NCBI Conserved Domain Search

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: 212.77 E-value: 1.87e-68

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177   6 YKIKDICEASHGREINTKYLRENQGIYPVYSSATSNEGEMGRIKTYDFDGEYVTWTTRWSYAGSIYYRNGKFSASSNCGI 85
Cdd:cd17255    1 KKLGDLFEIGRGRVISKKYISENPGDYPVYSSQTKNNGIMGYINTYDFDGEYITWTTDGANAGTVFYRNGKFSVTNVCGV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYALKKEAKKFVNTTSAiPILRTQKVVEIPIDFPPLQIQEKIATILDTFTelsaELSAELSAELSAE 165
Cdd:cd17255   81 LKVKNKNINNKFLYYALNLIAKKYVSFDGN-PKLMNNVMAKIKIPLPPLEEQEKIANILDKLD----ELINLLIAKLKKL 155

                        170
                 ....*....|.
gi 922323177 166 LRERKKQYAFY 176
Cdd:cd17255  156 IELRKKQLEYY 166

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: 125.16 E-value: 1.51e-34

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  183 PKNWKEenkyYKLGEIAQKvlvgGEKPADFSKEKNEVYKYPILS---NNSKAEEFLVYSKTFRVEEKSITVSARGTIGAV 259
Cdd:pfam01420   1 PEDWEV----FKLGDVFEI----KKGKTPKKKELKNNGKYPYIRagdLNNVVKGGLGYIKKYILPKGDITISSRATIGYV 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  260 FYRDFAYLPAVSLICFVPK-----EEFDIRFLFHALRAIKFKKQGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLY 334
Cdd:pfam01420  73 FYRDKPYYTNQHIIVLIPKnnikiTEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLD 152

                         170
                  ....*....|....*.
gi 922323177  335 SfFTDLNEGIPAEIEL 350
Cdd:pfam01420 153 N-TIELEKGILNELER 167

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: 108.75 E-value: 2.11e-28

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177   7 KIKDICEASHGREINTKYLRENqGIYPVYSSATSNegeMGRIKTYDFDGEYVTWTTRWSYAGSIYYRNGKFSASSNCGIL 86
Cdd:cd17291    2 KLGEIAEIKKGKQITKKELIEN-GKYPVIAGGIEP---SGYHNEYNREGNTITISASGASAGYVNYWKEPFWASDCCYIL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  87 KVLNKEINpKFLAYALKKEAKKFVN--TTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELSAelsa 164
Cdd:cd17291   78 SSKNELVN-KFLYYFLKNKQEEIYSlqRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFTELTAELPAELEA---- 152

                        170
                 ....*....|..
gi 922323177 165 elreRKKQYAFY 176
Cdd:cd17291  153 ----RKKQYEYY 160

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: 103.20 E-value: 2.75e-26

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177    4 KTYKIKDICEASHGREINTKYLRENqGIYPVYSSATSN---EGEMGRIKTYDFDGEYVTWTTRwSYAGSIYYRNGKFSAS 80
Cdd:pfam01420   5 EVFKLGDVFEIKKGKTPKKKELKNN-GKYPYIRAGDLNnvvKGGLGYIKKYILPKGDITISSR-ATIGYVFYRDKPYYTN 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177   81 SNCGILKVLNKEINPKFLAYAL--KKEAKKFVNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSaELSAEL 158
Cdd:pfam01420  83 QHIIVLIPKNNIKITEFLYLYLllKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDNTI-ELEKGI 161


                  ....
gi 922323177  159 SAEL 162
Cdd:pfam01420 162 LNEL 165

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: 100.66 E-value: 1.96e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 194 KLGEIAqKVLVGGEKPadfSKEKNEVYKYPILSNNSkaeEFLVYSKTFRVEEKSITVSARG-TIGAVFYRDFAYLPAVSL 272
Cdd:cd17291    2 KLGEIA-EIKKGKQIT---KKELIENGKYPVIAGGI---EPSGYHNEYNREGNTITISASGaSAGYVNYWKEPFWASDCC 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 273 ICFVPKEEFDIRFLFHALRA----IKFKKQGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPlysfFTDLNEGIPAEI 348
Cdd:cd17291   75 YILSSKNELVNKFLYYFLKNkqeeIYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDK----FTELTAELPAEL 150

                        170
                 ....*....|.
gi 922323177 349 ELCKKQLDYYQ 359
Cdd:cd17291  151 EARKKQYEYYR 161

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: 94.97 E-value: 2.65e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177   6 YKIKDICEASHGReINTKYLRENqGIYPVYSSATsnegEMGRIKTYDFDGEYVTWTTRWSYAGSIYYRNGKFSASSNCGI 85
Cdd:cd17269    1 KTLGEVAEIKTGK-LDANAANEN-GKYPFFTCSK----EPLRIDTYAFDEEAILIAGNGSGVGNVKYYNGKFNAYQRTYV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYALKKEAKKFVNTT---SAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTelsaelsaELSAEL 162
Cdd:cd17269   75 IHPFKEEIDPKFLYYYLKSYFKKYIEKNsvgSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFD--------ALTAEL 146

                        170       180
                 ....*....|....*....|
gi 922323177 163 SAELRERKKQYAFYCDYLLN 182
Cdd:cd17269  147 PAELEARKKQYEYYRDALLS 166

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

Pssm-ID: 341155 [Multi-domain] Cd Length: 159 Bit Score: 92.89 E-value: 1.10e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177   6 YKIKDICEASHGREINTKYLRENqGIYPVYSSatsNeGEMGRIKTYDFDGEYVTWTTRWSYAGSIYYRNGKFSASSNCGI 85
Cdd:cd17266    1 VKLGELCKIKSGKSITASKISEE-GDYPVYGG---N-GIIGYTDEYNHEGEYILIGRVGALCGNVHYVEGKFWVTDNALV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVlNKEINPKFLAYALKkeakkFVN-----TTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsa 160
Cdd:cd17266   76 VTP-KKENNIKFLYYLLK-----SLNlnqyaTGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKL-- 147

                        170
                 ....*....|...
gi 922323177 161 elsAELRERKKQY 173
Cdd:cd17266  148 ---EKLIELKKEL 157

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

Pssm-ID: 341170 Cd Length: 196 Bit Score: 79.56 E-value: 1.81e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  89 LNKEINPKFL---AYALKKEAKKFVNTTSaIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELSAELSAe 165
Cdd:cd17281  103 YKNKLDIKFLfyyFFVLGEWCKKNINIGG-FPSVDMNKLKKFKIPIPPLEEQEKIVEILDKFTKLTADLTAELPAELEA- 180

                         90
                 ....*....|....*..
gi 922323177 166 lreRKKQYAFYCDYLLN 182
Cdd:cd17281  181 ---RKKQYEYYRDKLLS 194

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

Pssm-ID: 341177 [Multi-domain] Cd Length: 163 Bit Score: 77.13 E-value: 8.02e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177   4 KTYKIKDICEASHGReiNTKYLreNQGIYPVYSSAtsneGEMGRIKTYDFDGEYV------TwttrwsyAGSIYYRNGKF 77
Cdd:cd17288    2 EVKKLGDLLKIKNGK--DYKHL--EDGNYPVYGSG----GIMGYVNDYLYDGESVligrkgT-------IDKPLYVNGPF 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  78 SAssncgilkV-------LNKEINPKFLAYALKKEAKKFVNTTSAIPILrTQKVVE-IPIDFPPLQIQEKIATILDTFTE 149
Cdd:cd17288   67 WT--------VdtmfyteIKKNNDPKFLYYLLKTIDFKKYNEATGVPSL-TQTTLNkIKIPIPPLEEQQKIASILDKLDA 137

                        170       180       190
                 ....*....|....*....|....*....|..
gi 922323177 150 LSAELsaelsaELSAELRERKKQYAFYCDYLL 181
Cdd:cd17288  138 KDALI------ELQEKLLEKLKQYKLALMQEL 163

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: 72.09 E-value: 7.44e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  94 NPKFLAYAL-----KKEAKKFVNTTSAIPILRTQ-KVVEIPIdfPPLQIQEKIATILDTFTELSAELSAELSAelsaelr 167
Cdd:cd17268  105 NPKYLSYLLnspafQKQKRKLGTGTKVVHISASDlAKIKIPV--PPLEEQERIVEILDKFDALIAGLPAEIEA------- 175


                 ....*....
gi 922323177 168 eRKKQYAFY 176
Cdd:cd17268  176 -RRKQYEYY 183

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: 69.77 E-value: 5.91e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 191 KYYKLGEIAQKVLVGGekPADFSKEKNEvykYPILSNN----------SKAEEFLVYSKTFRVEEKSITVSARGTIGAVF 260
Cdd:cd17272    2 EEKTLGDIAVDGFQNG--PAPNFDEKGE---IPVITSKnisngkidfeYVKYDFLSISKNRKINKGDILITMIGTIGETA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 261 Y----RDFAYLPAVSLiCFVPKEEFDIRFLFHALRAIKF-KKQGSAT---GQLTVAQFKEYGIHVPSLKKQKEIAAILDP 332
Cdd:cd17272   77 IvkclDPKFYTLNLYL-IRLKKEKLLPSYLKYFLDSEKFlNKSISATsgqGYLKANQIDKLEIPLPPLEEQQRIVKILDK 155

