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Conserved domains on  [gi|2735216693|ref|WP_346772545|]
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restriction endonuclease subunit S [Ligilactobacillus salivarius]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 218-389 1.82e-85

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: 257.07  E-value: 1.82e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 218 CRLNDHAIVTMGQSPNSKNYTNNQTDKILVQGNADLYKNKVLKRVFTTEITKTAIKNDILISVRAPVGDIARNQYEsVVI 297
Cdd:cd17494     1 KKLGEIAEITMGQSPSSKNYNDNPNGLPLVQGNADIKNGKVIPRIWTSEITKTANKGDIILSVRAPVGEVAKTNFD-ACI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 298 GRGIASIKGNDFLYYQLEKMKNSGFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSL 377
Cdd:cd17494    80 GRGVCAIKGNEFIFLYLYLLNIEGYWSKISQGSTFESINSNDIKNLKISIPSLEEQQKIATFLSTLDAEITLLEKKLEKL 159

                         170
                  ....*....|..
gi 2735216693 378 KKLKQFLLQNMF 389
Cdd:cd17494   160 KQLKKGLLQKLF 171
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-197 1.68e-83

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: 252.44  E-value: 1.68e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVNINKYITNKAVNDSAAKLIPANSIAIVTRVGVGKLA 94
Cdd:cd17513     1 VKLGELGK-FIGGGTPSTKNPEYWNGNIPWITSSDLSEDDIFKINIRKFITEEAIKNSATKIIPANSILIVTRVGVGKVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  95 YMSQEYSTSQDFLSLVDIKE-DLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRVFKILDN 173
Cdd:cd17513    80 INPFDICTSQDFTSLIPIKEvNPLFLAYLLYSLLQKLKSQLQGTSIKGITKDDLKNLKIPLP-PLEEQQKIAAILSKLDK 158

                         170       180
                  ....*....|....*....|....
gi 2735216693 174 SINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17513   159 LIEAHEKKLEKLKQLKKGLMQKLF 182
 
Name Accession Description Interval E-value
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 218-389 1.82e-85

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: 257.07  E-value: 1.82e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 218 CRLNDHAIVTMGQSPNSKNYTNNQTDKILVQGNADLYKNKVLKRVFTTEITKTAIKNDILISVRAPVGDIARNQYEsVVI 297
Cdd:cd17494     1 KKLGEIAEITMGQSPSSKNYNDNPNGLPLVQGNADIKNGKVIPRIWTSEITKTANKGDIILSVRAPVGEVAKTNFD-ACI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 298 GRGIASIKGNDFLYYQLEKMKNSGFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSL 377
Cdd:cd17494    80 GRGVCAIKGNEFIFLYLYLLNIEGYWSKISQGSTFESINSNDIKNLKISIPSLEEQQKIATFLSTLDAEITLLEKKLEKL 159

                         170
                  ....*....|..
gi 2735216693 378 KKLKQFLLQNMF 389
Cdd:cd17494   160 KQLKKGLLQKLF 171
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-197 1.68e-83

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: 252.44  E-value: 1.68e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVNINKYITNKAVNDSAAKLIPANSIAIVTRVGVGKLA 94
Cdd:cd17513     1 VKLGELGK-FIGGGTPSTKNPEYWNGNIPWITSSDLSEDDIFKINIRKFITEEAIKNSATKIIPANSILIVTRVGVGKVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  95 YMSQEYSTSQDFLSLVDIKE-DLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRVFKILDN 173
Cdd:cd17513    80 INPFDICTSQDFTSLIPIKEvNPLFLAYLLYSLLQKLKSQLQGTSIKGITKDDLKNLKIPLP-PLEEQQKIAAILSKLDK 158

                         170       180
                  ....*....|....*....|....
gi 2735216693 174 SINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17513   159 LIEAHEKKLEKLKQLKKGLMQKLF 182
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 11-179 1.30e-15

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


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 73.93  E-value: 1.30e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  11 TWERKKLGDVANsyINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVN-INKYItnkavndsaaklIPANSIAIVTRVG 89
Cdd:pfam01420   3 DWEVFKLGDVFE--IKKGKTPKKKELKNNGKYPYIRAGDLNNVVKGGLGyIKKYI------------LPKGDITISSRAT 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  90 VGKLAYMSQEYSTSQDFLSLVDIKEDLI--FIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRV 167
Cdd:pfam01420  69 IGYVFYRDKPYYTNQHIIVLIPKNNIKIteFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLP-PLEEQKKIAKI 147

                         170
                  ....*....|..
gi 2735216693 168 FKILDNSINLHE 179
Cdd:pfam01420 148 LSQLDNTIELEK 159
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
312-389 3.50e-09

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 53.52  E-value: 3.50e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2735216693 312 YQLEKMKNSGFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:COG0732     4 YYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 213-379 8.32e-09

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: 54.28  E-value: 8.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 213 EKWNQCRLNDHAIVTMGQSPNSKNYTNNQTDKILvqGNADLYKNKVLkrvfTTEITKTAI--KNDILISVRAPVGDIARN 290
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPKKKELKNNGKYPYI--RAGDLNNVVKG----GLGYIKKYIlpKGDITISSRATIGYVFYR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 291 QYESVV---IGRGIASIKGND--FLYYQLEKMKNSGfwNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTN 365
Cdd:pfam01420  76 DKPYYTnqhIIVLIPKNNIKIteFLYLYLLLKLKKL--KSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDN 153

                         170
                  ....*....|....
gi 2735216693 366 IIQLQEHKIDSLKK 379
Cdd:pfam01420 154 TIELEKGILNELER 167
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
127-197 2.93e-06

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 45.05  E-value: 2.93e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2735216693 127 ISKLSSSLQGTSIKGITKKELLNLSIsIVNNTAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:COG0732    12 REYLRSLATGSTQPNLNKKDLKKLPI-PLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
 
Name Accession Description Interval E-value
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 218-389 1.82e-85

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: 257.07  E-value: 1.82e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 218 CRLNDHAIVTMGQSPNSKNYTNNQTDKILVQGNADLYKNKVLKRVFTTEITKTAIKNDILISVRAPVGDIARNQYEsVVI 297
Cdd:cd17494     1 KKLGEIAEITMGQSPSSKNYNDNPNGLPLVQGNADIKNGKVIPRIWTSEITKTANKGDIILSVRAPVGEVAKTNFD-ACI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 298 GRGIASIKGNDFLYYQLEKMKNSGFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSL 377
Cdd:cd17494    80 GRGVCAIKGNEFIFLYLYLLNIEGYWSKISQGSTFESINSNDIKNLKISIPSLEEQQKIATFLSTLDAEITLLEKKLEKL 159

                         170
                  ....*....|..
gi 2735216693 378 KKLKQFLLQNMF 389
Cdd:cd17494   160 KQLKKGLLQKLF 171
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-197 1.68e-83

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: 252.44  E-value: 1.68e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVNINKYITNKAVNDSAAKLIPANSIAIVTRVGVGKLA 94
Cdd:cd17513     1 VKLGELGK-FIGGGTPSTKNPEYWNGNIPWITSSDLSEDDIFKINIRKFITEEAIKNSATKIIPANSILIVTRVGVGKVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  95 YMSQEYSTSQDFLSLVDIKE-DLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRVFKILDN 173
Cdd:cd17513    80 INPFDICTSQDFTSLIPIKEvNPLFLAYLLYSLLQKLKSQLQGTSIKGITKDDLKNLKIPLP-PLEEQQKIAAILSKLDK 158

                         170       180
                  ....*....|....*....|....
gi 2735216693 174 SINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17513   159 LIEAHEKKLEKLKQLKKGLMQKLF 182
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 219-389 1.47e-50

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: 167.33  E-value: 1.47e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 219 RLNDHAIVTMGQSPNSKNYTNNQTDKILVQGNADlYKNKVLK-RVFTTEITKTAIKNDILISVRAPVGDIARNQYESVvI 297
Cdd:cd17245     2 KLGEVAEIIMGQSPPSSTYNEEGEGLPFLQGKAD-FGEIYPTpRVWCTKPTKIAEKGDILISVRAPVGDVNIADEKCC-I 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 298 GRGIASIKGND-----FLYYQLEKMKNsgFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEH 372
Cdd:cd17245    80 GRGLAAIRANKdidnlFLYYYLKYNKP--ELEKLGTGSTFKAINKKDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKA 157

                         170
                  ....*....|....*..
gi 2735216693 373 KIDSLKKLKQFLLQNMF 389
Cdd:cd17245   158 LIEKLDELKKGLMQELF 174
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-197 2.55e-36

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: 130.60  E-value: 2.55e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVN-INKYITNKAVNDSAAKLIPANSIAIVTRVGV 90
Cdd:cd17273     1 WEVVKLGDVAE-IVGGGTPSTKNPEYWNGDIPWITPTDLTKLKGKYISdTERKITELGLKNSSAKLLPAGSVLLSSRAPI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  91 GKLAYMSQEYSTSQDFLSLV-DIKEDLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRVFK 169
Cdd:cd17273    80 GYVAIATNPLATNQGFKSIIpNEEIDNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEIPLP-PLEEQKKIAAILS 158

                         170       180
                  ....*....|....*....|....*...
gi 2735216693 170 ILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17273   159 KLDELIELLEKENEKLKELRDGLLPKLF 186
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 218-389 2.03e-34

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: 125.10  E-value: 2.03e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 218 CRLNDHAIVTMGQSPNSKNYTNNQTDKILVQGNADLYKNKVLKRVFTTEITKTAIKNDILISVRAPVGD--IARNQyesV 295
Cdd:cd17498     1 VKLGEIAEITMGQSPKSEFYNEDGIGLPFLQGNRTFGDKYPYIDTYTTDIKKIAKKGDILMSVRAPVGDlnIANKD---I 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 296 VIGRGIASIKG----NDFLYYQLEKMKNsgFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQE 371
Cdd:cd17498    78 CIGRGLCSIRMkngnNSFLYYLLKNNIK--NLINKSSGTVFGSINKDDIENLEVDIPEDEEQKRIANILSKIDDKIEINN 155

