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Conserved domains on  [gi|2496434|sp|P75159|]
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RecName: Full=Putative type I specificity subunit S.MpnORF638P; Short=S protein; Short=S.MpnORF638P

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 16-177 1.10e-38

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: 135.72  E-value: 1.10e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   16 KTLGSLFELKKGEMLEKELLAPDGKYEYFNGGIKASGRTNEFNTFKNTISII-IGGSCGYVRLADKDYFCGQSSCTLTVL 94
Cdd:cd17291   1 KKLGEIAEIKKGKQITKKELIENGKYPVIAGGIEPSGYHNEYNREGNTITISaSGASAGYVNYWKEPFWASDCCYILSSK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   95 DplEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEvNRKLR 174
Cdd:cd17291  81 N--ELVNKFLYYFLKNKQEEIYSLQRGAGQPHIYKKDIEKLKIPIP-PLEEQQKIVEILDKFTELTAELPAELE-ARKKQ 156


                ...
gi 2496434  175 DEY 177
Cdd:cd17291 157 YEY 159
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 204-365 5.58e-23

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.


The actual alignment was detected with superfamily member cd17291:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 161  Bit Score: 94.11  E-value: 5.58e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  204 ISLGEVFHLKSGKYLKADERFEDGKFPYYGAGIESTSFVNEPNTKGDTLSMIANGYSIGNIRYHTIPWFNGTGGIAMEAL 283
Cdd:cd17291   1 KKLGEIAEIKKGKQITKKELIENGKYPVIAGGIEPSGYHNEYNREGNTITISASGASAGYVNYWKEPFWASDCCYILSSK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  284 KPNKTYvpFFYCALKYMQKDLKERFKRDESPFISLKLAGEIKVPfVKSFALQRKAGKIiylLDKtLEECKEEAKSLISIR 363
Cdd:cd17291  81 NELVNK--FLYYFLKNKQEEIYSLQRGAGQPHIYKKDIEKLKIP-IPPLEEQQKIVEI---LDK-FTELTAELPAELEAR 153


                ..
gi 2496434  364 DN 365
Cdd:cd17291 154 KK 155
 
Name Accession Description Interval E-value
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 16-177 1.10e-38

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: 135.72  E-value: 1.10e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   16 KTLGSLFELKKGEMLEKELLAPDGKYEYFNGGIKASGRTNEFNTFKNTISII-IGGSCGYVRLADKDYFCGQSSCTLTVL 94
Cdd:cd17291   1 KKLGEIAEIKKGKQITKKELIENGKYPVIAGGIEPSGYHNEYNREGNTITISaSGASAGYVNYWKEPFWASDCCYILSSK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   95 DplEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEvNRKLR 174
Cdd:cd17291  81 N--ELVNKFLYYFLKNKQEEIYSLQRGAGQPHIYKKDIEKLKIPIP-PLEEQQKIVEILDKFTELTAELPAELE-ARKKQ 156


                ...
gi 2496434  175 DEY 177
Cdd:cd17291 157 YEY 159
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 10-169 5.37e-31

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: 115.53  E-value: 5.37e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434     10 NSNWTKKTLGSLFELKKGEMLEKELLAPDGKYEYFNGGIKAS------GRTNEFNTFKNTISIIIGGSCGYVRLADKDYF 83
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELKNNGKYPYIRAGDLNNvvkgglGYIKKYILPKGDITISSRATIGYVFYRDKPYY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434     84 CGQSSCTLTVLDPLEIDlKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHL 163
Cdd:pfam01420  81 TNQHIIVLIPKNNIKIT-EFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLP-PLEEQKKIAKILSQLDNTIELE 158


                  ....*.
gi 2496434    164 NELIEV 169
Cdd:pfam01420 159 KGILNE 164
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 204-365 5.58e-23

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: 94.11  E-value: 5.58e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  204 ISLGEVFHLKSGKYLKADERFEDGKFPYYGAGIESTSFVNEPNTKGDTLSMIANGYSIGNIRYHTIPWFNGTGGIAMEAL 283
Cdd:cd17291   1 KKLGEIAEIKKGKQITKKELIENGKYPVIAGGIEPSGYHNEYNREGNTITISASGASAGYVNYWKEPFWASDCCYILSSK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  284 KPNKTYvpFFYCALKYMQKDLKERFKRDESPFISLKLAGEIKVPfVKSFALQRKAGKIiylLDKtLEECKEEAKSLISIR 363
Cdd:cd17291  81 NELVNK--FLYYFLKNKQEEIYSLQRGAGQPHIYKKDIEKLKIP-IPPLEEQQKIVEI---LDK-FTELTAELPAELEAR 153


                ..
gi 2496434  364 DN 365
Cdd:cd17291 154 KK 155
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
106-183 9.40e-11

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 57.76  E-value: 9.40e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  106 YALKSQE--EKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKLFT 183
Cdd:COG0732   4 YYLRSPSfrEYLRSLATGSTQPNLNKKDLKKLPIPLP-PLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFT 82
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 203-350 1.35e-08

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: 53.90  E-value: 1.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434    203 EISLGEVFHLKSGKYLKADERFEDGKFPYYGAGI------ESTSFVNEPNTKGDTLSMIANGySIGNIRYHTIPWFNGTG 276
Cdd:pfam01420   6 VFKLGDVFEIKKGKTPKKKELKNNGKYPYIRAGDlnnvvkGGLGYIKKYILPKGDITISSRA-TIGYVFYRDKPYYTNQH 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2496434    277 GIAMEaLKPNKTYVPFFYCALKYMQKDLKERFKRDESPFISLKLAGEIKVPFVKSFAlQRKAGKIIYLLDKTLE 350
Cdd:pfam01420  85 IIVLI-PKNNIKITEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEE-QKKIAKILSQLDNTIE 156
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
61-199 1.85e-06

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 49.50  E-value: 1.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434    61 KNTISIIIGGSCGYVRLADKDYfcgQSSCTLTV-LDPLEIDLKFAYYALK------SQEEKITSLASGTTIKNIRLSDLK 133
Cdd:PRK09737  76 DRDIVISSAGSIGFSFLAQNPL---PSNVVFASfAIRLKPVNYFSEYFLKhflessDYRNQLSLMSAGNAVQNINAQSLS 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   134 DLPIPLVkSIQDQRTIAHALSVF-------DLRIEHLNELIE----------VNRKLRDEYAhklftlDPDFLTHWNLHE 196
Cdd:PRK09737 153 TLTFPIP-PIAEQKIIAEKLDTLlaqvdstKARLEQIPQILKrfrqavlgaaVSGKLTEEWR------WPDLPSTWSVHK 225


