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Conserved domains on  [gi|1063532573|ref|WP_069395825|]
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restriction endonuclease subunit S [Mycobacterium shimoidei]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 199-391 3.06e-105

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: 309.08  E-value: 3.06e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 199 PESWELVPLGDLGRIGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGQG 278
Cdd:cd17247     1 PEHWEVVRLGDVARVGNGSTPSRKNPDYWNGGTIPWVSSGEVNDNRITEADEFITELALKECSLPLVPPGSVLVAMIGQG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 279 KTLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGstKGALTCGFLRGMTVPRPPtIIEQQE 358
Cdd:cd17247    81 KTRGQAAILAIEATINQNLAAIRPNEERVLPEYLHYYLESQYDELRRIGSGGG--QGALNCGILKAFPIPLPP-LDEQRE 157

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1063532573 359 IAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17247   158 IVAELEALLAKIDLLEEKIARLIELLKELRQAL 190
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 58-181 3.24e-13

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


The actual alignment was detected with superfamily member cd17260:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 165  Bit Score: 67.08  E-value: 3.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  58 FEPGDVLYGKLRPYLD--KAVLAD----RAGVATTELLVLRPKLGVSPEYLACVVHSPAFVEFA---MQGVTGAQhpRTS 128
Cdd:cd17260    35 FRNGDVLLAKITPCFEngKTAIVDglpnGIGFGSTEFHVLRPKEGILPEFLYYLLRSPSFRKEAiksMTGSSGRQ--RVP 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063532573 129 WVHIRTFELPAHDRSEQASIAKLLWSLFELSMTTEQGIASASCLKRAAMQQLF 181
Cdd:cd17260   113 KDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
 
Name Accession Description Interval E-value
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 199-391 3.06e-105

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: 309.08  E-value: 3.06e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 199 PESWELVPLGDLGRIGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGQG 278
Cdd:cd17247     1 PEHWEVVRLGDVARVGNGSTPSRKNPDYWNGGTIPWVSSGEVNDNRITEADEFITELALKECSLPLVPPGSVLVAMIGQG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 279 KTLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGstKGALTCGFLRGMTVPRPPtIIEQQE 358
Cdd:cd17247    81 KTRGQAAILAIEATINQNLAAIRPNEERVLPEYLHYYLESQYDELRRIGSGGG--QGALNCGILKAFPIPLPP-LDEQRE 157

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1063532573 359 IAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17247   158 IVAELEALLAKIDLLEEKIARLIELLKELRQAL 190
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 199-382 1.21e-16

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: 77.01  E-value: 1.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 199 PESWELVPLGDLGRIGNGSTPKRStgAYWDGGTFPWLNSAKVYDrdiqdadqfVTDVALKECHLPVLEPGAVLVAITGqg 278
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKK--ELKNNGKYPYIRAGDLNN---------VVKGGLGYIKKYILPKGDITISSRA-- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 279 kTLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVAsgGGSTKGALTCGFLRGMTVPRPPtIIEQQE 358
Cdd:pfam01420  68 -TIGYVFYRDKPYYTNQHIIVLIPKNNIKITEFLYLYLLLKLKKLKSLK--FGSTQPKLTKERLKEIKIPLPP-LEEQKK 143

                         170       180
                  ....*....|....*....|....
gi 1063532573 359 IAQVLDVLDRKIELLGRKRDVLDR 382
Cdd:pfam01420 144 IAKILSQLDNTIELEKGILNELER 167
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
313-398 1.09e-15

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 72.01  E-value: 1.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 313 RAYLETQYDHLRAVASGGGSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:COG0732     3 KYYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPP-LEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81


                  ....*.
gi 1063532573 393 TGEISV 398
Cdd:COG0732    82 TGELRV 87
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 58-181 3.24e-13

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: 67.08  E-value: 3.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  58 FEPGDVLYGKLRPYLD--KAVLAD----RAGVATTELLVLRPKLGVSPEYLACVVHSPAFVEFA---MQGVTGAQhpRTS 128
Cdd:cd17260    35 FRNGDVLLAKITPCFEngKTAIVDglpnGIGFGSTEFHVLRPKEGILPEFLYYLLRSPSFRKEAiksMTGSSGRQ--RVP 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063532573 129 WVHIRTFELPAHDRSEQASIAKLLWSLFELSMTTEQGIASASCLKRAAMQQLF 181
Cdd:cd17260   113 KDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
104-186 2.27e-06

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 45.43  E-value: 2.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 104 CVVHSPAFVEFAMQGVTGAQHPRTSWVHIRTFELPAHDRSEQASIAKLLWSLFELSMTTEQGIASASCLKRAAMQQLFSR 183
Cdd:COG0732     4 YYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFTG 83


                  ...
gi 1063532573 184 GLR 186
Cdd:COG0732    84 ELR 86
 
Name Accession Description Interval E-value
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 199-391 3.06e-105

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: 309.08  E-value: 3.06e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 199 PESWELVPLGDLGRIGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGQG 278
Cdd:cd17247     1 PEHWEVVRLGDVARVGNGSTPSRKNPDYWNGGTIPWVSSGEVNDNRITEADEFITELALKECSLPLVPPGSVLVAMIGQG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 279 KTLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGstKGALTCGFLRGMTVPRPPtIIEQQE 358
Cdd:cd17247    81 KTRGQAAILAIEATINQNLAAIRPNEERVLPEYLHYYLESQYDELRRIGSGGG--QGALNCGILKAFPIPLPP-LDEQRE 157

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1063532573 359 IAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17247   158 IVAELEALLAKIDLLEEKIARLIELLKELRQAL 190
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 202-392 2.47e-54

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: 178.45  E-value: 2.47e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDLGRIGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGQGKTL 281
Cdd:cd17294     1 WEWKTLGEIAKIFSGGTPSTSNPEYWDGGTIPWLSSGEVNFKEIYETEKRITEEGLKNSSAKWIPKNSVLIALAGQGKTR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 282 GNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVasGGGSTKGALTCGFLRGMTVPRPPtIIEQQEIAQ 361
Cdd:cd17294    81 GTVAILKIPLTTNQSLAAIEPDEEIANSRFLYYNLSSRYEELRSL--SGGGGRGGLNLKIIKSLPIPLPP-LEEQKKIVA 157

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1063532573 362 VLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17294   158 ILDKFDALINDLKEGLPALLELRQKQYEYLR 188
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 205-393 4.54e-53

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: 174.98  E-value: 4.54e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWDGGtFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGQGKTLGNA 284
Cdd:cd17287     1 KKLGEIAKVSSGGTPSRSNPEYWNGG-IPWVKTGEVNFNEITDTEEKITEEGLKNSSAKLFPKGTLLMAMYGQGKTRGRV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 285 AVLSIRATINQHLAYLQTDlEKAEPKFVRAYLETQYDHLRAVASGGGstKGALTCGFLRGMTVPRPPtIIEQQEIAQVLD 364
Cdd:cd17287    80 AILGIEAATNQACAAILPN-DGINPDFLFYYLQSSYEELRDLSNGGG--QPNLNAGLIKSIEIPVPP-LDEQQKIAAFLS 155

                         170       180
                  ....*....|....*....|....*....
gi 1063532573 365 VLDRKIELLGRKRDVLDRLFKALLHKLMT 393
Cdd:cd17287   156 AIDAKIDALEQKLELLQELKKSLMQQLFT 184
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-392 5.11e-35

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: 127.55  E-value: 5.11e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWDGGTfPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGQgkTLGNA 284
Cdd:cd17515     1 VKLGDIGKWGSGGTPSRSNPEYYGGGI-PWIKSGELNDGYITSTEEKITEEGLKNSSAKLFPKGSVLIAMYGA--TAGKV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 285 AVLSIRATINQHLAYLQTDlEKAEPKFVRAYLETQYDHLRAVASGGGstKGALTCGFLRGMTVPRPPtIIEQQEIAQVLD 364
Cdd:cd17515    78 GILGIDAATNQAICAILPN-EEIDNEFLFYFLKSQKEYLISLGKGGA--QPNISQGIIKNIEIPLPP-LAEQKRIVAKLD 153