                         170
                  ....*....|....*...
gi 2735216693 372 HKIDSLKKLKQFLLQNMF 389
Cdd:cd17498   156 QINKNLEELAQAIFKHWF 173
RMtype1_S_Cep9333ORF4827P-TRD2-CR2_like cd17495
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 219-385 1.89e-33

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Crinalium epipsammum S subunit (S.Cep9333ORF4827P) TRD2-CR2 and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) T; The recognition sequences for Crinalium epipsammum S subunit (S.Cep9333ORF4827P) and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) 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: 341186 [Multi-domain]  Cd Length: 174  Bit Score: 122.57  E-value: 1.89e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 219 RLNDHAIVTMGQSPNSKNYTNNQTDKILVQGNADLYKNKVLKRVFTTEITKTAIKNDILISVRAPVGD--IArnqYESVV 296
Cdd:cd17495     2 TLGDIANITMGQSPKGESYNEDGEGLPFYQGVTDFGFRFPTNRVYTTAPTRFAEAGDILFSVRAPVGDinIA---NEKCC 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 297 IGRGIASIKGND----FLYYQLEKMKNsgFWNKYIAGST-FESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQE 371
Cdd:cd17495    79 IGRGLAAIRSKSgsqsFLFYQLKSLFK--EFDIFNGEGTvFGSINKKDLENLPIIIPSDEIIEAFEKLVSPIDQKIENNE 156

                         170
                  ....*....|....
gi 2735216693 372 HKIDSLKKLKQFLL 385
Cdd:cd17495   157 KENRTLAKLRDTLL 170
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 219-385 6.31e-32

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: 118.81  E-value: 6.31e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 219 RLNDHAIVTMGQSPNSKNYtNNQTDKI-LVQGNADLYKNKVLKRVFTTEITKTAIKNDILISVRAPVGD--IARNQYesv 295
Cdd:cd17497     2 KLKYVADIIMGQSPPSSTY-NTEGIGLpFLQGKAEFGKLYPTPRKWCSAPKKIAEKGDILLSVRAPVGPtnIADQEY--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 296 VIGRGIASIKGND-----FLYYQLEKMKNsgfW-NKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLT----N 365
Cdd:cd17497    78 CIGRGLAAIRPKKgldkkYLLYYLKSIEN---ElSSLGTGSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDELTakidQ 154

                         170       180
                  ....*....|....*....|
gi 2735216693 366 IIQLQEHKIDSLKKLKQFLL 385
Cdd:cd17497   155 LIALLEKAIELLKEYRQAVL 174
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 218-389 7.63e-32

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: 118.37  E-value: 7.63e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 218 CRLNDHAIVTMGQSPNSKNYTNNQTDKILVQGNADLYKNKVLKRVFTTEITKTAIKNDILISVRA-PVGD--IARNQYes 294
Cdd:cd17496     1 VKLGDIAEIIMGQSPKGESYNTEGIGIPLLNGPADFGDGYPIPKKWTTKPTKLCKKGDILFCVRGsTTGRlnIADDEY-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 295 vVIGRGIASIKGND-----FLYYQLEKMKNsgfwnkYIA----GSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTN 365
Cdd:cd17496    79 -CIGRGVAAIRPKNgidteFLYYLLESNLD------YLLaaatGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDE 151

                         170       180
                  ....*....|....*....|....
gi 2735216693 366 IIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17496   152 KIDKNKQEIEKLEELRDTLLPKLL 175
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 218-389 1.15e-30

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: 115.40  E-value: 1.15e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 218 CRLNDHAIVTMGQSPNSKNYtNNQTDKILV-QGNADlYKNKVLKR--VFTTEITKTAIKNDILISVRAPVGDIARNQyES 294
Cdd:cd17499     1 VRLGDVAEIIMGQSPEGKSY-NTNKEGLPFyQGKKE-FGDKYIKEpnTWTTSPTKIAEKNDILMSVRAPVGDVNITT-RK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 295 VVIGRGIASIKG-----NDFLYYQLEKMKNSgfWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQL 369
Cdd:cd17499    78 ICIGRGLAAIRAkknidKKYLFYFLLSNKDY--FKGKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFE 155

                         170       180
                  ....*....|....*....|
gi 2735216693 370 QEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17499   156 AKNNIEEALANAQQLFKSIL 175
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-197 4.02e-29

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: 111.44  E-value: 4.02e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANSYINGGTPDTQNKNYWIGDIPWIQSSDLKNDdiwnvNINK---YITNKAVNDSAAKLIPANSIAIVTRVGVG 91
Cdd:cd17285     1 KKLGDLVEKIVGGGTPSKSNPEYWNGDIPWASVKDLKGK-----YLTStedKITEEGLKNSSSNLIPKGTVIIATRMGLG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  92 KLAYMSQEYSTSQDfLSLVDIKEDlIFIMYMLYF------KISKLSSslqGTSIKGITKKELLNLSISIVnNTAEQNRIG 165
Cdd:cd17285    76 KVAINKIDVAINQD-LKALFPKDE-LDPEYLLYWflsieeTIESLGT---GTTVKGITLEDLKSLKIPLP-PLEEQKRIV 149

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2735216693 166 RVFKILDNSINLHEDHL-QFLHVFKSfLLQKMF 197
Cdd:cd17285   150 AILDELDELIDKLEAKLeKLKQLKKG-LMQSLL 181
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 13-197 2.50e-28

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: 109.56  E-value: 2.50e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  13 ERKKLGDVANSYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVNINKYITNKAVNDSAAKLIPANSIAIVTRVGVGK 92
Cdd:cd17275     1 EQVKLGELCEKMKSGGTPSTSNKEYYGGDIPFVKISDMTKSGKYIYSTEKYITEEGLKNSSAWIVPKGTILYAMYASVGK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  93 LAYMSQEYSTSQDFLSLV--DIKEDLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRVFKI 170
Cdd:cd17275    81 VAINKIDVATNQAILGIIpkDEKLDFEFLYYWLLSLKNELKRLIRTGTQANLNAEIVKNLPIPLP-PLEEQKKIAEILDK 159

                         170       180
                  ....*....|....*....|....*..
gi 2735216693 171 LDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17275   160 IDAEIDKLEEKIEKLRELKKGLLQKMF 186
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-183 2.04e-24

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: 98.71  E-value: 2.04e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANSYiNGGTPDTQNKNYWIGD-IPWIQSSDLKNDDIWNVNinKYITNKAVNDSAAKLIPANSIAIV----- 85
Cdd:cd17294     1 WEWKTLGEIAKIF-SGGTPSTSNPEYWDGGtIPWLSSGEVNFKEIYETE--KRITEEGLKNSSAKWIPKNSVLIAlagqg 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  86 -TRvgvGKLAYMSQEYSTSQDFLSLVDIKEDLI--FIMYML---YFKISKLSsslQGTSIKGITKKELLNLSISIvNNTA 159
Cdd:cd17294    78 kTR---GTVAILKIPLTTNQSLAAIEPDEEIANsrFLYYNLssrYEELRSLS---GGGGRGGLNLKIIKSLPIPL-PPLE 150

                         170       180
                  ....*....|....*....|....
gi 2735216693 160 EQNRIGRVFKILDNSINLHEDHLQ 183
Cdd:cd17294   151 EQKKIVAILDKFDALINDLKEGLP 174
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-196 7.14e-24

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: 97.14  E-value: 7.14e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVAnSYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVNInkYITNKAVNDSAAKLIPANSIAIVTRVGVGK-- 92
Cdd:cd17249     1 VRLGDLG-KFLSGGTPSKSNPEYWGGDIPWVSPKDMKSDYISDSED--HITELAVEESGTKLVPAGSVLIVVRGMILAht 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  93 --LAYMSQEYSTSQDFLSLV-DIKEDLIFIMYMLYFKISKLSSSLQGTSIkgITKK----ELLNLSISIVNnTAEQNRIG 165
Cdd:cd17249    78 fpVAITTRPVAFNQDIKALIpKEGIDPEFLLYALKANEDRILSLVDKAGH--GTGSldtdDLKNLPIPLPP-LEEQRRIA 154

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2735216693 166 RVFKILDNSINLHEDHLQFLHVFKSFLLQKM 196
Cdd:cd17249   155 AILDALDALIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-197 8.19e-24

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: 97.12  E-value: 8.19e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANSYiNGGTPDTQNKNYWIGDIPWIQSSDLKNDDIwnVNINKYITNKAVNDSAAKLIPANSIAI----VTrvgV 90
Cdd:cd17515     1 VKLGDIGKWG-SGGTPSRSNPEYYGGGIPWIKSGELNDGYI--TSTEEKITEEGLKNSSAKLFPKGSVLIamygAT---A 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  91 GKLAYMSQEYSTSQDFLSLV-DIKEDLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRVFK 169
Cdd:cd17515    75 GKVGILGIDAATNQAICAILpNEEIDNEFLFYFLKSQKEYLISLGKGGAQPNISQGIIKNIEIPLP-PLAEQKRIVAKLD 153

                         170       180
                  ....*....|....*....|....*...
gi 2735216693 170 ILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17515   154 KLDKLIEKLEKALEKLEELKKALMQKLL 181
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 13-178 8.81e-24

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: 97.14  E-value: 8.81e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  13 ERKKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVNINKYITNKAVNDSAAKLIPANSIAIVTRVGVGK 92
Cdd:cd17243     1 EVKSLSDVVD-IIGGGTPKTSVPEYWNGDIPWFSVKDVNNDSRFVLDTEKKITELGLKNSSTKLLPKGTTIISARGTVGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  93 LAYMSQEYSTSQdflSLVDIKEDLIFIMYMLYFKISKLSSSLQ----GTSIKGITKKELLNLSISIVnNTAEQNRIGRVF 168
Cdd:cd17243    80 LALLGIPMAMNQ---SCYGLRGKDGLSNYFLYYLLKNLIEELKqkahGSVFDTITRKTFDEIKVPLP-PEELQKSFENIV 155

