NCBI Conserved Domain Search

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

Pssm-ID: 341140 [Multi-domain] Cd Length: 185 Bit Score: 349.49 E-value: 1.60e-121

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 201 WKEKPLSFYGTIICGKTPSKKVQSYFNGDIPFIKIPDMHGNIFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIATVGLV 280
Cdd:cd17251    1 WEVKTLKDFGKIITGKTPSTKNKEYYGGDIPFIKIPDMHGNVFITKTEDYLSEEGANSQKNKTLPKNSICVSCIATVGLV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 281 SLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGTATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLF 360
Cdd:cd17251   81 SITTEESQTNQQINSIIPKKENYRYYLYFALKSLKELLEALGSGGSTTLNLNKGKFSKIKILLPSEDLLKKFHKIVSPLF 160

                        170       180
                 ....*....|....*....|....*
gi 814724563 361 DKIFFNQSQIHTLEKLRDTLLPKLM 385
Cdd:cd17251  161 DKILNNQKENQKLSQLRDTLLPKLM 185

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: 346.58 E-value: 2.63e-120

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCEQVLTGGTPLTKKSDYYLNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGQGDTAGRV 88
Cdd:cd17500    1 KLEDICIKITSGGTPSRSNKEYYNGGNIPWLKTKELNFKRIYDTEEKITEEGLKNSSAKLIPENTVIIAMYGAGKTAGRV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  89 AINKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLD 168
Cdd:cd17500   81 AINKIPLTTNQACCNLIIDNKKADYRFVYYSLKTQYEELVNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLD 160

                        170       180
                 ....*....|....*....|....*.
gi 814724563 169 DKIDLLHRQNKTLEAMAETLFRQWFV 194
Cdd:cd17500  161 DKIELNNRQNETLEAMAETLFKEWFV 186

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: 252.41 E-value: 2.73e-83

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEqVLTGGTPLTKKSDYYLNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGQGDT 84
Cdd:cd17294    1 WEWKTLGEIAK-IFSGGTPSTSNPEYWDGGTIPWLSSGEVNFKEIYETEKRITEEGLKNSSAKWIPKNSVLIALAGQGKT 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  85 AGRVAINKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASIL 164
Cdd:cd17294   80 RGTVAILKIPLTTNQSLAAIEPDEEIANSRFLYYNLSSRYEELRSLSGGGGRGGLNLKIIKSLPIPLPPLEEQKKIVAIL 159

                        170       180
                 ....*....|....*....|....*....
gi 814724563 165 SSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17294  160 DKFDALINDLKEGLPALLELRQKQYEYLR 188

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: 226.93 E-value: 2.23e-73

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGQgdTAGR 87
Cdd:cd17515    1 VKLGDIGK-WGSGGTPSRSNPEYY-GGGIPWIKSGELNDGYITSTEEKITEEGLKNSSAKLFPKGSVLIAMYGA--TAGK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKIPLATNQACCNLVIDNKIaDYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSL 167
Cdd:cd17515   77 VGILGIDAATNQAICAILPNEEI-DNEFLFYFLKSQKEYLISLGKGGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKL 155

                        170       180
                 ....*....|....*....|....*.
gi 814724563 168 DDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17515  156 DKLIEKLEKALEKLEELKKALMQKLL 181

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

Pssm-ID: 341176 [Multi-domain] Cd Length: 184 Bit Score: 221.98 E-value: 1.81e-71

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGQGDTAGR 87
Cdd:cd17287    1 KKLGEIAK-VSSGGTPSRSNPEYW-NGGIPWVKTGEVNFNEITDTEEKITEEGLKNSSAKLFPKGTLLMAMYGQGKTRGR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKIPLATNQACCNLvIDNKIADYHFIYYLLKNSYFElvLRK--TGSAQPNLNTKLLKDFDILLPPLPEQFTIASILS 165
Cdd:cd17287   79 VAILGIEAATNQACAAI-LPNDGINPDFLFYYLQSSYEE--LRDlsNGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLS 155

                        170       180
                 ....*....|....*....|....*...
gi 814724563 166 SLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17287  156 AIDAKIDALEQKLELLQELKKSLMQQLF 183

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: 202.39 E-value: 7.01e-64

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 210 GTIICGKTPSKKVQSYFNGDIPFIKIPDMHGNIFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIA-TVGLVSLNAKESQ 288
Cdd:cd17516    7 GKVVTGKTPSTKNPEYFGGDIPFITPSDMKGGKYIIKTERRLSSKGLEKVKNKLIPANSICVTCIGsDMGKVAITKEPSV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 289 TNQQINSIVPNENYYR-YYLYLTMRSSYDLLHSMASGGTATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFNQ 367
Cdd:cd17516   87 TNQQINSIIVNKNKFDpDFVYYLLKNNSKYLKSIAGGSTATPIINKSTFSNIEIPLPPLPEQKKIAAILSSLDDKIENNR 166

                        170
                 ....*....|....*...
gi 814724563 368 SQIHTLEKLRDTLLPKLM 385
Cdd:cd17516  167 RINKTLEEMAQALFKEWF 184

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: 183.53 E-value: 2.14e-56

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEQVLTGGTPLTKKSDYYLNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGQgdT 84
Cdd:cd17501    5 WEVGTILDLCYKTQSGGTPSRKNPEYWDGGIIPWLKTGELRDNIILDTEEKITEEGLKNSSAKLFPKGTVLVAMYGA--T 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  85 AGRVAINKIPLATNQACCNLVIDNKIaDYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPP--LPEQFTiaS 162
Cdd:cd17501   83 AGKLGILAKEATTNQACCALIPKEEY-SPFFLYLYLLNSRDYLANLASGSAQQNISQQIIKNTKVLIPPedLLEIFN--K 159

                        170       180
                 ....*....|....*....|....*.
gi 814724563 163 ILSSLDDKIDLLHRQNKTLEAMAETL 188
Cdd:cd17501  160 LVEPLFDKIINNLKENQKLAKLRDTL 185

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: 182.36 E-value: 5.23e-56

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   6 KECKLGDVCEQVLTGGTPLTKKSDYYlNGKIPWLK----TKEVNFcrINKTENYISELGLANSAAKLIPANSVIVAMYGq 81
Cdd:cd17275    1 EQVKLGELCEKMKSGGTPSTSNKEYY-GGDIPFVKisdmTKSGKY--IYSTEKYITEEGLKNSSAWIVPKGTILYAMYA- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  82 gdTAGRVAINKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIA 161
Cdd:cd17275   77 --SVGKVAINKIDVATNQAILGIIPKDEKLDFEFLYYWLLSLKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIA 154

                        170       180       190
                 ....*....|....*....|....*....|..
gi 814724563 162 SILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17275  155 EILDKIDAEIDKLEEKIEKLRELKKGLLQKMF 186

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoJA69PI TRD1-CR1, MjaXIP/S.MjaORF132P TRD2-CR2, and S.HspDL1ORF16625P TRD2-CR2; Escherichia coli UCD_JA69_pb S subunit (S.EcoJA69PI) recognizes 5'... CCANNNNNNNCTTC ... 3'. The recognition sequences of Methanococcus jannaschii MjaXIP/S.MjaORF132P TRD2-CR2 and Halobacterium species DL1 S subunit (S.HspDL1ORF16625P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various putative type II restriction enzymes and methyltransferases and may also include type I DNA methyltransferases.

Pssm-ID: 341162 [Multi-domain] Cd Length: 186 Bit Score: 177.60 E-value: 3.27e-54

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEqVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFCR---INKTENYISELGLANSAAKLIPANSVIV---Am 78
Cdd:cd17273    1 WEVVKLGDVAE-IVGGGTPSTKNPEYW-NGDIPWITPTDLTKLKgkyISDTERKITELGLKNSSAKLLPAGSVLLssrA- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  79 ygqgdTAGRVAINKIPLATNQACCNLVIDNKIaDYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQF 158
Cdd:cd17273   78 -----PIGYVAIATNPLATNQGFKSIIPNEEI-DNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEIPLPPLEEQK 151

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 814724563 159 TIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17273  152 KIAAILSKLDELIELLEKENEKLKELRDGLLPKLF 186

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: 177.34 E-value: 4.60e-54

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   4 EWKECKLGDVCEqVLTGGTPLTKKSDYYLNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGQGD 83
Cdd:cd17247    3 HWEVVRLGDVAR-VGNGSTPSRKNPDYWNGGTIPWVSSGEVNDNRITEADEFITELALKECSLPLVPPGSVLVAMIGQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  84 TAGRVAINKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYfeLVLRKTGS--AQPNLNTKLLKDFDILLPPLPEQFTIA 161
Cdd:cd17247   82 TRGQAAILAIEATINQNLAAIRPNEERVLPEYLHYYLESQY--DELRRIGSggGQGALNCGILKAFPIPLPPLDEQREIV 159

                        170       180
                 ....*....|....*....|....*..
gi 814724563 162 SILSSLDDKIDLLHRQNKTLEAMAETL 188
Cdd:cd17247  160 AELEALLAKIDLLEEKIARLIELLKEL 186

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: 175.43 E-value: 2.04e-53

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVcEQVLTGGTPLTKKSDYYlNGKIPWLK-TKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGQgdTAGR 87
Cdd:cd17516    2 KIGDL-GKVVTGKTPSTKNPEYF-GGDIPFITpSDMKGGKYIIKTERRLSSKGLEKVKNKLIPANSICVTCIGS--DMGK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYFEL-VLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSS 166
Cdd:cd17516   78 VAITKEPSVTNQQINSIIVNKNKFDPDFVYYLLKNNSKYLkSIAGGSTATPIINKSTFSNIEIPLPPLPEQKKIAAILSS 157

                        170       180
                 ....*....|....*....|....*..
gi 814724563 167 LDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17516  158 LDDKIENNRRINKTLEEMAQALFKEWF 184

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Arthrobacter chlorophenolicus A6 S subunit (S.AchA6I) TRD2-CR2; The S.AchA6I S subunit recognizes 5'... TGAANNNNNTCG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.AchA6I-TRD1 recognizes TGAA/TTCA, and TRD2 recognizes CGA/TCG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341132 [Multi-domain] Cd Length: 182 Bit Score: 165.70 E-value: 1.07e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   6 KECKLGDVCEqVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFC--RINKTENYISELGLANSAAKLIPANSVIVAMYGqgd 83
Cdd:cd17243    1 EVKSLSDVVD-IIGGGTPKTSVPEYW-NGDIPWFSVKDVNNDsrFVLDTEKKITELGLKNSSTKLLPKGTTIISARG--- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  84 TAGRVAINKIPLATNQACCNLVIDNKIADYhFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASI 163
Cdd:cd17243   76 TVGKLALLGIPMAMNQSCYGLRGKDGLSNY-FLYYLLKNLIEELKQKAHGSVFDTITRKTFDEIKVPLPPEELQKSFENI 154

                        170       180
                 ....*....|....*....|....*...
gi 814724563 164 LSSLDDKIDLLHRQNKTLEAMAETLFRQ 191
Cdd:cd17243  155 VSPLFDKILNNLKENQTLAQLRDTLLPK 182

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: 164.70 E-value: 2.94e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTPLTKKSDYYLNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGqgdTAGR 87
Cdd:cd17296    1 KKLGEICS-IQSGGTPSRSKKEYWNNGTIPWVKISDCKNKYVDETEEFITEEGLNNSSAKLLKKGTILIAIFA---TIGK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSL 167
Cdd:cd17296   77 VGILKIEATTNQAIAGIKPKNKSINPKYLYYYLKSLYEKFLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKF 156

                        170       180
                 ....*....|....*....|....*.
gi 814724563 168 DDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17296  157 EKLINKRQEGLQLLDELVKSLFEEMF 182

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: 154.49 E-value: 3.02e-45

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 201 WKEKPLSFYGTIICGKTPSKKVQSYFNGDIPFIKIPDMHGN--IFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIATVG 278
Cdd:cd17273    1 WEVVKLGDVAEIVGGGTPSTKNPEYWNGDIPWITPTDLTKLkgKYISDTERKITELGLKNSSAKLLPAGSVLLSSRAPIG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 279 LVSLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGTaTLNLNTGNFSQIPVLYPEQSVLEEFHSEVEP 358
Cdd:cd17273   81 YVAIATNPLATNQGFKSIIPNEEIDNEFLYYLLKNNKPEIESLASGST-FKEISKSTFKKIEIPLPPLEEQKKIAAILSK 159

                        170       180
                 ....*....|....*....|....*..
gi 814724563 359 LFDKIFFNQSQIHTLEKLRDTLLPKLM 385
Cdd:cd17273  160 LDELIELLEKENEKLKELRDGLLPKLF 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: 153.87 E-value: 5.24e-45

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 199 EGWKEKP-LSFYGTIICGKTPSKKVQSYF-NGDIPFIKIPDMHGNiFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCI-A 275
Cdd:cd17501    3 EGWEVGTiLDLCYKTQSGGTPSRKNPEYWdGGIIPWLKTGELRDN-IILDTEEKITEEGLKNSSAKLFPKGTVLVAMYgA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 276 TVGLVSLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGtATLNLNTGNFSQIPVLYPEQSVLEEFHSE 355
Cdd:cd17501   82 TAGKLGILAKEATTNQACCALIPKEEYSPFFLYLYLLNSRDYLANLASGS-AQQNISQQIIKNTKVLIPPEDLLEIFNKL 160