                 ...
gi 2496434   197 LHE 199
Cdd:PRK09737 226 YSE 228
 
Name Accession Description Interval E-value
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 16-177 1.10e-38

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: 135.72  E-value: 1.10e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   16 KTLGSLFELKKGEMLEKELLAPDGKYEYFNGGIKASGRTNEFNTFKNTISII-IGGSCGYVRLADKDYFCGQSSCTLTVL 94
Cdd:cd17291   1 KKLGEIAEIKKGKQITKKELIENGKYPVIAGGIEPSGYHNEYNREGNTITISaSGASAGYVNYWKEPFWASDCCYILSSK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   95 DplEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEvNRKLR 174
Cdd:cd17291  81 N--ELVNKFLYYFLKNKQEEIYSLQRGAGQPHIYKKDIEKLKIPIP-PLEEQQKIVEILDKFTELTAELPAELE-ARKKQ 156


                ...
gi 2496434  175 DEY 177
Cdd:cd17291 157 YEY 159
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 10-169 5.37e-31

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: 115.53  E-value: 5.37e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434     10 NSNWTKKTLGSLFELKKGEMLEKELLAPDGKYEYFNGGIKAS------GRTNEFNTFKNTISIIIGGSCGYVRLADKDYF 83
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELKNNGKYPYIRAGDLNNvvkgglGYIKKYILPKGDITISSRATIGYVFYRDKPYY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434     84 CGQSSCTLTVLDPLEIDlKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHL 163
Cdd:pfam01420  81 TNQHIIVLIPKNNIKIT-EFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLP-PLEEQKKIAKILSQLDNTIELE 158


                  ....*.
gi 2496434    164 NELIEV 169
Cdd:pfam01420 159 KGILNE 164
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 204-365 5.58e-23

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: 94.11  E-value: 5.58e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  204 ISLGEVFHLKSGKYLKADERFEDGKFPYYGAGIESTSFVNEPNTKGDTLSMIANGYSIGNIRYHTIPWFNGTGGIAMEAL 283
Cdd:cd17291   1 KKLGEIAEIKKGKQITKKELIENGKYPVIAGGIEPSGYHNEYNREGNTITISASGASAGYVNYWKEPFWASDCCYILSSK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  284 KPNKTYvpFFYCALKYMQKDLKERFKRDESPFISLKLAGEIKVPfVKSFALQRKAGKIiylLDKtLEECKEEAKSLISIR 363
Cdd:cd17291  81 NELVNK--FLYYFLKNKQEEIYSLQRGAGQPHIYKKDIEKLKIP-IPPLEEQQKIVEI---LDK-FTELTAELPAELEAR 153


                ..
gi 2496434  364 DN 365
Cdd:cd17291 154 KK 155
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 16-177 3.22e-17

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: 77.87  E-value: 3.22e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   16 KTLGSLFELKKGEMLEKELLAPDGKYEYF--NGGIkasGRTNEFNTFKNTisIIIG--GS-CGYVRLADKDYFcgqssct 90
Cdd:cd17266   1 VKLGELCKIKSGKSITASKISEEGDYPVYggNGII---GYTDEYNHEGEY--ILIGrvGAlCGNVHYVEGKFW------- 68

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   91 LT----VLDPL-EIDLKFAYYALKSQeeKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNE 165
Cdd:cd17266  69 VTdnalVVTPKkENNIKFLYYLLKSL--NLNQYATGSAQPLITVSKLKKLKIPLP-PLEEQKKIAAILDSLDAKIDLLEK 145

                       170
                ....*....|..
gi 2496434  166 LIEVNRKLRDEY 177
Cdd:cd17266 146 KLEKLIELKKEL 157
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 16-177 3.24e-17

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: 78.58  E-value: 3.24e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   16 KTLGSLFELKKGEmlekellAPDGKYEYFNGGI-----------------------KASGRTNEFNTFKNTISIIIGGSC 72
Cdd:cd16961   1 KKLGEIAEIISGK-------TPSSSSEYWDNGIipwirisdinnggiiltdekiteEGAEKLKKKILPKGDILISRSGTI 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   73 GYVRLADK--DYFCGQSSCTLTVLDplEIDLKFAYYALKSQE-EKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTI 149
Cdd:cd16961  74 GKVAIVKEndKALLNQAVIVIRPKD--EVDSEFLYYFLKSPFgKKLIEGSAGSTQPNLNKSDLKNLKIPLP-PLEEQKKI 150

                       170       180
                ....*....|....*....|....*...
gi 2496434  150 AHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd16961 151 ANILDKLDALIELLEQKLEKLEQLKQAL 178
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-182 2.85e-14

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: 70.23  E-value: 2.85e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17285  98 ELDPEYLLYWFLSIEETIESLGTGTTVKGITLEDLKSLKIPLP-PLEEQKRIVAILDELDELIDKLEAKLEKLKQLKKGL 176


                ....*
gi 2496434  178 AHKLF 182
Cdd:cd17285 177 MQSLL 181
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-182 2.93e-14

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: 70.26  E-value: 2.93e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17245  91 DIDNLFLYYYLKYNKPELEKLGTGSTFKAINKKDLEELKIPLP-PLEEQQKIAEILSTVDEAIEKTKALIEKLDELKKGL 169


                ....*
gi 2496434  178 AHKLF 182
Cdd:cd17245 170 MQELF 174
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 61-182 8.16e-14

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


Pssm-ID: 341164 [Multi-domain]  Cd Length: 186  Bit Score: 69.11  E-value: 8.16e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   61 KNTISIIIGGSCGYVRLADKDYFCGQSSCTLTVLDPLeIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLv 140
Cdd:cd17275  67 KGTILYAMYASVGKVAINKIDVATNQAILGIIPKDEK-LDFEFLYYWLLSLKNELKRLIRTGTQANLNAEIVKNLPIPL- 144

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 2496434  141 KSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKLF 182
Cdd:cd17275 145 PPLEEQKKIAEILDKIDAEIDKLEEKIEKLRELKKGLLQKMF 186
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 16-180 2.07e-13