                         170
                  ....*....|
gi 2735216693 169 KILDNSINLH 178
Cdd:cd17243   156 SPLFDKILNN 165
RMtype1_M_Cni19672ORF1405P_RMtype11G_Hci611ORFHP_T cd17277
Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 ...
 12-152 5.44e-23

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: 94.78  E-value: 5.44e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANsYINGGTPDTQNKNYWI-GDIPWIQSSDLKNDDIWNVNINKYITNKAVNDSAAKLIPANSIAIVTRVGV 90
Cdd:cd17277     1 WPIVKLGEVCE-IINGSTPSKKNEEYWNnGTIKWLTIPDIDERGLIISSTKQFITEKALEEKKVKLVPKNSVLLSCTATI 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2735216693  91 GKLAYMSQEYSTSQDFLSLVDIKEDLI--FIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSI 152
Cdd:cd17277    80 GKVAIAKIELTTNQQINALICKDSKILpeYLFYALKHIKQVLERLTTNPGVKHVNLSMLSNLQI 143
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 15-197 2.17e-22

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: 93.32  E-value: 2.17e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVAN--SyinGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVniNKYITNKAVNDSAAKLIPANSIAI------VT 86
Cdd:cd17287     1 KKLGEIAKvsS---GGTPSRSNPEYWNGGIPWVKTGEVNFNEITDT--EEKITEEGLKNSSAKLFPKGTLLMamygqgKT 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  87 RvgvGKLAYMSQEYSTSQDFLSLVDIKE-DLIFIMYML---YFKISKLSSSLQGTsikgitkkellNLSISIVNN----- 157
Cdd:cd17287    76 R---GRVAILGIEAATNQACAAILPNDGiNPDFLFYYLqssYEELRDLSNGGGQP-----------NLNAGLIKSieipv 141

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2735216693 158 --TAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17287   142 ppLDEQQKIAAFLSAIDAKIDALEQKLELLQELKKSLMQQLF 183
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 25-164 2.71e-21

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: 90.31  E-value: 2.71e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  25 INGGTPDTQNKNYWIGDIPWIQSSDL-KNDDIWNVNINKYITNKAVNDSAAKLIPANSIAIVTRVGVGKLAYMSQEYSTS 103
Cdd:cd17279    10 VNGSTPKSGEEDYWDGDIPWVTPADLsKLDGKYISSSQRKITEAGLESCGTSLVPAGSIILSTRAPIGYVAIATVELCTN 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2735216693 104 QDFLSLV-DIKEDLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVNNtAEQNRI 164
Cdd:cd17279    90 QGCKALVpNSDVDSRFLYYLLLAAKEELNSLGRGTTFLELSTDELANFKIPLPPL-SEQRAI 150
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 15-197 1.42e-20

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) TRD1-CR1, and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) TRD2-CR2; The recognition sequences of Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341175 [Multi-domain]  Cd Length: 179  Bit Score: 87.93  E-value: 1.42e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLkNDDIWNVNINKYITNKAVndSAAKLIPANSIaIVTRVG-VGKL 93
Cdd:cd17286     1 KKLGDLGE-IVTGNTPSTKNSEYYGGEILFVTPTDI-DGNKYIYKTEKKLSEKGF--KKARILPKGSI-LVTCIGsIGKN 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  94 AYMSQEYSTSQDFLSLV-DIKEDLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISiVNNTAEQNRIGRVFKILD 172
Cdd:cd17286    76 AIATEDCATNQQINAIIpNKNYDPEFLYYALENWSKKIKSLAGKQAVPIINKTEFSKIKIL-VPPLEEQQKIANFLSKLD 154

                         170       180
                  ....*....|....*....|....*
gi 2735216693 173 NSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17286   155 ELIELQQQKIEKLEELKKGLLQKLF 179
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-197 7.73e-20

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: 86.11  E-value: 7.73e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVAnSYINGGTPDTQNKNYWI-GDIPWIQSSDLKNDDIwnVNINKYITNKAVNDSAAKLIPANSIAIVTRVGVGKL 93
Cdd:cd17296     1 KKLGEIC-SIQSGGTPSRSKKEYWNnGTIPWVKISDCKNKYV--DETEEFITEEGLNNSSAKLLKKGTILIAIFATIGKV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  94 AYMSQEYSTSQDFLSLVdIKEDLI---FIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRVFKI 170
Cdd:cd17296    78 GILKIEATTNQAIAGIK-PKNKSInpkYLYYYLKSLYEKFLSLGRGVAQNNINLSILKNLKIPLP-PLEEQQRIVAILDK 155

                         170       180
                  ....*....|....*....|....*..
gi 2735216693 171 LDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17296   156 FEKLINKRQEGLQLLDELVKSLFEEMF 182
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-164 2.33e-18

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: 82.25  E-value: 2.33e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANSYINGGTPDTQNKNYWIGD-IPWIQSSDLKNDDIWNvNINKYITNKAVNDSAAKLIPANSIAIVTrVG--VG 91
Cdd:cd17290     1 KKLKRLAKSIKTGTTPPSENEEYYDGGiIPWFTPGDFNGDLILS-ESKRKLSELAIEDGEARLFPKNSVLVVG-IGatIG 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2735216693  92 KLAYMSQEYSTSQDFLSLVDIKE-DLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRI 164
Cdd:cd17290    79 KVGYSDKESSSNQQITGIIFNKDiNPKFLFYWLSSSKEELENLANGATLPILNQEKLKNIKLPVP-PLNEQQKI 151
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-180 3.10e-18

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: 81.66  E-value: 3.10e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVNInkYITNKAVNDSAAKLIPANSIAIVTRVGVGKLA 94
Cdd:cd16961     1 KKLGEIAE-IISGKTPSSSSEYWDNGIIPWIRISDINNGGIILTDE--KITEEGAEKLKKKILPKGDILISRSGTIGKVA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  95 YMSQE--YSTSQDFLSLVDIKE-DLIFIMYML-YFKISKLSSSLQGTSIKGITKKELLNLSISIVNNtAEQNRIGRVFKI 170
Cdd:cd16961    78 IVKENdkALLNQAVIVIRPKDEvDSEFLYYFLkSPFGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPL-EEQKKIANILDK 156

                         170
                  ....*....|
gi 2735216693 171 LDNSINLHED 180
Cdd:cd16961   157 LDALIELLEQ 166
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-183 6.94e-18

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


Pssm-ID: 341137 [Multi-domain]  Cd Length: 196  Bit Score: 81.04  E-value: 6.94e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVA--NSyinGGTPDTQNKNYWIGDIPWIQSSDLK-NDDIWNVNINKYITNKAVNDSAAKLIPANSIaIVTR- 87
Cdd:cd17248     4 WEVVPLTDVAklES---GHTPSRSRPEYWNGCIPWISLADVKqLRGDYIYETKEKISELGIANSSARLLPAGTV-VLSRt 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  88 VGVGKLAYMSQEYSTSQDFLSLVdIKEDLI--FIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSIsIVNNTAEQNRIG 165
Cdd:cd17248    80 ASVGKSAIMGRPMATSQDFANWV-CGPELDpeYLLYVLRAMKPEFERLAMGSTHKTIYMPDFKALRI-ALPPLEEQRKIV 157

                         170
                  ....*....|....*...
gi 2735216693 166 RVFKILDNSINLHEDHLQ 183
Cdd:cd17248   158 DRLEALDAKIDALERKLE 175
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 215-389 9.31e-18

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: 80.53  E-value: 9.31e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 215 WNQCRLNDHAIVTMGQSPNSKN--YTNnqtdkilvqGN------ADLYKNKVlKRVFTTE--ITKTAIKN---------D 275
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKNpeYWN---------GDipwitpTDLTKLKG-KYISDTErkITELGLKNssakllpagS 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 276 ILISVRAPVGDIARNQYE--------SVVIGRGIasikGNDFLYYQLEKMKnsgfwnKYI----AGSTFESITGKDLKNA 343
Cdd:cd17273    71 VLLSSRAPIGYVAIATNPlatnqgfkSIIPNEEI----DNEFLYYLLKNNK------PEIeslaSGSTFKEISKSTFKKI 140

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2735216693 344 KIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17273   141 EIPLPPLEEQKKIAAILSKLDELIELLEKENEKLKELRDGLLPKLF 186
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 15-197 1.81e-17

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: 79.42  E-value: 1.81e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANSyINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIwNVNINKYITNKAVndSAAKLIPANSIaIVTRVG--VGK 92
Cdd:cd17293     1 VKLGELGEV-VTGNTPSKKNPEYYGGDIPFIKPDDLNNGGI-ILTSEEYLSEEGA--KKARIVPKGSI-LVTCIGgsIGK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  93 LAYMSQEYSTSQDFLSLV-DIKEDLIFIMYML---YFKISKLSSSlqgtSIKGI-TKKELLNLSISIvNNTAEQNRIGRV 167
Cdd:cd17293    76 VGIADREVAFNQQINAIIpNKSVDPKFLYYQLlssKFQLQAIASS----TTLPIiNKSKFEKIEIPL-PPLEEQKRIVAK 150

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2735216693 168 FKILDNSINLHEDHLQ-FLHVFKSfLLQKMF 197
Cdd:cd17293   151 LDKLFALIDKLEESLEeLDELLKS-LFQSAF 180
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-183 2.18e-17