                        170       180       190
                 ....*....|....*....|....*....|.
gi 814724563 356 VEPLFDKIFFNQSQIHTLEKLRDTLLPKLMS 386
Cdd:cd17501  161 VEPLFDKIINNLKENQKLAKLRDTLLPKLMS 191

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Arthrobacter chlorophenolicus A6 S subunit (S.AchA6I) TRD2-CR2; The S.AchA6I S subunit recognizes 5'... TGAANNNNNTCG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.AchA6I-TRD1 recognizes TGAA/TTCA, and TRD2 recognizes CGA/TCG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341132 [Multi-domain] Cd Length: 182 Bit Score: 147.60 E-value: 1.05e-42

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 202 KEKPLSFYGTIICGKTPSKKVQSYFNGDIPFIKIPDMH-GNIFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIATVGLV 280
Cdd:cd17243    1 EVKSLSDVVDIIGGGTPKTSVPEYWNGDIPWFSVKDVNnDSRFVLDTEKKITELGLKNSSTKLLPKGTTIISARGTVGKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 281 SLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGT-ATLNLNTgnFSQIPVLYPEQSVLEEFHSEVEPL 359
Cdd:cd17243   81 ALLGIPMAMNQSCYGLRGKDGLSNYFLYYLLKNLIEELKQKAHGSVfDTITRKT--FDEIKVPLPPEELQKSFENIVSPL 158

                        170       180
                 ....*....|....*....|....
gi 814724563 360 FDKIFFNQSQIHTLEKLRDTLLPK 383
Cdd:cd17243  159 FDKILNNLKENQTLAQLRDTLLPK 182

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoR124I TRD2-CR2, S.Eco540I TRD2-CR2, S.Eco540AI TRD2-CR2, and S.Eco540ANI TRD2-CR2; Escherichia coli (R124) S subunit (S.EcoR124I), E. coli ST540 S subunit (S.Eco540I), E. coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540AN S subunit (S.Eco540ANI) recognize the sequence 5'... GAANNNNNNRTCG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoR124I -TRD1 recognizes GAA/TTC, and -TRD2 recognizes CGAY/RTCG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341138 [Multi-domain] Cd Length: 185 Bit Score: 146.06 E-value: 5.00e-42

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGqgdtaG- 86
Cdd:cd17249    1 VRLGDLGK-FLSGGTPSKSNPEYW-GGDIPWVSPKDMKSDYISDSEDHITELAVEESGTKLVPAGSVLIVVRG-----Mi 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  87 -----RVAINKIPLATNQACCNLVIDNKIaDYHFIYYLLK-NSYF--ELVLRKTGSAQpNLNTKLLKDFDILLPPLPEQF 158
Cdd:cd17249   74 lahtfPVAITTRPVAFNQDIKALIPKEGI-DPEFLLYALKaNEDRilSLVDKAGHGTG-SLDTDDLKNLPIPLPPLEEQR 151

                        170       180       190
                 ....*....|....*....|....*....|....
gi 814724563 159 TIASILSSLDDKIDLLHRQNKTLEAMAETLFRQW 192
Cdd:cd17249  152 RIAAILDALDALIDLLERKLAKLEELLKALMQAL 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: 145.22 E-value: 7.77e-42

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTPlTKKSDYYLNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGqgdTAGR 87
Cdd:cd16961    1 KKLGEIAE-IISGKTP-SSSSEYWDNGIIPWIRISDINNGGIILTDEKITEEGAEKLKKKILPKGDILISRSG---TIGK 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKI--PLATNQACCNLVIDNKIaDYHFIYYLLKNSYF-ELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASIL 164
Cdd:cd16961   76 VAIVKEndKALLNQAVIVIRPKDEV-DSEFLYYFLKSPFGkKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANIL 154

                        170       180
                 ....*....|....*....|....
gi 814724563 165 SSLDDKIDLLHRQNKTLEAMAETL 188
Cdd:cd16961  155 DKLDALIELLEQKLEKLEQLKQAL 178

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: 144.96 E-value: 1.06e-41

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEQVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVA--MygqgdTA 85
Cdd:cd17285    1 KKLGDLVEKIVGGGTPSKSNPEYW-NGDIPWASVKDLKGKYLTSTEDKITEEGLKNSSSNLIPKGTVIIAtrM-----GL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  86 GRVAINKIPLATNQACCNLVIDNKIADYhFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILS 165
Cdd:cd17285   75 GKVAINKIDVAINQDLKALFPKDELDPE-YLLYWFLSIEETIESLGTGTTVKGITLEDLKSLKIPLPPLEEQKRIVAILD 153

                        170       180
                 ....*....|....*....|....*.
gi 814724563 166 SLDDKIDLLHRQNKTLEAMAETLFRQ 191
Cdd:cd17285  154 ELDELIDKLEAKLEKLKQLKKGLMQS 179

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: 144.26 E-value: 2.31e-41

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCeQVLTGGTPLTKKSDYYLNG-KIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGQGDTAGR 87
Cdd:cd17276    2 KIGDIA-KTSSGGTPLRSNQEYYFNGgTIPWVKTTDLNNGVIYETEEKITEKALKETSCKLLPKGTVLVAMYGGFGQIGR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKIPLATNQACCNLVIDNKIADYHFI-YYLLKN-SYFELV---LRKtgsaQPNLNTKLLKDFDILLPPLPEQFTIAS 162
Cdd:cd17276   81 TGLLGIPAAINQAICAILPNEKKVNPEFLlRYLNFNrPYWMRVaasSRK----DPNITKDDVRNFPIPLPPLDEQRAIVE 156

                        170       180       190
                 ....*....|....*....|....*....|.
gi 814724563 163 ILSSLDDKID----LLHRQNKTLEAMAETLF 189
Cdd:cd17276  157 FLSDVDALIDsleaLIEKLRELKKGLMQQLL 187

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: 141.93 E-value: 1.47e-40

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEQVLTGGTPLTKKSDYYLNGKIPWLKTKEVNFCRINKTENYIS-ELGLANSAAKLIPANSVIVAMYGQGDTAG 86
Cdd:cd17514    1 VKIQDIAFEIINGGTPSRNEPEYWNNGDIPWLTSGETDDNFINNTSEKITtKNGLEDSSIRIVPKGTILIACTGQGYTRG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  87 RVAINKIPLATNQACcNLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSS 166
Cdd:cd17514   81 QVAVLQIDASTNQAI-AAIRCKENVNPKYLYYYLKTQKNNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNILET 159

                        170       180
                 ....*....|....*....|....*..
gi 814724563 167 LDDKIDllhRQNKTLEAMAETLFRQWF 193
Cdd:cd17514  160 LEFFEK---DSLRKIKETAQDINLMIN 183

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: 139.61 E-value: 1.23e-39

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCEQVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFCRINKTENYISELGLA-NSAAKLIPANSVIVAMYGQgdTAGR 87
Cdd:cd17280    2 KISHLFGLIGSGTTPKSDNEDYY-DGGIPWVTTGDLRDGIITETSKKITDKALDdYSALKIYPAGSLVIAMYGA--TIGR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKIPLATNQACCNLVIDNKIaDYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASIL--- 164
Cdd:cd17280   79 LGILGIDATTNQACCVLSGSNKI-DIKFLFYWLLANRDELISLASGGGQPNISQELIKSLRIPVPPLEEQKQIAAFLdkk 157

                        170
                 ....*....|....*....
gi 814724563 165 -SSLDDKIDLLHRQNKTLE 182
Cdd:cd17280  158 tAKIDSLIEKKERLIELLK 176

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: 137.27 E-value: 8.26e-39

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCEqVLTGGTPLTKKSDYYlNGKIPW-----LKTKEVNFCRINKtenYISELGLANSAAKLIPANSVIVAmygqgd 83
Cdd:cd17513    2 KLGELGK-FIGGGTPSTKNPEYW-NGNIPWitssdLSEDDIFKINIRK---FITEEAIKNSATKIIPANSILIV------ 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  84 T---AGRVAINKIPLATNQACCNLvIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTI 160
Cdd:cd17513   71 TrvgVGKVAINPFDICTSQDFTSL-IPIKEVNPLFLAYLLYSLLQKLKSQLQGTSIKGITKDDLKNLKIPLPPLEEQQKI 149

                        170       180       190
                 ....*....|....*....|....*....|...
gi 814724563 161 ASILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17513  150 AAILSKLDKLIEAHEKKLEKLKQLKKGLMQKLF 182

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: 137.27 E-value: 9.37e-39

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEQVLTGGTPltkkSDYYLNGKIPWLKTKEVNFCRIN-KTENYISELGLANSAAKLIP-ANSVIVAMYGqg 82
Cdd:cd17246    1 WEWVKLGEISSDITDGTHP----TPKYVESGIPFITSKNIKNGKIDfSDVKYISEEDHNEILKRSKLkKGDILFSIIG-- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  83 dTAGRVAI--NKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYF--ELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQF 158
Cdd:cd17246   75 -TIGRVAIvpEDLPANINQAVALIRPKKEKIDPKYLLYYLNSPIIqkQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQK 153

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 814724563 159 TIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17246  154 RIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLL 188

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: 136.05 E-value: 2.28e-38

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 204 KPLSFYGTIICGKTPSKKVQSYFNGDIPFIKIPDMHGNIFLFDTSDSLTEEGKRSQsnKTLPPKSICVSCIA-TVGLVSL 282
Cdd:cd17293    1 VKLGELGEVVTGNTPSKKNPEYYGGDIPFIKPDDLNNGGIILTSEEYLSEEGAKKA--RIVPKGSILVTCIGgSIGKVGI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 283 NAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGTATLnLNTGNFSQIPVLYP---EQSVLEEFHSEVEPL 359
Cdd:cd17293   79 ADREVAFNQQINAIIPNKSVDPKFLYYQLLSSKFQLQAIASSTTLPI-INKSKFEKIEIPLPpleEQKRIVAKLDKLFAL 157

                        170       180
                 ....*....|....*....|.
gi 814724563 360 FDKIffnQSQIHTLEKLRDTL 380
Cdd:cd17293  158 IDKL---EESLEELDELLKSL 175

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) TRD1-CR1, and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) TRD2-CR2; The recognition sequences of Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341175 [Multi-domain] Cd Length: 179 Bit Score: 134.93 E-value: 7.48e-38

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 204 KPLSFYGTIICGKTPSKKVQSYFNGDIPFIKIPDMHGNIFLFDTSDSLTEEGKRSQsnKTLPPKSICVSCIATVGLVSLN 283
Cdd:cd17286    1 KKLGDLGEIVTGNTPSTKNSEYYGGEILFVTPTDIDGNKYIYKTEKKLSEKGFKKA--RILPKGSILVTCIGSIGKNAIA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 284 AKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMAsGGTATLNLNTGNFSQIPVLYP---EQSVLEEFHSEVEplf 360
Cdd:cd17286   79 TEDCATNQQINAIIPNKNYDPEFLYYALENWSKKIKSLA-GKQAVPIINKTEFSKIKILVPpleEQQKIANFLSKLD--- 154

                        170       180
                 ....*....|....*....|....*
gi 814724563 361 DKIFFNQSQIHTLEKLRDTLLPKLM 385
Cdd:cd17286  155 ELIELQQQKIEKLEELKKGLLQKLF 179

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acetobacter pasteurianus S subunit (S.Apa101655I) TRD2-CR2; The S. Apa101655I S subunit recognizes 5'... TTAGNNNNNNTTC... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341133 [Multi-domain] Cd Length: 180 Bit Score: 124.51 E-value: 6.11e-34

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTPLTKKSDYYLNGKIPWLKTKEVNFCR-INKTENYISELGLANSAAKLIPANSVIVA--MygqgdT 84
Cdd:cd17244    1 VKLGDIFD-IKIGKTPPRKEPEYWSGDNIPWVSISDMGKGKyISDTKEYITDEAVKKFNVKLVPKGTLLMSfkL-----T 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  85 AGRVAINKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYFELvLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASIL 164
Cdd:cd17244   75 IGRVAIAGKDLYTNEAIAHFIPKDKKIDTEYLYYYLKSFDYSS-LGSTASKGKTLNSKKIKEIPIPLPPLEEQKRIAPIL 153

                        170       180
                 ....*....|....*....|....*
gi 814724563 165 SSLDDKIDLLHRQNKTLEAMAETLF 189
Cdd:cd17244  154 DKIDALIDQLETLIELLDELLPKLM 178

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: 124.18 E-value: 1.35e-33

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   4 EWKECKLGDVCEQVlTGGTPLTKKSDYYlNGKIPWLKTKEVNFCR---INKTENYISELGLANSAAKLIPANSVIV---A 77
Cdd:cd17248    3 HWEVVPLTDVAKLE-SGHTPSRSRPEYW-NGCIPWISLADVKQLRgdyIYETKEKISELGIANSSARLLPAGTVVLsrtA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  78 mygqgdTAGRVAINKIPLATNQACCNLVIDNKIaDYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQ 157
Cdd:cd17248   81 ------SVGKSAIMGRPMATSQDFANWVCGPEL-DPEYLLYVLRAMKPEFERLAMGSTHKTIYMPDFKALRIALPPLEEQ 153

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 814724563 158 FTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17248  154 RKIVDRLEALDAKIDALERKLERLIELLKELRQALL 189

