NCBI Conserved Domain Search

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2; This model contains Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2 and similar TRD-CR's. S.SonII recognizes 5'... GTCANNNNNNRTCA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.SonII TRD1-CR1 does not belong to this subfamily.

Pssm-ID: 341135 [Multi-domain] Cd Length: 189 Bit Score: 166.16 E-value: 3.61e-50

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 163 WNLCTLDQISAAIIDCPHSTPKWTEQGFICVRTNQFKPGYLDLNNSRYVSEQTYIERTQRLEPSYGDILYSREGGIlGVA 242
Cdd:cd17246     1 WEWVKLGEISSDITDGTHPTPKYVESGIPFITSKNIKNGKIDFSDVKYISEEDHNEILKRSKLKKGDILFSIIGTI-GRV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 243 CRVPEKIKICLGQRMMLIRPK-ENISSEYLEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKI 321
Cdd:cd17246    80 AIVPEDLPANINQAVALIRPKkEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQKRIAAIL 159

                         170       180
                  ....*....|....*....|....*...
gi 2181801761 322 NELNGVCEQLRSHIQSAQQTQLHLADAL 349
Cdd:cd17246   160 DSLDALIDKLEQKLEKLEDLKKGLMQDL 187

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: 114.17 E-value: 2.39e-30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 163 WNLCTLDQISAAIID--CPHSTPKWTEQGFI---CVRtnqfkPGYLDLNNSRYVSEQtyIERTQRLEPSYGDILYSREGG 237
Cdd:cd17261     1 WEWVRLGDLIEGIRNgwSPKPPDDETGWPVLklsAVT-----SGKFDPSENKYLPES--LEPASEYWLKPGDLLISRANT 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 238 IL--GVACRVPEKIKIC-LGQRMMLIRPKEN-ISSEYLEIVLNSPL----ITSLAQkmTTGGAAPRINVSTVKGYPIPYP 309
Cdd:cd17261    74 SElvGRAALVDGDPDNLiYPDKLIRLRVNEElLLPEYLALALNSPSarrqIESRAT--GTAGSMPKISQSDLKSLPIPLP 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2181801761 310 PLEEQNQIIEKINELNGVCEQLRSHIQSAQQTQLHLADAL 349
Cdd:cd17261   152 PLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191

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: 106.47 E-value: 1.93e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 187 EQGFICVRTNQFKPGYLDLNNSRYVSEQTY-IERTQRLEPsyGDILYS-RegGILGVACRVPEKIKICLGQRMMLIRPKE 264
Cdd:cd17264    25 DEGIPFINAGHLEDGTIDLSNMNFISEEKYnSLGSGKLQK--GDILYClR--GSLGKCAIVDNYDEGAIASSLVIIRPFA 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 265 NISSEYLEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQTQLH 344
Cdd:cd17264   101 KVDVRYLYYYLNSPLGKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQS 180


                  ....
gi 2181801761 345 LADA 348
Cdd:cd17264   181 LFQS 184

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: 104.89 E-value: 5.72e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 193 VRTNQFKPGYLDLNNSRYVSEQTY--IERTqRLEPsyGDILYSREGGIlGVACRVPEKIKIC-LGQRMMLIRPKENISSE 269
Cdd:cd17256    29 IRVTDIKNGGIDLDNLKYISPEIHekIKRY-TLSK--GDILISIVGTI-GRVGIVPKELDGAnLTENAARIRPKDSISPR 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2181801761 270 YLEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQTQLHLAD 347
Cdd:cd17256   105 YLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKALMQ 182

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

Pssm-ID: 341167 [Multi-domain] Cd Length: 189 Bit Score: 102.59 E-value: 4.89e-26

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 184 KWTEQGFICVRTNQFKPGYLDLNNSRYVSEqTYIERTQRLEPSYGDILYSREGGILGVACRVPEKIKIC-LGQRMMLIRP 262
Cdd:cd17278    22 DFSDEGIPVIRIGNIKNGGIDLDDNSKYPE-EPLEKYEKFLLKKGDILIAMTGGTVGKVAIVPEDDEPAlLNQRVGKFRP 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 263 KENISSEYLEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQTQ 342
Cdd:cd17278   101 KDKIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKLEQKLEKLRDLL 180


                  ....*..
gi 2181801761 343 LHLADAL 349
Cdd:cd17278   181 KPLLQSL 187

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR) and similar domains; The restriction-modification (RM) system S subunit generally consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily represents a single TRD-CR unit; in addition to type I TRD-CR units, it includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P, as well as TRD-CR-like sequence-recognition domains of the M subunit of putative type I DNA methyltransferase such as M2.CinURNWORF2828P and M.Mae7806ORF3969P.

Pssm-ID: 341131 [Multi-domain] Cd Length: 178 Bit Score: 100.15 E-value: 3.09e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 179 PHSTPKWTEQGFI-CVRTNQFKPGYLDLNNSRYVSEQTYIERTQRLEPsyGDILYSREGGIlGVACRVPEKIKICLGQRM 257
Cdd:cd16961    15 PSSSSEYWDNGIIpWIRISDINNGGIILTDEKITEEGAEKLKKKILPK--GDILISRSGTI-GKVAIVKENDKALLNQAV 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 258 MLIRPKENISSEYLEIVLNSPLITSLAqKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQS 337
Cdd:cd16961    92 IVIRPKDEVDSEFLYYFLKSPFGKKLI-EGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDALIELLEQKLEK 170


                  ....*...
gi 2181801761 338 AQQTQLHL 345
Cdd:cd16961   171 LEQLKQAL 178

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: 90.67 E-value: 1.49e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 187 EQGFICVRTNQFKPGYLDLNNSRYVSEQTYIERTQ-RLEPsyGDILYSREGGI---LGVACRVPEKIKICL-GQRMMLIR 261
Cdd:cd17517    25 GSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKELEKyLLKK--GDILFNRSNGSpelVGKCALVDEEDEPAIfASYLIRLR 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 262 PKEN-ISSEYLEIVLNSPLITSLAQKMTTGGAA-PRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQ 339
Cdd:cd17517   103 LDKKkILPEFLYYYLNSPLGRKQIEKIAKSAAGqANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLEKLE 182

                         170
                  ....*....|
gi 2181801761 340 QTQLHLADAL 349
Cdd:cd17517   183 QLFKSLMQSL 192

