NCBI Conserved Domain Search

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: 249.72 E-value: 3.64e-80

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 393 LGQVSTVKGGKRLPAGHQFSAYETAHVYIRVTDMKNGSINDSGLAYISPETHSLISQYTISSDDLYITIAGTIGDVGLVP 472
Cdd:cd17256     1 LGEIARVKGGGRLPKGESLSDGPTGVPYIRVTDIKNGGIDLDNLKYISPEIHEKIKRYTLSKGDILISIVGTIGRVGIVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 473 SRFNGMNLTENAAKL-MFRSIDKSWLKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELM 551
Cdd:cd17256    81 KELDGANLTENAARIrPKDSISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLD 160

                         170       180
                  ....*....|....*....|
gi 2026845886 552 FLCDQISARLQASQTTQQHL 571
Cdd:cd17256   161 AKIDALEKQLAKLEELKKAL 180

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: 220.02 E-value: 1.07e-68

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 108 RLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQSGSIIEPDKYLSESGLLNSEEANQGDVFTVCIGGSIGKSAIVHG 187
Cdd:cd17293     2 KLGELGEVVTGNTPSKKNPEYYGGDIPFIKPDDLNNGGIILTSEEYLSEEGAKKARIVPKGSILVTCIGGSIGKVGIADR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 188 RIGFNQQINAIKPIK-FSSAFLYSILSTRFFIDSmvSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCD 266
Cdd:cd17293    82 EVAFNQQINAIIPNKsVDPKFLYYQLLSSKFQLQ--AIASSTTLPIINKSKFEKIEIPLPPLEEQKRIVAKLDKLFALID 159

                         170       180
                  ....*....|....*....|.
gi 2026845886 267 QLEQKSEASLAAHQTLVETLL 287
Cdd:cd17293   160 KLEESLEELDELLKSLFQSAF 180

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: 127.28 E-value: 6.73e-34

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 108 RLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQSGSIIEPDKYLSESGlLNSEEAN---QGDVFTVCIGGSIGKSAI 184
Cdd:cd17516     2 KIGDLGKVVTGKTPSTKNPEYFGGDIPFITPSDMKGGKYIIKTERRLSSKG-LEKVKNKlipANSICVTCIGSDMGKVAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 185 VHGRIGFNQQINAIKPIK--FSSAFLYSILSTR-FFIDSMvsASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDEL 261
Cdd:cd17516    81 TKEPSVTNQQINSIIVNKnkFDPDFVYYLLKNNsKYLKSI--AGGSTATPIINKSTFSNIEIPLPPLPEQKKIAAILSSL 158

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: 122.22 E-value: 3.16e-32

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQSGSIIEPDKYLSESGLLNSEEANQGDVFTVCIgGSIGKSAIVH 186
Cdd:cd17286     1 KKLGDLGEIVTGNTPSTKNSEYYGGEILFVTPTDIDGNKYIYKTEKKLSEKGFKKARILPKGSILVTCI-GSIGKNAIAT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 187 GRIGFNQQINAIKPIK-FSSAFLYSILStrFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRI---VAKVDELM 262
Cdd:cd17286    80 EDCATNQQINAIIPNKnYDPEFLYYALE--NWSKKIKSLAGKQAVPIINKTEFSKIKILVPPLEEQQKIanfLSKLDELI 157

                         170
                  ....*....|.
gi 2026845886 263 SLCDQLEQKSE 273
Cdd:cd17286   158 ELQQQKIEKLE 168

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: 122.63 E-value: 3.38e-32

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQVST--VKGgkrlpAGHQFSAYETAHVYIRVTDMKNGSINDSGLAYISPETH-SLISQYTISSDDLYITIAGT 464
Cdd:cd17246     1 WEWVKLGEISSdiTDG-----THPTPKYVESGIPFITSKNIKNGKIDFSDVKYISEEDHnEILKRSKLKKGDILFSIIGT 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 465 IGDVGLVPSRFNgMNLTENAA--KLMFRSIDKSWLKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKR 542
Cdd:cd17246    76 IGRVAIVPEDLP-ANINQAVAliRPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQKR 154

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2026845886 543 IVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17246   155 IAAILDSLDALIDKLEQKLEKLEDLKKGLMQDL 187

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: 114.84 E-value: 1.64e-29

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQsGSIIEPDKYLSESGLLNSE----EANqgdvfTVCI---GGSI 179
Cdd:cd17515     1 VKLGDIGKWGSGGTPSRSNPEYYGGGIPWIKSGELND-GYITSTEEKITEEGLKNSSaklfPKG-----SVLIamyGATA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 180 GKSAIVHGRIGFNQQINAIKPI-KFSSAFLYSILstRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKV 258
Cdd:cd17515    75 GKVGILGIDAATNQAICAILPNeEIDNEFLFYFL--KSQKEYLISLGKGGAQPNISQGIIKNIEIPLPPLAEQKRIVAKL 152

                         170       180
                  ....*....|....*....|....*....
gi 2026845886 259 DELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17515   153 DKLDKLIEKLEKALEKLEELKKALMQKLL 181

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: 111.14 E-value: 3.14e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 108 RLGYVGVC-STGKTPSTSVNEYFNGD-IPFIGPGQITQSGSIIEPDKYLSESGLlnseEANQGDVFT------VCIGGSI 179
Cdd:cd17290     2 KLKRLAKSiKTGTTPPSENEEYYDGGiIPWFTPGDFNGDLILSESKRKLSELAI----EDGEARLFPknsvlvVGIGATI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 180 GKSAIVHGRIGFNQQINAIKPIK-FSSAFL-YSILSTRffiDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAK 257
Cdd:cd17290    78 GKVGYSDKESSSNQQITGIIFNKdINPKFLfYWLSSSK---EELENLANGATLPILNQEKLKNIKLPVPPLNEQQKIVEF 154

                         170
                  ....*....|....*...
gi 2026845886 258 VDELMSLCDQLEQKSEAS 275
Cdd:cd17290   155 LDKKTAKIDALIAKKEQL 172

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 115.36 E-value: 2.39e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 383 ELPEGWKMVRLGQVSTVKGGKRLPAGhQFSAYETA--HVYIRVTDMKNGSINDSGLAYISpETHSLISQYTISSDDLYIT 460
Cdd:PRK09737    5 KLPEGWVTTHISEICSVIRGVKPPKG-YATKSLTMgdLPFIRTTDITNGAVDLTTLPYCM-DAPEDVSKYQLQDRDIVIS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 461 IAGTIGDVGLVPSRF-NGMNLTENAAKL-MFRSIDKSWLKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIA 538
Cdd:PRK09737   83 SAGSIGFSFLAQNPLpSNVVFASFAIRLkPVNYFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIA 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2026845886 539 EQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEALVEGALN 581
Cdd:PRK09737  163 EQKIIAEKLDTLLAQVDSTKARLEQIPQILKRFRQAVLGAAVS 205

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: 107.85 E-value: 4.94e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQSGSIIEPDK-YLSESGLLNSEEANQGDVFTVCIGgSIGKSAIV 185
Cdd:cd16961     1 KKLGEIAEIISGKTPSSSSEYWDNGIIPWIRISDINNGGIILTDEKiTEEGAEKLKKKILPKGDILISRSG-TIGKVAIV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 186 HGRIG--FNQQINAIKPIK-FSSAFLYSILSTRFFiDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELM 262
Cdd:cd16961    80 KENDKalLNQAVIVIRPKDeVDSEFLYYFLKSPFG-KKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLD 158

                         170       180
                  ....*....|....*....|
gi 2026845886 263 SLCDQLEQKSEASLAAHQTL 282
Cdd:cd16961   159 ALIELLEQKLEKLEQLKQAL 178

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: 103.76 E-value: 1.85e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGyvGVCS-----TGKTPStsvneYFNGDIPFIGPGQITqSGSII-EPDKYLSEsgllnsEEANQ---------G 168
Cdd:cd17246     1 WEWVKLG--EISSditdgTHPTPK-----YVESGIPFITSKNIK-NGKIDfSDVKYISE------EDHNEilkrsklkkG 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 169 DVFTVCIGgSIGKSAIV--HGRIGFNQQINAIKPI--KFSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIP 244
Cdd:cd17246    67 DILFSIIG-TIGRVAIVpeDLPANINQAVALIRPKkeKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIP 145

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2026845886 245 CASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17246   146 LPPLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLL 188

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: 101.43 E-value: 1.16e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQVSTVKGGkrlpagHQF--SAY-ETAHVYIRVTDMKNGSINDSGLAYISPETHSLISQYTISSDDLYITI-AG 463
Cdd:cd17278     1 WEVVKLGDIADIQNG------YAFksSDFsDEGIPVIRIGNIKNGGIDLDDNSKYPEEPLEKYEKFLLKKGDILIAMtGG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 464 TIGDVGLVPSRFNGMNLTENAAKLMFRS-IDKSWLKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKR 542
Cdd:cd17278    75 TVGKVAIVPEDDEPALLNQRVGKFRPKDkIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKK 154

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2026845886 543 IVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17278   155 IAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSL 187

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: 101.48 E-value: 1.18e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKT--PSTSVNEYFNGDIPFIGPGQITQSGSIIEPDKYLSESglLNSEEA--NQGDVFTVCIGGS- 178
Cdd:cd17252     1 WEWVRLGEIAEIIRGVTykKSDASEEPSEGGIPVLRANNIQNGGLDFDDLVYVPKS--KVKEEQklKKGDILICMSSGSk 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 179 --IGKSAIVHGriGFNQQINA----IKP-IKFSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQ 251
Cdd:cd17252    79 elVGKAAFIDE--DTDYTFGAfcgvIRPkKEIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPLAEQ 156

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2026845886 252 HRIVAKVDELMSLCDQLEQKSEASLAAHQTLVE 284
Cdd:cd17252   157 KRIVAKLDKLDALIDKLKQALEKLDELLKSLFQ 189

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: 98.76 E-value: 7.74e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 421 IRVTDMKNGSINDSGLAYISPETHSLISQYTISSDDLYITIAGTIGDVGLVPSRFNGMNltenAAKLM----FRSIDKSW 496
Cdd:cd17264    31 INAGHLEDGTIDLSNMNFISEEKYNSLGSGKLQKGDILYCLRGSLGKCAIVDNYDEGAI----ASSLViirpFAKVDVRY 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2026845886 497 LKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEA 574
Cdd:cd17264   107 LYYYLNSPLGKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQSLFQS 184

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2; The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341136 [Multi-domain] Cd Length: 190 Bit Score: 96.83 E-value: 4.57e-23

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 101 PEGWEWCRLGYVGVCSTGKTPSTSVNEYFNGD-IPFIGPGQITQSgSIIEPDKYLSESGLLNSE----EANqgdvfTVCI 175
Cdd:cd17247     1 PEHWEVVRLGDVARVGNGSTPSRKNPDYWNGGtIPWVSSGEVNDN-RITEADEFITELALKECSlplvPPG-----SVLV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 176 -----GGSIGKSAIVHGRIGFNQQINAIKPI--KFSSAFLYSILSTRFfiDSMVSASTGSATPIINRSKWESLLIPCASM 248
Cdd:cd17247    75 amigqGKTRGQAAILAIEATINQNLAAIRPNeeRVLPEYLHYYLESQY--DELRRIGSGGGQGALNCGILKAFPIPLPPL 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2026845886 249 NEQHRIVAKVDELMSLCDQLEQKseasLAAHQTLVETLLATL 290
Cdd:cd17247   153 DEQREIVAELEALLAKIDLLEEK----IARLIELLKELRQAL 190

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: 93.34 E-value: 6.28e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTG---KTpstsvNEYFNGDIPFIGPGQITQSGSIIEPDKYLSESGLLNSEE--ANQGDVFTVCIGGS 178
Cdd:cd17278     1 WEVVKLGDIADIQNGyafKS-----SDFSDEGIPVIRIGNIKNGGIDLDDNSKYPEEPLEKYEKflLKKGDILIAMTGGT 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 179 IGKSAIV---HGRIGFNQQINAIKPI-KFSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRI 254
Cdd:cd17278    76 VGKVAIVpedDEPALLNQRVGKFRPKdKIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKI 155