                         170       180
                  ....*....|....*....|....*...
gi 1063532573 365 VLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17515   154 KLDKLIEKLEKALEKLEELKKALMQKLL 181
RMtype1_S_MmaGORF2198P_TRD1-CR1_like cd17500
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 212-387 1.08e-33

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: 124.32  E-value: 1.08e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 212 RIGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGQGKTLGNAAVLSIRA 291
Cdd:cd17500     8 KITSGGTPSRSNKEYYNGGNIPWLKTKELNFKRIYDTEEKITEEGLKNSSAKLIPENTVIIAMYGAGKTAGRVAINKIPL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 292 TINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGSTKgaLTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIE 371
Cdd:cd17500    88 TTNQACCNLIIDNKKADYRFVYYSLKTQYEELVNLASGAAQQN--LNSKLIKNFEIPLPP-LPEQKRIASILSSLDDKIE 164

                         170
                  ....*....|....*.
gi 1063532573 372 LLGRKRDVLDRLFKAL 387
Cdd:cd17500   165 LNNRQNETLEAMAETL 180
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-387 2.55e-32

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: 120.40  E-value: 2.55e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGqgkTLGNA 284
Cdd:cd17296     1 KKLGEICSIQSGGTPSRSKKEYWNNGTIPWVKISDCKNKYVDETEEFITEEGLNNSSAKLLKKGTILIAIFA---TIGKV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 285 AVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGSTKGALTcgFLRGMTVPRPPtIIEQQEIAQVLD 364
Cdd:cd17296    78 GILKIEATTNQAIAGIKPKNKSINPKYLYYYLKSLYEKFLSLGRGVAQNNINLS--ILKNLKIPLPP-LEEQQRIVAILD 154

                         170       180
                  ....*....|....*....|...
gi 1063532573 365 VLDRKIELLGRKRDVLDRLFKAL 387
Cdd:cd17296   155 KFEKLINKRQEGLQLLDELVKSL 177
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-367 5.20e-31

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: 116.89  E-value: 5.20e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLG-RIGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRDIQDADQFVT-DVALKECHLPVLEPGAVLVAITGQGKTLG 282
Cdd:cd17514     1 VKIQDIAfEIINGGTPSRNEPEYWNNGDIPWLTSGETDDNFINNTSEKITtKNGLEDSSIRIVPKGTILIACTGQGYTRG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 283 NAAVLSIRATINQHLAYLQTDlEKAEPKFVRAYLETQYDHLRAVASGGGstKGALTCGFLRGMTVPRPPtIIEQQEIAQV 362
Cdd:cd17514    81 QVAVLQIDASTNQAIAAIRCK-ENVNPKYLYYYLKTQKNNLRNLTSGVA--QKNLNIEMLRNLQIPLPP-KEEQQKIVNI 156


                  ....*
gi 1063532573 363 LDVLD 367
Cdd:cd17514   157 LETLE 161
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 207-392 5.31e-29

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: 111.52  E-value: 5.31e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 207 LGDLGRIGNGSTPKRSTGA-YWDGGTFPW-----LNSAKVYDRDIQdadqfVTDVALKECHLPVLEPGAVLVAITGQGKT 280
Cdd:cd17276     3 IGDIAKTSSGGTPLRSNQEyYFNGGTIPWvkttdLNNGVIYETEEK-----ITEKALKETSCKLLPKGTVLVAMYGGFGQ 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 281 LGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASggGSTKGA-LTCGFLRGMTVPRPPtIIEQQEI 359
Cdd:cd17276    78 IGRTGLLGIPAAINQAICAILPNEKKVNPEFLLRYLNFNRPYWMRVAA--SSRKDPnITKDDVRNFPIPLPP-LDEQRAI 154

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1063532573 360 AQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17276   155 VEFLSDVDALIDSLEALIEKLRELKKGLMQQLL 187
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-391 1.59e-28

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: 110.23  E-value: 1.59e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWDGGtFPWLnSAK-VYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAItgQGKTLGN 283
Cdd:cd17249     1 VRLGDLGKFLSGGTPSKSNPEYWGGD-IPWV-SPKdMKSDYISDSEDHITELAVEESGTKLVPAGSVLIVV--RGMILAH 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 284 ---AAVLSIRATINQhlaylqtDLeKA-------EPKFVRAYLETQYDHLRAVASGGGSTKGALTCGFLRGMTVPRPPtI 353
Cdd:cd17249    77 tfpVAITTRPVAFNQ-------DI-KAlipkegiDPEFLLYALKANEDRILSLVDKAGHGTGSLDTDDLKNLPIPLPP-L 147

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1063532573 354 IEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17249   148 EEQRRIAAILDALDALIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 203-392 4.14e-26

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: 103.78  E-value: 4.14e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 203 ELVPLGDL-GRIGNGSTPKRSTGAYWDGGTfPWL------NSAKVydrdIQDADQFVTDVALKECHLPVLEPGAVLVAIT 275
Cdd:cd17275     1 EQVKLGELcEKMKSGGTPSTSNKEYYGGDI-PFVkisdmtKSGKY----IYSTEKYITEEGLKNSSAWIVPKGTILYAMY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 276 GqgkTLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGgsTKGALTCGFLRGMTVPRPPtIIE 355
Cdd:cd17275    76 A---SVGKVAINKIDVATNQAILGIIPKDEKLDFEFLYYWLLSLKNELKRLIRTG--TQANLNAEIVKNLPIPLPP-LEE 149

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1063532573 356 QQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17275   150 QKKIAEILDKIDAEIDKLEEKIEKLRELKKGLLQKMF 186
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-387 4.17e-26

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: 103.61  E-value: 4.17e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRStGAYWDGGTFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGqgkTLGNA 284
Cdd:cd16961     1 KKLGEIAEIISGKTPSSS-SEYWDNGIIPWIRISDINNGGIILTDEKITEEGAEKLKKKILPKGDILISRSG---TIGKV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 285 AVLSI--RATINQHLAYLQTDlEKAEPKFVRAYLETQYDHlRAVASGGGSTKGALTCGFLRGMTVPRPPtIIEQQEIAQV 362
Cdd:cd16961    77 AIVKEndKALLNQAVIVIRPK-DEVDSEFLYYFLKSPFGK-KLIEGSAGSTQPNLNKSDLKNLKIPLPP-LEEQKKIANI 153

                         170       180
                  ....*....|....*....|....*
gi 1063532573 363 LDVLDRKIELLGRKRDVLDRLFKAL 387
Cdd:cd16961   154 LDKLDALIELLEQKLEKLEQLKQAL 178
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 202-392 4.25e-26

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: 103.64  E-value: 4.25e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDLGRIGNGSTPKRSTGAYWDGGTfPW--------LNSAKVYD--RDIqdadqfvTDVALKECHLPVLEPGAVL 271
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKNPEYWNGDI-PWitptdltkLKGKYISDteRKI-------TELGLKNSSAKLLPAGSVL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 272 vaitgqgktlgnaavLSIRATINqHLAYLQTDL------------EKAEPKFVRAYLETQYDHLRAVASGggST-----K 334
Cdd:cd17273    73 ---------------LSSRAPIG-YVAIATNPLatnqgfksiipnEEIDNEFLYYLLKNNKPEIESLASG--STfkeisK 134

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063532573 335 GALtcgflRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17273   135 STF-----KKIEIPLPP-LEEQKKIAAILSKLDELIELLEKENEKLKELRDGLLPKLF 186
RMtype1_M_Cni19672ORF1405P_RMtype11G_Hci611ORFHP_T cd17277
Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 ...
 202-381 4.55e-25

