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Conserved domains on  [gi|1589013687|gb|TCS78901|]
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type I restriction enzyme S subunit [Muricomes intestini]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_Cep9333ORF4827P-TRD2-CR2_like cd17495
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 209-382 2.89e-116

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Crinalium epipsammum S subunit (S.Cep9333ORF4827P) TRD2-CR2 and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) T; The recognition sequences for Crinalium epipsammum S subunit (S.Cep9333ORF4827P) and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


:

Pssm-ID: 341186 [Multi-domain]  Cd Length: 174  Bit Score: 335.59  E-value: 2.89e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 209 GTLSDIADITMGQSPSGSSYNEDGTGTIFFQGRAEFGFRFPSVRLYTTEPKRMARSNDTLMSVRAPVGDLNVAHMDCCIG 288
Cdd:cd17495     1 GTLGDIANITMGQSPKGESYNEDGEGLPFYQGVTDFGFRFPTNRVYTTAPTRFAEAGDILFSVRAPVGDINIANEKCCIG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 289 RGLAAIHSKSHHQSFVLYTMFSLKKQLDVFNGEGTVFGSINRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENC 368
Cdd:cd17495    81 RGLAAIRSKSGSQSFLFYQLKSLFKEFDIFNGEGTVFGSINKKDLENLPIIIPSDEIIEAFEKLVSPIDQKIENNEKENR 160

                         170
                  ....*....|....
gi 1589013687 369 RLQDIRDTLLPRLM 382
Cdd:cd17495   161 TLAKLRDTLLPKLM 174
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-198 2.37e-31

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 cd17246:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 189  Bit Score: 117.62  E-value: 2.37e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   4 KLIQLSDVITDIAAGPFGSnlkvSCFVNDGFPIIDGANLKSFKVTDNITKFVTEEKARSLH-RSIAKRGDIVVTISGTLG 82
Cdd:cd17246     2 EWVKLGEISSDITDGTHPT----PKYVESGIPFITSKNIKNGKIDFSDVKYISEEDHNEILkRSKLKKGDILFSIIGTIG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  83 QIAYIPDDsnyEEYLCSQRQFRVTFDTTKVYVPYLVFYFHTYEGKHKILSFANQVGVPALSqpLKNFRQISVQLPTLETQ 162
Cdd:cd17246    78 RVAIVPED---LPANINQAVALIRPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLS--LGDLKNLKIPLPPLEEQ 152

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1589013687 163 KKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17246   153 KRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLL 188
 
Name Accession Description Interval E-value
RMtype1_S_Cep9333ORF4827P-TRD2-CR2_like cd17495
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 209-382 2.89e-116

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Crinalium epipsammum S subunit (S.Cep9333ORF4827P) TRD2-CR2 and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) T; The recognition sequences for Crinalium epipsammum S subunit (S.Cep9333ORF4827P) and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341186 [Multi-domain]  Cd Length: 174  Bit Score: 335.59  E-value: 2.89e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 209 GTLSDIADITMGQSPSGSSYNEDGTGTIFFQGRAEFGFRFPSVRLYTTEPKRMARSNDTLMSVRAPVGDLNVAHMDCCIG 288
Cdd:cd17495     1 GTLGDIANITMGQSPKGESYNEDGEGLPFYQGVTDFGFRFPTNRVYTTAPTRFAEAGDILFSVRAPVGDINIANEKCCIG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 289 RGLAAIHSKSHHQSFVLYTMFSLKKQLDVFNGEGTVFGSINRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENC 368
Cdd:cd17495    81 RGLAAIRSKSGSQSFLFYQLKSLFKEFDIFNGEGTVFGSINKKDLENLPIIIPSDEIIEAFEKLVSPIDQKIENNEKENR 160

                         170
                  ....*....|....
gi 1589013687 369 RLQDIRDTLLPRLM 382
Cdd:cd17495   161 TLAKLRDTLLPKLM 174
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-198 2.37e-31

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: 117.62  E-value: 2.37e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   4 KLIQLSDVITDIAAGPFGSnlkvSCFVNDGFPIIDGANLKSFKVTDNITKFVTEEKARSLH-RSIAKRGDIVVTISGTLG 82
Cdd:cd17246     2 EWVKLGEISSDITDGTHPT----PKYVESGIPFITSKNIKNGKIDFSDVKYISEEDHNEILkRSKLKKGDILFSIIGTIG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  83 QIAYIPDDsnyEEYLCSQRQFRVTFDTTKVYVPYLVFYFHTYEGKHKILSFANQVGVPALSqpLKNFRQISVQLPTLETQ 162
Cdd:cd17246    78 RVAIVPED---LPANINQAVALIRPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLS--LGDLKNLKIPLPPLEEQ 152

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1589013687 163 KKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17246   153 KRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLL 188
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
119-198 1.64e-13

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 65.47  E-value: 1.64e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 119 FYFHTYEGKHKILSFANQVGVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:COG0732     4 YYLRSPSFREYLRSLATGSTQPNLNK--KDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
310-389 8.72e-13

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 63.54  E-value: 8.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 310 SLKKQLDvFNGEGTVFGSINRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPRLMSSELDVS 389
Cdd:COG0732    10 SFREYLR-SLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFTGELRVR 88
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 71-188 6.46e-10

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: 57.75  E-value: 6.46e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  71 GDIVVTISGTLGQIAYIPddsnyEEYLCSQRQFRVTFDTTKVYVPYLvFYFHTYEgKHKILSFANQVGVPALSQplKNFR 150
Cdd:pfam01420  59 GDITISSRATIGYVFYRD-----KPYYTNQHIIVLIPKNNIKITEFL-YLYLLLK-LKKLKSLKFGSTQPKLTK--ERLK 129

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1589013687 151 QISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQ 188
Cdd:pfam01420 130 EIKIPLPPLEEQKKIAKILSQLDNTIELEKGILNELER 167
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 204-354 5.46e-03

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: 37.33  E-value: 5.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 204 SDWAEGTLSDIADITMGQSPSGSSYNEDGT-----------GTIFFQGRAEFgFRFPsvrlyttepkrmarSNDTLMSVR 272
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPKKKELKNNGKypyiragdlnnVVKGGLGYIKK-YILP--------------KGDITISSR 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 273 APVGDLNVAHMDCCIGRGLAAIHSKSHH--QSFVLYTMFSLKKQLDVFNGeGTVFGSINRNSLNDMPILIPSD------- 343
Cdd:pfam01420  67 ATIGYVFYRDKPYYTNQHIIVLIPKNNIkiTEFLYLYLLLKLKKLKSLKF-GSTQPKLTKERLKEIKIPLPPLeeqkkia 145

                         170
                  ....*....|.
gi 1589013687 344 DILDEFERIVA 354
Cdd:pfam01420 146 KILSQLDNTIE 156
 
Name Accession Description Interval E-value
RMtype1_S_Cep9333ORF4827P-TRD2-CR2_like cd17495
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 209-382 2.89e-116

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Crinalium epipsammum S subunit (S.Cep9333ORF4827P) TRD2-CR2 and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) T; The recognition sequences for Crinalium epipsammum S subunit (S.Cep9333ORF4827P) and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341186 [Multi-domain]  Cd Length: 174  Bit Score: 335.59  E-value: 2.89e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 209 GTLSDIADITMGQSPSGSSYNEDGTGTIFFQGRAEFGFRFPSVRLYTTEPKRMARSNDTLMSVRAPVGDLNVAHMDCCIG 288
Cdd:cd17495     1 GTLGDIANITMGQSPKGESYNEDGEGLPFYQGVTDFGFRFPTNRVYTTAPTRFAEAGDILFSVRAPVGDINIANEKCCIG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 289 RGLAAIHSKSHHQSFVLYTMFSLKKQLDVFNGEGTVFGSINRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENC 368
Cdd:cd17495    81 RGLAAIRSKSGSQSFLFYQLKSLFKEFDIFNGEGTVFGSINKKDLENLPIIIPSDEIIEAFEKLVSPIDQKIENNEKENR 160

                         170
                  ....*....|....
gi 1589013687 369 RLQDIRDTLLPRLM 382
Cdd:cd17495   161 TLAKLRDTLLPKLM 174
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 210-382 1.30e-60

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: 193.52  E-value: 1.30e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 210 TLSDIADITMGQSPSGSSYNEDGTGTIFFQGRAEFGFRFPSVRLYTTEPKRMARSNDTLMSVRAPVGDLNVAHMDCCIGR 289
Cdd:cd17245     2 KLGEVAEIIMGQSPPSSTYNEEGEGLPFLQGKADFGEIYPTPRVWCTKPTKIAEKGDILISVRAPVGDVNIADEKCCIGR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 290 GLAAIHSKSH-HQSFVLYTMFSLKKQLDVfNGEGTVFGSINRNSLNDMPILIPSddiLDEFERIVA---PMDLTIRNNYD 365
Cdd:cd17245    82 GLAAIRANKDiDNLFLYYYLKYNKPELEK-LGTGSTFKAINKKDLEELKIPLPP---LEEQQKIAEilsTVDEAIEKTKA 157

                         170
                  ....*....|....*..
gi 1589013687 366 ENCRLQDIRDTLLPRLM 382
Cdd:cd17245   158 LIEKLDELKKGLMQELF 174
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 211-378 1.95e-57