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: 86.80 E-value: 3.69e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 199 KPGYLDLNNSRYVSEQtYIERTQRLEPSYGDILYSREGGILGVA---CRVPEKIKIC-LGQRMMLIRPKENISSEYLEIV 274
Cdd:cd17259    37 GVGEIRWDDTVYLPEE-YLEEYEKYLLKEGDIVIALDRPIISGGlkvARIPKSDLPAlLVQRVARIRPKDELNSDFLYYL 115

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2181801761 275 LNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQTQLHLADA 348
Cdd:cd17259   116 LQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKGLMQS 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: 84.83 E-value: 1.73e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 201 GYLDLNNSRYVS-EQTYIERTqRLEPsyGDILYSrEGG---ILGVACRVPEKIKICLGQ----RmmlIRPKEN-ISSEYL 271
Cdd:cd17253    41 GYLDLSEVKEIEvTEEELERY-RLRK--GDLLVT-EGGdsdKLGRGAIWRGEIPPCLHQnhlfR---VRPKDDlLLPEFL 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 272 EIVLNSPLITSLAQ---KMTTGGAAprINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQTQLHLADA 348
Cdd:cd17253   114 SYWLNSAYGRGYFLraaKQTTNLAS--INSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQA 191


                  .
gi 2181801761 349 L 349
Cdd:cd17253   192 L 192

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoKI TRD1-CR1, S.StySPI TRD1-CR1, S.Ara36733II TRD1-CR1, and S.Eco3722I TRD1-CR1; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) and Escherichia coli NCM3722 S subunit (S.Eco3722I) recognize 5'... AACNNNNNNGTGC ... 3', Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3', and Actinomyces radicidentis S subunit (S.Ara36733II) recognizes 5'... CATCNNNNNNCTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC, and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Treponema pedis T A4 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.TpeTA4ORF2695P. It may also include type I DNA methyltransferases.

Pssm-ID: 341141 [Multi-domain] Cd Length: 189 Bit Score: 81.07 E-value: 4.01e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 186 TEQGFICVRTNQFKPGYLDLNNSRYVSEQtYIERTQRLEPsyGDILY-----SREggILGVACRVPEKIKICLGQRMMLI 260
Cdd:cd17252    28 SEGGIPVLRANNIQNGGLDFDDLVYVPKS-KVKEEQKLKK--GDILIcmssgSKE--LVGKAAFIDEDTDYTFGAFCGVI 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 261 RPKENISSEYLEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQ 340
Cdd:cd17252   103 RPKKEIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQALEKLDE 182

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: 79.20 E-value: 1.93e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 259 LIR---PKENISSEYLEIVLNSPLITS-LAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSH 334
Cdd:cd17523    96 FIRmrlDQEKIDPEFLSYIFNSPLIRRkIERNFVTSAGQKTVNQGHIKSLPIPLPPLKEQKKIVARVEELFALIDQLESS 175

                          90
                  ....*....|....*
gi 2181801761 335 IQSAQQTQLHLADAL 349
Cdd:cd17523   176 LDLAQQLQNKLAQSI 190

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: 77.40 E-value: 6.62e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 184 KW--TEQG--FICVrTNQFKpGYLDLNNS-RYVSEQTYIERTQRLEPSYGDILYSREGGILG-VACRVPEKIKICLGQRM 257
Cdd:cd17518    17 NWqfTDEGikLLNV-TNIVN-GSLDLDKTdRYISTEEYNGKYKHFLIDEGDILIASSGNSWGkVAIVEKDHLPLMLNTST 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2181801761 258 MLIRPKEN-ISSEYLEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQL 331
Cdd:cd17518    95 IRFKFIDGlLDNNFLKYFLNSDYFKEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEAA 169

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: 75.23 E-value: 4.63e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 250 KICLGQRMMLIRPKENISSEYLEIVLNSpLITSLaQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCE 329
Cdd:cd17496    77 EYCIGRGVAAIRPKNGIDTEFLYYLLES-NLDYL-LAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKID 154

                          90       100
                  ....*....|....*....|
gi 2181801761 330 QLRSHIQSAQQTQLHLADAL 349
Cdd:cd17496   155 KNKQEIEKLEELRDTLLPKL 174

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: 71.34 E-value: 1.37e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKEN-ISSEYLEIVLNSPLITSLAQKMTTGGA--ApRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQ 336
Cdd:cd17524    98 IRLNEEkILPEYLNYFLNSPYGRKQIKSVATQGVgqA-NINATKLKAIPIPLPPLEEQKEIVEKLDELDALIDRLEALLE 176

                          90
                  ....*....|...
gi 2181801761 337 SAQQTQLHLADAL 349
Cdd:cd17524   177 EAEELLESLLQSL 189

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

Pssm-ID: 341202 [Multi-domain] Cd Length: 187 Bit Score: 70.97 E-value: 1.71e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 228 GDILYSREGGILGVACRVPEKIKICL--GqrmMLIR---PKENISSEYLEIVLNSPLITSLAQKMTTGGAAPRINVSTVK 302
Cdd:cd17521    64 GDILFARTGATVGKSYLYKEDDGKAVfaS---YLIRfrpNKKKVLPKYLFYFTQSSLYWKQIKSISSGSAQPNINAEKLK 140

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2181801761 303 GYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQT 341
Cdd:cd17521   141 SLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEEL 179

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: 69.84 E-value: 3.65e-14

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2181801761   1 SNIIPDFFFNTYSTVKIKGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQ 64
Cdd:cd17285   101 PEYLLYWFLSIEETIESLGTGTTVKGITLEDLKSLKIPLPPLEEQKRIVAILDELDELIDKLEA 164

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: 66.48 E-value: 7.61e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 163 WNLCTLDQISAAIIDCPHSTPKWTEQGFICVRTNQFKPGYLDLNNSRYVSEQTYIErTQRLEPSYGDILYSREG------ 236
Cdd:cd17512     1 WEEIRLGDIIDYQKGYAFKSKDYQDSGIRIVRVSDFTDDSIDINNLVYISEEKANK-YKKYELKENDIIITTVGswpsnp 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 237 -GILGVACRVPEKIK-ICLGQRMMLIRPKE-NISSEYLEIVLNSPL----ITSLAQkmttgGAA--PRINVSTVKGYPIP 307
Cdd:cd17512    80 dSVVGKVVRVPKEADgALLNQNAVKIRPKKgILDQSFLFYNLKSERfknyIESIAR-----GNAnqASITLGDIKKFKFL 154

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2181801761 308 YPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQTQ 342
Cdd:cd17512   155 LPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMK 189