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: 79.50  E-value: 2.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANSYiNGGTPDTQNKNYWIGD-IPWIQSSDLKNDDIwnVNINKYITNKAVNDSAAKLIPANS--IAIV--- 85
Cdd:cd17247     4 WEVVRLGDVARVG-NGSTPSRKNPDYWNGGtIPWVSSGEVNDNRI--TEADEFITELALKECSLPLVPPGSvlVAMIgqg 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  86 -TRvgvGKLAYMSQEYSTSQDFLSLVDIKEDL--IFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSIsIVNNTAEQN 162
Cdd:cd17247    81 kTR---GQAAILAIEATINQNLAAIRPNEERVlpEYLHYYLESQYDELRRIGSGGGQGALNCGILKAFPI-PLPPLDEQR 156

                         170       180
                  ....*....|....*....|.
gi 2735216693 163 RIGRVFKILDNSINLHEDHLQ 183
Cdd:cd17247   157 EIVAELEALLAKIDLLEEKIA 177
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 256-389 1.32e-16

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: 77.20  E-value: 1.32e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 256 NKVLKRVFTTE--ITKTAIKN---------DILISVRAPVGDIARNQYEsVVIGRGIASIKGND------FLYYQLEKMK 318
Cdd:cd17275    39 TKSGKYIYSTEkyITEEGLKNssawivpkgTILYAMYASVGKVAINKID-VATNQAILGIIPKDekldfeFLYYWLLSLK 117

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2735216693 319 NSgfWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17275   118 NE--LKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIAEILDKIDAEIDKLEEKIEKLRELKKGLLQKMF 186
RMtype1_S_NmaSCMORF606P_TRD2-CR2_like cd17271
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 17-197 1.37e-16

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: 77.31  E-value: 1.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  17 LGDVANSYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIwnVNINKYITNKAVNDSAAKLIPANS--IAIV------TRv 88
Cdd:cd17271     1 LGEVLKGLSSGATPSRGNPEYFNGDIPWITSGELNYNYI--TDTNEKITEEAVKNTNLKIHPKGTflIAITgleaagTR- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  89 gvGKLAYMSQEYSTSQD---FLSLVDIKEDLIFIMYMLY-----FKISklssslQGTSIKGITKKELLNLSIsIVNNTAE 160
Cdd:cd17271    78 --GKCAITGIPATTNQScmaFYPTKKLTTEFLFYWYKKYgnylgFKYA------QGTKQQSYTADIVKKLPI-LLPTLKE 148

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2735216693 161 QNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17271   149 QKKIANFLSDIDELIATLEKKIEKLKKIKKGLMQKLL 185
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-197 2.36e-16

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: 76.48  E-value: 2.36e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANSYINGgtpdtQNK-NYWIGDIPWIQSSDLKNDDIWNVNINKYITNKAVNDSAAKLIPANSIaIVTRVG- 89
Cdd:cd17284     4 WEVKRVGDVCDCIVPG-----RDKpKSFDGNIPWITIEDIKGKYISSSKSGLGVSEEEIKEMNLKVIPKGSV-IMSCVGd 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  90 VGKLAYMSQEYSTSQDFLSLVDIKE-DLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRVF 168
Cdd:cd17284    78 FGIVAIATNELVINQQLHAFVPSKKiNPEYLMYLLSLQKKYMEKIATGTTIPYLNKTNCESIPIPLP-PIEEQNKIAKIL 156

                         170       180
                  ....*....|....*....|....*....
gi 2735216693 169 KILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17284   157 DSIDKKIDLLIAKLEKLQQLKKGLMQQLF 185
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-197 4.26e-16

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: 75.66  E-value: 4.26e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWnVNINKYITNKAVNDSAAKLIPANSIAiVTRVG--VGK 92
Cdd:cd17516     1 VKIGDLGK-VVTGKTPSTKNPEYFGGDIPFITPSDMKGGKYI-IKTERRLSSKGLEKVKNKLIPANSIC-VTCIGsdMGK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  93 LAYMSQEYSTSQDFLSLVDIKE--DLIFIMYML---YFKISKLSSSLQGTSIkgITKKELLNLSISIVNNTaEQNRIGRV 167
Cdd:cd17516    78 VAITKEPSVTNQQINSIIVNKNkfDPDFVYYLLknnSKYLKSIAGGSTATPI--INKSTFSNIEIPLPPLP-EQKKIAAI 154

                         170       180       190
                  ....*....|....*....|....*....|
gi 2735216693 168 FKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17516   155 LSSLDDKIENNRRINKTLEEMAQALFKEWF 184
RMtype1_S_MmaGORF2198P_TRD1-CR1_like cd17500
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 16-177 1.16e-15

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: 74.63  E-value: 1.16e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  16 KLGDVANSYINGGTPDTQNKNYWI-GDIPWIQSSDLKNDDIWNVNinKYITNKAVNDSAAKLIPANSIaIVTRVG----V 90
Cdd:cd17500     1 KLEDICIKITSGGTPSRSNKEYYNgGNIPWLKTKELNFKRIYDTE--EKITEEGLKNSSAKLIPENTV-IIAMYGagktA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  91 GKLAYMSQEYSTSQDFLSLV--DIKEDLIFIMYML---YFKISKLSSslqGTSIKGITKKELLNLSISIvNNTAEQNRIG 165
Cdd:cd17500    78 GRVAINKIPLTTNQACCNLIidNKKADYRFVYYSLktqYEELVNLAS---GAAQQNLNSKLIKNFEIPL-PPLPEQKRIA 153

                         170
                  ....*....|..
gi 2735216693 166 RVFKILDNSINL 177
Cdd:cd17500   154 SILSSLDDKIEL 165
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 11-179 1.30e-15

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


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 73.93  E-value: 1.30e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  11 TWERKKLGDVANsyINGGTPDTQNKNYWIGDIPWIQSSDLKNDDIWNVN-INKYItnkavndsaaklIPANSIAIVTRVG 89
Cdd:pfam01420   3 DWEVFKLGDVFE--IKKGKTPKKKELKNNGKYPYIRAGDLNNVVKGGLGyIKKYI------------LPKGDITISSRAT 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  90 VGKLAYMSQEYSTSQDFLSLVDIKEDLI--FIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRV 167
Cdd:pfam01420  69 IGYVFYRDKPYYTNQHIIVLIPKNNIKIteFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLP-PLEEQKKIAKI 147

                         170
                  ....*....|..
gi 2735216693 168 FKILDNSINLHE 179
Cdd:pfam01420 148 LSQLDNTIELEK 159
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 218-382 9.67e-14

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: 68.95  E-value: 9.67e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 218 CRLNDHAIVTMGQSP-NSKNYTNNQTDKIL----VQGNADLYKNKVLKRVFTTEITKTAI-KNDILISVRAPVGDIAR-N 290
Cdd:cd16961     1 KKLGEIAEIISGKTPsSSSEYWDNGIIPWIrisdINNGGIILTDEKITEEGAEKLKKKILpKGDILISRSGTIGKVAIvK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 291 QYESVVIGRGIASIKGND-----FLYYQLekmkNSGFWNKYI---AGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSS 362
Cdd:cd16961    81 ENDKALLNQAVIVIRPKDevdseFLYYFL----KSPFGKKLIegsAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDK 156

                         170       180
                  ....*....|....*....|
gi 2735216693 363 LTNIIQLQEHKIDSLKKLKQ 382
Cdd:cd16961   157 LDALIELLEQKLEKLEQLKQ 176
RMtype1_S_HpyAXIII_TRD1-CR1_like cd17281
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-183 1.75e-13

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


Pssm-ID: 341170  Cd Length: 196  Bit Score: 68.39  E-value: 1.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANSYiNGGTPDTQNKNYWI-GDIPWIQSSDL-KNDDIWNvNINKYITNKAVNDSaaKLIPANSIAIVTRVG 89
Cdd:cd17281     2 VEWKKLGEIFDIR-NGYTPSKSNKEYWEnGTIPWFRMEDIrENGRILS-DSIQHITPSAVKGG--KLFPANSIILSTTAT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  90 VGKLAYMSQEYSTSQDF--LSLVDIKEDLIFIMYMLY--FKISK-LSSSLQGTSIKGITKKELLNLSISIvNNTAEQNRI 164
Cdd:cd17281    78 IGEHALITVDSLANQRFtnFSLKKSYKNKLDIKFLFYyfFVLGEwCKKNINIGGFPSVDMNKLKKFKIPI-PPLEEQEKI 156

                         170
                  ....*....|....*....
gi 2735216693 165 GRVFKILDNSINLHEDHLQ 183
Cdd:cd17281   157 VEILDKFTKLTADLTAELP 175
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-185 1.89e-13

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acetobacter pasteurianus S subunit (S.Apa101655I) TRD2-CR2; The S. Apa101655I S subunit recognizes 5'... TTAGNNNNNNTTC... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341133 [Multi-domain]  Cd Length: 180  Bit Score: 67.88  E-value: 1.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsyIN-GGTPDTQNKNYWIGD-IPWIQSSDLKNDDIWNvNINKYITNKAVNDSAAKLIPANSIAIVTRVGVGK 92
Cdd:cd17244     1 VKLGDIFD--IKiGKTPPRKEPEYWSGDnIPWVSISDMGKGKYIS-DTKEYITDEAVKKFNVKLVPKGTLLMSFKLTIGR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  93 LAYMSQEYSTSQDFLSLVdIKEDLIFIMYM-LYFKISKLsSSLQGTSIKGIT--KKELLNLSIsIVNNTAEQNRIGRVFK 169
Cdd:cd17244    78 VAIAGKDLYTNEAIAHFI-PKDKKIDTEYLyYYLKSFDY-SSLGSTASKGKTlnSKKIKEIPI-PLPPLEEQKRIAPILD 154

                         170
                  ....*....|....*.
gi 2735216693 170 ILDNSINLHEDHLQFL 185
Cdd:cd17244   155 KIDALIDQLETLIELL 170
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-172 2.74e-13

