NCBI Conserved Domain Search

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: 203.12 E-value: 1.99e-64

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSQPPKSTFKYELEDGYVRLLQIRDYKSDDNLTYIPESSTKKFCSKDDVMIGRYGPPVFQILRGLEGAY 85
Cdd:cd17263     1 VKLGEVCKFSKGKQPPISERFDEPKEGSVRYIQIEDLRNNNEKKYIENPKKSVICNEDDILIVRDGANAGEVGTGLEGAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  86 NVALMKAQPSEKV-DRDYLFYFLKQEKLFRLIdgLSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKR 164
Cdd:cd17263    81 ASTLFKIIPDKNIiDKDYLYYFLKSKEIQLNI--LTKAGSTIPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALIDKL 158

                         170
                  ....*....|....*....
gi 1675114791 165 QQATQLADDFLRSVFLDMF 183
Cdd:cd17263   159 KELIEKLIELKKGLFQELL 177

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: 166.16 E-value: 6.48e-50

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKITDGTHDTPSKVNEGVKFVTGKNIRPFKLDLTDLKYVTQYVHEEIYNRCNPEYGDLLLTNIGAgTGNA 272
Cdd:cd17246     1 WEWVKLGEISSDITDGTHPTPKYVESGIPFITSKNIKNGKIDFSDVKYISEEDHNEILKRSKLKKGDILFSIIGT-IGRV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 273 C-FNSLTEAFSMKNVALVKSSPNKLSGRFLEYLFNHEGFKsKLLGENSKGGAQKFLSLKVIREASIPVPTFKEQLKFSAI 351
Cdd:cd17246    80 AiVPEDLPANINQAVALIRPKKEKIDPKYLLYYLNSPIIQ-KQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQKRIAAI 158

                         170       180       190
                  ....*....|....*....|....*....|
gi 1675114791 352 VEKV-----KNGNLLDPNLSLKKvELFDSL 376
Cdd:cd17246   159 LDSLdalidKLEQKLEKLEDLKK-GLMQDL 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: 113.77 E-value: 6.69e-30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIggSQPPKSTFKYElEDGYvRLLQIRDYKSD----DNLTYIPESSTKKFCS-----KDDV---MIGRY 70
Cdd:cd17246     1 WEWVKLGEISSDI--TDGTHPTPKYV-ESGI-PFITSKNIKNGkidfSDVKYISEEDHNEILKrsklkKGDIlfsIIGTI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  71 GPPVFqILRGLEGAYNVALMKAQPS-EKVDRDYLFYFLKQEKLFRLIDGlSQRTAGQSGVDMNALKAYPMLLPPLEEQKR 149
Cdd:cd17246    77 GRVAI-VPEDLPANINQAVALIRPKkEKIDPKYLLYYLNSPIIQKQIEK-NAVGGTQKNLSLGDLKNLKIPLPPLEEQKR 154

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1675114791 150 IAAILDKADAIRRKRQQATQLADDFLRSVFLDMFG 184
Cdd:cd17246   155 IAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLLT 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: 96.68 E-value: 9.24e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSQPPKStfKYELEDGYVRLLQIRDYK------SDDNLTYIPESSTKKFCS-KDDVMIGRYGPP--VFQ 76
Cdd:cd16961     1 KKLGEIAEIISGKTPSSS--SEYWDNGIIPWIRISDINnggiilTDEKITEEGAEKLKKKILpKGDILISRSGTIgkVAI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  77 ILRGLEGAYNVALMKAQPSEKVDRDYLFYFLKQEKLFRLIDGLSqrTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDK 156
Cdd:cd16961    79 VKENDKALLNQAVIVIRPKDEVDSEFLYYFLKSPFGKKLIEGSA--GSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDK 156

                         170
                  ....*....|....*..
gi 1675114791 157 ADAIRRKRQQATQLADD 173
Cdd:cd16961   157 LDALIELLEQKLEKLEQ 173

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 99.96 E-value: 5.70e-23

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGSQPPKSTFKYELEDGYVRLLQIRDY-KSDDNLTYI------PESSTKKFCSKDDVMIGRYGPPVF 75
Cdd:PRK09737   10 WVTTHISEICSVIRGVKPPKGYATKSLTMGDLPFIRTTDItNGAVDLTTLpycmdaPEDVSKYQLQDRDIVISSAGSIGF 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  76 QILRGLEGAYNVAL----MKAQPSEKVDRDYLFYFLKQEKLFRLIDGLSQrTAGQSGVDMNALKAYPMLLPPLEEQKRIA 151
Cdd:PRK09737   90 SFLAQNPLPSNVVFasfaIRLKPVNYFSEYFLKHFLESSDYRNQLSLMSA-GNAVQNINAQSLSTLTFPIPPIAEQKIIA 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 152 AILD----KADAIRRKRQQATQLADDFLRSVFLDMFGDPVTN-------PMGWEVKQLNDVATKITDGTHDTPSKVNEGV 220
Cdd:PRK09737  169 EKLDtllaQVDSTKARLEQIPQILKRFRQAVLGAAVSGKLTEewrwpdlPSTWSVHKYSELVDSRLGGMSSKANNFGSAT 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 221 KFVTGKNIRPFKLDLTDLKYVTqyVHEEIYNRCNPEYGDLLLTNIGAGTGN---ACFNSLTEAFSMKNVALVKSS-PNKL 296
Cdd:PRK09737  249 PYLRNINVRWGSFDLEDLQDIL--ISDIERRELKLKLGDVLFCRGNEPLEVgrcAIWKEPQDIPVIYQKALIRARvKDDI 326

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 297 SGRFLEYLFNHEGFKSKLLGENSKGGAQKFLSLKVIREASIPVPTFKEQ----------LKFSAIVEKVKNGNLLDPNls 366
Cdd:PRK09737  327 IPEYLVYNLKSPDSRNISLSQLFTGTTQKHITGKALANYPIRVPPLEEQaeivrrveqlFAYADTIEKQVNNALARVN-- 404

                         410
                  ....*....|....*....
gi 1675114791 367 lkkvELFDSLSQKAFAGEL 385
Cdd:PRK09737  405 ----NLTQSILAKAFRGEL 419

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: 90.19 E-value: 2.41e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSQPPKSTFKY-----------ELEDGYVrllqirdYKSDDNLTY--IPESSTKKFcSKDDVMIGRYGP 72
Cdd:cd17515     1 VKLGDIGKWGSGGTPSRSNPEYygggipwiksgELNDGYI-------TSTEEKITEegLKNSSAKLF-PKGSVLIAMYGA 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  73 PVFQ--ILrGLEGAYNVALMKAQPSEKVDRDYLFYFLKQEKLfRLIdglSQRT-AGQSGVDMNALKAYPMLLPPLEEQKR 149
Cdd:cd17515    73 TAGKvgIL-GIDAATNQAICAILPNEEIDNEFLFYFLKSQKE-YLI---SLGKgGAQPNISQGIIKNIEIPLPPLAEQKR 147

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1675114791 150 IAAILDKADAIRRKRQQATQLADDFLRSVFLDMF 183
Cdd:cd17515   148 IVAKLDKLDKLIEKLEKALEKLEELKKALMQKLL 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: 88.77 E-value: 8.75e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGSQPPKSTFKYELEDGYVRLLQ---IRDYK-SDDNLTYIPES--STKKFCSKDDVMI--------- 67
Cdd:cd17252     1 WEWVRLGEIAEIIRGVTYKKSDASEEPSEGGIPVLRannIQNGGlDFDDLVYVPKSkvKEEQKLKKGDILIcmssgskel 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  68 -GRygppVFQILRGLEGAYNVALMKAQPSEKVDRDYLFYFLKQEKLFRLIDGLSQrTAGQSGVDMNALKAYPMLLPPLEE 146
Cdd:cd17252    81 vGK----AAFIDEDTDYTFGAFCGVIRPKKEIDPRYLFYFLQSPSYREYIRSLAS-GTNINNLSNEHLENLKIPLPPLAE 155

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1675114791 147 QKRIAAILDKADAIRRKRQQATQLADDFLRSVFL 180
Cdd:cd17252   156 QKRIVAKLDKLDALIDKLKQALEKLDELLKSLFQ 189

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: 87.66 E-value: 1.93e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSQPPKSTFKYeLEDGYVRLLQIRDYKS---DDNLTYIPE-----SSTKKFcSKDDVM------IGRYG 71
Cdd:cd17296     1 KKLGEICSIQSGGTPSRSKKEY-WNNGTIPWVKISDCKNkyvDETEEFITEeglnnSSAKLL-KKGTILiaifatIGKVG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  72 ppvfqILrGLEGAYNVALMKAQP-SEKVDRDYLFYFLKQEKLFRLIDGlsqRTAGQSGVDMNALKAYPMLLPPLEEQKRI 150
Cdd:cd17296    79 -----IL-KIEATTNQAIAGIKPkNKSINPKYLYYYLKSLYEKFLSLG---RGVAQNNINLSILKNLKIPLPPLEEQQRI 149

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1675114791 151 AAILDKADAIRRKRQQATQLADDFLRSVFLDMF 183
Cdd:cd17296   150 VAILDKFEKLINKRQEGLQLLDELVKSLFEEMF 182

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: 82.93 E-value: 9.67e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   5 VVELGSVVTfiGGSQPPKSTFKYELEDgyVRLLQIRDYKSD----DNLTYIPESSTKKF----CSKDDVMIGRYGPP--V 74
Cdd:cd17256     1 LGEIARVKG--GGRLPKGESLSDGPTG--VPYIRVTDIKNGgidlDNLKYISPEIHEKIkrytLSKGDILISIVGTIgrV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  75 FQILRGLEGAyNV--ALMKAQPSEKVDRDYLFYFLKQEKLFRLIDGlSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAA 152
Cdd:cd17256    77 GIVPKELDGA-NLteNAARIRPKDSISPRYLYYYLRSPFGQSQIES-ETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVA 154

                         170       180
                  ....*....|....*....|....*..
gi 1675114791 153 ILDKADA----IRRKRQQATQLADDFL 175
Cdd:cd17256   155 ILDSLDAkidaLEKQLAKLEELKKALM 181

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: 82.68 E-value: 1.43e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSQPPKstfKYEL-EDGYVRLLQIRDYKSDDNLTYIpeSSTKKFCSKDDVMI--GRYGPP---VF---- 75
Cdd:cd17250     1 VRLGDVCDFKAGSGFPE---KYQGkEDGEYPFYKVGDMNNSGNEKYL--STAENYISEEIVKElkAKLFPKgtiIFakig 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  76 --------QILrGLEGAYNVALMKAQPSEKVDRDYLFYFLKQEKLFRLIDG-----LSQRTagqsgvdmnaLKAYPMLLP 142
Cdd:cd17250    76 eaiklnrrAIL-SKDSCIDNNVMGLIPNEGIDSEYLYYWLKKVDLYKYSQAttvpsIRKST----------LESIPIPLP 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1675114791 143 PLEEQKRIAAILDKADAIRRKRQQATQLADDFLRSVFLDMF 183
Cdd:cd17250   145 PLEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGLRQSLL 185