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2026845886 255 VAKVDELMSLCDQLEQKSEASLAAHQTLVETLLA 288
Cdd:cd17278   156 AEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLFT 189

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: 92.55 E-value: 1.44e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKTPSTSVNEYFNGD-IPFIGPGQITQsGSIIEPDKYLSESGLLNSE----EANqgdvfTVCIG-- 176
Cdd:cd17294     1 WEWKTLGEIAKIFSGGTPSTSNPEYWDGGtIPWLSSGEVNF-KEIYETEKRITEEGLKNSSakwiPKN-----SVLIAla 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 177 GSiGKSAivhGRIGF-------NQQINAIKPIK--FSSAFLYSILSTRFfiDSMVSASTGSA-----TPIINrskweSLL 242
Cdd:cd17294    75 GQ-GKTR---GTVAIlkiplttNQSLAAIEPDEeiANSRFLYYNLSSRY--EELRSLSGGGGrgglnLKIIK-----SLP 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2026845886 243 IPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17294   144 IPLPPLEEQKKIVAILDKFDALINDLKEGLPALLELRQKQYEYLR 188

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: 92.06 E-value: 1.51e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 391 VRLGQVSTVKGGKRLPAGHQFSAYETaHVYIRVTDMKNGSINDSGLaYISPETHSLISQYTISSDDLYITIAGTIGDVGL 470
Cdd:cd16961     1 KKLGEIAEIISGKTPSSSSEYWDNGI-IPWIRISDINNGGIILTDE-KITEEGAEKLKKKILPKGDILISRSGTIGKVAI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 471 VPSRfNGMNLTENAAKL-MFRSIDKSWLKYTLRSKFSQSQFnEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDE 549
Cdd:cd16961    79 VKEN-DKALLNQAVIVIrPKDEVDSEFLYYFLKSPFGKKLI-EGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDK 156

                         170       180
                  ....*....|....*....|..
gi 2026845886 550 LMFLCDQISARLQASQTTQQHL 571
Cdd:cd16961   157 LDALIELLEQKLEKLEQLKQAL 178

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

Pssm-ID: 341145 [Multi-domain] Cd Length: 182 Bit Score: 90.64 E-value: 5.90e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 132 DIPFIGPGQITQSGSIIEPDKYLSEsgllNSEEA------NQGDVFtVCIGGSIGKSAIVHGRI-GFN--QQINAIKPI- 201
Cdd:cd17256    25 GVPYIRVTDIKNGGIDLDNLKYISP----EIHEKikrytlSKGDIL-ISIVGTIGRVGIVPKELdGANltENAARIRPKd 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 202 KFSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQT 281
Cdd:cd17256   100 SISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKA 179


                  .
gi 2026845886 282 L 282
Cdd:cd17256   180 L 180

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: 89.77 E-value: 1.24e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQSGS--IIEPDKYLSESGLLNSEeAN---QGDV-FTvcigg 177
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKNPEYWNGDIPWITPTDLTKLKGkyISDTERKITELGLKNSS-AKllpAGSVlLS----- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 178 S---IGKSAIVHGRIGFNQQINAIKP-IKFSSAFLYSILSTRffIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHR 253
Cdd:cd17273    75 SrapIGYVAIATNPLATNQGFKSIIPnEEIDNEFLYYLLKNN--KPEIESLASGSTFKEISKSTFKKIEIPLPPLEEQKK 152

                         170       180
                  ....*....|....*....|
gi 2026845886 254 IVAKVDELMSLCDQLEQKSE 273
Cdd:cd17273   153 IAAILSKLDELIELLEKENE 172

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: 88.66 E-value: 2.52e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 118 GKTPSTSVNEYFNGDIPFIGPGQITQSGS-IIEPDKYLSESGLLNS--EEANQGDVFtVCIGGSIGKSAIVHGRIGFNQQ 194
Cdd:cd17243    14 GGTPKTSVPEYWNGDIPWFSVKDVNNDSRfVLDTEKKITELGLKNSstKLLPKGTTI-ISARGTVGKLALLGIPMAMNQS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 195 INAIKP-IKFSSAFLYsiLSTRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSE 273
Cdd:cd17243    93 CYGLRGkDGLSNYFLY--YLLKNLIEELKQKAHGSVFDTITRKTFDEIKVPLPPEELQKSFENIVSPLFDKILNNLKENQ 170

                         170
                  ....*....|....
gi 2026845886 274 aSLAAhqtLVETLL 287
Cdd:cd17243   171 -TLAQ---LRDTLL 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: 88.36 E-value: 4.29e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQVST-VKGGKRLPAghqfSAYETAHVYIRVTDMKNGSINDSGLAYIsPETHSLISQYTISSDDLYITIAGTI- 465
Cdd:cd17261     1 WEWVRLGDLIEgIRNGWSPKP----PDDETGWPVLKLSAVTSGKFDPSENKYL-PESLEPASEYWLKPGDLLISRANTSe 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 466 --GDVGLVPsrfngmNLTENAA---KLM-FR----SIDKSWLKYTLRSKFSQSQF--NEKTNQLAQPKLALHRIESSIIA 533
Cdd:cd17261    76 lvGRAALVD------GDPDNLIypdKLIrLRvneeLLLPEYLALALNSPSARRQIesRATGTAGSMPKISQSDLKSLPIP 149

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2026845886 534 LPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17261   150 LPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191

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: 86.74 E-value: 1.12e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQSgSIIEPDKYLSESGLLNSEeANQGDVFTVCI---GGSIGKS- 182
Cdd:cd17249     1 VRLGDLGKFLSGGTPSKSNPEYWGGDIPWVSPKDMKSD-YISDSEDHITELAVEESG-TKLVPAGSVLIvvrGMILAHTf 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 183 --AIVHGRIGFNQQINAIKPIK-FSSAFL-YSILSTRFFIDSMVSAS---TGSatpiINRSKWESLLIPCASMNEQHRIV 255
Cdd:cd17249    79 pvAITTRPVAFNQDIKALIPKEgIDPEFLlYALKANEDRILSLVDKAghgTGS----LDTDDLKNLPIPLPPLEEQRRIA 154

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2026845886 256 AKVDELMSLCDQLEQKSEASLAAHQTLVETL 286
Cdd:cd17249   155 AILDALDALIDLLERKLAKLEELLKALMQAL 185

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

Pssm-ID: 341140 [Multi-domain] Cd Length: 185 Bit Score: 84.48 E-value: 8.38e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQSGSIIEPDKYLSESGllNSEEANQ----GDVFTVCIgGSI 179
Cdd:cd17251     1 WEVKTLKDFGKIITGKTPSTKNKEYYGGDIPFIKIPDMHGNVFITKTEDYLSEEG--ANSQKNKtlpkNSICVSCI-ATV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 180 GKSAIVHGRIGFNQQINAIKPIK-FSSAFLYSILSTRF-FIDSMvsASTGSATPIINRSKWESL--LIPCAS-MNEQHRI 254
Cdd:cd17251    78 GLVSITTEESQTNQQINSIIPKKeNYRYYLYFALKSLKeLLEAL--GSGGSTTLNLNKGKFSKIkiLLPSEDlLKKFHKI 155


                  ..
gi 2026845886 255 VA 256
Cdd:cd17251   156 VS 157

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Campylobacter species RM1670 S subunit (S.Csp16704I) TRD2-CR2, Aeromonas media WS S subunit (S.AmeWSORF2351P) TRD1-CR1, and Clos; Campylobacter species RM16704 S subunit (S.Csp16704I ) recognizes 5'... ACANNNNNNNNTCG ... 3', and the recognition sequences of Aeromonas media WS TRD1-CR1 S subunit (S.AmeWSORF2351P) and Clostridium carboxidivorans P7 S subunit (S.CcaPORF573P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341174 [Multi-domain] Cd Length: 181 Bit Score: 83.71 E-value: 1.42e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGyvGVCST---GKTPSTSVNEYFNGDIPFIGPGQITqSGSIIEPDKYLSESGLLNSEE--ANQGDVFtVCIGGSIGK 181
Cdd:cd17285     1 KKLG--DLVEKivgGGTPSKSNPEYWNGDIPWASVKDLK-GKYLTSTEDKITEEGLKNSSSnlIPKGTVI-IATRMGLGK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 182 SAIVHGRIGFNQQINAIKP-----IKFSSAFLYSILSTrffIDSMvsaSTGSATPIINRSKWESLLIPCASMNEQHRIVA 256
Cdd:cd17285    77 VAINKIDVAINQDLKALFPkdeldPEYLLYWFLSIEET---IESL---GTGTTVKGITLEDLKSLKIPLPPLEEQKRIVA 150

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2026845886 257 KVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17285   151 ILDELDELIDKLEAKLEKLKQLKKGLMQSLL 181

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: 83.36 E-value: 1.85e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 126 NEYFNGDIPFIGPGQItQSGSI-------IEPDKYlsesGLLNSEEANQGD-VFtvCIGGSIGKSAIVH----GRIgfNQ 193
Cdd:cd17264    21 SEFVDEGIPFINAGHL-EDGTIdlsnmnfISEEKY----NSLGSGKLQKGDiLY--CLRGSLGKCAIVDnydeGAI--AS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 194 QINAIKP-IKFSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKS 272
Cdd:cd17264    92 SLVIIRPfAKVDVRYLYYYLNSPLGKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQAL 171

                         170
                  ....*....|..
gi 2026845886 273 EASLAAHQTLVE 284
Cdd:cd17264   172 EKLEELLQSLFQ 183

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: 82.16 E-value: 3.58e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVCSTGKTP-STSVNEYFNGdIPFI-GPGQITqSGSIIePDKYLSESgllnSEEANQGDVFtVCIGGS-IGKSA 183
Cdd:cd17496     1 VKLGDIAEIIMGQSPkGESYNTEGIG-IPLLnGPADFG-DGYPI-PKKWTTKP----TKLCKKGDIL-FCVRGStTGRLN 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 184 IVHGR--IGfnQQINAIKPIK-FSSAFLYSILstRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDE 260
Cdd:cd17496    73 IADDEycIG--RGVAAIRPKNgIDTEFLYYLL--ESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDP 148

                         170       180
                  ....*....|....*....|....*..
gi 2026845886 261 LMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17496   149 LDEKIDKNKQEIEKLEELRDTLLPKLL 175

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: 81.42 E-value: 1.02e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 101 PEGWEWCRLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQ--SGSIIEPDKYLSESGLLNSEE----ANqgdvfTVC 174
Cdd:cd17248     1 PAHWEVVPLTDVAKLESGHTPSRSRPEYWNGCIPWISLADVKQlrGDYIYETKEKISELGIANSSArllpAG-----TVV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 175 IG--GSIGKSAIV--------HgrigFnqqINAIKPIKFSSAFLYSIL--STRFFIDSMvsasTGSATPIINRSKWESLL 242
Cdd:cd17248    76 LSrtASVGKSAIMgrpmatsqD----F---ANWVCGPELDPEYLLYVLraMKPEFERLA----MGSTHKTIYMPDFKALR 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2026845886 243 IPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLLA 288
Cdd:cd17248   145 IALPPLEEQRKIVDRLEALDAKIDALERKLERLIELLKELRQALLT 190

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

Pssm-ID: 341171 [Multi-domain] Cd Length: 186 Bit Score: 80.95 E-value: 1.33e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKT-------PStsvneYFNGDIPFIGPGQITQS-GSIIEPDKYLSESGLLNSEEANQGdvfTVC- 174
Cdd:cd17282     1 WEVKKLSDLGSLERGKFkhrprndPR-----LYGGDYPFIQTGDVARAnGYITSYSQTLNEKGLAQSKLFPKG---TLCi 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 175 -IGGSIGKSAI----------VhgrIGFNqqinaIKPIKFSSAFLYSILstRFFIDSMVSASTGSATPIINRSKWESLLI 243
Cdd:cd17282    73 tIAANIGDTAIlgfdacfpdsV---VGFI-----PNEEKIDVEFLEYYL--RTLKKELEAIAPQSAQKNINLEILRPLKI 142

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2026845886 244 PCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTL 282
Cdd:cd17282   143 PVPPLEEQKKIVEILDALDDLIDNLEKRIAKLEELKQSL 181

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) TRD2-CR2, Escherichia coli E24377A S subunit (S.EcoE24377ORF286P) TRD1-CR1 and Pseudoalteromonas species P1-1; Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) recognizes 5'... TCTANNNNNNRTTC ... 3', and the recognition sequences of Escherichia coli E24377A S subunit (S.EcoE24377ORF286P) and Pseudoalteromonas species P1-13-1a S subunit (S.Psp1bORF2093P) are undetermined. The restriction-modification (RM) system S subunit generally consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) TRD1 recognizes TCTA/TAGA, and -TRD2 recognizes GAAY/RTTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. In addition, this family includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P.