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: 100.94  E-value: 4.55e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDLGRIGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRD--IQDADQFVTDVALKECHLPVLEPGAVLVAITGqgk 279
Cdd:cd17277     1 WPIVKLGEVCEIINGSTPSKKNEEYWNNGTIKWLTIPDIDERGliISSTKQFITEKALEEKKVKLVPKNSVLLSCTA--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 280 TLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGsTKGaLTCGFLRGMTVPRPPTIIEQQEI 359
Cdd:cd17277    78 TIGKVAIAKIELTTNQQINALICKDSKILPEYLFYALKHIKQVLERLTTNPG-VKH-VNLSMLSNLQIPLPPLEVQKKIV 155

                         170       180
                  ....*....|....*....|..
gi 1063532573 360 AQVLDVLDRKIELlgrkRDVLD 381
Cdd:cd17277   156 AEIEKVEKVIQGL----RQKID 173
RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like cd17280
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter ...
 211-389 8.85e-22

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: 91.84  E-value: 8.85e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 211 GRIGNGSTPKRSTGAYWDGGTfPWLNSAKVYDRDIQDADQFVTDVALKECH-LPVLEPGAVLVAITGQgkTLGNAAVLSI 289
Cdd:cd17280     8 GLIGSGTTPKSDNEDYYDGGI-PWVTTGDLRDGIITETSKKITDKALDDYSaLKIYPAGSLVIAMYGA--TIGRLGILGI 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 290 RATINQHLAYLqTDLEKAEPKFVRAYLETQYDHLRAVASGGGSTKgaLTCGFLRGMTVPRPPtIIEQQEIAQVLDV---- 365
Cdd:cd17280    85 DATTNQACCVL-SGSNKIDIKFLFYWLLANRDELISLASGGGQPN--ISQELIKSLRIPVPP-LEEQKQIAAFLDKktak 160

                         170       180
                  ....*....|....*....|....
gi 1063532573 366 LDRKIELLGRKRDVLDRLFKALLH 389
Cdd:cd17280   161 IDSLIEKKERLIELLKERRQALIS 184
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-392 1.03e-20

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: 88.73  E-value: 1.03e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWDGGTfPWLNSAKVYDRDIQ--DADQFVTDVALKECHLPVLEPGAVLVAI-TGQGKTl 281
Cdd:cd17513     1 VKLGELGKFIGGGTPSTKNPEYWNGNI-PWITSSDLSEDDIFkiNIRKFITEEAIKNSATKIIPANSILIVTrVGVGKV- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 282 gnaAVLSIRATINQHLAYLqTDLEKAEPKFVRAYLETQYDHLrAVASGGGSTKGaLTCGFLRGMTVPRPPtIIEQQEIAQ 361
Cdd:cd17513    79 ---AINPFDICTSQDFTSL-IPIKEVNPLFLAYLLYSLLQKL-KSQLQGTSIKG-ITKDDLKNLKIPLPP-LEEQQKIAA 151

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1063532573 362 VLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17513   152 ILSKLDKLIEAHEKKLEKLKQLKKGLMQKLF 182
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 202-391 1.23e-20

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: 88.73  E-value: 1.23e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDLG-RIGNGSTPkrsTGAYWDGGtFPWLNSAKVYDRDIQDAD-QFVT----DVALKECHLpvlEPGAVLVAIT 275
Cdd:cd17246     1 WEWVKLGEISsDITDGTHP---TPKYVESG-IPFITSKNIKNGKIDFSDvKYISeedhNEILKRSKL---KKGDILFSII 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 276 GqgkTLGNAAVLSI--RATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGSTKGALTCGFLRGMTVPRPPtI 353
Cdd:cd17246    74 G---TIGRVAIVPEdlPANINQAVALIRPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPP-L 149

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1063532573 354 IEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17246   150 EEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDL 187
RMtype1_S_Vch69ORF1407P_TRD2-CR2_like cd17501
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio ...
 198-393 5.73e-20

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: 86.85  E-value: 5.73e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 198 IPESWELVP-LGDLGRIGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAItg 276
Cdd:cd17501     1 VPEGWEVGTiLDLCYKTQSGGTPSRKNPEYWDGGIIPWLKTGELRDNIILDTEEKITEEGLKNSSAKLFPKGTVLVAM-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 277 QGKTLGNAAVLSIRATINQHLAYLqTDLEKAEPKFVRAYLETQYDHLRAVASGGGSTKgaLTCGFLRGMTVPRPPT-IIE 355
Cdd:cd17501    79 YGATAGKLGILAKEATTNQACCAL-IPKEEYSPFFLYLYLLNSRDYLANLASGSAQQN--ISQQIIKNTKVLIPPEdLLE 155

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1063532573 356 qqEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLMT 393
Cdd:cd17501   156 --IFNKLVEPLFDKIINNLKENQKLAKLRDTLLPKLMS 191
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 203-388 1.32e-19

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: 85.58  E-value: 1.32e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 203 ELVPLGDLGRIGNGSTPKRSTGAYWDGGTfPWLNSAKV--YDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITGqgkT 280
Cdd:cd17243     1 EVKSLSDVVDIIGGGTPKTSVPEYWNGDI-PWFSVKDVnnDSRFVLDTEKKITELGLKNSSTKLLPKGTTIISARG---T 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 281 LGNAAVLSIRATINQHlAYLQTDLEKAEPKFVRAYLETQYDHLRAVASggGSTKGALTCGFLRGMTVPRPPtIIEQQEIA 360
Cdd:cd17243    77 VGKLALLGIPMAMNQS-CYGLRGKDGLSNYFLYYLLKNLIEELKQKAH--GSVFDTITRKTFDEIKVPLPP-EELQKSFE 152

                         170       180
                  ....*....|....*....|....*...
gi 1063532573 361 QVLDVLDRKIELLGRKRDVLDRLFKALL 388
Cdd:cd17243   153 NIVSPLFDKILNNLKENQTLAQLRDTLL 180
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 205-391 2.50e-19

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: 84.82  E-value: 2.50e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWdGGTFPWLNSAKV-YDRDIQDADQFVTDVALKecHLPVLEPGAVLVA-ItgqGKTLG 282
Cdd:cd17293     1 VKLGELGEVVTGNTPSKKNPEYY-GGDIPFIKPDDLnNGGIILTSEEYLSEEGAK--KARIVPKGSILVTcI---GGSIG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 283 NAAVLSIRATINQHLAYLQTDlEKAEPKFVRAYLETQYDHLRAVASGggSTKGALTCGFLRGMTVPRPPtIIEQQEIAQV 362
Cdd:cd17293    75 KVGIADREVAFNQQINAIIPN-KSVDPKFLYYQLLSSKFQLQAIASS--TTLPIINKSKFEKIEIPLPP-LEEQKRIVAK 150

                         170       180
                  ....*....|....*....|....*....
gi 1063532573 363 LDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17293   151 LDKLFALIDKLEESLEELDELLKSLFQSA 179
RMtype1_S_NmaSCMORF606P_TRD2-CR2_like cd17271
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 206-393 6.02e-19

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: 83.86  E-value: 6.02e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 206 PLGDLGRIGNGSTPKRSTGAYWDgGTFPWLNSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAITG---QGkTLG 282
Cdd:cd17271     1 LGEVLKGLSSGATPSRGNPEYFN-GDIPWITSGELNYNYITDTNEKITEEAVKNTNLKIHPKGTFLIAITGleaAG-TRG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 283 NAAVLSIRATINQH-LAYLQTDLEKAEPKFvraYLETQYDHLRAVASGGGSTKGALTCGFLRGMTVPRpPTIIEQQEIAQ 361
Cdd:cd17271    79 KCAITGIPATTNQScMAFYPTKKLTTEFLF---YWYKKYGNYLGFKYAQGTKQQSYTADIVKKLPILL-PTLKEQKKIAN 154