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: 185.19  E-value: 1.95e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 211 LSDIADITMGQSPSGSSYNEDGTGTIFFQGRAEFGFRFPSVRLYTTEPKRMARSNDTLMSVRAPVGDLNVAHMDCCIGRG 290
Cdd:cd17498     3 LGEIAEITMGQSPKSEFYNEDGIGLPFLQGNRTFGDKYPYIDTYTTDIKKIAKKGDILMSVRAPVGDLNIANKDICIGRG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 291 LAAIHSKSHHQSFVLYTMFSLKKQLDVfNGEGTVFGSINRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENCRL 370
Cdd:cd17498    83 LCSIRMKNGNNSFLYYLLKNNIKNLIN-KSSGTVFGSINKDDIENLEVDIPEDEEQKRIANILSKIDDKIEINNQINKNL 161


                  ....*...
gi 1589013687 371 QDIRDTLL 378
Cdd:cd17498   162 EELAQAIF 169
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 209-382 1.28e-51

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: 170.37  E-value: 1.28e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 209 GTLSDIADITMGQSPSGSSYNEDGTGTIFFQGRAEFGFRFPSVRLYTTEPKRMARSNDTLMSVRA-PVGDLNVAHMDCCI 287
Cdd:cd17496     1 VKLGDIAEIIMGQSPKGESYNTEGIGIPLLNGPADFGDGYPIPKKWTTKPTKLCKKGDILFCVRGsTTGRLNIADDEYCI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 288 GRGLAAIHSKS-HHQSFVLYTMFSLKKQLDVfNGEGTVFGSINRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDE 366
Cdd:cd17496    81 GRGVAAIRPKNgIDTEFLYYLLESNLDYLLA-AATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQE 159

                         170
                  ....*....|....*.
gi 1589013687 367 NCRLQDIRDTLLPRLM 382
Cdd:cd17496   160 IEKLEELRDTLLPKLL 175
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 211-357 4.58e-50

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2; 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: 166.19  E-value: 4.58e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 211 LSDIADITMGQSPSGSSYNEDGTGTIFFQGRAEFGFRFPSVRLYTTEPKRMARSNDTLMSVRAPVGDLNVAHMDCCIGRG 290
Cdd:cd17497     3 LKYVADIIMGQSPPSSTYNTEGIGLPFLQGKAEFGKLYPTPRKWCSAPKKIAEKGDILLSVRAPVGPTNIADQEYCIGRG 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1589013687 291 LAAIHSKSHH-QSFVLYTMFSLKKQLDvFNGEGTVFGSINRNSLNDMPILIPSddiLDEFERIVAPMD 357
Cdd:cd17497    83 LAAIRPKKGLdKKYLLYYLKSIENELS-SLGTGSTFKAISKEDLENLLIPLPP---LAEQKRIAAFLD 146
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 211-367 1.01e-46

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) TRD1-CR1 and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) TR; The recognition sequences for Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Helicobacter bizzozeronii CIII-1 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.HbiCORF8670P, and may also contain type I DNA methyltransferases.


Pssm-ID: 341190 [Multi-domain]  Cd Length: 175  Bit Score: 157.78  E-value: 1.01e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 211 LSDIADITMGQSPSGSSYNEDGTGTIFFQGRAEFGFRF---PSVrlYTTEPKRMARSNDTLMSVRAPVGDLNVAHMDCCI 287
Cdd:cd17499     3 LGDVAEIIMGQSPEGKSYNTNKEGLPFYQGKKEFGDKYikePNT--WTTSPTKIAEKNDILMSVRAPVGDVNITTRKICI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 288 GRGLAAIHSKSH-HQSFVLYTMFSLKKQLDVfNGEGTVFGSINRNSLNDMPILIPSddiLDEFERIVAPMDL------TI 360
Cdd:cd17499    81 GRGLAAIRAKKNiDKKYLFYFLLSNKDYFKG-KSGGSTFKSINKNQIKNIKIPLPP---LEEQKRIVSELDKlfklifEA 156


                  ....*..
gi 1589013687 361 RNNYDEN 367
Cdd:cd17499   157 KNNIEEA 163
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 210-343 7.10e-39

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: 136.88  E-value: 7.10e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 210 TLSDIADITMGQSPSGSSYNEDGTGTIFFQGRAEFGFRFPSVRLYTTEPKRMARSNDTLMSVRAPVGDLNVAHMDCCIGR 289
Cdd:cd17494     2 KLGEIAEITMGQSPSSKNYNDNPNGLPLVQGNADIKNGKVIPRIWTSEITKTANKGDIILSVRAPVGEVAKTNFDACIGR 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1589013687 290 GLAAIhsKSHHQSFVLYTMFSLKKQLDVFnGEGTVFGSINRNSLNDMPILIPSD 343
Cdd:cd17494    82 GVCAI--KGNEFIFLYLYLLNIEGYWSKI-SQGSTFESINSNDIKNLKISIPSL 132
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-198 2.37e-31

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: 117.62  E-value: 2.37e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   4 KLIQLSDVITDIAAGPFGSnlkvSCFVNDGFPIIDGANLKSFKVTDNITKFVTEEKARSLH-RSIAKRGDIVVTISGTLG 82
Cdd:cd17246     2 EWVKLGEISSDITDGTHPT----PKYVESGIPFITSKNIKNGKIDFSDVKYISEEDHNEILkRSKLKKGDILFSIIGTIG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  83 QIAYIPDDsnyEEYLCSQRQFRVTFDTTKVYVPYLVFYFHTYEGKHKILSFANQVGVPALSqpLKNFRQISVQLPTLETQ 162
Cdd:cd17246    78 RVAIVPED---LPANINQAVALIRPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLS--LGDLKNLKIPLPPLEEQ 152

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1589013687 163 KKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17246   153 KRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLL 188
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 31-195 1.76e-25

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: 101.81  E-value: 1.76e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  31 NDGFPIIDGANLKSFKV-TDNItKFVTEEKARSLHRSIAKRGDIVVTISGTLGQIAYIPDDsnYEEYLCSQRQFRVTFDT 109
Cdd:cd17256    23 PTGVPYIRVTDIKNGGIdLDNL-KYISPEIHEKIKRYTLSKGDILISIVGTIGRVGIVPKE--LDGANLTENAARIRPKD 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 110 TKVYvPYLVFYFHTYEGKHKILSFANQVGVPALsqPLKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQ 189
Cdd:cd17256   100 SISP-RYLYYYLRSPFGQSQIESETKGAAQPKL--NLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLEEL 176


                  ....*.
gi 1589013687 190 AQAIYQ 195
Cdd:cd17256   177 KKALMQ 182
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-197 2.21e-25

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: 101.85  E-value: 2.21e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   4 KLIQLSDVITDIAAGPFgsnlKVSCFVNDGFPIIDGANLKSFKVTDNITKFVTEEKARSLHRSIAKRGDIVVT-ISGT-- 80
Cdd:cd17517     2 EVVKLGDLLEDPRYGTS----KKSSYDGSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKELEKYLLKKGDILFNrSNGSpe 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  81 -LGQIAYIPDDSN---YEEYLcsqrqFRVTFDTTKVYVPYLVFYFHTYEGKHKILSFANQ-VGVPALSQplKNFRQISVQ 155
Cdd:cd17517    78 lVGKCALVDEEDEpaiFASYL-----IRLRLDKKKILPEFLYYYLNSPLGRKQIEKIAKSaAGQANINQ--KDLKKLPIP 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1589013687 156 LPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQM 197
Cdd:cd17517   151 LPPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-193 1.09e-22

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: 93.98  E-value: 1.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   8 LSDVItDIAAGPFGSNLKVscFVNDGF-PIIDGANLKSfKVTDNITKFVTEEKARSLHRSIAKRGDIVVTISGTLGQIAY 86
Cdd:cd16961     3 LGEIA-EIISGKTPSSSSE--YWDNGIiPWIRISDINN-GGIILTDEKITEEGAEKLKKKILPKGDILISRSGTIGKVAI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  87 IPDDsnyEEYLCSQRQFRVTFDTTkVYVPYLVFYFHTYEGKHKILSFANQVgVPALSQplKNFRQISVQLPTLETQKKIA 166
Cdd:cd16961    79 VKEN---DKALLNQAVIVIRPKDE-VDSEFLYYFLKSPFGKKLIEGSAGST-QPNLNK--SDLKNLKIPLPPLEEQKKIA 151

                         170       180
                  ....*....|....*....|....*..
gi 1589013687 167 SIVESINGKIEQNEIINNNLEQQAQAI 193
Cdd:cd16961   152 NILDKLDALIELLEQKLEKLEQLKQAL 178
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 29-195 2.76e-22

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: 92.99  E-value: 2.76e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  29 FVNDGFPIIDGANLKSFKVTDNITKFVTEEKARSLHRSIAKRGDIVVTISGTLGQIAYIPddsNYEE-----YLCSQRQF 103
Cdd:cd17264    23 FVDEGIPFINAGHLEDGTIDLSNMNFISEEKYNSLGSGKLQKGDILYCLRGSLGKCAIVD---NYDEgaiasSLVIIRPF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 104 RvtfdttKVYVPYLVFYFHTYEGKHKILSFANQVGVPALSqpLKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIIN 183
Cdd:cd17264   100 A------KVDVRYLYYYLNSPLGKSQIKKYDNGSAQPNLS--AKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQAL 171