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: 67.43  E-value: 2.07e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   16 KTLGSLFELKKGEMLEKELlAPDGKYE-YFNGGIkaSGRTNEFNTFKNTIsiIIG--GSCGYVRLADKDYFCgqSSCTLT 92
Cdd:cd17267   1 VKLGDVIELQYGKDLPKSR-RIPGPYPvYGSNGI--VGYHNEALVKGPGI--VVGrkGSIGKVHYSEEDFWP--IDTTLY 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   93 VLDPLEIDLKFAYYALKSQeeKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRK 172
Cdd:cd17267  74 VKDFKGNDPRFLYYLLKTL--DLERLNSGSAVPGLNRNDVYSLKVPLP-PLEEQKAIAAILDALDDKIELNRRQNQTLEE 150


                ....*...
gi 2496434  173 LRDEYAHK 180
Cdd:cd17267 151 LADALLPK 158
RMtype1_S_MmaGORF2198P_TRD1-CR1_like cd17500
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 61-169 2.42e-13

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: 67.70  E-value: 2.42e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   61 KNTISIII---GGSCGYVRLADKDYFCGQSSCTLtVLDPLEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPI 137
Cdd:cd17500  63 ENTVIIAMygaGKTAGRVAINKIPLTTNQACCNL-IIDNKKADYRFVYYSLKTQYEELVNLASGAAQQNLNSKLIKNFEI 141

                        90       100       110
                ....*....|....*....|....*....|..
gi 2496434  138 PLvKSIQDQRTIAHALSVFDLRIEHLNELIEV 169
Cdd:cd17500 142 PL-PPLPEQKRIASILSSLDDKIELNNRQNET 172
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 66-182 1.66e-12

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: 65.21  E-value: 1.66e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   66 III---GGSCGYVRLADKDYFCGQSSCTLTVLDplEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkS 142
Cdd:cd17496  59 ILFcvrGSTTGRLNIADDEYCIGRGVAAIRPKN--GIDTEFLYYLLESNLDYLLAAATGSTFPNISRDDLLNLKIPLP-P 135

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 2496434  143 IQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKLF 182
Cdd:cd17496 136 LEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTLLPKLL 175
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 61-182 3.20e-12

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: 64.46  E-value: 3.20e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   61 KNTISIIIGGSCGYVRLADKDYFCGQSSCTLTVLDplEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLV 140
Cdd:cd17513  64 ANSILIVTRVGVGKVAINPFDICTSQDFTSLIPIK--EVNPLFLAYLLYSLLQKLKSQLQGTSIKGITKDDLKNLKIPLP 141

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 2496434  141 kSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKLF 182
Cdd:cd17513 142 -PLEEQQKIAAILSKLDKLIEAHEKKLEKLKQLKKGLMQKLF 182
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-182 3.52e-12

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


Pssm-ID: 341162 [Multi-domain]  Cd Length: 186  Bit Score: 64.35  E-value: 3.52e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17273 103 EIDNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEIPLP-PLEEQKKIAAILSKLDELIELLEKENEKLKELRDGL 181


                ....*
gi 2496434  178 AHKLF 182
Cdd:cd17273 182 LPKLF 186
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-183 4.59e-12

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: 64.47  E-value: 4.59e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17248 106 ELDPEYLLYVLRAMKPEFERLAMGSTHKTIYMPDFKALRIAL-PPLEEQRKIVDRLEALDAKIDALERKLERLIELLKEL 184


                ....*.
gi 2496434  178 AHKLFT 183
Cdd:cd17248 185 RQALLT 190
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 95-182 6.29e-12

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: 63.62  E-value: 6.29e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   95 DPLEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPlVKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLR 174
Cdd:cd17282 100 NEEKIDVEFLEYYLRTLKKELEAIAPQSAQKNINLEILRPLKIP-VPPLEEQKKIVEILDALDDLIDNLEKRIAKLEELK 178


                ....*...
gi 2496434  175 DEYAHKLF 182
Cdd:cd17282 179 QSLLQEAF 186
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-182 7.36e-12

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: 63.61  E-value: 7.36e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17515  98 EIDNEFLFYFLKSQKEYLISLGKGGAQPNISQGIIKNIEIPLP-PLAEQKRIVAKLDKLDKLIEKLEKALEKLEELKKAL 176


                ....*
gi 2496434  178 AHKLF 182
Cdd:cd17515 177 MQKLL 181
RMtype1_S_PluTORF4319P-TRD2-CR2_like cd17269
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 16-183 2.93e-11

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: 61.45  E-value: 2.93e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   16 KTLGSLFELKKGEmLEKELLAPDGKYEYFNGGiKASGRTNEFnTFkNTISIII---GGSCGYVRladkdYFCG-----QS 87
Cdd:cd17269   1 KTLGEVAEIKTGK-LDANAANENGKYPFFTCS-KEPLRIDTY-AF-DEEAILIagnGSGVGNVK-----YYNGkfnayQR 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   88 SCTLTVLDPlEIDLKFAYYALKSQEEKITSLAS-GTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNEL 166
Cdd:cd17269  72 TYVIHPFKE-EIDPKFLYYYLKSYFKKYIEKNSvGSSVPYIRLPMLENFKIPLP-PLEEQKRIVRILDKFDALTAELPAE 149

                       170
                ....*....|....*..
gi 2496434  167 IEVNRKLRDEYAHKLFT 183
Cdd:cd17269 150 LEARKKQYEYYRDALLS 166
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 206-367 5.55e-11

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: 60.54  E-value: 5.55e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  206 LGEVFHLKSGKYLKADERFEDGKFPYYGA-GIesTSFVNEPNTKGDTLSMIANGYSIGNIRYHTIP-WFNGTggiAMeAL 283
Cdd:cd17266   3 LGELCKIKSGKSITASKISEEGDYPVYGGnGI--IGYTDEYNHEGEYILIGRVGALCGNVHYVEGKfWVTDN---AL-VV 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  284 KPNKTY-VPFFYCALKYMqkDLKerfKRDES---PFISLKLAGEIKVPFVkSFALQRKAGKIIYLLDKTLEECKEEAKSL 359
Cdd:cd17266  77 TPKKENnIKFLYYLLKSL--NLN---QYATGsaqPLITVSKLKKLKIPLP-PLEEQKKIAAILDSLDAKIDLLEKKLEKL 150


                ....*...
gi 2496434  360 ISIRDNLL 367
Cdd:cd17266 151 IELKKELM 158
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
106-183 9.40e-11

