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Conserved domains on  [gi|2574747319|ref|WP_308858781|]
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restriction endonuclease subunit S [Lactobacillus delbrueckii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 3-150 5.51e-71

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: 210.79  E-value: 5.51e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   3 KYKLAQLAEIKYGKDHKKLGKGSVPVYGTGGIMRYVNDFIYEGESVLIPRKGSLNNLFYVHGKFWTVDTIFWTKIDSKIV 82
Cdd:cd17288     3 VKKLGDLLKIKNGKDYKHLEDGNYPVYGSGGIMGYVNDYLYDGESVLIGRKGTIDKPLYVNGPFWTVDTMFYTEIKKNND 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2574747319  83 lPRYLYYYLSRIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17288    83 -PKFLYYLLKTIDFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDALIELQEKLL 149
 
Name Accession Description Interval E-value
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 3-150 5.51e-71

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: 210.79  E-value: 5.51e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   3 KYKLAQLAEIKYGKDHKKLGKGSVPVYGTGGIMRYVNDFIYEGESVLIPRKGSLNNLFYVHGKFWTVDTIFWTKIDSKIV 82
Cdd:cd17288     3 VKKLGDLLKIKNGKDYKHLEDGNYPVYGSGGIMGYVNDYLYDGESVLIGRKGTIDKPLYVNGPFWTVDTMFYTEIKKNND 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2574747319  83 lPRYLYYYLSRIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17288    83 -PKFLYYLLKTIDFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDALIELQEKLL 149
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 1-150 2.90e-15

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: 68.54  E-value: 2.90e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   1 MTKYKLAQLAEIKYGKDHKK---LGKGSVPVYGTG-------GIMRYVNDFIYEGESVLIPRKGSLNNLFYVHGKFWTVD 70
Cdd:pfam01420   4 WEVFKLGDVFEIKKGKTPKKkelKNNGKYPYIRAGdlnnvvkGGLGYIKKYILPKGDITISSRATIGYVFYRDKPYYTNQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  71 TIFWTKIDSKIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQIND 148
Cdd:pfam01420  84 HIIVLIPKNNIKITEFLYLYLLLKlkKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDNTIELEKGILN 163


                  ..
gi 2574747319 149 NL 150
Cdd:pfam01420 164 EL 165
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
89-150 1.83e-07

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 46.21  E-value: 1.83e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2574747319  89 YYLS----RIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:COG0732     4 YYLRspsfREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKL 69
 
Name Accession Description Interval E-value
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 3-150 5.51e-71

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: 210.79  E-value: 5.51e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   3 KYKLAQLAEIKYGKDHKKLGKGSVPVYGTGGIMRYVNDFIYEGESVLIPRKGSLNNLFYVHGKFWTVDTIFWTKIDSKIV 82
Cdd:cd17288     3 VKKLGDLLKIKNGKDYKHLEDGNYPVYGSGGIMGYVNDYLYDGESVLIGRKGTIDKPLYVNGPFWTVDTMFYTEIKKNND 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2574747319  83 lPRYLYYYLSRIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17288    83 -PKFLYYLLKTIDFKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDALIELQEKLL 149
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 5-152 1.14e-39

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: 130.98  E-value: 1.14e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   5 KLAQLAEIKYGKD--HKKLGKGSVPVYGTGGIMRYVNDFIYEGESVLIPRKGSLNNLFYVHGKFWTVDTIFWTKiDSKIV 82
Cdd:cd17267     2 KLGDVIELQYGKDlpKSRRIPGPYPVYGSNGIVGYHNEALVKGPGIVVGRKGSIGKVHYSEEDFWPIDTTLYVK-DFKGN 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  83 LPRYLYYYLSRIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNLVA 152
Cdd:cd17267    81 DPRFLYYLLKTLDLERLNSGSAVPGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEE 150
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-150 3.46e-31

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: 109.46  E-value: 3.46e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   4 YKLAQLAEIKYGK---DHKKLGKGSVPVYGTGGIMRYVNDFIYEGESVLIPRKGSL-NNLFYVHGKFWTVDTIFWTKIDS 79
Cdd:cd17266     1 VKLGELCKIKSGKsitASKISEEGDYPVYGGNGIIGYTDEYNHEGEYILIGRVGALcGNVHYVEGKFWVTDNALVVTPKK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2574747319  80 KIVLpRYLYYYLSRIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17266    81 ENNI-KFLYYLLKSLNLNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKL 150
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 23-152 2.27e-25