                         170
                  ....*....|..
gi 1589013687 184 NNLEQQAQAIYQ 195
Cdd:cd17264   172 EKLEELLQSLFQ 183
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 29-199 1.05e-20

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: 88.72  E-value: 1.05e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  29 FVNDGFPIIDGANLKSFKVTDNITKFVTEEKARSLHRSIAKRGDIVVTISG-TLGQIAYIPDDsnYEEYLCSQR--QFRV 105
Cdd:cd17278    23 FSDEGIPVIRIGNIKNGGIDLDDNSKYPEEPLEKYEKFLLKKGDILIAMTGgTVGKVAIVPED--DEPALLNQRvgKFRP 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 106 TfdtTKVYVPYLVFYFHTYEGKHKILSFANQVGVPALSqpLKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNN 185
Cdd:cd17278   101 K---DKIDKEFLYYLLRSDSFRNQIKSSATGTAQPNIS--PKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKLEQKLEK 175

                         170
                  ....*....|....
gi 1589013687 186 LEQQAQAIYQQMFI 199
Cdd:cd17278   176 LRDLLKPLLQSLFT 189
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-196 1.46e-20

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: 88.34  E-value: 1.46e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   4 KLIQLSDVItDIAAG-PFGSNLkvscFVNDGFPIIDGANLKSFKVTDNITKFVTEEKARSLHRSIAKRGDIVV-----TI 77
Cdd:cd17259     2 EWVKLGDVA-DILSGyAFKSSE----FSESGIRLLRGANVGVGEIRWDDTVYLPEEYLEEYEKYLLKEGDIVIaldrpII 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  78 SGTLgQIAYIPDdsNYEEYLCSQRQFRVTFDTtKVYVPYLVFYFHTYEGKHKILSFANQVGVPALSqpLKNFRQISVQLP 157
Cdd:cd17259    77 SGGL-KVARIPK--SDLPALLVQRVARIRPKD-ELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHIS--TKQIKNFKIPLP 150

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1589013687 158 TLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQ 196
Cdd:cd17259   151 PLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKGLMQS 189
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 4-196 2.12e-18

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


Pssm-ID: 341193 [Multi-domain]  Cd Length: 195  Bit Score: 82.66  E-value: 2.12e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   4 KLIQLSDVITDIAAGPFGSNLkvscFVNDGFPIIDGANLKSFKVTDNITKFVTEEKARSLHRSIAKRGDIVVTISG---- 79
Cdd:cd17512     2 EEIRLGDIIDYQKGYAFKSKD----YQDSGIRIVRVSDFTDDSIDINNLVYISEEKANKYKKYELKENDIIITTVGswps 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  80 ----TLGQIAYIPDDSNyeEYLCSQRQFRVTFDTTKVYVPYLVFYFHTYEGKHKILSF----ANQVGVpALSQpLKNFRq 151
Cdd:cd17512    78 npdsVVGKVVRVPKEAD--GALLNQNAVKIRPKKGILDQSFLFYNLKSERFKNYIESIargnANQASI-TLGD-IKKFK- 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1589013687 152 isVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQ 196
Cdd:cd17512   153 --FLLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQALYQE 195
RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like cd17289
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 54-198 4.48e-18

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: 81.53  E-value: 4.48e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  54 FVTEEKARSLHRS--IAKRGDIVVTISGTLGQIAYIPDDSNYeeYlcsqrqFR---VTF--DTTKVYVPYLVFYFHTYEG 126
Cdd:cd17289    50 FISEERYEEIKSKygVPKKGDILITSVGTIGIPYLVKNDDPF--Y------FKdgnLTWfkNIKDINSKFLYYWFQSSIF 121

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1589013687 127 KHKILSFANQVGVPALSqpLKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17289   122 KNQINSITIGSTQKALT--IEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEELAKTLFQYWF 191
RMtype1_S_Vch69ORF1407P_TRD2-CR2_like cd17501
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio ...
 264-383 3.49e-17

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: 79.15  E-value: 3.49e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 264 SNDTLMSVRAP-VGDL---------NVAhmdCCigrglaAIHSKSHHQSFVLYtmFSLKKQLDVFNGEGtvFGS----IN 329
Cdd:cd17501    71 KGTVLVAMYGAtAGKLgilakeattNQA---CC------ALIPKEEYSPFFLY--LYLLNSRDYLANLA--SGSaqqnIS 137

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1589013687 330 RNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPRLMS 383
Cdd:cd17501   138 QQIIKNTKVLIPPEDLLEIFNKLVEPLFDKIINNLKENQKLAKLRDTLLPKLMS 191
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 208-380 4.42e-15

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: 72.87  E-value: 4.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 208 EGTLSDIADITMGQSP--SGSSY-NedgtGTI-FFQGrAEFGFrfPSVRLYTTEPK-----------RMARSNDTLMSVR 272
Cdd:cd17243     2 VKSLSDVVDIIGGGTPktSVPEYwN----GDIpWFSV-KDVNN--DSRFVLDTEKKitelglknsstKLLPKGTTIISAR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 273 APVGDLNVAHMDCCIGRGLAAIHSKSHHQSFVLYtmFSLKKQLDVF--NGEGTVFGSINRNSLNDMPILIPSDDILDEFE 350
Cdd:cd17243    75 GTVGKLALLGIPMAMNQSCYGLRGKDGLSNYFLY--YLLKNLIEELkqKAHGSVFDTITRKTFDEIKVPLPPEELQKSFE 152

                         170       180       190
                  ....*....|....*....|....*....|
gi 1589013687 351 RIVAPMDLTIRNNYDENCRLQDIRDTLLPR 380
Cdd:cd17243   153 NIVSPLFDKILNNLKENQTLAQLRDTLLPK 182
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17251
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 206-382 4.67e-15

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


Pssm-ID: 341140 [Multi-domain]  Cd Length: 185  Bit Score: 72.92  E-value: 4.67e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 206 WAEGTLSDIADITMGQSPSGSsyNEDgtgtiFFQGRAEFgFRFPSVR--LYTTEPKRM-------ARSNDTLmsvraPVG 276
Cdd:cd17251     1 WEVKTLKDFGKIITGKTPSTK--NKE-----YYGGDIPF-IKIPDMHgnVFITKTEDYlseeganSQKNKTL-----PKN 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 277 DLNVAhmdcCIGR-GLAAIHS---------------KSHHQSFVLYTMFSLKKQLDVFNGEGTVFGSINRNSLNDMPILI 340
Cdd:cd17251    68 SICVS----CIATvGLVSITTeesqtnqqinsiipkKENYRYYLYFALKSLKELLEALGSGGSTTLNLNKGKFSKIKILL 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1589013687 341 PSDDILDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPRLM 382
Cdd:cd17251   144 PSEDLLKKFHKIVSPLFDKILNNQKENQKLSQLRDTLLPKLM 185
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 206-382 1.95e-14

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: 70.90  E-value: 1.95e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 206 WAEGTLSDIADITMGQSPSGS--SYNEDG------------TGTIFFQGRA---EFGFRFPSVRLYttePKrmarsNDTL 268
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKnpEYWNGDipwitptdltklKGKYISDTERkitELGLKNSSAKLL---PA-----GSVL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 269 MSVRAPVGDLNVAHMDCCIGRGLAAIH-SKSHHQSFVLYTMFSLKKQLDvFNGEGTVFGSINRNSLNDMPILIPSddiLD 347
Cdd:cd17273    73 LSSRAPIGYVAIATNPLATNQGFKSIIpNEEIDNEFLYYLLKNNKPEIE-SLASGSTFKEISKSTFKKIEIPLPP---LE 148

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1589013687 348 EFERIVAP---MDLTIRNNYDENCRLQDIRDTLLPRLM 382
Cdd:cd17273   149 EQKKIAAIlskLDELIELLEKENEKLKELRDGLLPKLF 186
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 25-198 2.76e-14

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: 70.65  E-value: 2.76e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  25 KVSCFVNDGFPIIDGANLKSFKVTDNITKFVTEEKARSLHRSIAKRGDIVVT-ISGTLGQIAYIPDDS--NyeeylcsQR 101
Cdd:cd17516    18 KNPEYFGGDIPFITPSDMKGGKYIIKTERRLSSKGLEKVKNKLIPANSICVTcIGSDMGKVAITKEPSvtN-------QQ 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 102 QFRVTFDTTKvYVPYLVFYFHTYEGKHkILSFANQ-VGVPALSqplKN-FRQISVQLPTLETQKKIASIVESINGKIEQN 179
Cdd:cd17516    91 INSIIVNKNK-FDPDFVYYLLKNNSKY-LKSIAGGsTATPIIN---KStFSNIEIPLPPLPEQKKIAAILSSLDDKIENN 165

                         170
                  ....*....|....*....
gi 1589013687 180 EIINNNLEQQAQAIYQQMF 198
Cdd:cd17516   166 RRINKTLEEMAQALFKEWF 184
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 103-198 8.07e-14