                        170       180       190
                 ....*....|....*....|....*....|..
gi 922323177 333 LYSFFTDLNEGIPAEIELCKKQLDYYQNFLFN 364
Cdd:cd17272  156 FDTLCNDITEGLPAEIEARQKQYEYYRDLLLS 187

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: 68.28 E-value: 1.67e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 271 SLICFVPKEE-FDIRFLFHALRA----IKFKKQGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIP 345
Cdd:cd17294   95 SLAAIEPDEEiANSRFLYYNLSSryeeLRSLSGGGGRGGLNLKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLP 174

                         90
                 ....*....|...
gi 922323177 346 AEIELCKKQLDYY 358
Cdd:cd17294  175 ALLELRQKQYEYL 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: 67.79 E-value: 2.04e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 193 YKLGEIA--QKVLVGGEKPADFSKEKNEVYK-------YPILSNNSKAEEFLVYSKTFRVEEKSITVSARGTIGAVFYRD 263
Cdd:cd16961    1 KKLGEIAeiISGKTPSSSSEYWDNGIIPWIRisdinngGIILTDEKITEEGAEKLKKKILPKGDILISRSGTIGKVAIVK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 264 FaYLPAV---SLICFVPKEEFDIRFLFHALRAIKFKKQ-----GSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYS 335
Cdd:cd16961   81 E-NDKALlnqAVIVIRPKDEVDSEFLYYFLKSPFGKKLiegsaGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDA 159

                        170       180
                 ....*....|....*....|
gi 922323177 336 FFTDLNEGIPAEIELcKKQL 355
Cdd:cd16961  160 LIELLEQKLEKLEQL-KQAL 178

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: 66.18 E-value: 7.71e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  70 IYYRNGKFSASSNCGILKVLNKEINPKFLAYAL-KKEAKKFVNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFT 148
Cdd:cd17519   81 INLTDQEFYLNQRVGKFIPNEEILNNRYLYHFLlSKQNEKYILAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILDKFR 160

                         90       100       110
                 ....*....|....*....|....*....|.
gi 922323177 149 ELSAELSAELSaelsaelrERKKQYAFYCDY 179
Cdd:cd17519  161 ELTNELESELN--------LRLKQYEYYRDY 183

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: 64.64 E-value: 2.92e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 275 FVPKEEF-DIRFLFHALRAIKFKKQGSATG---QLTVAQFKEYGIHVPSLKKQKEIAAILDPlysfFTDLNEGIPAEIEL 350
Cdd:cd17519   97 FIPNEEIlNNRYLYHFLLSKQNEKYILAGGsqpNLSSEKLKKIKIPIPSLEVQEEIVSILDK----FRELTNELESELNL 172

                         90
                 ....*....|
gi 922323177 351 CKKQLDYYQN 360
Cdd:cd17519  173 RLKQYEYYRD 182

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: 63.77 E-value: 4.15e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 278 KEEFDIRFLFHALRA-----IKFKKQGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPlysfFTDLNEGIPAEIELCK 352
Cdd:cd17269   79 KEEIDPKFLYYYLKSyfkkyIEKNSVGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDK----FDALTAELPAELEARK 154

                         90
                 ....*....|..
gi 922323177 353 KQLDYYQNFLFN 364
Cdd:cd17269  155 KQYEYYRDALLS 166

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

Pssm-ID: 341170 Cd Length: 196 Bit Score: 64.54 E-value: 4.18e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 238 SKTFrvEEKSITVSARGTIGavfyrDFAYLPAVSL-----ICFVPKEEF----DIRFLFHALRAI-KFKKQGSATGQL-- 305
Cdd:cd17281   62 GKLF--PANSIILSTTATIG-----EHALITVDSLanqrfTNFSLKKSYknklDIKFLFYYFFVLgEWCKKNINIGGFps 134

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 306 -TVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIPAEIELCKKQLDYYQNFLFN 364
Cdd:cd17281  135 vDMNKLKKFKIPIPPLEEQEKIVEILDKFTKLTADLTAELPAELEARKKQYEYYRDKLLS 194

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: 62.78 E-value: 1.15e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177   6 YKIKDICEASHGREINTKYLRENQGIYPVYSSATSNEGEMGRIKTYDFDGEYVTWTTRWSYAGSIYY------------- 72
Cdd:cd16961    1 KKLGEIAEIISGKTPSSSSEYWDNGIIPWIRISDINNGGIILTDEKITEEGAEKLKKKILPKGDILIsrsgtigkvaivk 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  73 RNGKFSASSNCGILKVlNKEINPKFLAYALK-KEAKKFVN--TTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTE 149
Cdd:cd16961   81 ENDKALLNQAVIVIRP-KDEVDSEFLYYFLKsPFGKKLIEgsAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDA 159

                        170       180
                 ....*....|....*....|....
gi 922323177 150 LSAELSAELSaelsaELRERKKQY 173
Cdd:cd16961  160 LIELLEQKLE-----KLEQLKQAL 178

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: 62.45 E-value: 1.19e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  29 QGIYPVYSsATsneGEMGRIKTYDFDGEYV----------TWTTRwsyagsIYYR-NGKFSASSNCGILKVlNKEINPKF 97
Cdd:cd17262   29 QGNYPYYG-AS---GIVDYVDDYIFDGEYVligedganllSRGTP------IAFYvSGKFWVNNHAHVLKG-KNGISTEF 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 922323177  98 LAYALK-KEAKKFVnTTSAIPILrTQKVVE-IPIDFPPLQIQEKIATILDTFTELSAELSAELSAELsaELRERKKQY 173
Cdd:cd17262   98 LYYYLNsIDISPYV-TGAAQPKL-NQANLNsIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLI--ELKKALLQK 171

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: 62.93 E-value: 1.41e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 191 KYYKLGEIAQKVLVGGEKPADFSKE-------KNeVYKYPILSNNSK---AEEFLVYSKTFRVEEKSITVSARGTIG--A 258
Cdd:cd17246    2 EWVKLGEISSDITDGTHPTPKYVESgipfitsKN-IKNGKIDFSDVKyisEEDHNEILKRSKLKKGDILFSIIGTIGrvA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 259 VFYRDFAYLPAVSLICFVPKEEF-DIRFLFHALRAIKFKKQ------GSATGQLTVAQFKEYGIHVPSLKKQKEIAAILD 331
Cdd:cd17246   81 IVPEDLPANINQAVALIRPKKEKiDPKYLLYYLNSPIIQKQieknavGGTQKNLSLGDLKNLKIPLPPLEEQKRIAAILD 160

                        170       180
                 ....*....|....*....|....
gi 922323177 332 PLYSFFTDLNEGIPAEIELcKKQL 355
Cdd:cd17246  161 SLDALIDKLEQKLEKLEDL-KKGL 183

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

Pssm-ID: 341155 [Multi-domain] Cd Length: 159 Bit Score: 61.31 E-value: 2.82e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 277 PKEEFDIRFLFHALRAIKFKK--QGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIPAEIELCKKQ 354
Cdd:cd17266   78 PKKENNIKFLYYLLKSLNLNQyaTGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKEL 157


                 ..
gi 922323177 355 LD 356
Cdd:cd17266  158 MQ 159

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: 60.52 E-value: 9.75e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  82 NCGILKVLNKEINPKFLAYAL--KKEAKKFVNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELS 159
Cdd:cd17272   89 NLYLIRLKKEKLLPSYLKYFLdsEKFLNKSISATSGQGYLKANQIDKLEIPLPPLEEQQRIVKILDKFDTLCNDITEGLP 168

                         90       100
                 ....*....|....*....|...
gi 922323177 160 AELSAelreRKKQYAFYCDYLLN 182
Cdd:cd17272  169 AEIEA----RQKQYEYYRDLLLS 187

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

Pssm-ID: 341135 [Multi-domain] Cd Length: 189 Bit Score: 59.84 E-value: 1.34e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  74 NGKFSASSNCGILKVLNKEINPKFLAYALKKE-AKKFVN---TTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTE 149
Cdd:cd17246   85 DLPANINQAVALIRPKKEKIDPKYLLYYLNSPiIQKQIEknaVGGTQKNLSLGDLKNLKIPLPPLEEQKRIAAILDSLDA 164

                         90       100
                 ....*....|....*....|....
gi 922323177 150 LSAELSAELSaelsaELRERKKQY 173
Cdd:cd17246  165 LIDKLEQKLE-----KLEDLKKGL 183

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: 58.75 E-value: 3.21e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  88 VLNKEINPKFLAYALK--KEAKKFVNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELsAELSAELSAE 165
Cdd:cd17290   97 IFNKDINPKFLFYWLSssKEELENLANGATLPILNQEKLKNIKLPVPPLNEQQKIVEFLDKKTAKIDAL-IAKKEQLIEL 175


