NINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQ 395
Cdd:cd17283  137 NLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLEELKKGLMQ 181

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: 42.06 E-value: 1.77e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 928790070 351 NINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17254  126 NIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLEELRKALLQSLL 173

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: 41.84 E-value: 2.54e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  21 WEEKKLGNLTTKIGSGKTPKGGSenyTNKGIPFLRSQNIRNGKLNLNDLVYISkdIDDEMKNS-RTYYGDVLL------- 92
Cdd:cd17523    1 WEWVRLGDLIPEFQNGLSKRGGS---DGEPIIVLRLADIKNNKISFENLRRIK--LTEKEIEKySLSKGDLLIirvngsp 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  93 NITGASIGRTAINSIVethanLNQHVCIIRLKKEYYYNFFGQYLL-SRKGKRKI---FLAQSGgsREGLNFKEIANLKIF 168
Cdd:cd17523   76 DLVGRFILFKGYEDVA-----YCDHFIRMRLDQEKIDPEFLSYIFnSPLIRRKIernFVTSAG--QKTVNQGHIKSLPIP 148

                        170
                 ....*....|.
gi 928790070 169 TPTIfEEQQKI 179
Cdd:cd17523  149 LPPL-KEQKKI 158

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: 41.67 E-value: 2.77e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 312 VVKSNDHNLFFMnYYL--NFKELRAFV--AGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLK 387
Cdd:cd17249   97 IPKEGIDPEFLL-YALkaNEDRILSLVdkAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLE 175

                         90
                 ....*....|
gi 928790070 388 ERKKGLLQKM 397
Cdd:cd17249  176 ELLKALMQAL 185

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: 41.30 E-value: 3.00e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  98 SIGRTAINSIVETHanlNQHVCIIRLKK-----EYYYNFFGQYLLSRKGKRkiflaQSGGSreGLNFKEIANLKIFTPTI 172
Cdd:cd17244   74 TIGRVAIAGKDLYT---NEAIAHFIPKDkkidtEYLYYYLKSFDYSSLGST-----ASKGK--TLNSKKIKEIPIPLPPL 143

                         90
                 ....*....|....*...
gi 928790070 173 fEEQQKIGKFFSKLDRQI 190
Cdd:cd17244  144 -EEQKRIAPILDKIDALI 160

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: 41.38 E-value: 3.08e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTTkIGSGKTPKGGSENYTNKGIPFLRSqNIRNGKLNLNDLVYISKDIddemKNSRTyyGDVLLNITgASIGRTa 103
Cdd:cd17497    1 KKLKYVAD-IIMGQSPPSSTYNTEGIGLPFLQG-KAEFGKLYPTPRKWCSAPK----KIAEK--GDILLSVR-APVGPT- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 104 insivethaNL-NQHVCI------IRLKKEYYYNFFGQYL------LSRKGKRKIFLAQSGgsreglnfKEIANLKIFTP 170
Cdd:cd17497   71 ---------NIaDQEYCIgrglaaIRPKKGLDKKYLLYYLksieneLSSLGTGSTFKAISK--------EDLENLLIPLP 133

                        170       180
                 ....*....|....*....|....
gi 928790070 171 TiFEEQQKIGKF----FSKLDRQI 190
Cdd:cd17497  134 P-LAEQKRIAAFldelTAKIDQLI 156

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: 41.08 E-value: 3.96e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 306 VNNHAHVVKSN---DHNLFFmnYYLNFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNR 382
Cdd:cd17250   92 IDNNVMGLIPNegiDSEYLY--YWLKKVDLYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQA 169

                         90
                 ....*....|....*.
gi 928790070 383 IELLKERKKGLLQKMF 398
Cdd:cd17250  170 LEAAKEQLKGLRQSLL 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: 40.55 E-value: 5.23e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 928790070 161 EIANLKIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIFT 213
Cdd:cd17274  120 EYSKFKIPLPPL-EEQNKIVRILDKFDELIAELEAKLELLKKQKKYYLQKLFT 171