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: 121.02 E-value: 1.18e-32

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCEqVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFCRINKT-ENYISELGLANsaAKLIPANSVIVAMYGQgdTAGR 87
Cdd:cd17293    2 KLGELGE-VVTGNTPSKKNPEYY-GGDIPFIKPDDLNNGGIILTsEEYLSEEGAKK--ARIVPKGSILVTCIGG--SIGK 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKIPLATNQACcNLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLN-TKLLKdFDILLPPLPEQFTIASILSS 166
Cdd:cd17293   76 VGIADREVAFNQQI-NAIIPNKSVDPKFLYYQLLSSKFQLQAIASSTTLPIINkSKFEK-IEIPLPPLEEQKRIVAKLDK 153

                        170       180
                 ....*....|....*....|...
gi 814724563 167 LDDKIDLLHRQNKTLEAMAETLF 189
Cdd:cd17293  154 LFALIDKLEESLEELDELLKSLF 176

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: 119.15 E-value: 7.83e-32

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEqvLTGGTPLtkKSDYYLNGKIPWLKTKEVNFCRINKTENYISELGLANSAAK-LIPANSVIVAMygQGD 83
Cdd:cd17278    1 WEVVKLGDIAD--IQNGYAF--KSSDFSDEGIPVIRIGNIKNGGIDLDDNSKYPEEPLEKYEKfLLKKGDILIAM--TGG 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  84 TAGRVAI---NKIPLATNQACCNLVIDNKIaDYHFIYYLLKNSYFE--LVLRKTGSAQPNLNTKLLKDFDILLPPLPEQF 158
Cdd:cd17278   75 TVGKVAIvpeDDEPALLNQRVGKFRPKDKI-DKEFLYYLLRSDSFRnqIKSSATGTAQPNISPKDIESIKIPLPPLEEQK 153

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 814724563 159 TIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWFV 194
Cdd:cd17278  154 KIAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLFT 189

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: 115.83 E-value: 1.08e-30

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  10 LGDVCEQVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYG--QGDTAGR 87
Cdd:cd17271    1 LGEVLKGLSSGATPSRGNPEYF-NGDIPWITSGELNYNYITDTNEKITEEAVKNTNLKIHPKGTFLIAITGleAAGTRGK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKIPLATNQACCNLVIDNKIaDYHFIYYLLKNSYFELVLRKT-GSAQPNLNTKLLKDFDILLPPLPEQFTIASILSS 166
Cdd:cd17271   80 CAITGIPATTNQSCMAFYPTKKL-TTEFLFYWYKKYGNYLGFKYAqGTKQQSYTADIVKKLPILLPTLKEQKKIANFLSD 158

                        170       180
                 ....*....|....*....|
gi 814724563 167 LDDKIDLLhrqNKTLEAMAE 186
Cdd:cd17271  159 IDELIATL---EKKIEKLKK 175

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: 113.99 E-value: 3.52e-30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563    4 EWKECKLGDVCEqVLTGGTPltKKSDYYLNGKIPWLKTKEVNfcrinktENYISELGLANsaAKLIPANSVIVAMYGqgd 83
Cdd:pfam01420   3 DWEVFKLGDVFE-IKKGKTP--KKKELKNNGKYPYIRAGDLN-------NVVKGGLGYIK--KYILPKGDITISSRA--- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   84 TAGRVAINKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASI 163
Cdd:pfam01420  68 TIGYVFYRDKPYYTNQHIIVLIPKNNIKITEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKI 147

                         170       180
                  ....*....|....*....|
gi 814724563  164 LSSLDDKIDLLHRQNKTLEA 183
Cdd:pfam01420 148 LSQLDNTIELEKGILNELER 167

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: 114.51 E-value: 3.61e-30

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTPLTKKSDYYlNGKIPWLKTKEVNFCR-INKTENYISELGLAnsAAKLIPANSVIVAMYGqgdTAG 86
Cdd:cd17286    1 KKLGDLGE-IVTGNTPSTKNSEYY-GGEILFVTPTDIDGNKyIYKTEKKLSEKGFK--KARILPKGSILVTCIG---SIG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  87 RVAINKIPLATNQACcNLVIDNKIADYHFIYYLLKNsYFELVLRKTG-SAQPNLNTKLLKDFDILLPPLPEQFTIASILS 165
Cdd:cd17286   74 KNAIATEDCATNQQI-NAIIPNKNYDPEFLYYALEN-WSKKIKSLAGkQAVPIINKTEFSKIKILVPPLEEQQKIANFLS 151

                        170       180
                 ....*....|....*....|....*...
gi 814724563 166 SLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17286  152 KLDELIELQQQKIEKLEELKKGLLQKLF 179

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: 112.68 E-value: 1.47e-29

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCEQVLTGGTPLTKKSDYYLNGKIPWLKTKEVN-FCRINKTENYISELGLANSAAKLIPANSVIVAmyGQGDTAGR 87
Cdd:cd17290    2 KLKRLAKSIKTGTTPPSENEEYYDGGIIPWFTPGDFNgDLILSESKRKLSELAIEDGEARLFPKNSVLVV--GIGATIGK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  88 VAINKIPLATNQAcCNLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSL 167
Cdd:cd17290   80 VGYSDKESSSNQQ-ITGIIFNKDINPKFLFYWLSSSKEELENLANGATLPILNQEKLKNIKLPVPPLNEQQKIVEFLDKK 158


                 ....*..
gi 814724563 168 DDKIDLL 174
Cdd:cd17290  159 TAKIDAL 165

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: 110.64 E-value: 9.91e-29

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 215 GKTPSKKVQSYFNGD-IPFIKIPDMHGNIFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIATVGLVSLNAKESQTNQQI 293
Cdd:cd17244   12 GKTPPRKEPEYWSGDnIPWVSISDMGKGKYISDTKEYITDEAVKKFNVKLVPKGTLLMSFKLTIGRVAIAGKDLYTNEAI 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 294 NSIVPNENYY-RYYLYLTMRS-SYDLLHSMASGGTAtlnLNTGNFSQIPVLYPEqsvlEEFHSEVEPLFDKIFFNQSQIH 371
Cdd:cd17244   92 AHFIPKDKKIdTEYLYYYLKSfDYSSLGSTASKGKT---LNSKKIKEIPIPLPP----LEEQKRIAPILDKIDALIDQLE 164

                        170
                 ....*....|....*.
gi 814724563 372 TLEKLRDTLLPKLMSG 387
Cdd:cd17244  165 TLIELLDELLPKLMSG 180

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: 109.11 E-value: 2.98e-28

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTP------LTKKSDYylngkIPWLK----TKEVNFcrINKTENYISELGLANSaaKLIPANSVIVA 77
Cdd:cd17283    1 KKLGDISE-IVRGASPrpigdpITFDGDG-----IPWIKigdvTKDGKY--ITKTKEKITEEGAKKS--RLVKPGDLILS 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  78 MYGqgdTAGRVAINKIplatnQACCN---LVIDNKIADYH--FIYYLLKNSYFELVLRKTGSAQ-PNLNTKLLKDFDILL 151
Cdd:cd17283   71 NSM---SFGRPYILKI-----DGCIHdgwLVFSDLKKKLDkdFLYYLLSSITVQLQFSAQAGGGtKNLNTDIVKNLKIPL 142

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 814724563 152 PPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLF 189
Cdd:cd17283  143 PPLEEQKRIAEILDSLDALIDALEEKLEKLEELKKGLM 180

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Burkholderia multivorans CF2 S subunit (S.BmuCF2ORF3362P) TRD1-CR1 and and Halomonas campaniensis LS21 S subunit (S.HcaLS21ORF99; The recognition sequences of Burkholderia multivorans CF2 S subunit (S.BmuCF2ORF3362P) and Halomonas campaniensis LS21 S subunit (S.HcaLS21ORF9970P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341168 [Multi-domain] Cd Length: 184 Bit Score: 107.26 E-value: 1.86e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  17 VLTGGTPLTKKSDYYlNGKIPWLKTKEVNF---CRINKTENYISELGLANSAAKLIPANSVIVAmygqgdT---AGRVAI 90
Cdd:cd17279    9 IVNGSTPKSGEEDYW-DGDIPWVTPADLSKldgKYISSSQRKITEAGLESCGTSLVPAGSIILS------TrapIGYVAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  91 NKIPLATNQACCNLVIDNKIaDYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDK 170
Cdd:cd17279   82 ATVELCTNQGCKALVPNSDV-DSRFLYYLLLAAKEELNSLGRGTTFLELSTDELANFKIPLPPLSEQRAIADFLDRETAK 160

                        170
                 ....*....|....*..
gi 814724563 171 ID-LLHRQNKTLEAMAE 186
Cdd:cd17279  161 IDaLIAKKQQLIELLKE 177

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

Pssm-ID: 341166 [Multi-domain] Cd Length: 184 Bit Score: 105.95 E-value: 6.06e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEqVLTGGTPLTKKSDYYLNGKIPWLKTK--EVNFCRINKTENYISELGLANSAAKLIPANSVIVAMYGqg 82
Cdd:cd17277    1 WPIVKLGEVCE-IINGSTPSKKNEEYWNNGTIKWLTIPdiDERGLIISSTKQFITEKALEEKKVKLVPKNSVLLSCTA-- 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 814724563  83 dTAGRVAINKIPLATNQACCNLVI-DNKIADyHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTI 160
Cdd:cd17277   78 -TIGKVAIAKIELTTNQQINALICkDSKILP-EYLFYALKHIKQVLERLTTNPGVKHVNLSMLSNLQIPLPPLEVQKKI 154

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: 104.94 E-value: 1.33e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 209 YGTIICGKTPSKKVQSYFNGDIPFIKIPDM-HGNIFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIATVGLVSLNAKES 287
Cdd:cd17275    9 CEKMKSGGTPSTSNKEYYGGDIPFVKISDMtKSGKYIYSTEKYITEEGLKNSSAWIVPKGTILYAMYASVGKVAINKIDV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 288 QTNQQINSIVPNENY-YRYYLYLTMRSSYDLLHSMASGGTATlNLNTGNFSQIPVLYP---EQSVLEEFHSEVEPLFDKI 363
Cdd:cd17275   89 ATNQAILGIIPKDEKlDFEFLYYWLLSLKNELKRLIRTGTQA-NLNAEIVKNLPIPLPpleEQKKIAEILDKIDAEIDKL 167

                        170       180
                 ....*....|....*....|..
gi 814724563 364 ffnQSQIHTLEKLRDTLLPKLM 385
Cdd:cd17275  168 ---EEKIEKLRELKKGLLQKMF 186

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: 104.83 E-value: 1.34e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEqVLTGgtpltkKSDY-------YLNGKIPWLKTKEV---NFcRINKTENYISELGLANSaaKLIPANSV 74
Cdd:cd17282    1 WEVKKLSDLGS-LERG------KFKHrprndprLYGGDYPFIQTGDVaraNG-YITSYSQTLNEKGLAQS--KLFPKGTL 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  75 ---IVAmygqgdTAGRVAINKIPlatnqACC-----NLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKD 146
Cdd:cd17282   71 citIAA------NIGDTAILGFD-----ACFpdsvvGFIPNEEKIDVEFLEYYLRTLKKELEAIAPQSAQKNINLEILRP 139

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 814724563 147 FDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17282  140 LKIPVPPLEEQKKIVEILDALDDLIDNLEKRIAKLEELKQSLLQEAF 186

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: 102.98 E-value: 7.00e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEqvLTGGTPLtkKSDYYLNGKIPWLKTKEVNFCRIN-KTENYISElGLANSAAK-LIPANSVIVAMYGQG 82
Cdd:cd17259    1 WEWVKLGDVAD--ILSGYAF--KSSEFSESGIRLLRGANVGVGEIRwDDTVYLPE-EYLEEYEKyLLKEGDIVIALDRPI 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  83 DTAG-RVAI---NKIPLATNQACCNLVIDNKIaDYHFIYYLLKNSYFE--LVLRKTGSAQPNLNTKLLKDFDILLPPLPE 156
Cdd:cd17259   76 ISGGlKVARipkSDLPALLVQRVARIRPKDEL-NSDFLYYLLQSDFFLnyVEPVLTGTDVPHISTKQIKNFKIPLPPLEE 154

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 814724563 157 QFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQ 191
Cdd:cd17259  155 QKKIAEFLSSLDALIDLLEQKLEKLQQLKKGLMQS 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: 100.53 E-value: 4.70e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 204 KPLSFYGTIICGKTPSKKVQSYFNGDIPFIKIPDMHGNiFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIATVGLVSLN 283
Cdd:cd16961    1 KKLGEIAEIISGKTPSSSSEYWDNGIIPWIRISDINNG-GIILTDEKITEEGAEKLKKKILPKGDILISRSGTIGKVAIV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 284 AKESQ--TNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGTATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFD 361
Cdd:cd16961   80 KENDKalLNQAVIVIRPKDEVDSEFLYYFLKSPFGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDA 159

                        170
                 ....*....|....*....
gi 814724563 362 KIFFNQSQIHTLEKLRDTL 380
Cdd:cd16961  160 LIELLEQKLEKLEQLKQAL 178