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: 81.40 E-value: 3.59e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVV-TFIGGSQPPKStfKYELEDGYVRLLQIRDYKsDDNLT----YIPE----SSTKKFCSKDDVMIG-RYGPPVF 75
Cdd:cd17285     1 KKLGDLVeKIVGGGTPSKS--NPEYWNGDIPWASVKDLK-GKYLTstedKITEeglkNSSSNLIPKGTVIIAtRMGLGKV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  76 QILRglegaYNVAL---MKA-QPSEKVDRDYLFYFLKqeKLFRLIDGLSQRTAGQsGVDMNALKAYPMLLPPLEEQKRIA 151
Cdd:cd17285    78 AINK-----IDVAInqdLKAlFPKDELDPEYLLYWFL--SIEETIESLGTGTTVK-GITLEDLKSLKIPLPPLEEQKRIV 149

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1675114791 152 AILDKADAIRRKRQQATQLADDFLRSVFLDMF 183
Cdd:cd17285   150 AILDELDELIDKLEAKLEKLKQLKKGLMQSLL 181

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

Pssm-ID: 341134 [Multi-domain] Cd Length: 174 Bit Score: 80.66 E-value: 4.87e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSQPPKSTfkYELEDGYVRLLQirdYKSDDNLTYiPE-----SSTKKFCSKDDVMIG-RygPPVfqilr 79
Cdd:cd17245     1 VKLGEVAEIIMGQSPPSST--YNEEGEGLPFLQ---GKADFGEIY-PTprvwcTKPTKIAEKGDILISvR--APV----- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  80 gleGAYNVALMKA---------QPSEKVDRDYLFYFLKQEKLFrlidgLSQRTAGQ--SGVDMNALKAYPMLLPPLEEQK 148
Cdd:cd17245    68 ---GDVNIADEKCcigrglaaiRANKDIDNLFLYYYLKYNKPE-----LEKLGTGStfKAINKKDLEELKIPLPPLEEQQ 139

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1675114791 149 RIAAILDKADAIRRKRQQATQLADDFLRSVFLDMF 183
Cdd:cd17245   140 KIAEILSTVDEAIEKTKALIEKLDELKKGLMQELF 174

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: 79.57 E-value: 2.06e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGSqPPKSTfKYElEDGyVRLLQIRDYKSD----DNLTYIPESSTKKF----CSKDDVMIGRYG--P 72
Cdd:cd17512     1 WEEIRLGDIIDYQKGY-AFKSK-DYQ-DSG-IRIVRVSDFTDDsidiNNLVYISEEKANKYkkyeLKENDIIITTVGswP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  73 P--------VFQILRGLEGAY---NVALMKAQpSEKVDRDYLFYFLKQEKLFRLIDGLSQRTAGQSGVDMNALKAYPMLL 141
Cdd:cd17512    77 SnpdsvvgkVVRVPKEADGALlnqNAVKIRPK-KGILDQSFLFYNLKSERFKNYIESIARGNANQASITLGDIKKFKFLL 155

                         170
                  ....*....|....*..
gi 1675114791 142 PPLEEQKRIAAILDKAD 158
Cdd:cd17512   156 PPLEEQKKIASILSAYD 172

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: 79.12 E-value: 2.64e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   8 LGSVVTFIGGSQ----PPKSTFKYE---------LEDGYVrllqirdykSDDNLTYIPEsstKKFCS-------KDDVMI 67
Cdd:cd17264     2 LGDIAEFINGDRgknyPSKSEFVDEgipfinaghLEDGTI---------DLSNMNFISE---EKYNSlgsgklqKGDILY 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  68 grygppvfqILRG-----------LEGAYNVALMKAQPSEKVDRDYLFYFLK----QEKLFRLIDGLSQR--TAGQsgvd 130
Cdd:cd17264    70 ---------CLRGslgkcaivdnyDEGAIASSLVIIRPFAKVDVRYLYYYLNsplgKSQIKKYDNGSAQPnlSAKS---- 136

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1675114791 131 mnaLKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLADDFLRSVFL 180
Cdd:cd17264   137 ---LKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQSLFQ 183

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

Pssm-ID: 341167 [Multi-domain] Cd Length: 189 Bit Score: 75.24 E-value: 5.88e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGSQPPKSTFKyelEDGY--VRLLQIRD-YKSDDNLTYIPESSTKKF----CSKDDVMI----GRYG 71
Cdd:cd17278     1 WEVVKLGDIADIQNGYAFKSSDFS---DEGIpvIRIGNIKNgGIDLDDNSKYPEEPLEKYekflLKKGDILIamtgGTVG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  72 PPVFqILRGLEGAY---NVALMKaqPSEKVDRDYLFYFLKQEKLFRLIDGLSQRTAgQSGVDMNALKAYPMLLPPLEEQK 148
Cdd:cd17278    78 KVAI-VPEDDEPALlnqRVGKFR--PKDKIDKEFLYYLLRSDSFRNQIKSSATGTA-QPNISPKDIESIKIPLPPLEEQK 153

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1675114791 149 RIAAILDKADAIRRKRQQATQLADDFLRSVFLDMFG 184
Cdd:cd17278   154 KIAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLFT 189

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

Pssm-ID: 341138 [Multi-domain] Cd Length: 185 Bit Score: 74.41 E-value: 1.05e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSQPPKSTFKY-----------ELEDGYVrllqirdYKSDDNLTY--IPESSTKkFCSKDDV------M 66
Cdd:cd17249     1 VRLGDLGKFLSGGTPSKSNPEYwggdipwvspkDMKSDYI-------SDSEDHITElaVEESGTK-LVPAGSVlivvrgM 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  67 IGRYGPPVfqilrglegAYN---VAL---MKA-QPSEKVDRDYLFYFLK--QEKLFRLIDglsqrTAGqSGV---DMNAL 134
Cdd:cd17249    73 ILAHTFPV---------AITtrpVAFnqdIKAlIPKEGIDPEFLLYALKanEDRILSLVD-----KAG-HGTgslDTDDL 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1675114791 135 KAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLADDFLRSVFLDM 182
Cdd:cd17249   138 KNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEELLKALMQAL 185

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: 73.78 E-value: 2.37e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  95 SEKVDRDYL---FYFLKQEKLFRlidGLSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLA 171
Cdd:cd17526   104 KSKINPEFLaryLHLLWRSGYFK---KLCTNWVNQAGINSDTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEAL 180

                          90
                  ....*....|..
gi 1675114791 172 DDFLRSVFLDMF 183
Cdd:cd17526   181 LELAKSLFEDLL 192

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: 72.95 E-value: 4.45e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  95 SEKVDRDYLFYFLKQEKLFRLIDGLSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLADDF 174
Cdd:cd17522   103 KNIVDPKYLYYLLKSDRFRNQFRSIAKKAVNQASINQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEKLKEL 182


                  ....*...
gi 1675114791 175 LRSVFLDM 182
Cdd:cd17522   183 KKGLFQKL 190

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: 72.11 E-value: 6.42e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSqppksTFKYE--LEDGY--VRLLQIRDYKSDDNLT--YIPEsstKKFCSKDDVMIGR---YGPpvfQ 76
Cdd:cd17254     1 VKLGDLATFINGR-----AFKPSewSDSGLpiIRIQNLNGGNAPFNYYsgLLDE---KYYVEKGDLLFSWsasFGP---F 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  77 ILRGLEGAYNVALMKAQPSEKVDRDYLFYFLKQeklfrLIDGLSQRTAGqSG---VDMNALKAYPMLLPPLEEQKRIAAI 153
Cdd:cd17254    70 IWNGGKAILNQHIFKVVPDEEIDKDYLYYLLKA-----LTEEIESQAHG-STmvhITKGDLENIKVPLPPLEEQKRIAAI 143

                         170       180       190
                  ....*....|....*....|....*....|
gi 1675114791 154 LDKADAIRRKRQQATQLADDFLRSVFLDMF 183
Cdd:cd17254   144 LDELDALIDALEEQLKKLEELRKALLQSLL 173

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to TRD2-CR2's of StySKI, S.EcoAI, S.EcoJA17PI, and S.EcoJA23PI; Salmonella kaduna CDC-388 S subunit (StySKI) recognizes 5'... CGATNNNNNNNGTTA ... 3' while Escherichia coli Type-1 restriction enzyme EcoAI specificity protein (S.EcoAI), Escherichia coli UCD_JA17_pb S subunit (S.EcoJA17PI) and Escherichia coli UCD_JA23_pb S subunit (S.EcoJA23PI) recognize 5'... GAGNNNNNNNGTCA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341148 [Multi-domain] Cd Length: 189 Bit Score: 71.39 E-value: 1.53e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGSQPPKSTFKyelEDGyVRLLQI----RDYKSDDNLTYIPESSTKKFCS----KDDVMIGRYGPpv 74
Cdd:cd17259     1 WEWVKLGDVADILSGYAFKSSEFS---ESG-IRLLRGanvgVGEIRWDDTVYLPEEYLEEYEKyllkEGDIVIALDRP-- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  75 fQILRGLegayNVALMKAQ--------------PSEKVDRDYLFYFLKQEKLFRLIDglsqrtAGQSGVD-----MNALK 135
Cdd:cd17259    75 -IISGGL----KVARIPKSdlpallvqrvarirPKDELNSDFLYYLLQSDFFLNYVE------PVLTGTDvphisTKQIK 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1675114791 136 AYPMLLPPLEEQKRIAAILD----KADAIRRKRQQATQLADDFLRS 177
Cdd:cd17259   144 NFKIPLPPLEEQKKIAEFLSsldaLIDLLEQKLEKLQQLKKGLMQS 189

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: 3.26e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  54 SSTKKFCSKDDVMIGRYGPPVfqilrgleGAYNVA---------LMKAQPSEKVDRDYLFYFLKQeklfrLIDGLSQRTA 124
Cdd:cd17496    48 TKPTKLCKKGDILFCVRGSTT--------GRLNIAddeycigrgVAAIRPKNGIDTEFLYYLLES-----NLDYLLAAAT 114

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1675114791 125 G--QSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLADDFLRSVFLDMF 183
Cdd:cd17496   115 GstFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTLLPKLL 175

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: 69.77 E-value: 3.73e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  94 PSEKVDRDYLFYFLKQEKlFRLIdGLSQRT--AGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLA 171
Cdd:cd17260    76 PKEGILPEFLYYLLRSPS-FRKE-AIKSMTgsSGRQRVPKDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETL 153

                          90
                  ....*....|..
gi 1675114791 172 DDFLRSVFLDMF 183
Cdd:cd17260   154 EELLDALLPKLL 165

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: 70.24 E-value: 3.85e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSQPPKSTFKY-----------ELEDGYVRLLQIRDYKSDDNltyIPESSTKKfCSKDDVMIG-RYGpp 73
Cdd:cd17513     1 VKLGELGKFIGGGTPSTKNPEYwngnipwitssDLSEDDIFKINIRKFITEEA---IKNSATKI-IPANSILIVtRVG-- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  74 VfqilrgleGayNVALMKAQ-----------PSEKVDRDYLFYFLKqeklfRLIDGLSQRTAGQS--GVDMNALKAYPML 140
Cdd:cd17513    75 V--------G--KVAINPFDictsqdftsliPIKEVNPLFLAYLLY-----SLLQKLKSQLQGTSikGITKDDLKNLKIP 139

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1675114791 141 LPPLEEQKRIAAILDKADAIRRKRQQATQLADDFLRSVFLDMF 183
Cdd:cd17513   140 LPPLEEQQKIAAILSKLDKLIEAHEKKLEKLKQLKKGLMQKLF 182