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: 40.22 E-value: 5.36e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  71 YISKDIDDEMKNSRTY--YGDVLLNITGaSIGRTAI----------NSIVETHANLNQhvciirLKKEYYYNFFgqylls 138
Cdd:cd17292   13 YISRELFEEYKSKYSYpkKGDILISASG-TIGRTVIydgedayfqdSNIVWLDNDESK------VLNKFLYYFY------ 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 928790070 139 rkgKRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17292   80 ---QIIKWKKTEGSTIKRLYNDNLLNTKIPVPSL-DEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYLF 149

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: 40.61 E-value: 6.29e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 928790070 353 NLKIPC--LTEQDKVSALL----KSIDNKMNNQMNRIELLKERKKGL 393
Cdd:cd17280  136 SLRIPVppLEEQKQIAAFLdkktAKIDSLIEKKERLIELLKERRQAL 182

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: 40.67 E-value: 6.46e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 928790070 319 NLFFMNYYLNFkelrafVAGNA-PAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQK 396
Cdd:cd17512  123 SERFKNYIESI------ARGNAnQASITLGDIKKFKFLLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQALYQE 195

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: 40.19 E-value: 6.65e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 928790070 117 HVCIIRLKKEYYYNFFGQYLLSRKgkRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSKLD 187
Cdd:cd17291   73 CCYILSSKNELVNKFLYYFLKNKQ--EEIYSLQRGAGQPHIYKKDIEKLKIPIPPL-EEQQKIVEILDKFT 140

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: 40.26 E-value: 8.04e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 312 VVKSNDHNLFFMNYYLNFKelRAF---VAGNA---PaKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIEL 385
Cdd:cd17276   98 LPNEKKVNPEFLLRYLNFN--RPYwmrVAASSrkdP-NITKDDVRNFPIPLPPLDEQRAIVEFLSDVDALIDSLEALIEK 174

                         90
                 ....*....|...
gi 928790070 386 LKERKKGLLQKMF 398
Cdd:cd17276  175 LRELKKGLMQQLL 187

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: 39.97 E-value: 9.22e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKGGSENYTNKGIPFLRSQNIRNGKLNLNDlVYISkDIDDEMKNsrtyyGDVLLNITgASIGRta 103
Cdd:cd17498    1 VKLGEIA-EITMGQSPKSEFYNEDGIGLPFLQGNRTFGDKYPYID-TYTT-DIKKIAKK-----GDILMSVR-APVGD-- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 104 INsIVETHANLNQHVCIIRLKKeyYYNFFGQYLLsrKGKRKIFLAQSGGSREG-LNFKEIANLKIFTPTIfEEQQKIGKF 182
Cdd:cd17498   70 LN-IANKDICIGRGLCSIRMKN--GNNSFLYYLL--KNNIKNLINKSSGTVFGsINKDDIENLEVDIPED-EEQKRIANI 143


                 ....*...
gi 928790070 183 FSKLDRQI 190
Cdd:cd17498  144 LSKIDDKI 151

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: 39.82 E-value: 1.04e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  20 EWEEKKLGNLTtKIGSGKTPKGGSENYTNKGIPF--------LRSQNIRNGKLNLNDLvyiskdiddEMKNS-------R 84
Cdd:cd17248    3 HWEVVPLTDVA-KLESGHTPSRSRPEYWNGCIPWisladvkqLRGDYIYETKEKISEL---------GIANSsarllpaG 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  85 TyygdVLLNITgASIGRTAI------NSivethanlnQH----VCIIRLKKEYYYNFFgqyllsrKGKRKIFLAQSGGSR 154
Cdd:cd17248   73 T----VVLSRT-ASVGKSAImgrpmaTS---------QDfanwVCGPELDPEYLLYVL-------RAMKPEFERLAMGST 131

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 928790070 155 EG-LNFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQIELEEQKLELLQQQKKGYMQKIFTQELRFK 219
Cdd:cd17248  132 HKtIYMPDFKALRIALPPL-EEQRKIVDRLEALDAKIDALERKLERLIELLKELRQALLTAAVTGK 196

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: 39.38 E-value: 1.43e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 928790070 351 NINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQK 396
Cdd:cd17244  135 EIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDELLPKLMSG 180