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1063532573 362 VLDVLDRKIELLGRKRDVLDRLFKALLHKLMT 393
Cdd:cd17271   155 FLSDIDELIATLEKKIEKLKKIKKGLMQKLLT 186
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-388 1.73e-18

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: 82.55  E-value: 1.73e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGR--IGnGSTPKRSTGAYWDGGtFPWlnsAKVYD---RDIQDADQFVTDVALKECHLPVLEPGAVLVAiTGQGk 279
Cdd:cd17285     1 KKLGDLVEkiVG-GGTPSKSNPEYWNGD-IPW---ASVKDlkgKYLTSTEDKITEEGLKNSSSNLIPKGTVIIA-TRMG- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 280 tLGNAAVLSIRATINQHLAYLQTDlEKAEPKFVRAYLETQYDHLraVASGGGST-KGaLTCGFLRGMTVPRPPtIIEQQE 358
Cdd:cd17285    74 -LGKVAINKIDVAINQDLKALFPK-DELDPEYLLYWFLSIEETI--ESLGTGTTvKG-ITLEDLKSLKIPLPP-LEEQKR 147

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1063532573 359 IAQVLDVLDRKI----ELLGRKRDVLDRLFKALL 388
Cdd:cd17285   148 IVAILDELDELIdkleAKLEKLKQLKKGLMQSLL 181
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-392 4.96e-17

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: 78.36  E-value: 4.96e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWdGGTFPWlnsakVYDRDIQDADQFVTDV---------ALKECHLPvlePGAVLVaiT 275
Cdd:cd17516     1 VKIGDLGKVVTGKTPSTKNPEYF-GGDIPF-----ITPSDMKGGKYIIKTErrlsskgleKVKNKLIP---ANSICV--T 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 276 GQGKTLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGST----KGAltcgFLRgMTVPRPP 351
Cdd:cd17516    70 CIGSDMGKVAITKEPSVTNQQINSIIVNKNKFDPDFVYYLLKNNSKYLKSIAGGSTATpiinKST----FSN-IEIPLPP 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1063532573 352 tIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17516   145 -LPEQKKIAAILSSLDDKIENNRRINKTLEEMAQALFKEWF 184
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 199-395 1.02e-16

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: 77.96  E-value: 1.02e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 199 PESWELVPLGDLGRIGNGSTPKRSTGAYWDGGtFPWL---NSAKVYDRDIQDADQFVTDVALKECHLPVLEPGAVLVAIT 275
Cdd:cd17248     1 PAHWEVVPLTDVAKLESGHTPSRSRPEYWNGC-IPWIslaDVKQLRGDYIYETKEKISELGIANSSARLLPAGTVVLSRT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 276 GqgkTLGNAAVLSIRATINQHLAYLQTDlEKAEPKFVRAYLETQYDHLRAVASggGSTKGALTCGFLRGMTVPRPPtIIE 355
Cdd:cd17248    80 A---SVGKSAIMGRPMATSQDFANWVCG-PELDPEYLLYVLRAMKPEFERLAM--GSTHKTIYMPDFKALRIALPP-LEE 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1063532573 356 QQEIAQVLDVLDRKIELLGRK----RDVLDRLFKALLHKLMTGE 395
Cdd:cd17248   153 QRKIVDRLEALDAKIDALERKlerlIELLKELRQALLTAAVTGK 196
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 199-382 1.21e-16

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: 77.01  E-value: 1.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 199 PESWELVPLGDLGRIGNGSTPKRStgAYWDGGTFPWLNSAKVYDrdiqdadqfVTDVALKECHLPVLEPGAVLVAITGqg 278
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKK--ELKNNGKYPYIRAGDLNN---------VVKGGLGYIKKYILPKGDITISSRA-- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 279 kTLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVAsgGGSTKGALTCGFLRGMTVPRPPtIIEQQE 358
Cdd:pfam01420  68 -TIGYVFYRDKPYYTNQHIIVLIPKNNIKITEFLYLYLLLKLKKLKSLK--FGSTQPKLTKERLKEIKIPLPP-LEEQKK 143

                         170       180
                  ....*....|....*....|....
gi 1063532573 359 IAQVLDVLDRKIELLGRKRDVLDR 382
Cdd:pfam01420 144 IAKILSQLDNTIELEKGILNELER 167
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
313-398 1.09e-15

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 72.01  E-value: 1.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 313 RAYLETQYDHLRAVASGGGSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:COG0732     3 KYYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPP-LEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81


                  ....*.
gi 1063532573 393 TGEISV 398
Cdd:COG0732    82 TGELRV 87
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 199-392 2.21e-15

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: 73.79  E-value: 2.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 199 PESWELVPLGDL------GRigngSTPKRstgaywDGGTFPW-----LNSAKVYDRDIQdadQFVTDVALKECHLPVLEP 267
Cdd:cd17284     1 PEGWEVKRVGDVcdcivpGR----DKPKS------FDGNIPWitiedIKGKYISSSKSG---LGVSEEEIKEMNLKVIPK 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 268 GAVLVAITGqgkTLGNAAVLSIRATINQHLAYLQTDlEKAEPKFVRAYLETQYDHLRAVASGGgstkgalTCGFL----- 342
Cdd:cd17284    68 GSVIMSCVG---DFGIVAIATNELVINQQLHAFVPS-KKINPEYLMYLLSLQKKYMEKIATGT-------TIPYLnktnc 136

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063532573 343 RGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17284   137 ESIPIPLPP-IEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQQLF 185
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-387 3.05e-15

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: 73.36  E-value: 3.05e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWDGGtFPWLNSA---KVYDRDIQDADQFVTDVALKECHLPVLEPGAVlvaitgqgktl 281
Cdd:cd17279     1 VPLKRIFRIVNGSTPKSGEEDYWDGD-IPWVTPAdlsKLDGKYISSSQRKITEAGLESCGTSLVPAGSI----------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 282 gnaaVLSIRATINqHLAYLQTDL------------EKAEPKFVRAYLETQYDHLRAVasGGGSTKGALTCGFLRGMTVPR 349
Cdd:cd17279    69 ----ILSTRAPIG-YVAIATVELctnqgckalvpnSDVDSRFLYYLLLAAKEELNSL--GRGTTFLELSTDELANFKIPL 141

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1063532573 350 PPtIIEQQEIAQVLDV----LDRKIELLGRKRDVLDRLFKAL 387
Cdd:cd17279   142 PP-LSEQRAIADFLDRetakIDALIAKKQQLIELLKEKRQAL 182
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 205-392 1.93e-14

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: 70.99  E-value: 1.93e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWDGGtFPWLNSAKVYD-RDIQDADQFVTDVALKEC-HLPvlePGAVLVAITGqgkTLG 282
Cdd:cd17286     1 KKLGDLGEIVTGNTPSTKNSEYYGGE-ILFVTPTDIDGnKYIYKTEKKLSEKGFKKArILP---KGSILVTCIG---SIG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 283 NAAVLSIRATINQhlaylQ----TDLEKAEPKFVRAYLETQYDHLRAVASGGgstkgaltcgflrgmTVP---------- 348
Cdd:cd17286    74 KNAIATEDCATNQ-----QinaiIPNKNYDPEFLYYALENWSKKIKSLAGKQ---------------AVPiinktefski 133

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1063532573 349 --RPPTIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17286   134 kiLVPPLEEQQKIANFLSKLDELIELQQQKIEKLEELKKGLLQKLF 179
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-387 4.05e-14