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: 69.07  E-value: 8.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 103 FRVTFDTTKVYVPYLVFYFHTYEGKHKILSFANqVGVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEII 182
Cdd:cd17263    85 FKIIPDKNIIDKDYLYYFLKSKEIQLNILTKAG-STIPHVNK--KDLENLKIPLPSLEEQKKIAEILDKLDALIDKLKEL 161

                          90
                  ....*....|....*.
gi 1589013687 183 NNNLEQQAQAIYQQMF 198
Cdd:cd17263   162 IEKLIELKKGLFQELL 177
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
119-198 1.64e-13

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 65.47  E-value: 1.64e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 119 FYFHTYEGKHKILSFANQVGVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:COG0732     4 YYLRSPSFREYLRSLATGSTQPNLNK--KDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
310-389 8.72e-13

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 63.54  E-value: 8.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 310 SLKKQLDvFNGEGTVFGSINRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPRLMSSELDVS 389
Cdd:COG0732    10 SFREYLR-SLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFTGELRVR 88
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 67-198 1.40e-12

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: 65.40  E-value: 1.40e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  67 IAKRGDIVVTISGTLGQIAYIPDDSNYEEYLCSQRqfrvtfdTTKVYVPYLVFYFHTYegKHKILSFANQVGVPALSQP- 145
Cdd:cd17498    53 IAKKGDILMSVRAPVGDLNIANKDICIGRGLCSIR-------MKNGNNSFLYYLLKNN--IKNLINKSSGTVFGSINKDd 123

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1589013687 146 LKNFRqisVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17498   124 IENLE---VDIPEDEEQKRIANILSKIDDKIEINNQINKNLEELAQAIFKHWF 173
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 73-196 1.16e-11

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: 62.42  E-value: 1.16e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  73 IVVTISGTLGQIAYIPDDsnyeeylcsqrqfrvtF---DTT------KVYVPYLVFYF-HTyegkHKILSFANQVGVPAL 142
Cdd:cd17267    47 IVVGRKGSIGKVHYSEED----------------FwpiDTTlyvkdfKGNDPRFLYYLlKT----LDLERLNSGSAVPGL 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1589013687 143 SQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQ 196
Cdd:cd17267   107 NR--NDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADALLPK 158
RMtype1_S_MmaGORF2198P_TRD1-CR1_like cd17500
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 118-199 3.00e-11

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: 61.92  E-value: 3.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 118 VFYF--HTYEgkhKILSFANQVGVPALSQPL-KNFRqisVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIY 194
Cdd:cd17500   108 VYYSlkTQYE---ELVNLASGAAQQNLNSKLiKNFE---IPLPPLPEQKRIASILSSLDDKIELNNRQNETLEAMAETLF 181


                  ....*
gi 1589013687 195 QQMFI 199
Cdd:cd17500   182 KEWFV 186
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 210-377 3.55e-11

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: 61.63  E-value: 3.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 210 TLSDIADITMGQSPSGSS-YNEDG-----TGTIFFQGRAEFGFRFPSVRLYTTEPKRMARSNDTLMSVRAPVGDLNVAH- 282
Cdd:cd16961     2 KLGEIAEIISGKTPSSSSeYWDNGiipwiRISDINNGGIILTDEKITEEGAEKLKKKILPKGDILISRSGTIGKVAIVKe 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 283 -MDCCIGRGLAAIHSKSH-HQSFVLYTMFSLKKQLDVFNGEGTVFGSINRNSLNDMPILIPSDDILDEFERIVAPMDLTI 360
Cdd:cd16961    82 nDKALLNQAVIVIRPKDEvDSEFLYYFLKSPFGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDALI 161

                         170
                  ....*....|....*..
gi 1589013687 361 RNNYDENCRLQDIRDTL 377
Cdd:cd16961   162 ELLEQKLEKLEQLKQAL 178
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 12-197 4.83e-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: 61.34  E-value: 4.83e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  12 ITDIaaGPFGSNLKvscfvNDGFPIIDGANLKSFKVtdnitkfvteekarslhrsiaKRGDIVVTISG-TLGQIAYIpdD 90
Cdd:cd17521    33 ITDI--QDDGVLWD-----TVPYCSISEEDAEKYLL---------------------KDGDILFARTGaTVGKSYLY--K 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  91 SNYEE-----YLcsqrqFRVTFDTTKVYVPYLVFYFHTYEGKHKILSFANQVGVPALS-QPLKNFRqisVQLPTLETQKK 164
Cdd:cd17521    83 EDDGKavfasYL-----IRFRPNKKKVLPKYLFYFTQSSLYWKQIKSISSGSAQPNINaEKLKSLK---IPLPPLEEQKR 154

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1589013687 165 IASIVESINGKIEQNEIINNNLEQQAQAIYQQM 197
Cdd:cd17521   155 IVAILDALDAKIDALEELLEKLEELLKELLQSL 187
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 31-198 7.12e-11

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: 60.59  E-value: 7.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  31 NDGFPIIDGAnlksfkvTD------NITKFVTEEKArslhrsIAKRGDIVVTISG-TLGQIAYIPDdsnyeEYlCSQRQ- 102
Cdd:cd17496    24 GIGIPLLNGP-------ADfgdgypIPKKWTTKPTK------LCKKGDILFCVRGsTTGRLNIADD-----EY-CIGRGv 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 103 --FRVTFDTTKVYVPYLVfyfhtyegKHKILSFANQ-VG--VPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIE 177
Cdd:cd17496    85 aaIRPKNGIDTEFLYYLL--------ESNLDYLLAAaTGstFPNISR--DDLLNLKIPLPPLEEQKRIVAILDPLDEKID 154

                         170       180
                  ....*....|....*....|.
gi 1589013687 178 QNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17496   155 KNKQEIEKLEELRDTLLPKLL 175
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 147-198 1.28e-10

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: 60.11  E-value: 1.28e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1589013687 147 KNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17273   135 STFKKIEIPLPPLEEQKKIAAILSKLDELIELLEKENEKLKELRDGLLPKLF 186
RMtype1_S_HpyCR35ORFAP-TRD1-CR1_like cd17519
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 21-168 1.30e-10

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) TRD1-CR1 and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190; The recognition sequences of Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341200 [Multi-domain]  Cd Length: 183  Bit Score: 60.01  E-value: 1.30e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  21 GSNLKVSCFVNDGFPIIDGANLKSFKV-TDNITKFVTEEKARSLHRSIAKRGDIVVTISG-TLGQIAYipDDSNYEEYLc 98
Cdd:cd17519    14 GFAFKSSKYRESGFPIIRITNIQNGKIdTDNLKYFDLNDYKENLDKYIVRPGDIVIAMSGaTTGKVGI--NLTDQEFYL- 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  99 SQRQFRVTFDTTKVYVPYLvfyFHTYEGKHKILSFANQVGVPALSqpLKNFRQISVQLPTLETQKKIASI 168
Cdd:cd17519    91 NQRVGKFIPNEEILNNRYL---YHFLLSKQNEKYILAGGSQPNLS--SEKLKKIKIPIPSLEVQEEIVSI 155
RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like cd17258
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 53-198 2.83e-10

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: 58.96  E-value: 2.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  53 KFVTEEKARSLHRS-IAKRGDIVVTISGTLGQIAYIPDdsnyEEYLCSQRQFRVTFDTTKVYVPYLVFYFHTYEGKHKIL 131
Cdd:cd17258    33 KIVEPDYKIGLKQSkIFKKGDVLITRHGTIGRVSIILS----EEACLSSHVAGFNSKEGISDNKFIKYLFNSKKIKNRLM 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1589013687 132 SFANQVGVPALsqPLKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17258   109 SYGASSTQPAL--NLSRLLKIKFPNPPLEEQQKIGKILSTWDRAIELTEQKLELLQQQKKGLMQQLF 173
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 104-197 3.63e-10

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: 58.70  E-value: 3.63e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 104 RVTFDTTKVYVPYLVFYFHTYEGKHKILSFANQ-VGVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEII 182
Cdd:cd17522    98 RLRPNKNIVDPKYLYYLLKSDRFRNQFRSIAKKaVNQASINQ--TELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEK 175

                          90
                  ....*....|....*
gi 1589013687 183 NNNLEQQAQAIYQQM 197
Cdd:cd17522   176 IEKLKELKKGLFQKL 190
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 8-196 4.02e-10

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: 58.70  E-value: 4.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   8 LSDVITDIAAG--PFGSN-------LKVSCfVNDGfpiidganlkSFKVTDNitKFVTEEKARSLHRSIaKRGDIVVTIS 78
Cdd:cd17261     6 LGDLIEGIRNGwsPKPPDdetgwpvLKLSA-VTSG----------KFDPSEN--KYLPESLEPASEYWL-KPGDLLISRA 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  79 GTL---GQIAYIPDDsnYEEYLCSQRQFRVTFDTTKVYVPYLVFYFHTYEGKHKILSFA-----NQVGVpalSQplKNFR 150
Cdd:cd17261    72 NTSelvGRAALVDGD--PDNLIYPDKLIRLRVNEELLLPEYLALALNSPSARRQIESRAtgtagSMPKI---SQ--SDLK 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1589013687 151 QISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQ 196
Cdd:cd17261   145 SLPIPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQA 190
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 71-188 6.46e-10