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: 69.45 E-value: 6.11e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 198 LNDVATKITDG-THDTPSKVNE--GVKFVTGKNIRPFKLDLTDLKYVTQYVHEEIYN-RCNPeyGDLLLTnIgAGT-GNA 272
Cdd:cd17256     1 LGEIARVKGGGrLPKGESLSDGptGVPYIRVTDIKNGGIDLDNLKYISPEIHEKIKRyTLSK--GDILIS-I-VGTiGRV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 273 CF--------NsLTEafsmkNVALVKSSPNKLSgRFLEYLFNHEGFKSKLLGEnSKGGAQKFLSLKVIREASIPVPTFKE 344
Cdd:cd17256    77 GIvpkeldgaN-LTE-----NAARIRPKDSISP-RYLYYYLRSPFGQSQIESE-TKGAAQPKLNLKRIRELPIPLPPLEE 148

                         170
                  ....*....|.
gi 1675114791 345 QLKFSAIVEKV 355
Cdd:cd17256   149 QKRIVAILDSL 159

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: 69.50 E-value: 6.84e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  94 PSEKVDRDYLFYFLK--QEKLFRLIDGLSQR--TAGQsgvdmnaLKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQ 169
Cdd:cd17275   100 KDEKLDFEFLYYWLLslKNELKRLIRTGTQAnlNAEI-------VKNLPIPLPPLEEQKKIAEILDKIDAEIDKLEEKIE 172

                          90
                  ....*....|....
gi 1675114791 170 LADDFLRSVFLDMF 183
Cdd:cd17275   173 KLRELKKGLLQKMF 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: 68.71 E-value: 8.98e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGSqpPkstFKYEL---EDGYVRLLQIRDYKSDDNLTYIPESSTKKF-CSKDDVMIGRYGPpvFQIL 78
Cdd:cd17257     1 WEVVRLGDVADVQNGF--P---FKSKLfndEGGGLPLIRIRDLKSGDTETYYTGEYDEKYlVKNGDILIGMDGD--FNAA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  79 R--GLEGAYNVALMKAQP-SEKVDRDYLFYFLkqEKLFRLIDG---------LSQRTagqsgvdmnaLKAYPMLLPPLEE 146
Cdd:cd17257    74 IwkGGDALLNQRVCRIRPkSEELDKRFLYYAL--PPPLKAIEDttssttvkhLSSKD----------IDEIELPLPPLEE 141

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1675114791 147 QKRIAAILDKADAIRRKRQQATQLADDFLRSVFLD 181
Cdd:cd17257   142 QRRIAEILDELDALIDKLIAKLEKLRDLLLPLLQS 176

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

Pssm-ID: 341133 [Multi-domain] Cd Length: 180 Bit Score: 68.65 E-value: 1.13e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  96 EKVDRDYLFYFLKQeklfRLIDGLSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLADDFL 175
Cdd:cd17244    99 KKIDTEYLYYYLKS----FDYSSLGSTASKGKTLNSKKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDELL 174


                  ....*.
gi 1675114791 176 RSVFLD 181
Cdd:cd17244   175 PKLMSG 180

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

Pssm-ID: 341150 [Multi-domain] Cd Length: 191 Bit Score: 68.72 E-value: 1.52e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFI--GGSQPPKstfkyELEDGY--VRL--LQIRDYKSDDNlTYIPESSTKK---FCSKDDVMIGRYGPP 73
Cdd:cd17261     1 WEWVRLGDLIEGIrnGWSPKPP-----DDETGWpvLKLsaVTSGKFDPSEN-KYLPESLEPAseyWLKPGDLLISRANTS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  74 ----VFQILRGLEgaYNVA----LMKAQPSE-KVDRDYLFYFLKQEKLFRLIDGLSQRTAG-QSGVDMNALKAYPMLLPP 143
Cdd:cd17261    75 elvgRAALVDGDP--DNLIypdkLIRLRVNEeLLLPEYLALALNSPSARRQIESRATGTAGsMPKISQSDLKSLPIPLPP 152

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1675114791 144 LEEQKRIAAILD----KADAIRRKRQQATQLADDFLRSV 178
Cdd:cd17261   153 LAEQKRIVARVDellaLIDRLEAQLAAALQLLDRLRQAL 191

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR),similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Salmonella enterica subsp. enterica serovar Potsdam S sub; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3' and Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 both recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2.It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.

Pssm-ID: 341198 [Multi-domain] Cd Length: 192 Bit Score: 68.33 E-value: 1.72e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTfiggsqPPKS--TFKYELEDGYVRLLQIRDYKS-----DDNLTYI--PESSTKKF-CSKDDVMIGR--- 69
Cdd:cd17517     1 WEVVKLGDLLE------DPRYgtSKKSSYDGSGTPVLRIPNIYDggidlDDLKKRVdlSEKELEKYlLKKGDILFNRsng 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  70 --------------YGPPVFqilrgleGAYnvaLMKAQP-SEKVDRDYLFYFLKQEKLFRLIDGLSQRTAGQSGVDMNAL 134
Cdd:cd17517    75 spelvgkcalvdeeDEPAIF-------ASY---LIRLRLdKKKILPEFLYYYLNSPLGRKQIEKIAKSAAGQANINQKDL 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1675114791 135 KAYPMLLPPLEEQKRIAAILD----KADAIRRKRQQATQLADDFLRSV 178
Cdd:cd17517   145 KKLPIPLPPLEEQKEIVEILEsldsKIDLLEKKLEKLEQLFKSLMQSL 192

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: 67.89 E-value: 2.10e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVtfiggsqppkSTFKY------ELEDGYVRLLQIRD------YKSDDNLTYIPESSTKKFC-SKDDVMIGR 69
Cdd:cd17521     1 WEVKKLGELS----------EKIQYgytasaAYEDGGPRYLRITDiqddgvLWDTVPYCSISEEDAEKYLlKDGDILFAR 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  70 YGPPV---FQILRGLEGA----YnvaLMKAQP-SEKVDRDYLFYFLKQEKLFRLIDGLSQRTAgQSGVDMNALKAYPMLL 141
Cdd:cd17521    71 TGATVgksYLYKEDDGKAvfasY---LIRFRPnKKKVLPKYLFYFTQSSLYWKQIKSISSGSA-QPNINAEKLKSLKIPL 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1675114791 142 PPLEEQKRIAAILDKADA----IRRKRQQATQLADDFLRSV 178
Cdd:cd17521   147 PPLEEQKRIVAILDALDAkidaLEELLEKLEELLKELLQSL 187

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: 66.71 E-value: 5.62e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  94 PSEKVDRDYLFYFLKQEKlFRLidglsQRTAGQSGV------DMNALkayPMLLPPLEEQKRIAAILDKADAIRRKRQQA 167
Cdd:cd17293    94 PNKSVDPKFLYYQLLSSK-FQL-----QAIASSTTLpiinksKFEKI---EIPLPPLEEQKRIVAKLDKLFALIDKLEES 164

                          90
                  ....*....|....*.
gi 1675114791 168 TQLADDFLRSVFLDMF 183
Cdd:cd17293   165 LEELDELLKSLFQSAF 180

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: 66.25 E-value: 7.07e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 196 KQLNDVAtKITDGThdTPSKVNE-----GVKFVTGKNIRPFKLDLTDLKYVtqYVHEEIYNRCNPEYGDLLLTNIGaGTG 270
Cdd:cd16961     1 KKLGEIA-EIISGK--TPSSSSEywdngIIPWIRISDINNGGIILTDEKIT--EEGAEKLKKKILPKGDILISRSG-TIG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 271 NACFNSLTEAFSMKNVALVKSSPNKLSGRFLEYLFNHEGFKSKLlgENSKGGAQKFLSLKVIREASIPVPTFKEQLKFSA 350
Cdd:cd16961    75 KVAIVKENDKALLNQAVIVIRPKDEVDSEFLYYFLKSPFGKKLI--EGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIAN 152


                  ....
gi 1675114791 351 IVEK 354
Cdd:cd16961   153 ILDK 156

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: 66.35 E-value: 7.53e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFI-GGSQPPKSTFKYELEDGYVRLlQIRDYKSDDN-LTYIPESSTKK------FCSKDDVMI---GRYGPPV 74
Cdd:cd17283     1 KKLGDISEIVrGASPRPIGDPITFDGDGIPWI-KIGDVTKDGKyITKTKEKITEEgakksrLVKPGDLILsnsMSFGRPY 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  75 fqILrGLEGAYN---VALMKaqPSEKVDRDYLFYFLKQEKLFRLidglSQRTAGQSGVDMNA--LKAYPMLLPPLEEQKR 149
Cdd:cd17283    80 --IL-KIDGCIHdgwLVFSD--LKKKLDKDFLYYLLSSITVQLQ----FSAQAGGGTKNLNTdiVKNLKIPLPPLEEQKR 150

                         170       180       190
                  ....*....|....*....|....*....|
gi 1675114791 150 IAAILDKADA----IRRKRQQATQLADDFL 175
Cdd:cd17283   151 IAEILDSLDAlidaLEEKLEKLEELKKGLM 180

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: 65.97 E-value: 1.15e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  53 ESSTKKFCsKDDVMIGRYGppvfQ--------ILrGLEGAYNVALMKAQPSEKVDRDYLFYFLKqeKLFRLIDGLSqRTA 124
Cdd:cd17287    54 NSSAKLFP-KGTLLMAMYG----QgktrgrvaIL-GIEAATNQACAAILPNDGINPDFLFYYLQ--SSYEELRDLS-NGG 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1675114791 125 GQSgvDMNA--LKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLADDFLRSV 178
Cdd:cd17287   125 GQP--NLNAglIKSIEIPVPPLDEQQKIAAFLSAIDAKIDALEQKLELLQELKKSL 178

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: 65.61 E-value: 1.68e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVAT-------KitdgthdtpSK--VNEGVKFVTGKNIRPFKLDLTDLKYVTqYVHEEIYNRCNPEYGDLLLT 263
Cdd:cd17278     1 WEVVKLGDIADiqngyafK---------SSdfSDEGIPVIRIGNIKNGGIDLDDNSKYP-EEPLEKYEKFLLKKGDILIA 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 264 NIGAGTGNACFNSLTEAFSMKN--VALVKSSpNKLSGRFLEYLFNHEGFKSKLLGeNSKGGAQKFLSLKVIREASIPVPT 341
Cdd:cd17278    71 MTGGTVGKVAIVPEDDEPALLNqrVGKFRPK-DKIDKEFLYYLLRSDSFRNQIKS-SATGTAQPNISPKDIESIKIPLPP 148

                         170
                  ....*....|....
gi 1675114791 342 FKEQLKFSAIVEKV 355
Cdd:cd17278   149 LEEQKKIAEILDSL 162

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: 64.35 E-value: 3.66e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  94 PSEKVDRDYLFYFLKQEKlfRLIDGLSqrtagqSG-----VDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQAT 168
Cdd:cd17273   100 PNEEIDNEFLYYLLKNNK--PEIESLA------SGstfkeISKSTFKKIEIPLPPLEEQKKIAAILSKLDELIELLEKEN 171