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: 70.31  E-value: 4.05e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGR-IGNGSTPKRSTGAYWDGGTFPWLNSAKVYDRD-IQDADQFVTDVALKECHLPVLEPGAVLvaITGQGKTLG 282
Cdd:cd17290     1 KKLKRLAKsIKTGTTPPSENEEYYDGGIIPWFTPGDFNGDLiLSESKRKLSELAIEDGEARLFPKNSVL--VVGIGATIG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 283 NAAVLSIRATINQHLAYLQTDlEKAEPKFVRAYLETQYDHLRAVASggGSTKGALTCGFLRGMTVPRPPtIIEQQEIAQV 362
Cdd:cd17290    79 KVGYSDKESSSNQQITGIIFN-KDINPKFLFYWLSSSKEELENLAN--GATLPILNQEKLKNIKLPVPP-LNEQQKIVEF 154

                         170       180
                  ....*....|....*....|....*....
gi 1063532573 363 LD----VLDRKIELLGRKRDVLDRLFKAL 387
Cdd:cd17290   155 LDkktaKIDALIAKKEQLIELLKEYRQAL 183
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 58-181 3.24e-13

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: 67.08  E-value: 3.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  58 FEPGDVLYGKLRPYLD--KAVLAD----RAGVATTELLVLRPKLGVSPEYLACVVHSPAFVEFA---MQGVTGAQhpRTS 128
Cdd:cd17260    35 FRNGDVLLAKITPCFEngKTAIVDglpnGIGFGSTEFHVLRPKEGILPEFLYYLLRSPSFRKEAiksMTGSSGRQ--RVP 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063532573 129 WVHIRTFELPAHDRSEQASIAKLLWSLFELSMTTEQGIASASCLKRAAMQQLF 181
Cdd:cd17260   113 KDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-389 4.58e-13

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: 67.12  E-value: 4.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPkRSTGA--YWDGGTFPWLnsaKVYD-----RDIQDADQFVTDVALKECHLpvLEPGAVLVAITGq 277
Cdd:cd17283     1 KKLGDISEIVRGASP-RPIGDpiTFDGDGIPWI---KIGDvtkdgKYITKTKEKITEEGAKKSRL--VKPGDLILSNSM- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 278 gkTLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGSTKGaLTCGFLRGMTVPRPPtIIEQQ 357
Cdd:cd17283    74 --SFGRPYILKIDGCIHDGWLVFSDLKKKLDKDFLYYLLSSITVQLQFSAQAGGGTKN-LNTDIVKNLKIPLPP-LEEQK 149

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1063532573 358 EIAQVLDVLDRKIELLGRKRDVLDRLFKALLH 389
Cdd:cd17283   150 RIAEILDSLDALIDALEEKLEKLEELKKGLMQ 181
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 202-391 5.03e-13

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: 67.18  E-value: 5.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDL-GRIGNGSTPKRStgaYWDGGTfPWLNSAKVYD--RDIQDADQFVtDVALKECHLPVLEPGAVLVA-ITGQ 277
Cdd:cd17517     1 WEVVKLGDLlEDPRYGTSKKSS---YDGSGT-PVLRIPNIYDggIDLDDLKKRV-DLSEKELEKYLLKKGDILFNrSNGS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 278 GKTLGNAAVLS------------IRATINQhlaylqtdlEKAEPKFVRAYLETQY--DHLRAVASGGG-----STKGalt 338
Cdd:cd17517    76 PELVGKCALVDeedepaifasylIRLRLDK---------KKILPEFLYYYLNSPLgrKQIEKIAKSAAgqaniNQKD--- 143

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063532573 339 cgfLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17517   144 ---LKKLPIPLPP-LEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-390 9.74e-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: 65.96  E-value: 9.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYWDGGTFPW-----LNSAKVydrdIQDADQFVTDVALKECHLPVLEPGAVLVAItgqgK 279
Cdd:cd17244     1 VKLGDIFDIKIGKTPPRKEPEYWSGDNIPWvsisdMGKGKY----ISDTKEYITDEAVKKFNVKLVPKGTLLMSF----K 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 280 -TLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQ-YDHLRAVASGGGSTKGALtcgfLRGMTVPRPPtIIEQQ 357
Cdd:cd17244    73 lTIGRVAIAGKDLYTNEAIAHFIPKDKKIDTEYLYYYLKSFdYSSLGSTASKGKTLNSKK----IKEIPIPLPP-LEEQK 147

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1063532573 358 EIAQVLDVLDRKIELLGRKRDVLDRLFKALLHK 390
Cdd:cd17244   148 RIAPILDKIDALIDQLETLIELLDELLPKLMSG 180
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 207-389 3.24e-12

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: 64.83  E-value: 3.24e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 207 LGDLGR-IGNGSTPKRSTGAYWDGGtFPWLNSAKVYDRDIQDAD-QFVTDVALKECHLPVLEPGAVLVAITGqgkTLGNA 284
Cdd:cd17256     1 LGEIARvKGGGRLPKGESLSDGPTG-VPYIRVTDIKNGGIDLDNlKYISPEIHEKIKRYTLSKGDILISIVG---TIGRV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 285 AVLSI---RATINQHLAYLqTDLEKAEPKFVRAYLETQY--DHLRAvaSGGGSTKGALTCGFLRGMTVPRPPtIIEQQEI 359
Cdd:cd17256    77 GIVPKeldGANLTENAARI-RPKDSISPRYLYYYLRSPFgqSQIES--ETKGAAQPKLNLKRIRELPIPLPP-LEEQKRI 152

                         170       180       190
                  ....*....|....*....|....*....|
gi 1063532573 360 AQVLDVLDRKIELLGRKRDVLDRLFKALLH 389
Cdd:cd17256   153 VAILDSLDAKIDALEKQLAKLEELKKALMQ 182
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 202-393 5.80e-12

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: 64.07  E-value: 5.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDLGRIGNG----STPKRSTGaY--------WDGGTFpWLNSAKVYDRDIQDADQFVtdvalkechlpvLEPGA 269
Cdd:cd17278     1 WEVVKLGDIADIQNGyafkSSDFSDEG-IpvirigniKNGGID-LDDNSKYPEEPLEKYEKFL------------LKKGD 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 270 VLVAITGqgKTLGNAAVL---SIRATINQHLAYLQTDlEKAEPKFVRAYLETQY--DHLRAVASGGG----STKGaltcg 340
Cdd:cd17278    67 ILIAMTG--GTVGKVAIVpedDEPALLNQRVGKFRPK-DKIDKEFLYYLLRSDSfrNQIKSSATGTAqpniSPKD----- 138

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063532573 341 fLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLMT 393
Cdd:cd17278   139 -IESIKIPLPP-LEEQKKIAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLFT 189
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 202-391 1.06e-11

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: 63.27  E-value: 1.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDLgrIGN---GSTpkrSTGAYWDGGTfpwlnsakVYDR--DIQDADQFVTDVALKECHLPV-----LEPGAVL 271
Cdd:cd17521     1 WEVKKLGEL--SEKiqyGYT---ASAAYEDGGP--------RYLRitDIQDDGVLWDTVPYCSISEEDaekylLKDGDIL 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 272 VAITGQ--GKTL------GNAAVLS--IRATINQhlaylqtdlEKAEPKFVRAYLETQY--DHLRAVASGGG-----STK 334
Cdd:cd17521    68 FARTGAtvGKSYlykeddGKAVFASylIRFRPNK---------KKVLPKYLFYFTQSSLywKQIKSISSGSAqpninAEK 138

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063532573 335 galtcgfLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17521   139 -------LKSLKIPLPP-LEEQKRIVAILDALDAKIDALEELLEKLEELLKELLQSL 187
RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like cd17258
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 265-391 2.41e-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: 62.04  E-value: 2.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 265 LEPGAVLVAITGQ-GKTlgnAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGGGSTKGALTCGFLR 343
Cdd:cd17258    49 FKKGDVLITRHGTiGRV---SIILSEEACLSSHVAGFNSKEGISDNKFIKYLFNSKKIKNRLMSYGASSTQPALNLSRLL 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1063532573 344 GMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17258   126 KIKFPNPP-LEEQQKIGKILSTWDRAIELTEQKLELLQQQKKGLMQQL 172
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 305-392 1.84e-10