Pssm-ID: 341202 [Multi-domain] Cd Length: 187 Bit Score: 79.83 E-value: 2.92e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVgvCSTGKTPSTSVNEYFNGDIPFIgpgQIT---QSGSIIEPDKYLSesglLNSEEANQ-----GD-VF--T 172
Cdd:cd17521     1 WEVKKLGEL--SEKIQYGYTASAAYEDGGPRYL---RITdiqDDGVLWDTVPYCS----ISEEDAEKyllkdGDiLFarT 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 173 vciGGSIGKSAIVHgrigfNQQINAI----------KPIKFSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLL 242
Cdd:cd17521    72 ---GATVGKSYLYK-----EDDGKAVfasylirfrpNKKKVLPKYLFYFTQSSLYWKQIKSISSGSAQPNINAEKLKSLK 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2026845886 243 IPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETL 286
Cdd:cd17521   144 IPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLKELLQSL 187

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) TRD2-CR2 and Shewanella xiamenensis BC01 S subunit (S.SxiBC01OR; The recognition sequences of Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) and Shewanella xiamenensis BC01 S subunit (S.SxiBC01ORF77P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341173 [Multi-domain] Cd Length: 185 Bit Score: 77.64 E-value: 2.07e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 101 PEGWEWCRLGYVGVCSTgktPSTSVNEYFNGDIPFIgpgqitqsgsIIE--PDKYLSESGL---LNSEEANQ-------- 167
Cdd:cd17284     1 PEGWEVKRVGDVCDCIV---PGRDKPKSFDGNIPWI----------TIEdiKGKYISSSKSglgVSEEEIKEmnlkvipk 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 168 GDVFTVCIGgSIGKSAIVHGRIGFNQQINAIKPIK-FSSAFLYSILStrFFIDSMVSASTGSATPIINRSKWESLLIPCA 246
Cdd:cd17284    68 GSVIMSCVG-DFGIVAIATNELVINQQLHAFVPSKkINPEYLMYLLS--LQKKYMEKIATGTTIPYLNKTNCESIPIPLP 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2026845886 247 SMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17284   145 PIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQQLF 185

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 81.08 E-value: 3.49e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886  99 ELPEGWEWCRLGYVGVCSTGKTPST--SVNEYFNGDIPFIGPGQITQSGSIIEPDKYLSESGLLNSEEANQGDVFTVCIG 176
Cdd:PRK09737    5 KLPEGWVTTHISEICSVIRGVKPPKgyATKSLTMGDLPFIRTTDITNGAVDLTTLPYCMDAPEDVSKYQLQDRDIVISSA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 177 GSIGKSAIVHGRIGFNQQINA----IKPIK-FSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQ 251
Cdd:PRK09737   85 GSIGFSFLAQNPLPSNVVFASfairLKPVNyFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAEQ 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 252 HRIVAKVDelmslcdqleqkseaslaahqtlveTLLATLtesaDSGElaqnwARLAQYFDSLfttqssiDALKQTILQLA 331
Cdd:PRK09737  165 KIIAEKLD-------------------------TLLAQV----DSTK-----ARLEQIPQIL-------KRFRQAVLGAA 203

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 332 VMGKLvpqdpndepasvlleriaaekarlvkegkikksnplpeiTDDEKPFELPEGWKMVRLGQVSTVKGGKRLPAGHQF 411
Cdd:PRK09737  204 VSGKL---------------------------------------TEEWRWPDLPSTWSVHKYSELVDSRLGGMSSKANNF 244

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 412 SayeTAHVYIRVTDMKNGSINDSGLAYISPEThSLISQYTISSDDLYITIAGTIGDVGL--VPSRFNGMNLTENAAKLMF 489
Cdd:PRK09737  245 G---SATPYLRNINVRWGSFDLEDLQDILISD-IERRELKLKLGDVLFCRGNEPLEVGRcaIWKEPQDIPVIYQKALIRA 320

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 490 RSIDK---SWLKYTLRSKFS-QSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQI-----SAR 560
Cdd:PRK09737  321 RVKDDiipEYLVYNLKSPDSrNISLSQLFTGTTQKHITGKALANYPIRVPPLEEQAEIVRRVEQLFAYADTIekqvnNAL 400

                         490
                  ....*....|....
gi 2026845886 561 LQASQTTQQHLAEA 574
Cdd:PRK09737  401 ARVNNLTQSILAKA 414

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: 75.24 E-value: 1.36e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQVSTVKggkrlpAGHQFSAYETAHVYIRV---TDMKNGSINDSGLAYISPETHSLISQYTISSDDLYITIAGT 464
Cdd:cd17259     1 WEWVKLGDVADIL------SGYAFKSSEFSESGIRLlrgANVGVGEIRWDDTVYLPEEYLEEYEKYLLKEGDIVIALDRP 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 465 IGDVGL----VPSRFNGMNLTENAAKLMFRS-IDKSWLKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAE 539
Cdd:cd17259    75 IISGGLkvarIPKSDLPALLVQRVARIRPKDeLNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEE 154

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2026845886 540 QKRIVAKVDELMFLCDQISARLQASQTTQQHLAEA 574
Cdd:cd17259   155 QKKIAEFLSSLDALIDLLEQKLEKLQQLKKGLMQS 189

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: 75.37 E-value: 1.37e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQVSTVKGGKRLpagHQfSAYETAHV-YIR---VTDMKNGSINDSGLaYISPETHSLI-SQY-TISSDDLYITI 461
Cdd:cd17289     1 WEWKKLGDIAEITSSKRI---FK-SEYVDSGIpFYRskeIIELFNGEEISTEL-FISEERYEEIkSKYgVPKKGDILITS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 462 AGTIGDVGLVPSR----FNGMNLT--ENaaklmFRSIDKSWLKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALP 535
Cdd:cd17289    76 VGTIGIPYLVKNDdpfyFKDGNLTwfKN-----IKDINSKFLYYWFQSSIFKNQINSITIGSTQKALTIEKLKKTKIPLP 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2026845886 536 PIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17289   151 PLEEQKKIVSILSALDEKIDLNKKQLQKLEELAKTLFQYW 190

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: 74.56 E-value: 2.03e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVCSTGKTPSTSVNEYF-NGDIPFIGPGQItQSGSIIEPDKYLSESGLLNSEeANQGDVFTVCIG--GSIGKSA 183
Cdd:cd17296     1 KKLGEICSIQSGGTPSRSKKEYWnNGTIPWVKISDC-KNKYVDETEEFITEEGLNNSS-AKLLKKGTILIAifATIGKVG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 184 IVHGRIGFNQQINAIKPI--KFSSAFLYSILstRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDEL 261
Cdd:cd17296    79 ILKIEATTNQAIAGIKPKnkSINPKYLYYYL--KSLYEKFLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKF 156


                  ....*....
gi 2026845886 262 MSLCDQLEQ 270
Cdd:cd17296   157 EKLINKRQE 165

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: 74.59 E-value: 2.13e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 128 YFNGDIPFIGPGQITQSGSiiepDKYLSESGLLNSEEANQ---GDVF---TVC---IGGSI--GKSAIVHGRIGFNQQIN 196
Cdd:cd17250    22 KEDGEYPFYKVGDMNNSGN----EKYLSTAENYISEEIVKelkAKLFpkgTIIfakIGEAIklNRRAILSKDSCIDNNVM 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 197 AIKPI-KFSSAFLYSILSTrffIDsMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEAS 275
Cdd:cd17250    98 GLIPNeGIDSEYLYYWLKK---VD-LYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQALEAA 173

                         170
                  ....*....|..
gi 2026845886 276 LAAHQTLVETLL 287
Cdd:cd17250   174 KEQLKGLRQSLL 185

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: 74.47 E-value: 2.37e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKT-PSTsvnEYFNGDIPF-----IGPGQITqsgsiIEPDKYLSESGLLNSEE--ANQGDVftVcI 175
Cdd:cd17259     1 WEWVKLGDVADILSGYAfKSS---EFSESGIRLlrganVGVGEIR-----WDDTVYLPEEYLEEYEKylLKEGDI--V-I 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 176 G--GSIGKSAIVHGRIG-------FNQQINAIKPIK-FSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIPC 245
Cdd:cd17259    70 AldRPIISGGLKVARIPksdlpalLVQRVARIRPKDeLNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPL 149

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2026845886 246 ASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTL 282
Cdd:cd17259   150 PPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKGL 186

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

Pssm-ID: 341198 [Multi-domain] Cd Length: 192 Bit Score: 74.11 E-value: 3.46e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVgVCSTGKTPSTSVNEYFNGdIPFIGPGQITQSGSIIEPDKYLSEsglLNSEEANQ-----GDVFTVCIGGS 178
Cdd:cd17517     1 WEVVKLGDL-LEDPRYGTSKKSSYDGSG-TPVLRIPNIYDGGIDLDDLKKRVD---LSEKELEKyllkkGDILFNRSNGS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 179 ---IGKSAIVHG------------RIGFNQQinaikpiKFSSAFLYSILSTRFFIDSMVSASTGSA-TPIINRSKWESLL 242
Cdd:cd17517    76 pelVGKCALVDEedepaifasyliRLRLDKK-------KILPEFLYYYLNSPLGRKQIEKIAKSAAgQANINQKDLKKLP 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2026845886 243 IPCASMNEQHRIVAKVDELMSLCDQLEQKSEASlaahQTLVETLLATL 290
Cdd:cd17517   149 IPLPPLEEQKEIVEILESLDSKIDLLEKKLEKL----EQLFKSLMQSL 192

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: 74.11 E-value: 3.50e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQVST-VKGGKRLPAghqfSAYETAHVYIRVTDMKNGSINDSGLAYISPETHSLISQYTISSDDLYIT----IA 462
Cdd:cd17517     1 WEVVKLGDLLEdPRYGTSKKS----SYDGSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKELEKYLLKKGDILFNrsngSP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 463 GTIGDVGLVPSRFNGmnlTENAAKLM-FR----SIDKSWLKYTLRSKFSQSQFNEKTNQLA-QPKLALHRIESSIIALPP 536
Cdd:cd17517    77 ELVGKCALVDEEDEP---AIFASYLIrLRldkkKILPEFLYYYLNSPLGRKQIEKIAKSAAgQANINQKDLKKLPIPLPP 153

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2026845886 537 IAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17517   154 LEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192

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: 74.18 E-value: 3.75e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQ-VSTVKGGKrlpaghqFSA--YETAHVYI-RVTDMKNGSINDSGLAYISPETHSLISQYTISSDDLYITIAG 463
Cdd:cd17512     1 WEEIRLGDiIDYQKGYA-------FKSkdYQDSGIRIvRVSDFTDDSIDINNLVYISEEKANKYKKYELKENDIIITTVG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 464 --------TIGDVGLVPSRFNGMNLTENAAKLMFRS--IDKSWLKYTLRSKFSQsQFNEKTNQLA--QPKLALHRIESSI 531
Cdd:cd17512    74 swpsnpdsVVGKVVRVPKEADGALLNQNAVKIRPKKgiLDQSFLFYNLKSERFK-NYIESIARGNanQASITLGDIKKFK 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2026845886 532 IALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHL 571
Cdd:cd17512   153 FLLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQAL 192