                          90
                  ....*....|....*
gi 1675114791 169 QLADDFLRSVFLDMF 183
Cdd:cd17273   172 EKLKELRDGLLPKLF 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: 63.32 E-value: 8.91e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   2 SWPVVELGSVVTfIG-GSQPPKSTFKYELEDGY-------VRLLQIRDykSDDNLTY--IPESSTKKFcSKDDVMIGRYG 71
Cdd:cd17247     3 HWEVVRLGDVAR-VGnGSTPSRKNPDYWNGGTIpwvssgeVNDNRITE--ADEFITElaLKECSLPLV-PPGSVLVAMIG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  72 ppvfQ--------ILRgLEGAYNVALMKAQPSE-KVDRDYLFYFLKQ--EKLFRLIDGlsqrtAGQSGVDMNALKAYPML 140
Cdd:cd17247    79 ----QgktrgqaaILA-IEATINQNLAAIRPNEeRVLPEYLHYYLESqyDELRRIGSG-----GGQGALNCGILKAFPIP 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1675114791 141 LPPLEEQKRIAAILD----KADAIRRKRQQATQLADDFLRSV 178
Cdd:cd17247   149 LPPLDEQREIVAELEallaKIDLLEEKIARLIELLKELRQAL 190

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1 and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) TRD2-CR; The recognition sequences of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341183 [Multi-domain] Cd Length: 188 Bit Score: 62.89 E-value: 1.39e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGSQPPKSTFKYeLEDGYVRLL---QIRD---YKSDDNLTY--IPESSTKkFCSKDDVMIGRYGppv 74
Cdd:cd17294     1 WEWKTLGEIAKIFSGGTPSTSNPEY-WDGGTIPWLssgEVNFkeiYETEKRITEegLKNSSAK-WIPKNSVLIALAG--- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  75 fQ--------ILRgLEGAYN--VALMKAQPsEKVDRDYLFYFLKQ--EKLfRLIDGLSQRtagqSGVDMNALKAYPMLLP 142
Cdd:cd17294    76 -QgktrgtvaILK-IPLTTNqsLAAIEPDE-EIANSRFLYYNLSSryEEL-RSLSGGGGR----GGLNLKIIKSLPIPLP 147

                         170       180
                  ....*....|....*....|....*....
gi 1675114791 143 PLEEQKRIAAILDKADA-IRRKRQQATQL 170
Cdd:cd17294   148 PLEEQKKIVAILDKFDAlINDLKEGLPAL 176

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: 61.69 E-value: 1.80e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  90 MKAQPSEKVDRDYLFYFLKQEKLFRLIDGlsqrtAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQ 169
Cdd:cd17266    74 LVVTPKKENNIKFLYYLLKSLNLNQYATG-----SAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLE 148

                          90
                  ....*....|
gi 1675114791 170 LADDFLRSVF 179
Cdd:cd17266   149 KLIELKKELM 158

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: 61.78 E-value: 3.41e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKITDGTHDTPSKVNEGVKFVTGKNIRPFKLDLTDLKYVTQyVHEEIYNRCNPEYGDLLLTNIG---AGT 269
Cdd:cd17517     1 WEVVKLGDLLEDPRYGTSKKSSYDGSGTPVLRIPNIYDGGIDLDDLKKRVD-LSEKELEKYLLKKGDILFNRSNgspELV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 270 GNAC-FNSLTE--AFS---MKnvalVKSSPNKLSGRFLEYLFNHEGFKSKLLGeNSKGGAQKF-LSLKVIREASIPVPTF 342
Cdd:cd17517    80 GKCAlVDEEDEpaIFAsylIR----LRLDKKKILPEFLYYYLNSPLGRKQIEK-IAKSAAGQAnINQKDLKKLPIPLPPL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1675114791 343 KEQLKFSAIVEKVKngNLLDPNLSLKKV--ELFDSLSQKA 380
Cdd:cd17517   155 EEQKEIVEILESLD--SKIDLLEKKLEKleQLFKSLMQSL 192

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: 61.31 E-value: 4.37e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 258 GDLLLT---NIGAgTG----NACF-NSLteafsmknVALVkSSPNKLSGRFLEYLFNHegFKSKLLgENSKGGAQKFLSL 329
Cdd:cd17282    68 GTLCITiaaNIGD-TAilgfDACFpDSV--------VGFI-PNEEKIDVEFLEYYLRT--LKKELE-AIAPQSAQKNINL 134

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1675114791 330 KVIREASIPVPTFKEQLKFSAIVEKVkNGNLLDPNLSLKKVE-LFDSLSQKAF 381
Cdd:cd17282   135 EILRPLKIPVPPLEEQKKIVEILDAL-DDLIDNLEKRIAKLEeLKQSLLQEAF 186

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.MgeORF438P TRD1-CR1 and TRD2-CR2, and to Escherichia coli G5 S subunit (S.Eco16445ORF5013P ) TRD2-CR2 and Acetobacter pasteuri; The recognition sequences of Mycoplasma genitalium G-37 S subunit (S.MgeORF438P), Escherichia coli G5 S subunit (S.Eco16445ORF5013P), and Acetobacter pasteurianus IFO 3283-01 S subunit (S2.Apa3283ORF14230P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341180 [Multi-domain] Cd Length: 161 Bit Score: 60.22 E-value: 6.22e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  93 QPSEKVDRDYLFYFLK--QEKLFRLidglsQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAI---------R 161
Cdd:cd17291    78 SSKNELVNKFLYYFLKnkQEEIYSL-----QRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFTELtaelpaeleA 152


                  ....
gi 1675114791 162 RKRQ 165
Cdd:cd17291   153 RKKQ 156

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: 60.26 E-value: 9.40e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  54 SSTKKFCSKDDVMIG-RygPPVfqilrgleGAYNVA---------LMKAQPSEKVDRDYLFYFLK--QEKLFRLIDGlSQ 121
Cdd:cd17497    48 SAPKKIAEKGDILLSvR--APV--------GPTNIAdqeycigrgLAAIRPKKGLDKKYLLYYLKsiENELSSLGTG-ST 116

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1675114791 122 RTAgqsgVDMNALKAYPMLLPPLEEQKRIAAILDKA----DAIRRKRQQATQLADDFLRSV 178
Cdd:cd17497   117 FKA----ISKEDLENLLIPLPPLAEQKRIAAFLDELtakiDQLIALLEKAIELLKEYRQAV 173

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 57.76 E-value: 1.10e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 303 YLFNHEGFKSKLLgENSKGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKVKNgNLLDPNLSLKKV-ELFDSLSQKAF 381
Cdd:COG0732     4 YYLRSPSFREYLR-SLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFD-KIAALEKEIEKLkELRDALLPKLF 81


                  ....
gi 1675114791 382 AGEL 385
Cdd:COG0732    82 TGEL 85

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: 59.58 E-value: 2.06e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  95 SEKVDRDYLFYFLKQEKLFRLIDGLSQrTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLADDF 174
Cdd:cd17289   104 IKDINSKFLYYWFQSSIFKNQINSITI-GSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEEL 182


                  ....*....
gi 1675114791 175 LRSVFLDMF 183
Cdd:cd17289   183 AKTLFQYWF 191

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: 58.60 E-value: 2.72e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  64 DVMIGRYGPPVFQIlrglEGAYNV-----ALmkaQPSEKVDRDYLFYFLKQEKLFRLIDGlsqrtAGQSGVDMNALKAYP 138
Cdd:cd17262    61 ANLLSRGTPIAFYV----SGKFWVnnhahVL---KGKNGISTEFLYYYLNSIDISPYVTG-----AAQPKLNQANLNSIP 128

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1675114791 139 MLLPPLEEQKRIAAILDKADA-IRRKRQQATQL 170
Cdd:cd17262   129 IPLPPLEEQKKIVAILDKLDAlIDLLEEELEKL 161

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: 58.98 E-value: 3.29e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATkitDGTHDTP---SKVNEGVKFVTGKNIRPFKLDLTDLKYVtqyvHEEIYNRCNPEYGDLLLTNIGAGT 269
Cdd:cd17272     1 VEEKTLGDIAV---DGFQNGPapnFDEKGEIPVITSKNISNGKIDFEYVKYD----FLSISKNRKINKGDILITMIGTIG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 270 GNACFNSLTEAFSMKNVALVKSSPNKLSGRFLEYLFNHEGFKSKllgENSKGGAQKFLSLKVIREASIPVPTFKEQLKFS 349
Cdd:cd17272    74 ETAIVKCLDPKFYTLNLYLIRLKKEKLLPSYLKYFLDSEKFLNK---SISATSGQGYLKANQIDKLEIPLPPLEEQQRIV 150


                  ....*
gi 1675114791 350 AIVEK 354
Cdd:cd17272   151 KILDK 155

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: 57.16 E-value: 1.47e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  94 PSEKVDRDYLFYFLKQEK--LFRLIDGLSQRTAGqsgvdMNALKAYPMLLPPLEEQKRIAAILD----KADAIRRKRQQA 167
Cdd:cd17248   103 CGPELDPEYLLYVLRAMKpeFERLAMGSTHKTIY-----MPDFKALRIALPPLEEQRKIVDRLEaldaKIDALERKLERL 177


                  ....*
gi 1675114791 168 TQLAD 172
Cdd:cd17248   178 IELLK 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: 55.82 E-value: 2.38e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGSQPPKSTFKYELEDGYVRllqiRDYKSDDNLTYIPESSTKKFcSKDDVMIGRYGPPVFQILRGLE 82
Cdd:pfam01420   4 WEVFKLGDVFEIKKGKTPKKKELKNNGKYPYIR----AGDLNNVVKGGLGYIKKYIL-PKGDITISSRATIGYVFYRDKP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  83 GAYNVALMKAQPSEK---VDRDYLFYFLKQEKLFRLIDGlsqrtAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADA 159
Cdd:pfam01420  79 YYTNQHIIVLIPKNNikiTEFLYLYLLLKLKKLKSLKFG-----STQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDN 153

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 53.91 E-value: 2.43e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1675114791 105 YFLKQEKLFRLIDGLSQRTAgQSGVDMNALKAYPMLLPPLEEQKRIAAILDKA-DAIRRKRQQATQL 170
Cdd:COG0732     4 YYLRSPSFREYLRSLATGST-QPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLfDKIAALEKEIEKL 69

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: 55.48 E-value: 2.55e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1675114791 102 YLFYFLKQEKLFRLIDGlsqrtAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLADDFLRSVF 179
Cdd:cd17267    84 FLYYLLKTLDLERLNSG-----SAVPGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADALL 156

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: 56.01 E-value: 3.20e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 213 PSK---VNEGVKFVTGKNIRPFKLDLTDLKYVTQYVHEEIyNRCNPEYGDLLLTNIGAGTGNACFNSLTEAFSMKNVALV 289
Cdd:cd17264    18 PSKsefVDEGIPFINAGHLEDGTIDLSNMNFISEEKYNSL-GSGKLQKGDILYCLRGSLGKCAIVDNYDEGAIASSLVII 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1675114791 290 KSSPNKLSgRFLEYLFNHEGFKSKLLGENSkGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17264    97 RPFAKVDV-RYLYYYLNSPLGKSQIKKYDN-GSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDEL 160