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: 67.58  E-value: 2.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANSYINGGTPDTQNKNYWI-GDIPWIQSSDLKNDDIWNVNInKYITNKAVNDSAAKLIPANSIAIV---TRVGV 90
Cdd:cd17514     1 VKIQDIAFEIINGGTPSRNEPEYWNnGDIPWLTSGETDDNFINNTSE-KITTKNGLEDSSIRIVPKGTILIActgQGYTR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  91 GKLAYMSQEYSTSQDFLSLVDIKEDL-IFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIvNNTAEQNRIGRVFK 169
Cdd:cd17514    80 GQVAVLQIDASTNQAIAAIRCKENVNpKYLYYYLKTQKNNLRNLTSGVAQKNLNIEMLRNLQIPL-PPKEEQQKIVNILE 158


                  ...
gi 2735216693 170 ILD 172
Cdd:cd17514   159 TLE 161
RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like cd17280
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter ...
 27-84 1.23e-12

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: 66.03  E-value: 1.23e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2735216693  27 GGTPDTQNKNYWIGDIPWIQSSDLKNDDIwnVNINKYITNKAVND-SAAKLIPANSIAI 84
Cdd:cd17280    13 GTTPKSDNEDYYDGGIPWVTTGDLRDGII--TETSKKITDKALDDySALKIYPAGSLVI 69
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 307-389 1.32e-12

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) TRD1-CR1, and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) TRD2-CR2; The recognition sequences of Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341175 [Multi-domain]  Cd Length: 179  Bit Score: 65.59  E-value: 1.32e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEkmknsgFWNKYI----AGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQ 382
Cdd:cd17286    99 PEFLYYALE------NWSKKIkslaGKQAVPIINKTEFSKIKILVPPLEEQQKIANFLSKLDELIELQQQKIEKLEELKK 172


                  ....*..
gi 2735216693 383 FLLQNMF 389
Cdd:cd17286   173 GLLQKLF 179
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 273-389 1.83e-12

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: 65.21  E-value: 1.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 273 KNDILISVR----APVGDIA--RNQYESVVIGRGIASIKG--NDFLYYQLekmkNSGFWNKYIA---GSTFESITGKDLK 341
Cdd:cd17265    58 EGDILICVRngsrALIGKNAliDKEAEGMTFGAFMTVFRSeyNDYLFHLF----NSDLFKKQIGsflTATINQITNGNLN 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2735216693 342 NAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17265   134 NFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKELMQQLI 181
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-389 7.21e-12

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: 62.56  E-value: 7.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKnsgfWNKyIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17292    72 NKFLYYFYQIIK----WKK-TEGSTIKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQ 146


                  ...
gi 2735216693 387 NMF 389
Cdd:cd17292   147 YLF 149
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 15-175 3.12e-11

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: 61.83  E-value: 3.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVAnSYINGGTPDTQNKNYWI--GDIPWIQSSDLKNDDIWNVNInkYITNKAVNDSAAKLIPANSIAIVTRVG--- 89
Cdd:cd17276     1 KKIGDIA-KTSSGGTPLRSNQEYYFngGTIPWVKTTDLNNGVIYETEE--KITEKALKETSCKLLPKGTVLVAMYGGfgq 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  90 VGKLAYMSQEYSTSQDfLSLVDIKEDLIFIMYMLYFKISKLS--SSLQGTSIKG--ITKKELLNLSISIVnNTAEQNRIG 165
Cdd:cd17276    78 IGRTGLLGIPAAINQA-ICAILPNEKKVNPEFLLRYLNFNRPywMRVAASSRKDpnITKDDVRNFPIPLP-PLDEQRAIV 155

                         170
                  ....*....|
gi 2735216693 166 RVFKILDNSI 175
Cdd:cd17276   156 EFLSDVDALI 165
RMtype1_S_Vch69ORF1407P_TRD2-CR2_like cd17501
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio ...
 12-179 3.36e-11

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


Pssm-ID: 341192 [Multi-domain]  Cd Length: 191  Bit Score: 61.81  E-value: 3.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANSYINGGTPDTQNKNYWI-GDIPWIQSSDLKNDDIwnVNINKYITNKAVNDSAAKLIPANSIAI----VT 86
Cdd:cd17501     5 WEVGTILDLCYKTQSGGTPSRKNPEYWDgGIIPWLKTGELRDNII--LDTEEKITEEGLKNSSAKLFPKGTVLVamygAT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  87 rvgVGKLAYMSQEYSTSQDFLSLVDIKEDLIFIMYM-LYFKISKLSSSLQGTSIKGITKKELLNLSISIVNNTAEQNRIG 165
Cdd:cd17501    83 ---AGKLGILAKEATTNQACCALIPKEEYSPFFLYLyLLNSRDYLANLASGSAQQNISQQIIKNTKVLIPPEDLLEIFNK 159

                         170
                  ....*....|....
gi 2735216693 166 RVFKILDNSINLHE 179
Cdd:cd17501   160 LVEPLFDKIINNLK 173
RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like cd17258
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 235-389 6.97e-11

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: 60.50  E-value: 6.97e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 235 KNYTNNQTDKILVqgnaDLYKNKVLKRvftteiTKTAIKNDILISVRAPVGDIARNQYESVVIGRGIA------SIKGND 308
Cdd:cd17258    23 KNELINSLKVKIV----EPDYKIGLKQ------SKIFKKGDVLITRHGTIGRVSIILSEEACLSSHVAgfnskeGISDNK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 309 FLYYQLE--KMKNSGfwNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17258    93 FIKYLFNskKIKNRL--MSYGASSTQPALNLSRLLKIKFPNPPLEEQQKIGKILSTWDRAIELTEQKLELLQQQKKGLMQ 170


                  ...
gi 2735216693 387 NMF 389
Cdd:cd17258   171 QLF 173
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 273-389 1.20e-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: 60.23  E-value: 1.20e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 273 KNDILISVRAPVGDIAR-NQYESVVIGRGIASIKG------NDFLYYQLekmkNSGFWNKYI----AGSTFESITGKDLK 341
Cdd:cd17246    65 KGDILFSIIGTIGRVAIvPEDLPANINQAVALIRPkkekidPKYLLYYL----NSPIIQKQIeknaVGGTQKNLSLGDLK 140

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2735216693 342 NAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17246   141 NLKIPLPPLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLL 188
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-197 1.88e-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: 1.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVAnSYINGGTPDTqnKNYWIGDIPWIQSSDLKNDDIwNVNINKYITNKAVNDSAAKLIP-ANSIaIVTRVG- 89
Cdd:cd17246     1 WEWVKLGEIS-SDITDGTHPT--PKYVESGIPFITSKNIKNGKI-DFSDVKYISEEDHNEILKRSKLkKGDI-LFSIIGt 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  90 VGKLAY--MSQEYSTSQDfLSLVDIKEDLIFIMYMLYF-----KISKLSSSLQGTSIKGITKKELLNLSISIVNnTAEQN 162
Cdd:cd17246    76 IGRVAIvpEDLPANINQA-VALIRPKKEKIDPKYLLYYlnspiIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPP-LEEQK 153

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2735216693 163 RIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17246   154 RIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLL 188
RMtype1_S_Sba223ORF3470P-TRD1-CR1_like cd17270
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-196 2.27e-09

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: 56.56  E-value: 2.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsYINGGTPDTQNKNYWIGD---IPWIQSSDLKNDDIWNVNINKYITNKAVNDSAakLIPANSIaIVTRVG-V 90
Cdd:cd17270     1 KTLGEVAK-FRRGSFPQPYGNSEWYDGegsMPFVQVADVGDNFKLVEKTKQKISKLAQPKSV--FVPKGTV-IVTLQGsI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  91 GKLA------YMSQEYSTSQDFLSLVDIKedliFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVNNtAEQNRI 164
Cdd:cd17270    77 GRVAitqydaYVDRTLLIFESYKININKK----FFAYQLKLKFEIEKEKAPGGTIKTITKEELSKFEIPIPSL-EEQKEI 151

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2735216693 165 GRVFKILDNSINLHEDHLQFLHVFKSFLLQKM 196
Cdd:cd17270   152 VNILDKFDELITELQLRKKQLEYYKKALLSFM 183
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-388 3.15e-09

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


Pssm-ID: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 55.52  E-value: 3.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKnsgfWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17262    95 TEFLYYYLNSID----ISPYVTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQ 170


                  ..
gi 2735216693 387 NM 388
Cdd:cd17262   171 KL 172
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-386 3.39e-09

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: 55.15  E-value: 3.39e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKnsgfWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17266    84 IKFLYYLLKSLN----LNQYATGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKELMQ 159
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
312-389 3.50e-09

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 53.52  E-value: 3.50e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2735216693 312 YQLEKMKNSGFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:COG0732     4 YYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 213-379 8.32e-09

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: 54.28  E-value: 8.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 213 EKWNQCRLNDHAIVTMGQSPNSKNYTNNQTDKILvqGNADLYKNKVLkrvfTTEITKTAI--KNDILISVRAPVGDIARN 290
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPKKKELKNNGKYPYI--RAGDLNNVVKG----GLGYIKKYIlpKGDITISSRATIGYVFYR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 291 QYESVV---IGRGIASIKGND--FLYYQLEKMKNSGfwNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTN 365
Cdd:pfam01420  76 DKPYYTnqhIIVLIPKNNIKIteFLYLYLLLKLKKL--KSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQLDN 153

                         170
                  ....*....|....
gi 2735216693 366 IIQLQEHKIDSLKK 379
Cdd:pfam01420 154 TIELEKGILNELER 167
RMtype1_S_Sba223ORF3470P-TRD1-CR1_like cd17270
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 251-388 1.10e-08