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 57.76  E-value: 9.40e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  106 YALKSQE--EKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKLFT 183
Cdd:COG0732   4 YYLRSPSfrEYLRSLATGSTQPNLNKKDLKKLPIPLP-PLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFT 82
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-181 1.45e-10

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: 59.77  E-value: 1.45e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSL--ASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRD 175
Cdd:cd17249 101 GIDPEFLLYALKANEDRILSLvdKAGHGTGSLDTDDLKNLPIPLP-PLEEQRRIAAILDALDALIDLLERKLAKLEELLK 179


                ....*.
gi 2496434  176 EYAHKL 181
Cdd:cd17249 180 ALMQAL 185
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 70-177 1.49e-10

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: 59.88  E-value: 1.49e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   70 GSCGYVRlADKDY----FCGqssctltVLDPL-EIDLKFAYYALKSQE--EKITSLASGTTIKNIRLSDLKDLPIPLVkS 142
Cdd:cd17252  82 GKAAFID-EDTDYtfgaFCG-------VIRPKkEIDPRYLFYFLQSPSyrEYIRSLASGTNINNLSNEHLENLKIPLP-P 152

                        90       100       110
                ....*....|....*....|....*....|....*
gi 2496434  143 IQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17252 153 LAEQKRIVAKLDKLDALIDKLKQALEKLDELLKSL 187
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 65-175 1.72e-10

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


Pssm-ID: 341168 [Multi-domain]  Cd Length: 184  Bit Score: 59.50  E-value: 1.72e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   65 SIIIggSC----GYVRLADKDYFCGQSSCTLTVLDPleIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLv 140
Cdd:cd17279  67 SIIL--STrapiGYVAIATVELCTNQGCKALVPNSD--VDSRFLYYLLLAAKEELNSLGRGTTFLELSTDELANFKIPL- 141

                        90       100       110
                ....*....|....*....|....*....|....*
gi 2496434  141 KSIQDQRTIAHALsvfDLRIEHLNELIEVNRKLRD 175
Cdd:cd17279 142 PPLSEQRAIADFL---DRETAKIDALIAKKQQLIE 173
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 64-183 1.92e-10

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


Pssm-ID: 341135 [Multi-domain]  Cd Length: 189  Bit Score: 59.46  E-value: 1.92e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   64 ISIIigGSCGYVRLADKDY-FCGQSSCTLTVLDPLEIDLKFAYYALKSQ--EEKITSLASGTTIKNIRLSDLKDLPIPLV 140
Cdd:cd17246  70 FSII--GTIGRVAIVPEDLpANINQAVALIRPKKEKIDPKYLLYYLNSPiiQKQIEKNAVGGTQKNLSLGDLKNLKIPLP 147

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 2496434  141 kSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKLFT 183
Cdd:cd17246 148 -PLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLLT 189
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 61-174 2.30e-10

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: 59.14  E-value: 2.30e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   61 KNTISII-IGGSCGYVRLADKDYFCGQSsctLTVLDPLE-IDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIP 138
Cdd:cd17290  65 KNSVLVVgIGATIGKVGYSDKESSSNQQ---ITGIIFNKdINPKFLFYWLSSSKEELENLANGATLPILNQEKLKNIKLP 141

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 2496434  139 LVkSIQDQRTIAHAL----SVFDLRIEHLNELIEVNRKLR 174
Cdd:cd17290 142 VP-PLNEQQKIVEFLdkktAKIDALIAKKEQLIELLKEYR 180
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 73-177 2.94e-10

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


Pssm-ID: 341188 [Multi-domain]  Cd Length: 174  Bit Score: 58.72  E-value: 2.94e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   73 GYVRLADKDYFCGQSSCTLTVLDplEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHA 152
Cdd:cd17497  68 GPTNIADQEYCIGRGLAAIRPKK--GLDKKYLLYYLKSIENELSSLGTGSTFKAISKEDLENLLIPLP-PLAEQKRIAAF 144

                        90       100
                ....*....|....*....|....*
gi 2496434  153 LSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17497 145 LDELTAKIDQLIALLEKAIELLKEY 169
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-182 5.36e-10

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: 57.85  E-value: 5.36e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17254  90 EIDKDYLYYLLKALTEEIESQAHGSTMVHITKGDLENIKVPL-PPLEEQKRIAAILDELDALIDALEEQLKKLEELRKAL 168


                ....*
gi 2496434  178 AHKLF 182
Cdd:cd17254 169 LQSLL 173
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 61-175 7.93e-10

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: 57.61  E-value: 7.93e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   61 KNTISIIIGGSCGYVRLADKDYFCGQSSCTLTVLDpLEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLV 140
Cdd:cd17296  63 KGTILIAIFATIGKVGILKIEATTNQAIAGIKPKN-KSINPKYLYYYLKSLYEKFLSLGRGVAQNNINLSILKNLKIPLP 141

                        90       100       110
                ....*....|....*....|....*....|....*
gi 2496434  141 kSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRD 175
Cdd:cd17296 142 -PLEEQQRIVAILDKFEKLINKRQEGLQLLDELVK 175
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 99-183 1.17e-09

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: 57.11  E-value: 1.17e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   99 IDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPlVKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYA 178
Cdd:cd17287 101 INPDFLFYYLQSSYEELRDLSNGGGQPNLNAGLIKSIEIP-VPPLDEQQKIAAFLSAIDAKIDALEQKLELLQELKKSLM 179


                ....*
gi 2496434  179 HKLFT 183
Cdd:cd17287 180 QQLFT 184
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 70-181 2.95e-09

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: 56.01  E-value: 2.95e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   70 GSCGYVRLADKDY------FCGQssctltvLDPLEIDLKFAYYALKSQE--EKITSLASGT--TIKNIRLSDLKDLPIPL 139
Cdd:cd17261  78 GRAALVDGDPDNLiypdklIRLR-------VNEELLLPEYLALALNSPSarRQIESRATGTagSMPKISQSDLKSLPIPL 150

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 2496434  140 VkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKL 181
Cdd:cd17261 151 P-PLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 84-176 3.14e-09

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: 55.96  E-value: 3.14e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   84 CGQSSCTLTVlDPLEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHL 163
Cdd:cd17294  92 TNQSLAAIEP-DEEIANSRFLYYNLSSRYEELRSLSGGGGRGGLNLKIIKSLPIPL-PPLEEQKKIVAILDKFDALINDL 169