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: 39.03 E-value: 1.43e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 232 KFIKDIFIFenNRRKPITSS-LREKGLYPYYGATGIIDYVKDYLFNNEERLLIGEDGAkwgqfeTSSFIA--NGQYWVNN 308
Cdd:cd17291    1 KKLGEIAEI--KKGKQITKKeLIENGKYPVIAGGIEPSGYHNEYNREGNTITISASGA------SAGYVNywKEPFWASD 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 309 HAHVVKSNDHNL-FFMNYYLNFKE--LRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMnrIEL 385
Cdd:cd17291   73 CCYILSSKNELVnKFLYYFLKNKQeeIYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFTELTAELP--AEL 150


                 ....*.
gi 928790070 386 LKERKK 391
Cdd:cd17291  151 EARKKQ 156

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: 39.06 E-value: 1.73e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 313 VKSNDHNLFFMNYYLNFKELRAFV-------AGNAPaKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIEL 385
Cdd:cd17261  101 VNEELLLPEYLALALNSPSARRQIesratgtAGSMP-KISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDRLEAQLAA 179

                         90
                 ....*....|
gi 928790070 386 LKERKKGLLQ 395
Cdd:cd17261  180 ALQLLDRLRQ 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: 38.66 E-value: 1.75e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 113 NLNQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIflaqSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQIEL 192
Cdd:cd17255   73 SVTNVCGVLKVKNKNINNKFLYYALNLIAKKYV----SFDGNPKLMNNVMAKIKIPLPPL-EEQEKIANILDKLDELINL 147

                         90
                 ....*....|....*....
gi 928790070 193 EEQKLELLQQQKKGYMQKI 211
Cdd:cd17255  148 LIAKLKKLIELRKKQLEYY 166

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: 38.58 E-value: 1.79e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 928790070 120 IIRLKKEYYYNFFGqYLLSRKGKRKIflaQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQI 190
Cdd:cd17266   75 VVTPKKENNIKFLY-YLLKSLNLNQY---ATGSAQPLITVSKLKKLKIPLPPL-EEQKKIAAILDSLDAKI 140

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: 38.99 E-value: 1.87e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 322 FMNYYLNFKELRAFVAGNApaklTHA-NLCNIN------LKIPC--LTEQDKVSALLKSIDNKMNNQMNRIELLKERKKG 392
Cdd:cd17524  109 YLNYFLNSPYGRKQIKSVA----TQGvGQANINatklkaIPIPLppLEEQKEIVEKLDELDALIDRLEALLEEAEELLES 184


                 ....
gi 928790070 393 LLQK 396
Cdd:cd17524  185 LLQS 188

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: 39.12 E-value: 1.95e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 309 HAHVVKSNDHNLFFMnYYLNFKE--LRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELL 386
Cdd:cd17284   95 HAFVPSKKINPEYLM-YLLSLQKkyMEKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKL 173

                         90
                 ....*....|..
gi 928790070 387 KERKKGLLQKMF 398
Cdd:cd17284  174 QQLKKGLMQQLF 185

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: 38.70 E-value: 2.71e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  24 KKLGNLTtKIGSGKTPKGGSENYTNKGIPFlrsqnIRNGKLNLNDLVYIS---KDIDDE-MKNSRTYY---GDVLLNiTG 96
Cdd:cd17279    1 VPLKRIF-RIVNGSTPKSGEEDYWDGDIPW-----VTPADLSKLDGKYISssqRKITEAgLESCGTSLvpaGSIILS-TR 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  97 ASIGRTAINsivETHANLNQH----VCIIRLKKEYYYnffgqYLLSRKGKRKIFLAQsggsreGLNFKEI-----ANLKI 167
Cdd:cd17279   74 APIGYVAIA---TVELCTNQGckalVPNSDVDSRFLY-----YLLLAAKEELNSLGR------GTTFLELstdelANFKI 139

                        170       180
                 ....*....|....*....|....*..
gi 928790070 168 FTPTIfEEQQKIGKFF----SKLDRQI 190
Cdd:cd17279  140 PLPPL-SEQRAIADFLdretAKIDALI 165

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: 38.42 E-value: 3.11e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 322 FMNYYL--NFKELRAFVAGNAPAKLTHANLCNINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMFI 399
Cdd:cd17500  107 FVYYSLktQYEELVNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLDDKIELNNRQNETLEAMAETLFKEWFV 186