                 ....*
gi 922323177 166 LRERK 170
Cdd:cd17290  176 LKEYR 180

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: 57.65 E-value: 8.34e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 248 ITVSARGTIGAVFY----RDFaYLPAVSLICFVPKEEFDIRFLFHALRAIKFKKQ------GSATGQLTVAQFKEYGIHV 317
Cdd:cd17289   71 ILITSVGTIGIPYLvkndDPF-YFKDGNLTWFKNIKDINSKFLYYWFQSSIFKNQinsitiGSTQKALTIEKLKKTKIPL 149

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 922323177 318 PSLKKQKEIAAILDPLYSFFTDLNEGIPAEIELCKKQLDYY 358
Cdd:cd17289  150 PPLEEQKKIVSILSALDEKIDLNKKQLQKLEELAKTLFQYW 190

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: 56.67 E-value: 1.48e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  76 KFSASSN---CGILkvLNKEINPKFLAYALKKEAKKFVNTT--SAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTEL 150
Cdd:cd17515   81 GIDAATNqaiCAIL--PNEEIDNEFLFYFLKSQKEYLISLGkgGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKL 158

                         90       100
                 ....*....|....*....|....*
gi 922323177 151 SAELSAELsaELSAELRERKKQYAF 175
Cdd:cd17515  159 IEKLEKAL--EKLEELKKALMQKLL 181

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) TRD1-CR1, Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) TRD1-CR1; The recognition sequences of Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) and Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341182 [Multi-domain] Cd Length: 180 Bit Score: 56.31 E-value: 1.82e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  88 VLNKEINPKFLAYALKkeAKKFVN----TTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaELS 163
Cdd:cd17293   93 IPNKSVDPKFLYYQLL--SSKFQLqaiaSSTTLPIINKSKFEKIEIPLPPLEEQKRIVAKLDKLFALIDKLEESL--EEL 168

                         90
                 ....*....|..
gi 922323177 164 AELRERKKQYAF 175
Cdd:cd17293  169 DELLKSLFQSAF 180

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

Pssm-ID: 341157 [Multi-domain] Cd Length: 185 Bit Score: 56.30 E-value: 2.25e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 274 CFVPKEEFDIRFLFHALRAIKFKKQGSATGQ------LTVAQFKEYGIHVPSLKKQKEIAAILDPlysfFTDLNEGIPAE 347
Cdd:cd17268   97 IIIFRHSQNPKYLSYLLNSPAFQKQKRKLGTgtkvvhISASDLAKIKIPVPPLEEQERIVEILDK----FDALIAGLPAE 172

                         90
                 ....*....|...
gi 922323177 348 IELCKKQLDYYQN 360
Cdd:cd17268  173 IEARRKQYEYYRD 185

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

Pssm-ID: 341139 [Multi-domain] Cd Length: 185 Bit Score: 56.10 E-value: 3.00e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  81 SNCGILKVLNKeINPKFLAYALKKEA-KKFVNTTSaIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELs 159
Cdd:cd17250   94 NNVMGLIPNEG-IDSEYLYYWLKKVDlYKYSQATT-VPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQAL- 170

                         90
                 ....*....|.
gi 922323177 160 AELSAELRERK 170
Cdd:cd17250  171 EAAKEQLKGLR 181

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: 55.92 E-value: 3.47e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  88 VLNKEINPKFLAYALKKEAKKFVNTTSAIPI----LRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaels 163
Cdd:cd17249   97 IPKEGIDPEFLLYALKANEDRILSLVDKAGHgtgsLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKL----- 171

                         90
                 ....*....|
gi 922323177 164 AELRERKKQY 173
Cdd:cd17249  172 AKLEELLKAL 181

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

Pssm-ID: 341172 [Multi-domain] Cd Length: 181 Bit Score: 55.56 E-value: 4.21e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  89 LNKEINPKFLAYALKKEAKKFV---NTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaelsAE 165
Cdd:cd17283   97 LKKKLDKDFLYYLLSSITVQLQfsaQAGGGTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKL-----EK 171


                 ....*...
gi 922323177 166 LRERKKQY 173
Cdd:cd17283  172 LEELKKGL 179

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: 54.71 E-value: 5.01e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177   7 KIKDICEASHGREInTKYLRENqGIYPVYSSAtsneGEMGRIKTYDFDGEYVTwTTRWSYAGSIYYRNGKFSassncgil 86
Cdd:cd17267    2 KLGDVIELQYGKDL-PKSRRIP-GPYPVYGSN----GIVGYHNEALVKGPGIV-VGRKGSIGKVHYSEEDFW-------- 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  87 kVLN--------KEINPKFLAYALKKEAKKFVNTTSAIPIL-RTQkVVEIPIDFPPLQIQEKIATILDTFTELSAELSAE 157
Cdd:cd17267   67 -PIDttlyvkdfKGNDPRFLYYLLKTLDLERLNSGSAVPGLnRND-VYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQ 144

                        170
                 ....*....|....
gi 922323177 158 LS--AELSAELRER 169
Cdd:cd17267  145 NQtlEELADALLPK 158

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: 54.75 E-value: 5.76e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 277 PKEEFDIRFLFHALRAIKFKK--QGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIPAEIELCKKQ 354
Cdd:cd17262   89 GKNGISTEFLYYYLNSIDISPyvTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKAL 168


                 ....
gi 922323177 355 LDYY 358
Cdd:cd17262  169 LQKL 172

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: 54.33 E-value: 6.61e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 237 YSKTFRVEEKSITVSARGTIGAVFY--RDF-----AYlpavslicFV-PKEEFDIRFLFHALRAIKFKKQGSATGQLTV- 307
Cdd:cd17267   36 YHNEALVKGPGIVVGRKGSIGKVHYseEDFwpidtTL--------YVkDFKGNDPRFLYYLLKTLDLERLNSGSAVPGLn 107

                         90       100
                 ....*....|....*....|....*..
gi 922323177 308 -AQFKEYGIHVPSLKKQKEIAAILDPL 333
Cdd:cd17267  108 rNDVYSLKVPLPPLEEQKAIAAILDAL 134

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: 54.87 E-value: 7.48e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  69 SIYYRNGKFSASSNCGILKVlNKEINPKFLAYALK-KEAKKFVN---TTSAIPILRTQKVVEIPIDFPPLQIQEKIATIL 144
Cdd:cd17252   85 AFIDEDTDYTFGAFCGVIRP-KKEIDPRYLFYFLQsPSYREYIRslaSGTNINNLSNEHLENLKIPLPPLAEQKRIVAKL 163

                         90
                 ....*....|....*...
gi 922323177 145 DTFTELSAELSAELSAEL 162
Cdd:cd17252  164 DKLDALIDKLKQALEKLD 181

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: 54.43 E-value: 9.75e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVL--NKEINPKFLAYALKKEAKKFVN-----TTSAIpilRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAEL 158
Cdd:cd17285   90 LKALfpKDELDPEYLLYWFLSIEETIESlgtgtTVKGI---TLEDLKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKL 166

                         90
                 ....*....|....*..
gi 922323177 159 SAELsaELRERKKQYAF 175
Cdd:cd17285  167 EKLK--QLKKGLMQSLL 181

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: 53.30 E-value: 2.00e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYALKKEAKKFVNTTSAIPI--LRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaels 163
Cdd:cd17257   89 IRPKSEELDKRFLYYALPPPLKAIEDTTSSTTVkhLSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLIAKL----- 163

                         90
                 ....*....|
gi 922323177 164 AELRERKKQY 173
Cdd:cd17257  164 EKLRDLLLPL 173

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

Pssm-ID: 341173 [Multi-domain] Cd Length: 185 Bit Score: 53.37 E-value: 2.12e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  88 VLNKEINPKFLAYALKKEAKKF--VNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaelsAE 165
Cdd:cd17284   98 VPSKKINPEYLMYLLSLQKKYMekIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKL-----EK 172


                 ....*....
gi 922323177 166 LRERKKQYA 174
Cdd:cd17284  173 LQQLKKGLM 181

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

Pssm-ID: 341153 [Multi-domain] Cd Length: 184 Bit Score: 52.15 E-value: 5.68e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 253 RGTIGAV----FYRDFAYlpAVSLICFVPKEEFDIRFLFHALRAIKFKKQ------GSATGQLTVAQFKEYGIHVPSLKK 322
Cdd:cd17264   72 RGSLGKCaivdNYDEGAI--ASSLVIIRPFAKVDVRYLYYYLNSPLGKSQikkydnGSAQPNLSAKSLKKFLIPLPPLEE 149

                         90       100       110
                 ....*....|....*....|....*....|....
gi 922323177 323 QKEIAAILDPLYSFFTDLNEGIPAEIELCKKQLD 356
Cdd:cd17264  150 QKRIVAKLDELDALIDKLKQALEKLEELLQSLFQ 183

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

Pssm-ID: 341183 [Multi-domain] Cd Length: 188 Bit Score: 52.11 E-value: 5.78e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  76 KFSASSN--CGILKVLNKEINPKFLAYALKKEAKKFVNTTSA-------IPILRtqkvvEIPIDFPPLQIQEKIATILDT 146
Cdd:cd17294   87 KIPLTTNqsLAAIEPDEEIANSRFLYYNLSSRYEELRSLSGGggrgglnLKIIK-----SLPIPLPPLEEQKKIVAILDK 161

