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Conserved domains on  [gi|497036889|ref|WP_009443044|]
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restriction endonuclease subunit S, partial [Selenomonas sp. oral taxon 149]

Protein Classification

restriction endonuclease subunit S domain-containing protein( domain architecture ID 1000239)

type I restriction-modification system specificity (S) subunit (HsdS) dictates DNA sequence specificity; it consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs; each TRD binds to different specific sequences in the DNA

PubMed:  24068554

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 26-201 1.28e-40

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 cd17254:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 173  Bit Score: 136.05  E-value: 1.28e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  26 LTDIAEYLNGLAmqkFRPQN-EQESLPVLKIKELRQGQCDINseRCSLDIKPQYIIHDGDVIFSWSGSLLVDFWCGGICG 104
Cdd:cd17254    3 LGDLATFINGRA---FKPSEwSDSGLPIIRIQNLNGGNAPFN--YYSGLLDEKYYVEKGDLLFSWSASFGPFIWNGGKAI 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 105 LNQHLFKVHSKQYAP--WLYYSWtKYYLAEFVAMAAdkATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAH 182
Cdd:cd17254   78 LNQHIFKVVPDEEIDkdYLYYLL-KALTEEIESQAH--GSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDAL 154

                        170
                 ....*....|....*....
gi 497036889 183 RVEIRKLSTLRNTLLPRLM 201
Cdd:cd17254  155 EEQLKKLEELRKALLQSLL 173
 
Name Accession Description Interval E-value
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 26-201 1.28e-40

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: 136.05  E-value: 1.28e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  26 LTDIAEYLNGLAmqkFRPQN-EQESLPVLKIKELRQGQCDINseRCSLDIKPQYIIHDGDVIFSWSGSLLVDFWCGGICG 104
Cdd:cd17254    3 LGDLATFINGRA---FKPSEwSDSGLPIIRIQNLNGGNAPFN--YYSGLLDEKYYVEKGDLLFSWSASFGPFIWNGGKAI 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 105 LNQHLFKVHSKQYAP--WLYYSWtKYYLAEFVAMAAdkATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAH 182
Cdd:cd17254   78 LNQHIFKVVPDEEIDkdYLYYLL-KALTEEIESQAH--GSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDAL 154

                        170
                 ....*....|....*....
gi 497036889 183 RVEIRKLSTLRNTLLPRLM 201
Cdd:cd17254  155 EEQLKKLEELRKALLQSLL 173
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
122-208 2.46e-15

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 68.16  E-value: 2.46e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 122 YYSWTKYYLAEFVAMAadKATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLSTLRNTLLPRLM 201
Cdd:COG0732    4 YYLRSPSFREYLRSLA--TGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81


                 ....*..
gi 497036889 202 SGEIDVS 208
Cdd:COG0732   82 TGELRVR 88
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 18-179 1.14e-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: 38.11  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889   18 PKGWQEGYLTDIAEYLNGLAMQKFRPqNEQESLPVLKIKELRQGQCDInsercsLDIKPQYIIHDGDVIFSWSGSLLVDF 97
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKEL-KNNGKYPYIRAGDLNNVVKGG------LGYIKKYILPKGDITISSRATIGYVF 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889   98 WCGGICGLNQHLFKVHSKQYAPWLYYSWtkYYLAEFVA--MAADKATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPL 175
Cdd:pfam01420  74 YRDKPYYTNQHIIVLIPKNNIKITEFLY--LYLLLKLKklKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQL 151


                  ....
gi 497036889  176 YDAI 179
Cdd:pfam01420 152 DNTI 155
 
Name Accession Description Interval E-value
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 26-201 1.28e-40