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

Pssm-ID: 341142 [Multi-domain] Cd Length: 193 Bit Score: 73.66 E-value: 5.67e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 103 GWEWCRLGYVGVCSTGKT--PSTSVNE--------------YFN-GDIPFIGpgqITQSgsiiEPDKYLsesgLLNseea 165
Cdd:cd17253     1 GWEWVRLGDVAEVQSGITkgKKRRGGElevpylrvanvqdgYLDlSEVKEIE---VTEE----ELERYR----LRK---- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 166 nqGDVFtVCIGGS---IGKSAIVHGRIG--FNQqiNAI-----KPIKFSSAFLYSILSTRFFIDSMVSASTGSaTPI--I 233
Cdd:cd17253    66 --GDLL-VTEGGDsdkLGRGAIWRGEIPpcLHQ--NHLfrvrpKDDLLLPEFLSYWLNSAYGRGYFLRAAKQT-TNLasI 139

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2026845886 234 NRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17253   140 NSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193

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: 72.27 E-value: 1.40e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 421 IRVTDMKNGSINDSGLAYISPETHSlISQYTISSDDLYIT-IAGTIGDVGlvpsRFNGMNLTENAA--------KLMFRS 491
Cdd:cd17523    31 LRLADIKNNKISFENLRRIKLTEKE-IEKYSLSKGDLLIIrVNGSPDLVG----RFILFKGYEDVAycdhfirmRLDQEK 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 492 IDKSWLKYTLRSKFSQSQFNEKTNQLA-QPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQH 570
Cdd:cd17523   106 IDPEFLSYIFNSPLIRRKIERNFVTSAgQKTVNQGHIKSLPIPLPPLKEQKKIVARVEELFALIDQLESSLDLAQQLQNK 185


                  ....*
gi 2026845886 571 LAEAL 575
Cdd:cd17523   186 LAQSI 190

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: 71.67 E-value: 2.24e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKTPSTSVNEYF-NGDIPFIGPGQITQSGSIIEPDK-YLSESGLlnsEEAN-----QGDVFtVCIG 176
Cdd:cd17277     1 WPIVKLGEVCEIINGSTPSKKNEEYWnNGTIKWLTIPDIDERGLIISSTKqFITEKAL---EEKKvklvpKNSVL-LSCT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 177 GSIGKSAIVHGRIGFNQQINAI--KPIKFSSAFLYSILstRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRI 254
Cdd:cd17277    77 ATIGKVAIAKIELTTNQQINALicKDSKILPEYLFYAL--KHIKQVLERLTTNPGVKHVNLSMLSNLQIPLPPLEVQKKI 154

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2026845886 255 VAKVDELmslcDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17277   155 VAEIEKV----EKVIQGLRQKIDEYQPLINAIL 183

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: 71.36 E-value: 3.25e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQVSTvkggkrlpaGHQFSAYETA------HVYIRVTDMKNGSINDSGLAYISPEThSLISQYTISSDDlyITI 461
Cdd:cd17521     1 WEVKKLGELSE---------KIQYGYTASAayedggPRYLRITDIQDDGVLWDTVPYCSISE-EDAEKYLLKDGD--ILF 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 462 A---GTIGDVGLVPsrfngmNLTENA--------AKLMFRSIDKSWLKYTLRSKFSQSQFNEKTNQLAQP-----KLAlh 525
Cdd:cd17521    69 ArtgATVGKSYLYK------EDDGKAvfasylirFRPNKKKVLPKYLFYFTQSSLYWKQIKSISSGSAQPninaeKLK-- 140

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2026845886 526 rieSSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17521   141 ---SLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLKELLQSL 187

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: 71.01 E-value: 3.80e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 108 RLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQIT-QSGSIIEPDKYLSESGLLNSeEANqgdvftVCIGGSI------- 179
Cdd:cd17513     2 KLGELGKFIGGGTPSTKNPEYWNGNIPWITSSDLSeDDIFKINIRKFITEEAIKNS-ATK------IIPANSIlivtrvg 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 180 -GKSAIVHGRIGFNQQINAIKPIK-----FSSAFLYSILStrfFIDSMVSASTgsatpI--INRSKWESLLIPCASMNEQ 251
Cdd:cd17513    75 vGKVAINPFDICTSQDFTSLIPIKevnplFLAYLLYSLLQ---KLKSQLQGTS-----IkgITKDDLKNLKIPLPPLEEQ 146

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2026845886 252 HRIVAKVDELMSLCDQLEQKSEASLAAHQTL 282
Cdd:cd17513   147 QKIAAILSKLDKLIEAHEKKLEKLKQLKKGL 177

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: 71.03 E-value: 4.28e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYV-GVCSTGKTPSTSVNEyfnGDIPFIGPGQITqSGSIIEPD-KYLSESGLLNSE-EANQGDVFtVCIGGSI- 179
Cdd:cd17261     1 WEWVRLGDLiEGIRNGWSPKPPDDE---TGWPVLKLSAVT-SGKFDPSEnKYLPESLEPASEyWLKPGDLL-ISRANTSe 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 180 --GKSAIVHG------------RIGFNQQINaikpikfSSAFLYSILST---RFFIDSMVSASTGSaTPIINRSKWESLL 242
Cdd:cd17261    76 lvGRAALVDGdpdnliypdkliRLRVNEELL-------LPEYLALALNSpsaRRQIESRATGTAGS-MPKISQSDLKSLP 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2026845886 243 IPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETL 286
Cdd:cd17261   148 IPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191

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: 70.65 E-value: 4.42e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 105 EWCRLGYVgvCSTGK---TPSTSVNEYFNGDIPFIGPGQITQSGSIIE-PDKYLSESGLLNSE----EANqgdvfTVC-- 174
Cdd:cd17275     1 EQVKLGEL--CEKMKsggTPSTSNKEYYGGDIPFVKISDMTKSGKYIYsTEKYITEEGLKNSSawivPKG-----TILya 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 175 IGGSIGKSAIVHGRIGFNQQINAIKP--IKFSSAFLYSILStrFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQH 252
Cdd:cd17275    74 MYASVGKVAINKIDVATNQAILGIIPkdEKLDFEFLYYWLL--SLKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQK 151

                         170
                  ....*....|....*....
gi 2026845886 253 RIVAKVDELMSLCDQLEQK 271
Cdd:cd17275   152 KIAEILDKIDAEIDKLEEK 170

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: 69.82 E-value: 1.01e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVCSTGKTPSTSVNEYFNGDIPFIGPGQItQSGSIIEPDKYLSESGLLNSeeanQGDVF---TVCI-----GGS 178
Cdd:cd17287     1 KKLGEIAKVSSGGTPSRSNPEYWNGGIPWVKTGEV-NFNEITDTEEKITEEGLKNS----SAKLFpkgTLLMamygqGKT 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 179 IGKSAIvhgrIGF----NQQINAIKPI-KFSSAFLYSILSTRFfiDSMVSASTGSATPIINRSKWESLLIPCASMNEQHR 253
Cdd:cd17287    76 RGRVAI----LGIeaatNQACAAILPNdGINPDFLFYYLQSSY--EELRDLSNGGGQPNLNAGLIKSIEIPVPPLDEQQK 149

                         170       180
                  ....*....|....*....|....*....
gi 2026845886 254 IVAKVDELMSLCDQLEQKSEASLAAHQTL 282
Cdd:cd17287   150 IAAFLSAIDAKIDALEQKLELLQELKKSL 178

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: 68.00 E-value: 3.60e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 108 RLGYVGVCSTGKTPSTSVNE-YFNGD-IPFIGPGQITqSGSIIEPDKYLSESGLLNSE----EANqgdvfTVCI-----G 176
Cdd:cd17276     2 KIGDIAKTSSGGTPLRSNQEyYFNGGtIPWVKTTDLN-NGVIYETEEKITEKALKETSckllPKG-----TVLVamyggF 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 177 GSIGKSAIvhgrIGF----NQQINAIKPI--KFSSAFLYSILStrFFIDS-MVSASTGSATPIINRSKWESLLIPCASMN 249
Cdd:cd17276    76 GQIGRTGL----LGIpaaiNQAICAILPNekKVNPEFLLRYLN--FNRPYwMRVAASSRKDPNITKDDVRNFPIPLPPLD 149

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2026845886 250 EQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17276   150 EQRAIVEFLSDVDALIDSLEALIEKLRELKKGLMQQLL 187

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: 67.00 E-value: 6.40e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 101 PEGWEWCRLGYVGVCSTGKTPSTSvNEYFNGDIPFIGPGqITQSGSIIEPDKYlsesgllnSEEANQGDVFTVCIGGSIG 180
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKK-ELKNNGKYPYIRAG-DLNNVVKGGLGYI--------KKYILPKGDITISSRATIG 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 181 KSAIVHGRIGFNQQINAI--KPIKFSSAFLYSILSTrfFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKV 258
Cdd:pfam01420  71 YVFYRDKPYYTNQHIIVLipKNNIKITEFLYLYLLL--KLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKIL 148

                         170
                  ....*....|....*...
gi 2026845886 259 DELmSLCDQLEQKSEASL 276
Cdd:pfam01420 149 SQL-DNTIELEKGILNEL 165

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2, Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1, and re; The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 3'. The recognition sequence of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. It also includes the TRD-CR-like domains of putative type II restriction enzymes and methyltransferases, such as Helicobacter cinaedi PAGU611 Hci611ORFHP which may recognize 5'... GAGNNNNNGT ... 3', and type I N6-adenine DNA methyltransferases, such as Calditerrivibrio nitroreducens M.Cni19672ORF1405P whose recognition sequence is undetermined.

Pssm-ID: 341195 [Multi-domain] Cd Length: 183 Bit Score: 66.43 E-value: 1.28e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVC-STGKTPSTSVNEYFN-GDIPFIGPGQiTQSGSIIEPDKYLSESGLLNSEEAN---QGDVFTVC--IGGSI 179
Cdd:cd17514     1 VKIQDIAFEiINGGTPSRNEPEYWNnGDIPWLTSGE-TDDNFINNTSEKITTKNGLEDSSIRivpKGTILIACtgQGYTR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 180 GKSAIVHGRIGFNQQINAIKPIK-FSSAFLYSILSTRFfiDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKV 258
Cdd:cd17514    80 GQVAVLQIDASTNQAIAAIRCKEnVNPKYLYYYLKTQK--NNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNIL 157

                         170       180
                  ....*....|....*....|....*..
gi 2026845886 259 DEL-MSLCDQLEQKSEaslAAHQTLVE 284
Cdd:cd17514   158 ETLeFFEKDSLRKIKE---TAQDINLM 181

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: 66.34 E-value: 1.34e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 116 STGKTPSTSVNEYFNGD-IPFIGPGQITQSGSIIEPDKYLSESGLLNSeeanqgDVFTVCIGG-------SIGKSAIVHG 187
Cdd:cd17244    10 KIGKTPPRKEPEYWSGDnIPWVSISDMGKGKYISDTKEYITDEAVKKF------NVKLVPKGTllmsfklTIGRVAIAGK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 188 RIGFNQQINAIKP--IKFSSAFLYSILSTrFFIDSMVSASTGSATpiINRSKWESLLIPCASMNEQHRIVAKVDELMSLC 265
Cdd:cd17244    84 DLYTNEAIAHFIPkdKKIDTEYLYYYLKS-FDYSSLGSTASKGKT--LNSKKIKEIPIPLPPLEEQKRIAPILDKIDALI 160

                         170
                  ....*....|....*...
gi 2026845886 266 DQLEQKSEASLAAHQTLV 283
Cdd:cd17244   161 DQLETLIELLDELLPKLM 178

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: 65.54 E-value: 2.55e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 459 ITIAGTIGD--------------VGLVPSRFNgmnltenaaklmfrsIDKSWLKYTLRskFSQSQFNEKTNQLAQPKLAL 524
Cdd:cd17282    72 ITIAANIGDtailgfdacfpdsvVGFIPNEEK---------------IDVEFLEYYLR--TLKKELEAIAPQSAQKNINL 134

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2026845886 525 HRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEALV 576
Cdd:cd17282   135 EILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIAKLEELKQSLLQEAF 186