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: 57.75  E-value: 6.46e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  71 GDIVVTISGTLGQIAYIPddsnyEEYLCSQRQFRVTFDTTKVYVPYLvFYFHTYEgKHKILSFANQVGVPALSQplKNFR 150
Cdd:pfam01420  59 GDITISSRATIGYVFYRD-----KPYYTNQHIIVLIPKNNIKITEFL-YLYLLLK-LKKLKSLKFGSTQPKLTK--ERLK 129

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1589013687 151 QISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQ 188
Cdd:pfam01420 130 EIKIPLPPLEEQKKIAKILSQLDNTIELEKGILNELER 167
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 3-198 7.40e-10

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: 57.50  E-value: 7.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   3 RKLIQLSDVITdiaagpfGS--NLKVSCFVNDGFPIIDGANLKSFKVTDNITKFVTE---EKARSLhrsiaKRGDIVVTI 77
Cdd:cd17286     1 KKLGDLGEIVT-------GNtpSTKNSEYYGGEILFVTPTDIDGNKYIYKTEKKLSEkgfKKARIL-----PKGSILVTC 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  78 SGTLG-------------QI-AYIPDDSNYEEYLcsqrqfrvtfdttkvyvpYLVFYFHTYegkhKILSFANQVGVPALS 143
Cdd:cd17286    69 IGSIGknaiatedcatnqQInAIIPNKNYDPEFL------------------YYALENWSK----KIKSLAGKQAVPIIN 126

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1589013687 144 QplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17286   127 K--TEFSKIKILVPPLEEQQKIANFLSKLDELIELQQQKIEKLEELKKGLLQKLF 179
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 108-198 1.08e-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: 57.45  E-value: 1.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 108 DTTKVYVPYLVFYFHTYegKHKILSFAnqvgvPALSQP---LKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINN 184
Cdd:cd17282   100 NEEKIDVEFLEYYLRTL--KKELEAIA-----PQSAQKninLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIA 172

                          90
                  ....*....|....
gi 1589013687 185 NLEQQAQAIYQQMF 198
Cdd:cd17282   173 KLEELKQSLLQEAF 186
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 116-197 1.41e-09

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


Pssm-ID: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 56.67  E-value: 1.41e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 116 YLVFYFHTYegkhKILSFANQVGVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQ 195
Cdd:cd17262    97 FLYYYLNSI----DISPYVTGAAQPKLNQ--ANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQ 170


                  ..
gi 1589013687 196 QM 197
Cdd:cd17262   171 KL 172
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 29-198 2.70e-09

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: 55.93  E-value: 2.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  29 FVNDGFPIIDGANLksfkvTDNITKF------VTEEKarslhrsIAKRGDIVVTISGTLGqiAYIpddSNYEEYLCSQRQ 102
Cdd:cd17254    20 WSDSGLPIIRIQNL-----NGGNAPFnyysglLDEKY-------YVEKGDLLFSWSASFG--PFI---WNGGKAILNQHI 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 103 FRVTFDTT--KVYVPYLVFYFhtyegKHKILSFANQVGvpalsqpLK-----NFRQISVQLPTLETQKKIASIVESINGK 175
Cdd:cd17254    83 FKVVPDEEidKDYLYYLLKAL-----TEEIESQAHGST-------MVhitkgDLENIKVPLPPLEEQKRIAAILDELDAL 150

                         170       180
                  ....*....|....*....|...
gi 1589013687 176 IEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17254   151 IDALEEQLKKLEELRKALLQSLL 173
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 110-198 2.87e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to MjaXIP/S.MjaORF132P TRD1-CR1, S.Sau1132ORF3780P TRD1-CR1, S.Mca353ORF290P TRD1-CR1, and other TRD-CR's; The Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 3'. The recognition sequence of Methanococcus jannaschii S subunit (MjaXIP/S.MjaORF132P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG, and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341196 [Multi-domain]  Cd Length: 181  Bit Score: 55.90  E-value: 2.87e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 110 TKVYVPYLvFYFHTYEgKHKILSFANQVGVPALSQP-LKNFrqiSVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQ 188
Cdd:cd17515    97 EEIDNEFL-FYFLKSQ-KEYLISLGKGGAQPNISQGiIKNI---EIPLPPLAEQKRIVAKLDKLDKLIEKLEKALEKLEE 171

                          90
                  ....*....|
gi 1589013687 189 QAQAIYQQMF 198
Cdd:cd17515   172 LKKALMQKLL 181
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 35-198 3.17e-09

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: 55.99  E-value: 3.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  35 PIIDGANLKSFKVTD-NITKFVTEEkarSLHRSIAK---RGDI-VVTISGtLGQIAYIPDDsnyeeyLCSQRQFRVTFDT 109
Cdd:cd17513    28 PWITSSDLSEDDIFKiNIRKFITEE---AIKNSATKiipANSIlIVTRVG-VGKVAINPFD------ICTSQDFTSLIPI 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 110 TKVYVPYLVFYFHTYEgkhKILSFANQ----VGVPAlsqplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNN 185
Cdd:cd17513    98 KEVNPLFLAYLLYSLL---QKLKSQLQgtsiKGITK-----DDLKNLKIPLPPLEEQQKIAAILSKLDKLIEAHEKKLEK 169

                         170
                  ....*....|...
gi 1589013687 186 LEQQAQAIYQQMF 198
Cdd:cd17513   170 LKQLKKGLMQKLF 182
RMtype1_S_Cje2232P-TRD2-CR2_like cd17526
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 8-198 5.11e-09

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: 55.67  E-value: 5.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   8 LSDVITDIAAGpFGSNLKVScfVNDGFP------IIDGANLksfkVTDNITKFVTEEKARslHRSIAKRGDIVV--TISG 79
Cdd:cd17526     6 LGDIILDIQSG-FASGKQNE--DEDGVPqlrphnITTDGEL----DLDKLIKIVPSPKER--KRYLLQKGDVLFnnTNSQ 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  80 TL-GQIAYIPDDsnyEEYLCSQRQFRVTFDTTKVYVPYLVFYFHTY--EGKHKILS--FANQVGVPalSQPLKNFRqisV 154
Cdd:cd17526    77 ELvGKTALFDGE---EPYVFSNHMTRIRVKKSKINPEFLARYLHLLwrSGYFKKLCtnWVNQAGIN--SDTLANLK---I 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1589013687 155 QLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17526   149 PLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 6-191 9.36e-09

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: 54.48  E-value: 9.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687   6 IQLSDVITDIAAGPFGSNLKVSCFVNDGFPIIDGANLKSFKVTDNiTKFVTEEKARSLHRS-IAKRGDIVVTISG---TL 81
Cdd:cd17514     1 VKIQDIAFEIINGGTPSRNEPEYWNNGDIPWLTSGETDDNFINNT-SEKITTKNGLEDSSIrIVPKGTILIACTGqgyTR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  82 GQIAYIpddsnyeEYLCSQRQFRVTFDTTKVYVPYLVFYFHTYEgKHKILSFANQVGVPALSqpLKNFRQISVQLPTLET 161
Cdd:cd17514    80 GQVAVL-------QIDASTNQAIAAIRCKENVNPKYLYYYLKTQ-KNNLRNLTSGVAQKNLN--IEMLRNLQIPLPPKEE 149

                         170       180       190
                  ....*....|....*....|....*....|
gi 1589013687 162 QKKIASIVESINGKIEQNEIINNNLEQQAQ 191
Cdd:cd17514   150 QQKIVNILETLEFFEKDSLRKIKETAQDIN 179
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 144-195 9.74e-09

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


Pssm-ID: 341155 [Multi-domain]  Cd Length: 159  Bit Score: 53.99  E-value: 9.74e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1589013687 144 QPL---KNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQ 195
Cdd:cd17266   105 QPLitvSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKELMQ 159
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 43-198 9.98e-09

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: 54.47  E-value: 9.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  43 KSFKVTDNITKFVTEE--KARSLHrsIAKRGDIVVTISGTLGQIAYipddsNYEEYLCSQRQFRVTFDTTKVYVPYLvFY 120
Cdd:cd17275    40 KSGKYIYSTEKYITEEglKNSSAW--IVPKGTILYAMYASVGKVAI-----NKIDVATNQAILGIIPKDEKLDFEFL-YY 111

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1589013687 121 FHTYEgKHKILSFANQVGVPALSqpLKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17275   112 WLLSL-KNELKRLIRTGTQANLN--AEIVKNLPIPLPPLEEQKKIAEILDKIDAEIDKLEEKIEKLRELKKGLLQKMF 186
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 69-198 1.01e-08

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: 53.70  E-value: 1.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  69 KRGDIVVTISGTLGQI-------AYIpDDSNYeeylcsqrqfrV--TFDTTKVYVPYLvfyFHTYegkhKILSFANQVG- 138
Cdd:cd17292    30 KKGDILISASGTIGRTviydgedAYF-QDSNI-----------VwlDNDESKVLNKFL---YYFY----QIIKWKKTEGs 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1589013687 139 -VPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17292    91 tIKRLYN--DNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYLF 149
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 42-197 1.20e-08