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

Pssm-ID: 341142 [Multi-domain] Cd Length: 193 Bit Score: 55.94 E-value: 3.77e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 192 GWEVKQLNDVATkitdgthdtpskVNEGV----KFVTGKNIRPF---------KLDLTDLKYVTqyVHEEIYNRCNPEYG 258
Cdd:cd17253     1 GWEWVRLGDVAE------------VQSGItkgkKRRGGELEVPYlrvanvqdgYLDLSEVKEIE--VTEEELERYRLRKG 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 259 DLLLT------NIGAGT------GNACF-NSLteaFSmknvalVKSSPNKLSGRFLEYLFNHEGFKSKLLGE-------N 318
Cdd:cd17253    67 DLLVTeggdsdKLGRGAiwrgeiPPCLHqNHL---FR------VRPKDDLLLPEFLSYWLNSAYGRGYFLRAakqttnlA 137

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1675114791 319 SkggaqkfLSLKVIREASIPVPTFKEQLKFSAIVEKV-----KNGNLLDpnlslKKVELFDSLSQKAF 381
Cdd:cd17253   138 S-------INSTKLKALPVPLPPLEEQRRIVERLDELlalidALEASLA-----KLEELLKALRQALL 193

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: 55.78 E-value: 4.05e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   8 LGSVVTFIGGSqPPKSTFKYELEDGYVRLLQIRDYKSD-DNLTYIPESSTKKFCSK-----DDVMIGRYGPPVFQI---L 78
Cdd:cd17519     5 LGEVCKFQNGF-AFKSSKYRESGFPIIRITNIQNGKIDtDNLKYFDLNDYKENLDKyivrpGDIVIAMSGATTGKVginL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  79 RGLEGAYNVALMKAQP-SEKVDRDYLFYFL--KQEKLFrlidglSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILD 155
Cdd:cd17519    84 TDQEFYLNQRVGKFIPnEEILNNRYLYHFLlsKQNEKY------ILAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILD 157


                  .
gi 1675114791 156 K 156
Cdd:cd17519   158 K 158

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: 55.51 E-value: 5.05e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1675114791  84 AYNVALMKAQPsEKVDRDYLFYFLKQEKLFRLIDglsQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAI 160
Cdd:cd17272    87 TLNLYLIRLKK-EKLLPSYLKYFLDSEKFLNKSI---SATSGQGYLKANQIDKLEIPLPPLEEQQRIVKILDKFDTL 159

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: 54.93 E-value: 5.76e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGsQPPKSTFKYELEDGyvrlLQIRDYKSDDNLTYIPESST-----KKFCSKDDV-MIGRygPPVfqilr 79
Cdd:cd17499     1 VRLGDVAEIIMG-QSPEGKSYNTNKEG----LPFYQGKKEFGDKYIKEPNTwttspTKIAEKNDIlMSVR--APV----- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  80 gleGAYNVA---------LMKAQPSEKVDRDYLFYFLK-QEKLFRLIDGLSQRTAgqsgVDMNALKAYPMLLPPLEEQKR 149
Cdd:cd17499    69 ---GDVNITtrkicigrgLAAIRAKKNIDKKYLFYFLLsNKDYFKGKSGGSTFKS----INKNQIKNIKIPLPPLEEQKR 141

                         170
                  ....*....|....*..
gi 1675114791 150 IAAILDKADAIRRKRQQ 166
Cdd:cd17499   142 IVSELDKLFKLIFEAKN 158

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: 55.13 E-value: 6.19e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 302 EYLFNH-EGFKSKLLgENSKGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKVKNG-NLLDPNLSLKKvELFDSLSQK 379
Cdd:cd17515   102 EFLFYFlKSQKEYLI-SLGKGGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKLiEKLEKALEKLE-ELKKALMQK 179


                  ..
gi 1675114791 380 AF 381
Cdd:cd17515   180 LL 181

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: 54.52 E-value: 7.12e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  96 EKVDRDYLFYFLKqeKLFRLIDGLSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADA--------IRRKRQQA 167
Cdd:cd17269    80 EEIDPKFLYYYLK--SYFKKYIEKNSVGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDAltaelpaeLEARKKQY 157


                  ....*....
gi 1675114791 168 TQLADDFLR 176
Cdd:cd17269   158 EYYRDALLS 166

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

Pssm-ID: 341204 [Multi-domain] Cd Length: 190 Bit Score: 54.55 E-value: 9.31e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1675114791  94 PSEKVDRDYLFYFLKQEKLFRLIDGLSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLA 171
Cdd:cd17523   102 DQEKIDPEFLSYIFNSPLIRRKIERNFVTSAGQKTVNQGHIKSLPIPLPPLKEQKKIVARVEELFALIDQLESSLDLA 179

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: 54.33 E-value: 1.11e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGSQPPKSTFKYeLEDGYVRLLQIRDYksDDNLTYIpeSSTKKFCSK---DD--------------- 64
Cdd:cd17277     1 WPIVKLGEVCEIINGSTPSKKNEEY-WNNGTIKWLTIPDI--DERGLII--SSTKQFITEkalEEkkvklvpknsvllsc 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  65 -VMIGRYGppvfqILRGlEGAYN---VALMKAQpsEKVDRDYLFYFLKQEKlFRLIDglSQRTAGQSGVDMNALKAYPML 140
Cdd:cd17277    76 tATIGKVA-----IAKI-ELTTNqqiNALICKD--SKILPEYLFYALKHIK-QVLER--LTTNPGVKHVNLSMLSNLQIP 144

                         170
                  ....*....|..
gi 1675114791 141 LPPLEEQKRIAA 152
Cdd:cd17277   145 LPPLEVQKKIVA 156

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: 54.40 E-value: 1.37e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  95 SEKVDRDYLFYFLKQEKLFRLIDGLSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILD----KADAIRRKRQQATQL 170
Cdd:cd17253   105 DDLLLPEFLSYWLNSAYGRGYFLRAAKQTTNLASINSTKLKALPVPLPPLEEQRRIVERLDellaLIDALEASLAKLEEL 184


                  ....*....
gi 1675114791 171 ADDFLRSVF 179
Cdd:cd17253   185 LKALRQALL 193

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) TRD2-CR2 and Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) TRD2-CR2; Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) recognizes 5'... CCANNNNNNNCTTC ... 3' and the recognition sequence of Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.

Pssm-ID: 341205 [Multi-domain] Cd Length: 189 Bit Score: 53.62 E-value: 2.10e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIG-GSqppkSTFKYELEDGY--VRLLQIRDYKSDD-NLTY--IPESSTKKFC-SKDDVMI-------- 67
Cdd:cd17524     1 WEWVTIGDLVTSVQyGT----SEKKSEDEGGYpvLRMGNIQDGGIDDdDLKYvdLDEKEFEKYLlKKGDVLFnrtnspel 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  68 -GRYGppVFQilrgLEGAYNVA--LMKAQP-SEKVDRDYLFYFLKQEKLFRLIDGLSQRTAGQSGVdmNA--LKAYPMLL 141
Cdd:cd17524    77 vGKTA--IFR----GDGPATFAsyLIRIRLnEEKILPEYLNYFLNSPYGRKQIKSVATQGVGQANI--NAtkLKAIPIPL 148

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1675114791 142 PPLEEQKRIAAILDKADAIRRKRQQATQLADDFLRSVF 179
Cdd:cd17524   149 PPLEEQKEIVEKLDELDALIDRLEALLEEAEELLESLL 186

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

Pssm-ID: 341150 [Multi-domain] Cd Length: 191 Bit Score: 53.31 E-value: 2.76e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKITDGTHDTPSKVNEGVKFVTGKNIRPFKLDLTDLKYVTqyVHEEIYNRCNPEYGDLLLTNigAGT--- 269
Cdd:cd17261     1 WEWVRLGDLIEGIRNGWSPKPPDDETGWPVLKLSAVTSGKFDPSENKYLP--ESLEPASEYWLKPGDLLISR--ANTsel 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 270 -GNAC-FNSLTEAFS-----MKnvalVKSSPNKLSGRFLEYLFNHEGFKSKLLgENSKG--GAQKFLSLKVIREASIPVP 340
Cdd:cd17261    77 vGRAAlVDGDPDNLIypdklIR----LRVNEELLLPEYLALALNSPSARRQIE-SRATGtaGSMPKISQSDLKSLPIPLP 151

                         170
                  ....*....|....*.
gi 1675114791 341 TFKEQLkfsAIVEKVK 356
Cdd:cd17261   152 PLAEQK---RIVARVD 164

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: 52.47 E-value: 3.82e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   3 WPVVELGSVVTFIGGsqppkstfkyeledgyvrllqiRDYKSDDNLTY-------IPESSTKKFCSKDDVMIGRYGP--- 72
Cdd:cd17288     1 WEVKKLGDLLKIKNG----------------------KDYKHLEDGNYpvygsggIMGYVNDYLYDGESVLIGRKGTidk 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  73 PVFqilrgLEGAY-NVALM-KAQPSEKVDRDYLFYFLKQEKLFRLIDG-----LSQRTagqsgvdmnaLKAYPMLLPPLE 145
Cdd:cd17288    59 PLY-----VNGPFwTVDTMfYTEIKKNNDPKFLYYLLKTIDFKKYNEAtgvpsLTQTT----------LNKIKIPIPPLE 123

                         170       180
                  ....*....|....*....|....*..
gi 1675114791 146 EQKRIAAILDKADAIRRKRQQATQLAD 172
Cdd:cd17288   124 EQQKIASILDKLDAKDALIELQEKLLE 150

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: 52.68 E-value: 4.37e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  38 QIRDYKSDDNLTYIPE----SSTKKFCSKDDVMIGRYGppvfqilrglEG--AYNVALMKA-----QP-------SEKVD 99
Cdd:cd17500    35 ELNFKRIYDTEEKITEeglkNSSAKLIPENTVIIAMYG----------AGktAGRVAINKIplttnQAccnliidNKKAD 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 100 RDYLFYFLK--QEKLFRLIDGlsqrtAGQSGVDMNALKAYPMLLPPLEEQKRIAAIL----DKADAIRRKRQQATQLADD 173
Cdd:cd17500   105 YRFVYYSLKtqYEELVNLASG-----AAQQNLNSKLIKNFEIPLPPLPEQKRIASILssldDKIELNNRQNETLEAMAET 179


                  ....*.
gi 1675114791 174 FLRSVF 179
Cdd:cd17500   180 LFKEWF 185

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: 52.37 E-value: 5.42e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  97 KVDRDYLFYFLK----QEKLFRLIDGLSQRTAGQSgvdmnALKAYPMLLPPLEEQKRIAAILDKADAirrKRQQATQLAD 172
Cdd:cd17518   103 LLDNNFLKYFLNsdyfKEQLDLLITGGAQPNFGPS-----HLKKIKIPLPPLEEQKRIAEILDDADD---AIEAALEALR 174


                  ....
gi 1675114791 173 DFLR 176
Cdd:cd17518   175 KKKQ 178

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: 52.48 E-value: 5.51e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKITDGTHDTPSKVNEGVKFVTGKNIRPFKLDLTDLKYVTqyVHEEIYNRCNPEYGDLLLTNIGAGTG-- 270
Cdd:cd17521     1 WEVKKLGELSEKIQYGYTASAAYEDGGPRYLRITDIQDDGVLWDTVPYCS--ISEEDAEKYLLKDGDILFARTGATVGks 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 271 --------NACFNSlteaFsmknvaLVKSSPNK--LSGRFLEYLFNHEGFKsKLLGENSKGGAQKFLSLKVIREASIPVP 340
Cdd:cd17521    79 ylykeddgKAVFAS----Y------LIRFRPNKkkVLPKYLFYFTQSSLYW-KQIKSISSGSAQPNINAEKLKSLKIPLP 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1675114791 341 TFKEQLKFSAIVEKVKngNLLDPNLSL--KKVELFDSLSQK 379
Cdd:cd17521   148 PLEEQKRIVAILDALD--AKIDALEELleKLEELLKELLQS 186