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: 54.25  E-value: 1.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 251 ADLYKNKVLKRVFTTEITKTAI-------KNDILISVRAPVGDIARNQYESVViGRGIASIKGND------FLYYQLeKM 317
Cdd:cd17270    36 ADVGDNFKLVEKTKQKISKLAQpksvfvpKGTVIVTLQGSIGRVAITQYDAYV-DRTLLIFESYKininkkFFAYQL-KL 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2735216693 318 KNSgFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNM 388
Cdd:cd17270   114 KFE-IEKEKAPGGTIKTITKEELSKFEIPIPSLEEQKEIVNILDKFDELITELQLRKKQLEYYKKALLSFM 183
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 273-386 1.25e-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: 54.04  E-value: 1.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 273 KNDILISVRAPVGDIAR--------NQYESVVIgrgIASIKG--NDFLYYQL--EKMKNsgFWNKYIAGSTFESITGKDL 340
Cdd:cd17256    62 KGDILISIVGTIGRVGIvpkeldgaNLTENAAR---IRPKDSisPRYLYYYLrsPFGQS--QIESETKGAAQPKLNLKRI 136

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2735216693 341 KNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17256   137 RELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKALMQ 182
RMtype1_S_Eco540ANI-TRD1-CR1_like cd17274
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 305-390 2.62e-08

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


Pssm-ID: 341163  Cd Length: 171  Bit Score: 52.88  E-value: 2.62e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 305 KGNDFLYYQLEKMKNSgfwnKYIAG-------STFESItgkdlknaKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSL 377
Cdd:cd17274    91 NNNVNLKFVYEALQTI----KYVPGdhkrhwiSEYSKF--------KIPLPPLEEQNKIVRILDKFDELIAELEAKLELL 158

                          90
                  ....*....|...
gi 2735216693 378 KKLKQFLLQNMFI 390
Cdd:cd17274   159 KKQKKYYLQKLFT 171
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 308-389 5.45e-08

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: 52.08  E-value: 5.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 308 DFLYYQLEKMKNSgfWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQN 387
Cdd:cd17254    94 DYLYYLLKALTEE--IESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLEELRKALLQS 171


                  ..
gi 2735216693 388 MF 389
Cdd:cd17254   172 LL 173
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17251
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 12-151 6.36e-08

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


Pssm-ID: 341140 [Multi-domain]  Cd Length: 185  Bit Score: 52.12  E-value: 6.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLKNdDIWNVNINKYITNKAVNDSAAKLIPANSIaIVTRVG-V 90
Cdd:cd17251     1 WEVKTLKDFGK-IITGKTPSTKNKEYYGGDIPFIKIPDMHG-NVFITKTEDYLSEEGANSQKNKTLPKNSI-CVSCIAtV 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2735216693  91 GKLAYMSQEYSTSQDFLSLVDIKEDLifiMYMLYFKISKLSSSLQGTSIKGITkkeLLNLS 151
Cdd:cd17251    78 GLVSITTEESQTNQQINSIIPKKENY---RYYLYFALKSLKELLEALGSGGST---TLNLN 132
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 117-197 7.39e-08

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: 51.75  E-value: 7.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 117 IFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVNNtAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKM 196
Cdd:cd17494    92 IFLYLYLLNIEGYWSKISQGSTFESINSNDIKNLKISIPSL-EEQQKIATFLSTLDAEITLLEKKLEKLKQLKKGLLQKL 170


                  .
gi 2735216693 197 F 197
Cdd:cd17494   171 F 171
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 252-389 1.15e-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: 51.35  E-value: 1.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 252 DLYKNKVLKRVFTTEITKTAIKNDILIsVR--APVGDIARNqyESVVIGRGIASIK------GNDFLYYQLekmKNSGFW 323
Cdd:cd17263    36 DLRNNNEKKYIENPKKSVICNEDDILI-VRdgANAGEVGTG--LEGAIASTLFKIIpdkniiDKDYLYYFL---KSKEIQ 109

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2735216693 324 NKYI--AGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17263   110 LNILtkAGSTIPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALIDKLKELIEKLIELKKGLFQELL 177
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 75-197 1.81e-07

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: 50.61  E-value: 1.81e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  75 KLIPANSIAIVTRVGVGKLAYMSQEYSTSQDFLSLVDIKE-DLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSIS 153
Cdd:cd17245    52 KIAEKGDILISVRAPVGDVNIADEKCCIGRGLAAIRANKDiDNLFLYYYLKYNKPELEKLGTGSTFKAINKKDLEELKIP 131

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2735216693 154 IVnNTAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17245   132 LP-PLEEQQKIAEILSTVDEAIEKTKALIEKLDELKKGLMQELF 174
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 308-386 4.11e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to TRD2-CR2's of StySKI, S.EcoAI, S.EcoJA17PI, and S.EcoJA23PI; Salmonella kaduna CDC-388 S subunit (StySKI) recognizes 5'... CGATNNNNNNNGTTA ... 3' while Escherichia coli Type-1 restriction enzyme EcoAI specificity protein (S.EcoAI), Escherichia coli UCD_JA17_pb S subunit (S.EcoJA17PI) and Escherichia coli UCD_JA23_pb S subunit (S.EcoJA23PI) recognize 5'... GAGNNNNNNNGTCA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341148 [Multi-domain]  Cd Length: 189  Bit Score: 49.82  E-value: 4.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 308 DFLYYQLekmkNSGFWNKYIAGSTFES----ITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQF 383
Cdd:cd17259   110 DFLYYLL----QSDFFLNYVEPVLTGTdvphISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKG 185


                  ...
gi 2735216693 384 LLQ 386
Cdd:cd17259   186 LMQ 188
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-194 5.28e-07

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


Pssm-ID: 341141 [Multi-domain]  Cd Length: 189  Bit Score: 49.48  E-value: 5.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVAnSYINGGT--PDTQNKNYWIGDIPW-----IQSSDLKNDDIWNVNINKyitnkaVNDSaaKLIPANSIAI 84
Cdd:cd17252     1 WEWVRLGEIA-EIIRGVTykKSDASEEPSEGGIPVlrannIQNGGLDFDDLVYVPKSK------VKEE--QKLKKGDILI 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  85 VTRVG----VGKLAYMSQEY-STSQDFLSLVDIKEDLI--FIMYML---YFKiSKLSSSLQGTSIKGITKKELLNLSISI 154
Cdd:cd17252    72 CMSSGskelVGKAAFIDEDTdYTFGAFCGVIRPKKEIDprYLFYFLqspSYR-EYIRSLASGTNINNLSNEHLENLKIPL 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2735216693 155 VnNTAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQ 194
Cdd:cd17252   151 P-PLAEQKRIVAKLDKLDALIDKLKQALEKLDELLKSLFQ 189
RMtype1_S_NmaSCMORF606P_TRD2-CR2_like cd17271
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 307-389 1.12e-06

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: 48.42  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKNS-GFwnKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLL 385
Cdd:cd17271   104 TEFLFYWYKKYGNYlGF--KYAQGTKQQSYTADIVKKLPILLPTLKEQKKIANFLSDIDELIATLEKKIEKLKKIKKGLM 181


                  ....
gi 2735216693 386 QNMF 389
Cdd:cd17271   182 QKLL 185
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 256-385 1.33e-06

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


Pssm-ID: 341132 [Multi-domain]  Cd Length: 182  Bit Score: 48.22  E-value: 1.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 256 NKVLKRVFTTE--ITKTAIKN---------DILISVRAPVGDIAR-------NQyeSVVigrGIASIKG--NDFLYYQL- 314
Cdd:cd17243    38 NNDSRFVLDTEkkITELGLKNsstkllpkgTTIISARGTVGKLALlgipmamNQ--SCY---GLRGKDGlsNYFLYYLLk 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2735216693 315 ---EKMKNSGfwnkyiAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLL 385
Cdd:cd17243   113 nliEELKQKA------HGSVFDTITRKTFDEIKVPLPPEELQKSFENIVSPLFDKILNNLKENQTLAQLRDTLL 180
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 110-197 1.92e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.FclI TRD1-CR1; The recognition sequence of Flavobacterium columnare G4 S subunit (S.FclI) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also contains TRD-CR-like sequence-recognition domains of type I DNA methyltransferases, such as putative Type I N6-adenine DNA methyltransferases from Microbacterium ketosireducens (M.Msp12510ORF408P) and Treponema primitia ZAS-2 (M.TprZAS2ORF3630P). It may also include various type II restriction enzymes and methyltransferases.


Pssm-ID: 341143 [Multi-domain]  Cd Length: 173  Bit Score: 47.45  E-value: 1.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 110 VDIKE--DLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVNnTAEQNRIGRVFKILDNSINLHEDHLQFLHV 187
Cdd:cd17254    85 VVPDEeiDKDYLYYLLKALTEEIESQAHGSTMVHITKGDLENIKVPLPP-LEEQKRIAAILDELDALIDALEEQLKKLEE 163

                          90
                  ....*....|
gi 2735216693 188 FKSFLLQKMF 197
Cdd:cd17254   164 LRKALLQSLL 173
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 215-390 1.93e-06

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


Pssm-ID: 341167 [Multi-domain]  Cd Length: 189  Bit Score: 47.89  E-value: 1.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 215 WNQCRLNDHAIVTMGQSPNSKNYTNNQTdKILVQGN-----ADLYKNKVLKRVFTTEITKTAI-KNDILIS-VRAPVGDI 287
Cdd:cd17278     1 WEVVKLGDIADIQNGYAFKSSDFSDEGI-PVIRIGNiknggIDLDDNSKYPEEPLEKYEKFLLkKGDILIAmTGGTVGKV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 288 ARNQYESVV------IGRGIASIKGN-DFLYYQLekmKNSGFWNKYIA---GSTFESITGKDLKNAKIYTTNSDEERKIG 357
Cdd:cd17278    80 AIVPEDDEPallnqrVGKFRPKDKIDkEFLYYLL---RSDSFRNQIKSsatGTAQPNISPKDIESIKIPLPPLEEQKKIA 156