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoEI TRD1-CR1, S.EcoJA17PI TRD1-CR1, S.EcoJA23PI TRD1-CR1, and S.StyLTIII TRD1-CR1; Escherichia coli A58 S subunit (S.EcoEI) recognizes 5'... GAGNNNNNNNATGC ... 3', Escherichia coli UCD_JA17_pb S subunit (S.EcoJA17PI) and Escherichia coli UCD_JA23_pb S subunit (S.EcoJA23PI) recognize 5'... GAGNNNNNNNGTCA ... 3', and Salmonella typhimurium LT7 S subunit (S.StyLTIII) recognizes 5'... GAGNNNNNNRTAYG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example: S.EcoEI TRD1 and S.StyLTIII TRD1 recognize GAG/CTC, S.EcoEI TRD2 recognizes GCAT/ATGC, and S.StyLTIII TRD2 recognizes CRTAY/RTAYG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferas RM.PpiI and Porphyromonas macacae COT-192 OH2631 RM.Pma2631ORF8845P, as well as type I DNA methyltransferases such as Chlorobium limicola M.Cli245ORF128P. RM.PpiI recognizes the sequence 5' ... GAACNNNNNCTC ... 3'.

Pssm-ID: 341149 [Multi-domain] Cd Length: 165 Bit Score: 37.80 E-value: 3.45e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 928790070 351 NINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17260  118 NYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165

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

Pssm-ID: 341201 [Multi-domain] Cd Length: 180 Bit Score: 38.21 E-value: 3.86e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  47 TNKGIPFLRSQNIRNGKLNLNDLVYIskdiDDEMKNSRTYY---GDVLLNITGASIgRTAI----NSIVETHANlnqhVC 119
Cdd:cd17520   21 KPGSISVLNISNIEDGEIDYSGMDTI----EEEERKVKRYElrdGDLVLSCRGTAI-KVAVfreqKKIVIASAN----II 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 928790070 120 IIRLKKEYYYNFFGQYLLSRKGKRKIFLAQSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSK 185
Cdd:cd17520   92 VIRPNEKVLSEYLKIFLESPVGTALIKSFQRGTTVMNINHSDIAEMEIPLLPL-EEQKKIAEEYRK 156

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: 37.41 E-value: 6.37e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 115 NQHVCIIRLKKEYYYNFFGQYLLSRKGKRKIflaqSGGSREGLNFKEIANLKIFTPTIfEEQQKIGKFFSKLDRQIELEE 194
Cdd:cd17262   81 NNHAHVLKGKNGISTEFLYYYLNSIDISPYV----TGAAQPKLNQANLNSIPIPLPPL-EEQKKIVAILDKLDALIDLLE 155

                         90
                 ....*....|....*..
gi 928790070 195 QKLELLQQQKKGYMQKI 211
Cdd:cd17262  156 EELEKLIELKKALLQKL 172

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: 37.23 E-value: 7.99e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070  25 KLGNLTT-KIGSGKTpkGGSENYTNKGIPFLRSQNIR---NGKLNLNDLVYISKDIDDEMKNSRTYYGDVLLNITGASIg 100
Cdd:cd17250    2 RLGDVCDfKAGSGFP--EKYQGKEDGEYPFYKVGDMNnsgNEKYLSTAENYISEEIVKELKAKLFPKGTIIFAKIGEAI- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928790070 101 RTAINSIVETHANLNQHVCIIRLKKEYYYNFFgqYLLSRKGKRKIFlaQSGGSREGLNFKEIANLKIFTPTIfEEQQKIG 180
Cdd:cd17250   79 KLNRRAILSKDSCIDNNVMGLIPNEGIDSEYL--YYWLKKVDLYKY--SQATTVPSIRKSTLESIPIPLPPL-EEQKRIA 153

                        170       180       190
                 ....*....|....*....|....*....|..
gi 928790070 181 KFFSKLDRQIELEEQKLELLQQQKKGYMQKIF 212
Cdd:cd17250  154 AKLDELFEKLDKLKQALEAAKEQLKGLRQSLL 185

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: 36.89 E-value: 9.47e-03

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                 ....*....|....*....|....*....|....*....|....*...
gi 928790070 351 NINLKIPCLTEQDKVSALLKSIDNKMNNQMNRIELLKERKKGLLQKMF 398
Cdd:cd17498  126 NLEVDIPEDEEQKRIANILSKIDDKIEINNQINKNLEELAQAIFKHWF 173