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2 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: 59.47  E-value: 1.84e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 305 EKAEPKFVRAYLETQYDHLRAVasGGGSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLF 384
Cdd:cd17245    90 KDIDNLFLYYYLKYNKPELEKL--GTGSTFKAINKKDLEELKIPLPP-LEEQQKIAEILSTVDEAIEKTKALIEKLDELK 166


                  ....*...
gi 1063532573 385 KALLHKLM 392
Cdd:cd17245   167 KGLMQELF 174
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 305-392 2.57e-10

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: 59.05  E-value: 2.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 305 EKAEPKFVRAYLETQYDHLRAVASGggSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLF 384
Cdd:cd17496    91 NGIDTEFLYYLLESNLDYLLAAATG--STFPNISRDDLLNLKIPLPP-LEEQKRIVAILDPLDEKIDKNKQEIEKLEELR 167


                  ....*...
gi 1063532573 385 KALLHKLM 392
Cdd:cd17496   168 DTLLPKLL 175
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 201-391 2.75e-10

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I), Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) TRD2-CR2, and Streptomyces species SirexAA-E S subu; Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I) recognizes 5'... CACNNNNNNNCTGG ... 3' and Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) recognizes 5'... RTCANNNNNNNNGTGG ... 3'. The recognition sequence of Streptomyces species SirexAA-E S subunit (S.SspAAEORF2129P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Eco2071ORF3585P TRD1 recognizes RTCA/TGAY and S.Eco2071ORF3585P TRD2 recognizes CCAC/GTGG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341142 [Multi-domain]  Cd Length: 193  Bit Score: 59.41  E-value: 2.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 201 SWELVPLGDLGRIGNGST--PKRSTGAYwdggTFPWLNSAKVYDR--DIQDADQF-VTDVALKECHLpvlEPGAVLVaiT 275
Cdd:cd17253     1 GWEWVRLGDVAEVQSGITkgKKRRGGEL----EVPYLRVANVQDGylDLSEVKEIeVTEEELERYRL---RKGDLLV--T 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 276 -GQGKT-LGNAAVL--SIRATINQ-HLAYLQTDLEKAEPKFVRAYLETQY--DHLRAVASGggSTKGA-LTCGFLRGMTV 347
Cdd:cd17253    72 eGGDSDkLGRGAIWrgEIPPCLHQnHLFRVRPKDDLLLPEFLSYWLNSAYgrGYFLRAAKQ--TTNLAsINSTKLKALPV 149

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1063532573 348 PRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17253   150 PLPP-LEEQRRIVERLDELLALIDALEASLAKLEELLKALRQAL 192
RMtype1_S_EcoUTORF5051P-TRD2-CR2_like cd17524
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 202-391 3.83e-10

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) TRD2-CR2 and Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) TRD2-CR2; Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) recognizes 5'... CCANNNNNNNCTTC ... 3' and the recognition sequence of Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341205 [Multi-domain]  Cd Length: 189  Bit Score: 59.02  E-value: 3.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDLGRIGN-GSTPKRSTgaywDGGTFP------------WLNSAKVYDRDIQDADQFVtdvalkechlpvLEPG 268
Cdd:cd17524     1 WEWVTIGDLVTSVQyGTSEKKSE----DEGGYPvlrmgniqdggiDDDDLKYVDLDEKEFEKYL------------LKKG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 269 AVL---------VaitgqGKTlgnaAV--LSIRATInqhlA-YL---QTDLEKAEPKFVRAYLETQY--DHLRAVASGGG 331
Cdd:cd17524    65 DVLfnrtnspelV-----GKT----AIfrGDGPATF----AsYLiriRLNEEKILPEYLNYFLNSPYgrKQIKSVATQGV 131

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063532573 332 S------TKgaltcgfLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17524   132 GqaninaTK-------LKAIPIPLPP-LEEQKEIVEKLDELDALIDRLEALLEEAEELLESLLQSL 189
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 305-391 2.67e-09

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: 56.30  E-value: 2.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 305 EKAEPKFVRAYLETQYDHLRAVASGggSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLF 384
Cdd:cd17282   102 EKIDVEFLEYYLRTLKKELEAIAPQ--SAQKNINLEILRPLKIPVPP-LEEQKKIVEILDALDDLIDNLEKRIAKLEELK 178


                  ....*..
gi 1063532573 385 KALLHKL 391
Cdd:cd17282   179 QSLLQEA 185
RMtype1_S_HpyAXIII_TRD1-CR1_like cd17281
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 202-373 9.91e-08

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: 51.83  E-value: 9.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDLGRIGNGSTPKRSTGAYWDGGTFPWLnsaKVYD-----RDIQDADQFVTDVALKECHLpvLEPGAVLVAITG 276
Cdd:cd17281     2 VEWKKLGEIFDIRNGYTPSKSNKEYWENGTIPWF---RMEDirengRILSDSIQHITPSAVKGGKL--FPANSIILSTTA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 277 qgkTLGNAAVLSIRATINQHLAYLQ--TDLEKA-EPKFVRAYLETQYDHLRAVASGGG----STKGaltcgfLRGMTVPR 349
Cdd:cd17281    77 ---TIGEHALITVDSLANQRFTNFSlkKSYKNKlDIKFLFYYFFVLGEWCKKNINIGGfpsvDMNK------LKKFKIPI 147

                         170       180
                  ....*....|....*....|....
gi 1063532573 350 PPtIIEQQEIAQVLDVLDRKIELL 373
Cdd:cd17281   148 PP-LEEQEKIVEILDKFTKLTADL 170
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 294-392 2.03e-07

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: 50.54  E-value: 2.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 294 NQHLAYLQTDlEKAEPKFVRAYLETQYDHLRAvaSGGGSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELL 373
Cdd:cd17254    79 NQHIFKVVPD-EEIDKDYLYYLLKALTEEIES--QAHGSTMVHITKGDLENIKVPLPP-LEEQKRIAAILDELDALIDAL 154

                          90
                  ....*....|....*....
gi 1063532573 374 GRKRDVLDRLFKALLHKLM 392
Cdd:cd17254   155 EEQLKKLEELRKALLQSLL 173
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 309-391 2.60e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.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: 50.58  E-value: 2.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 309 PKFVRAYLETQYDHlRAVASGGGSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALL 388
Cdd:cd17265   100 NDYLFHLFNSDLFK-KQIGSFLTATINQITNGNLNNFKIPLPP-LEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKELM 177


                  ...
gi 1063532573 389 HKL 391
Cdd:cd17265   178 QQL 180
RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like cd17289
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 303-392 2.74e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus amyloliquefaciens JRS5 S subunit (S.BamJRS5ORF1993P) TRD1-CR1 and Bacillus pumilus Jo2 S subunit (S.BpuJo2I) TRD1-CR1; The recognition sequences of Bacillus amyloliquefaciens JRS5 S subunit (S.BamJRS5ORF1993P) and Bacillus pumilus Jo2 S subunit (S.BpuJo2I) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341178 [Multi-domain]  Cd Length: 191  Bit Score: 50.72  E-value: 2.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 303 DLEKAEPKFVRAYLETQY--DHLRAVASGggSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVL 380
Cdd:cd17289   103 NIKDINSKFLYYWFQSSIfkNQINSITIG--STQKALTIEKLKKTKIPLPP-LEEQKKIVSILSALDEKIDLNKKQLQKL 179

                          90
                  ....*....|..
gi 1063532573 381 DRLFKALLHKLM 392
Cdd:cd17289   180 EELAKTLFQYWF 191
RMtype1_S_Eco540ANI-TRD1-CR1_like cd17274
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 345-393 4.32e-07