                         90       100       110
                 ....*....|....*....|....*....|
gi 922323177 147 FTELSAELSAELSAELSaelrERKKQYAFY 176
Cdd:cd17294  162 FDALINDLKEGLPALLE----LRQKQYEYL 187

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: 51.77 E-value: 1.01e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  74 NGKFSASSNCGILKVLNKEINPKFLAYAL-----KKEAKKFVNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFT 148
Cdd:cd17517   89 DEPAIFASYLIRLRLDKKKILPEFLYYYLnsplgRKQIEKIAKSAAGQANINQKDLKKLPIPLPPLEEQKEIVEILESLD 168

                         90       100
                 ....*....|....*....|...
gi 922323177 149 ELSAELSAELSA--ELSAELRER 169
Cdd:cd17517  169 SKIDLLEKKLEKleQLFKSLMQS 191

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: 51.41 E-value: 1.09e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 191 KYYKLGEIAQkvLVGG--EKPADFSKEKNEVYkYPIL-SNNSKAEEF----LVY------SKTFRVEEKSITVSA----R 253
Cdd:cd17252    2 EWVRLGEIAE--IIRGvtYKKSDASEEPSEGG-IPVLrANNIQNGGLdfddLVYvpkskvKEEQKLKKGDILICMssgsK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 254 GTIG--AVFYRDFAYlpAVSLICFV--PKEEFDIRFLFHALRAIKFKK------QGSATGQLTVAQFKEYGIHVPSLKKQ 323
Cdd:cd17252   79 ELVGkaAFIDEDTDY--TFGAFCGVirPKKEIDPRYLFYFLQSPSYREyirslaSGTNINNLSNEHLENLKIPLPPLAEQ 156

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 922323177 324 KEIAAILDPLYSFFTDLNEgipaEIELCKKQLDYY 358
Cdd:cd17252  157 KRIVAKLDKLDALIDKLKQ----ALEKLDELLKSL 187

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: 51.36 E-value: 1.35e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYALKKEAKKF----VNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaelsAE 165
Cdd:cd17259  104 KDELNSDFLYYLLQSDFFLNyvepVLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKL-----EK 178


                 ....*..
gi 922323177 166 LRERKKQ 172
Cdd:cd17259  179 LQQLKKG 185

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: 51.32 E-value: 1.46e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYAL-----KKEAKKFVNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELSA 160
Cdd:cd17253  101 VRPKDDLLLPEFLSYWLnsaygRGYFLRAAKQTTNLASINSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEASLAK 180

                         90
                 ....*....|.
gi 922323177 161 --ELSAELRER 169
Cdd:cd17253  181 leELLKALRQA 191

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: 51.06 E-value: 1.60e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  76 KFSASSNCGI--LKVLNKEINPKFLAYALKKEAKKFVNTTSAIP-------ILRTQKvveIPIdfPPLQIQEKIATILDT 146
Cdd:cd17296   81 KIEATTNQAIagIKPKNKSINPKYLYYYLKSLYEKFLSLGRGVAqnninlsILKNLK---IPL--PPLEEQQRIVAILDK 155

                         90       100
                 ....*....|....*....|....*....
gi 922323177 147 FTELSAELSAELsaELSAELRERKKQYAF 175
Cdd:cd17296  156 FEKLINKRQEGL--QLLDELVKSLFEEMF 182

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: 50.20 E-value: 2.58e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 277 PKEEFDIRFLFHALRAI--KFKKQGSATgqlTVA-----QFKEYGIHVPSLKKQKEIAAILDplySFFTDLNEGIpAEIE 349
Cdd:cd17285   95 PKDELDPEYLLYWFLSIeeTIESLGTGT---TVKgitleDLKSLKIPLPPLEEQKRIVAILD---ELDELIDKLE-AKLE 167

                         90
                 ....*....|....
gi 922323177 350 LCKKQLDYYQNFLF 363
Cdd:cd17285  168 KLKQLKKGLMQSLL 181

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus licheniformis S subunit (S1.BliBORF2384P) TRD1-CR1 and Chlorobium tepidum TLS S subunit (S.CteTORF675P) TRD1-CR1; The recognition sequences for Bacillus licheniformis S subunit (S1.BliBORF2384P) and Chlorobium tepidum TLS S subunit (S.CteTORF675P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341187 [Multi-domain] Cd Length: 175 Bit Score: 50.19 E-value: 2.64e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYALKKEAKKFVNTT--SAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaELSAELR 167
Cdd:cd17496   90 KNGIDTEFLYYLLESNLDYLLAAAtgSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEI--EKLEELR 167


                 ....*...
gi 922323177 168 ERKKQYAF 175
Cdd:cd17496  168 DTLLPKLL 175

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Sba223ORF3470P TRD1-CR1; The recognition sequence of Shewanella baltica OS223 S subunit (S.Sba223ORF3470P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341159 [Multi-domain] Cd Length: 183 Bit Score: 50.40 E-value: 2.69e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  85 ILKVLNKEINPKFLAYALK----KEAKKFVNTTSAIPILRTQKVVEIPIdfPPLQIQEKIATILDTFTelsaelsaelsa 160
Cdd:cd17270   94 IFESYKININKKFFAYQLKlkfeIEKEKAPGGTIKTITKEELSKFEIPI--PSLEEQKEIVNILDKFD------------ 159

                         90       100
                 ....*....|....*....|..
gi 922323177 161 ELSAELRERKKQYAFYCDYLLN 182
Cdd:cd17270  160 ELITELQLRKKQLEYYKKALLS 181

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: 50.23 E-value: 2.77e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYALK-----KEAKKFVNTTSA----IpilrTQKVV-EIPIDFPPLQIQEKIATILDTFTELSAELS 155
Cdd:cd17261   99 LRVNEELLLPEYLALALNspsarRQIESRATGTAGsmpkI----SQSDLkSLPIPLPPLAEQKRIVARVDELLALIDRLE 174

                         90
                 ....*....|....*.
gi 922323177 156 AELSA--ELSAELRER 169
Cdd:cd17261  175 AQLAAalQLLDRLRQA 190

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Methanococcus maripaludis C5 S subunit (S.MmaC5ORF1169P) TRD1-CR1, and Methanobacterium formicicum S subunit (S.Mfo3637ORF3708P); The recognition sequences of Methanococcus maripaludis C5 S subunit (S.MmaC5ORF1169P) and Methanobacterium formicicum S subunit (S.Mfo3637ORF3708P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341184 [Multi-domain] Cd Length: 182 Bit Score: 49.91 E-value: 2.96e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 254 GTIGAVFYRDF--AYLPAVSLIcfVPKEE-FDIRFLFHALRAIK--FKKQGSATGQ--LTVAQFKEYGIHVPSLKKQKEI 326
Cdd:cd17296   72 ATIGKVGILKIeaTTNQAIAGI--KPKNKsINPKYLYYYLKSLYekFLSLGRGVAQnnINLSILKNLKIPLPPLEEQQRI 149

                         90       100       110
                 ....*....|....*....|....*....|..
gi 922323177 327 AAILDPLYSFFTDLNEGIPAEIELCKKQLDYY 358
Cdd:cd17296  150 VAILDKFEKLINKRQEGLQLLDELVKSLFEEM 181

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Eco540ANI TRD1-CR1, S.Eco2747AII TRD1-CR1, S.Eco540AI TRD1-CR1, S.Eco2747II TRD1-CR1, and S.Eco540I TRD1-CR1; Escherichia coli ST540AN S subunit (S.Eco540ANI ), Escherichia coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540 S subunit (S.Eco540I) recognize 5'... GAANNNNNNRTCG ... 3'. Escherichia coli ST2747A S subunit (S.Eco2747AII) and Escherichia coli ST2747 S subunit (S.Eco2747II) recognize 5'... GAANNNNNNNTAAA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341163 Cd Length: 171 Bit Score: 49.80 E-value: 3.28e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  80 SSNCGILKVLNKEINPKFLAYALKKeaKKFVNTTSA---IpilrtQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSA 156
Cdd:cd17274   81 SSAMKILTPKNNNVNLKFVYEALQT--IKYVPGDHKrhwI-----SEYSKFKIPLPPLEEQNKIVRILDKFDELIAELEA 153

                         90       100
                 ....*....|....*....|....*
gi 922323177 157 ELSAelsaelreRKKQYAFYCDYLL 181
Cdd:cd17274  154 KLEL--------LKKQKKYYLQKLF 170

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: 49.80 E-value: 3.50e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  88 VLNKEINPKFLAYALK-KEAKKFVN---TTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaels 163
Cdd:cd17256   96 RPKDSISPRYLYYYLRsPFGQSQIEsetKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQL----- 170

                         90
                 ....*....|
gi 922323177 164 AELRERKKQY 173
Cdd:cd17256  171 AKLEELKKAL 180