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: 94.81  E-value: 2.27e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  23 KGSVPVYGTGGIMRYVNDFIYEGESVLIP------RKGSLNNLFYVHGKFWT-----VdtifwtkIDSK-IVLPRYLYYY 90
Cdd:cd17262    29 QGNYPYYGASGIVDYVDDYIFDGEYVLIGedganlLSRGTPIAFYVSGKFWVnnhahV-------LKGKnGISTEFLYYY 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2574747319  91 LSRIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNLVA 152
Cdd:cd17262   102 LNSIDISPYVTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIE 163
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 1-150 2.90e-15

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: 68.54  E-value: 2.90e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   1 MTKYKLAQLAEIKYGKDHKK---LGKGSVPVYGTG-------GIMRYVNDFIYEGESVLIPRKGSLNNLFYVHGKFWTVD 70
Cdd:pfam01420   4 WEVFKLGDVFEIKKGKTPKKkelKNNGKYPYIRAGdlnnvvkGGLGYIKKYILPKGDITISSRATIGYVFYRDKPYYTNQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  71 TIFWTKIDSKIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQIND 148
Cdd:pfam01420  84 HIIVLIPKNNIKITEFLYLYLLLKlkKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDNTIELEKGILN 163


                  ..
gi 2574747319 149 NL 150
Cdd:pfam01420 164 EL 165
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 5-137 3.07e-15

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: 68.31  E-value: 3.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   5 KLAQLAEIKYGKD-HKK--LGKGSVPVYGtGGI--MRYVNDFIYEGESVLIP-RKGSLNNLFYVHGKFWTVDTiFWTKID 78
Cdd:cd17291     2 KLGEIAEIKKGKQiTKKelIENGKYPVIA-GGIepSGYHNEYNREGNTITISaSGASAGYVNYWKEPFWASDC-CYILSS 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2574747319  79 SKIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIE 137
Cdd:cd17291    80 KNELVNKFLYYFLKNKqeEIYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFT 140
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-150 5.70e-14

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: 65.24  E-value: 5.70e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   4 YKLAQLAEIKYG-----KDHKKLgKGSVPVYGT----GGIMRYVNDFIYEGESVLIPRKGS-LNNLFYVHGKFWTVDTIF 73
Cdd:cd17255     1 KKLGDLFEIGRGrviskKYISEN-PGDYPVYSSqtknNGIMGYINTYDFDGEYITWTTDGAnAGTVFYRNGKFSVTNVCG 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2574747319  74 WTKIDSKIVLPRYLYYYLSRIdLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17255    80 VLKVKNKNINNKFLYYALNLI-AKKYVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIAKLKKL 155
RMtype1_S_PluTORF4319P-TRD2-CR2_like cd17269
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-150 3.38e-13

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: 63.00  E-value: 3.38e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   4 YKLAQLAEIKYGKDHKKLGK--GSVPVYGTGGIMRYVNDFIYEGESVLIPRKGSLN-NLFYVHGKFWT-----VDTIFWT 75
Cdd:cd17269     1 KTLGEVAEIKTGKLDANAANenGKYPFFTCSKEPLRIDTYAFDEEAILIAGNGSGVgNVKYYNGKFNAyqrtyVIHPFKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  76 KIDskivlPRYLYYYLS----RIDLTSyNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKL-----------TAIENKI 140
Cdd:cd17269    81 EID-----PKFLYYYLKsyfkKYIEKN-SVGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILdkfdaltaelpAELEARK 154

                         170
                  ....*....|
gi 2574747319 141 KINEQINDNL 150
Cdd:cd17269   155 KQYEYYRDAL 164
RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like cd17289
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 48-150 6.13e-11

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: 6.13e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  48 VLIPRKGSLNNLFYV--HGKFWTVD-TIFWTKiDSKIVLPRYLYYYLS----RIDLTSYNVGSAVPSLTISLLNELVLDI 120
Cdd:cd17289    71 ILITSVGTIGIPYLVknDDPFYFKDgNLTWFK-NIKDINSKFLYYWFQssifKNQINSITIGSTQKALTIEKLKKTKIPL 149