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: 136.05  E-value: 1.28e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  26 LTDIAEYLNGLAmqkFRPQN-EQESLPVLKIKELRQGQCDINseRCSLDIKPQYIIHDGDVIFSWSGSLLVDFWCGGICG 104
Cdd:cd17254    3 LGDLATFINGRA---FKPSEwSDSGLPIIRIQNLNGGNAPFN--YYSGLLDEKYYVEKGDLLFSWSASFGPFIWNGGKAI 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 105 LNQHLFKVHSKQYAP--WLYYSWtKYYLAEFVAMAAdkATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAH 182
Cdd:cd17254   78 LNQHIFKVVPDEEIDkdYLYYLL-KALTEEIESQAH--GSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDAL 154

                        170
                 ....*....|....*....
gi 497036889 183 RVEIRKLSTLRNTLLPRLM 201
Cdd:cd17254  155 EEQLKKLEELRKALLQSLL 173
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
122-208 2.46e-15

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 68.16  E-value: 2.46e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 122 YYSWTKYYLAEFVAMAadKATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLSTLRNTLLPRLM 201
Cdd:COG0732    4 YYLRSPSFREYLRSLA--TGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81


                 ....*..
gi 497036889 202 SGEIDVS 208
Cdd:COG0732   82 TGELRVR 88
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 21-202 1.96e-14

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: 68.32  E-value: 1.96e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  21 WQEGYLTDIAEYLNGLAMQ--KFRpqNEQESLPVLKIKELRQGQCDINSERcslDIKPQYIIHDGDVIFSWSGSLLVDFW 98
Cdd:cd17257    1 WEVVRLGDVADVQNGFPFKskLFN--DEGGGLPLIRIRDLKSGDTETYYTG---EYDEKYLVKNGDILIGMDGDFNAAIW 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  99 CGGICGLNQHLFKVHSKQYapwlyySWTKYYLAEFVAMAADK------ATTMGHI-KRDaLENARVLIPcsddylKIEEQ 171
Cdd:cd17257   76 KGGDALLNQRVCRIRPKSE------ELDKRFLYYALPPPLKAiedttsSTTVKHLsSKD-IDEIELPLP------PLEEQ 142

                        170       180       190
                 ....*....|....*....|....*....|....
gi 497036889 172 ---LQPLYDAIIAHRVEIRKLSTLRNTLLPRLMS 202
Cdd:cd17257  143 rriAEILDELDALIDKLIAKLEKLRDLLLPLLQS 176
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 26-196 6.74e-14

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


Pssm-ID: 341131 [Multi-domain]  Cd Length: 178  Bit Score: 67.02  E-value: 6.74e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  26 LTDIAEYLNGLAMQKFRPQNEQESLPVLKIKELRQGQCDINSERCS---LDIKPQYIIHDGDVIFSWSGSL----LVDFW 98
Cdd:cd16961    3 LGEIAEIISGKTPSSSSEYWDNGIIPWIRISDINNGGIILTDEKITeegAEKLKKKILPKGDILISRSGTIgkvaIVKEN 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  99 CGGICglNQHLFKVHSK--QYAPWLYY---SWTKYYLAEFVAMaadkaTTMGHIKRDALENARVLIPCSDDYLKIEEQLQ 173
Cdd:cd16961   83 DKALL--NQAVIVIRPKdeVDSEFLYYflkSPFGKKLIEGSAG-----STQPNLNKSDLKNLKIPLPPLEEQKKIANILD 155

                        170       180
                 ....*....|....*....|...
gi 497036889 174 PLYDAIIAHRVEIRKLSTLRNTL 196
Cdd:cd16961  156 KLDALIELLEQKLEKLEQLKQAL 178
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 21-205 7.38e-13

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


Pssm-ID: 341167 [Multi-domain]  Cd Length: 189  Bit Score: 64.45  E-value: 7.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  21 WQEGYLTDIAEYLNGLAmqkFRPQN-EQESLPVLKIKELRQGQCDINSERC----SLDIKPQYIIHDGDVIFSWSGSLL- 94
Cdd:cd17278    1 WEVVKLGDIADIQNGYA---FKSSDfSDEGIPVIRIGNIKNGGIDLDDNSKypeePLEKYEKFLLKKGDILIAMTGGTVg 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  95 ----VDFwCGGICGLNQH--LFKVHSKQYAPWLYYS-WTKYYLAEFVAMAadKATTMGHIKRDALENARVLIPCSDDYLK 167
Cdd:cd17278   78 kvaiVPE-DDEPALLNQRvgKFRPKDKIDKEFLYYLlRSDSFRNQIKSSA--TGTAQPNISPKDIESIKIPLPPLEEQKK 154