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: 97.91 E-value: 5.31e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 204 KPLSFYGTIICGKTPSKKVQSYFNGDIPFI--KipDMHGNiFLFDTSDSLTEEGKRSQSNKTLPPKSICV---SCIatvg 278
Cdd:cd17249    1 VRLGDLGKFLSGGTPSKSNPEYWGGDIPWVspK--DMKSD-YISDSEDHITELAVEESGTKLVPAGSVLIvvrGMI---- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 279 L-----VSLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASG-GTATLNLNTGNFSQIPVLYPEQSVLEEF 352
Cdd:cd17249   74 LahtfpVAITTRPVAFNQDIKALIPKEGIDPEFLLYALKANEDRILSLVDKaGHGTGSLDTDDLKNLPIPLPPLEEQRRI 153

                        170       180       190
                 ....*....|....*....|....*....|..
gi 814724563 353 HSEVEPLFDKIFFNQSQIHTLEKLRDTLLPKL 384
Cdd:cd17249  154 AAILDALDALIDLLERKLAKLEELLKALMQAL 185

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: 97.28 E-value: 9.66e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   3 GEWKECKLGDVCEQVLTG-GTPltkKSdyyLNGKIPWLKTKEVNFCRINKT--ENYISELGLANSAAKLIPANSVIVAMY 79
Cdd:cd17284    2 EGWEVKRVGDVCDCIVPGrDKP---KS---FDGNIPWITIEDIKGKYISSSksGLGVSEEEIKEMNLKVIPKGSVIMSCV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  80 GqgdTAGRVAINKIPLATNQACCNLVIDNKIaDYHFIYYLL--KNSYFELVlrKTGSAQPNLNTKLLKDFDILLPPLPEQ 157
Cdd:cd17284   76 G---DFGIVAIATNELVINQQLHAFVPSKKI-NPEYLMYLLslQKKYMEKI--ATGTTIPYLNKTNCESIPIPLPPIEEQ 149

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 814724563 158 FTIASILSSLDDKIDL----LHRQNKTLEAMAETLF 189
Cdd:cd17284  150 NKIAKILDSIDKKIDLliakLEKLQQLKKGLMQQLF 185

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.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: 96.17 E-value: 2.43e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCEqvLTGGTPLTKKSDYYLNGKIPWLKTKEVNFC----RINKTENYISELGLANSAAKLIPANSVIVAMYGQGDT 84
Cdd:cd17250    2 RLGDVCD--FKAGSGFPEKYQGKEDGEYPFYKVGDMNNSgnekYLSTAENYISEEIVKELKAKLFPKGTIIFAKIGEAIK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  85 AGRVAINKIPLATNQACCNLVIDNKIaDYHFIYYLLKNsyFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASIL 164
Cdd:cd17250   80 LNRRAILSKDSCIDNNVMGLIPNEGI-DSEYLYYWLKK--VDLYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKL 156

                        170       180
                 ....*....|....*....|....*....
gi 814724563 165 SSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17250  157 DELFEKLDKLKQALEAAKEQLKGLRQSLL 185

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: 95.43 E-value: 4.23e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 212 IICGKTPSKKVQSYF-NGDIPFIKIPDMHGNiFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCI---ATVGLVSLNAKES 287
Cdd:cd17500    9 ITSGGTPSRSNKEYYnGGNIPWLKTKELNFK-RIYDTEEKITEEGLKNSSAKLIPENTVIIAMYgagKTAGRVAINKIPL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 288 QTNQQINSIVPNENYYRY-YLYLTMRSSYDLLHSMASGGtATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFN 366
Cdd:cd17500   88 TTNQACCNLIIDNKKADYrFVYYSLKTQYEELVNLASGA-AQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLDDKIELN 166

                        170
                 ....*....|....
gi 814724563 367 QSQIHTLEKLRDTL 380
Cdd:cd17500  167 NRQNETLEAMAETL 180

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: 95.25 E-value: 4.34e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 201 WKEKPLSFYGTIICGKTPSKKVQSYFNGD-IPFIKIPDMHGNiFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCI---AT 276
Cdd:cd17294    1 WEWKTLGEIAKIFSGGTPSTSNPEYWDGGtIPWLSSGEVNFK-EIYETEKRITEEGLKNSSAKWIPKNSVLIALAgqgKT 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 277 VGLVSLNAKESQTNQQINSIVPNENYYRY-YLYLTMRSSYDLLHSMASGGTATlNLNTGNFSQIPVLYPEQSVLEEFHSE 355
Cdd:cd17294   80 RGTVAILKIPLTTNQSLAAIEPDEEIANSrFLYYNLSSRYEELRSLSGGGGRG-GLNLKIIKSLPIPLPPLEEQKKIVAI 158

                        170       180       190
                 ....*....|....*....|....*....|
gi 814724563 356 VEPLFDKIFFNQSQIHTLEKLRDTLLPKLM 385
Cdd:cd17294  159 LDKFDALINDLKEGLPALLELRQKQYEYLR 188

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: 94.00 E-value: 5.65e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 105 VIDNKIADYHFIYYLLKNsyFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAM 184
Cdd:cd17267   74 VKDFKGNDPRFLYYLLKT--LDLERLNSGSAVPGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEEL 151


                 ....*..
gi 814724563 185 AETLFRQ 191
Cdd:cd17267  152 ADALLPK 158

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: 94.19 E-value: 9.97e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 211 TIICGKTPSKKVQSYFNGD-IPFIKIPDMHGNIFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCI-ATVGLVSLNAKESQ 288
Cdd:cd17290    9 SIKTGTTPPSENEEYYDGGiIPWFTPGDFNGDLILSESKRKLSELAIEDGEARLFPKNSVLVVGIgATIGKVGYSDKESS 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 814724563 289 TNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGgtATLN-LNTGNFSQIPVLYP---EQ 346
Cdd:cd17290   89 SNQQITGIIFNKDINPKFLFYWLSSSKEELENLANG--ATLPiLNQEKLKNIKLPVPplnEQ 148

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: 94.20 E-value: 1.18e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 199 EGWKEKPLSFYGTIIcgkTPSK-KVQSyFNGDIPFIKIPDMHGNiFLFDTSD--SLTEEGKRSQSNKTLPPKSICVSCIA 275
Cdd:cd17284    2 EGWEVKRVGDVCDCI---VPGRdKPKS-FDGNIPWITIEDIKGK-YISSSKSglGVSEEEIKEMNLKVIPKGSVIMSCVG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 276 TVGLVSLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASgGTATLNLNTGNFSQIPVLYP---EQSVLEEF 352
Cdd:cd17284   77 DFGIVAIATNELVINQQLHAFVPSKKINPEYLMYLLSLQKKYMEKIAT-GTTIPYLNKTNCESIPIPLPpieEQNKIAKI 155

                        170       180       190
                 ....*....|....*....|....*....|...
gi 814724563 353 HSEVEPLFDKIffnQSQIHTLEKLRDTLLPKLM 385
Cdd:cd17284  156 LDSIDKKIDLL---IAKLEKLQQLKKGLMQQLF 185

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: 92.17 E-value: 4.81e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 108 NKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAET 187
Cdd:cd17496   90 KNGIDTEFLYYLLESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDT 169


                 ....*.
gi 814724563 188 LFRQWF 193
Cdd:cd17496  170 LLPKLL 175

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: 91.44 E-value: 1.39e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEQVLTGgtpLTKKSDYYLNGkIPWLKTKEV-NFCRINKTENYISELGLANSAA-KLIPANSVIVAMYGQG 82
Cdd:cd17517    1 WEVVKLGDLLEDPRYG---TSKKSSYDGSG-TPVLRIPNIyDGGIDLDDLKKRVDLSEKELEKyLLKKGDILFNRSNGSP 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  83 DTAGRVAInkIPLATNQA--CCNLV---IDNKIADYHFIYYLLKNSYF--ELVLRKTGSA-QPNLNTKLLKDFDILLPPL 154
Cdd:cd17517   77 ELVGKCAL--VDEEDEPAifASYLIrlrLDKKKILPEFLYYYLNSPLGrkQIEKIAKSAAgQANINQKDLKKLPIPLPPL 154

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 814724563 155 PEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQW 192
Cdd:cd17517  155 EEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192

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: 90.64 E-value: 2.05e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCEqvLTGGT--PLTKKSDYYLNGKIPWLKTKevnFCRINKTENYISElglaNSAAKLIPANSVIVAMYGQgdTAG 86
Cdd:cd17263    2 KLGEVCK--FSKGKqpPISERFDEPKEGSVRYIQIE---DLRNNNEKKYIEN----PKKSVICNEDDILIVRDGA--NAG 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  87 RV------AIN----KIplatnqaccnlVIDNKIADYHFIYYLLKNSYFEL-VLRKTGSAQPNLNTKLLKDFDILLPPLP 155
Cdd:cd17263   71 EVgtglegAIAstlfKI-----------IPDKNIIDKDYLYYFLKSKEIQLnILTKAGSTIPHVNKKDLENLKIPLPSLE 139

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 814724563 156 EQFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17263  140 EQKKIAEILDKLDALIDKLKELIEKLIELKKGLFQELL 177

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

Pssm-ID: 341145 [Multi-domain] Cd Length: 182 Bit Score: 90.64 E-value: 2.12e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  10 LGDVCEqVLTGGtpLTKKSDYYLNGK--IPWLKTKEVNFCRINkTEN--YISElglaNSAAKLipANSVIVAmygqGD-- 83
Cdd:cd17256    1 LGEIAR-VKGGG--RLPKGESLSDGPtgVPYIRVTDIKNGGID-LDNlkYISP----EIHEKI--KRYTLSK----GDil 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  84 -----TAGRVAInkIPLATN-----QACCNLVIDNKIaDYHFIYYLLKNSYF--ELVLRKTGSAQPNLNTKLLKDFDILL 151
Cdd:cd17256   67 isivgTIGRVGI--VPKELDganltENAARIRPKDSI-SPRYLYYYLRSPFGqsQIESETKGAAQPKLNLKRIRELPIPL 143

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 814724563 152 PPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLF 189
Cdd:cd17256  144 PPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKALM 181

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

Pssm-ID: 341166 [Multi-domain] Cd Length: 184 Bit Score: 90.54 E-value: 2.22e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 201 WKEKPLSFYGTIICGKTPSKKVQSYF-NGDIPFIKIPDMHGN-IFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIATVG 278
Cdd:cd17277    1 WPIVKLGEVCEIINGSTPSKKNEEYWnNGTIKWLTIPDIDERgLIISSTKQFITEKALEEKKVKLVPKNSVLLSCTATIG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 279 LVSLNAKESQTNQQINSIVPNENYY--RYYLYLTMRSSYDLLHSmaSGGTATLNLNTGNFSQIPVLYPEQSVLEEFHSEV 356
Cdd:cd17277   81 KVAIAKIELTTNQQINALICKDSKIlpEYLFYALKHIKQVLERL--TTNPGVKHVNLSMLSNLQIPLPPLEVQKKIVAEI 158


                 .
gi 814724563 357 E 357
Cdd:cd17277  159 E 159

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: 90.44 E-value: 2.24e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTPltkKSDYY--LNGKIPWL---KTKEVNFCRINKTENYISelglansaaKLIPANSVIVAMYGQg 82
Cdd:cd17498    1 VKLGEIAE-ITMGQSP---KSEFYneDGIGLPFLqgnRTFGDKYPYIDTYTTDIK---------KIAKKGDILMSVRAP- 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  83 dtAGRVAINKIPLATNQACCnlVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIAS 162
Cdd:cd17498   67 --VGDLNIANKDICIGRGLC--SIRMKNGNNSFLYYLLKNNIKNLINKSSGTVFGSINKDDIENLEVDIPEDEEQKRIAN 142

                        170       180       190
                 ....*....|....*....|....*....|.
gi 814724563 163 ILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17498  143 ILSKIDDKIEINNQINKNLEELAQAIFKHWF 173

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: 90.75 E-value: 2.28e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEqvLTGGTPLtkKSDYYLNGKIPWLKTKEVNFCRI-NKTENYISElglaNSAAK----LIPANSVIVAMY 79
Cdd:cd17512    1 WEEIRLGDIID--YQKGYAF--KSKDYQDSGIRIVRVSDFTDDSIdINNLVYISE----EKANKykkyELKENDIIITTV 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  80 G-----QGDTAGRVAinKIPLAT-----NQaccNLVI---DNKIADYHFIYYLLKNSYFE--LVLRKTGSA-QPNLNTKL 143
Cdd:cd17512   73 GswpsnPDSVVGKVV--RVPKEAdgallNQ---NAVKirpKKGILDQSFLFYNLKSERFKnyIESIARGNAnQASITLGD 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 814724563 144 LKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQ 191
Cdd:cd17512  148 IKKFKFLLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQALYQE 195

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: 90.01 E-value: 3.84e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 115 FIYYLLKNSYF--ELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQW 192
Cdd:cd17289  111 FLYYWFQSSIFknQINSITIGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEELAKTLFQYW 190


                 .
gi 814724563 193 F 193
Cdd:cd17289  191 F 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: 85.61 E-value: 1.50e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 104 LVIDNKIADYHFIYYLLK-NSYFELV-LRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTL 181
Cdd:cd17521   97 FRPNKKKVLPKYLFYFTQsSLYWKQIkSISSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKL 176