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) TRD2-CR2 and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) T; The recognition sequences of Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341172 [Multi-domain] Cd Length: 181 Bit Score: 65.58 E-value: 2.58e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 128 YFNGD-IPFIGPGQITQSGSIIEPDK-YLSESGLLNSEEANQGDvFTVCIGGSIGKSAIVhgriGFNQQIN----AIKPI 201
Cdd:cd17283    23 TFDGDgIPWIKIGDVTKDGKYITKTKeKITEEGAKKSRLVKPGD-LILSNSMSFGRPYIL----KIDGCIHdgwlVFSDL 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 202 --KFSSAFLYSILSTrFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAH 279
Cdd:cd17283    98 kkKLDKDFLYYLLSS-ITVQLQFSAQAGGGTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLEELK 176


                  ...
gi 2026845886 280 QTL 282
Cdd:cd17283   177 KGL 179

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: 64.30 E-value: 5.19e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 385 PEGWKMVRLGQVSTVKGGKRLPAGhQFSAYETAhVYIRVTDMKNGSIndSGLAYISpethslisQYTISSDDLYITIAGT 464
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKK-ELKNNGKY-PYIRAGDLNNVVK--GGLGYIK--------KYILPKGDITISSRAT 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 465 IGDVGLVPSRFNgmnltenAAKLMFRSIDKSWLKYTLRS----KFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQ 540
Cdd:pfam01420  69 IGYVFYRDKPYY-------TNQHIIVLIPKNNIKITEFLylylLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQ 141

                         170
                  ....*....|
gi 2026845886 541 KRIVAKVDEL 550
Cdd:pfam01420 142 KKIAKILSQL 151

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: 64.89 E-value: 5.52e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQVSTVKGGKRLPAGHQFSAY-ETAHVYIRVTDMKNGSINDSGLAYISPETHSlISQYtISSDDLYITIA-GTI 465
Cdd:cd17252     1 WEWVRLGEIAEIIRGVTYKKSDASEEPsEGGIPVLRANNIQNGGLDFDDLVYVPKSKVK-EEQK-LKKGDILICMSsGSK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 466 GDVGLVPSRFNGMNLTENAaklmFRSI-------DKSWLKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIA 538
Cdd:cd17252    79 ELVGKAAFIDEDTDYTFGA----FCGVirpkkeiDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPLA 154

                         170       180
                  ....*....|....*....|....*..
gi 2026845886 539 EQKRIVAKVDELMFLCDQISARLQASQ 565
Cdd:cd17252   155 EQKRIVAKLDKLDALIDKLKQALEKLD 181

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: 63.68 E-value: 1.10e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 108 RLGYVGVCSTGKTP--STSVNEYFNGDIPFIGPGQITQSgsiiEPDKYLSESglLNSEEANQGDVFTVCIGGSIGKsaIV 185
Cdd:cd17263     2 KLGEVCKFSKGKQPpiSERFDEPKEGSVRYIQIEDLRNN----NEKKYIENP--KKSVICNEDDILIVRDGANAGE--VG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 186 HGRIG-FNQQINAIKPIK--FSSAFLYSILSTRFFIdSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELM 262
Cdd:cd17263    74 TGLEGaIASTLFKIIPDKniIDKDYLYYFLKSKEIQ-LNILTKAGSTIPHVNKKDLENLKIPLPSLEEQKKIAEILDKLD 152

                         170       180
                  ....*....|....*....|....*
gi 2026845886 263 SLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17263   153 ALIDKLKELIEKLIELKKGLFQELL 177

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: 63.22 E-value: 2.10e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKMVRLGQVstVKGGKRLPAGHQFSAyETAHVYIRVTDMKNGSINdsgLAYISPETHSLISQYTISSDDLYITIAGTIGD 467
Cdd:cd17272     1 VEEKTLGDI--AVDGFQNGPAPNFDE-KGEIPVITSKNISNGKID---FEYVKYDFLSISKNRKINKGDILITMIGTIGE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 468 VGLVpSRFNGMNLTENAAKLMFRS--IDKSWLKYTL-RSKFSQSQFNektNQLAQPKLALHRIESSIIALPPIAEQKRIV 544
Cdd:cd17272    75 TAIV-KCLDPKFYTLNLYLIRLKKekLLPSYLKYFLdSEKFLNKSIS---ATSGQGYLKANQIDKLEIPLPPLEEQQRIV 150

                         170
                  ....*....|....*....
gi 2026845886 545 AKVDELMFLCDQISARLQA 563
Cdd:cd17272   151 KILDKFDTLCNDITEGLPA 169

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: 62.87 E-value: 2.53e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVgVCS----TGKTPSTSvneyfNGDIPFIGPGQITQSGSIIEPDKYLSesglLNSEEA-----NQGDV-F-- 171
Cdd:cd17524     1 WEWVTIGDL-VTSvqygTSEKKSED-----EGGYPVLRMGNIQDGGIDDDDLKYVD----LDEKEFekyllKKGDVlFnr 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 172 T-----VciggsiGKSAIVHG-----------RIGFNQQInaIKPiKFSSAFLYSILsTRFFIDSMVSASTGSATpiINR 235
Cdd:cd17524    71 TnspelV------GKTAIFRGdgpatfasyliRIRLNEEK--ILP-EYLNYFLNSPY-GRKQIKSVATQGVGQAN--INA 138

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2026845886 236 SKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASlaahQTLVETLLATL 290
Cdd:cd17524   139 TKLKAIPIPLPPLEEQKEIVEKLDELDALIDRLEALLEEA----EELLESLLQSL 189

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: 62.88 E-value: 2.75e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 387 GWKMVRLGQVSTVKGGKRLpaGHQFSAYETAHVYIRVTDMKNGSINDSGLAYIS-PETHslISQYTISSDDLYITIAGTI 465
Cdd:cd17253     1 GWEWVRLGDVAEVQSGITK--GKKRRGGELEVPYLRVANVQDGYLDLSEVKEIEvTEEE--LERYRLRKGDLLVTEGGDS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 466 GDVG---LVPSRFNGMnLTENAakLM-FRSIDKS----WLKYTLRSKFSQSQFNE---KTNQLAqpklalH----RIESS 530
Cdd:cd17253    77 DKLGrgaIWRGEIPPC-LHQNH--LFrVRPKDDLllpeFLSYWLNSAYGRGYFLRaakQTTNLA------SinstKLKAL 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2026845886 531 IIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEALV 576
Cdd:cd17253   148 PVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193

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: 61.80 E-value: 5.16e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 116 STGKTPSTSVNEYFNGDIPFIGPGQITQsGSIIEPDKYLSESGL-----LNSEEANqgdvfTVCI---GGSIGKSAIVhg 187
Cdd:cd17280    11 GSGTTPKSDNEDYYDGGIPWVTTGDLRD-GIITETSKKITDKALddysaLKIYPAG-----SLVIamyGATIGRLGIL-- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 188 RIGF--NQQINAIKPIK-FSSAFL-YSILSTRffiDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMS 263
Cdd:cd17280    83 GIDAttNQACCVLSGSNkIDIKFLfYWLLANR---DELISLASGGGQPNISQELIKSLRIPVPPLEEQKQIAAFLDKKTA 159

                         170
                  ....*....|...
gi 2026845886 264 LCDQLEQKSEASL 276
Cdd:cd17280   160 KIDSLIEKKERLI 172

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 58.53 E-value: 7.53e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 498 KYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEALVE 577
Cdd:COG0732     3 KYYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFT 82


                  ...
gi 2026845886 578 GAL 580
Cdd:COG0732    83 GEL 85

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: 60.98 E-value: 9.93e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 391 VRLGQVSTVKGGKRLPAGHQFSAY-ETAHVYIRVTDMKNGSINDsglaYISPETHSLIsqytISSDDLYIT----IAGTI 465
Cdd:cd17263     1 VKLGEVCKFSKGKQPPISERFDEPkEGSVRYIQIEDLRNNNEKK----YIENPKKSVI----CNEDDILIVrdgaNAGEV 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 466 --GDVGLVPSrfngmnlteNAAKLMFRS--IDKSWLKYTLRSKFSQSQFNeKTNQLAQPKLALHRIESSIIALPPIAEQK 541
Cdd:cd17263    73 gtGLEGAIAS---------TLFKIIPDKniIDKDYLYYFLKSKEIQLNIL-TKAGSTIPHVNKKDLENLKIPLPSLEEQK 142

                         170       180       190
                  ....*....|....*....|....*....|
gi 2026845886 542 RIVAKVDELMFLCDQISARLQASQTTQQHL 571
Cdd:cd17263   143 KIAEILDKLDALIDKLKELIEKLIELKKGL 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: 60.57 E-value: 1.21e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 491 SIDKSWLKYTLRSKFSQSQFNEKTNQlAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQH 570
Cdd:cd17283   100 KLDKDFLYYLLSSITVQLQFSAQAGG-GTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLEELKKG 178


                  .
gi 2026845886 571 L 571
Cdd:cd17283   179 L 179

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: 60.64 E-value: 1.27e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 197 AIKPIK-FSSAFLYSILstRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEAS 275
Cdd:cd17497    85 AIRPKKgLDKKYLLYYL--KSIENELSSLGTGSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDELTAKIDQLIALLEKA 162

                          90
                  ....*....|..
gi 2026845886 276 LAAHQTLVETLL 287
Cdd:cd17497   163 IELLKEYRQAVL 174

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: 59.94 E-value: 2.58e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 188 RIGFNQQInaIKPIkFSSAFLYSILSTRFFIDSMVSaSTGSATpiINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQ 267
Cdd:cd17523    98 RMRLDQEK--IDPE-FLSYIFNSPLIRRKIERNFVT-SAGQKT--VNQGHIKSLPIPLPPLKEQKKIVARVEELFALIDQ 171

                          90       100
                  ....*....|....*....|
gi 2026845886 268 LEQkseaSLAAHQTLVETLL 287
Cdd:cd17523   172 LES----SLDLAQQLQNKLA 187

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: 59.17 E-value: 4.19e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVCSTGKTP-STSVNEYFNGdIPFigpgqitQSGSIIEPDKYLSESGLLNSE---EANQGDVFtVCIGGSIGKS 182
Cdd:cd17499     1 VRLGDVAEIIMGQSPeGKSYNTNKEG-LPF-------YQGKKEFGDKYIKEPNTWTTSptkIAEKNDIL-MSVRAPVGDV 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 183 AIVHGRIGFNQQINAIKPIK-FSSAFLYSILSTrfFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDEL 261
Cdd:cd17499    72 NITTRKICIGRGLAAIRAKKnIDKKYLFYFLLS--NKDYFKGKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSELDKL 149

                         170       180
                  ....*....|....*....|....*.
gi 2026845886 262 MSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17499   150 FKLIFEAKNNIEEALANAQQLFKSIL 175

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: 59.53 E-value: 4.24e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 103 GWEWCRLGYVGVCSTGKTPSTSVNEYF-NGDIPFIGPGQITQSGSIiepdkyLSESGLLNSEEA-NQGDVFT-----VCI 175
Cdd:cd17281     1 GVEWKKLGEIFDIRNGYTPSKSNKEYWeNGTIPWFRMEDIRENGRI------LSDSIQHITPSAvKGGKLFPansiiLST 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 176 GGSIGKSAIVhgRIGF--NQQIN--AIKPiKFSSAFLYSILSTRFFI--DSMVSASTGSATPIINRSKWESLLIPCASMN 249
Cdd:cd17281    75 TATIGEHALI--TVDSlaNQRFTnfSLKK-SYKNKLDIKFLFYYFFVlgEWCKKNINIGGFPSVDMNKLKKFKIPIPPLE 151

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2026845886 250 EQHRIVAKVDELMSLCDQLEQKSEASLAAHQ 280
Cdd:cd17281   152 EQEKIVEILDKFTKLTADLTAELPAELEARK 182

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: 59.37 E-value: 4.71e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKTPSTSVNEyfNGDIPFIGPGQITQSGSIIEPDKYLSESGLLNSEEaNQGDVFTVCIGgSIGKSA 183
Cdd:cd17272     1 VEEKTLGDIAVDGFQNGPAPNFDE--KGEIPVITSKNISNGKIDFEYVKYDFLSISKNRKI-NKGDILITMIG-TIGETA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 184 IVHGR----IGFNQQINAIKPIKFSSAFLYSILSTRFFIDSMVSASTGSatPIINRSKWESLLIPCASMNEQHRIVAKVD 259
Cdd:cd17272    77 IVKCLdpkfYTLNLYLIRLKKEKLLPSYLKYFLDSEKFLNKSISATSGQ--GYLKANQIDKLEIPLPPLEEQQRIVKILD 154