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 497036889 168 IEEQLQPLYDAIIahrVEIRKLSTLRNTLLPRLMSGEI 205
Cdd:cd17278  155 IAEILDSLDAKID---KLEQKLEKLRDLLKPLLQSLFT 189
RMtype1_S_Cep9333ORF4827P-TRD2-CR2_like cd17495
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 112-201 2.87e-12

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: 62.48  E-value: 2.87e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 112 VHSKQYAP-WLYYSwTKYYLAEFvAMAADKATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLS 190
Cdd:cd17495   86 IRSKSGSQsFLFYQ-LKSLFKEF-DIFNGEGTVFGSINKKDLENLPIIIPSDEIIEAFEKLVSPIDQKIENNEKENRTLA 163

                         90
                 ....*....|.
gi 497036889 191 TLRNTLLPRLM 201
Cdd:cd17495  164 KLRDTLLPKLM 174
RMtype1_S_Vch69ORF1407P_TRD2-CR2_like cd17501
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio ...
 115-202 2.12e-11

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


Pssm-ID: 341192 [Multi-domain]  Cd Length: 191  Bit Score: 60.27  E-value: 2.12e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 115 KQYAPWLYYSWTKYYLAEFVAMAADKATTmgHIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLSTLRN 194
Cdd:cd17501  106 EEYSPFFLYLYLLNSRDYLANLASGSAQQ--NISQQIIKNTKVLIPPEDLLEIFNKLVEPLFDKIINNLKENQKLAKLRD 183


                 ....*...
gi 497036889 195 TLLPRLMS 202
Cdd:cd17501  184 TLLPKLMS 191
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 120-199 3.21e-10

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: 57.08  E-value: 3.21e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 120 WLYYsWTKYYLAEFVAMAAdkattmG----HIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLSTLRNT 195
Cdd:cd17243  106 FLYY-LLKNLIEELKQKAH------GsvfdTITRKTFDEIKVPLPPEELQKSFENIVSPLFDKILNNLKENQTLAQLRDT 178


                 ....
gi 497036889 196 LLPR 199
Cdd:cd17243  179 LLPK 182
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 110-201 5.18e-09

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: 53.56  E-value: 5.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 110 FK---VHSKQYAPWLYYsWTKYYLAEFVAMAAdkATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEI 186
Cdd:cd17273   95 FKsiiPNEEIDNEFLYY-LLKNNKPEIESLAS--GSTFKEISKSTFKKIEIPLPPLEEQKKIAAILSKLDELIELLEKEN 171

                         90
                 ....*....|....*
gi 497036889 187 RKLSTLRNTLLPRLM 201
Cdd:cd17273  172 EKLKELRDGLLPKLF 186
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17251
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 113-201 1.72e-08

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


Pssm-ID: 341140 [Multi-domain]  Cd Length: 185  Bit Score: 52.12  E-value: 1.72e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 113 HSKQYAPWLYYSWTKYYlAEFVAMAADkATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLSTL 192
Cdd:cd17251   99 KKENYRYYLYFALKSLK-ELLEALGSG-GSTTLNLNKGKFSKIKILLPSEDLLKKFHKIVSPLFDKILNNQKENQKLSQL 176


                 ....*....
gi 497036889 193 RNTLLPRLM 201
Cdd:cd17251  177 RDTLLPKLM 185
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 21-185 2.55e-07