                          90       100       110
                  ....*....|....*....|....*....|
gi 2574747319 121 PPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17289   150 PPLEEQKKIVSILSALDEKIDLNKKQLQKL 179
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-150 1.04e-10

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: 56.62  E-value: 1.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319   4 YKLAQLAEIKYGKDHKKLGK----GSVPVYGTGGIMR----------------YVNDFIYEGESVLIPRKGSLNNLFYVH 63
Cdd:cd16961     1 KKLGEIAEIISGKTPSSSSEywdnGIIPWIRISDINNggiiltdekiteegaeKLKKKILPKGDILISRSGTIGKVAIVK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  64 G--KFWTVDTIFWTKIDsKIVLPRYLYYYLSRIDLTSY---NVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIEN 138
Cdd:cd16961    81 EndKALLNQAVIVIRPK-DEVDSEFLYYFLKSPFGKKLiegSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDA 159

                         170
                  ....*....|..
gi 2574747319 139 KIKINEQINDNL 150
Cdd:cd16961   160 LIELLEQKLEKL 171
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 77-151 4.73e-10

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: 55.00  E-value: 4.73e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2574747319  77 IDSKIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNLV 151
Cdd:cd17498    86 IRMKNGNNSFLYYLLKNNikNLINKSSGTVFGSINKDDIENLEVDIPEDEEQKRIANILSKIDDKIEINNQINKNLE 162
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 79-150 2.19e-09

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: 53.21  E-value: 2.19e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2574747319  79 SKIVLPRYLYYYLS--RIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17515    96 NEEIDNEFLFYFLKsqKEYLISLGKGGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKLIEKLEKALEKL 169
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 48-150 2.32e-09

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: 53.30  E-value: 2.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  48 VLIPRKGSLNNLFYV--HGKFWTVDTIFWTKIDSKIVLPRYLYYYLS----RIDLTSYNVGSAVPSLTISLLNELVLDIP 121
Cdd:cd17246    68 ILFSIIGTIGRVAIVpeDLPANINQAVALIRPKKEKIDPKYLLYYLNspiiQKQIEKNAVGGTQKNLSLGDLKNLKIPLP 147

                          90       100
                  ....*....|....*....|....*....
gi 2574747319 122 PISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17246   148 PLEEQKRIAAILDSLDALIDKLEQKLEKL 176
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 76-150 2.41e-09

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: 53.25  E-value: 2.41e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2574747319  76 KIDSKIVLPRYLYYYL-SRI---DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17521    98 RPNKKKVLPKYLFYFTqSSLywkQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKL 176
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 77-150 1.01e-08

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: 51.35  E-value: 1.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  77 IDSKIVLPRYLYYYL------SRIDLTSYnvGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17256    96 RPKDSISPRYLYYYLrspfgqSQIESETK--GAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKL 173
RMtype1_S_MmaGORF2198P_TRD1-CR1_like cd17500
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 77-150 1.03e-08

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: 51.52  E-value: 1.03e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2574747319  77 IDSKIVLPRYLYYYL--SRIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17500    98 IDNKKADYRFVYYSLktQYEELVNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLDDKIELNNRQNETL 173
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 76-150 1.18e-08

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: 51.38  E-value: 1.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  76 KIDSKIVLPRYLYYYLSRIDLTSYNVGSA-----VPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17517   102 RLDKKKILPEFLYYYLNSPLGRKQIEKIAksaagQANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLEKL 181
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 80-150 1.74e-08

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: 50.57  E-value: 1.74e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2574747319  80 KIVLPRYLYYYLSRIDLTSYN--VGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17496    91 NGIDTEFLYYLLESNLDYLLAaaTGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKL 163
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 44-147 2.02e-08

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: 50.63  E-value: 2.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  44 EGESVLIPRKGSLnnLFYVHGKFWTVDTIFWTKIDS------------KIVLPRYLYYYLS--RIDLTSYNVGSAVPSLT 109
Cdd:cd17514    56 EDSSIRIVPKGTI--LIACTGQGYTRGQVAVLQIDAstnqaiaairckENVNPKYLYYYLKtqKNNLRNLTSGVAQKNLN 133