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


Pssm-ID: 341136 [Multi-domain]  Cd Length: 190  Bit Score: 54.46  E-value: 1.20e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  42 LKSFKVTDNI----TKFVTEEKARSLHRSIAKRGDIVVTISG---TLGQIAY--IPDDSNyeeylcsQRQFRVTFDTTKV 112
Cdd:cd17247    37 VSSGEVNDNRiteaDEFITELALKECSLPLVPPGSVLVAMIGqgkTRGQAAIlaIEATIN-------QNLAAIRPNEERV 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 113 YVPYLVFYFHT-YEgkhKILSFANQVGVPALS-QPLKNFRqisVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQA 190
Cdd:cd17247   110 LPEYLHYYLESqYD---ELRRIGSGGGQGALNcGILKAFP---IPLPPLDEQREIVAELEALLAKIDLLEEKIARLIELL 183


                  ....*..
gi 1589013687 191 QAIYQQM 197
Cdd:cd17247   184 KELRQAL 190
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 103-198 2.06e-08

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: 53.63  E-value: 2.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 103 FRVTFDTTKVYVPYLVFYFHTYEGKHKILSFANQV-GVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEI 181
Cdd:cd17253    99 FRVRPKDDLLLPEFLSYWLNSAYGRGYFLRAAKQTtNLASINS--TKLKALPVPLPPLEEQRRIVERLDELLALIDALEA 176

                          90
                  ....*....|....*..
gi 1589013687 182 INNNLEQQAQAIYQQMF 198
Cdd:cd17253   177 SLAKLEELLKALRQALL 193
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 138-198 3.44e-08

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: 52.47  E-value: 3.44e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1589013687 138 GVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17288   103 GVPSLTQ--TTLNKIKIPIPPLEEQQKIASILDKLDAKDALIELQEKLLEKLKQYKLALMQ 161
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 69-195 4.13e-08

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: 52.95  E-value: 4.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  69 KRGDIVV-TISGT---LGQIAYIPDDSNYeeylcsqrqfrvTFD--------TTKVYVPYLVFYFHTYEGKHKILSFANQ 136
Cdd:cd17252    65 KKGDILIcMSSGSkelVGKAAFIDEDTDY------------TFGafcgvirpKKEIDPRYLFYFLQSPSYREYIRSLASG 132

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1589013687 137 VGVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQ 195
Cdd:cd17252   133 TNINNLSN--EHLENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQALEKLDELLKSLFQ 189
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 149-198 4.90e-08

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: 52.05  E-value: 4.90e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1589013687 149 FRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17260   116 LENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 31-197 9.28e-08

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: 51.68  E-value: 9.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  31 NDGFPIIDGANLKSFKVTDNITKfVTEEKARSLHRSIAKRGDI-VVTISGTLgqiayipddsnyeeylcsQRQFRVTF-- 107
Cdd:cd17249    24 GGDIPWVSPKDMKSDYISDSEDH-ITELAVEESGTKLVPAGSVlIVVRGMIL------------------AHTFPVAItt 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 108 -DTT-----KVYVP-------YLVFYFHTYEgkHKILSFANQVGVPALSQPLKNFRQISVQLPTLETQKKIASIVESING 174
Cdd:cd17249    85 rPVAfnqdiKALIPkegidpeFLLYALKANE--DRILSLVDKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDALDA 162

                         170       180
                  ....*....|....*....|...
gi 1589013687 175 KIEQNEIINNNLEQQAQAIYQQM 197
Cdd:cd17249   163 LIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 115-198 1.43e-07

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: 50.95  E-value: 1.43e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 115 PYLVFYF--HTYEgkhKILSFANQVGVPALSQPLknFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQA 192
Cdd:cd17287   103 PDFLFYYlqSSYE---ELRDLSNGGGQPNLNAGL--IKSIEIPVPPLDEQQKIAAFLSAIDAKIDALEQKLELLQELKKS 177


                  ....*.
gi 1589013687 193 IYQQMF 198
Cdd:cd17287   178 LMQQLF 183
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 31-198 1.98e-07

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: 50.53  E-value: 1.98e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  31 NDGFPIIDGANLKSFKVTDNITKFVTEE---KARslhrsIAKRGDIVVT-ISGTLG-------------QI-AYIPDDSN 92
Cdd:cd17293    24 GGDIPFIKPDDLNNGGIILTSEEYLSEEgakKAR-----IVPKGSILVTcIGGSIGkvgiadrevafnqQInAIIPNKSV 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  93 YEEYLcsqrqfrvtfdttkvyvpYLVFYFhtyeGKHKILSFANQVGVPALSqplK-NFRQISVQLPTLETQKKIASIVES 171
Cdd:cd17293    99 DPKFL------------------YYQLLS----SKFQLQAIASSTTLPIIN---KsKFEKIEIPLPPLEEQKRIVAKLDK 153

                         170       180
                  ....*....|....*....|....*..
gi 1589013687 172 INGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17293   154 LFALIDKLEESLEELDELLKSLFQSAF 180
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 150-195 2.21e-07

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


Pssm-ID: 341172 [Multi-domain]  Cd Length: 181  Bit Score: 50.56  E-value: 2.21e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1589013687 150 RQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQ 195
Cdd:cd17283   136 KNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLEELKKGLMQ 181
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 206-383 2.77e-07

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


Pssm-ID: 341146 [Multi-domain]  Cd Length: 176  Bit Score: 50.22  E-value: 2.77e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 206 WAEGTLSDIADITMGQSPSGSSYNEDGTGTiffqgraefgfrfPSVRL----------YTTEPkrmaRSNDTLmsVRApv 275
Cdd:cd17257     1 WEVVRLGDVADVQNGFPFKSKLFNDEGGGL-------------PLIRIrdlksgdtetYYTGE----YDEKYL--VKN-- 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 276 GDLnVAHMD----CCI-GRGLAA-------IHSKS--HHQSFVLYtmfSLKKQLDVFNGEgTVFGS---INRNSLNDMPI 338
Cdd:cd17257    60 GDI-LIGMDgdfnAAIwKGGDALlnqrvcrIRPKSeeLDKRFLYY---ALPPPLKAIEDT-TSSTTvkhLSSKDIDEIEL 134

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1589013687 339 LIPSddiLDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPRLMS 383
Cdd:cd17257   135 PLPP---LEEQRRIAEILDELDALIDKLIAKLEKLRDLLLPLLQS 176
RMtype1_S_Eco2747II-TRD2-CR2-like cd17272
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 33-170 3.15e-07

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


Pssm-ID: 341161 [Multi-domain]  Cd Length: 189  Bit Score: 50.12  E-value: 3.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  33 GFPIIDGANLKSFKVTdniTKFVTEEKARSLHRSIAKRGDIVVTISGTLGQIAYIPDDSNYEeYLCSQRQFRvtFDTTKV 112
Cdd:cd17272    27 EIPVITSKNISNGKID---FEYVKYDFLSISKNRKINKGDILITMIGTIGETAIVKCLDPKF-YTLNLYLIR--LKKEKL 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1589013687 113 YVPYLVFYFHTYEGKHKILSFANQVGvpalSQPLKNFRQISVQLPTLETQKKIASIVE 170
Cdd:cd17272   101 LPSYLKYFLDSEKFLNKSISATSGQG----YLKANQIDKLEIPLPPLEEQQRIVKILD 154
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 46-198 4.20e-07

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


Pssm-ID: 341184 [Multi-domain]  Cd Length: 182  Bit Score: 49.91  E-value: 4.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  46 KVTDNITKFVTEEkarSLHRSIAK---RGDIVVTISGTLGQIAYIPDDSNyeeylCSQRQFRVTFDTTKVYVPYLvFYFH 122
Cdd:cd17296    39 KYVDETEEFITEE---GLNNSSAKllkKGTILIAIFATIGKVGILKIEAT-----TNQAIAGIKPKNKSINPKYL-YYYL 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1589013687 123 TYEgKHKILSFANQVGVPALSQP-LKNFRqisVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17296   110 KSL-YEKFLSLGRGVAQNNINLSiLKNLK---IPLPPLEEQQRIVAILDKFEKLINKRQEGLQLLDELVKSLFEEMF 182
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 327-380 5.82e-07

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: 48.94  E-value: 5.82e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1589013687 327 SINRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPR 380
Cdd:cd17267   105 GLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADALLPK 158
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 328-384 1.09e-06

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: 48.62  E-value: 1.09e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1589013687 328 INRNSLNDMPILIPSddiLDEFERIVAPMDlTIRNNYDENCRLQDIRDTLLPRLMSS 384
Cdd:cd17244   128 LNSKKIKEIPIPLPP---LEEQKRIAPILD-KIDALIDQLETLIELLDELLPKLMSG 180
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 55-198 1.12e-06

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: 48.36  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  55 VTEEKARSLHRSIAKRGDIVVTISGTLG------------Q--IAYIPDDSNYEEYLCSqrqfrvtfdttkvYVPYLVFY 120
Cdd:cd17284    52 VSEEEIKEMNLKVIPKGSVIMSCVGDFGivaiatnelvinQqlHAFVPSKKINPEYLMY-------------LLSLQKKY 118