                         90
                 ....*....|.
gi 814724563 182 EAMAETLFRQW 192
Cdd:cd17521  177 EELLKELLQSL 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: 85.23 E-value: 1.74e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 204 KPLSFYGTIICGKTPSKKVQSYFNGDIPFIKIPDMHGNIfLFDTSDSLTEEGKRSQSNKTLPPKSICVSCI---ATVGLV 280
Cdd:cd17287    1 KKLGEIAKVSSGGTPSRSNPEYWNGGIPWVKTGEVNFNE-ITDTEEKITEEGLKNSSAKLFPKGTLLMAMYgqgKTRGRV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 281 SLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGTATlNLNTGNFSQIPVLYP---EQSVLEEFHSEVE 357
Cdd:cd17287   80 AILGIEAATNQACAAILPNDGINPDFLFYYLQSSYEELRDLSNGGGQP-NLNAGLIKSIEIPVPpldEQQKIAAFLSAID 158

                        170       180
                 ....*....|....*....|....*....
gi 814724563 358 plfDKIFFNQSQIHTLEKLRDTLLPKLMS 386
Cdd:cd17287  159 ---AKIDALEQKLELLQELKKSLMQQLFT 184

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: 84.13 E-value: 4.35e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCEqVLTG--GTPLTKKSDYYLNGkIPWLKTKEVNFCRINKTE-NYISE-----LGlansAAKLIPANSV------ 74
Cdd:cd17264    1 RLGDIAE-FINGdrGKNYPSKSEFVDEG-IPFINAGHLEDGTIDLSNmNFISEekynsLG----SGKLQKGDILyclrgs 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  75 -----IVAMYGQGdtagrvAINKiplatnqaccNLVI----DNKIADYhfIYYLLKNSYFELVLRK--TGSAQPNLNTKL 143
Cdd:cd17264   75 lgkcaIVDNYDEG------AIAS----------SLVIirpfAKVDVRY--LYYYLNSPLGKSQIKKydNGSAQPNLSAKS 136

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 814724563 144 LKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLF 189
Cdd:cd17264  137 LKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQSLF 182

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) TRD2-CR2; Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3'. The RM system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example S.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341155 [Multi-domain] Cd Length: 159 Bit Score: 82.88 E-value: 7.35e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 105 VIDNKIADYHFIYYLLKNsyfeLVLRK--TGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLE 182
Cdd:cd17266   76 VTPKKENNIKFLYYLLKS----LNLNQyaTGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLI 151


                 ....*...
gi 814724563 183 AMAETLFR 190
Cdd:cd17266  152 ELKKELMQ 159

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 78.56 E-value: 4.08e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 307 LYLTMRSSYDLLHSMASGgTATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFNQSQIHTLEKLRDTLLPKLMS 386
Cdd:COG0732    4 YYLRSPSFREYLRSLATG-STQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFT 82


                 ....*.
gi 814724563 387 GEVRVE 392
Cdd:COG0732   83 GELRVR 88

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: 81.07 E-value: 5.07e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 204 KPLSFYGTIICGKTPSKKVQSYFNGDIPFIKIPDMHG--NIFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIATVGLVS 281
Cdd:cd17279    1 VPLKRIFRIVNGSTPKSGEEDYWDGDIPWVTPADLSKldGKYISSSQRKITEAGLESCGTSLVPAGSIILSTRAPIGYVA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814724563 282 LNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASgGTATLNLNTGNFSQIPVLYPEQS 347
Cdd:cd17279   81 IATVELCTNQGCKALVPNSDVDSRFLYYLLLAAKEELNSLGR-GTTFLELSTDELANFKIPLPPLS 145

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: 80.27 E-value: 7.65e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 108 NKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAET 187
Cdd:cd17245   89 NKDIDNLFLYYYLKYNKPELEKLGTGSTFKAINKKDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKLDELKKG 168


                 ....*.
gi 814724563 188 LFRQWF 193
Cdd:cd17245  169 LMQELF 174

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Crinalium epipsammum S subunit (S.Cep9333ORF4827P) TRD2-CR2 and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) T; The recognition sequences for Crinalium epipsammum S subunit (S.Cep9333ORF4827P) and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341186 [Multi-domain] Cd Length: 174 Bit Score: 80.20 E-value: 8.89e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 303 YRYYLYLTMRSSYDLLHSMASGGTATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFNQSQIHTLEKLRDTLLP 382
Cdd:cd17495   92 SQSFLFYQLKSLFKEFDIFNGEGTVFGSINKKDLENLPIIIPSDEIIEAFEKLVSPIDQKIENNEKENRTLAKLRDTLLP 171


                 ...
gi 814724563 383 KLM 385
Cdd:cd17495  172 KLM 174

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: 79.18 E-value: 2.35e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 211 TIICGKTPSKKVQSYF-NGDIPFIKIPDMHGNiFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIATVGLVSLNAKESQT 289
Cdd:cd17296    8 SIQSGGTPSRSKKEYWnNGTIPWVKISDCKNK-YVDETEEFITEEGLNNSSAKLLKKGTILIAIFATIGKVGILKIEATT 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814724563 290 NQQINSIVPNENYY-RYYLYLTMRSSYDLLHSMASGGtATLNLNTGNFSQIPVLYP---EQ----SVLEEFHSEVE 357
Cdd:cd17296   87 NQAIAGIKPKNKSInPKYLYYYLKSLYEKFLSLGRGV-AQNNINLSILKNLKIPLPpleEQqrivAILDKFEKLIN 161

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) TRD1-CR1, Neisseria meningitidis 510612 S subunit ; Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) recognizes 5'... CTANNNNNNNNTGT ... 3', and the recognition sequences of Neisseria meningitidis 510612 S subunit (S.Nme510612ORF1157P) and Streptococcus mitis SVGS_061 S subunit (S2.Smi61ORF7905P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) TRD1 recognizes CTA/TAG, and TRD2 recognizes ACA/TGT. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341170 Cd Length: 196 Bit Score: 77.63 E-value: 1.25e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   4 EWKecKLGDVCEqVLTGGTPLTKKSDYYLNGKIPWLKTKEVnfcRIN-----KTENYISELGLANSaaKLIPANSVIVAM 78
Cdd:cd17281    3 EWK--KLGEIFD-IRNGYTPSKSNKEYWENGTIPWFRMEDI---RENgrilsDSIQHITPSAVKGG--KLFPANSIILST 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  79 YGqgdTAGRVAINKIPLATNQACCNLVI----DNKIaDYHFIYYllknsYFELV---LRK--TGSAQPNLNTKLLKDFDI 149
Cdd:cd17281   75 TA---TIGEHALITVDSLANQRFTNFSLkksyKNKL-DIKFLFY-----YFFVLgewCKKniNIGGFPSVDMNKLKKFKI 145

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 814724563 150 LLPPLPEQFTIASILSSLDdkiDLLHRQNKTLEAMAETLFRQWfveeadEGWKEKPLSF 208
Cdd:cd17281  146 PIPPLEEQEKIVEILDKFT---KLTADLTAELPAELEARKKQY------EYYRDKLLSF 195

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 73.55 E-value: 2.78e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 118 YLLKNSYF--ELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWFVE 195
Cdd:COG0732    4 YYLRSPSFreYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFTG 83


                 ...
gi 814724563 196 EAD 198
Cdd:COG0732   84 ELR 86

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: 76.03 E-value: 4.32e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 199 EGWKEKPLSFYGTIICGKTPSKKVQSYFNGD-IPFIKIPDMHGNIFLfDTSDSLTEEGKRSQSNKTLPPKSICVSCIA-- 275
Cdd:cd17247    2 EHWEVVRLGDVARVGNGSTPSRKNPDYWNGGtIPWVSSGEVNDNRIT-EADEFITELALKECSLPLVPPGSVLVAMIGqg 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 276 -TVGLVSLNAKESQTNQQINSIVPNENY-YRYYLYLTMRSSYDLLHSMASGGtatlN---LNTGNFSQIPVLYPEQSVLE 350
Cdd:cd17247   81 kTRGQAAILAIEATINQNLAAIRPNEERvLPEYLHYYLESQYDELRRIGSGG----GqgaLNCGILKAFPIPLPPLDEQR 156

                        170       180       190
                 ....*....|....*....|....*....|....
gi 814724563 351 EFHSEVEPLFDKIFFNQSQIHTLEKLRDTLLPKL 384
Cdd:cd17247  157 EIVAELEALLAKIDLLEEKIARLIELLKELRQAL 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, 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: 75.29 E-value: 7.60e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 212 IICGKTPSKKVQSYFN-GDIPFIKIPDMHGNiFLFDTSDSLTEE-GKRSQSNKTLPPKSICVSCIA---TVGLVSLNAKE 286
Cdd:cd17514   10 IINGGTPSRNEPEYWNnGDIPWLTSGETDDN-FINNTSEKITTKnGLEDSSIRIVPKGTILIACTGqgyTRGQVAVLQID 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814724563 287 SQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGtATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDK 362
Cdd:cd17514   89 ASTNQAIAAIRCKENVNPKYLYYYLKTQKNNLRNLTSGV-AQKNLNIEMLRNLQIPLPPKEEQQKIVNILETLEFF 163

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: 74.78 E-value: 8.21e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 108 NKIADYHFIYYLLKN-SYFELVlrkTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAE 186
Cdd:cd17262   90 KNGISTEFLYYYLNSiDISPYV---TGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKK 166


                 ....*.
gi 814724563 187 TLFRQW 192
Cdd:cd17262  167 ALLQKL 172

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

Pssm-ID: 341149 [Multi-domain] Cd Length: 165 Bit Score: 74.39 E-value: 8.69e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 108 NKIADYHFIYYLLKNSYFelvlRK------TGSA-QPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKT 180
Cdd:cd17260   77 KEGILPEFLYYLLRSPSF----RKeaiksmTGSSgRQRVPKDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIET 152

                         90
                 ....*....|...
gi 814724563 181 LEAMAETLFRQWF 193
Cdd:cd17260  153 LEELLDALLPKLL 165

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Actinosynnema mirum DSM 43827 S subunit (S. AmiI) TRD2-CR2; The S. AmiI S subunit recognizes 5'... CAGNNNNNNNTCGA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S. AmiI -TRD1 recognizes CAG/CTG, and TRD2 recognizes TCGA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341137 [Multi-domain] Cd Length: 196 Bit Score: 74.49 E-value: 1.56e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 199 EGWKEKPLSFYGTIICGKTPSKKVQSYFNGDIPFIKIPDMHGN--IFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIAT 276
Cdd:cd17248    2 AHWEVVPLTDVAKLESGHTPSRSRPEYWNGCIPWISLADVKQLrgDYIYETKEKISELGIANSSARLLPAGTVVLSRTAS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 277 VGLVSLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGTatlnLNT---GNFSQIPVLYP---EQsvlE 350
Cdd:cd17248   82 VGKSAIMGRPMATSQDFANWVCGPELDPEYLLYVLRAMKPEFERLAMGST----HKTiymPDFKALRIALPpleEQ---R 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 814724563 351 EFHSEVEPLFDKIFFNQSQIHTLEKLRDTLLPKLMSGEVRVE 392
Cdd:cd17248  155 KIVDRLEALDAKIDALERKLERLIELLKELRQALLTAAVTGK 196

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: 73.71 E-value: 2.47e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 210 GTIICGKTPSKKVQSYFNGDIPFIKIPDMHGN-IFLFDTSDSLTEEGKRSQSNKTLPPKSIcvsCIAT---VGLVSLNAK 285
Cdd:cd17513    7 GKFIGGGTPSTKNPEYWNGNIPWITSSDLSEDdIFKINIRKFITEEAIKNSATKIIPANSI---LIVTrvgVGKVAINPF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 286 ESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASgGTATLNLNTGNFSQIPVLYP---EQSVLEEFHSEVEplfDK 362
Cdd:cd17513   84 DICTSQDFTSLIPIKEVNPLFLAYLLYSLLQKLKSQLQ-GTSIKGITKDDLKNLKIPLPpleEQQKIAAILSKLD---KL 159

                        170       180
                 ....*....|....*....|...
gi 814724563 363 IFFNQSQIHTLEKLRDTLLPKLM 385
Cdd:cd17513  160 IEAHEKKLEKLKQLKKGLMQKLF 182

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: 72.77 E-value: 3.42e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  199 EGWKEKPLSFYGTIICGKTPSKKvQSYFNGDIPFIKIPDMHGNiflfdtsdslTEEGKRSQSNKTLPPKSICVSCIATVG 278
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPKKK-ELKNNGKYPYIRAGDLNNV----------VKGGLGYIKKYILPKGDITISSRATIG 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  279 LVSLNAKESQTNQQINSIVP----NENYYRYYLYLTMRSSydllHSMASGGTATLNLNTGNFSQIPVLYPeqsVLEEFHS 354
Cdd:pfam01420  71 YVFYRDKPYYTNQHIIVLIPknniKITEFLYLYLLLKLKK----LKSLKFGSTQPKLTKERLKEIKIPLP---PLEEQKK 143

                         170
                  ....*....|....*...
gi 814724563  355 EVEPLFDkiFFNQSQIHT 372
Cdd:pfam01420 144 IAKILSQ--LDNTIELEK 159