                         170       180
                  ....*....|....*....|.
gi 2026845886 260 ELMSLCDQLEQKSEASLAAHQ 280
Cdd:cd17272   155 KFDTLCNDITEGLPAEIEARQ 175

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: 58.98 E-value: 4.92e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 464 TIGDVGLvpsrfNGMNLTEN---AAKLMFRSIDKSWLKYTLRSKfsQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQ 540
Cdd:cd17515    73 TAGKVGI-----LGIDAATNqaiCAILPNEEIDNEFLFYFLKSQ--KEYLISLGKGGAQPNISQGIIKNIEIPLPPLAEQ 145

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2026845886 541 KRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17515   146 KRIVAKLDKLDKLIEKLEKALEKLEELKKALMQKL 180

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: 58.09 E-value: 9.86e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 388 WKmvRLGQVSTVKggkrlpAGHQFSAY---ETAHVYIRVTDMKNGSINDSGLAYISPETHS-LISQYTISSDDLYITIAG 463
Cdd:cd17519     2 YK--TLGEVCKFQ------NGFAFKSSkyrESGFPIIRITNIQNGKIDTDNLKYFDLNDYKeNLDKYIVRPGDIVIAMSG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 464 -TIGDVGLVPSRFNGMnLTENAAKLMFRS--IDKSWLKYTLRSKFSQSQFnekTNQLAQPKLALHRIESSIIALPPIAEQ 540
Cdd:cd17519    74 aTTGKVGINLTDQEFY-LNQRVGKFIPNEeiLNNRYLYHFLLSKQNEKYI---LAGGSQPNLSSEKLKKIKIPIPSLEVQ 149

                         170       180
                  ....*....|....*....|.
gi 2026845886 541 KRIVAKVDELMFLCDQISARL 561
Cdd:cd17519   150 EEIVSILDKFRELTNELESEL 170

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter sp. S subunit (S.Asp27244ORF1181P) TRD1-CR1; The recognition sequence of Acinetobacter sp. S subunit (S.Asp27244ORF1181P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341199 [Multi-domain] Cd Length: 180 Bit Score: 57.76 E-value: 1.06e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 133 IPFIGPGQITQsGSII--EPDKYLSEsgllnsEEANQ---------GDVFTVCIGGSIGKSAIV---HGRIGFNQQINAI 198
Cdd:cd17518    25 IKLLNVTNIVN-GSLDldKTDRYIST------EEYNGkykhflideGDILIASSGNSWGKVAIVekdHLPLMLNTSTIRF 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2026845886 199 KPI--KFSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMslcDQLEQKSEA 274
Cdd:cd17518    98 KFIdgLLDNNFLKYFLNSDYFKEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDAD---DAIEAALEA 172

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

Pssm-ID: 341206 [Multi-domain] Cd Length: 190 Bit Score: 58.01 E-value: 1.08e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGyvGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQSGSIIEPD-KYLSESGL-LNSEEANQGDVF-----TVCIg 176
Cdd:cd17525     1 WEWVKLG--DILSSTQLGLVRSNSEDPNGYPYIKMGNIGRGGINLLKVeTYVDATELeVEKYLLEDGDLLfntrnTLEL- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 177 gsIGKSAIVHG---RIGFNQQINAIK-PIKFSSAFLYSILSTRFFI---DSMVSASTGSATpiINRSKWESLLIPCASMN 249
Cdd:cd17525    78 --VGKVAIWRGelpKALFNNNILRIRfDDIVLPYFINYYLNSPDGKkqlESIASGTTSVAA--IYQKDLKKLKLPLPPLD 153

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2026845886 250 EQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETL 286
Cdd:cd17525   154 EQREIVSFLSELDAKIDQLEQKLEKLLQIKKALMQQL 190

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.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: 58.03 E-value: 1.17e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 391 VRLGQVSTVKGGKRLPAGHQFSAyETAHVYIRVTDMKNgsINDSGlaYISPethsliSQYTISSDDLYITIA-----GTI 465
Cdd:cd17250     1 VRLGDVCDFKAGSGFPEKYQGKE-DGEYPFYKVGDMNN--SGNEK--YLST------AENYISEEIVKELKAklfpkGTI 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 466 gdvgLVPSRfnGMNLTENAAKLMFRS---------------IDKSWLKYTLRsKFSQSQFNEKTNQlaqPKLALHRIESS 530
Cdd:cd17250    70 ----IFAKI--GEAIKLNRRAILSKDscidnnvmglipnegIDSEYLYYWLK-KVDLYKYSQATTV---PSIRKSTLESI 139

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2026845886 531 IIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEALV 576
Cdd:cd17250   140 PIPLPPLEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGLRQSLL 185

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: 57.45 E-value: 1.33e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 180 GKSAIVHG---RIGF----------NQQInaikpikfSSAFLYSILSTRFFID----SMvsasTGSA------TPIInrs 236
Cdd:cd17260    52 GKTAIVDGlpnGIGFgstefhvlrpKEGI--------LPEFLYYLLRSPSFRKeaikSM----TGSSgrqrvpKDFL--- 116

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2026845886 237 kwESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17260   117 --ENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165

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: 57.47 E-value: 1.42e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 427 KNGSINDSGLAYISPETHS---LISQYTISSDDLYIT-IAGTIGDVGLV--PSRFNgmnlteNAAKLmFRSIDKSWLKYT 500
Cdd:cd17293    31 KPDDLNNGGIILTSEEYLSeegAKKARIVPKGSILVTcIGGSIGKVGIAdrEVAFNqq---iNAIIP-NKSVDPKFLYYQ 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 501 LRSKFSQsqfnektNQLAQPKLALHRI-----ESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17293   107 LLSSKFQ-------LQAIASSTTLPIInkskfEKIEIPLPPLEEQKRIVAKLDKLFALIDKLEESLEELDELLKSLFQSA 179


                  .
gi 2026845886 576 V 576
Cdd:cd17293   180 F 180

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: 56.60 E-value: 2.66e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 421 IRVTDMKNGSIN-DSGLAYIS-PETHSLISQYTISSDDLYITIAGTI-GDVGLVPSRfnGMNLTENAAKLMFRSI----D 493
Cdd:cd17518    28 LNVTNIVNGSLDlDKTDRYIStEEYNGKYKHFLIDEGDILIASSGNSwGKVAIVEKD--HLPLMLNTSTIRFKFIdgllD 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2026845886 494 KSWLKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMF-LCDQISARLQASQTT 567
Cdd:cd17518   106 NNFLKYFLNSDYFKEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDaIEAALEALRKKKQAA 180

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: 56.74 E-value: 2.81e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 435 GLAYIS-----PETHSLISQYTIS------SDDLYITIAG-TIGdvglvpsrfnGMNlteNAAK-------LM-FRS--- 491
Cdd:cd17496    26 GIPLLNgpadfGDGYPIPKKWTTKptklckKGDILFCVRGsTTG----------RLN---IADDeycigrgVAaIRPkng 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 492 IDKSWLKYTLRSKFSQsqFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHL 571
Cdd:cd17496    93 IDTEFLYYLLESNLDY--LLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTL 170


                  ....*
gi 2026845886 572 AEALV 576
Cdd:cd17496   171 LPKLL 175

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: 56.29 E-value: 3.78e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 198 IKPIK-FSSAFLYSILStRFFIDSMVsasTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASL 276
Cdd:cd17262    87 LKGKNgISTEFLYYYLN-SIDISPYV---TGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLI 162

                          90
                  ....*....|
gi 2026845886 277 AAHQTLVETL 286
Cdd:cd17262   163 ELKKALLQKL 172

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: 55.93 E-value: 4.03e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 191 FNQQINAIKPIK-FSSAFLYSILstRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLE 269
Cdd:cd17254    78 LNQHIFKVVPDEeIDKDYLYYLL--KALTEEIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALE 155

                          90
                  ....*....|....*...
gi 2026845886 270 QKSEASLAAHQTLVETLL 287
Cdd:cd17254   156 EQLKKLEELRKALLQSLL 173

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: 56.30 E-value: 4.76e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKTPSTSvnEYFNGDIPFIGPGQI-TQSG-SIIEPDKYLSESGLLNSEEANQGDVFtvcIGGS--- 178
Cdd:cd17268     1 VEWKTLGEIGEFIRGKGITKK--DFVESGVPCIHYGEIyTKYGiYTTKTKSFISEELAKKLRKAKPGDLL---IAGTget 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 179 ---IGKS--------AIVHGrigfnqQINAIKPiKFSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIPCAS 247
Cdd:cd17268    76 iedIGKAvawlgdeeVAAGG------DIIIFRH-SQNPKYLSYLLNSPAFQKQKRKLGTGTKVVHISASDLAKIKIPVPP 148

                         170       180
                  ....*....|....*....|....*..
gi 2026845886 248 MNEQHRIVAKVDELMSLCDQLEQKSEA 274
Cdd:cd17268   149 LEEQERIVEILDKFDALIAGLPAEIEA 175

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 53.52 E-value: 5.00e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 212 LSTRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASlaahqtlvETLLATLT 291
Cdd:COG0732     6 LRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKL--------KELRDALL 77


                  ....*...
gi 2026845886 292 ESADSGEL 299
Cdd:COG0732    78 PKLFTGEL 85

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: 55.30 E-value: 8.36e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 420 YIRVTDMKNGSINDSGLaYISPETHSLISQYTISSDDLYITIAGTIGDVGL--VPSRFN----GMNLTENaaklmfrSID 493
Cdd:cd17296    30 WVKISDCKNKYVDETEE-FITEEGLNNSSAKLLKKGTILIAIFATIGKVGIlkIEATTNqaiaGIKPKNK-------SIN 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2026845886 494 KSWLKYTLRSKFSQsqFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQ 562
Cdd:cd17296   102 PKYLYYYLKSLYEK--FLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKFEKLINKRQEGLQ 168

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio cholerae 1311-69 S subunit (S.Vch69ORF1407P) TRD2-CR2, and Methanococcoides methylutens MM1 S subunit (S.MmeMM1ORF456P) TRD2-CR2; The recognition sequences of Vibrio cholerae 1311-69 S subunit (S.Vch69ORF1407P) and Methanococcoides methylutens MM1 S subunit (S.MmeMM1ORF456P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341192 [Multi-domain] Cd Length: 191 Bit Score: 54.49 E-value: 1.87e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 100 LPEGWEwcRLGYVGVC---STGKTPSTSVNEYF-NGDIPFIGPGQITQSgSIIEPDKYLSESGLLNSE----EANqgdvf 171
Cdd:cd17501     1 VPEGWE--VGTILDLCyktQSGGTPSRKNPEYWdGGIIPWLKTGELRDN-IILDTEEKITEEGLKNSSaklfPKG----- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 172 TVCI---GGSIGKSAIVHGRIGFNQQINAIKPIK-FSSAFLY-SILSTRffiDSMVSASTGSATPIINRSKWESLLIPCA 246
Cdd:cd17501    73 TVLVamyGATAGKLGILAKEATTNQACCALIPKEeYSPFFLYlYLLNSR---DYLANLASGSAQQNISQQIIKNTKVLIP 149


                  .
gi 2026845886 247 S 247
Cdd:cd17501   150 P 150

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: 53.37 E-value: 3.83e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 421 IRVTDMKNGSINDS--GLaYISPETHSLISQYTISSDDLYITIAGTIGDVGLvpsrfNGMNLTENA---AKLMFRSIDKS 495
Cdd:cd17284    33 ITIEDIKGKYISSSksGL-GVSEEEIKEMNLKVIPKGSVIMSCVGDFGIVAI-----ATNELVINQqlhAFVPSKKINPE 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 496 WLKYTLRskFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17284   107 YLMYLLS--LQKKYMEKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQQL 184