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


Pssm-ID: 341163  Cd Length: 171  Bit Score: 49.41  E-value: 4.32e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063532573 345 MTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLMT 393
Cdd:cd17274   124 FKIPLPP-LEEQNKIVRILDKFDELIAELEAKLELLKKQKKYYLQKLFT 171
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 310-391 5.32e-07

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


Pssm-ID: 341152 [Multi-domain]  Cd Length: 177  Bit Score: 49.42  E-value: 5.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 310 KFVRAYLETQYDHLRAVASGGgSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLH 389
Cdd:cd17263    97 DYLYYFLKSKEIQLNILTKAG-STIPHVNKKDLENLKIPLPS-LEEQKKIAEILDKLDALIDKLKELIEKLIELKKGLFQ 174


                  ..
gi 1063532573 390 KL 391
Cdd:cd17263   175 EL 176
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 331-391 5.86e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) 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: 49.35  E-value: 5.86e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063532573 331 GSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17262   113 GAAQPKLNQANLNSIPIPLPP-LEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQKL 172
RMtype1_S_Sba223ORF3470P-TRD1-CR1_like cd17270
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 205-391 9.59e-07

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


Pssm-ID: 341159 [Multi-domain]  Cd Length: 183  Bit Score: 48.85  E-value: 9.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 205 VPLGDLGRIGNGSTPKRSTGAYW--DGGTFPWLnsaKVYDRD-----IQDADQFVTDVALKechLPVLEP-GAVLVAITG 276
Cdd:cd17270     1 KTLGEVAKFRRGSFPQPYGNSEWydGEGSMPFV---QVADVGdnfklVEKTKQKISKLAQP---KSVFVPkGTVIVTLQG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 277 qgkTLGNAAVLSIRATINQHLAYLQTDLEKAEPKFVRAYLETQYDHLRAVASGG---GSTKGALTcgflrGMTVPRPPtI 353
Cdd:cd17270    75 ---SIGRVAITQYDAYVDRTLLIFESYKININKKFFAYQLKLKFEIEKEKAPGGtikTITKEELS-----KFEIPIPS-L 145

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1063532573 354 IEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17270   146 EEQKEIVNILDKFDELITELQLRKKQLEYYKKALLSFM 183
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 59-182 1.28e-06

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: 48.67  E-value: 1.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  59 EPGDVLYGKLRPyLDKAVLADRAGVATT--ELLVLRPKLG-VSPEYLACVVHSPAFVE-FAMQGVTGAQhPRTSWVHIRT 134
Cdd:cd17246    64 KKGDILFSIIGT-IGRVAIVPEDLPANInqAVALIRPKKEkIDPKYLLYYLNSPIIQKqIEKNAVGGTQ-KNLSLGDLKN 141

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1063532573 135 FELPAHDRSEQASIAKLLWSLFELSMTTEQGIASASCLKRAAMQQLFS 182
Cdd:cd17246   142 LKIPLPPLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLLT 189
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-391 1.66e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) TRD2-CR2 and Lactobacillus amylovorus GRL 1112 S subunit (S1.L; The recognition sequences of Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) and Lactobacillus amylovorus GRL 1112 S subunit (S1.LamGRLORF5415P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341185 [Multi-domain]  Cd Length: 171  Bit Score: 47.90  E-value: 1.66e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063532573 351 PTIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17494   130 PSLEEQQKIATFLSTLDAEITLLEKKLEKLKQLKKGLLQKL 170
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 202-391 1.83e-06

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Escherichia coli A58 S subunit (S.EcoEI) TRD2-CR2, and Aminomonas paucivorans S subunit (S.Apa12260I); Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3', Escherichia coli A58 S subunit (S.EcoEI) recognizes 5'... GAGNNNNNNNATGC ... 3', and Aminomonas paucivorans S subunit (S.Apa12260I) recognizes 5'... GCCNNNNNCTCC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 recognizes AAC/GTT and S.EcoKI-TRD2 recognizes GCAC/GTGC, S.EcoEI TRD1 recognizes GAG/CTC and S.EcoEI TRD2 recognizes GCAT/ATGC, and S.Apa12260I TRD1 recognizes GCC/GGC and S.Apa12260I TRD2 recognizes GGAG/CTCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341150 [Multi-domain]  Cd Length: 191  Bit Score: 47.92  E-value: 1.83e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 202 WELVPLGDL-GRIGNGSTPKRSTgaYWDG-----------GTFpWLNSAKVYDRDIQDADQFVtdvalkechlpvLEPGA 269
Cdd:cd17261     1 WEWVRLGDLiEGIRNGWSPKPPD--DETGwpvlklsavtsGKF-DPSENKYLPESLEPASEYW------------LKPGD 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 270 VLvaIT-GQGKTL-GNAAVLSiraTINQHLAY------LQTDLEKAEPKFVRAYLETQY--DHLRAVASG-GGSTKGaLT 338
Cdd:cd17261    66 LL--ISrANTSELvGRAALVD---GDPDNLIYpdklirLRVNEELLLPEYLALALNSPSarRQIESRATGtAGSMPK-IS 139

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063532573 339 CGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17261   140 QSDLKSLPIPLPP-LAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
104-186 2.27e-06

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 45.43  E-value: 2.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 104 CVVHSPAFVEFAMQGVTGAQHPRTSWVHIRTFELPAHDRSEQASIAKLLWSLFELSMTTEQGIASASCLKRAAMQQLFSR 183
Cdd:COG0732     4 YYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFTG 83


                  ...
gi 1063532573 184 GLR 186
Cdd:COG0732    84 ELR 86
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 341-392 3.50e-06

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: 46.66  E-value: 3.50e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1063532573 341 FLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17260   115 FLENYKIPLPP-LEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 347-390 3.60e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoAO83I TRD1-CR1 and S.AbaB8342I TRD2-CR2; Escherichia coli strain A0 34/86 S subunit (S.EcoAO83I) recognizes 5'... GGANNNNNNNNATGC ... 3, and Acinetobacter baumannii B8342 S subunit (S.AbaB8342I) recognizes 5'... TTCANNNNNNTCC ... 3. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example S.AbaB8342I-TRD1 recognizes TTCA/TGAA and S.AbaB8342I-TRD2 recognizes GGA/TCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Type IIG restriction enzyme/N6-adenine DNA methyltransferases from Thermus scotoductus RFL1 (RM.TstI) and Acinetobacter lwoffi Ks 4-8 (RM.AloI), as well as type I DNA methyltransferases such as Sideroxydans lithotrophicus ES-1 Type I N6-adenine DNA methyltransferase (M.SliESORF1090P). RM.TstI recognizes 5' ... CACNNNNNNTCC ... 3' and RM.AloI recognizes 5' ... GAACNNNNNNTCC ... 3'.