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: 49.77 E-value: 3.53e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 922323177 276 VPKEEFDIRFLFHALRA----IKFKKQGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPL 333
Cdd:cd17254   86 VPDEEIDKDYLYYLLKAlteeIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDEL 147

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: 49.90 E-value: 3.85e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 272 LICFVPKEEFDIRFLFHALRAIK--FKKQGSATGQLTVAQ--FKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIPAE 347
Cdd:cd17284   94 LHAFVPSKKINPEYLMYLLSLQKkyMEKIATGTTIPYLNKtnCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKL 173


                 ....*...
gi 922323177 348 IELCKKQL 355
Cdd:cd17284  174 QQLKKGLM 181

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

Pssm-ID: 341172 [Multi-domain] Cd Length: 181 Bit Score: 49.79 E-value: 3.88e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 277 PKEEFDIRFLFHALRAI--KFKKQGSATGQ---LTVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIPAEIELC 351
Cdd:cd17283   97 LKKKLDKDFLYYLLSSItvQLQFSAQAGGGtknLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLEELK 176


                 ....
gi 922323177 352 KKQL 355
Cdd:cd17283  177 KGLM 180

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: 49.79 E-value: 4.25e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYALKKEA-KKFVN---TTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELSAE 161
Cdd:cd17521   97 FRPNKKKVLPKYLFYFTQSSLyWKQIKsisSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKL 176

                         90
                 ....*....|..
gi 922323177 162 LsaELRERKKQY 173
Cdd:cd17521  177 E--ELLKELLQS 186

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

Pssm-ID: 341197 [Multi-domain] Cd Length: 184 Bit Score: 49.47 E-value: 5.32e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 922323177  86 LKVLNKEINPKFLAYALK---KEAKKFVNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTEL 150
Cdd:cd17516   94 IIVNKNKFDPDFVYYLLKnnsKYLKSIAGGSTATPIINKSTFSNIEIPLPPLPEQKKIAAILSSLDDK 161

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: 48.98 E-value: 7.10e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 248 ITVSArgTIGAVFYRDF-AYLPAvSLICFVPKEE-FDIRFLFHALRAIK--FKKQGSATGQ--LTVAQFKEYGIHVPSLK 321
Cdd:cd17282   72 ITIAA--NIGDTAILGFdACFPD-SVVGFIPNEEkIDVEFLEYYLRTLKkeLEAIAPQSAQknINLEILRPLKIPVPPLE 148

                         90       100       110
                 ....*....|....*....|....*....|....
gi 922323177 322 KQKEIAAILDPLYSFFTDLNEGIpAEIELCKKQL 355
Cdd:cd17282  149 EQKKIVEILDALDDLIDNLEKRI-AKLEELKQSL 181

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: 48.99 E-value: 7.29e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 274 CFVPKEEFDIRFLFHALRAIK------FKKQGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIPAE 347
Cdd:cd17249   95 ALIPKEGIDPEFLLYALKANEdrilslVDKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKL 174


                 ....*...
gi 922323177 348 IELcKKQL 355
Cdd:cd17249  175 EEL-LKAL 181

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

Pssm-ID: 341152 [Multi-domain] Cd Length: 177 Bit Score: 48.65 E-value: 8.06e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  80 SSNCGILKVLNKEINPKFLAYALK-KEAKKFVNT--TSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSA 156
Cdd:cd17263   81 ASTLFKIIPDKNIIDKDYLYYFLKsKEIQLNILTkaGSTIPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALIDKLKE 160

                         90
                 ....*....|....*..
gi 922323177 157 ELsaelsAELRERKKQY 173
Cdd:cd17263  161 LI-----EKLIELKKGL 172

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: 48.30 E-value: 1.03e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYALKKEAKKFVN-----TTSAIpilrTQKVVE-IPIDFPPLQIQEKIATILDTftelsAELSAELSAELS 163
Cdd:cd17245   89 NKDIDNLFLYYYLKYNKPELEKlgtgsTFKAI----NKKDLEeLKIPLPPLEEQQKIAEILST-----VDEAIEKTKALI 159


                 ....*...
gi 922323177 164 AELRERKK 171
Cdd:cd17245  160 EKLDELKK 167

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: 47.89 E-value: 1.57e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 274 CFVPKEEFDIRFLFHALRAIKFKKQ------GSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYsfftdlnegipAE 347
Cdd:cd17278   97 KFRPKDKIDKEFLYYLLRSDSFRNQikssatGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLD-----------AK 165

                         90
                 ....*....|....*
gi 922323177 348 IELCKKQLDYYQNFL 362
Cdd:cd17278  166 IDKLEQKLEKLRDLL 180

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

Pssm-ID: 341162 [Multi-domain] Cd Length: 186 Bit Score: 48.17 E-value: 1.58e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 247 SITVSARGTIGAVfyrdfaylpAVSL---------ICFVPKEEFDIRFLFHALRAIKFKKQGSATG----QLTVAQFKEY 313
Cdd:cd17273   70 SVLLSSRAPIGYV---------AIATnplatnqgfKSIIPNEEIDNEFLYYLLKNNKPEIESLASGstfkEISKSTFKKI 140

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 922323177 314 GIHVPSLKKQKEIAAILDPLYsfftdlnegipAEIELCKKQLD 356
Cdd:cd17273  141 EIPLPPLEEQKKIAAILSKLD-----------ELIELLEKENE 172

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

Pssm-ID: 341168 [Multi-domain] Cd Length: 184 Bit Score: 47.94 E-value: 1.87e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 209 PADFSKEKNEvykypILSNNSK--AEEFLVYSKTFRVEEKSITVSARGTIGAVFYRDFAYlpAVSLICF--VPKEEFDIR 284
Cdd:cd17279   32 PADLSKLDGK-----YISSSQRkiTEAGLESCGTSLVPAGSIILSTRAPIGYVAIATVEL--CTNQGCKalVPNSDVDSR 104

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 922323177 285 FLFHALRAIKFKKQGSATG----QLTVAQFKEYGIHVPSLKKQKEIAAILD 331
Cdd:cd17279  105 FLYYLLLAAKEELNSLGRGttflELSTDELANFKIPLPPLSEQRAIADFLD 155

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Sba223ORF3470P TRD1-CR1; The recognition sequence of Shewanella baltica OS223 S subunit (S.Sba223ORF3470P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341159 [Multi-domain] Cd Length: 183 Bit Score: 47.31 E-value: 2.32e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 238 SKTFRVEEKSITVSARGTIGAVFYRDF-AYLPAVSLICFVPKEEFDIRFLFHALRAiKF-----KKQGSATGQLTVAQFK 311
Cdd:cd17270   58 PKSVFVPKGTVIVTLQGSIGRVAITQYdAYVDRTLLIFESYKININKKFFAYQLKL-KFeiekeKAPGGTIKTITKEELS 136

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 922323177 312 EYGIHVPSLKKQKEIAAILDplysfftDLNEgIPAEIELCKKQLDYYQNFLFN 364
Cdd:cd17270  137 KFEIPIPSLEEQKEIVNILD-------KFDE-LITELQLRKKQLEYYKKALLS 181

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) TRD1-CR1, Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) TRD1-CR1; The recognition sequences of Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) and Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341182 [Multi-domain] Cd Length: 180 Bit Score: 47.45 E-value: 2.43e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 922323177 275 FVPKEEFDIRFLFHALRAIKFKKQGSATGQlTVA-----QFKEYGIHVPSLKKQKEIAAILD 331
Cdd:cd17293   92 IIPNKSVDPKFLYYQLLSSKFQLQAIASST-TLPiinksKFEKIEIPLPPLEEQKRIVAKLD 152

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: 47.07 E-value: 2.44e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  85 ILKV-LNKEINPKFLAYALKKEAKKFVNTTSAIPILRTQK--VVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaE 161
Cdd:cd17254   82 IFKVvPDEEIDKDYLYYLLKALTEEIESQAHGSTMVHITKgdLENIKVPLPPLEEQKRIAAILDELDALIDALEEQL--K 159

                         90
                 ....*....|.
gi 922323177 162 LSAELRERKKQ 172
Cdd:cd17254  160 KLEELRKALLQ 170

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: 46.38 E-value: 3.24e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 922323177 284 RFLFHALRAIKFKK-QGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIPAEIELCKKQLDYY 358
Cdd:cd17292   73 KFLYYFYQIIKWKKtEGSTIKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYL 148

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: 46.34 E-value: 4.62e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 277 PKEEFDIRFLFHALRAI--KFKKQ--GSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYsfftdlnegipAEIELCK 352
Cdd:cd17496   89 PKNGIDTEFLYYLLESNldYLLAAatGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLD-----------EKIDKNK 157


                 ....
gi 922323177 353 KQLD 356
Cdd:cd17496  158 QEIE 161

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: 46.78 E-value: 4.78e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 922323177  76 KFSASSNCGILKV-LNKEINPKFLAYALKKEAKKFVNTTS--AIPILRTQKVVEIPIDFPPLQIQEKIATILDT 146
Cdd:cd17514   86 QIDASTNQAIAAIrCKENVNPKYLYYYLKTQKNNLRNLTSgvAQKNLNIEMLRNLQIPLPPKEEQQKIVNILET 159