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: 52.40 E-value: 5.47e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2026845886 207 FLYSILSTrFFIDSMvsaSTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTL 282
Cdd:cd17267    84 FLYYLLKT-LDLERL---NSGSAVPGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADAL 155

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: 52.43 E-value: 6.97e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2026845886 518 AQPKL---ALHRIEssiIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17262   115 AQPKLnqaNLNSIP---IPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQKL 172

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

Pssm-ID: 341200 [Multi-domain] Cd Length: 183 Bit Score: 52.31 E-value: 9.19e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 105 EWCRLGyvGVCSTGKTPSTSVNEYFNGDIPFIGPGQItQSGSIIEPD-KYLSES---GLLNSEEANQGDVFTVCIGGSIG 180
Cdd:cd17519     1 EYKTLG--EVCKFQNGFAFKSSKYRESGFPIIRITNI-QNGKIDTDNlKYFDLNdykENLDKYIVRPGDIVIAMSGATTG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 181 KSAIVHGRIGF--NQQINAIKP--IKFSSAFLYSILSTRFfIDSMVSAstGSATPIINRSKWESLLIPCASMNEQHRIVA 256
Cdd:cd17519    78 KVGINLTDQEFylNQRVGKFIPneEILNNRYLYHFLLSKQ-NEKYILA--GGSQPNLSSEKLKKIKIPIPSLEVQEEIVS 154

                         170
                  ....*....|....*
gi 2026845886 257 KVDELMSLCDQLEQK 271
Cdd:cd17519   155 ILDKFRELTNELESE 169

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: 52.29 E-value: 9.23e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 116 STGKTPSTSVNEYF-NGDIPFIGPGQItQSGSIIEPDKYLSESGLLNSE----EANqgdvfTVCI-----GGSIGKSAIV 185
Cdd:cd17500    10 TSGGTPSRSNKEYYnGGNIPWLKTKEL-NFKRIYDTEEKITEEGLKNSSakliPEN-----TVIIamygaGKTAGRVAIN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 186 HGRIGFNQQINA--IKPIKFSSAFLYSILSTRFfiDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIvakVDELMS 263
Cdd:cd17500    84 KIPLTTNQACCNliIDNKKADYRFVYYSLKTQY--EELVNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRI---ASILSS 158


                  ....*.
gi 2026845886 264 LCDQLE 269
Cdd:cd17500   159 LDDKIE 164

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: 51.68 E-value: 9.96e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2026845886 225 STGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTL 282
Cdd:cd17266   100 ATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKEL 157

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: 51.69 E-value: 1.14e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 489 FRSIDKSWLKYTLrsKFSQSQFNEKTNQLAQpklaLH----RIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQAS 564
Cdd:cd17254    88 DEEIDKDYLYYLL--KALTEEIESQAHGSTM----VHitkgDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKL 161

                          90
                  ....*....|.
gi 2026845886 565 QTTQQHLAEAL 575
Cdd:cd17254   162 EELRKALLQSL 172

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

Pssm-ID: 341205 [Multi-domain] Cd Length: 189 Bit Score: 52.08 E-value: 1.23e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 490 RSIDKSWLKYTLRSKFSQSQ-FNEKTNQLAQ-----PKLAlhRIEssiIALPPIAEQKRIVAKVDELMFLCDQISARLQA 563
Cdd:cd17524   103 EKILPEYLNYFLNSPYGRKQiKSVATQGVGQaninaTKLK--AIP---IPLPPLEEQKEIVEKLDELDALIDRLEALLEE 177

                          90
                  ....*....|..
gi 2026845886 564 SQTTQQHLAEAL 575
Cdd:cd17524   178 AEELLESLLQSL 189

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

Pssm-ID: 341188 [Multi-domain] Cd Length: 174 Bit Score: 51.78 E-value: 1.34e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2026845886 527 IESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEALV 576
Cdd:cd17497   125 LENLLIPLPPLAEQKRIAAFLDELTAKIDQLIALLEKAIELLKEYRQAVL 174

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: 51.79 E-value: 1.47e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 118 GKTPSTSVNEYFNGDIPFIGPGQI--TQSGSIIEPDKYLSESGLLNSE----EANqgdvfTVCIggS----IGKSAIVHG 187
Cdd:cd17279    12 GSTPKSGEEDYWDGDIPWVTPADLskLDGKYISSSQRKITEAGLESCGtslvPAG-----SIIL--StrapIGYVAIATV 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 188 RIGFNQQINAIKPI-KFSSAFLYSILSTRffIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIV-------AKVD 259
Cdd:cd17279    85 ELCTNQGCKALVPNsDVDSRFLYYLLLAA--KEELNSLGRGTTFLELSTDELANFKIPLPPLSEQRAIAdfldretAKID 162

                         170
                  ....*....|....*....
gi 2026845886 260 ELMSLCDQ----LEQKSEA 274
Cdd:cd17279   163 ALIAKKQQlielLKEKRQA 181

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: 51.38 E-value: 2.09e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 179 IGKSAI--------VHG----RIGFNQQInaikpikFSSAFLYSILSTRFFIDSMVS--------AStgsatpiINRSKW 238
Cdd:cd17522    77 IGKTAIydgdpeplIHGmnllRLRPNKNI-------VDPKYLYYLLKSDRFRNQFRSiakkavnqAS-------INQTEL 142

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2026845886 239 ESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKseasLAAHQTLVETLLATL 290
Cdd:cd17522   143 KKIKIPLPPLEEQQKIASILEKLDKKIEKRKEK----IEKLKELKKGLFQKL 190

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: 51.30 E-value: 2.39e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2026845886 521 KLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17249   131 SLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEELLKALMQAL 185

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: 49.75 E-value: 4.02e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 466 GDVGLVPSRFNgmnLTENA--AKLmFRSIDKSWLKYTLRSkfsqSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRI 543
Cdd:cd17266    58 GNVHYVEGKFW---VTDNAlvVTP-KKENNIKFLYYLLKS----LNLNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKI 129

                          90       100
                  ....*....|....*....|....*...
gi 2026845886 544 VAKVDELMFLCDQISARLQASQTTQQHL 571
Cdd:cd17266   130 AAILDSLDAKIDLLEKKLEKLIELKKEL 157

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Campylobacter species RM1670 S subunit (S.Csp16704I) TRD2-CR2, Aeromonas media WS S subunit (S.AmeWSORF2351P) TRD1-CR1, and Clos; Campylobacter species RM16704 S subunit (S.Csp16704I ) recognizes 5'... ACANNNNNNNNTCG ... 3', and the recognition sequences of Aeromonas media WS TRD1-CR1 S subunit (S.AmeWSORF2351P) and Clostridium carboxidivorans P7 S subunit (S.CcaPORF573P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341174 [Multi-domain] Cd Length: 181 Bit Score: 49.81 E-value: 5.78e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2026845886 527 IESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17285   132 LKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEKLKQLKKGLMQSL 180

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: 48.74 E-value: 1.08e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 492 IDKSWLKYTLRSKFSQSQFNeKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHL 571
Cdd:cd17269    82 IDPKFLYYYLKSYFKKYIEK-NSVGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAELPAELEARKKQYEYY 160


                  ....
gi 2026845886 572 AEAL 575
Cdd:cd17269   161 RDAL 164

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: 48.56 E-value: 1.58e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 126 NEYF-NGDIPFIGPGQITQSGSIIEPDKYLSESGLLNSEEANQGDVFtVCIGGSIGKSAIVH-GRIGFNQQINAIKP--I 201
Cdd:cd17258     9 PELFcNGNIKLVCIKNELINSLKVKIVEPDYKIGLKQSKIFKKGDVL-ITRHGTIGRVSIILsEEACLSSHVAGFNSkeG 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 202 KFSSAFLYSILSTRFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVA---KVDELMSLCDQL 268
Cdd:cd17258    88 ISDNKFIKYLFNSKKIKNRLMSYGASSTQPALNLSRLLKIKFPNPPLEEQQKIGKilsTWDRAIELTEQK 157

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: 47.82 E-value: 2.14e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2026845886 527 IESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17260   116 LENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKL 164

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: 48.30 E-value: 2.15e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 477 GMNLtenaakLMFRS----IDKSWLKYTLRSKFSQSQFNEKTNQ-LAQPKLALHRIESSIIALPPIAEQKRIVAKVDELM 551
Cdd:cd17522    93 GMNL------LRLRPnkniVDPKYLYYLLKSDRFRNQFRSIAKKaVNQASINQTELKKIKIPLPPLEEQQKIASILEKLD 166

                          90       100
                  ....*....|....*....|
gi 2026845886 552 FLCDQISARLQASQTTQQHL 571
Cdd:cd17522   167 KKIEKRKEKIEKLKELKKGL 186

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: 47.78 E-value: 2.29e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 489 FRSIDKSWLKYTLRSkFSQSQFNEKTnqlAQPKL---ALHRIEssiIALPPIAEQKRIVAKVDELMflcDQISARLQASQ 565
Cdd:cd17267    77 FKGNDPRFLYYLLKT-LDLERLNSGS---AVPGLnrnDVYSLK---VPLPPLEEQKAIAAILDALD---DKIELNRRQNQ 146

                          90
                  ....*....|
gi 2026845886 566 TTQQhLAEAL 575
Cdd:cd17267   147 TLEE-LADAL 155

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: 47.20 E-value: 6.45e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2026845886 233 INRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17526   138 INSDTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192

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: 46.75 E-value: 9.10e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2026845886 519 QPKLALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17247   134 QGALNCGILKAFPIPLPPLDEQREIVAELEALLAKIDLLEEKIARLIELLKELRQAL 190

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: 46.07 E-value: 1.49e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2026845886 532 IALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17525   147 LPLPPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKKALMQQL 190

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: 45.21 E-value: 3.12e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2026845886 532 IALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEALVEGA 579
Cdd:cd17248   145 IALPPLEEQRKIVDRLEALDAKIDALERKLERLIELLKELRQALLTAA 192

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: 44.91 E-value: 3.49e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGyvGVCSTGKTPSTSVNEYFNGDIPFIGPGQITQSGSIIEPDKYLSEsgllnsEEANQ--------GDVF--TV 173
Cdd:cd17512     1 WEEIRLG--DIIDYQKGYAFKSKDYQDSGIRIVRVSDFTDDSIDINNLVYISE------EKANKykkyelkeNDIIitTV 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 174 cigGS--------IGKSAIV---HGRIGFNQQINAIKPIK--FSSAFLYSILSTRFFIDSMVSASTGSATPI---INRSK 237
Cdd:cd17512    73 ---GSwpsnpdsvVGKVVRVpkeADGALLNQNAVKIRPKKgiLDQSFLFYNLKSERFKNYIESIARGNANQAsitLGDIK 149

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2026845886 238 WESLLIPcaSMNEQHRIVAKVDELMSLCDQLEQK 271
Cdd:cd17512   150 KFKFLLP--PLEEQKKIASILSAYDDLIENNEKR 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: 44.51 E-value: 3.66e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 207 FLYSILSTrFFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETL 286
Cdd:cd17269    86 FLYYYLKS-YFKKYIEKNSVGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAELPAELEARKKQYEYYRDAL 164


                  .
gi 2026845886 287 L 287
Cdd:cd17269   165 L 165

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: 43.55 E-value: 6.89e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 423 VTDMKNGSINDSGLAYISPETHSLI---SQYTISSDDLYITIAGTIGDVGLVPSrfNGMNLTENaaKLMFRS----IDKS 495
Cdd:cd17258    17 IKLVCIKNELINSLKVKIVEPDYKIglkQSKIFKKGDVLITRHGTIGRVSIILS--EEACLSSH--VAGFNSkegiSDNK 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 496 WLKYTLRSKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVA---KVDELMFLCDQISARLQ 562
Cdd:cd17258    93 FIKYLFNSKKIKNRLMSYGASSTQPALNLSRLLKIKFPNPPLEEQQKIGKilsTWDRAIELTEQKLELLQ 162

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: 43.73 E-value: 8.74e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2026845886 532 IALPPIAEQKRIVAKVDELMFLCDQISARLQASQTtqqhLAEALVE 577
Cdd:cd17526   148 IPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLE----LAKSLFE 189