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

Pssm-ID: 341170 Cd Length: 196 Bit Score: 52.21 E-value: 6.18e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1675114791  91 KAQPSEKVDRDYLFYFlkqeklFRLIDGLSQRTAGQSG---VDMNALKAYPMLLPPLEEQKRIAAILDKADA 159
Cdd:cd17281   100 KKSYKNKLDIKFLFYY------FFVLGEWCKKNINIGGfpsVDMNKLKKFKIPIPPLEEQEKIVEILDKFTK 165

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

Pssm-ID: 341171 [Multi-domain] Cd Length: 186 Bit Score: 52.06 E-value: 6.30e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  96 EKVDRDYLFYFLKQEKlfRLIDGLSQRTAgQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQLADDFL 175
Cdd:cd17282   102 EKIDVEFLEYYLRTLK--KELEAIAPQSA-QKNINLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIAKLEELK 178


                  ....*...
gi 1675114791 176 RSVFLDMF 183
Cdd:cd17282   179 QSLLQEAF 186

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) TRD1-CR1 and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190; The recognition sequences of Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341200 [Multi-domain] Cd Length: 183 Bit Score: 51.54 E-value: 1.12e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 227 NIRPFKLDLTDLKYVTQYVHEEIYNRCNPEYGDLLLTNIGAGTGNACFNSLTEAFSM-KNVALVKSSPNKLSGRFL-EYL 304
Cdd:cd17519    34 NIQNGKIDTDNLKYFDLNDYKENLDKYIVRPGDIVIAMSGATTGKVGINLTDQEFYLnQRVGKFIPNEEILNNRYLyHFL 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1675114791 305 FNHEGFKSKLlgensKGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEK 354
Cdd:cd17519   114 LSKQNEKYIL-----AGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILDK 158

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: 51.33 E-value: 1.15e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1675114791 319 SKGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKVKNG-NLLDPNLSLKKvELFDSLSQKAF 381
Cdd:cd17287   121 SNGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAKiDALEQKLELLQ-ELKKSLMQQLF 183

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: 51.10 E-value: 1.38e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATkITDgthdtpSK-------VNEGVKFVTGKNIrpfkLDLTDLKYVTQ--YVHEEIYNRCNPEYG----- 258
Cdd:cd17289     1 WEWKKLGDIAE-ITS------SKrifkseyVDSGIPFYRSKEI----IELFNGEEISTelFISEERYEEIKSKYGvpkkg 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 259 DLLLTNIGAgTGNACFNSLTEAFSMK--NVALVKSSpNKLSGRFLEYLFNHEGFKSKLLGEnSKGGAQKFLSLKVIREAS 336
Cdd:cd17289    70 DILITSVGT-IGIPYLVKNDDPFYFKdgNLTWFKNI-KDINSKFLYYWFQSSIFKNQINSI-TIGSTQKALTIEKLKKTK 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1675114791 337 IPVPTFKEQLKFSAIVEKV-----KNGNLLDPNLSLKKvELFDSL 376
Cdd:cd17289   147 IPLPPLEEQKKIVSILSALdekidLNKKQLQKLEELAK-TLFQYW 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: 50.10 E-value: 2.80e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 216 VNEGVKFVTGKNIRpfkLDLTDLKYVTQYVHEEIYNRCNPEYGDLLLTNIGA-------GTGNACFNSlteafsmkNVAL 288
Cdd:cd17258    13 CNGNIKLVCIKNEL---INSLKVKIVEPDYKIGLKQSKIFKKGDVLITRHGTigrvsiiLSEEACLSS--------HVAG 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1675114791 289 VKSSPNKLSGRFLEYLFNHEGFKSKLLgENSKGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEK 354
Cdd:cd17258    82 FNSKEGISDNKFIKYLFNSKKIKNRLM-SYGASSTQPALNLSRLLKIKFPNPPLEEQQKIGKILST 146

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: 49.96 E-value: 3.22e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  80 GLEGAYNVALMKAQPSEKVDRDYLFYFLKQEKLFrLIDGLSQRTAGQSgvdMNA--LKAYPMLLPPLEEQKRIAAILDKA 157
Cdd:cd17271    84 GIPATTNQSCMAFYPTKKLTTEFLFYWYKKYGNY-LGFKYAQGTKQQS---YTAdiVKKLPILLPTLKEQKKIANFLSDI 159


                  ..
gi 1675114791 158 DA 159
Cdd:cd17271   160 DE 161

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: 49.86 E-value: 3.66e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKIT----DGTHDTPSKVNEGVKFVTGKNIRPFKLDLTDLKYV-------TQYVHEeiynrcnpeyGDLL 261
Cdd:cd17252     1 WEWVRLGEIAEIIRgvtyKKSDASEEPSEGGIPVLRANNIQNGGLDFDDLVYVpkskvkeEQKLKK----------GDIL 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 262 ltnIGAGTG-------NACFNSLTE----AFsmknVALVKSSPNKLSgRFLEYLFNHEGFKsKLLGENSKGGAQKFLSLK 330
Cdd:cd17252    71 ---ICMSSGskelvgkAAFIDEDTDytfgAF----CGVIRPKKEIDP-RYLFYFLQSPSYR-EYIRSLASGTNINNLSNE 141

                         170       180
                  ....*....|....*....|....*
gi 1675114791 331 VIREASIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17252   142 HLENLKIPLPPLAEQKRIVAKLDKL 166

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: 49.89 E-value: 3.70e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGSQPPKSTFKYELEDG---YVRLLQIRD---YKSDDNLT--YIPESSTKKFcSKDDVMIGRYGPpvF-Q 76
Cdd:cd17276     1 KKIGDIAKTSSGGTPLRSNQEYYFNGGtipWVKTTDLNNgviYETEEKITekALKETSCKLL-PKGTVLVAMYGG--FgQ 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  77 I----LRGLEGAYNVALMKAQPSEK-VDRDYLFYFLKqekLFRlidGLSQRTAGQSGVDMNA----LKAYPMLLPPLEEQ 147
Cdd:cd17276    78 IgrtgLLGIPAAINQAICAILPNEKkVNPEFLLRYLN---FNR---PYWMRVAASSRKDPNItkddVRNFPIPLPPLDEQ 151

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1675114791 148 KRIAAILDKADA--------IRRKRQQATQLADDFL 175
Cdd:cd17276   152 RAIVEFLSDVDAlidslealIEKLRELKKGLMQQLL 187

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: 48.32 E-value: 1.27e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  94 PSEKVDRDYLFYFLK--QEKLFRLIDGlsqrtAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKA-----DAIRRKRQQ 166
Cdd:cd17280    97 GSNKIDIKFLFYWLLanRDELISLASG-----GGQPNISQELIKSLRIPVPPLEEQKQIAAFLDKKtakidSLIEKKERL 171


                  ....*.
gi 1675114791 167 ATQLAD 172
Cdd:cd17280   172 IELLKE 177

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to TRD2-CR2's of StySKI, S.EcoAI, S.EcoJA17PI, and S.EcoJA23PI; Salmonella kaduna CDC-388 S subunit (StySKI) recognizes 5'... CGATNNNNNNNGTTA ... 3' while Escherichia coli Type-1 restriction enzyme EcoAI specificity protein (S.EcoAI), Escherichia coli UCD_JA17_pb S subunit (S.EcoJA17PI) and Escherichia coli UCD_JA23_pb S subunit (S.EcoJA23PI) recognize 5'... GAGNNNNNNNGTCA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341148 [Multi-domain] Cd Length: 189 Bit Score: 48.28 E-value: 1.44e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVAtKITDGtHDTPSK--VNEGVKFVTGKNIRPFKLDLTDLKYVTQYVHEEiYNRCNPEYGDLLL----TNIG 266
Cdd:cd17259     1 WEWVKLGDVA-DILSG-YAFKSSefSESGIRLLRGANVGVGEIRWDDTVYLPEEYLEE-YEKYLLKEGDIVIaldrPIIS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 267 AGtgnacfnslteafsmKNVALVKSS--P-------------NKLSGRFLEYLFNHEGFKSKLLgENSKGGAQKFLSLKV 331
Cdd:cd17259    78 GG---------------LKVARIPKSdlPallvqrvarirpkDELNSDFLYYLLQSDFFLNYVE-PVLTGTDVPHISTKQ 141

                         170       180
                  ....*....|....*....|....
gi 1675114791 332 IREASIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17259   142 IKNFKIPLPPLEEQKKIAEFLSSL 165

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: 47.16 E-value: 3.04e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  96 EKVDRDYLFYFLKQE-KLFRLIDGLSQRTagqSGVDMNALKAYPMLLPPLEEQKRIAAIL----DKADAIRRKRQQATQL 170
Cdd:cd17516    99 NKFDPDFVYYLLKNNsKYLKSIAGGSTAT---PIINKSTFSNIEIPLPPLPEQKKIAAILssldDKIENNRRINKTLEEM 175


                  ....*....
gi 1675114791 171 ADDFLRSVF 179
Cdd:cd17516   176 AQALFKEWF 184

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: 46.97 E-value: 3.77e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 218 EGVKFVTGKNIRPFKLDL--TDlKYVTQYVHEEIYNRCNPEYGDLLLTNIGAGTGN-ACFNSLTEAFSMKNVAL-VKSSP 293
Cdd:cd17518    23 EGIKLLNVTNIVNGSLDLdkTD-RYISTEEYNGKYKHFLIDEGDILIASSGNSWGKvAIVEKDHLPLMLNTSTIrFKFID 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1675114791 294 NKLSGRFLEYLFNHEGFKSKLLGENSkGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17518   102 GLLDNNFLKYFLNSDYFKEQLDLLIT-GGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDA 162

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: 46.69 E-value: 4.69e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKITDGTHDTPSKVNEGVKFVTGKNIRPFKLDLTDLKYVTqyVHEEIYNRCNPEYGDLLL--TN------ 264
Cdd:cd17524     1 WEWVTIGDLVTSVQYGTSEKKSEDEGGYPVLRMGNIQDGGIDDDDLKYVD--LDEKEFEKYLLKKGDVLFnrTNspelvg 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 265 ---IGAGTGNACFNSLteafsmknvaLV--KSSPNKLSGRFLEYLFNHEGFKSKLLGENSKGG------AQKFLSLKvir 333
Cdd:cd17524    79 ktaIFRGDGPATFASY----------LIriRLNEEKILPEYLNYFLNSPYGRKQIKSVATQGVgqaninATKLKAIP--- 145

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1675114791 334 easIPVPTFKEQLKFSAIVEKVKNGNLLDPNLSLKKVELFDSLSQKA 380
Cdd:cd17524   146 ---IPLPPLEEQKEIVEKLDELDALIDRLEALLEEAEELLESLLQSL 189