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: 72.16 E-value: 4.84e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCEqvLTGGTPLTKKSDYyLNGKIPwlktkeVnfcrINkteNYISELGLANSAakLIPANSVIVAmyGQGDTAGRV 88
Cdd:cd17291    2 KLGEIAE--IKKGKQITKKELI-ENGKYP------V----IA---GGIEPSGYHNEY--NREGNTITIS--ASGASAGYV 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  89 AINKIPL-ATNqaCCNLVIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILssl 167
Cdd:cd17291   62 NYWKEPFwASD--CCYILSSKNELVNKFLYYFLKNKQEEIYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEIL--- 136

                        170       180
                 ....*....|....*....|....
gi 814724563 168 dDKIDLLhrqnkTLEAMAETLFRQ 191
Cdd:cd17291  137 -DKFTEL-----TAELPAELEARK 154

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: 72.54 E-value: 6.33e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 211 TIICGKTPSKKVQSYFNGDIPFIKIPDMHGNiFLFDTSDSLTEEGKRSQSNKTLPPKSIcvsCIAT---VGLVSLNAKES 287
Cdd:cd17285    9 KIVGGGTPSKSNPEYWNGDIPWASVKDLKGK-YLTSTEDKITEEGLKNSSSNLIPKGTV---IIATrmgLGKVAINKIDV 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 288 QTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGT-ATLNLNTGNFSQIPVL-YPEQ----SVLEEFHSEVEPLFD 361
Cdd:cd17285   85 AINQDLKALFPKDELDPEYLLYWFLSIEETIESLGTGTTvKGITLEDLKSLKIPLPpLEEQkrivAILDELDELIDKLEA 164

                        170       180
                 ....*....|....*....|
gi 814724563 362 KIffnQSQIHTLEKLRDTLL 381
Cdd:cd17285  165 KL---EKLKQLKKGLMQSLL 181

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: 70.86 E-value: 2.41e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  49 INKTENYISELGLANSAAKLIPANSVIVaMYGQGDTAGRVAINK---IPLATNQACCNLVIDNKIADYHFIYYLLKNSYF 125
Cdd:cd17518   40 LDKTDRYISTEEYNGKYKHFLIDEGDIL-IASSGNSWGKVAIVEkdhLPLMLNTSTIRFKFIDGLLDNNFLKYFLNSDYF 118

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 814724563 126 --ELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKID 172
Cdd:cd17518  119 keQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIE 167

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: 70.22 E-value: 3.27e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 292 QINSIVPNENYYRYYLYLTMRSSYDLLHSMASGgTATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFNQSQIH 371
Cdd:cd17496   83 GVAAIRPKNGIDTEFLYYLLESNLDYLLAAATG-STFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIE 161

                         90
                 ....*....|....
gi 814724563 372 TLEKLRDTLLPKLM 385
Cdd:cd17496  162 KLEELRDTLLPKLL 175

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: 69.66 E-value: 6.30e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   9 KLGDVCE-------QvltggtPLTKKSDYYLNGKIPWLKTKEV--NFCRINKTENYISELGLANSAakLIPANSVIVAMY 79
Cdd:cd17270    2 TLGEVAKfrrgsfpQ------PYGNSEWYDGEGSMPFVQVADVgdNFKLVEKTKQKISKLAQPKSV--FVPKGTVIVTLQ 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  80 GqgdTAGRVAINKIPLATNQACcnLVIDNKIADYH--FIYYLLKNSyFELVLRKT-GSAQPNLNTKLLKDFDILLPPLPE 156
Cdd:cd17270   74 G---SIGRVAITQYDAYVDRTL--LIFESYKININkkFFAYQLKLK-FEIEKEKApGGTIKTITKEELSKFEIPIPSLEE 147

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 814724563 157 QFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQ 191
Cdd:cd17270  148 QKEIVNILDKFDELITELQLRKKQLEYYKKALLSF 182

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.FclI TRD1-CR1; The recognition sequence of Flavobacterium columnare G4 S subunit (S.FclI) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also contains TRD-CR-like sequence-recognition domains of type I DNA methyltransferases, such as putative Type I N6-adenine DNA methyltransferases from Microbacterium ketosireducens (M.Msp12510ORF408P) and Treponema primitia ZAS-2 (M.TprZAS2ORF3630P). It may also include various type II restriction enzymes and methyltransferases.

Pssm-ID: 341143 [Multi-domain] Cd Length: 173 Bit Score: 69.03 E-value: 7.92e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 105 VIDNKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAM 184
Cdd:cd17254   85 VVPDEEIDKDYLYYLLKALTEEIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLEEL 164


                 ....*....
gi 814724563 185 AETLFRQWF 193
Cdd:cd17254  165 RKALLQSLL 173

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: 67.68 E-value: 3.50e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 215 GKTPSKKVQSYFNGDIPFIKIPDMHGNIfLFDTSDSLTEEGKRSQSNKTLPPKSIcvsCIATVGL--------VSLNAKE 286
Cdd:cd17271   11 GATPSRGNPEYFNGDIPWITSGELNYNY-ITDTNEKITEEAVKNTNLKIHPKGTF---LIAITGLeaagtrgkCAITGIP 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 287 SQTNQQINSIVPNENYYRYYLYltmrsSYDLLHSMASG-----GTATLNLNTGNFSQIPVLYP---EQSVLEEFHSEVEp 358
Cdd:cd17271   87 ATTNQSCMAFYPTKKLTTEFLF-----YWYKKYGNYLGfkyaqGTKQQSYTADIVKKLPILLPtlkEQKKIANFLSDID- 160

                        170       180
                 ....*....|....*....|....*...
gi 814724563 359 lfDKIFFNQSQIHTLEKLRDTLLPKLMS 386
Cdd:cd17271  161 --ELIATLEKKIEKLKKIKKGLMQKLLT 186

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: 66.73 E-value: 5.03e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 225 YFNGD-IPFIKIPDMH-GNIFLFDTSDSLTEEGkrsqSNKT--LPPKSICVSCIATVGL--------------VSLNAKE 286
Cdd:cd17283   23 TFDGDgIPWIKIGDVTkDGKYITKTKEKITEEG----AKKSrlVKPGDLILSNSMSFGRpyilkidgcihdgwLVFSDLK 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 287 SQTNQQinsivpnenyyryYLYLTMRSSYDLLHSMASGGTATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFN 366
Cdd:cd17283   99 KKLDKD-------------FLYYLLSSITVQLQFSAQAGGGTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDAL 165

                        170
                 ....*....|....*.
gi 814724563 367 QSQIHTLEKLRDTLLP 382
Cdd:cd17283  166 EEKLEKLEELKKGLMQ 181

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: 66.04 E-value: 1.04e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEQV--LTGGTplTKKSDYYLNGKIPWLKTKEVNFCRINKTEN-YISELGLANSaaKLIPANSVIVAM-YG 80
Cdd:cd17252    1 WEWVRLGEIAEIIrgVTYKK--SDASEEPSEGGIPVLRANNIQNGGLDFDDLvYVPKSKVKEE--QKLKKGDILICMsSG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  81 QGDTAGRVAInkIPLATNQA----CCNLVIDNKIaDYHFIYYLLKNSYFELVLRKT--GSAQPNLNTKLLKDFDILLPPL 154
Cdd:cd17252   77 SKELVGKAAF--IDEDTDYTfgafCGVIRPKKEI-DPRYLFYFLQSPSYREYIRSLasGTNINNLSNEHLENLKIPLPPL 153

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 814724563 155 PEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLF 189
Cdd:cd17252  154 AEQKRIVAKLDKLDALIDKLKQALEKLDELLKSLF 188

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Photorhabdus luminescens S subunit (S.PluTORF4319P) TRD2-CR2; The recognition sequence of Photorhabdus luminescens S subunit (S.PluTORF4319P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341158 [Multi-domain] Cd Length: 168 Bit Score: 64.92 E-value: 2.12e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 104 LVIDNKIADYHFIYYLLKNSYFELVLRKT-GSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKID----LLHRQN 178
Cdd:cd17269   75 IHPFKEEIDPKFLYYYLKSYFKKYIEKNSvGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAelpaELEARK 154

                         90
                 ....*....|....
gi 814724563 179 KTLEAMAETLFRQW 192
Cdd:cd17269  155 KQYEYYRDALLSFA 168

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: 65.02 E-value: 2.13e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   6 KECKLGDVCEqVLTGgtpLTKKSDYYLNGKIPWLKTKEVNFCRINKTE-NYISELGLANSAAK-LIPANSVIVAMygQGD 83
Cdd:cd17519    1 EYKTLGEVCK-FQNG---FAFKSSKYRESGFPIIRITNIQNGKIDTDNlKYFDLNDYKENLDKyIVRPGDIVIAM--SGA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  84 TAGRVAINK--IPLATNQACCNLVIDNKIADYHFIYYLL---KNSYFELVlrktGSAQPNLNTKLLKDFDILLPPLPEQF 158
Cdd:cd17519   75 TTGKVGINLtdQEFYLNQRVGKFIPNEEILNNRYLYHFLlskQNEKYILA----GGSQPNLSSEKLKKIKIPIPSLEVQE 150


                 ....*.
gi 814724563 159 TIASIL 164
Cdd:cd17519  151 EIVSIL 156

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Lactococcus lactis S subunit (S.LlaAI06ORF1089P) TRD1-CR1 and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) TRD2-CR2; The recognition sequences of Lactococcus lactis S subunit (S.LlaAI06ORF1089P) and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341177 [Multi-domain] Cd Length: 163 Bit Score: 64.41 E-value: 2.87e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 115 FIYYLLKNsyFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWFV 194
Cdd:cd17288   85 FLYYLLKT--IDFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDALIELQEKLLEKLKQYKLALMQE 162

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli G4/9 S subunit (S.Eco16444ORF1681P) TRD1-CR1 and Zobellia galactanivorans DsiJT S subunit (S.ZgaJTORF2697P)TRD2; The recognition sequences of Escherichia coli G4/9 S subunit (S.Eco16444ORF1681P) and Zobellia galactanivorans DsiJT S subunit (S.ZgaJTORF2697P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various putative type II restriction enzymes and methyltransferases and may also include type I DNA methyltransferases.

Pssm-ID: 341171 [Multi-domain] Cd Length: 186 Bit Score: 64.39 E-value: 4.53e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 201 WKEKPLSFYGTIICGKtpSK----KVQSYFNGDIPFIKIPDMHG-NIFLFDTSDSLTEEGKrSQSnKTLPPKSICVSCIA 275
Cdd:cd17282    1 WEVKKLSDLGSLERGK--FKhrprNDPRLYGGDYPFIQTGDVARaNGYITSYSQTLNEKGL-AQS-KLFPKGTLCITIAA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 276 TVG--------------LVSLNAKESQTNqqinsivpnenyyRYYLYLTMRSSYDLLHSMASGgTATLNLNTGNFSQIPV 341
Cdd:cd17282   77 NIGdtailgfdacfpdsVVGFIPNEEKID-------------VEFLEYYLRTLKKELEAIAPQ-SAQKNINLEILRPLKI 142

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 814724563 342 LYPEQSVLEEFHSEVEPLFDKIFFNQSQIHTLEKLRDTLLPKL 384
Cdd:cd17282  143 PVPPLEEQKKIVEILDALDDLIDNLEKRIAKLEELKQSLLQEA 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: 63.71 E-value: 7.74e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 104 LVIDNKIADYHFIYYLLKNSYF-ELVLRKTGSA--QPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKT 180
Cdd:cd17522   99 LRPNKNIVDPKYLYYLLKSDRFrNQFRSIAKKAvnQASINQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEK 178

                         90
                 ....*....|..
gi 814724563 181 LEAMAETLFRQW 192
Cdd:cd17522  179 LKELKKGLFQKL 190

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: 62.04 E-value: 2.18e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  26 KKSDYYLNGKIP----WLKTKEVNFCRINKTENYISELGLansaaKLIPANSVIVAMYGqgdTAGRVAInkipLATNQAC 101
Cdd:cd17258    7 KDPELFCNGNIKlvciKNELINSLKVKIVEPDYKIGLKQS-----KIFKKGDVLITRHG---TIGRVSI----ILSEEAC 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 102 CN-----LVIDNKIADYHFIYYLLKNSYF-ELVLRKTGSA-QPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLL 174
Cdd:cd17258   75 LSshvagFNSKEGISDNKFIKYLFNSKKIkNRLMSYGASStQPALNLSRLLKIKFPNPPLEEQQKIGKILSTWDRAIELT 154

                        170
                 ....*....|....*....
gi 814724563 175 HRQNKTLEAMAETLFRQWF 193
Cdd:cd17258  155 EQKLELLQQQKKGLMQQLF 173

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: 61.40 E-value: 4.62e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 104 LVIDNKIADYHFIYYLLKN----SYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNK 179
Cdd:cd17261   99 LRVNEELLLPEYLALALNSpsarRQIESRATGTAGSMPKISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDRLEAQLA 178


                 ....*....
gi 814724563 180 TLEAMAETL 188
Cdd:cd17261  179 AALQLLDRL 187

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: 61.39 E-value: 5.34e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 201 WKEKPLsfyGTIIC----GKTPSKKvqsYFNGDIPFIKIPDMHGNIFLFDTSDSLTEEG-----KRSQsnktLPPKSICV 271
Cdd:cd17246    1 WEWVKL---GEISSditdGTHPTPK---YVESGIPFITSKNIKNGKIDFSDVKYISEEDhneilKRSK----LKKGDILF 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 272 SCIATVG---LVSLNAKESqTNQQINSIVPN-ENYYRYYLYLTMRSSY--DLLHSMASGGTATlNLNTGNFSQIPVLYP- 344
Cdd:cd17246   71 SIIGTIGrvaIVPEDLPAN-INQAVALIRPKkEKIDPKYLLYYLNSPIiqKQIEKNAVGGTQK-NLSLGDLKNLKIPLPp 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 814724563 345 --EQ----SVLEEfhsevepLFDKIFFNQSQIHTLEKLRDTLLPKL 384
Cdd:cd17246  149 leEQkriaAILDS-------LDALIDKLEQKLEKLEDLKKGLMQDL 187