                        90
                ....*....|...
gi 2496434  164 NELIEVNRKLRDE 176
Cdd:cd17294 170 KEGLPALLELRQK 182
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 57-173 4.59e-09

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: 55.25  E-value: 4.59e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   57 FNTFKNTI----SII---IGGSCGYVRLADKDYFCGQSSCTLTVlDPLEIDLKFAYYALKSQEEKITSLASG-TTIKNIR 128
Cdd:cd17516  53 LEKVKNKLipanSICvtcIGSDMGKVAITKEPSVTNQQINSIIV-NKNKFDPDFVYYLLKNNSKYLKSIAGGsTATPIIN 131

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 2496434  129 LSDLKDLPIPLVkSIQDQRTIAHALSVFDlriehlnELIEVNRKL 173
Cdd:cd17516 132 KSTFSNIEIPLP-PLPEQKKIAAILSSLD-------DKIENNRRI 168
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 203-350 1.35e-08

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: 53.90  E-value: 1.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434    203 EISLGEVFHLKSGKYLKADERFEDGKFPYYGAGI------ESTSFVNEPNTKGDTLSMIANGySIGNIRYHTIPWFNGTG 276
Cdd:pfam01420   6 VFKLGDVFEIKKGKTPKKKELKNNGKYPYIRAGDlnnvvkGGLGYIKKYILPKGDITISSRA-TIGYVFYRDKPYYTNQH 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2496434    277 GIAMEaLKPNKTYVPFFYCALKYMQKDLKERFKRDESPFISLKLAGEIKVPFVKSFAlQRKAGKIIYLLDKTLE 350
Cdd:pfam01420  85 IIVLI-PKNNIKITEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEE-QKKIAKILSQLDNTIE 156
RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like cd17280
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter ...
 84-168 1.37e-08

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


Pssm-ID: 341169 [Multi-domain]  Cd Length: 187  Bit Score: 54.09  E-value: 1.37e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   84 CGQSSCTLTvlDPLEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPlVKSIQDQRTIA----HALSVFDLR 159
Cdd:cd17280  88 TNQACCVLS--GSNKIDIKFLFYWLLANRDELISLASGGGQPNISQELIKSLRIP-VPPLEEQKQIAafldKKTAKIDSL 164


                ....*....
gi 2496434  160 IEHLNELIE 168
Cdd:cd17280 165 IEKKERLIE 173
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-183 1.62e-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: 54.05  E-value: 1.62e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQE--EKITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRD 175
Cdd:cd17278 103 KIDKEFLYYLLRSDSfrNQIKSSATGTAQPNISPKDIESIKIPL-PPLEEQKKIAEILDSLDAKIDKLEQKLEKLRDLLK 181


                ....*...
gi 2496434  176 EYAHKLFT 183
Cdd:cd17278 182 PLLQSLFT 189
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 24-179 2.48e-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: 53.27  E-value: 2.48e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   24 LKKGEMLEKEllapDGKYEYF------NGGIKASG--RTNE--FNTFKNT------ISIIIGGSCGYVRLADKDY---FC 84
Cdd:cd17256  13 LPKGESLSDG----PTGVPYIrvtdikNGGIDLDNlkYISPeiHEKIKRYtlskgdILISIVGTIGRVGIVPKELdgaNL 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   85 GQSSCTLTVLDplEIDLKFAYYALKSQ--EEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEH 162
Cdd:cd17256  89 TENAARIRPKD--SISPRYLYYYLRSPfgQSQIESETKGAAQPKLNLKRIRELPIPLP-PLEEQKRIVAILDSLDAKIDA 165

                       170
                ....*....|....*..
gi 2496434  163 LNELIEVNRKLRDEYAH 179
Cdd:cd17256 166 LEKQLAKLEELKKALMQ 182
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 99-182 6.69e-08

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


Pssm-ID: 341173 [Multi-domain]  Cd Length: 185  Bit Score: 52.21  E-value: 6.69e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   99 IDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYA 178
Cdd:cd17284 103 INPEYLMYLLSLQKKYMEKIATGTTIPYLNKTNCESIPIPLP-PIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLM 181


                ....
gi 2496434  179 HKLF 182
Cdd:cd17284 182 QQLF 185
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-181 9.01e-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; 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: 51.76  E-value: 9.01e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17247 108 RVLPEYLHYYLESQYDELRRIGSGGGQGALNCGILKAFPIPL-PPLDEQREIVAELEALLAKIDLLEEKIARLIELLKEL 186


                ....
gi 2496434  178 AHKL 181
Cdd:cd17247 187 RQAL 190
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 94-181 1.07e-07

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: 1.07e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   94 LDPLEIDLKFAYYALKSQEEK--ITSLASGTTIK-NIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVN 170
Cdd:cd17517 103 LDKKKILPEFLYYYLNSPLGRkqIEKIAKSAAGQaNINQKDLKKLPIPLP-PLEEQKEIVEILESLDSKIDLLEKKLEKL 181

                        90
                ....*....|.
gi 2496434  171 RKLRDEYAHKL 181
Cdd:cd17517 182 EQLFKSLMQSL 192
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 91-182 1.72e-07

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: 50.76  E-value: 1.72e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   91 LTVLDPLEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPlVKSIQDQRTIAHALSVFDLRIEHLNELIEVN 170
Cdd:cd17498  83 LCSIRMKNGNNSFLYYLLKNNIKNLINKSSGTVFGSINKDDIENLEVD-IPEDEEQKRIANILSKIDDKIEINNQINKNL 161

                        90
                ....*....|..
gi 2496434  171 RKLRDEYAHKLF 182
Cdd:cd17498 162 EELAQAIFKHWF 173
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 99-182 2.07e-07

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: 50.71  E-value: 2.07e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   99 IDLKFAYYALKSQEekITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYA 178
Cdd:cd17250 105 IDSEYLYYWLKKVD--LYKYSQATTVPSIRKSTLESIPIPL-PPLEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGLR 181


                ....
gi 2496434  179 HKLF 182
Cdd:cd17250 182 QSLL 185
RMtype1_S_Sba223ORF3470P-TRD1-CR1_like cd17270
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 61-181 2.88e-07