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1589013687 121 FHtyegkhkilSFANQVGVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17284   119 ME---------KIATGTTIPYLNK--TNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQQLF 185
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 45-194 1.35e-06

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


Pssm-ID: 341132 [Multi-domain]  Cd Length: 182  Bit Score: 48.22  E-value: 1.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  45 FKVTD--NITKFV--TEEK--ARSLHRSIAK---RGDIVVTISGTLGQIAYIPDD-----SNYeeylcsqrQFRVTFDTT 110
Cdd:cd17243    32 FSVKDvnNDSRFVldTEKKitELGLKNSSTKllpKGTTIISARGTVGKLALLGIPmamnqSCY--------GLRGKDGLS 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 111 KVYVpylvfYFHTyegKHKILSF-ANQVGvpalSQ----PLKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNN 185
Cdd:cd17243   104 NYFL-----YYLL---KNLIEELkQKAHG----SVfdtiTRKTFDEIKVPLPPEELQKSFENIVSPLFDKILNNLKENQT 171


                  ....*....
gi 1589013687 186 LEQQAQAIY 194
Cdd:cd17243   172 LAQLRDTLL 180
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 147-198 1.86e-06

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: 47.53  E-value: 1.86e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1589013687 147 KNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17245   123 KDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKLDELKKGLMQELF 174
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 31-193 2.70e-06

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: 47.58  E-value: 2.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  31 NDGFPIIDGANLKSFKVTDNITKFVTEEKARSLHRSIAKRGDI-VVTISGTLGQIAYIPDDSnyeeylCSQRQFRVTFDT 109
Cdd:cd17290    26 GGIIPWFTPGDFNGDLILSESKRKLSELAIEDGEARLFPKNSVlVVGIGATIGKVGYSDKES------SSNQQITGIIFN 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 110 TKVYVPYLVFYFHTYegKHKILSFANQVGVPALSQplKNFRQISVQLPTLETQKKIASIVES----INGKIEQNEIINNN 185
Cdd:cd17290   100 KDINPKFLFYWLSSS--KEELENLANGATLPILNQ--EKLKNIKLPVPPLNEQQKIVEFLDKktakIDALIAKKEQLIEL 175


                  ....*...
gi 1589013687 186 LEQQAQAI 193
Cdd:cd17290   176 LKEYRQAL 183
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 328-381 2.74e-06

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: 47.04  E-value: 2.74e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1589013687 328 INRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPRL 381
Cdd:cd17262   119 LNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQKL 172
RMtype1_S_EcoUTORF5051P-TRD2-CR2_like cd17524
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 96-196 3.02e-06

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: 47.46  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  96 YLcsqrqFRVTFDTTKVYVPYLVFYFHTYEGKHKILSFA----NQVGVPAlsqplKNFRQISVQLPTLETQKKIASIVES 171
Cdd:cd17524    94 YL-----IRIRLNEEKILPEYLNYFLNSPYGRKQIKSVAtqgvGQANINA-----TKLKAIPIPLPPLEEQKEIVEKLDE 163

                          90       100
                  ....*....|....*....|....*
gi 1589013687 172 INGKIEQNEIINNNLEQQAQAIYQQ 196
Cdd:cd17524   164 LDALIDRLEALLEEAEELLESLLQS 188
RMtype1_S_Asp27244ORF1181P-TRD1-CR1_like cd17518
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 29-192 4.02e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter sp. S subunit (S.Asp27244ORF1181P) TRD1-CR1; The recognition sequence of Acinetobacter sp. S subunit (S.Asp27244ORF1181P) 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: 341199 [Multi-domain]  Cd Length: 180  Bit Score: 46.97  E-value: 4.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  29 FVNDGFPIIDGANLKSFKVT-DNITKFVTEEKARS--LHRSIaKRGDIVVTISGTL-GQIAYIPDDsnYEEYLCSQRQFR 104
Cdd:cd17518    20 FTDEGIKLLNVTNIVNGSLDlDKTDRYISTEEYNGkyKHFLI-DEGDILIASSGNSwGKVAIVEKD--HLPLMLNTSTIR 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 105 VTFDTTKVYVPYLVFYFHTyegkhkiLSFANQVGVPALSQPLKNF-----RQISVQLPTLETQKKIASIVESINGKIEQN 179
Cdd:cd17518    97 FKFIDGLLDNNFLKYFLNS-------DYFKEQLDLLITGGAQPNFgpshlKKIKIPLPPLEEQKRIAEILDDADDAIEAA 169

                         170
                  ....*....|...
gi 1589013687 180 EIinnNLEQQAQA 192
Cdd:cd17518   170 LE---ALRKKKQA 179
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 260-353 4.66e-06

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: 46.78  E-value: 4.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 260 RMARSNDTLMSVRAPVGDLNVAHMDCCIGRG------LAAIHSKshhqsFVLYTMFSLKKQLDVFnGEGTVFGSINRNSL 333
Cdd:cd17279    61 SLVPAGSIILSTRAPIGYVAIATVELCTNQGckalvpNSDVDSR-----FLYYLLLAAKEELNSL-GRGTTFLELSTDEL 134

                          90       100
                  ....*....|....*....|
gi 1589013687 334 NDMPILIPSddiLDEFERIV 353
Cdd:cd17279   135 ANFKIPLPP---LSEQRAIA 151
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 146-198 7.11e-06

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: 45.96  E-value: 7.11e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1589013687 146 LKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17285   129 LEDLKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEKLKQLKKGLMQSLL 181
RMtype1_S_Eco15ORF14057P-TRD1-CR1_like cd17525
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 104-197 1.29e-05

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: 45.30  E-value: 1.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 104 RVTFDttKVYVPYLV-FYFHTYEGKHKILSFAnqVG---VPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQN 179
Cdd:cd17525    99 RIRFD--DIVLPYFInYYLNSPDGKKQLESIA--SGttsVAAIYQ--KDLKKLKLPLPPLDEQREIVSFLSELDAKIDQL 172

                          90
                  ....*....|....*...
gi 1589013687 180 EIINNNLEQQAQAIYQQM 197
Cdd:cd17525   173 EQKLEKLLQIKKALMQQL 190
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 116-198 1.82e-05

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


Pssm-ID: 341139 [Multi-domain]  Cd Length: 185  Bit Score: 44.93  E-value: 1.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 116 YLVFYFHTYEgkhkILSFANQVGVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQ 195
Cdd:cd17250   109 YLYYWLKKVD----LYKYSQATTVPSIRK--STLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGLRQ 182


                  ...
gi 1589013687 196 QMF 198
Cdd:cd17250   183 SLL 185
RMtype1_S_NmaSCMORF606P_TRD2-CR2_like cd17271
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 25-198 4.67e-05

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: 43.80  E-value: 4.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  25 KVSCFVNDGFPIIDGANLKSFKVTDNITKfVTEEKARSLHRSIAKRGDIVVTI-----SGTLGQIAYIPDDSNyeeylCS 99
Cdd:cd17271    17 GNPEYFNGDIPWITSGELNYNYITDTNEK-ITEEAVKNTNLKIHPKGTFLIAItgleaAGTRGKCAITGIPAT-----TN 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 100 QRQFRVtFDTTKVYVPYLvFYFHTYEGKHKILSFANqvGVPALSQPLKNFRQISVQLPTLETQKKIASIVESINGKIEQN 179
Cdd:cd17271    91 QSCMAF-YPTKKLTTEFL-FYWYKKYGNYLGFKYAQ--GTKQQSYTADIVKKLPILLPTLKEQKKIANFLSDIDELIATL 166

                         170
                  ....*....|....*....
gi 1589013687 180 EIINNNLEQQAQAIYQQMF 198
Cdd:cd17271   167 EKKIEKLKKIKKGLMQKLL 185
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 74-196 6.24e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.MgeORF438P TRD1-CR1 and TRD2-CR2, and to Escherichia coli G5 S subunit (S.Eco16445ORF5013P ) TRD2-CR2 and Acetobacter pasteuri; The recognition sequences of Mycoplasma genitalium G-37 S subunit (S.MgeORF438P), Escherichia coli G5 S subunit (S.Eco16445ORF5013P), and Acetobacter pasteurianus IFO 3283-01 S subunit (S2.Apa3283ORF14230P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341180 [Multi-domain]  Cd Length: 161  Bit Score: 42.88  E-value: 6.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  74 VVTISGTLGQIAYIpddsNY--EEYLCSQRQFrvTFDTTKVYVPYLVFYFHTYEgKHKILSFANQVGVPALSqpLKNFRQ 151
Cdd:cd17291    48 TITISASGASAGYV----NYwkEPFWASDCCY--ILSSKNELVNKFLYYFLKNK-QEEIYSLQRGAGQPHIY--KKDIEK 118

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1589013687 152 ISVQLPTLETQKKIASIVESINGKIEQNEIinNNLEQQAQAIYQQ 196
Cdd:cd17291   119 LKIPIPPLEEQQKIVEILDKFTELTAELPA--ELEARKKQYEYYR 161
RMtype1_S_Eco540ANI-TRD1-CR1_like cd17274
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 148-199 1.20e-04

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: 42.48  E-value: 1.20e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1589013687 148 NFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMFI 199
Cdd:cd17274   120 EYSKFKIPLPPLEEQNKIVRILDKFDELIAELEAKLELLKKQKKYYLQKLFT 171
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 149-197 2.07e-04

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: 41.36  E-value: 2.07e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1589013687 149 FRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQM 197
Cdd:cd17255   118 MAKIKIPLPPLEEQEKIANILDKLDELINLLIAKLKKLIELRKKQLEYY 166
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 67-198 3.03e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) TRD1-CR1 and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) TR; The recognition sequences for Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Helicobacter bizzozeronii CIII-1 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.HbiCORF8670P, and may also contain type I DNA methyltransferases.