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: 60.98 E-value: 6.72e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 210 GTIICGK-TPSKKVQSYFNGDIPFIKIPDMHGNIFLFD----TSDSLTEEGKRSqsnkTLPPKSICVSCIATVGLV---- 280
Cdd:cd17256    5 ARVKGGGrLPKGESLSDGPTGVPYIRVTDIKNGGIDLDnlkyISPEIHEKIKRY----TLSKGDILISIVGTIGRVgivp 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 281 -SLNakESQTNQQINSIVPNENYYRYYLYLTMRSSY--DLLHSMASGGT-ATLNLntGNFSQIPVLYPEQSVLEEFHSEV 356
Cdd:cd17256   81 kELD--GANLTENAARIRPKDSISPRYLYYYLRSPFgqSQIESETKGAAqPKLNL--KRIRELPIPLPPLEEQKRIVAIL 156

                        170       180
                 ....*....|....*....|....*
gi 814724563 357 EPLFDKIFFNQSQIHTLEKLRDTLL 381
Cdd:cd17256  157 DSLDAKIDALEKQLAKLEELKKALM 181

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

Pssm-ID: 341167 [Multi-domain] Cd Length: 189 Bit Score: 59.45 E-value: 1.99e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 201 WKEKPLSFYGTIICG---KtpSKKvqsYFNGDIPFIKIPDMHGNIFLFDTSDSLTEEGKRSQSNKTLPPKSICVS-CIAT 276
Cdd:cd17278    1 WEVVKLGDIADIQNGyafK--SSD---FSDEGIPVIRIGNIKNGGIDLDDNSKYPEEPLEKYEKFLLKKGDILIAmTGGT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 277 VGLVSLNAKESQT---NQQINSIVPNENYYRYYLYLTMRSSY--DLLHSMAsGGTATLNLNTGNFSQIPVLYPEQSVLEE 351
Cdd:cd17278   76 VGKVAIVPEDDEPallNQRVGKFRPKDKIDKEFLYYLLRSDSfrNQIKSSA-TGTAQPNISPKDIESIKIPLPPLEEQKK 154

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 814724563 352 FHSEVEPLFDKIffnQSQIHTLEKLRDTLLPKLMSGEV 389
Cdd:cd17278  155 IAEILDSLDAKI---DKLEQKLEKLRDLLKPLLQSLFT 189

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoAO83I TRD1-CR1 and S.AbaB8342I TRD2-CR2; Escherichia coli strain A0 34/86 S subunit (S.EcoAO83I) recognizes 5'... GGANNNNNNNNATGC ... 3, and Acinetobacter baumannii B8342 S subunit (S.AbaB8342I) recognizes 5'... TTCANNNNNNTCC ... 3. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example S.AbaB8342I-TRD1 recognizes TTCA/TGAA and S.AbaB8342I-TRD2 recognizes GGA/TCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Type IIG restriction enzyme/N6-adenine DNA methyltransferases from Thermus scotoductus RFL1 (RM.TstI) and Acinetobacter lwoffi Ks 4-8 (RM.AloI), as well as type I DNA methyltransferases such as Sideroxydans lithotrophicus ES-1 Type I N6-adenine DNA methyltransferase (M.SliESORF1090P). RM.TstI recognizes 5' ... CACNNNNNNTCC ... 3' and RM.AloI recognizes 5' ... GAACNNNNNNTCC ... 3'.

Pssm-ID: 341156 [Multi-domain] Cd Length: 158 Bit Score: 57.80 E-value: 4.46e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 298 PNENYYRYYLYLTMRssydlLHSMaSGGTA--TLNLNtgNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFNQSQIHTLEK 375
Cdd:cd17267   79 GNDPRFLYYLLKTLD-----LERL-NSGSAvpGLNRN--DVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEE 150


                 ....*...
gi 814724563 376 LRDTLLPK 383
Cdd:cd17267  151 LADALLPK 158

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: 57.85 E-value: 5.51e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 290 NQQINSIVPNENYYRYYLYLTMRssYDLLHSMASGGTATL-NLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFNQS 368
Cdd:cd17254   79 NQHIFKVVPDEEIDKDYLYYLLK--ALTEEIESQAHGSTMvHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEE 156

                         90
                 ....*....|....*..
gi 814724563 369 QIHTLEKLRDTLLPKLM 385
Cdd:cd17254  157 QLKKLEELRKALLQSLL 173

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

Pssm-ID: 341142 [Multi-domain] Cd Length: 193 Bit Score: 58.26 E-value: 6.38e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  80 GQG-DTAGRVAI--NKIPLATNQaccNLVI----DNKIADYHFIYYLLkNS-----YFELVLRKTgSAQPNLNTKLLKDF 147
Cdd:cd17253   73 GGDsDKLGRGAIwrGEIPPCLHQ---NHLFrvrpKDDLLLPEFLSYWL-NSaygrgYFLRAAKQT-TNLASINSTKLKAL 147

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 814724563 148 DILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17253  148 PVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193

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: 57.12 E-value: 1.09e-09

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814724563 113 YHFIYYLLKNSYFELVLRKTGSAQPN-LNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLL-HRQNKTLEAMAE 186
Cdd:cd17265  100 NDYLFHLFNSDLFKKQIGSFLTATINqITNGNLNNFKIPLPPLEEQEKIAEFLSSLDAKIDKLiKKIEKLIELKKE 175

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Eco2747II TRD2-CR2 and S.Eco2747AII TRD2-CR2; Escherichia coli ST2747 S subunit (S.Eco2747II) and Escherichia coli ST2747A s SUBUNIT (S.Eco2747AII) recognize 5'... GAANNNNNNNTAAA ... 3'. Generally The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains mainly TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341161 [Multi-domain] Cd Length: 189 Bit Score: 57.05 E-value: 1.68e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCeqvlTGGTPLTKKSDYYLNGKIPWLKTKEVNFCRINKTenYISELGLANSAAKLIPANSVIVAMYGQ-GD 83
Cdd:cd17272    1 VEEKTLGDIA----VDGFQNGPAPNFDEKGEIPVITSKNISNGKIDFE--YVKYDFLSISKNRKINKGDILITMIGTiGE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  84 TAGRVAINKIPLATNQACCNLVIDNKIADYHFIYYLLKNSYFELVLRKTGsaQPNLNTKLLKDFDILLPPLPEQFTIASI 163
Cdd:cd17272   75 TAIVKCLDPKFYTLNLYLIRLKKEKLLPSYLKYFLDSEKFLNKSISATSG--QGYLKANQIDKLEIPLPPLEEQQRIVKI 152

                        170
                 ....*....|.
gi 814724563 164 LssldDKIDLL 174
Cdd:cd17272  153 L----DKFDTL 159

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Flavobacterium columnare S subunit (S.Fco49512ORF2615P) TRD2-CR2; The recognition sequence of Flavobacterium columnare S subunit (S.Fco49512ORF2615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341144 [Multi-domain] Cd Length: 166 Bit Score: 56.00 E-value: 2.21e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 101 CCNLVIDNKIADYHFIYYLLKNSYFELVlrkTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKT 180
Cdd:cd17255   78 CGVLKVKNKNINNKFLYYALNLIAKKYV---SFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIAKLKK 154

                         90
                 ....*....|.
gi 814724563 181 LEAMAETLFRQ 191
Cdd:cd17255  155 LIELRKKQLEY 165

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: 56.06 E-value: 3.39e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 105 VIDNKIaDYHFIYYLL----KNSYFELVLRKTGSaQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKT 180
Cdd:cd17526  102 VKKSKI-NPEFLARYLhllwRSGYFKKLCTNWVN-QAGINSDTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEA 179

                         90
                 ....*....|...
gi 814724563 181 LEAMAETLFRQWF 193
Cdd:cd17526  180 LLELAKSLFEDLL 192

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: 55.70 E-value: 3.40e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   8 CKLGDVCEqVLTGGTPltkKSDYY--LNGKIPWLKTKeVNFcrinkTENYISELGL-ANSAAKLIPANSVIVAMygqgdt 84
Cdd:cd17499    1 VRLGDVAE-IIMGQSP---EGKSYntNKEGLPFYQGK-KEF-----GDKYIKEPNTwTTSPTKIAEKNDILMSV------ 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  85 agRVAINKIPLATNQAC---------CNLVIDNKiadyhFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLP 155
Cdd:cd17499   65 --RAPVGDVNITTRKICigrglaairAKKNIDKK-----YLFYFLLSNKDYFKGKSGGSTFKSINKNQIKNIKIPLPPLE 137

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 814724563 156 EQFTIASILSSLDDKIDLLHRQNKTLEAMAETLFRQWF 193
Cdd:cd17499  138 EQKRIVSELDKLFKLIFEAKNNIEEALANAQQLFKSIL 175

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2; 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: 54.48 E-value: 8.17e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 108 NKIADYHFIYYLLKNSYFELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKID-LLHRQNKTLEAMAE 186
Cdd:cd17497   89 KKGLDKKYLLYYLKSIENELSSLGTGSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDELTAKIDqLIALLEKAIELLKE 168


                 ....*
gi 814724563 187 tlFRQ 191
Cdd:cd17497  169 --YRQ 171

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 56.81 E-value: 1.03e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   4 EWKECKLGDVCEqVLTGGTPLTKKSDYYLN-GKIPWLKTKEVNFCRINKTENYISELGLANSAAKLIPANSVIVAmygQG 82
Cdd:PRK09737   9 GWVTTHISEICS-VIRGVKPPKGYATKSLTmGDLPFIRTTDITNGAVDLTTLPYCMDAPEDVSKYQLQDRDIVIS---SA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  83 DTAGRVAINKIPLATNQACCNLVIDNKIADYHFIYYL---LKNSYF--ELVLRKTGSAQPNLNTKLLKDFDILLPPLPEQ 157
Cdd:PRK09737  85 GSIGFSFLAQNPLPSNVVFASFAIRLKPVNYFSEYFLkhfLESSDYrnQLSLMSAGNAVQNINAQSLSTLTFPIPPIAEQ 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 158 FTIASILSSLDDKIDllhRQNKTLEAMAETL--FRQ--------------WFVEEADEGWKEKPLSFYGTIICGKTPSKK 221
Cdd:PRK09737 165 KIIAEKLDTLLAQVD---STKARLEQIPQILkrFRQavlgaavsgklteeWRWPDLPSTWSVHKYSELVDSRLGGMSSKA 241

                        250       260
                 ....*....|....*....|....*...
gi 814724563 222 VQsyFNGDIPFIKIPDMHGniFLFDTSD 249
Cdd:PRK09737 242 NN--FGSATPYLRNINVRW--GSFDLED 265

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: 53.97 E-value: 1.34e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 298 PNENYYRYYLYLTMrSSYDLLHSMAsgGTATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFNQSQIHTLEKLR 377
Cdd:cd17262   89 GKNGISTEFLYYYL-NSIDISPYVT--GAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELK 165


                 ....*..
gi 814724563 378 DTLLPKL 384
Cdd:cd17262  166 KALLQKL 172

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: 53.74 E-value: 2.00e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 204 KPLSFYGTIICGKTPS-KKVQSYFNGD-IPFIKIPDMHgNIFLFDTSDSLTEEGKRSQSNKTLPPKSICVsciA------ 275
Cdd:cd17276    1 KKIGDIAKTSSGGTPLrSNQEYYFNGGtIPWVKTTDLN-NGVIYETEEKITEKALKETSCKLLPKGTVLV---Amyggfg 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 276 TVGLVSLNAKESQTNQQINSIVPNEN-YYRYYLYLTMRSSYDLLHSMASGGTATLNLNTGNFSQIPVLYP---EQSVLEE 351
Cdd:cd17276   77 QIGRTGLLGIPAAINQAICAILPNEKkVNPEFLLRYLNFNRPYWMRVAASSRKDPNITKDDVRNFPIPLPpldEQRAIVE 156

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 814724563 352 FHSEVEPLFDKiffnqsQIHTLEKLRDtLLPKLMS 386
Cdd:cd17276  157 FLSDVDALIDS------LEALIEKLRE-LKKGLMQ 184

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: 53.32 E-value: 2.60e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 204 KPLS-FYGTIICGKTPSKKVQSYFNGDIPFIKIPDMHgNIFLFDTSDSLTEEGKRSQSN-KTLPPKSICVSCI-ATVGLV 280
Cdd:cd17280    1 WKIShLFGLIGSGTTPKSDNEDYYDGGIPWVTTGDLR-DGIITETSKKITDKALDDYSAlKIYPAGSLVIAMYgATIGRL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 281 SLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGTATlNLNTGNFSQIPVLYP---EQ----SVLEEFH 353
Cdd:cd17280   80 GILGIDATTNQACCVLSGSNKIDIKFLFYWLLANRDELISLASGGGQP-NISQELIKSLRIPVPpleEQkqiaAFLDKKT 158