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: 66.12 E-value: 9.64e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 205 LNNSR-YVSEQTYIERTQRLEPSyGDILYSREGG--------ILGVACrvpekikiCLGQRMMLIRPKENISSEYLEIVL 275
Cdd:cd17250    44 LSTAEnYISEEIVKELKAKLFPK-GTIIFAKIGEaiklnrraILSKDS--------CIDNNVMGLIPNEGIDSEYLYYWL 114

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2181801761 276 NSPLITSLAQkmttGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQ 340
Cdd:cd17250   115 KKVDLYKYSQ----ATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQALEAAKE 175

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: 65.55 E-value: 1.34e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 236 GGILgvACRVP---EKIKICLGQRMMLIRPKENISSEYL--EIVLNSPLITSLAQKMTTGgaAPRINVSTVKGYPIPYPP 310
Cdd:cd17249    71 GMIL--AHTFPvaiTTRPVAFNQDIKALIPKEGIDPEFLlyALKANEDRILSLVDKAGHG--TGSLDTDDLKNLPIPLPP 146

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2181801761 311 LEEQNQIIEKINELNGVCEQLRSHIQSAQQTQLHLADAL 349
Cdd:cd17249   147 LEEQRRIAAILDALDALIDLLERKLAKLEELLKALMQAL 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: 64.76 E-value: 1.44e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKENISSEYLEIVLNSPLITSLA-QKMTtgGAA--PRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQ 336
Cdd:cd17260    74 LRPKEGILPEFLYYLLRSPSFRKEAiKSMT--GSSgrQRVPKDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIE 151

                          90
                  ....*....|....*...
gi 2181801761 337 SAQQtqlhLADALTEAAI 354
Cdd:cd17260   152 TLEE----LLDALLPKLL 165

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: 64.56 E-value: 2.22e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 250 KICLGQRMMLIRPKENISSEYLEIVLNSplITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKinelngvCE 329
Cdd:cd17499    77 KICIGRGLAAIRAKKNIDKKYLFYFLLS--NKDYFKGKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSE-------LD 147

                          90       100
                  ....*....|....*....|....*.
gi 2181801761 330 QLRSHIQSAQQTQLhLADALTEAAIN 355
Cdd:cd17499   148 KLFKLIFEAKNNIE-EALANAQQLFK 172

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

Pssm-ID: 341136 [Multi-domain] Cd Length: 190 Bit Score: 63.70 E-value: 7.14e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 248 KIKICLGQRMMLIRPKEN-ISSEYLEIVLnsplitsLAQ-----KMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKI 321
Cdd:cd17247    90 AIEATINQNLAAIRPNEErVLPEYLHYYL-------ESQydelrRIGSGGGQGALNCGILKAFPIPLPPLDEQREIVAEL 162

                          90       100
                  ....*....|....*....|....*...
gi 2181801761 322 NELNGVCEQLRSHIQSAQQTQLHLADAL 349
Cdd:cd17247   163 EALLAKIDLLEEKIARLIELLKELRQAL 190

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 60.46 E-value: 9.08e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 274 VLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQtqlhLADALTEAA 353
Cdd:COG0732     5 YLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKE----LRDALLPKL 80


                  ..
gi 2181801761 354 IN 355
Cdd:COG0732    81 FT 82

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: 60.91 E-value: 4.72e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKENISSEYLEIVLN----SPLITslaqkmttGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHI 335
Cdd:cd17262    87 LKGKNGISTEFLYYYLNsidiSPYVT--------GAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEEL 158

                          90
                  ....*....|....*..
gi 2181801761 336 QSAQQtqlhLADALTEA 352
Cdd:cd17262   159 EKLIE----LKKALLQK 171

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

Pssm-ID: 341201 [Multi-domain] Cd Length: 180 Bit Score: 60.93 E-value: 4.98e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 212 SEQTYIERTQRLEPSY----GDILYSREGGILGVACRVPEKIKICLGQRMMLIRPKENISSEYLEIVLNSPLITSLAQKM 287
Cdd:cd17520    41 SGMDTIEEEERKVKRYelrdGDLVLSCRGTAIKVAVFREQKKIVIASANIIVIRPNEKVLSEYLKIFLESPVGTALIKSF 120

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2181801761 288 TTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINE 323
Cdd:cd17520   121 QRGTTVMNINHSDIAEMEIPLLPLEEQKKIAEEYRK 156

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 63.36 E-value: 5.25e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 193 VRTNQFKPGYLDLNNSRYVSEQtyIERTQRLEPSYGDILYSREGGIlGVACRVPEKI--KICLGQRMMLIRPKENISSEY 270
Cdd:PRK09737   44 IRTTDITNGAVDLTTLPYCMDA--PEDVSKYQLQDRDIVISSAGSI-GFSFLAQNPLpsNVVFASFAIRLKPVNYFSEYF 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2181801761 271 LEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINEL 324
Cdd:PRK09737  121 LKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAEQKIIAEKLDTL 174

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: 60.14 E-value: 8.88e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKENISSEYLEIVLNS--PLITSLAQkmttGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQS 337
Cdd:cd17515    93 ILPNEEIDNEFLFYFLKSqkEYLISLGK----GGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKLIEKLEKALEK 168


                  ...
gi 2181801761 338 AQQ 340
Cdd:cd17515   169 LEE 171

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: 59.80 E-value: 1.14e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 259 LIRPKENISSEYLEIVLNSPLITSLAQKMTTGGAaPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSA 338
Cdd:cd17283    94 FSDLKKKLDKDFLYYLLSSITVQLQFSAQAGGGT-KNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKL 172


                  ...
gi 2181801761 339 QQT 341
Cdd:cd17283   173 EEL 175

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 62.59 E-value: 1.14e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 201 GYLDLNNSRYVSEQTyIERtQRLEPSYGDILYSREGGILGVA-CRV---PEKIKICLGQRMMLIRPKENISSEYLEIVLN 276
Cdd:PRK09737  259 GSFDLEDLQDILISD-IER-RELKLKLGDVLFCRGNEPLEVGrCAIwkePQDIPVIYQKALIRARVKDDIIPEYLVYNLK 336

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2181801761 277 SPLIT--SLAQKMTTGGAApRINVSTVKGYPIPYPPLEEQNQIIEKINEL 324
Cdd:PRK09737  337 SPDSRniSLSQLFTGTTQK-HITGKALANYPIRVPPLEEQAEIVRRVEQL 385