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: 45.95 E-value: 6.18e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 256 EYGDLLLTNIGAGTGNacfnsLTEAFSM----KNVALVKSSpNKLSGRFLEYLFNHegFKSKLLgENSKGGAQKFLSLKV 331
Cdd:cd17496    55 KKGDILFCVRGSTTGR-----LNIADDEycigRGVAAIRPK-NGIDTEFLYYLLES--NLDYLL-AAATGSTFPNISRDD 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1675114791 332 IREASIPVPTFKEQLKFSAIVEKVKngNLLDPNLSL--KKVELFDSLSQKAF 381
Cdd:cd17496   126 LLNLKIPLPPLEEQKRIVAILDPLD--EKIDKNKQEieKLEELRDTLLPKLL 175

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: 45.62 E-value: 1.06e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 258 GDLLLTNIGAGTGNACfnslteafsmknvaLVKSSPNKLSGRFLEYLFNheGFKSKLLGEnSKGGAQKFLSLKVIREASI 337
Cdd:cd17280    77 GRLGILGIDATTNQAC--------------CVLSGSNKIDIKFLFYWLL--ANRDELISL-ASGGGQPNISQELIKSLRI 139

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1675114791 338 PVPTFKEQLKfsaIVekvkngNLLDpnlslKKVELFDSLSQKA 380
Cdd:cd17280   140 PVPPLEEQKQ---IA------AFLD-----KKTAKIDSLIEKK 168

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: 45.24 E-value: 1.24e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  94 PSEKVDRDYLFYFLK--QEKLFRLIDG-----LSQrtagqsgvdmNALKAYPMLLPPLEEQKRIAAILD----KADAIRR 162
Cdd:cd17279    97 PNSDVDSRFLYYLLLaaKEELNSLGRGttfleLST----------DELANFKIPLPPLSEQRAIADFLDretaKIDALIA 166


                  ....
gi 1675114791 163 KRQQ 166
Cdd:cd17279   167 KKQQ 170

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: 44.51 E-value: 2.43e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  93 QPSEKVDRDYLFYFL-KQEKLFRLIdglsqrTAGQSGVDMN--ALKAYPMLLPPLEEQKRIAAILDKADAIR----RKRQ 165
Cdd:cd17284    98 VPSKKINPEYLMYLLsLQKKYMEKI------ATGTTIPYLNktNCESIPIPLPPIEEQNKIAKILDSIDKKIdlliAKLE 171

                          90
                  ....*....|....
gi 1675114791 166 QATQLADDFLRSVF 179
Cdd:cd17284   172 KLQQLKKGLMQQLF 185

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

Pssm-ID: 341189 [Multi-domain] Cd Length: 173 Bit Score: 44.21 E-value: 2.46e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   6 VELGSVVTFIGGsQPPKSTFKYELEDGYVRLLQIRDYksDDNLTYIPESST--KKFCSKDDVMIGrygppvfqiLRGLEG 83
Cdd:cd17498     1 VKLGEIAEITMG-QSPKSEFYNEDGIGLPFLQGNRTF--GDKYPYIDTYTTdiKKIAKKGDILMS---------VRAPVG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  84 AYNVALMK--------AQPSEKVDRDYLFYFLKQeklfrLIDGLSQRTAGQ--SGVDMNALKAYPMLLPPLEEQKRIAAI 153
Cdd:cd17498    69 DLNIANKDicigrglcSIRMKNGNNSFLYYLLKN-----NIKNLINKSSGTvfGSINKDDIENLEVDIPEDEEQKRIANI 143


                  ....*.
gi 1675114791 154 LDKADA 159
Cdd:cd17498   144 LSKIDD 149

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: 44.37 E-value: 2.98e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 196 KQLNDVATKITdGThdTPSKVNEG-----VKFVTGKNIRPFKLDLTDLKYVTqyvhEEIYN--RCNPEyGDLLLTNIGAG 268
Cdd:cd17293     1 VKLGELGEVVT-GN--TPSKKNPEyyggdIPFIKPDDLNNGGIILTSEEYLS----EEGAKkaRIVPK-GSILVTCIGGS 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 269 TGNACFNSLTEAFsmkNV---ALVkssPNK-LSGRFLEYLFNHEGFKSKLLGEN------SKGgaqKFLSLKvireasIP 338
Cdd:cd17293    73 IGKVGIADREVAF---NQqinAII---PNKsVDPKFLYYQLLSSKFQLQAIASSttlpiiNKS---KFEKIE------IP 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1675114791 339 VPTFKEQLKFSAIVEKV-KNGNLLDPNLSLKKvELFDSLSQKAF 381
Cdd:cd17293   138 LPPLEEQKRIVAKLDKLfALIDKLEESLEELD-ELLKSLFQSAF 180

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: 43.68 E-value: 4.57e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKITDGTHDTPSKVNEGVKfVT-------GKnirpfkLDLTDLKYVtqYVHEEIYNRCNPEYGDLLLTNI 265
Cdd:cd17522     1 WKVVKLGDVLEEIRNGTTVKQNKEGGGYP-VTrietisnGT------IDLNRVGYA--ITNEEKIEKYKLQKGDILFSHI 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 266 gagtgnacfNSL-----TEAFSMKNVALV--------KSSPNKLSGRFLEYLFNHEGFKSKLLGENSKGGAQKFLSLKVI 332
Cdd:cd17522    72 ---------NSIehigkTAIYDGDPEPLIhgmnllrlRPNKNIVDPKYLYYLLKSDRFRNQFRSIAKKAVNQASINQTEL 142

                         170       180
                  ....*....|....*....|...
gi 1675114791 333 REASIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17522   143 KKIKIPLPPLEEQQKIASILEKL 165

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: 43.59 E-value: 5.64e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791   5 VVELGSVVTFIGGSQPPKSTFKYEleDGYVRLLQIRDYKSDDNLTYIPE----------SSTKKFcSKDDVMI------G 68
Cdd:cd17243     2 VKSLSDVVDIIGGGTPKTSVPEYW--NGDIPWFSVKDVNNDSRFVLDTEkkitelglknSSTKLL-PKGTTIIsargtvG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  69 RYGppvfqiLRGLEGAYN---VALmkaQPSEKVDRDYLFYFLKqeklfRLIDGLSQRTAG--QSGVDMNALKAYPMLLPP 143
Cdd:cd17243    79 KLA------LLGIPMAMNqscYGL---RGKDGLSNYFLYYLLK-----NLIEELKQKAHGsvFDTITRKTFDEIKVPLPP 144

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1675114791 144 LEEQKRIAAIL----DKADAIRRKRQQATQLADDFL 175
Cdd:cd17243   145 EELQKSFENIVsplfDKILNNLKENQTLAQLRDTLL 180

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: 43.29 E-value: 6.62e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 190 PMGWEVKQLNDVAtKITDGThdTPSKVNEgvKFVTGKNIrPF----KLDLTDLKYVTQYVHEEIYNRCN-PEY--GDLLL 262
Cdd:cd17247     1 PEHWEVVRLGDVA-RVGNGS--TPSRKNP--DYWNGGTI-PWvssgEVNDNRITEADEFITELALKECSlPLVppGSVLV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 263 TNIGAGT--GN-------ACFNslteafsmKNVALVKSSPNKLSGRFLEYLFnheGFKSKLLGENSKGGAQKFLSLKVIR 333
Cdd:cd17247    75 AMIGQGKtrGQaailaieATIN--------QNLAAIRPNEERVLPEYLHYYL---ESQYDELRRIGSGGGQGALNCGILK 143

                         170       180
                  ....*....|....*....|
gi 1675114791 334 EASIPVPTFKEQLKFSAIVE 353
Cdd:cd17247   144 AFPIPLPPLDEQREIVAELE 163

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2, 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: 42.54 E-value: 1.12e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  53 ESSTKKFCSKDDVMIGRYGPPVfqiLRG------LEGAYNVALMKAQPSEKVDRDYLFYFLKQEKlfRLIDGLSqRTAGQ 126
Cdd:cd17514    56 EDSSIRIVPKGTILIACTGQGY---TRGqvavlqIDASTNQAIAAIRCKENVNPKYLYYYLKTQK--NNLRNLT-SGVAQ 129

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1675114791 127 SGVDMNALKAYPMLLPPLEEQKRIAAILDK-----ADAIRRKRQQATQ 169
Cdd:cd17514   130 KNLNIEMLRNLQIPLPPKEEQQKIVNILETleffeKDSLRKIKETAQD 177

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: 42.22 E-value: 1.67e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  84 AYNVALMKAQPSEKVDRDYLFYFLKQEKLFRLIDGLSQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKADAirrK 163
Cdd:cd17525    92 LFNNNILRIRFDDIVLPYFINYYLNSPDGKKQLESIASGTTSVAAIYQKDLKKLKLPLPPLDEQREIVSFLSELDA---K 168

                          90
                  ....*....|..
gi 1675114791 164 RQQATQLADDFL 175
Cdd:cd17525   169 IDQLEQKLEKLL 180

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: 41.74 E-value: 1.94e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1675114791 281 FSMKNVALV-KSSPNKLSGRFLEYLFNHEGFKSKllgenSKGGAQKfLSLKVIREASIPVPTFKEQLKFSAIVEKVKN 357
Cdd:cd17255    72 FSVTNVCGVlKVKNKNINNKFLYYALNLIAKKYV-----SFDGNPK-LMNNVMAKIKIPLPPLEEQEKIANILDKLDE 143

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: 41.19 E-value: 3.20e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 190 PMGWEVKQLNDVATKITDGTHDTPSKVNEGVKFVTGKNIRPfKLDLTDLKYVTQYVHEEiynrcnpeyGDLLLTnIGAGT 269
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELKNNGKYPYIRAGDLN-NVVKGGLGYIKKYILPK---------GDITIS-SRATI 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 270 GNACFNSLTEAFSmKNVALVKSSPNKLSGRFLEYLFNHegfKSKLLGENSKGGAQKFLSLKVIREASIPVPTFKEQLKFS 349
Cdd:pfam01420  70 GYVFYRDKPYYTN-QHIIVLIPKNNIKITEFLYLYLLL---KLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIA 145

                         170
                  ....*....|..
gi 1675114791 350 AIVEKVKNGNLL 361
Cdd:pfam01420 146 KILSQLDNTIEL 157

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: 40.51 E-value: 3.74e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1675114791 287 ALVKSSPNKLSGRFLEYLFnhegfKSKLLGENSKGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17266    73 ALVVTPKKENNIKFLYYLL-----KSLNLNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSL 136

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: 40.85 E-value: 4.40e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  28 ELEDGYVRLLQIR-------DYKSDDNLTYIPESSTKKFCsKDDVMI---GRYGPPVFQILRGLEGAYNVALMKAqPSEK 97
Cdd:cd17258    11 LFCNGNIKLVCIKnelinslKVKIVEPDYKIGLKQSKIFK-KGDVLItrhGTIGRVSIILSEEACLSSHVAGFNS-KEGI 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1675114791  98 VDR---DYLFYFLK-QEKLFRLidglsQRTAGQSGVDMNALKAYPMLLPPLEEQKRIAAILDKAD 158
Cdd:cd17258    89 SDNkfiKYLFNSKKiKNRLMSY-----GASSTQPALNLSRLLKIKFPNPPLEEQQKIGKILSTWD 148