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2735216693 358 NIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMFI 390
Cdd:cd17278   157 EILDSLDAKIDKLEQKLEKLRDLLKPLLQSLFT 189
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 215-386 2.18e-06

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


Pssm-ID: 341193 [Multi-domain]  Cd Length: 195  Bit Score: 47.99  E-value: 2.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 215 WNQCRLNDHAIVTMGQSPNSKNYTN-----------------NQTDKILVQGNADLYKNKVLKrvftteitktaiKNDIL 277
Cdd:cd17512     1 WEEIRLGDIIDYQKGYAFKSKDYQDsgirivrvsdftddsidINNLVYISEEKANKYKKYELK------------ENDII 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 278 ISVrapVGDIArNQYESVViGRGI---------------------ASIKGNDFLYYQLekmKNSGFWNkYIA----GSTF 332
Cdd:cd17512    69 ITT---VGSWP-SNPDSVV-GKVVrvpkeadgallnqnavkirpkKGILDQSFLFYNL---KSERFKN-YIEsiarGNAN 139

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2735216693 333 E-SITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17512   140 QaSITLGDIKKFKFLLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQALYQ 194
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
127-197 2.93e-06

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 45.05  E-value: 2.93e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2735216693 127 ISKLSSSLQGTSIKGITKKELLNLSIsIVNNTAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:COG0732    12 REYLRSLATGSTQPNLNKKDLKKLPI-PLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-389 3.75e-06

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: 47.04  E-value: 3.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKNsgfwnKYIA---GSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQF 383
Cdd:cd17515   101 NEFLFYFLKSQKE-----YLISlgkGGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKLIEKLEKALEKLEELKKA 175


                  ....*.
gi 2735216693 384 LLQNMF 389
Cdd:cd17515   176 LMQKLL 181
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 307-389 5.22e-06

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: 46.71  E-value: 5.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQL----EKMKNSGfwnkyiAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQ 382
Cdd:cd17287   103 PDFLFYYLqssyEELRDLS------NGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAKIDALEQKLELLQELKK 176


                  ....*..
gi 2735216693 383 FLLQNMF 389
Cdd:cd17287   177 SLMQQLF 183
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 309-388 6.15e-06

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


Pssm-ID: 341177 [Multi-domain]  Cd Length: 163  Bit Score: 45.92  E-value: 6.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 309 FLYYQLEKMKnsgfWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTN---IIQLQEHKIDSLKKLKQFLL 385
Cdd:cd17288    85 FLYYLLKTID----FKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAkdaLIELQEKLLEKLKQYKLALM 160


                  ...
gi 2735216693 386 QNM 388
Cdd:cd17288   161 QEL 163
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-197 7.85e-06

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: 45.96  E-value: 7.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsyINGGTP-------DTQNKNYwigdIPWIQSSDLKNDdiwnvNINKYItnkaVNDSAAKLIPANSIAIVT- 86
Cdd:cd17263     1 VKLGEVCK--FSKGKQppiserfDEPKEGS----VRYIQIEDLRNN-----NEKKYI----ENPKKSVICNEDDILIVRd 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  87 -----RVGVGKLAYMSqeySTsqdfLSLVDIKEDLIFIMYMLYF----KISKLSSSLQGTSIKGITKKELLNLSISIVNn 157
Cdd:cd17263    66 ganagEVGTGLEGAIA---ST----LFKIIPDKNIIDKDYLYYFlkskEIQLNILTKAGSTIPHVNKKDLENLKIPLPS- 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2735216693 158 TAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17263   138 LEEQKKIAEILDKLDALIDKLKELIEKLIELKKGLFQELL 177
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-388 1.05e-05

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: 45.21  E-value: 1.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKNsgfwnKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17255    90 NKFLYYALNLIAK-----KYVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIAKLKKLIELRKKQLE 164


                  ..
gi 2735216693 387 NM 388
Cdd:cd17255   165 YY 166
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 89-197 1.30e-05

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: 45.18  E-value: 1.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  89 GVGKLAYMSQEYSTSQDFLSL-VDIKEDLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVNNtAEQNRIGRV 167
Cdd:cd17496    67 TTGRLNIADDEYCIGRGVAAIrPKNGIDTEFLYYLLESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPL-EEQKRIVAI 145

                          90       100       110
                  ....*....|....*....|....*....|
gi 2735216693 168 FKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17496   146 LDPLDEKIDKNKQEIEKLEELRDTLLPKLL 175
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-196 1.53e-05

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: 45.22  E-value: 1.53e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANSYINGGTpdtQNKNYWIGDIPWIQSSDLKNDDIWNVNINKYITNKAVNDSAAKLIPaNSIaIVTRV--- 88
Cdd:cd17517     1 WEVVKLGDLLEDPRYGTS---KKSSYDGSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKELEKYLLKK-GDI-LFNRSngs 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  89 --GVGKLAYMSQE-----YSTsqdFLSLVDIKEDLI---FIMYMLYFKISK---LSSSLQGTSIKGITKKELLNLSIsIV 155
Cdd:cd17517    76 peLVGKCALVDEEdepaiFAS---YLIRLRLDKKKIlpeFLYYYLNSPLGRkqiEKIAKSAAGQANINQKDLKKLPI-PL 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2735216693 156 NNTAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKM 196
Cdd:cd17517   152 PPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 334-388 2.00e-05

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P/MjaXIIP) TRD1-CR1; The recognition sequence of Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P, also called MjaXIIP) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341203 [Multi-domain]  Cd Length: 190  Bit Score: 44.84  E-value: 2.00e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2735216693 334 SITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNM 388
Cdd:cd17522   136 SINQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEKLKELKKGLFQKL 190
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-388 2.01e-05

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: 44.84  E-value: 2.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLekmkNSGFWNKYIAGST-----FESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLK 381
Cdd:cd17517   110 PEFLYYYL----NSPLGRKQIEKIAksaagQANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLF 185


                  ....*..
gi 2735216693 382 QFLLQNM 388
Cdd:cd17517   186 KSLMQSL 192
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 308-389 5.45e-05

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: 43.69  E-value: 5.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 308 DFLYYQLekmKNSGFWNKYIAG----------STFESItgkdlknaKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSL 377
Cdd:cd17516   104 DFVYYLL---KNNSKYLKSIAGgstatpiinkSTFSNI--------EIPLPPLPEQKKIAAILSSLDDKIENNRRINKTL 172

                          90
                  ....*....|..
gi 2735216693 378 KKLKQFLLQNMF 389
Cdd:cd17516   173 EEMAQALFKEWF 184
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 132-197 6.04e-05

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: 42.92  E-value: 6.04e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2735216693 132 SSLQGTSIKGITKKELLNLSISIVNnTAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17292    85 KKTEGSTIKRLYNDNLLNTKIPVPS-LDEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYLF 149
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 262-386 6.21e-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: 6.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 262 VFTTE--ITKTAI---------KNDILISVRAPVGDIARN---QYESVvIGRGIASIKGND------FLYYQLEKmkNSG 321
Cdd:cd17276    42 IYETEekITEKALketsckllpKGTVLVAMYGGFGQIGRTgllGIPAA-INQAICAILPNEkkvnpeFLLRYLNF--NRP 118

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2735216693 322 FWNKYIAGSTFE-SITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17276   119 YWMRVAASSRKDpNITKDDVRNFPIPLPPLDEQRAIVEFLSDVDALIDSLEALIEKLRELKKGLMQ 184
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 268-382 6.52e-05

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: 43.32  E-value: 6.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 268 TKTAIKNDILISVRAPVGDIARNQYESVV-IG-RGIASIKGND--FLYYQL----EKMKNSGfwnkyiAGSTFESITGKD 339
Cdd:cd17279    60 TSLVPAGSIILSTRAPIGYVAIATVELCTnQGcKALVPNSDVDsrFLYYLLlaakEELNSLG------RGTTFLELSTDE 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2735216693 340 LKNAKIYTTNSDEERKIGNIFSSLT----NIIQLQEHKIDSLKKLKQ 382
Cdd:cd17279   134 LANFKIPLPPLSEQRAIADFLDRETakidALIAKKQQLIELLKEKRQ 180
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 215-389 6.65e-05

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: 43.25  E-value: 6.65e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 215 WNQCRLNDHAIVTMGQSPNSKN--YTNNQTDKILVQGNADLyknkvlKRVFTTE--ITKTAIKN---------DILISVR 281
Cdd:cd17294     1 WEWKTLGEIAKIFSGGTPSTSNpeYWDGGTIPWLSSGEVNF------KEIYETEkrITEEGLKNssakwipknSVLIALA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 282 ---APVGDIARNQYESVvIGRGIASIKGND------FLYYQL----EKMKNSGfwnkyiAGSTFESITGKDLKNAKIYTT 348
Cdd:cd17294    75 gqgKTRGTVAILKIPLT-TNQSLAAIEPDEeiansrFLYYNLssryEELRSLS------GGGGRGGLNLKIIKSLPIPLP 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2735216693 349 NSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17294   148 PLEEQKKIVAILDKFDALINDLKEGLPALLELRQKQYEYLR 188
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 115-196 1.52e-04

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


Pssm-ID: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 42.03  E-value: 1.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 115 DLIFIMYmlYFKISKLSSSLQGTSIKGITKKELLNLSIsIVNNTAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQ 194
Cdd:cd17262    94 STEFLYY--YLNSIDISPYVTGAAQPKLNQANLNSIPI-PLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQ 170


                  ..
gi 2735216693 195 KM 196
Cdd:cd17262   171 KL 172
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 272-386 1.66e-04

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: 42.14  E-value: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 272 IKNDILISVRAPVGDIARnqYESVVIGrGIAS---------IKGNDFLYYQLEKMKNSGFWNKYIAGSTFESITGKDLKN 342
Cdd:cd17264    63 QKGDILYCLRGSLGKCAI--VDNYDEG-AIASslviirpfaKVDVRYLYYYLNSPLGKSQIKKYDNGSAQPNLSAKSLKK 139