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: 59.01 E-value: 2.52e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 189 GFIC-VRTNQFKPGYLDLNNSRYVSEQtyIERTQRLEPSyGDILYSREGGILGVACRVpeKIKICLGQRMMLIRPKENIS 267
Cdd:cd17293    25 GDIPfIKPDDLNNGGIILTSEEYLSEE--GAKKARIVPK-GSILVTCIGGSIGKVGIA--DREVAFNQQINAIIPNKSVD 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 268 SEYLEIVLNSPLitSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQtqlhLAD 347
Cdd:cd17293   100 PKFLYYQLLSSK--FQLQAIASSTTLPIINKSKFEKIEIPLPPLEEQKRIVAKLDKLFALIDKLEESLEELDE----LLK 173


                  ....*.
gi 2181801761 348 ALTEAA 353
Cdd:cd17293   174 SLFQSA 179

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: 57.18 E-value: 9.48e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 248 KIKICLGQRMMLIRPKENISSEYLEIVLNSplITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELN-G 326
Cdd:cd17514    86 QIDASTNQAIAAIRCKENVNPKYLYYYLKT--QKNNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNILETLEfF 163

                          90       100
                  ....*....|....*....|
gi 2181801761 327 VCEQLRSHIQSAQQTQLHLA 346
Cdd:cd17514   164 EKDSLRKIKETAQDINLMIN 183

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: 56.79 E-value: 1.36e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2181801761  18 KGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQLVE 78
Cdd:cd17497   111 LGTGSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDELTAKIDQLIALLEKAIELLKEYRQ 171

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) TRD1-CR1; Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) recognizes 5'... GAYNNNNNNNTCYC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341152 [Multi-domain] Cd Length: 177 Bit Score: 56.36 E-value: 1.63e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 228 GDILYSREGgILGVAcrvpekikiclgqrMMLIRPKENI-SSEYLEIVLNSPliTSLAQKMTTGGAA-PRINVSTVKGYP 305
Cdd:cd17263    70 GEVGTGLEG-AIAST--------------LFKIIPDKNIiDKDYLYYFLKSK--EIQLNILTKAGSTiPHVNKKDLENLK 132

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2181801761 306 IPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQT 341
Cdd:cd17263   133 IPLPSLEEQKKIAEILDKLDALIDKLKELIEKLIEL 168

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: 56.36 E-value: 2.18e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKENISSEYLE--IVLNSPLITSLAQKMTTGGaaprINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQS 337
Cdd:cd17285    93 LFPKDELDPEYLLywFLSIEETIESLGTGTTVKG----ITLEDLKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEK 168


                  ...
gi 2181801761 338 AQQ 340
Cdd:cd17285   169 LKQ 171

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: 56.01 E-value: 3.12e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 201 GYLDLNNSRYVSEQTYIERTQRLEPsyGDILYSReggI-----LG-VACRVPEKIKICLGQRMMLIRP-KENISSEYLEI 273
Cdd:cd17522    39 GTIDLNRVGYAITNEEKIEKYKLQK--GDILFSH---InsiehIGkTAIYDGDPEPLIHGMNLLRLRPnKNIVDPKYLYY 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2181801761 274 VLNSPLITSLAQKMttggaAPR------INVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQT 341
Cdd:cd17522   114 LLKSDRFRNQFRSI-----AKKavnqasINQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEKLKEL 182

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: 54.90 E-value: 6.27e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 186 TEQGFICVRTNQFKP-GYLDLN-NSRYVSEQTYIERTqRLEPsyGDILY----SREggILGVACRVPEKIKICLGQRMML 259
Cdd:cd17526    25 DEDGVPQLRPHNITTdGELDLDkLIKIVPSPKERKRY-LLQK--GDVLFnntnSQE--LVGKTALFDGEEPYVFSNHMTR 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKEN-ISSEYLEIVLNSPLITSLAQKMTT---GGAAprINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHI 335
Cdd:cd17526   100 IRVKKSkINPEFLARYLHLLWRSGYFKKLCTnwvNQAG--INSDTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEA 177


                  ....
gi 2181801761 336 QSAQ 339
Cdd:cd17526   178 EALL 181

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: 54.76 E-value: 6.59e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKEN-ISSEYLEIVLNS--PLITSLAqkmtTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQ 336
Cdd:cd17282    97 FIPNEEkIDVEFLEYYLRTlkKELEAIA----PQSAQKNINLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIA 172

                          90
                  ....*....|....
gi 2181801761 337 -SAQQTQLHLADAL 349
Cdd:cd17282   173 kLEELKQSLLQEAF 186

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: 54.53 E-value: 8.22e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 248 KIKICLGQRMMLIRPKE-NISSEYLEIVLNSplITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELng 326
Cdd:cd17296    81 KIEATTNQAIAGIKPKNkSINPKYLYYYLKS--LYEKFLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKF-- 156

                          90       100
                  ....*....|....*....|...
gi 2181801761 327 vcEQLRSHIQSAQQTQLHLADAL 349
Cdd:cd17296   157 --EKLINKRQEGLQLLDELVKSL 177

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: 54.34 E-value: 1.16e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 262 PKENISSEYLEIVLNSplITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQt 341
Cdd:cd17273   100 PNEEIDNEFLYYLLKN--NKPEIESLASGSTFKEISKSTFKKIEIPLPPLEEQKKIAAILSKLDELIELLEKENEKLKE- 176


                  ....*...
gi 2181801761 342 qlhLADAL 349
Cdd:cd17273   177 ---LRDGL 181

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: 53.08 E-value: 2.97e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 184 KWTEQGFICVRTNQFKPGYLDLNNSRYVSEQTYIERTQRLEPSYGDILYSREGGILGvacrvpeKIKI-------CLGQR 256
Cdd:cd17519    21 KYRESGFPIIRITNIQNGKIDTDNLKYFDLNDYKENLDKYIVRPGDIVIAMSGATTG-------KVGInltdqefYLNQR 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 257 MMLIRPKENI-SSEYL-EIVLNSPLItslaQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSH 334
Cdd:cd17519    94 VGKFIPNEEIlNNRYLyHFLLSKQNE----KYILAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILDKFRELTNELESE 169