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


Pssm-ID: 341159 [Multi-domain]  Cd Length: 183  Bit Score: 50.01  E-value: 2.88e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   61 KNTISIIIGGSCGYVRLADKDYFCGQsscTLTVLDPL--EIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIP 138
Cdd:cd17270  65 KGTVIVTLQGSIGRVAITQYDAYVDR---TLLIFESYkiNINKKFFAYQLKLKFEIEKEKAPGGTIKTITKEELSKFEIP 141

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 2496434  139 LvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKL 181
Cdd:cd17270 142 I-PSLEEQKEIVNILDKFDELITELQLRKKQLEYYKKALLSFM 183
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 90-182 3.15e-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: 49.81  E-value: 3.15e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   90 TLTVLDPLE--IDLKFAYYALKSQEEKITSLA-SGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNEL 166
Cdd:cd17263  83 TLFKIIPDKniIDKDYLYYFLKSKEIQLNILTkAGSTIPHVNKKDLENLKIPL-PSLEEQKKIAEILDKLDALIDKLKEL 161

                        90
                ....*....|....*.
gi 2496434  167 IEVNRKLRDEYAHKLF 182
Cdd:cd17263 162 IEKLIELKKGLFQELL 177
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 16-181 4.17e-07

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: 49.45  E-value: 4.17e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   16 KTLGSLFELKKGE-MLEKELLAPDGKYE-Y----FNGGIKasGRTNEFNTFKNTISIIIGGSC-GYVRLADKDYFCGQSS 88
Cdd:cd17255   1 KKLGDLFEIGRGRvISKKYISENPGDYPvYssqtKNNGIM--GYINTYDFDGEYITWTTDGANaGTVFYRNGKFSVTNVC 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   89 CTLTVLDPlEIDLKFAYYALKSQEEKitSLASGTTIKnIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIE 168
Cdd:cd17255  79 GVLKVKNK-NINNKFLYYALNLIAKK--YVSFDGNPK-LMNNVMAKIKIPLP-PLEEQEKIANILDKLDELINLLIAKLK 153

                       170
                ....*....|...
gi 2496434  169 VNRKLRDEYAHKL 181
Cdd:cd17255 154 KLIELRKKQLEYY 166
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 94-182 4.98e-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: 49.78  E-value: 4.98e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   94 LDPLEIDLKFAYYALKSQEEK--ITSLASGTT-IKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVN 170
Cdd:cd17253 103 PKDDLLLPEFLSYWLNSAYGRgyFLRAAKQTTnLASINSTKLKALPVPLP-PLEEQRRIVERLDELLALIDALEASLAKL 181

                        90
                ....*....|..
gi 2496434  171 RKLRDEYAHKLF 182
Cdd:cd17253 182 EELLKALRQALL 193
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 95-182 1.22e-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: 47.54  E-value: 1.22e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   95 DPLEIDLKFAYYALKSQEEKITSlasGTTIKNIRLSDLKDLPIPlVKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLR 174
Cdd:cd17292  66 DESKVLNKFLYYFYQIIKWKKTE---GSTIKRLYNDNLLNTKIP-VPSLDEQRKIAEFLSLLDALIALLQKKLEKLIALK 141


                ....*...
gi 2496434  175 DEYAHKLF 182
Cdd:cd17292 142 KGLMQYLF 149
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
61-199 1.85e-06

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 49.50  E-value: 1.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434    61 KNTISIIIGGSCGYVRLADKDYfcgQSSCTLTV-LDPLEIDLKFAYYALK------SQEEKITSLASGTTIKNIRLSDLK 133
Cdd:PRK09737  76 DRDIVISSAGSIGFSFLAQNPL---PSNVVFASfAIRLKPVNYFSEYFLKhflessDYRNQLSLMSAGNAVQNINAQSLS 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   134 DLPIPLVkSIQDQRTIAHALSVF-------DLRIEHLNELIE----------VNRKLRDEYAhklftlDPDFLTHWNLHE 196
Cdd:PRK09737 153 TLTFPIP-PIAEQKIIAEKLDTLlaqvdstKARLEQIPQILKrfrqavlgaaVSGKLTEEWR------WPDLPSTWSVHK 225


                 ...
gi 2496434   197 LHE 199
Cdd:PRK09737 226 YSE 228
RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like cd17289
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 99-176 2.54e-06

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: 47.64  E-value: 2.54e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   99 IDLKFAYYALKSQEEK--ITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDE 176
Cdd:cd17289 107 INSKFLYYWFQSSIFKnqINSITIGSTQKALTIEKLKKTKIPL-PPLEEQKKIVSILSALDEKIDLNKKQLQKLEELAKT 185
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-175 3.56e-06

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: 47.12  E-value: 3.56e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQE--EKITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRD 175
Cdd:cd17259 106 ELNSDFLYYLLQSDFflNYVEPVLTGTDVPHISTKQIKNFKIPL-PPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKK 184
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 68-182 5.91e-06

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: 46.30  E-value: 5.91e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   68 IGGSCGYVRLADKDYFCGQSSCTLTVLDplEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQR 147
Cdd:cd17293  69 IGGSIGKVGIADREVAFNQQINAIIPNK--SVDPKFLYYQLLSSKFQLQAIASSTTLPIINKSKFEKIEIPLP-PLEEQK 145

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 2496434  148 TIAH----ALSVFDLRIEHLNELIEvnrkLRDEYAHKLF 182
Cdd:cd17293 146 RIVAkldkLFALIDKLEESLEELDE----LLKSLFQSAF 180
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 103-182 9.96e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) TRD2-CR2 and Lactobacillus amylovorus GRL 1112 S subunit (S1.L; The recognition sequences of Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) and Lactobacillus amylovorus GRL 1112 S subunit (S1.LamGRLORF5415P) 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: 341185 [Multi-domain]  Cd Length: 171  Bit Score: 45.59  E-value: 9.96e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  103 FAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVKSIQDQRtIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKLF 182
Cdd:cd17494  93 FLYLYLLNIEGYWSKISQGSTFESINSNDIKNLKISIPSLEEQQK-IATFLSTLDAEITLLEKKLEKLKQLKKGLLQKLF 171
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-366 1.20e-05