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2574747319 110 ISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQIN 147
Cdd:cd17514   134 IEMLRNLQIPLPPKEEQQKIVNILETLEFFEKDSLRKI 171
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 84-150 4.42e-08

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: 49.85  E-value: 4.42e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  84 PRYLYYYLS-RIDL--TSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17516   103 PDFVYYLLKnNSKYlkSIAGGSTATPIINKSTFSNIEIPLPPLPEQKKIAAILSSLDDKIENNRRINKTL 172
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 76-145 4.92e-08

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: 49.39  E-value: 4.92e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2574747319  76 KIDSKIVLPRYLYYYLSRIDLTSYN----VGSAVPSltiSLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQ 145
Cdd:cd17244    95 IPKDKKIDTEYLYYYLKSFDYSSLGstasKGKTLNS---KKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLET 165
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 81-141 5.21e-08

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: 49.56  E-value: 5.21e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2574747319  81 IVLPRYLYYYLSRIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIK 141
Cdd:cd17250   104 GIDSEYLYYWLKKVDLYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLD 164
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 77-150 6.90e-08

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: 49.43  E-value: 6.90e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2574747319  77 IDSKIVLPRYLYYYLSRIDLTSY----NVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17259   102 RPKDELNSDFLYYLLQSDFFLNYvepvLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKLEKL 179
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 77-150 8.63e-08

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: 49.02  E-value: 8.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  77 IDSKIVLPRYLYYYLSridlTSYNV------GSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17287    96 LPNDGINPDFLFYYLQ----SSYEElrdlsnGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAKIDALEQKLELL 171
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 80-150 9.63e-08

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


Pssm-ID: 341167 [Multi-domain]  Cd Length: 189  Bit Score: 49.05  E-value: 9.63e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2574747319  80 KIVLPRYLYYYLS----RIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17278   102 DKIDKEFLYYLLRsdsfRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKLEQKLEKL 176
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 77-150 1.01e-07

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: 48.64  E-value: 1.01e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2574747319  77 IDSKIVLPRYLYYYLSR--IDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17294   101 PDEEIANSRFLYYNLSSryEELRSLSGGGGRGGLNLKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLPAL 176
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
89-150 1.83e-07

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 46.21  E-value: 1.83e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2574747319  89 YYLS----RIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:COG0732     4 YYLRspsfREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKL 69
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 79-152 3.14e-07

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


Pssm-ID: 341149 [Multi-domain]  Cd Length: 165  Bit Score: 47.05  E-value: 3.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  79 SKIVLPRYLYYYLS----RIDLTSYNVGSA----VPSltiSLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17260    77 KEGILPEFLYYLLRspsfRKEAIKSMTGSSgrqrVPK---DFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETL 153


                  ..
gi 2574747319 151 VA 152
Cdd:cd17260   154 EE 155
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 77-145 3.29e-07

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: 47.47  E-value: 3.29e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2574747319  77 IDSKIVLPRYLYYYLSRIDLTSYNVGSAV-----PSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQ 145
Cdd:cd17253   103 PKDDLLLPEFLSYWLNSAYGRGYFLRAAKqttnlASINSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEA 176
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 71-150 3.75e-07

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: 47.11  E-value: 3.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  71 TIFWTKIDSKIVLPRYLYYYL---SRIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQIN 147
Cdd:cd17263    83 TLFKIIPDKNIIDKDYLYYFLkskEIQLNILTKAGSTIPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALIDKLKELI 162


                  ...
gi 2574747319 148 DNL 150
Cdd:cd17263   163 EKL 165
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 79-150 5.27e-07

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: 46.70  E-value: 5.27e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2574747319  79 SKIVLPRYLYYYLSRIDLTSYNVGSA---VPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17283    98 KKKLDKDFLYYLLSSITVQLQFSAQAgggTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKL 172
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 78-150 5.63e-07

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: 46.67  E-value: 5.63e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2574747319  78 DSKIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17282   100 NEEKIDVEFLEYYLRTLkkELEAIAPQSAQKNINLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIAKL 174
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 79-150 8.66e-07

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: 46.40  E-value: 8.66e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2574747319  79 SKIVLPRYLYYYLS----RIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17252   105 KKEIDPRYLFYFLQspsyREYIRSLASGTNINNLSNEHLENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQALEKL 180
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 79-147 1.67e-06