                  .
gi 2181801761 335 I 335
Cdd:cd17519   170 L 170

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

Pssm-ID: 341134 [Multi-domain] Cd Length: 174 Bit Score: 52.54 E-value: 3.44e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 228 GDILYSREG--GILGVAcrvpeKIKICLGQRMMLIRPKENISSEYLEIVL--NSPLITSLAQkmttGGAAPRINVSTVKG 303
Cdd:cd17245    57 GDILISVRApvGDVNIA-----DEKCCIGRGLAAIRANKDIDNLFLYYYLkyNKPELEKLGT----GSTFKAINKKDLEE 127

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2181801761 304 YPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQ 340
Cdd:cd17245   128 LKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKLDE 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: 52.06 E-value: 4.03e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 258 MLIRPKENISSEYLEIVLNS----PLITSLAQkmttggaaPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRS 333
Cdd:cd17266    74 LVVTPKKENNIKFLYYLLKSlnlnQYATGSAQ--------PLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEK 145


                  ....*..
gi 2181801761 334 HIQSAQQ 340
Cdd:cd17266   146 KLEKLIE 152

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: 52.17 E-value: 4.59e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 228 GDILYSREG--GILGVAcrvpeKIKICLGQRMMLIRPKENISSEYLEIVLNSplITSLAQKMTTGGAAPRINVSTVKGYP 305
Cdd:cd17497    57 GDILLSVRApvGPTNIA-----DQEYCIGRGLAAIRPKKGLDKKYLLYYLKS--IENELSSLGTGSTFKAISKEDLENLL 129

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2181801761 306 IPYPPLEEQNQIIEKINELNGVCEQLRSHIQsAQQTQLH 344
Cdd:cd17497   130 IPLPPLAEQKRIAAFLDELTAKIDQLIALLE-KAIELLK 167

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

Pssm-ID: 341173 [Multi-domain] Cd Length: 185 Bit Score: 52.60 E-value: 4.60e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 262 PKENISSEYLEIVLNspLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQT 341
Cdd:cd17284    99 PSKKINPEYLMYLLS--LQKKYMEKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQL 176


                  ....*...
gi 2181801761 342 QLHLADAL 349
Cdd:cd17284   177 KKGLMQQL 184

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: 52.13 E-value: 5.41e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2181801761   6 DFFFNTYSTVKikgTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd17259   119 DFFLNYVEPVL---TGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKGL 186

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: 51.79 E-value: 7.95e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   1 SNIIPDFFF-----NTY-STVKIKGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQ 74
Cdd:cd17252   106 KEIDPRYLFyflqsPSYrEYIRSLASGTNINNLSNEHLENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQALEKLDELLK 185


                  ....
gi 2181801761  75 QLVE 78
Cdd:cd17252   186 SLFQ 189

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: 51.77 E-value: 8.95e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   3 IIPDF---FFNT-----YSTVKIKGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQ 74
Cdd:cd17261   106 LLPEYlalALNSpsarrQIESRATGTAGSMPKISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLD 185


                  ..
gi 2181801761  75 QL 76
Cdd:cd17261   186 RL 187

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) TRD2-CR2 and Shewanella oneidensis MR-1 S subunit (S.SonIV) TRD1-CR1; Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) recognizes 5'... TACNNNNNNNRTRTC ... 3 while Shewanella oneidensis MR-1 S subunit (S.SonIV) recognizes 5'... TACNNNNNNGTNGT ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.SonIV-TRD1 recognizes TAC/GTA and S.SonIV-TRD2 recognizes ACNAC/GTNGT. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341139 [Multi-domain] Cd Length: 185 Bit Score: 51.10 E-value: 1.40e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2181801761  21 GTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQLVE 78
Cdd:cd17250   125 ATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGLRQ 182

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Sau13435ORF2165P TRD1-CR1 and S.SauL3067ORFAP TRD1-CR1; Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) recognizes 5'... TCTANNNNNNRTTC ... 3'; the recognition sequence of Staphylococcus aureus 3067 S.Sau3067ORFAP S subunit is as yet undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Sau13435ORF2165P TRD1 recognizes TCTA/TAGA, and S.Sau13435ORF2165P TRD2 recognizes GAAY/RTTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains mostly TRD1-CR1. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341147 [Multi-domain] Cd Length: 173 Bit Score: 50.48 E-value: 2.01e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 228 GDILYSREGGILGVACRVPEKIkiCLGQRMMLIRPKENIS-SEYLEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPI 306
Cdd:cd17258    52 GDVLITRHGTIGRVSIILSEEA--CLSSHVAGFNSKEGISdNKFIKYLFNSKKIKNRLMSYGASSTQPALNLSRLLKIKF 129

                          90
                  ....*....|.
gi 2181801761 307 PYPPLEEQNQI 317
Cdd:cd17258   130 PNPPLEEQQKI 140

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: 49.52 E-value: 4.42e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2181801761   2 NIIPDFFFNTYSTVK----IKGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd17284   102 KINPEYLMYLLSLQKkymeKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGL 180

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: 49.43 E-value: 4.68e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   1 SNIIPDFFFNTYST------VKIKGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQ 74
Cdd:cd17278   102 DKIDKEFLYYLLRSdsfrnqIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKLEQKLEKLRDLLK 181


                  ..
gi 2181801761  75 QL 76
Cdd:cd17278   182 PL 183

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

Pssm-ID: 341157 [Multi-domain] Cd Length: 185 Bit Score: 48.98 E-value: 6.17e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKENISseYLEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQ 339
Cdd:cd17268   100 FRHSQNPK--YLSYLLNSPAFQKQKRKLGTGTKVVHISASDLAKIKIPVPPLEEQERIVEILDKFDALIAGLPAEIEARR 177


                  .
gi 2181801761 340 Q 340
Cdd:cd17268   178 K 178

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: 49.03 E-value: 6.43e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2181801761  18 KGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQLVE 78
Cdd:cd17496   112 AATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTLLP 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: 48.61 E-value: 8.60e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKENISSEYLEIVLNSplITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQ 339
Cdd:cd17254    85 VVPDEEIDKDYLYYLLKA--LTEEIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLE 162

                          90
                  ....*....|....*
gi 2181801761 340 QtqlhLADALTEAAI 354
Cdd:cd17254   163 E----LRKALLQSLL 173

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: 48.29 E-value: 9.99e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 253 LGQRMMLIRPK-ENISSEYLEIVLNSPL--ItslaQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCE 329
Cdd:cd17257    82 LNQRVCRIRPKsEELDKRFLYYALPPPLkaI----EDTTSSTTVKHLSSKDIDEIELPLPPLEEQRRIAEILDELDALID 157