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

Pssm-ID: 341177 [Multi-domain] Cd Length: 163 Bit Score: 45.92 E-value: 5.73e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 276 VPKEEFDIRFLFHALRAIKFKKQGSATG--QLTVAQFKEYGIHVPSLKKQKEIAAILDPLYSffTDLNEGIPAEIELCKK 353
Cdd:cd17288   76 EIKKNNDPKFLYYLLKTIDFKKYNEATGvpSLTQTTLNKIKIPIPPLEEQQKIASILDKLDA--KDALIELQEKLLEKLK 153


                 ....*
gi 922323177 354 QLDYY 358
Cdd:cd17288  154 QYKLA 158

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: 46.39 E-value: 6.40e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  76 KFSASSNCGIL--KVLNKEINPKFLAYAL---KKEAKKFVNTTSAiPILRTQKVVEIPIDFPPLQIQEKIATILDTFTEL 150
Cdd:cd17275   85 KIDVATNQAILgiIPKDEKLDFEFLYYWLlslKNELKRLIRTGTQ-ANLNAEIVKNLPIPLPPLEEQKKIAEILDKIDAE 163

                         90       100
                 ....*....|....*....|.
gi 922323177 151 SAELSAELSaelsaELRERKK 171
Cdd:cd17275  164 IDKLEEKIE-----KLRELKK 179

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: 45.96 E-value: 8.06e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  73 RNGKFsassncgilkVLNKEINPKFLAYALKKEA--KKFVN--TTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFT 148
Cdd:cd17278   94 RVGKF----------RPKDKIDKEFLYYLLRSDSfrNQIKSsaTGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLD 163

                         90       100
                 ....*....|....*....|....*
gi 922323177 149 ELSAELSAELSaelsaELRERKKQY 173
Cdd:cd17278  164 AKIDKLEQKLE-----KLRDLLKPL 183

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

Pssm-ID: 341202 [Multi-domain] Cd Length: 187 Bit Score: 45.94 E-value: 8.26e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 252 AR--GTIGAVFYRDFAYLPAV--S-LICFVPKEE-FDIRFLFHALR------AIKFKKQGSATGQLTVAQFKEYGIHVPS 319
Cdd:cd17521   69 ARtgATVGKSYLYKEDDGKAVfaSyLIRFRPNKKkVLPKYLFYFTQsslywkQIKSISSGSAQPNINAEKLKSLKIPLPP 148

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 922323177 320 LKKQKEIAAILDPLYSFFTDLNEGIPAEIELCKKQLDYY 358
Cdd:cd17521  149 LEEQKRIVAILDALDAKIDALEELLEKLEELLKELLQSL 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: 45.70 E-value: 8.82e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 276 VPKEEFDIRFLFHALRAIKFKK--QGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDplySFFTDLNEGIpAEIELCKK 353
Cdd:cd17250  100 IPNEGIDSEYLYYWLKKVDLYKysQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLD---ELFEKLDKLK-QALEAAKE 175


                 ....*
gi 922323177 354 QLDYY 358
Cdd:cd17250  176 QLKGL 180

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Eco540ANI TRD1-CR1, S.Eco2747AII TRD1-CR1, S.Eco540AI TRD1-CR1, S.Eco2747II TRD1-CR1, and S.Eco540I TRD1-CR1; Escherichia coli ST540AN S subunit (S.Eco540ANI ), Escherichia coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540 S subunit (S.Eco540I) recognize 5'... GAANNNNNNRTCG ... 3'. Escherichia coli ST2747A S subunit (S.Eco2747AII) and Escherichia coli ST2747 S subunit (S.Eco2747II) recognize 5'... GAANNNNNNNTAAA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341163 Cd Length: 171 Bit Score: 45.56 E-value: 9.43e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 278 KEEFDIRFLFHALRAIKFKKQG------SatgqlTVAQFKeygIHVPSLKKQKEIAAILDPlysfFTDLNEGIPAEIELC 351
Cdd:cd17274   91 NNNVNLKFVYEALQTIKYVPGDhkrhwiS-----EYSKFK---IPLPPLEEQNKIVRILDK----FDELIAELEAKLELL 158

                         90
                 ....*....|..
gi 922323177 352 KKQLDYYQNFLF 363
Cdd:cd17274  159 KKQKKYYLQKLF 170

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

Pssm-ID: 341149 [Multi-domain] Cd Length: 165 Bit Score: 45.50 E-value: 9.71e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 277 PKEEFDIRFLFHALRAIKFKKQGS-----ATGQ--LTVAQFKEYGIHVPSLKKQKEIAAILDPLysffTDLNEGIPAEIE 349
Cdd:cd17260   76 PKEGILPEFLYYLLRSPSFRKEAIksmtgSSGRqrVPKDFLENYKIPLPPLEEQKRIAAILDSL----DAKIDALEAEIE 151

                         90
                 ....*....|....
gi 922323177 350 LCKKQLDYYQNFLF 363
Cdd:cd17260  152 TLEELLDALLPKLL 165

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: 45.56 E-value: 1.04e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYALKKEAKKFVNT--TSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaelsAELR 167
Cdd:cd17286   94 NKNYDPEFLYYALENWSKKIKSLagKQAVPIINKTEFSKIKILVPPLEEQQKIANFLSKLDELIELQQQKI-----EKLE 168


                 ....
gi 922323177 168 ERKK 171
Cdd:cd17286  169 ELKK 172

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: 45.09 E-value: 1.37e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  88 VLNKEINPKFLAYALKKEAKKFVN----TT----SAipilrtqKVVE-IPIDFPPLQIQEKIATILDTFTELSAELSAEL 158
Cdd:cd17273   99 IPNEEIDNEFLYYLLKNNKPEIESlasgSTfkeiSK-------STFKkIEIPLPPLEEQKKIAAILSKLDELIELLEKEN 171

                         90
                 ....*....|...
gi 922323177 159 saelsAELRERKK 171
Cdd:cd17273  172 -----EKLKELRD 179

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: 45.18 E-value: 1.55e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 241 FRVEEKSITVSARGTIGAVFY-----------RDFAYLpavslicfVPKEEFDIRFLFHALRAIKFKKQ------GSATG 303
Cdd:cd17256   58 YTLSKGDILISIVGTIGRVGIvpkeldganltENAARI--------RPKDSISPRYLYYYLRSPFGQSQiesetkGAAQP 129

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 922323177 304 QLTVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIPAEIELCKK 353
Cdd:cd17256  130 KLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKA 179

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

Pssm-ID: 341194 [Multi-domain] Cd Length: 182 Bit Score: 44.82 E-value: 1.67e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  88 VLNKEINPKFLAYALKKEAKKFVNT---TSAIPILRTQkVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaelsA 164
Cdd:cd17513   95 IPIKEVNPLFLAYLLYSLLQKLKSQlqgTSIKGITKDD-LKNLKIPLPPLEEQQKIAAILSKLDKLIEAHEKKL-----E 168


                 ....*..
gi 922323177 165 ELRERKK 171
Cdd:cd17513  169 KLKQLKK 175

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: 44.89 E-value: 1.70e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYAL---------KKEAKKFVNTtSAIpilRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSA 156
Cdd:cd17526  100 IRVKKSKINPEFLARYLhllwrsgyfKKLCTNWVNQ-AGI---NSDTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRA 175

                         90
                 ....*....|....*..
gi 922323177 157 ELSAelsaeLRERKKQY 173
Cdd:cd17526  176 EAEA-----LLELAKSL 187

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: 44.84 E-value: 1.79e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 238 SKTFRVEEK-SITVSARGTIGAVFYRDFAYLPAVSLICFVPKEEFDIRFLFHALRAIKFKKQGSATGQ----LTVAQFKE 312
Cdd:cd17245   48 TKPTKIAEKgDILISVRAPVGDVNIADEKCCIGRGLAAIRANKDIDNLFLYYYLKYNKPELEKLGTGStfkaINKKDLEE 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 922323177 313 YGIHVPSLKKQKEIAAILDPlysfftdlnegIPAEIELCKKQLDYYQNFL 362
Cdd:cd17245  128 LKIPLPPLEEQQKIAEILST-----------VDEAIEKTKALIEKLDELK 166

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: 44.94 E-value: 1.91e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYALK-KEAKKFVNT---TSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELSAELsaE 165
Cdd:cd17289  104 IKDINSKFLYYWFQsSIFKNQINSitiGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLE--E 181

                         90
                 ....*....|
gi 922323177 166 LRERKKQYAF 175
Cdd:cd17289  182 LAKTLFQYWF 191

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: 44.35 E-value: 2.29e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 274 CFVPKEEFDIRFLFHALRAIK--FKKQGSATGQ--LTVAQFKEYGIHVPSLKKQKEIAAILDPLYsfftdlnegipAEIE 349
Cdd:cd17515   92 AILPNEEIDNEFLFYFLKSQKeyLISLGKGGAQpnISQGIIKNIEIPLPPLAEQKRIVAKLDKLD-----------KLIE 160