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: 41.05 E-value: 4.66e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKITDGTHDTPSKVNEGVKFVTGKNIRPFKLDLTDLKYVTQYVHEEiYNRCNPEYGDLLLTNIGAG---- 268
Cdd:cd17512     1 WEEIRLGDIIDYQKGYAFKSKDYQDSGIRIVRVSDFTDDSIDINNLVYISEEKANK-YKKYELKENDIIITTVGSWpsnp 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 269 ---TGNACF--NSLTEAFSMKNVALVKSSPNKLSGRFLEYLFNHEGFKSKLLGEnSKGGA-QKFLSLKVIREASIPVPTF 342
Cdd:cd17512    80 dsvVGKVVRvpKEADGALLNQNAVKIRPKKGILDQSFLFYNLKSERFKNYIESI-ARGNAnQASITLGDIKKFKFLLPPL 158

                         170
                  ....*....|
gi 1675114791 343 KEQLKFSAIV 352
Cdd:cd17512   159 EEQKKIASIL 168

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: 40.56 E-value: 5.56e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1675114791 101 DYLFYFLKQEKLFRlidglsqrtagQSGVDMNA---------LKAYPMLLPPLEEQKRIAAILDKADA 159
Cdd:cd17265   101 DYLFHLFNSDLFKK-----------QIGSFLTAtinqitngnLNNFKIPLPPLEEQEKIAEFLSSLDA 157

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: 40.51 E-value: 5.75e-04

                          10        20
                  ....*....|....*....|....*...
gi 1675114791 132 NALKAYPMLLPPLEEQKRIAAILDKADA 159
Cdd:cd17268   137 SDLAKIKIPVPPLEEQERIVEILDKFDA 164

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.MgeORF438P TRD1-CR1 and TRD2-CR2, and to Escherichia coli G5 S subunit (S.Eco16445ORF5013P ) TRD2-CR2 and Acetobacter pasteuri; The recognition sequences of Mycoplasma genitalium G-37 S subunit (S.MgeORF438P), Escherichia coli G5 S subunit (S.Eco16445ORF5013P), and Acetobacter pasteurianus IFO 3283-01 S subunit (S2.Apa3283ORF14230P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341180 [Multi-domain] Cd Length: 161 Bit Score: 40.19 E-value: 6.06e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 265 IGAGTGNACFNSL-TEAFSMKNVALVKSSPNKLSGRFLEY--LFNHEGFKSKllgenSKGGAQKFLSLKVIREASIPVPT 341
Cdd:cd17291    51 ISASGASAGYVNYwKEPFWASDCCYILSSKNELVNKFLYYflKNKQEEIYSL-----QRGAGQPHIYKKDIEKLKIPIPP 125

                          90
                  ....*....|...
gi 1675114791 342 FKEQLKFSAIVEK 354
Cdd:cd17291   126 LEEQQKIVEILDK 138

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: 40.20 E-value: 6.09e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1675114791 102 YLFYFLKqEKLFRLIDGLSQRTAGQsgvdmNALKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQ 166
Cdd:cd17255    92 FLYYALN-LIAKKYVSFDGNPKLMN-----NVMAKIKIPLPPLEEQEKIANILDKLDELINLLIA 150

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: 40.47 E-value: 6.75e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVAtKITDGThdTPSKVNE------GVKFVTGKNIRPFKLDLTDLK-YVTQYVHEEIYNRCNPEyGDLLLTnI 265
Cdd:cd17277     1 WPIVKLGEVC-EIINGS--TPSKKNEeywnngTIKWLTIPDIDERGLIISSTKqFITEKALEEKKVKLVPK-NSVLLS-C 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 266 GAGTGNACFNSLTEAFSMKNVALVkSSPNKLSGRFLEYLFNHegFKSKLLGENSKGGaQKFLSLKVIREASIPVPTFKEQ 345
Cdd:cd17277    76 TATIGKVAIAKIELTTNQQINALI-CKDSKILPEYLFYALKH--IKQVLERLTTNPG-VKHVNLSMLSNLQIPLPPLEVQ 151

                         170
                  ....*....|
gi 1675114791 346 LKFSAIVEKV 355
Cdd:cd17277   152 KKIVAEIEKV 161

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: 40.26 E-value: 7.42e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  94 PSEKVDRDYLFYFLK-QEKLFRLidglsqrTAGQSGVD-MNA--LKAYPMLLPPLEEQKRIAAILDKADAIRRKRQQATQ 169
Cdd:cd17290    98 FNKDINPKFLFYWLSsSKEELEN-------LANGATLPiLNQekLKNIKLPVPPLNEQQKIVEFLDKKTAKIDALIAKKE 170

                          90
                  ....*....|....
gi 1675114791 170 LADDFLRSVFLDMF 183
Cdd:cd17290   171 QLIELLKEYRQALI 184

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2, 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: 39.85 E-value: 9.87e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 196 KQLNDVATKITDGThdTPSKV------NEGVKFVTGKNIRPFKLDLTDLKYVTQYVHEEIYNRCNPEyGDLLLTNIGAGT 269
Cdd:cd17514     1 VKIQDIAFEIINGG--TPSRNepeywnNGDIPWLTSGETDDNFINNTSEKITTKNGLEDSSIRIVPK-GTILIACTGQGY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 270 --GNACFnSLTEAFSMKNVALVKSSPNKLSGRFLEYLFnhegFKSKLLGENSKGGAQKFLSLKVIREASIPVPTFKEQLK 347
Cdd:cd17514    78 trGQVAV-LQIDASTNQAIAAIRCKENVNPKYLYYYLK----TQKNNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQK 152

                         170       180
                  ....*....|....*....|....
gi 1675114791 348 FSAIVEKVKNGNlldpNLSLKKVE 371
Cdd:cd17514   153 IVNILETLEFFE----KDSLRKIK 172

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: 39.01 E-value: 1.59e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791  94 PSEKVDRDYLFYFL--KQEKLfrlidglsQRTAGQSGVDM---NALKAYPMLLPPLEEQKRIAAILDKAD-AIRRKRQQA 167
Cdd:cd17286    93 PNKNYDPEFLYYALenWSKKI--------KSLAGKQAVPIinkTEFSKIKILVPPLEEQQKIANFLSKLDeLIELQQQKI 164


                  ...
gi 1675114791 168 TQL 170
Cdd:cd17286   165 EKL 167

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: 38.35 E-value: 2.56e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1675114791 279 EAFSMKNVALVKSSPNKLSGRFLEYLFnhEGFKSKLLGeNSKGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17296    83 EATTNQAIAGIKPKNKSINPKYLYYYL--KSLYEKFLS-LGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKF 156

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: 38.37 E-value: 3.37e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKITDGTHDTPSKVNEGVKFVTGKNI-RPFKLDLTDLKYVTqyVHEEIYNRCNPEYGDLL--------LT 263
Cdd:cd17525     1 WEWVKLGDILSSTQLGLVRSNSEDPNGYPYIKMGNIgRGGINLLKVETYVD--ATELEVEKYLLEDGDLLfntrntleLV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 264 NIGA----GTGNACFNSlteafsmkNVALVKSSPNKLSGrFLEYLFNHEGFKSKLlgENSKGG--------AQKFLSLKv 331
Cdd:cd17525    79 GKVAiwrgELPKALFNN--------NILRIRFDDIVLPY-FINYYLNSPDGKKQL--ESIASGttsvaaiyQKDLKKLK- 146

                         170       180
                  ....*....|....*....|....
gi 1675114791 332 ireasIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17525   147 -----LPLPPLDEQREIVSFLSEL 165

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: 37.90 E-value: 3.48e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1675114791 294 NKLSGRFLEYLFNhegFKSKLLGENSKGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKVKN 357
Cdd:cd17245    90 KDIDNLFLYYYLK---YNKPELEKLGTGSTFKAINKKDLEELKIPLPPLEEQQKIAEILSTVDE 150

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

Pssm-ID: 341191 [Multi-domain] Cd Length: 186 Bit Score: 38.04 E-value: 3.50e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 197 QLNDVATKITDGThdTPSKVNEGvkFVTGKNIRPFKLDLTDLKYVTQ---YVHEEIYNRCN----PE-------YGD--- 259
Cdd:cd17500     1 KLEDICIKITSGG--TPSRSNKE--YYNGGNIPWLKTKELNFKRIYDteeKITEEGLKNSSakliPEntviiamYGAgkt 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 260 ---LLLTNIGAGTGNACFNSLTEafsmknvalvkssPNKLSGRFLEYLFNHEGFKSKLLgenSKGGAQKFLSLKVIREAS 336
Cdd:cd17500    77 agrVAINKIPLTTNQACCNLIID-------------NKKADYRFVYYSLKTQYEELVNL---ASGAAQQNLNSKLIKNFE 140

                         170
                  ....*....|....*..
gi 1675114791 337 IPVPTFKEQLKFSAIVE 353
Cdd:cd17500   141 IPLPPLPEQKRIASILS 157

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

Pssm-ID: 341204 [Multi-domain] Cd Length: 190 Bit Score: 37.99 E-value: 3.86e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1675114791 289 VKSSPNKLSGRFLEYLFNHEGFKSKLLgENSKGGA-QKFLSLKVIREASIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17523    99 MRLDQEKIDPEFLSYIFNSPLIRRKIE-RNFVTSAgQKTVNQGHIKSLPIPLPPLKEQKKIVARVEEL 165

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1 and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) TRD2-CR; The recognition sequences of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341183 [Multi-domain] Cd Length: 188 Bit Score: 37.85 E-value: 4.05e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 193 WEVKQLNDVATKITDGThdtPSKVNEgvKFVTGKNIRPFKLDLTDLKYVT---QYVHEEIYNRCN----PEyGDLLltnI 265
Cdd:cd17294     1 WEWKTLGEIAKIFSGGT---PSTSNP--EYWDGGTIPWLSSGEVNFKEIYeteKRITEEGLKNSSakwiPK-NSVL---I 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 266 G-AGTG-----------NACFNslteafsmKNVALVKSSPNKLSGRFLEYLF--NHEGFKSkLLGENSKGGaqkfLSLKV 331
Cdd:cd17294    72 AlAGQGktrgtvailkiPLTTN--------QSLAAIEPDEEIANSRFLYYNLssRYEELRS-LSGGGGRGG----LNLKI 138

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1675114791 332 IREASIPVPTFKEQLKFSAIVEKV-----KNGNLLDPNLSLKKvELFDSL 376
Cdd:cd17294   139 IKSLPIPLPPLEEQKKIVAILDKFdalinDLKEGLPALLELRQ-KQYEYL 187

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) TRD2-CR2 and Moraxella catarrhalis S subunit (S.Mca353ORF290P) TRD2; Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) recognizes 5'... GCANNNNNNTGT ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341151 [Multi-domain] Cd Length: 172 Bit Score: 37.41 E-value: 4.68e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675114791 294 NKLSGRFLEYLFNH---EGFKSkllgenskGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKV-----KNGNLLDPNL 365
Cdd:cd17262    91 NGISTEFLYYYLNSidiSPYVT--------GAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLdalidLLEEELEKLI 162

                          90
                  ....*....|.
gi 1675114791 366 SLKKvELFDSL 376
Cdd:cd17262   163 ELKK-ALLQKL 172

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: 36.69 E-value: 9.24e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1675114791 294 NKLSGRFLEYLFNHEgfKSKLLGENSKGGAQKFLSLKVIREASIPVPTFKEQLKFSAIVEKV 355
Cdd:cd17283    99 KKLDKDFLYYLLSSI--TVQLQFSAQAGGGTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSL 158