                          90
                  ....*....|..
gi 2181801761 330 QLRSHIQSAQQT 341
Cdd:cd17257   158 KLIAKLEKLRDL 169

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: 48.27 E-value: 1.02e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 257 MMLIRPKENissEYLEIVLNSPLITSLAQKMTTGgaapRIN---VSTVKGYPIPYPPLEEQNQIIEKineLNGVCEQLRS 333
Cdd:cd17265    92 MTVFRSEYN---DYLFHLFNSDLFKKQIGSFLTA----TINqitNGNLNNFKIPLPPLEEQEKIAEF---LSSLDAKIDK 161

                          90
                  ....*....|....*...
gi 2181801761 334 HIQSAQQTQLHLADALTE 351
Cdd:cd17265   162 LIKKIEKLIELKKELMQQ 179

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

Pssm-ID: 341144 [Multi-domain] Cd Length: 166 Bit Score: 47.91 E-value: 1.09e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 257 MMLIRPKENISSEYLEIVLNSplitsLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQI---IEKINELNGVCEQLRS 333
Cdd:cd17255    79 GVLKVKNKNINNKFLYYALNL-----IAKKYVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIaniLDKLDELINLLIAKLK 153

                          90
                  ....*....|.
gi 2181801761 334 HIQSAQQTQLH 344
Cdd:cd17255   154 KLIELRKKQLE 164

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: 48.25 E-value: 1.26e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKENISSEYLEIVLNSPL--ITSLAQkmttGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQS 337
Cdd:cd17287    95 ILPNDGINPDFLFYYLQSSYeeLRDLSN----GGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAKIDALEQKLEL 170


                  ...
gi 2181801761 338 AQQ 340
Cdd:cd17287   171 LQE 173

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

Pssm-ID: 396139 [Multi-domain] Cd Length: 167 Bit Score: 47.74 E-value: 1.43e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 228 GDILYSREGGILGVACRvpeKIKICLGQRMMLIRPKENI---SSEYLEIVLNSPLITSLAQkmttGGAAPRINVSTVKGY 304
Cdd:pfam01420  59 GDITISSRATIGYVFYR---DKPYYTNQHIIVLIPKNNIkitEFLYLYLLLKLKKLKSLKF----GSTQPKLTKERLKEI 131

                          90
                  ....*....|....*..
gi 2181801761 305 PIPYPPLEEQNQIIEKI 321
Cdd:pfam01420 132 KIPLPPLEEQKKIAKIL 148

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: 48.00 E-value: 1.50e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 201 GYLDLNNSRYVSEQTYIERTQRLEpsYGDILY----SREggILGVACRVPEKI-KICLGQRMMLIRPKENISSEYLEIVL 275
Cdd:cd17525    40 GINLLKVETYVDATELEVEKYLLE--DGDLLFntrnTLE--LVGKVAIWRGELpKALFNNNILRIRFDDIVLPYFINYYL 115

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2181801761 276 NSPLITSLAQKM---TTGGAAprINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQTQLHLADAL 349
Cdd:cd17525   116 NSPDGKKQLESIasgTTSVAA--IYQKDLKKLKLPLPPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKKALMQQL 190

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: 47.84 E-value: 1.65e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2181801761  39 FPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQLVE 78
Cdd:cd17293   138 LPPLEEQKRIVAKLDKLFALIDKLEESLEELDELLKSLFQ 177

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

Pssm-ID: 341206 [Multi-domain] Cd Length: 190 Bit Score: 47.61 E-value: 2.29e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   1 SNIIPDFFFNTYSTVK----IKgTGTT-VEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQ 75
Cdd:cd17525   107 LPYFINYYLNSPDGKKqlesIA-SGTTsVAAIYQKDLKKLKLPLPPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKKA 185


                  .
gi 2181801761  76 L 76
Cdd:cd17525   186 L 186

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: 47.09 E-value: 2.82e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   1 SNIIPDF---FFNT---YSTVKIKGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQ 74
Cdd:cd17521   102 KKVLPKYlfyFTQSslyWKQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLK 181


                  ....
gi 2181801761  75 QLVE 78
Cdd:cd17521   182 ELLQ 185

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: 47.23 E-value: 2.97e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2181801761  39 FPPFNEQNKIVVKVKELMSLCDQLEQHsltsLDAHQQLVE 78
Cdd:cd17523   149 LPPLKEQKKIVARVEELFALIDQLESS----LDLAQQLQN 184

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: 47.04 E-value: 3.13e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 186 TEQGFICVRTNQFKPGYLDLNNSRYvseqTYIERTQRLEPSYGDILYSREGGILGVAcRVPEKIKICLGQRMMLIRPKEN 265
Cdd:cd17272    24 EKGEIPVITSKNISNGKIDFEYVKY----DFLSISKNRKINKGDILITMIGTIGETA-IVKCLDPKFYTLNLYLIRLKKE 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2181801761 266 -ISSEYLEIVLNSPLITSLAQKMTTGgaAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQL 331
Cdd:cd17272    99 kLLPSYLKYFLDSEKFLNKSISATSG--QGYLKANQIDKLEIPLPPLEEQQRIVKILDKFDTLCNDI 163

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: 47.06 E-value: 3.35e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2181801761  16 KIKGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd17249   121 LVDKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEELLKAL 181

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

Pssm-ID: 341183 [Multi-domain] Cd Length: 188 Bit Score: 46.71 E-value: 3.73e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 248 KIKICLGQRMMLIRPKE----------NISSEYLEIvlnsplitslaQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQI 317
Cdd:cd17294    87 KIPLTTNQSLAAIEPDEeiansrflyyNLSSRYEEL-----------RSLSGGGGRGGLNLKIIKSLPIPLPPLEEQKKI 155

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2181801761 318 IEKINEL----NGVCEQLRSHIQsAQQTQLH 344
Cdd:cd17294   156 VAILDKFdaliNDLKEGLPALLE-LRQKQYE 185

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: 46.87 E-value: 4.16e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 185 WTEQGFICVRTNQFKPGYLDLNNSR--YVSEQTYIE-RTQRLEPSYGDILYSrEGGILGVACRVPEKIKICLGQRMML-I 260
Cdd:cd17289    23 YVDSGIPFYRSKEIIELFNGEEISTelFISEERYEEiKSKYGVPKKGDILIT-SVGTIGIPYLVKNDDPFYFKDGNLTwF 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 261 RPKENISSEYLEIVLNSPLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQ 340
Cdd:cd17289   102 KNIKDINSKFLYYWFQSSIFKNQINSITIGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEE 181