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

Pssm-ID: 341177 [Multi-domain] Cd Length: 163 Bit Score: 43.23 E-value: 9.18e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKTPSTSVNeyfnGDIPFIGPGQITQSGsiiepDKYLSEsgllnsEEanqgdvfTVCIG--GSIGK 181
Cdd:cd17288     1 WEVKKLGDLLKIKNGKDYKHLED----GNYPVYGSGGIMGYV-----NDYLYD------GE-------SVLIGrkGTIDK 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 182 SAIVHGRI-----GFNQQINAIKPIKFssafLYSILSTrffID--SMvsaSTGSATPIINRSKWESLLIPCASMNEQHRI 254
Cdd:cd17288    59 PLYVNGPFwtvdtMFYTEIKKNNDPKF----LYYLLKT---IDfkKY---NEATGVPSLTQTTLNKIKIPIPPLEEQQKI 128

                         170       180
                  ....*....|....*....|
gi 2026845886 255 VA---KVDELMSLCDQLEQK 271
Cdd:cd17288   129 ASildKLDAKDALIELQEKL 148

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: 43.23 E-value: 1.11e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2026845886 527 IESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTtqqhLAEALVEG 578
Cdd:cd17244   133 IKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDE----LLPKLMSG 180

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: 42.87 E-value: 1.51e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 489 FRSIDKSWLKYTLRSKFSQSQFNE---KT-NQLAQPKLAlhrieSSIIALPPIAEQKRIVAKVDELMFLCDQISARLQAS 564
Cdd:cd17265    95 FRSEYNDYLFHLFNSDLFKKQIGSfltATiNQITNGNLN-----NFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKL 169

                          90
                  ....*....|.
gi 2026845886 565 QTTQQHLAEAL 575
Cdd:cd17265   170 IELKKELMQQL 180

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: 42.26 E-value: 2.27e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 115 CSTGKTPSTSVNEYFNGDIPFIGPGQItQSGSIIEPDKYLSESGLlnsEEAN----QGDVFTVCI-----GGSIGKSAIV 185
Cdd:cd17271     8 LSSGATPSRGNPEYFNGDIPWITSGEL-NYNYITDTNEKITEEAV---KNTNlkihPKGTFLIAItgleaAGTRGKCAIT 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 186 HGRIGFNQQINAIKPI-KFSSAFLYS-------ILSTRFfidsmvsaSTGSATPIINRSKWESLLIPCASMNEQHRIVAK 257
Cdd:cd17271    84 GIPATTNQSCMAFYPTkKLTTEFLFYwykkygnYLGFKY--------AQGTKQQSYTADIVKKLPILLPTLKEQKKIANF 155

                         170
                  ....*....|....*.
gi 2026845886 258 VDELMSLCDQLEQKSE 273
Cdd:cd17271   156 LSDIDELIATLEKKIE 171

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: 41.47 E-value: 4.37e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 104 WEWCRLGYVGVCSTGKtpSTSVNEYFNGDIPFIGPGQITQ--SGSIIEPDKYLSESglLNSEEANQ------GDVFtVCI 175
Cdd:cd17289     1 WEWKKLGDIAEITSSK--RIFKSEYVDSGIPFYRSKEIIElfNGEEISTELFISEE--RYEEIKSKygvpkkGDIL-ITS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 176 GGSIGKSAIVHGRIGF---NQQINAIKPIK-FSSAFLYSILSTRFF---IDSMVSASTGSATPIinrSKWESLLIPCASM 248
Cdd:cd17289    76 VGTIGIPYLVKNDDPFyfkDGNLTWFKNIKdINSKFLYYWFQSSIFknqINSITIGSTQKALTI---EKLKKTKIPLPPL 152

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2026845886 249 NEQHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17289   153 EEQKKIVSILSALDEKIDLNKKQLQKLEELAKTLFQYWF 191

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

Pssm-ID: 341146 [Multi-domain] Cd Length: 176 Bit Score: 41.36 E-value: 4.67e-04

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2026845886 527 IESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQA 563
Cdd:cd17257   129 IDEIELPLPPLEEQRRIAEILDELDALIDKLIAKLEK 165

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: 41.42 E-value: 4.88e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 457 LYITIAGTIGDVGLV--PSRFN----GMNLTEnaaklmfrSIDKSWLKYTLRSkfSQSQFNEKTNQLAQPKLALHRIESS 530
Cdd:cd17290    69 LVVGIGATIGKVGYSdkESSSNqqitGIIFNK--------DINPKFLFYWLSS--SKEELENLANGATLPILNQEKLKNI 138

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2026845886 531 IIALPPIAEQKRIVAkvdelmFLcDQISARLQASQTTQQHLAEALVE 577
Cdd:cd17290   139 KLPVPPLNEQQKIVE------FL-DKKTAKIDALIAKKEQLIELLKE 178

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 42.56 E-value: 6.62e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886  60 EPASVLLERIAAEKARLVKEGKIKK-----------SKPLAEITDDEkpfELPEGWEWCRLGYVGVCSTGKTPSTSVNey 128
Cdd:PRK09737  169 EKLDTLLAQVDSTKARLEQIPQILKrfrqavlgaavSGKLTEEWRWP---DLPSTWSVHKYSELVDSRLGGMSSKANN-- 243

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 129 FNGDIPFIGPGQItQSGSIIEPD-KYLSESGL-LNSEEANQGDVFtVCIGGS---IGKSAIVHGRigfnQQINAIKPIKF 203
Cdd:PRK09737  244 FGSATPYLRNINV-RWGSFDLEDlQDILISDIeRRELKLKLGDVL-FCRGNEpleVGRCAIWKEP----QDIPVIYQKAL 317

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 204 SSA-------------FLYSILSTRFfidSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELMSLCDQLEQ 270
Cdd:PRK09737  318 IRArvkddiipeylvyNLKSPDSRNI---SLSQLFTGTTQKHITGKALANYPIRVPPLEEQAEIVRRVEQLFAYADTIEK 394

                         250       260       270
                  ....*....|....*....|....*....|...
gi 2026845886 271 KSEASLAAHQTLVETLLAtlteSADSGELAQNW 303
Cdd:PRK09737  395 QVNNALARVNNLTQSILA----KAFRGELTAQW 423

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: 40.61 E-value: 7.80e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 430 SINDSGL----AYISPETHSLISQYtissddlyitiaGTIGDVGlvpsrFNGMNLTENAAKL--MFRS--IDKSWLKYTL 501
Cdd:cd17275    51 YITEEGLknssAWIVPKGTILYAMY------------ASVGKVA-----INKIDVATNQAILgiIPKDekLDFEFLYYWL 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2026845886 502 rsKFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAkvdelmFLcDQISARLQASQTTQQHLAEALVE 577
Cdd:cd17275   114 --LSLKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIAE------IL-DKIDAEIDKLEEKIEKLRELKKG 180

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

Pssm-ID: 341180 [Multi-domain] Cd Length: 161 Bit Score: 40.19 E-value: 1.01e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2026845886 207 FLYSILSTR-FFIDSMVSastGSATPIINRSKWESLLIPCASMNEQHRIVAKVDELmslcDQLEQKSEASLAAHQ 280
Cdd:cd17291    87 FLYYFLKNKqEEIYSLQR---GAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDKF----TELTAELPAELEARK 154

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S.Sau1132ORF3780P TRD1-CR1, and S.Mca353ORF290P TRD1-CR1; The Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG, and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341165 [Multi-domain] Cd Length: 187 Bit Score: 40.26 E-value: 1.13e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2026845886 526 RIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHLAEAL 575
Cdd:cd17276   137 DVRNFPIPLPPLDEQRAIVEFLSDVDALIDSLEALIEKLRELKKGLMQQL 186

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

Pssm-ID: 341189 [Multi-domain] Cd Length: 173 Bit Score: 39.97 E-value: 1.20e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 107 CRLGYVGVCSTGKTP-STSVNEyFNGDIPFIgpgQITQSGSIIEP--DKYLSESgllnSEEANQGDV-FTVciGGSIGKS 182
Cdd:cd17498     1 VKLGEIAEITMGQSPkSEFYNE-DGIGLPFL---QGNRTFGDKYPyiDTYTTDI----KKIAKKGDIlMSV--RAPVGDL 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 183 AIVHGRIGFNQQINAIKPIKFSSAFLYSILSTrfFIDSMVSASTGSATPIINRSKWESLLIPCASMNEQHRIVA---KVD 259
Cdd:cd17498    71 NIANKDICIGRGLCSIRMKNGNNSFLYYLLKN--NIKNLINKSSGTVFGSINKDDIENLEVDIPEDEEQKRIANilsKID 148


                  ..
gi 2026845886 260 EL 261
Cdd:cd17498   149 DK 150

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: 39.82 E-value: 1.31e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 192 NQQINAIKPI--KFSSAFLYSILstRFFIDsMVSASTGSATpIINRSKW--ESLLIPCASMNEQHRIVAKVDELMSLCDQ 267
Cdd:cd17257    83 NQRVCRIRPKseELDKRFLYYAL--PPPLK-AIEDTTSSTT-VKHLSSKdiDEIELPLPPLEEQRRIAEILDELDALIDK 158

                          90
                  ....*....|....*
gi 2026845886 268 LEQKSEASLAAHQTL 282
Cdd:cd17257   159 LIAKLEKLRDLLLPL 173

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) TRD1-CR1 and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) TR; The recognition sequences for Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Helicobacter bizzozeronii CIII-1 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.HbiCORF8670P, and may also contain type I DNA methyltransferases.

Pssm-ID: 341190 [Multi-domain] Cd Length: 175 Bit Score: 39.91 E-value: 1.41e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 492 IDKSWLKYTLRSKfsQSQFNEK----------TNQlaqpklalhrIESSIIALPPIAEQKRIVAKVDELmflcDQISARL 561
Cdd:cd17499    93 IDKKYLFYFLLSN--KDYFKGKsggstfksinKNQ----------IKNIKIPLPPLEEQKRIVSELDKL----FKLIFEA 156

                          90
                  ....*....|....*....
gi 2026845886 562 QASQTTQQHLAEALVEGAL 580
Cdd:cd17499   157 KNNIEEALANAQQLFKSIL 175

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: 39.39 E-value: 2.00e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2026845886 522 LALHRIESSIIALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQ 569
Cdd:cd17294   134 LNLKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLPALLELRQ 181

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: 39.31 E-value: 2.74e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2026845886 532 IALPPIAEQKRIVAKVDELMFLCDQISARLQASQTTQQHL 571
Cdd:cd17273   142 IPLPPLEEQKKIAAILSKLDELIELLEKENEKLKELRDGL 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.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: 38.25 E-value: 5.18e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 177 GS---IGKSAIVHGRIGfNQQINAIKPIkFSS---AFLYSILSTRFFiDSMVSASTGSATPIINRSKWESLLIPCASMNE 250
Cdd:cd17265    68 GSralIGKNALIDKEAE-GMTFGAFMTV-FRSeynDYLFHLFNSDLF-KKQIGSFLTATINQITNGNLNNFKIPLPPLEE 144

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2026845886 251 QHRIVAKVDELMSLCDQLEQKSEASLAAHQTLVETLL 287
Cdd:cd17265   145 QEKIAEFLSSLDAKIDKLIKKIEKLIELKKELMQQLI 181

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2, Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1, and re; The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 3'. The recognition sequence of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. It also includes the TRD-CR-like domains of putative type II restriction enzymes and methyltransferases, such as Helicobacter cinaedi PAGU611 Hci611ORFHP which may recognize 5'... GAGNNNNNGT ... 3', and type I N6-adenine DNA methyltransferases, such as Calditerrivibrio nitroreducens M.Cni19672ORF1405P whose recognition sequence is undetermined.

Pssm-ID: 341195 [Multi-domain] Cd Length: 183 Bit Score: 37.92 E-value: 6.86e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2026845886 504 KFSQSQFNEKTNQLAQPKLALHRIESSIIALPPIAEQKRIVAKVDELMFL-CDQISARLQASQTTQQHLA 572
Cdd:cd17514   114 KTQKNNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNILETLEFFeKDSLRKIKETAQDINLMIN 183