                         90
                 ....*....|.
gi 922323177 350 LCKKQLDYYQN 360
Cdd:cd17515  161 KLEKALEKLEE 171

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: 44.39 E-value: 2.52e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYALKKEAKKFVNTTSAI-PILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaELSA 164
Cdd:cd17244   94 FIPKDKKIDTEYLYYYLKSFDYSSLGSTASKgKTLNSKKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLI--ELLD 171


                 ....*...
gi 922323177 165 ELRERKKQ 172
Cdd:cd17244  172 ELLPKLMS 179

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: 44.45 E-value: 2.81e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYALKKE---------AKKFVNTTSaipiLRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSA 156
Cdd:cd17522   99 LRPNKNIVDPKYLYYLLKSDrfrnqfrsiAKKAVNQAS----INQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKE 174

                         90
                 ....*....|....*
gi 922323177 157 ELSaelsaELRERKK 171
Cdd:cd17522  175 KIE-----KLKELKK 184

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) TRD2-CR2; The recognition sequence of Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341193 [Multi-domain] Cd Length: 195 Bit Score: 44.52 E-value: 2.88e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 272 LICFVPKEEFDI-RFLFHALRAIKFKK------QGSAT-GQLTVAQFKEYGIHVPSLKKQKEIAAILDPLysfftDlneg 343
Cdd:cd17512  102 AVKIRPKKGILDqSFLFYNLKSERFKNyiesiaRGNANqASITLGDIKKFKFLLPPLEEQKKIASILSAY-----D---- 172

                         90
                 ....*....|....*.
gi 922323177 344 ipAEIELCKKQLDYYQ 359
Cdd:cd17512  173 --DLIENNEKRIKLLE 186

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 41.97 E-value: 3.33e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 922323177 104 KEAKKFVNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaELSAELRE 168
Cdd:COG0732   12 REYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEI--EKLKELRD 74

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: 43.20 E-value: 7.81e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYALKKEAKKFVN--TTSA-----IPILRTqkvveIPIDFPPLQIQEKIATILDTFTELSAELSAEL 158
Cdd:cd17282   97 FIPNEEKIDVEFLEYYLRTLKKELEAiaPQSAqkninLEILRP-----LKIPVPPLEEQKKIVEILDALDDLIDNLEKRI 171

                         90
                 ....*....|....
gi 922323177 159 saelsAELRERKKQ 172
Cdd:cd17282  172 -----AKLEELKQS 180

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: 42.84 E-value: 8.18e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  86 LKVLNKEINPKFLAYAL---------KKEAKKFVNTT--SAipilrtQKVVEIPIDFPPLQIQEKIATILDTFTELSAEL 154
Cdd:cd17524   98 IRLNEEKILPEYLNYFLnspygrkqiKSVATQGVGQAniNA------TKLKAIPIPLPPLEEQKEIVEKLDELDALIDRL 171

                         90
                 ....*....|....*..
gi 922323177 155 SAELSA--ELSAELRER 169
Cdd:cd17524  172 EALLEEaeELLESLLQS 188

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 40.81 E-value: 8.77e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 288 HALRAIKFKKQ------GSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEgipaEIELCKKQLDYYQNF 361
Cdd:COG0732    4 YYLRSPSFREYlrslatGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEK----EIEKLKELRDALLPK 79


                 ...
gi 922323177 362 LFN 364
Cdd:COG0732   80 LFT 82

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: 42.90 E-value: 8.85e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 278 KEEFDIRFLFHALRAI--KFKKQGSATGQ--LTVAQFKEYGIHVPSLKKQKEIAAILDPLYSFFTDLNEGIPAEIELCKK 353
Cdd:cd17247  106 EERVLPEYLHYYLESQydELRRIGSGGGQgaLNCGILKAFPIPLPPLDEQREIVAELEALLAKIDLLEEKIARLIELLKE 185


                 ...
gi 922323177 354 QLD 356
Cdd:cd17247  186 LRQ 188

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) TRD2-CR2 and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) TRD2-CR; Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) recognizes 5'... GAGNNNNNGTTY ... 3', and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) recognizes 5'... YTCANNNNNNGTTY ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Eco4255III-TRD1 recognizes GAG/CTC and S.EcoNIH1II-TRD1 recognizes YTCA/TGAR, while both S.EcoNIH1II-TRD2 and S.Eco4255III-TRD2 recognize RAAC/GTTY. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341154 [Multi-domain] Cd Length: 181 Bit Score: 42.49 E-value: 1.07e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 922323177 284 RFLFHALRAIKFKKQ-----GSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDplysfftDLNEGIPAEIELCKKQLDY 357
Cdd:cd17265  101 DYLFHLFNSDLFKKQigsflTATINQITNGNLNNFKIPLPPLEEQEKIAEFLS-------SLDAKIDKLIKKIEKLIEL 172

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

Pssm-ID: 341197 [Multi-domain] Cd Length: 184 Bit Score: 42.54 E-value: 1.14e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 922323177 271 SLICFvpKEEFDIRFLFHALRAIKFKKQGSATGQLTV-----AQFKEYGIHVPSLKKQKEIAAILDPL 333
Cdd:cd17516   93 SIIVN--KNKFDPDFVYYLLKNNSKYLKSIAGGSTATpiinkSTFSNIEIPLPPLPEQKKIAAILSSL 158

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: 41.89 E-value: 1.75e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 922323177  88 VLNKEI-NPKFLAYALKKEAKKFVN--TTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTEL 150
Cdd:cd17500   97 IIDNKKaDYRFVYYSLKTQYEELVNlaSGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLDDK 162

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: 41.45 E-value: 2.09e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  91 KEINPKFLAYALKKEAKKFVN-----TTSAIpilrTQKVVE-IPIDFPPLQIQEKIATILDTFTELSAELSaELSAELSA 164
Cdd:cd17499   91 KNIDKKYLFYFLLSNKDYFKGksggsTFKSI----NKNQIKnIKIPLPPLEEQKRIVSELDKLFKLIFEAK-NNIEEALA 165


                 ....*....
gi 922323177 165 ELRERKKQY 173
Cdd:cd17499  166 NAQQLFKSI 174

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: 41.73 E-value: 2.50e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 274 CFVPKEEFDIRFLFHALRAIKFKK--QGSATGQ----LTVAQFKEYGIHVPSLKKQKEIAAILDPLYsfftdlnegipAE 347
Cdd:cd17259  100 RIRPKDELNSDFLYYLLQSDFFLNyvEPVLTGTdvphISTKQIKNFKIPLPPLEEQKKIAEFLSSLD-----------AL 168

                         90
                 ....*....|...
gi 922323177 348 IELCKKQLDYYQN 360
Cdd:cd17259  169 IDLLEQKLEKLQQ 181

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

Pssm-ID: 341188 [Multi-domain] Cd Length: 174 Bit Score: 41.38 E-value: 2.76e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 922323177 277 PKEEFDIRFLFHALRAIKFKKQGSATGQ----LTVAQFKEYGIHVPSLKKQKEIAAILD 331
Cdd:cd17497   88 PKKGLDKKYLLYYLKSIENELSSLGTGStfkaISKEDLENLLIPLPPLAEQKRIAAFLD 146

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

Pssm-ID: 341189 [Multi-domain] Cd Length: 173 Bit Score: 39.97 E-value: 6.48e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177   6 YKIKDICEASHGREINTKYLRENQGIYPVYSSATSnegeMGRIKTYdFDgeyvTWTTRW---SYAGSIYyrngkFSASSN 82
Cdd:cd17498    1 VKLGEIAEITMGQSPKSEFYNEDGIGLPFLQGNRT----FGDKYPY-ID----TYTTDIkkiAKKGDIL-----MSVRAP 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  83 CGILKVLNKEI--------------NPKFLAYALKKEAKKFVNTTS-----AIpilrTQKVVE-IPIDFPPLQIQEKIAT 142
Cdd:cd17498   67 VGDLNIANKDIcigrglcsirmkngNNSFLYYLLKNNIKNLINKSSgtvfgSI----NKDDIEnLEVDIPEDEEQKRIAN 142


                 ....*...
gi 922323177 143 ILDTFTEL 150
Cdd:cd17498  143 ILSKIDDK 150

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: 40.13 E-value: 8.00e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 247 SITVSARGTIGAVfyrdfAYL--PAV---SLICFVPKEEFDIRFLFHALR-AIKFKKQgSATG----QLTVAQFKEYGIH 316
Cdd:cd17243   68 TTIISARGTVGKL-----ALLgiPMAmnqSCYGLRGKDGLSNYFLYYLLKnLIEELKQ-KAHGsvfdTITRKTFDEIKVP 141

                         90
                 ....*....|....*...
gi 922323177 317 VPSLKKQKEIAAILDPLY 334
Cdd:cd17243  142 LPPEELQKSFENIVSPLF 159

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

Pssm-ID: 341164 [Multi-domain] Cd Length: 186 Bit Score: 39.84 E-value: 8.41e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 243 VEEKSITVSARGTIGAVfyrDFAYLPAVS---LICFVPKEEF-DIRFLFHALRAIK--FKKQGSATGQ--LTVAQFKEYG 314
Cdd:cd17275   65 VPKGTILYAMYASVGKV---AINKIDVATnqaILGIIPKDEKlDFEFLYYWLLSLKneLKRLIRTGTQanLNAEIVKNLP 141