Pssm-ID: 341156 [Multi-domain]  Cd Length: 158  Bit Score: 46.62  E-value: 3.60e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063532573 347 VPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHK 390
Cdd:cd17267   116 VPLPP-LEEQKAIAAILDALDDKIELNRRQNQTLEELADALLPK 158
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 50-158 3.85e-06

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: 46.99  E-value: 3.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  50 DATSQKAAFEPGDVLYGK--------LRPYLDKAVLADRagvatteLLVLRPKLGVSPEYLACVVHSPAFVEFAMQGVTG 121
Cdd:cd16961    52 AEKLKKKILPKGDILISRsgtigkvaIVKENDKALLNQA-------VIVIRPKDEVDSEFLYYFLKSPFGKKLIEGSAGS 124

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1063532573 122 AQhPRTSWVHIRTFELPAHDRSEQASIAKLLWSLFEL 158
Cdd:cd16961   125 TQ-PNLNKSDLKNLKIPLPPLEEQKKIANILDKLDAL 160
RMtype1_S_Eco15ORF14057P-TRD1-CR1_like cd17525
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 305-391 4.46e-06

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: 46.84  E-value: 4.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 305 EKAEPKFVRAYLETQY--DHLRAVASGGGSTkGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDR 382
Cdd:cd17525   104 DIVLPYFINYYLNSPDgkKQLESIASGTTSV-AAIYQKDLKKLKLPLPP-LDEQREIVSFLSELDAKIDQLEQKLEKLLQ 181


                  ....*....
gi 1063532573 383 LFKALLHKL 391
Cdd:cd17525   182 IKKALMQQL 190
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 28-178 7.26e-06

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: 46.34  E-value: 7.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  28 PYLGLEHLEPGRLRATGFGRASDATSQK---AAFEPGDVLY---------GKLRPYLDKAVLAdrAGVAttellVLRPKL 95
Cdd:cd17256    27 PYIRVTDIKNGGIDLDNLKYISPEIHEKikrYTLSKGDILIsivgtigrvGIVPKELDGANLT--ENAA-----RIRPKD 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  96 GVSPEYLACVVHSPAFVEFAMQGVTGAQHPRTSWVHIRTFELPAHDRSEQASIAKLLWSLFELSMTTEQGIASASCLKRA 175
Cdd:cd17256   100 SISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKA 179


                  ...
gi 1063532573 176 AMQ 178
Cdd:cd17256   180 LMQ 182
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 291-388 1.59e-05

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: 45.20  E-value: 1.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 291 ATINQHLAYLQTDlEKAEPKFVRAYLETQY--DHLRAVASGGG----STKGaltcgfLRGMTVPRPPtIIEQQEIAQVLD 364
Cdd:cd17259    92 ALLVQRVARIRPK-DELNSDFLYYLLQSDFflNYVEPVLTGTDvphiSTKQ------IKNFKIPLPP-LEEQKKIAEFLS 163

                          90       100
                  ....*....|....*....|....
gi 1063532573 365 VLDRKIELLGRKRDVLDRLFKALL 388
Cdd:cd17259   164 SLDALIDLLEQKLEKLQQLKKGLM 187
RMtype1_S_Cje2232P-TRD2-CR2_like cd17526
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 278-392 1.60e-05

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) TRD2-CR2 and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) TRD1-CR1; The recognition sequences of Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. Also included in this subfamily is the C-terminal TRD-CR-like sequence-recognition domain of Microcystis aeruginosa putative type I N6-adenine DNA methyltransferase M subunit (M.Mae7806ORF3969P). The recognition sequence of M.Mae7806ORF3969P is undetermined.


Pssm-ID: 341207 [Multi-domain]  Cd Length: 192  Bit Score: 45.27  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 278 GKTlgnaAVLSIRA--TINQHLAYLQTDLEKAEPKFVRAYLETQYDH--LRAVA------SGGGSTKgaltcgfLRGMTV 347
Cdd:cd17526    80 GKT----ALFDGEEpyVFSNHMTRIRVKKSKINPEFLARYLHLLWRSgyFKKLCtnwvnqAGINSDT-------LANLKI 148

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1063532573 348 PRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17526   149 PLPP-LPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 332-389 2.19e-05

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: 44.36  E-value: 2.19e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063532573 332 STKGA---LTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLH 389
Cdd:cd17266   100 ATGSAqplITVSKLKKLKIPLPP-LEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKELMQ 159
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 88-179 3.94e-05

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: 44.04  E-value: 3.94e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  88 LLV-----LRPKLGVSPEYLACVVHSPAFVEFAMQGVTGAQHPRTSWVHIRTFELPAHDRSEQASIAKLLWSLFELSMTT 162
Cdd:cd17259    93 LLVqrvarIRPKDELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLL 172

                          90
                  ....*....|....*..
gi 1063532573 163 EQGIASASCLKRAAMQQ 179
Cdd:cd17259   173 EQKLEKLQQLKKGLMQS 189
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 342-391 8.68e-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: 43.29  E-value: 8.68e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063532573 342 LRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17522   142 LKKIKIPLPP-LEEQQKIASILEKLDKKIEKRKEKIEKLKELKKGLFQKL 190
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 305-388 3.20e-04

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


Pssm-ID: 341188 [Multi-domain]  Cd Length: 174  Bit Score: 41.38  E-value: 3.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 305 EKAEPKFVRAYLETQYDHLRAVASGggSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLD----VLDRKIELLGRKRDVL 380
Cdd:cd17497    90 KGLDKKYLLYYLKSIENELSSLGTG--STFKAISKEDLENLLIPLPP-LAEQKRIAAFLDeltaKIDQLIALLEKAIELL 166


                  ....*...
gi 1063532573 381 DRLFKALL 388
Cdd:cd17497   167 KEYRQAVL 174
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-392 3.80e-04

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: 40.92  E-value: 3.80e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1063532573 351 PTIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKLM 392
Cdd:cd17288   120 PPLEEQQKIASILDKLDAKDALIELQEKLLEKLKQYKLALMQ 161
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 342-391 5.00e-04

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: 40.22  E-value: 5.00e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063532573 342 LRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17292   100 LLNTKIPVPS-LDEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYL 148
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 89-181 8.73e-04

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: 40.11  E-value: 8.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  89 LVLRPKLGVSPEYL--ACVVHSPAFVEfamQGVTGAQhPRTSWVHIRTFELPAHDRSEQASIAKLLWSLFELSMTTEQGI 166
Cdd:cd17515    91 CAILPNEEIDNEFLfyFLKSQKEYLIS---LGKGGAQ-PNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKLIEKLEKAL 166

                          90
                  ....*....|....*
gi 1063532573 167 ASASCLKRAAMQQLF 181
Cdd:cd17515   167 EKLEELKKALMQKLL 181
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 91-182 9.32e-04

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: 40.19  E-value: 9.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573  91 LRPKLGVSPEYLACVVHSPAFVEFAMQGVTGAQHPRTSWVHIRTFELPAHDRSEQASIAKLLWSLFELSMTTEQGIASAS 170
Cdd:cd17278    98 FRPKDKIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKLEQKLEKLR 177

                          90
                  ....*....|..
gi 1063532573 171 CLKRAAMQQLFS 182
Cdd:cd17278   178 DLLKPLLQSLFT 189
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 309-389 2.53e-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: 38.69  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 309 PKFVRAYLETQY--DHLRAVASGGGS---TKGALTCgflrgMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRL 383
Cdd:cd17252   110 PRYLFYFLQSPSyrEYIRSLASGTNInnlSNEHLEN-----LKIPLPP-LAEQKRIVAKLDKLDALIDKLKQALEKLDEL 183


                  ....*.
gi 1063532573 384 FKALLH 389
Cdd:cd17252   184 LKSLFQ 189
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 144-181 3.61e-03

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


Pssm-ID: 341181 [Multi-domain]  Cd Length: 149  Bit Score: 37.52  E-value: 3.61e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1063532573 144 EQASIAKLLWSLFELSMTTEQGIASASCLKRAAMQQLF 181
Cdd:cd17292   112 EQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYLF 149
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 331-390 4.66e-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: 37.66  E-value: 4.66e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063532573 331 GSTKGALTCGFLRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHK 390
Cdd:cd17498   113 GTVFGSINKDDIENLEVDIPE-DEEQKRIANILSKIDDKIEINNQINKNLEELAQAIFKH 171
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 342-390 7.73e-03

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: 37.13  E-value: 7.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063532573 342 LRGMTVPRPPtIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHK 390
Cdd:cd17264   137 LKKFLIPLPP-LEEQKRIVAKLDELDALIDKLKQALEKLEELLQSLFQS 184
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-391 8.69e-03

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: 36.74  E-value: 8.69e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063532573 351 PTIIEQQEIAQVLDVLDRKIELLGRKRDVLDRLFKALLHKL 391
Cdd:cd17255   126 PPLEEQEKIANILDKLDELINLLIAKLKKLIELRKKQLEYY 166
 
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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