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2735216693 343 AKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17264   140 FLIPLPPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQSLFQ 183
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 16-193 3.28e-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.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: 41.08  E-value: 3.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  16 KLGDVANSYINGGTP-DTQNKNYwiGDIPWIQSSDLKNDD--IWNVNINKYITNKAVNDSAAKLIPANSIaIVTRVG--- 89
Cdd:cd17250     2 RLGDVCDFKAGSGFPeKYQGKED--GEYPFYKVGDMNNSGneKYLSTAENYISEEIVKELKAKLFPKGTI-IFAKIGeai 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  90 -VGKLAYMSQEystsqdflSLVD------IKEDLIFIMYMLYF-KISKLSSSLQGTSIKGITKKELLNLSISIvNNTAEQ 161
Cdd:cd17250    79 kLNRRAILSKD--------SCIDnnvmglIPNEGIDSEYLYYWlKKVDLYKYSQATTVPSIRKSTLESIPIPL-PPLEEQ 149

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2735216693 162 NRIGRV----FKILDNSINLHEDHLQFLHVFKSFLL 193
Cdd:cd17250   150 KRIAAKldelFEKLDKLKQALEAAKEQLKGLRQSLL 185
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-195 3.83e-04

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


Pssm-ID: 341193 [Multi-domain]  Cd Length: 195  Bit Score: 41.05  E-value: 3.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVANsYINGGTpdTQNKNYWIGDIPWIQSSDLKNDDIwNVNINKYITNKAVNDSAAKLIPANSIaIVTRVG-- 89
Cdd:cd17512     1 WEEIRLGDIID-YQKGYA--FKSKDYQDSGIRIVRVSDFTDDSI-DINNLVYISEEKANKYKKYELKENDI-IITTVGsw 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  90 -------VGKLAYMSQEYSTS---QDFLSLVDIKEDL--IFIMYMLYFK--ISKLSSSLQGTSIK-GITKKELLNLSISI 154
Cdd:cd17512    76 psnpdsvVGKVVRVPKEADGAllnQNAVKIRPKKGILdqSFLFYNLKSErfKNYIESIARGNANQaSITLGDIKKFKFLL 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2735216693 155 VNNTaEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQK 195
Cdd:cd17512   156 PPLE-EQKKIASILSAYDDLIENNEKRIKLLEQMKQALYQE 195
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-389 8.41e-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.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: 39.93  E-value: 8.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKNSgfwnKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17250   107 SEYLYYWLKKVDLY----KYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGLRQ 182


                  ...
gi 2735216693 387 NMF 389
Cdd:cd17250   183 SLL 185
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 15-197 1.00e-03

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


Pssm-ID: 341189 [Multi-domain]  Cd Length: 173  Bit Score: 39.59  E-value: 1.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  15 KKLGDVANsYINGGTPDTQNKNYWIGDIPWIQSSDLKND-----DIWNVNINKYitnkavndsaAKlipANSIAIVTRVG 89
Cdd:cd17498     1 VKLGEIAE-ITMGQSPKSEFYNEDGIGLPFLQGNRTFGDkypyiDTYTTDIKKI----------AK---KGDILMSVRAP 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  90 VGKLAYMSQEYSTSQDFLSLVDIKEDLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLSISIVNNTaEQNRIGRVFK 169
Cdd:cd17498    67 VGDLNIANKDICIGRGLCSIRMKNGNNSFLYYLLKNNIKNLINKSSGTVFGSINKDDIENLEVDIPEDE-EQKRIANILS 145

                         170       180
                  ....*....|....*....|....*...
gi 2735216693 170 ILDNSINLHEDHLQFLHVFKSFLLQKMF 197
Cdd:cd17498   146 KIDDKIEINNQINKNLEELAQAIFKHWF 173
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-389 1.21e-03

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: 39.50  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKNsgFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17284   105 PEYLMYLLSLQKK--YMEKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQ 182


                  ...
gi 2735216693 387 NMF 389
Cdd:cd17284   183 QLF 185
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 273-389 1.34e-03

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: 39.35  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 273 KNDILISVRAPVGDIARNQYE-----SVVigrGIASIKG---NDFLYYQLEKMKNsgFWNKYIAGSTFESITGKDLKNAK 344
Cdd:cd17282    67 KGTLCITIAANIGDTAILGFDacfpdSVV---GFIPNEEkidVEFLEYYLRTLKK--ELEAIAPQSAQKNINLEILRPLK 141

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2735216693 345 IYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17282   142 IPVPPLEEQKKIVEILDALDDLIDNLEKRIAKLEELKQSLLQEAF 186
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 307-388 1.38e-03

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


Pssm-ID: 341202 [Multi-domain]  Cd Length: 187  Bit Score: 39.39  E-value: 1.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLekmkNSGFWNKYI----AGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQ 382
Cdd:cd17521   106 PKYLFYFT----QSSLYWKQIksisSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLK 181


                  ....*.
gi 2735216693 383 FLLQNM 388
Cdd:cd17521   182 ELLQSL 187
RMtype1_S_PluTORF4319P-TRD2-CR2_like cd17269
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 309-389 1.49e-03

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: 39.11  E-value: 1.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 309 FLYYQLEKmknsgFWNKYIA----GSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFL 384
Cdd:cd17269    86 FLYYYLKS-----YFKKYIEknsvGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAELPAELEARKKQYEYY 160


                  ....*
gi 2735216693 385 LQNMF 389
Cdd:cd17269   161 RDALL 165
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-386 1.70e-03

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: 39.00  E-value: 1.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKNSGFWNKYIAGSTfesitgKDL-----KNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLK 381
Cdd:cd17283   103 KDFLYYLLSSITVQLQFSAQAGGGT------KNLntdivKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLEELK 176


                  ....*
gi 2735216693 382 QFLLQ 386
Cdd:cd17283   177 KGLMQ 181
RMtype1_S_Eco15ORF14057P-TRD1-CR1_like cd17525
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 335-388 1.70e-03

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


Pssm-ID: 341206 [Multi-domain]  Cd Length: 190  Bit Score: 39.14  E-value: 1.70e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2735216693 335 ITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNM 388
Cdd:cd17525   137 IYQKDLKKLKLPLPPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKKALMQQL 190
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-195 1.78e-03

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: 39.03  E-value: 1.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  12 WERKKLGDVAN----------SYINGGTPDTQNKNYWIGDIPWiqssdlknddiwnvNINKYITNKAVNDSAAKLIPANS 81
Cdd:cd17259     1 WEWVKLGDVADilsgyafkssEFSESGIRLLRGANVGVGEIRW--------------DDTVYLPEEYLEEYEKYLLKEGD 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  82 IAI-VTR--VGVG-KLAYMSQEYSTS---Q---DFLSLVDIKEDLIFIMYMLYFKISKLSSSLQGTSIKGITKKELLNLS 151
Cdd:cd17259    67 IVIaLDRpiISGGlKVARIPKSDLPAllvQrvaRIRPKDELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFK 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2735216693 152 ISiVNNTAEQNRIGRVFKILDNSINLHEDHLQFLHVFKSFLLQK 195
Cdd:cd17259   147 IP-LPPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKGLMQS 189
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 299-387 2.08e-03

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


Pssm-ID: 341146 [Multi-domain]  Cd Length: 176  Bit Score: 38.66  E-value: 2.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 299 RGIASIKGNDFLYYQLEK-MKnsgFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSL 377
Cdd:cd17257    90 RPKSEELDKRFLYYALPPpLK---AIEDTTSSTTVKHLSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLIAKLEKL 166

                          90
                  ....*....|
gi 2735216693 378 KKLKQFLLQN 387
Cdd:cd17257   167 RDLLLPLLQS 176
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 37-183 3.24e-03

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: 38.25  E-value: 3.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693  37 YWIGDIPWIQSSDLKNDDIWNVNInKYITnkavnDSAAKLIPaNSI-----AIVTRVG-VGKLAYMSQEYS---TSQDFL 107
Cdd:cd17256    21 DGPTGVPYIRVTDIKNGGIDLDNL-KYIS-----PEIHEKIK-RYTlskgdILISIVGtIGRVGIVPKELDganLTENAA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 108 SLVDIKEDL-IFIMYML---YFKiSKLSSSLQGTSIKGITKKELLNLSISIVnNTAEQNRIGRVFKILDNSINLHEDHLQ 183
Cdd:cd17256    94 RIRPKDSISpRYLYYYLrspFGQ-SQIESETKGAAQPKLNLKRIRELPIPLP-PLEEQKRIVAILDSLDAKIDALEKQLA 171
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 272-386 4.47e-03

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: 37.92  E-value: 4.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 272 IKNDILISV----RAPVGDIAR-NQYESVVIG--RGIASIKGN---DFLYYQLekmkNSGFWNKYI----AGSTFESITG 337
Cdd:cd17252    65 KKGDILICMssgsKELVGKAAFiDEDTDYTFGafCGVIRPKKEidpRYLFYFL----QSPSYREYIrslaSGTNINNLSN 140

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2735216693 338 KDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17252   141 EHLENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQALEKLDELLKSLFQ 189
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-386 6.03e-03

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


Pssm-ID: 341137 [Multi-domain]  Cd Length: 196  Bit Score: 37.51  E-value: 6.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2735216693 307 NDFLYYQLEKMKnsGFWNKYIAGSTFESITGKDLKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQ 386
Cdd:cd17248   109 PEYLLYVLRAMK--PEFERLAMGSTHKTIYMPDFKALRIALPPLEEQRKIVDRLEALDAKIDALERKLERLIELLKELRQ 186
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 340-389 9.23e-03

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: 36.65  E-value: 9.23e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2735216693 340 LKNAKIYTTNSDEERKIGNIFSSLTNIIQLQEHKIDSLKKLKQFLLQNMF 389
Cdd:cd17260   116 LENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
 
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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