                  .
gi 2181801761 341 T 341
Cdd:cd17289   182 L 182

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: 46.76 E-value: 4.88e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   3 IIPDF---FFNTY---STVKIKGTGTTVE-GIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQH 65
Cdd:cd17517   108 ILPEFlyyYLNSPlgrKQIEKIAKSAAGQaNINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKK 177

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

Pssm-ID: 341180 [Multi-domain] Cd Length: 161 Bit Score: 45.58 E-value: 6.49e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2181801761 260 IRPKENISSEYLEIVL--NSPLITSLAqkmtTGGAAPRINVSTVKGYPIPYPPLEEQNQIIE---KINELN 325
Cdd:cd17291    77 LSSKNELVNKFLYYFLknKQEEIYSLQ----RGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEildKFTELT 143

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: 45.91 E-value: 7.26e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKENISSEYLEIVLNSpLITSLaQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNgvcEQLRSHIQSAQ 339
Cdd:cd17243    96 LRGKDGLSNYFLYYLLKN-LIEEL-KQKAHGSVFDTITRKTFDEIKVPLPPEELQKSFENIVSPLF---DKILNNLKENQ 170

                          90
                  ....*....|.
gi 2181801761 340 Q-TQlhLADAL 349
Cdd:cd17243   171 TlAQ--LRDTL 179

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: 45.66 E-value: 8.21e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 255 QRMMLIRP-KENISSEYLEIVLNSpLITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRS 333
Cdd:cd17269    70 QRTYVIHPfKEEIDPKFLYYYLKS-YFKKYIEKNSVGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAELPA 148

                          90       100
                  ....*....|....*....|
gi 2181801761 334 HIQSAQQTQLHLADALTEAA 353
Cdd:cd17269   149 ELEARKKQYEYYRDALLSFA 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: 45.21 E-value: 1.26e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   1 SNIIPDF---FFNTYSTVKI---KGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQ 74
Cdd:cd17246   102 EKIDPKYllyYLNSPIIQKQiekNAVGGTQKNLSLGDLKNLKIPLPPLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKK 181


                  ....
gi 2181801761  75 QLVE 78
Cdd:cd17246   182 GLMQ 185

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter species EN3 S subunit (S.MspEN3ORF6650P) TRD1-CR1, Methanothermobacter marburgensis str. Marburg S subunit (S.Mma2133ORF14720P) TRD2-CR2 and Nostoc species NIES; The recognition sequences of Marinobacter species EN3 S subunit (S.MspEN3ORF6650P), Methanothermobacter marburgensis str. Marburg S subunit (S.Mma2133ORF14720P), and Nostoc species NIES-3756 S subunit (S.Nsp3756ORF27100P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341169 [Multi-domain] Cd Length: 187 Bit Score: 44.08 E-value: 3.24e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 264 ENISSEYLEIVLNS--PLITSLAQkmttGGAAPRINVSTVKGYPIPYPPLEEQNQIiekINELNGVCEQLRSHIQSAQQT 341
Cdd:cd17280    99 NKIDIKFLFYWLLAnrDELISLAS----GGGQPNISQELIKSLRIPVPPLEEQKQI---AAFLDKKTAKIDSLIEKKERL 171

                          90
                  ....*....|....*.
gi 2181801761 342 QLHLAD---ALTEAAI 354
Cdd:cd17280   172 IELLKErrqALISEAV 187

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: 44.07 E-value: 3.28e-05

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2181801761  40 PPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQLVE 78
Cdd:cd17264   145 PPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQSLFQ 183

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: 43.60 E-value: 3.98e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   1 SNIIPDFFFNT--YSTVKIK--GTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd17254    89 EEIDKDYLYYLlkALTEEIEsqAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLEELRKAL 168

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: 43.62 E-value: 4.86e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2181801761 260 IRPKEN-ISSEYLEIVLNSPLITSLAQKmTTGGAAprINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQ 336
Cdd:cd17244    94 FIPKDKkIDTEYLYYYLKSFDYSSLGST-ASKGKT--LNSKKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIE 168

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: 43.34 E-value: 5.61e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2181801761 294 PRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQTQLHLADAL 349
Cdd:cd17276   131 PNITKDDVRNFPIPLPPLDEQRAIVEFLSDVDALIDSLEALIEKLRELKKGLMQQL 186

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 40.81 E-value: 7.34e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2181801761   7 FFFNT---YSTVKIKGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMslcDQLEQHSlTSLDAHQQL 76
Cdd:COG0732     4 YYLRSpsfREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLF---DKIAALE-KEIEKLKEL 72

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: 42.75 E-value: 9.03e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   2 NIIPDF---FFNTYSTVKIK--GTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd16961    99 EVDSEFlyyFLKSPFGKKLIegSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDALIELLEQKLEKLEQLKQAL 178

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: 42.78 E-value: 9.49e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 206 NNSRYVSEQTYIERTQRLEPSyGDILYSREGGILGVACrvpEKIKICLGQRMMLIRPKEN-ISSEYLEIVLnsPLITSLA 284
Cdd:cd17277    48 STKQFITEKALEEKKVKLVPK-NSVLLSCTATIGKVAI---AKIELTTNQQINALICKDSkILPEYLFYAL--KHIKQVL 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2181801761 285 QKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQ 340
Cdd:cd17277   122 ERLTTNPGVKHVNLSMLSNLQIPLPPLEVQKKIVAEIEKVEKVIQGLRQKIDEYQP 177

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

Pssm-ID: 341145 [Multi-domain] Cd Length: 182 Bit Score: 42.10 E-value: 1.61e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2181801761  20 TGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd17256   124 KGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKAL 180

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: 40.94 E-value: 2.95e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 260 IRPKENISSEYL--EIVLNSPLITSLAQKMTTggaaPRINVSTVKGYPIPYPPLEEQNQII-------EKINELNGVCEQ 330
Cdd:cd17286    91 IIPNKNYDPEFLyyALENWSKKIKSLAGKQAV----PIINKTEFSKIKILVPPLEEQQKIAnflskldELIELQQQKIEK 166

                          90
                  ....*....|
gi 2181801761 331 LRSHIQSAQQ 340
Cdd:cd17286   167 LEELKKGLLQ 176