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: 45.22  E-value: 1.67e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2574747319  79 SKIVLPRYLYYYLS----RIDLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKI-KINEQIN 147
Cdd:cd17264    99 FAKVDVRYLYYYLNsplgKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIdKLKQALE 172
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 86-150 1.88e-06

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


Pssm-ID: 341132 [Multi-domain]  Cd Length: 182  Bit Score: 45.14  E-value: 1.88e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2574747319  86 YLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17243   106 FLYYLLKNLieELKQKAHGSVFDTITRKTFDEIKVPLPPEELQKSFENIVSPLFDKILNNLKENQTL 172
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 76-146 3.16e-06

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: 44.51  E-value: 3.16e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2574747319  76 KIDSKIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKI-KINEQI 146
Cdd:cd17296    94 KPKNKSINPKYLYYYLKSLyeKFLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKFEKLInKRQEGL 167
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 72-150 3.49e-06

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: 44.07  E-value: 3.49e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2574747319  72 IFWTKIDSKIVLPRYLYYYLSRIDLTSYNvGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17292    60 IVWLDNDESKVLNKFLYYFYQIIKWKKTE-GSTIKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKL 137
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 78-145 4.66e-06

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: 44.06  E-value: 4.66e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  78 DSKIVLPRYLYYYL-SRID-LTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQ 145
Cdd:cd17247   105 NEERVLPEYLHYYLeSQYDeLRRIGSGGGQGALNCGILKAFPIPLPPLDEQREIVAELEALLAKIDLLEE 174
RMtype1_S_HpyCR35ORFAP-TRD1-CR1_like cd17519
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 57-133 5.13e-06

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: 44.22  E-value: 5.13e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2574747319  57 NNLFYVHGKFWTVDtifwtkIDSKIVLPRYLYYYLSRIDLTSY-NVGSAVPSLTISLLNELVLDIPPISVQKDVVNKL 133
Cdd:cd17519    85 DQEFYLNQRVGKFI------PNEEILNNRYLYHFLLSKQNEKYiLAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSIL 156
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 82-150 8.72e-06

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: 43.21  E-value: 8.72e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2574747319  82 VLPRYLYYY--------LSRIDLTSYNVGSavpsLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17249   102 IDPEFLLYAlkanedriLSLVDKAGHGTGS----LDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKL 174
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 79-150 1.16e-05

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: 42.98  E-value: 1.16e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2574747319  79 SKIVLPRYLYYYLSRIDLTSYNV----GSAVP-SLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17512   109 KGILDQSFLFYNLKSERFKNYIEsiarGNANQaSITLGDIKKFKFLLPPLEEQKKIASILSAYDDLIENNEKRIKLL 185
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 76-150 3.06e-05

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: 41.75  E-value: 3.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  76 KIDSKIVLPRYLYYYLS----RIDLTSYnVGSAV--PSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDN 149
Cdd:cd17522   100 RPNKNIVDPKYLYYLLKsdrfRNQFRSI-AKKAVnqASINQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEK 178


                  .
gi 2574747319 150 L 150
Cdd:cd17522   179 L 179
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 77-150 5.33e-05

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: 41.35  E-value: 5.33e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2574747319  77 IDSKIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17513    95 IPIKEVNPLFLAYLLYSLlqKLKSQLQGTSIKGITKDDLKNLKIPLPPLEEQQKIAAILSKLDKLIEAHEKKLEKL 170
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 72-150 5.58e-05

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: 40.91  E-value: 5.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  72 IFwtKID-SKIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQIND 148
Cdd:cd17254    82 IF--KVVpDEEIDKDYLYYLLKALteEIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLK 159


                  ..
gi 2574747319 149 NL 150
Cdd:cd17254   160 KL 161
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 82-150 1.70e-04

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


Pssm-ID: 341162 [Multi-domain]  Cd Length: 186  Bit Score: 39.70  E-value: 1.70e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2574747319  82 VLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17273   104 IDNEFLYYLLKNNkpEIESLASGSTFKEISKSTFKKIEIPLPPLEEQKKIAAILSKLDELIELLEKENEKL 174
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 80-150 2.83e-04