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 922323177 315 IHVPSLKKQKEIAAILDplysfftdlneGIPAEIELCKKQLDYYQNFL 362
Cdd:cd17275  142 IPLPPLEEQKKIAEILD-----------KIDAEIDKLEEKIEKLRELK 178

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: 38.68 E-value: 1.36e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYALKkeAKKFVNTT-SAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELSAELSAelre 168
Cdd:cd17292   67 ESKVLNKFLYYFYQ--IIKWKKTEgSTIKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIAL---- 140


                 ....*...
gi 922323177 169 RKKQYAFY 176
Cdd:cd17292  141 KKGLMQYL 148

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: 39.39 E-value: 1.39e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 922323177 274 CFV--PKEEFDIRFLFHALRAI--KFKKQGSATGQ--LTVAQFKEYGIHVPSLKKQKEIAAILD 331
Cdd:cd17287   92 CAAilPNDGINPDFLFYYLQSSyeELRDLSNGGGQpnLNAGLIKSIEIPVPPLDEQQKIAAFLS 155

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

Pssm-ID: 341137 [Multi-domain] Cd Length: 196 Bit Score: 39.44 E-value: 1.44e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 269 AVS--LICFVPKEEFDIRFLFHALRAIK--FKKQGSATGQLTV--AQFKEYGIHVPSLKKQKEIAAILDplysfftDLNE 342
Cdd:cd17248   93 ATSqdFANWVCGPELDPEYLLYVLRAMKpeFERLAMGSTHKTIymPDFKALRIALPPLEEQRKIVDRLE-------ALDA 165

                         90
                 ....*....|....
gi 922323177 343 GIPAEIELCKKQLD 356
Cdd:cd17248  166 KIDALERKLERLIE 179

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: 39.07 E-value: 1.70e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 922323177 275 FVPKEEFDIRFLFHALRAIKFKKQGSATG-------QLTVAQFKeygIHVPSLKKQKEIAAILD 331
Cdd:cd17280   95 LSGSNKIDIKFLFYWLLANRDELISLASGggqpnisQELIKSLR---IPVPPLEEQKQIAAFLD 155

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: 39.06 E-value: 1.75e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYAL-----KKEAKKFvNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaelsA 164
Cdd:cd17264   99 FAKVDVRYLYYYLnsplgKSQIKKY-DNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQAL-----E 172

                         90
                 ....*....|
gi 922323177 165 ELRERKKQYA 174
Cdd:cd17264  173 KLEELLQSLF 182

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: 38.62 E-value: 2.33e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  76 KFSASSN--CGILKvLNKEINPKFLAYALKK---EAKKFVNTTSAiPILRTQKVVEIPIDFPPLQIQEKIATILDTFTEL 150
Cdd:cd17287   83 GIEAATNqaCAAIL-PNDGINPDFLFYYLQSsyeELRDLSNGGGQ-PNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAK 160

                         90       100
                 ....*....|....*....|..
gi 922323177 151 ------SAELSAELSAELSAEL 166
Cdd:cd17287  161 idaleqKLELLQELKKSLMQQL 182

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: 38.19 E-value: 2.45e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYALK-----KEAKKFVNTTSA---IPilrTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELsaE 161
Cdd:cd17260   77 KEGILPEFLYYLLRspsfrKEAIKSMTGSSGrqrVP---KDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEI--E 151

                         90
                 ....*....|....
gi 922323177 162 LSAELRERKKQYAF 175
Cdd:cd17260  152 TLEELLDALLPKLL 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: 37.98 E-value: 3.05e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 277 PKEEFDIRFLFHALRAIK--FKKQGSAT--GQLTVAQFKEYGIHVPSLKKQKEIAAILDPLYSfftdlnegIPAEIELCK 352
Cdd:cd17499   89 AKKNIDKKYLFYFLLSNKdyFKGKSGGStfKSINKNQIKNIKIPLPPLEEQKRIVSELDKLFK--------LIFEAKNNI 160

                         90
                 ....*....|....*
gi 922323177 353 KQLDYYQNFLFNWVQ 367
Cdd:cd17499  161 EEALANAQQLFKSIL 175

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

Pssm-ID: 341168 [Multi-domain] Cd Length: 184 Bit Score: 38.31 E-value: 3.06e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  88 VLNKEINPKFLAYALK--KEAKKFVNTTSAIPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELSAELSAELSAELSAe 165
Cdd:cd17279   96 VPNSDVDSRFLYYLLLaaKEELNSLGRGTTFLELSTDELANFKIPLPPLSEQRAIADFLDRETAKIDALIAKKQQLIEL- 174


                 ....*.
gi 922323177 166 LRERKK 171
Cdd:cd17279  175 LKEKRQ 180

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: 38.28 E-value: 3.16e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 274 CFVPKEEF-DIRFLFHALRA-IKF--KKQGSAT-GQLTVAQFKEYGIHVPSLKKQKEIAAILDplysfftDLNEGIPAEI 348
Cdd:cd17257   88 RIRPKSEElDKRFLYYALPPpLKAieDTTSSTTvKHLSSKDIDEIELPLPPLEEQRRIAEILD-------ELDALIDKLI 160


                 ....*...
gi 922323177 349 ELCKKQLD 356
Cdd:cd17257  161 AKLEKLRD 168

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

Pssm-ID: 341191 [Multi-domain] Cd Length: 186 Bit Score: 38.04 E-value: 3.26e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 922323177 278 KEEFDIRFLFHALR----AIKFKKQGSATGQLTVAQFKEYGIHVPSLKKQKEIAAIL 330
Cdd:cd17500  100 NKKADYRFVYYSLKtqyeELVNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASIL 156

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: 37.77 E-value: 3.70e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  80 SSNCGILKVLNKEINPKFLAYALK-KEAKKFVNTTSA---IPILRTQKVVEIPIDFPPLQIQEKIATILDTFTELsaels 155
Cdd:cd17258   76 SSHVAGFNSKEGISDNKFIKYLFNsKKIKNRLMSYGAsstQPALNLSRLLKIKFPNPPLEEQQKIGKILSTWDRA----- 150

                         90
                 ....*....|....*...
gi 922323177 156 AELSAELSAELRERKKQY 173
Cdd:cd17258  151 IELTEQKLELLQQQKKGL 168

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

Pssm-ID: 341194 [Multi-domain] Cd Length: 182 Bit Score: 37.88 E-value: 4.01e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177 275 FVPKEEFDIRFLFHALRAI----KFKKQGSATGQLTVAQFKEYGIHVPSLKKQKEIAAILDplysfftdlneGIPAEIEL 350
Cdd:cd17513   94 LIPIKEVNPLFLAYLLYSLlqklKSQLQGTSIKGITKDDLKNLKIPLPPLEEQQKIAAILS-----------KLDKLIEA 162


                 ....*....
gi 922323177 351 CKKQLDYYQ 359
Cdd:cd17513  163 HEKKLEKLK 171

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: 37.56 E-value: 5.25e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  73 RNG--KFSASSN---CGILkVLNKEINPKFLAYALKKEAKKFVNTTSAipiLR-----TQKVVE-IPIDFPPLQIQEKIA 141
Cdd:cd17276   80 RTGllGIPAAINqaiCAIL-PNEKKVNPEFLLRYLNFNRPYWMRVAAS---SRkdpniTKDDVRnFPIPLPPLDEQRAIV 155

                         90       100       110
                 ....*....|....*....|....*....|.
gi 922323177 142 TILDTFTELSAELSAELsAELSAELRERKKQ 172
Cdd:cd17276  156 EFLSDVDALIDSLEALI-EKLRELKKGLMQQ 185

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: 37.14 E-value: 5.74e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYALKKEAKKFV-----NTTSAIpilrTQKVVE-IPIDFPPLQIQEKIATILDTFTELSAELSAELsaELS 163
Cdd:cd17497   89 KKGLDKKYLLYYLKSIENELSslgtgSTFKAI----SKEDLEnLLIPLPPLAEQKRIAAFLDELTAKIDQLIALL--EKA 162


                 ....*....
gi 922323177 164 AELRERKKQ 172
Cdd:cd17497  163 IELLKEYRQ 171

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

Pssm-ID: 341137 [Multi-domain] Cd Length: 196 Bit Score: 37.51 E-value: 5.88e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922323177  90 NKEINPKFLAYAL---KKEAKKFVN----TTSAIPILRtqkvvEIPIDFPPLQIQEKIATILDTFTELSAELSAELSAeL 162
Cdd:cd17248  104 GPELDPEYLLYVLramKPEFERLAMgsthKTIYMPDFK-----ALRIALPPLEEQRKIVDRLEALDAKIDALERKLER-L 177

                         90
                 ....*....|
gi 922323177 163 SAELRERKKQ 172
Cdd:cd17248  178 IELLKELRQA 187