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 42.56 E-value: 3.28e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   2 NIIPD---FFFNTYSTVKI----KGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQ 64
Cdd:PRK09737  325 DIIPEylvYNLKSPDSRNIslsqLFTGTTQKHITGKALANYPIRVPPLEEQAEIVRRVEQLFAYADTIEK 394

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: 40.46 E-value: 3.63e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2181801761 286 KMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQSAQQtqlhLADAL 349
Cdd:cd17267    96 RLNSGSAVPGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEE----LADAL 155

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: 40.73 E-value: 4.01e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2181801761 265 NISSEYLEIVLNSplitslaqkmtTGGAAPRINVSTVKGYPIPYPPLEEQNQI 317
Cdd:cd17500   111 SLKTQYEELVNLA-----------SGAAQQNLNSKLIKNFEIPLPPLPEQKRI 152

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Algibacter lectus S subunit (S.AleSS8ORF2795P) TRD1-CR1 and Vibrio parahaemolyticus O1:K33 CDC_K4557 S subunit (S.Vpa4557ORF2259; The recognition sequences of Algibacter lectus S subunit (S.AleSS8ORF2795P) and Vibrio parahaemolyticus O1:K33 CDC_K4557 S subunit (S.Vpa4557ORF22590P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341179 [Multi-domain] Cd Length: 184 Bit Score: 40.65 E-value: 4.71e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 198 FKPGYLD----LNNS-RYVSEQTYIERTQRLEPSyGDILYSREGGILGvacrvpekiKICL-------GQRMMLIRPKEN 265
Cdd:cd17290    32 FTPGDFNgdliLSESkRKLSELAIEDGEARLFPK-NSVLVVGIGATIG---------KVGYsdkesssNQQITGIIFNKD 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2181801761 266 ISSEYLEIVLNSplITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQIIEKINELNGVCEQLRSHIQ 336
Cdd:cd17290   102 INPKFLFYWLSS--SKEELENLANGATLPILNQEKLKNIKLPVPPLNEQQKIVEFLDKKTAKIDALIAKKE 170

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

Pssm-ID: 341190 [Multi-domain] Cd Length: 175 Bit Score: 39.91 E-value: 7.79e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761   1 SNIIPDFFFNTYSTVKI----KGTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd17499    91 KNIDKKYLFYFLLSNKDyfkgKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNNIEEALANAQQL 170


                  ..
gi 2181801761  77 VE 78
Cdd:cd17499   171 FK 172

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: 40.15 E-value: 8.19e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2181801761  39 FPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQLVE 78
Cdd:cd17253   151 LPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQ 190

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: 39.35 E-value: 1.01e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2181801761  26 GIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd17266   107 LITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKEL 157

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: 38.54 E-value: 1.65e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2181801761   2 NIIPDFFFNTYSTVKIK--GTGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd17267    79 GNDPRFLYYLLKTLDLErlNSGSAVPGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADAL 155

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: 38.30 E-value: 2.47e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2181801761 248 KIKICLGQRMMLIRPKEN-ISSEYLEIVLNSplITSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQI 317
Cdd:cd17275    85 KIDVATNQAILGIIPKDEkLDFEFLYYWLLS--LKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKI 153

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: 37.83 E-value: 3.76e-03

                          10        20
                  ....*....|....*....|....*.
gi 2181801761  40 PPFNEQNKIVVKVKELMSLCDQLEQH 65
Cdd:cd17524   149 PPLEEQKEIVEKLDELDALIDRLEAL 174

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to the S subunit TRD2-CR2 regions of Lactococcus lactis subsp. cremoris A17 (S.LlaA17I), Haemophilus influenzae Rd (S.HindORF215P) ; Lactococcus lactis subsp. cremoris A17 S subunit (S.LlaA17I) recognizes 5'... CAANNNNNNNNTAYG... 3', while the recognition sequences of Clostridium species ASF502 S subunit (S.Csp502ORF478P) and Haemophilus influenzae Rd S subunit (S.HindORF215P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Porphyromonas species COT-108 OH1349 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.Psp1349ORF730P) of unknown recognition sequence. It may also include type I DNA methyltransferases.

Pssm-ID: 341181 [Multi-domain] Cd Length: 149 Bit Score: 37.14 E-value: 5.36e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 288 TTGGAAPRINVSTVKGYPIPYPPLEEQNQIIE-------KINELNGVCEQLRSHIQSAQQ 340
Cdd:cd17292    87 TEGSTIKRLYNDNLLNTKIPVPSLDEQRKIAEflslldaLIALLQKKLEKLIALKKGLMQ 146

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

Pssm-ID: 341160 [Multi-domain] Cd Length: 186 Bit Score: 37.25 E-value: 6.24e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 255 QRMMLIRPKENISSEYLE--IVLNSpliTSLAQKMTTGGAAPRINVSTVKGYPIPYPPLEEQNQII-------EKINELN 325
Cdd:cd17271    91 QSCMAFYPTKKLTTEFLFywYKKYG---NYLGFKYAQGTKQQSYTADIVKKLPILLPTLKEQKKIAnflsdidELIATLE 167

                          90
                  ....*....|....*
gi 2181801761 326 GVCEQLRSHIQSAQQ 340
Cdd:cd17271   168 KKIEKLKKIKKGLMQ 182

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

Pssm-ID: 341151 [Multi-domain] Cd Length: 172 Bit Score: 37.03 E-value: 6.47e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2181801761   1 SNIIPDFFFNTYSTVKIKG--TGTTVEGIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQL 76
Cdd:cd17262    91 NGISTEFLYYYLNSIDISPyvTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKAL 168

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: 37.19 E-value: 6.56e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2181801761  26 GIKQEQLVNYITGFPPFNEQNKIVVKVKELMSLCDQLEQHSLTSLDAHQQLVE 78
Cdd:cd17526   137 GINSDTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFE 189

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

Pssm-ID: 341189 [Multi-domain] Cd Length: 173 Bit Score: 36.51 E-value: 9.01e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181801761 228 GDILYSREG--GILGVAcrvpeKIKICLGQRMMLIRPKeNISSEYLEIVLNSpLITSLAqKMTTGGAAPRINVSTVKGYP 305
Cdd:cd17498    57 GDILMSVRApvGDLNIA-----NKDICIGRGLCSIRMK-NGNNSFLYYLLKN-NIKNLI-NKSSGTVFGSINKDDIENLE 128

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2181801761 306 IPYPPLEEQNQI----------IEKINELNGVCEQLR 332
Cdd:cd17498   129 VDIPEDEEQKRIanilskiddkIEINNQINKNLEELA 165