Pssm-ID: 341190 [Multi-domain]  Cd Length: 175  Bit Score: 41.06  E-value: 3.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  67 IAKRGDIVVTISGTLGQIAYIPDDSNYEEYLCSqrqFRVTFDTTKVYVPYLVFYFHTYEGKHKILSFanqvgVPALSQpl 146
Cdd:cd17499    54 IAEKNDILMSVRAPVGDVNITTRKICIGRGLAA---IRAKKNIDKKYLFYFLLSNKDYFKGKSGGST-----FKSINK-- 123

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1589013687 147 KNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17499   124 NQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNNIEEALANAQQLFKSIL 175
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 147-198 3.39e-04

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: 40.97  E-value: 3.39e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1589013687 147 KNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17494   120 NDIKNLKISIPSLEEQQKIATFLSTLDAEITLLEKKLEKLKQLKKGLLQKLF 171
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 115-198 3.48e-04

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


Pssm-ID: 341154 [Multi-domain]  Cd Length: 181  Bit Score: 40.95  E-value: 3.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 115 PYLVFYFHTYEGKHKILSFA----NQVGVpalsqplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQA 190
Cdd:cd17265   101 DYLFHLFNSDLFKKQIGSFLtatiNQITN-------GNLNNFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELK 173


                  ....*...
gi 1589013687 191 QAIYQQMF 198
Cdd:cd17265   174 KELMQQLI 181
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 149-198 3.83e-04

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


Pssm-ID: 341137 [Multi-domain]  Cd Length: 196  Bit Score: 41.36  E-value: 3.83e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1589013687 149 FRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17248   140 FKALRIALPPLEEQRKIVDRLEALDAKIDALERKLERLIELLKELRQALL 189
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 210-382 4.69e-04

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: 40.61  E-value: 4.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 210 TLSDIADITMGQSPSGSS---YNEDG---TGTIFFQGRaefgFRFPSVRLYTTEPKRMARSNdtlmsvRAPVGDLNVahm 283
Cdd:cd17516     2 KIGDLGKVVTGKTPSTKNpeyFGGDIpfiTPSDMKGGK----YIIKTERRLSSKGLEKVKNK------LIPANSICV--- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 284 dCCIGR--GLAAIHSKS----------------HHQSFVLYTMFSLKKQLDVFNGEGTVFGSINRNSLNDMPILIPSDDI 345
Cdd:cd17516    69 -TCIGSdmGKVAITKEPsvtnqqinsiivnknkFDPDFVYYLLKNNSKYLKSIAGGSTATPIINKSTFSNIEIPLPPLPE 147

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1589013687 346 LDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPRLM 382
Cdd:cd17516   148 QKKIAAILSSLDDKIENNRRINKTLEEMAQALFKEWF 184
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 260-381 4.70e-04

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: 40.90  E-value: 4.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 260 RMARSNDTLMSVRA-------PVGdlnVAHMDCCIGRGLAAIHSKSHHQS-FVLYTMFSLKKQ-LDVFNGEGTVFGSINR 330
Cdd:cd17249    58 KLVPAGSVLIVVRGmilahtfPVA---ITTRPVAFNQDIKALIPKEGIDPeFLLYALKANEDRiLSLVDKAGHGTGSLDT 134

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1589013687 331 NSLNDMPILIPSddiLDEFERIVA---PMDLTIRNNYDENCRLQDIRDTLLPRL 381
Cdd:cd17249   135 DDLKNLPIPLPP---LEEQRRIAAildALDALIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_PluTORF4319P-TRD2-CR2_like cd17269
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 100-198 8.67e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Photorhabdus luminescens S subunit (S.PluTORF4319P) TRD2-CR2; The recognition sequence of Photorhabdus luminescens S subunit (S.PluTORF4319P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341158 [Multi-domain]  Cd Length: 168  Bit Score: 39.88  E-value: 8.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 100 QRQFRVTFDTTKVYVPYLVFYFHTYEgKHKILSFANQVGVPALSQP-LKNFrqiSVQLPTLETQKKIASIVESINGKIEQ 178
Cdd:cd17269    70 QRTYVIHPFKEEIDPKFLYYYLKSYF-KKYIEKNSVGSSVPYIRLPmLENF---KIPLPPLEEQKRIVRILDKFDALTAE 145

                          90       100
                  ....*....|....*....|
gi 1589013687 179 NEIINNNLEQQAQAIYQQMF 198
Cdd:cd17269   146 LPAELEARKKQYEYYRDALL 165
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 206-383 8.95e-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: 8.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 206 WAEGTLSDIADITMGQSPSGSSYNEDGTGtIF----FQGRAEFGFRFPSVRLYTTE-PKR-MARSNDTLMS-VRAPVGdl 278
Cdd:cd17278     1 WEVVKLGDIADIQNGYAFKSSDFSDEGIP-VIrignIKNGGIDLDDNSKYPEEPLEkYEKfLLKKGDILIAmTGGTVG-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 279 NVAHMDCCIGRGL-----AAIHSKS-HHQSFVLYTMFSLKKQLDVFNGE-GTVFGSINRNSLNDMPILIPSDDILDEFER 351
Cdd:cd17278    78 KVAIVPEDDEPALlnqrvGKFRPKDkIDKEFLYYLLRSDSFRNQIKSSAtGTAQPNISPKDIESIKIPLPPLEEQKKIAE 157

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1589013687 352 IVAPMDLTIRNNYDencRLQDIRDTLLPRLMS 383
Cdd:cd17278   158 ILDSLDAKIDKLEQ---KLEKLRDLLKPLLQS 186
RMtype1_M_Cni19672ORF1405P_RMtype11G_Hci611ORFHP_T cd17277
Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 ...
 45-196 1.06e-03

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: 39.70  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687  45 FKVTDNITKFVTEEKARSLHRSIAKRGDIVVTISGTLGQIAYipddsNYEEYLCSQRQFRVTFDTTKVYVPYLVFYFHTY 124
Cdd:cd17277    43 GLIISSTKQFITEKALEEKKVKLVPKNSVLLSCTATIGKVAI-----AKIELTTNQQINALICKDSKILPEYLFYALKHI 117

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1589013687 125 egKHKILSFANQVGVPALSQP-LKNFRqisVQLPTLETQKKIASivesingKIEQNEIINNNLEQQAQAiYQQ 196
Cdd:cd17277   118 --KQVLERLTTNPGVKHVNLSmLSNLQ---IPLPPLEVQKKIVA-------EIEKVEKVIQGLRQKIDE-YQP 177
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 135-196 1.41e-03

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: 39.38  E-value: 1.41e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1589013687 135 NQVGVPALSQplKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQ 196
Cdd:cd17244   121 TASKGKTLNS--KKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDELLPKLMSG 180
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 146-198 1.72e-03

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: 39.01  E-value: 1.72e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1589013687 146 LKNFRQISVQLPTLETQKKIASIVESINGKIEQNEIINNNLEQQAQAIYQQMF 198
Cdd:cd17294   136 LKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLPALLELRQKQYEYLR 188
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 328-382 3.61e-03

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


Pssm-ID: 341149 [Multi-domain]  Cd Length: 165  Bit Score: 37.80  E-value: 3.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1589013687 328 INRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPRLM 382
Cdd:cd17260   111 VPKDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 204-354 5.46e-03

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: 37.33  E-value: 5.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 204 SDWAEGTLSDIADITMGQSPSGSSYNEDGT-----------GTIFFQGRAEFgFRFPsvrlyttepkrmarSNDTLMSVR 272
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPKKKELKNNGKypyiragdlnnVVKGGLGYIKK-YILP--------------KGDITISSR 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 273 APVGDLNVAHMDCCIGRGLAAIHSKSHH--QSFVLYTMFSLKKQLDVFNGeGTVFGSINRNSLNDMPILIPSD------- 343
Cdd:pfam01420  67 ATIGYVFYRDKPYYTNQHIIVLIPKNNIkiTEFLYLYLLLKLKKLKSLKF-GSTQPKLTKERLKEIKIPLPPLeeqkkia 145

                         170
                  ....*....|.
gi 1589013687 344 DILDEFERIVA 354
Cdd:pfam01420 146 KILSQLDNTIE 156
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 303-383 7.05e-03

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: 37.06  E-value: 7.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589013687 303 FVLYtmFSLKKQLDVFNgEGTVFGSINRNSLNDMPILIPSDDILDEFERIVAPMDLTIRNNYDENCRLQDIRDTLLPRLM 382
Cdd:cd17288    85 FLYY--LLKTIDFKKYN-EATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDALIELQEKLLEKLKQYKLALMQ 161


                  .
gi 1589013687 383 S 383
Cdd:cd17288   162 E 162
 
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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