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: 39.06  E-value: 2.83e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2574747319  80 KIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNL 150
Cdd:cd17245    90 KDIDNLFLYYYLKYNkpELEKLGTGSTFKAINKKDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKL 162
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 82-152 3.12e-04

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: 39.05  E-value: 3.12e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2574747319  82 VLPRYLYYYL--SRIDLTSYNVGSAVPslTISL--LNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDNLVA 152
Cdd:cd17248   107 LDPEYLLYVLraMKPEFERLAMGSTHK--TIYMpdFKALRIALPPLEEQRKIVDRLEALDAKIDALERKLERLIE 179
RMtype1_S_HpyAXIII_TRD1-CR1_like cd17281
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 71-141 3.56e-04

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: 39.11  E-value: 3.56e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2574747319  71 TIFWTKID-SKIVLPRYLYYYLSRID---LTSYNVGSaVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIK 141
Cdd:cd17281    95 TNFSLKKSyKNKLDIKFLFYYFFVLGewcKKNINIGG-FPSVDMNKLKKFKIPIPPLEEQEKIVEILDKFTKLTA 168
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 79-145 3.73e-04

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: 38.59  E-value: 3.73e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2574747319  79 SKIVLPRYLYYYLsridLTSYNV------GSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQ 145
Cdd:cd17293    95 NKSVDPKFLYYQL----LSSKFQlqaiasSTTLPIINKSKFEKIEIPLPPLEEQKRIVAKLDKLFALIDKLEE 163
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 70-150 8.64e-04

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: 37.90  E-value: 8.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  70 DTIFWTKIDSKIVLPRYLYYYLS----RIDLTSYNVGSA--VPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKI-KI 142
Cdd:cd17261    94 DKLIRLRVNEELLLPEYLALALNspsaRRQIESRATGTAgsMPKISQSDLKSLPIPLPPLAEQKRIVARVDELLALIdRL 173


                  ....*...
gi 2574747319 143 NEQINDNL 150
Cdd:cd17261   174 EAQLAAAL 181
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 82-147 1.68e-03

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: 36.80  E-value: 1.68e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2574747319  82 VLPRYLYYYLSRI-----DLTSYNVgsaVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKI-----KINEQIN 147
Cdd:cd17290   102 INPKFLFYWLSSSkeeleNLANGAT---LPILNQEKLKNIKLPVPPLNEQQKIVEFLDKKTAKIdaliaKKEQLIE 174
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 79-140 1.73e-03

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: 36.71  E-value: 1.73e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2574747319  79 SKIVLPRYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKI 140
Cdd:cd17285    96 KDELDPEYLLYWFLSIeeTIESLGTGTTVKGITLEDLKSLKIPLPPLEEQKRIVAILDELDELI 159
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 45-146 2.90e-03

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: 36.32  E-value: 2.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  45 GESVLIPRKgslnNLFYVHGKFWTVdtifwtkIDSKivLPRYLYYYLSRIDLTSY---NVGSAVPSLTISLLNELVLDIP 121
Cdd:cd17265    74 GKNALIDKE----AEGMTFGAFMTV-------FRSE--YNDYLFHLFNSDLFKKQigsFLTATINQITNGNLNNFKIPLP 140

                          90       100
                  ....*....|....*....|....*.
gi 2574747319 122 PISVQKDVVNKLTAIENKI-KINEQI 146
Cdd:cd17265   141 PLEEQEKIAEFLSSLDAKIdKLIKKI 166
RMtype1_S_Eco540ANI-TRD1-CR1_like cd17274
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 76-150 5.40e-03

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: 35.55  E-value: 5.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2574747319  76 KIDSKIVLPRYLYYYLSRIDLTS------YnvgsavpsltISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQINDN 149
Cdd:cd17274    88 TPKNNNVNLKFVYEALQTIKYVPgdhkrhW----------ISEYSKFKIPLPPLEEQNKIVRILDKFDELIAELEAKLEL 157


                  .
gi 2574747319 150 L 150
Cdd:cd17274   158 L 158
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 85-146 8.17e-03

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: 34.90  E-value: 8.17e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2574747319  85 RYLYYYLSRI--DLTSYNVGSAVPSLTISLLNELVLDIPPISVQKDVVNKLTAIENKIKINEQI 146
Cdd:cd17499    96 KYLFYFLLSNkdYFKGKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNN 159
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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