                        170       180
                 ....*....|....*....|....*..
gi 814724563 354 SEVEPLFDKIffnQSQIHTLEKLRDTL 380
Cdd:cd17280  159 AKIDSLIEKK---ERLIELLKERRQAL 182

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: 52.85 E-value: 3.74e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 104 LVIDNKIADYHFIYYLLKNSYFELVLR---KTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKT 180
Cdd:cd17524   98 IRLNEEKILPEYLNYFLNSPYGRKQIKsvaTQGVGQANINATKLKAIPIPLPPLEEQKEIVEKLDELDALIDRLEALLEE 177

                         90
                 ....*....|.
gi 814724563 181 LEAMAETLFRQ 191
Cdd:cd17524  178 AEELLESLLQS 188

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 54.89 E-value: 4.04e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 199 EGWKEKPLSFYGTIICGKTPSKK--VQSYFNGDIPFIKIPDM-HGNiflFDTSD-SLTEEGKRSQSNKTLPPKSICVSCI 274
Cdd:PRK09737   8 EGWVTTHISEICSVIRGVKPPKGyaTKSLTMGDLPFIRTTDItNGA---VDLTTlPYCMDAPEDVSKYQLQDRDIVISSA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 275 ATVGLVSLNAKESQTNQQINSIV----PNENYYRYYL-YLTMRSSYDLLHSMASGGTATLNLNTGNFSQIPVLYPEqsvl 349
Cdd:PRK09737  85 GSIGFSFLAQNPLPSNVVFASFAirlkPVNYFSEYFLkHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPP---- 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 814724563 350 eefhseveplfdkifFNQSQIhTLEKLrDTLLPKLMSGEVRVE 392
Cdd:PRK09737 161 ---------------IAEQKI-IAEKL-DTLLAQVDSTKARLE 186

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoBI TRD1-CR1, S.EcoSanI TRD1-CR1, and S.EcoVR50I TRD1-CR1; Escherichia coli B S subunit (S.EcoBI) and Escherichia coli VR50 S subunit (S.EcoVR50I) recognize 5'... TGANNNNNNNNTGCT ... 3', while Escherichia coli Sanji S subunit (S.EcoSanI) recognizes 5'... TGANNNNNNCTTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341146 [Multi-domain] Cd Length: 176 Bit Score: 52.14 E-value: 5.39e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  98 NQACCNLVIDNKIADYHFIYYLLKnSYFELVLRKTGSAQ-PNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHR 176
Cdd:cd17257   83 NQRVCRIRPKSEELDKRFLYYALP-PPLKAIEDTTSSTTvKHLSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLIA 161

                         90
                 ....*....|....*
gi 814724563 177 QNKTLEAMAETLFRQ 191
Cdd:cd17257  162 KLEKLRDLLLPLLQS 176

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: 49.85 E-value: 1.98e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 107 DNKIADYHFIYYLLKNSYFELVlrkTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQNKTLEAMAE 186
Cdd:cd17292   66 DESKVLNKFLYYFYQIIKWKKT---EGSTIKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIALKK 142


                 ....*..
gi 814724563 187 TLFRQWF 193
Cdd:cd17292  143 GLMQYLF 149

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) TRD1-CR1, Neisseria meningitidis 510612 S subunit ; Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) recognizes 5'... CTANNNNNNNNTGT ... 3', and the recognition sequences of Neisseria meningitidis 510612 S subunit (S.Nme510612ORF1157P) and Streptococcus mitis SVGS_061 S subunit (S2.Smi61ORF7905P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) TRD1 recognizes CTA/TAG, and TRD2 recognizes ACA/TGT. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341170 Cd Length: 196 Bit Score: 49.90 E-value: 5.23e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 200 GWKEKPLSFYGTIICGKTPSKKVQSYF-NGDIPFIKIPD--MHGNIfLFDTSDSLTEEG-KRSqsnKTLPPKSICVSCIA 275
Cdd:cd17281    1 GVEWKKLGEIFDIRNGYTPSKSNKEYWeNGTIPWFRMEDirENGRI-LSDSIQHITPSAvKGG---KLFPANSIILSTTA 76

                         90       100
                 ....*....|....*....|....*..
gi 814724563 276 TVGLVSLNAKESQTNQQINSIVPNENY 302
Cdd:cd17281   77 TIGEHALITVDSLANQRFTNFSLKKSY 103

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) TRD2-CR2 and Lactobacillus amylovorus GRL 1112 S subunit (S1.L; The recognition sequences of Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) and Lactobacillus amylovorus GRL 1112 S subunit (S1.LamGRLORF5415P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341185 [Multi-domain] Cd Length: 171 Bit Score: 46.75 E-value: 3.35e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814724563 112 DYHFIYYLLKNSYFELVlrKTGSAQPNLNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLLHRQ 177
Cdd:cd17494   92 IFLYLYLLNIEGYWSKI--SQGSTFESINSNDIKNLKISIPSLEEQQKIATFLSTLDAEITLLEKK 155

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: 45.12 E-value: 1.32e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 814724563 336 FSQIPVLYPEQSVLEEFHSEVEPLFDKIFFNQSQIHTLEKLRDTLLPKLM 385
Cdd:cd17260  116 LENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165

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: 44.38 E-value: 2.31e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 297 VPNENYYRYYLYLTMrSSYDLLhSMASGgTATLNLNTGNFSQIPVLYPEQSVLEEFHSEVEPLFDKIFFNQSQIHTLEKL 376
Cdd:cd17288   76 EIKKNNDPKFLYYLL-KTIDFK-KYNEA-TGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDALIELQEKLLEKL 152

                         90
                 ....*....|.
gi 814724563 377 RDTLLPKLMSG 387
Cdd:cd17288  153 KQYKLALMQEL 163

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoBI TRD1-CR1, S.EcoSanI TRD1-CR1, and S.EcoVR50I TRD1-CR1; Escherichia coli B S subunit (S.EcoBI) and Escherichia coli VR50 S subunit (S.EcoVR50I) recognize 5'... TGANNNNNNNNTGCT ... 3', while Escherichia coli Sanji S subunit (S.EcoSanI) recognizes 5'... TGANNNNNNCTTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341146 [Multi-domain] Cd Length: 176 Bit Score: 44.44 E-value: 2.61e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 290 NQQINSIVPNENYY-RYYLYLTMRSSYDLLHSMASGGTATlNLNTGNFSQIPVLYPEqsvLEEFHSEVEPLFDKIFFNQS 368
Cdd:cd17257   83 NQRVCRIRPKSEELdKRFLYYALPPPLKAIEDTTSSTTVK-HLSSKDIDEIELPLPP---LEEQRRIAEILDELDALIDK 158

                         90
                 ....*....|....*...
gi 814724563 369 QIHTLEKLRDTLLPKLMS 386
Cdd:cd17257  159 LIAKLEKLRDLLLPLLQS 176

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: 43.78 E-value: 4.13e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 220 KKVQSYFNGDIPFIKIPDMH---GNIFLFDTSDSLTEEGKRSQSNKTLPPKSICVSCIAtvGLVSLN-----AKESQTNQ 291
Cdd:cd17250   17 EKYQGKEDGEYPFYKVGDMNnsgNEKYLSTAENYISEEIVKELKAKLFPKGTIIFAKIG--EAIKLNrrailSKDSCIDN 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 292 QINSIVPNENYYRYYLYLTMRSS--YDLlhsmaSGGTATLNLNTGNFSQIPVLYP---EQ----SVLEEFHSEVEPLFDK 362
Cdd:cd17250   95 NVMGLIPNEGIDSEYLYYWLKKVdlYKY-----SQATTVPSIRKSTLESIPIPLPpleEQkriaAKLDELFEKLDKLKQA 169

                        170
                 ....*....|....*....
gi 814724563 363 IFFNQSQihtLEKLRDTLL 381
Cdd:cd17250  170 LEAAKEQ---LKGLRQSLL 185

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 44.87 E-value: 6.19e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEQVLTGGTPLTKKS----DYYLNGKIPWLKTKEVNFCRINKTENYISELGLANsaaklipaNSVIVAMYG 80
Cdd:PRK09737 221 WSVHKYSELVDSRLGGMSSKANNFgsatPYLRNINVRWGSFDLEDLQDILISDIERRELKLKL--------GDVLFCRGN 292

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  81 QGDTAGRVAINK----IPLATNQACCNL-VIDNKIADYhfIYYLLKN---SYFELVLRKTGSAQPNLNTKLLKDFDILLP 152
Cdd:PRK09737 293 EPLEVGRCAIWKepqdIPVIYQKALIRArVKDDIIPEY--LVYNLKSpdsRNISLSQLFTGTTQKHITGKALANYPIRVP 370

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 814724563 153 PLPEQFTIASILSSL---DDKID-----LLHRQNKTLEAMAETLFR-----QWFVEEAD 198
Cdd:PRK09737 371 PLEEQAEIVRRVEQLfayADTIEkqvnnALARVNNLTQSILAKAFRgeltaQWRAENPS 429

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

Pssm-ID: 341157 [Multi-domain] Cd Length: 185 Bit Score: 43.20 E-value: 7.05e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563   5 WKECKLGDVCEqvLTGGTPLTKKsDYYLNGkIPWLK-----TKEVNFcrINKTENYISElglaNSAAKLIPANS--VIVA 77
Cdd:cd17268    1 VEWKTLGEIGE--FIRGKGITKK-DFVESG-VPCIHygeiyTKYGIY--TTKTKSFISE----ELAKKLRKAKPgdLLIA 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563  78 myGQGDTA---GR-VA-INKIPLATNQACCNL--VIDNKiadyhFIYYLLKNSYFELVLRK--TGSAQPNLNTKLLKDFD 148
Cdd:cd17268   71 --GTGETIediGKaVAwLGDEEVAAGGDIIIFrhSQNPK-----YLSYLLNSPAFQKQKRKlgTGTKVVHISASDLAKIK 143

                        170       180
                 ....*....|....*....|....*....
gi 814724563 149 ILLPPLPEQFTIASILSSLDDKIDLLHRQ 177
Cdd:cd17268  144 IPVPPLEEQERIVEILDKFDALIAGLPAE 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: 41.45 E-value: 2.94e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 814724563 108 NKIADYHFIYYLLKNSYFELVLRKTGSAQPN---LNTKLLKDFDILLPPLPEQFTIASILSSLDDKIDLL-HRQNKTLE 182
Cdd:cd17525  103 DDIVLPYFINYYLNSPDGKKQLESIASGTTSvaaIYQKDLKKLKLPLPPLDEQREIVSFLSELDAKIDQLeQKLEKLLQ 181

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: 40.94 E-value: 3.47e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 108 NKIADYHFIYYLLKNSYFELvlrktgsaqpnlntkllKD-----------FDILLPPLPEQFTIASILSSLDDKIDLLHR 176
Cdd:cd17274   91 NNNVNLKFVYEALQTIKYVP-----------------GDhkrhwiseyskFKIPLPPLEEQNKIVRILDKFDELIAELEA 153

                         90
                 ....*....|....*...
gi 814724563 177 QNKTLEAMAETLFRQWFV 194
Cdd:cd17274  154 KLELLKKQKKYYLQKLFT 171

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2 and Aminobacterium colombiense DSM 12261 S subunit (S.Aco12; The S.Aco12261I S subunit recognizes 5'... GCANNNNNNTGT ... 3', while the recognition sequence is undetermined for S.TteMORF1547P TRD2-CR2. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. S.TteMORF1547P TRD1-CR1 and S.Aco12261I TRD2-CR2 do not belong to this family. This family may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341134 [Multi-domain] Cd Length: 174 Bit Score: 40.60 E-value: 4.66e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 258 SQSNKTLPPKSICVSCIATVGLVSLNAKESQTNQQINSIVPNENYYRYYLYLTMRSSYDLLHSMASGGTATlNLNTGNFS 337
Cdd:cd17245   48 TKPTKIAEKGDILISVRAPVGDVNIADEKCCIGRGLAAIRANKDIDNLFLYYYLKYNKPELEKLGTGSTFK-AINKKDLE 126

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 814724563 338 QIPVLYPEQSVLEEFHSEVEPLFDKIFFNQSQIHTLEKLRDTLLPKLM 385
Cdd:cd17245  127 ELKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKLDELKKGLMQELF 174

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: 38.67 E-value: 2.52e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 201 WKEKPL------SFYGTiicgktpSKKvQSYFNGDIPFIKIPDM-HGNIFLFDTSDSLTEEGK---------------RS 258
Cdd:cd17517    1 WEVVKLgdlledPRYGT-------SKK-SSYDGSGTPVLRIPNIyDGGIDLDDLKKRVDLSEKelekyllkkgdilfnRS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814724563 259 QSNKTLppksicvscIATVGLVSLNAKESqtnqqINS-----IVPNENYYR-YYLYLTMRSSY--DLLHSMASGGTATLN 330
Cdd:cd17517   73 NGSPEL---------VGKCALVDEEDEPA-----IFAsylirLRLDKKKILpEFLYYYLNSPLgrKQIEKIAKSAAGQAN 138

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 814724563 331 LNTGNFSQIPVLYP---EQsvlEEFHSEVEPLFDKIFFNQSQIHTLEKLRDTLLPKL 384
Cdd:cd17517  139 INQKDLKKLPIPLPpleEQ---KEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192