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: 45.45  E-value: 1.20e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  205 SLGEVFHLKSGKYLKADERF-EDGKFPYYGAGIESTSFVNEPNT----------------KGDTL-SMIAngySIGNIRY 266
Cdd:cd16961   2 KLGEIAEIISGKTPSSSSEYwDNGIIPWIRISDINNGGIILTDEkiteegaeklkkkilpKGDILiSRSG---TIGKVAI 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  267 HTI--PWFNGTGGIAmeaLKPNKTYVP-FFYCALKYM-QKDLKERFKRDESPFISLKLAGEIKVPFVkSFALQRKAGKII 342
Cdd:cd16961  79 VKEndKALLNQAVIV---IRPKDEVDSeFLYYFLKSPfGKKLIEGSAGSTQPNLNKSDLKNLKIPLP-PLEEQKKIANIL 154

                       170       180
                ....*....|....*....|....
gi 2496434  343 YLLDKTLEECKEEAKSLISIRDNL 366
Cdd:cd16961 155 DKLDALIELLEQKLEKLEQLKQAL 178
RMtype1_S_HpyCR35ORFAP-TRD1-CR1_like cd17519
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 95-177 1.52e-05

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: 44.99  E-value: 1.52e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   95 DPLEIDLKFAYYALKSQEEKITSLASGTtIKNIRLSDLKDLPIPlVKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLR 174
Cdd:cd17519 100 NEEILNNRYLYHFLLSKQNEKYILAGGS-QPNLSSEKLKKIKIP-IPSLEVQEEIVSILDKFRELTNELESELNLRLKQY 177


                ...
gi 2496434  175 DEY 177
Cdd:cd17519 178 EYY 180
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-177 1.93e-05

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


Pssm-ID: 341146 [Multi-domain]  Cd Length: 176  Bit Score: 44.82  E-value: 1.93e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17257  95 ELDKRFLYYALPPPLKAIEDTTSSTTVKHLSSKDIDEIELPL-PPLEEQRRIAEILDELDALIDKLIAKLEKLRDLLLPL 173
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-177 1.95e-05

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: 44.78  E-value: 1.95e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEKITSLASGTTI-KNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDE 176
Cdd:cd17283 100 KLDKDFLYYLLSSITVQLQFSAQAGGGtKNLNTDIVKNLKIPL-PPLEEQKRIAEILDSLDALIDALEEKLEKLEELKKG 178


                .
gi 2496434  177 Y 177
Cdd:cd17283 179 L 179
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 206-369 2.09e-05

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: 44.31  E-value: 2.09e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  206 LGEVFHLKSGKYLKADERfEDGKFPYYGA-GIesTSFVNEPNTKGDTL----SmianGySIGNIRYHTIPWF--NgTggi 278
Cdd:cd17267   3 LGDVIELQYGKDLPKSRR-IPGPYPVYGSnGI--VGYHNEALVKGPGIvvgrK----G-SIGKVHYSEEDFWpiD-T--- 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  279 ameAL--KPNKTYVP-FFYCALKYMqkDLkERFKRDES-PFISLKLAGEIKVPFVkSFALQRKAGKIIYLLDKTLEECKE 354
Cdd:cd17267  71 ---TLyvKDFKGNDPrFLYYLLKTL--DL-ERLNSGSAvPGLNRNDVYSLKVPLP-PLEEQKAIAAILDALDDKIELNRR 143

                       170
                ....*....|....*
gi 2496434  355 EAKSLISIRDNLLGK 369
Cdd:cd17267 144 QNQTLEELADALLPK 158
RMtype1_S_Ara36733I_TRD1-CR1_like cd17268
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 102-177 3.86e-05

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


Pssm-ID: 341157 [Multi-domain]  Cd Length: 185  Bit Score: 43.97  E-value: 3.86e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2496434  102 KFAYYALKS---QEEKItSLASGTTIKNIRLSDLKDLPIPlVKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEY 177
Cdd:cd17268 107 KYLSYLLNSpafQKQKR-KLGTGTKVVHISASDLAKIKIP-VPPLEEQERIVEILDKFDALIAGLPAEIEARRKQYEYY 183
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 86-182 5.56e-05

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


Pssm-ID: 341165 [Multi-domain]  Cd Length: 187  Bit Score: 43.34  E-value: 5.56e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   86 QSSCTLtVLDPLEIDLKFAYYALKSQEEKITSLASGTTIK-NIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLN 164
Cdd:cd17276  92 QAICAI-LPNEKKVNPEFLLRYLNFNRPYWMRVAASSRKDpNITKDDVRNFPIPLP-PLDEQRAIVEFLSDVDALIDSLE 169

                        90
                ....*....|....*...
gi 2496434  165 ELIEVNRKLRDEYAHKLF 182
Cdd:cd17276 170 ALIEKLRELKKGLMQQLL 187
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-176 5.66e-05

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: 43.29  E-value: 5.66e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQEEK--ITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHAL----SVFDLRIEHLNELIEVNR 171
Cdd:cd17264 101 KVDVRYLYYYLNSPLGKsqIKKYDNGSAQPNLSAKSLKKFLIPL-PPLEEQKRIVAKLdeldALIDKLKQALEKLEELLQ 179


                ....*
gi 2496434  172 KLRDE 176
Cdd:cd17264 180 SLFQS 184
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 99-161 5.76e-05

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: 43.37  E-value: 5.76e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2496434   99 IDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLV-KSIQdQRTIAHALSVFDLRIE 161
Cdd:cd17499  93 IDKKYLFYFLLSNKDYFKGKSGGSTFKSINKNQIKNIKIPLPpLEEQ-KRIVSELDKLFKLIFE 155
RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like cd17258
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 61-182 1.29e-04

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


Pssm-ID: 341147 [Multi-domain]  Cd Length: 173  Bit Score: 42.39  E-value: 1.29e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   61 KNTISIIIGGSCGYVRLADKDYFCGQSSCTLTVLDPLEIDLKFAYYALKSQ--EEKITSLASGTTIKNIRLSDLKDLPIP 138
Cdd:cd17258  51 KGDVLITRHGTIGRVSIILSEEACLSSHVAGFNSKEGISDNKFIKYLFNSKkiKNRLMSYGASSTQPALNLSRLLKIKFP 130

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 2496434  139 lVKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHKLF 182
Cdd:cd17258 131 -NPPLEEQQKIGKILSTWDRAIELTEQKLELLQQQKKGLMQQLF 173
RMtype1_M_Cni19672ORF1405P_RMtype11G_Hci611ORFHP_T cd17277
Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 ...
 61-168 1.60e-04

Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 Calditerrivibrio nitroreducens M.Cni19672ORF1405P TRD1-CR1 and RMtype11G Helicobacter cinaedi PAGU611 RM.Hci611ORFHP TRD1-CR1; The recognition sequence of Calditerrivibrio nitroreducens M.Cni19672ORF1405P is undetermined, and the predicted recognition sequence of RM.Hci611ORFHP is 5'... GAGNNNNNGT ... 3'. M.Cni19672ORF1405P is a putative type I N6-adenine DNA methyltransferase. RM.Hci611ORFHP is a type II subtype gamma (also called type IIG and type IIC) N6-adenine DNA methyltransferase. Both are DNA methyltransferase-specificity subunit fusion proteins, they each have a domain corresponding to a HsdM methylation (M) subunit followed by a C-terminal, TRD-CR-like domain for sequence-recognition, which corresponds to the HsdS specificty (S) subunit. The latter consists of two variable TRDs, and two CRs which separate the TRDs; the TRDs each bind to different specific sequences in the DNA. RM.Hci611ORFHP has an additional N-terminal HSDR_N domain. Restriction-modification (RM) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit, two modification (M) subunits, and two restriction (R) subunits.


Pssm-ID: 341166 [Multi-domain]  Cd Length: 184  Bit Score: 42.01  E-value: 1.60e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   61 KNTISIIIGGSCGYVRLADKDYFCGQSSCTLtVLDPLEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPL- 139
Cdd:cd17277  68 KNSVLLSCTATIGKVAIAKIELTTNQQINAL-ICKDSKILPEYLFYALKHIKQVLERLTTNPGVKHVNLSMLSNLQIPLp 146

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 2496434  140 --------VKSIQD-QRTIAHALSVfdlrIEHLNELIE 168
Cdd:cd17277 147 plevqkkiVAEIEKvEKVIQGLRQK----IDEYQPLIN 180
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 102-182 2.17e-04

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: 41.72  E-value: 2.17e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  102 KFAYYALKSQE-EKITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDEYAHK 180
Cdd:cd17265 101 DYLFHLFNSDLfKKQIGSFLTATINQITNGNLNNFKIPL-PPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKELMQQ 179


                ..
gi 2496434  181 LF 182
Cdd:cd17265 180 LI 181
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-182 2.94e-04

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: 40.88  E-value: 2.94e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   98 EIDLKFAYYALKSQE--EKITSLASGTT-IKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLR 174
Cdd:cd17260  79 GILPEFLYYLLRSPSfrKEAIKSMTGSSgRQRVPKDFLENYKIPLP-PLEEQKRIAAILDSLDAKIDALEAEIETLEELL 157


                ....*...
gi 2496434  175 DEYAHKLF 182
Cdd:cd17260 158 DALLPKLL 165
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 285-371 5.70e-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: 40.47  E-value: 5.70e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434  285 PNKTYVP-FFYCALKYMQKDLKER-----FKrdEspfISLKLAGEIKVPfVKSFALQRKAGKIIYLLDKTLEECKEEAKS 358
Cdd:cd17273 100 PNEEIDNeFLYYLLKNNKPEIESLasgstFK--E---ISKSTFKKIEIP-LPPLEEQKKIAAILSKLDELIELLEKENEK 173

                        90
                ....*....|...
gi 2496434  359 LISIRDNLLGKLF 371
Cdd:cd17273 174 LKELRDGLLPKLF 186
RMtype1_S_Eco2747II-TRD2-CR2-like cd17272
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 60-183 7.53e-04

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


Pssm-ID: 341161 [Multi-domain]  Cd Length: 189  Bit Score: 40.11  E-value: 7.53e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   60 FKNTISIIIGGSCGYVRL--ADKDYFCGQSScTLTVLDPLEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPI 137
Cdd:cd17272  60 NKGDILITMIGTIGETAIvkCLDPKFYTLNL-YLIRLKKEKLLPSYLKYFLDSEKFLNKSISATSGQGYLKANQIDKLEI 138

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 2496434  138 PLvKSIQDQRTIAHALSVFDLRIEHLNE----LIEVNRKLRDEYAHKLFT 183
Cdd:cd17272 139 PL-PPLEEQQRIVKILDKFDTLCNDITEglpaEIEARQKQYEYYRDLLLS 187
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 103-176 2.05e-03

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: 38.59  E-value: 2.05e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2496434  103 FAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLVkSIQDQRTIAHALSVFDLRIEHLNELIEVNRKLRDE 176
Cdd:cd17243 106 FLYYLLKNLIEELKQKAHGSVFDTITRKTFDEIKVPLP-PEELQKSFENIVSPLFDKILNNLKENQTLAQLRDT 178
RMtype1_S_NmaSCMORF606P_TRD2-CR2_like cd17271
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 70-183 2.07e-03

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


Pssm-ID: 341160 [Multi-domain]  Cd Length: 186  Bit Score: 38.79  E-value: 2.07e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   70 GSCGYVRladKDYFCGQSSCTLTVLDPLEIDLKFAYYaLKSQEEKITSLASGTTIKNIRLSDLKDLPIpLVKSIQDQRTI 149
Cdd:cd17271  78 GKCAITG---IPATTNQSCMAFYPTKKLTTEFLFYWY-KKYGNYLGFKYAQGTKQQSYTADIVKKLPI-LLPTLKEQKKI 152

                        90       100       110
                ....*....|....*....|....*....|....
gi 2496434  150 AHALSVFDLRIEHLNELIEVNRKLRDEYAHKLFT 183
Cdd:cd17271 153 ANFLSDIDELIATLEKKIEKLKKIKKGLMQKLLT 186
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 19-157 5.18e-03

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


Pssm-ID: 341195 [Multi-domain]  Cd Length: 183  Bit Score: 37.54  E-value: 5.18e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2496434   19 GSLFELKKGEMLEKELLAPDGKYEYFNGGIKASGRTNEfntfKNTISIII---GGSCGYVRLADKDYFCGQSSCTLTVLD 95
Cdd:cd17514  27 GDIPWLTSGETDDNFINNTSEKITTKNGLEDSSIRIVP----KGTILIACtgqGYTRGQVAVLQIDASTNQAIAAIRCKE 102

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2496434   96 plEIDLKFAYYALKSQEEKITSLASGTTIKNIRLSDLKDLPIPLvKSIQDQRTIAHALSVFD 157
Cdd:cd17514 103 --NVNPKYLYYYLKTQKNNLRNLTSGVAQKNLNIEMLRNLQIPL-PPKEEQQKIVNILETLE 161
 
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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