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: 49.07  E-value: 2.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  21 WQEGYLTDIAEYL-NGLAmqkFRPQNEQESLPVLKIKELRQGQCDINSER---CSLDIKPQYIIHDGDVIFSWS-GSLLV 95
Cdd:cd17261    1 WEWVRLGDLIEGIrNGWS---PKPPDDETGWPVLKLSAVTSGKFDPSENKylpESLEPASEYWLKPGDLLISRAnTSELV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  96 dfwcgGICGL----NQHL--------FKVHSKQYAP-WLYYSW-TKYYLAEFVAMAADKATTMGHIKRDALENARVLIPC 161
Cdd:cd17261   78 -----GRAALvdgdPDNLiypdklirLRVNEELLLPeYLALALnSPSARRQIESRATGTAGSMPKISQSDLKSLPIPLPP 152

                        170       180
                 ....*....|....*....|....
gi 497036889 162 sddylkIEEQLQplydaiIAHRVE 185
Cdd:cd17261  153 ------LAEQKR------IVARVD 164
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 83-201 3.54e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus licheniformis S subunit (S1.BliBORF2384P) TRD1-CR1 and Chlorobium tepidum TLS S subunit (S.CteTORF675P) TRD1-CR1; The recognition sequences for Bacillus licheniformis S subunit (S1.BliBORF2384P) and Chlorobium tepidum TLS S subunit (S.CteTORF675P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341187 [Multi-domain]  Cd Length: 175  Bit Score: 45.57  E-value: 3.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  83 GDVIFSWSGS-----LLVDF-WC-G-GICGLnqhlfKVHSKQYAPWLYYsWTKYYLAEFVAMAAdkATTMGHIKRDALEN 154
Cdd:cd17496   57 GDILFCVRGSttgrlNIADDeYCiGrGVAAI-----RPKNGIDTEFLYY-LLESNLDYLLAAAT--GSTFPNISRDDLLN 128

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 497036889 155 ARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLSTLRNTLLPRLM 201
Cdd:cd17496  129 LKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTLLPKLL 175
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 18-179 1.14e-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: 38.11  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889   18 PKGWQEGYLTDIAEYLNGLAMQKFRPqNEQESLPVLKIKELRQGQCDInsercsLDIKPQYIIHDGDVIFSWSGSLLVDF 97
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKEL-KNNGKYPYIRAGDLNNVVKGG------LGYIKKYILPKGDITISSRATIGYVF 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889   98 WCGGICGLNQHLFKVHSKQYAPWLYYSWtkYYLAEFVA--MAADKATTMGHIKRDALENARVLIPCSDDYLKIEEQLQPL 175
Cdd:pfam01420  74 YRDKPYYTNQHIIVLIPKNNIKITEFLY--LYLLLKLKklKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKILSQL 151


                  ....
gi 497036889  176 YDAI 179
Cdd:pfam01420 152 DNTI 155
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 128-201 1.79e-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: 37.42  E-value: 1.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 128 YYLA---EFVAMAADKAT-TMGHiKR---DALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLSTLRNTLLPRL 200
Cdd:cd17260   86 YYLLrspSFRKEAIKSMTgSSGR-QRvpkDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKL 164


                 .
gi 497036889 201 M 201
Cdd:cd17260  165 L 165
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 98-200 1.91e-03

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: 37.84  E-value: 1.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889  98 WCGGI--CgLNQ-HLFKV--HSKQYAPW--LYYSWTKYYLAEFVAmAADKATTMGHIKRDALENARVLIPCSDDYLKIEE 170
Cdd:cd17253   85 WRGEIppC-LHQnHLFRVrpKDDLLLPEflSYWLNSAYGRGYFLR-AAKQTTNLASINSTKLKALPVPLPPLEEQRRIVE 162

                         90       100       110
                 ....*....|....*....|....*....|
gi 497036889 171 QLQPLYDAIIAHRVEIRKLSTLRNTLLPRL 200
Cdd:cd17253  163 RLDELLALIDALEASLAKLEELLKALRQAL 192
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 121-203 3.14e-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: 37.07  E-value: 3.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497036889 121 LYYSWTKYYLAEF----VAMAADKATTmghIKRDALENARVLIPCsddylkIEEQLQ--PLYDAIIAHRVEIRKLSTLRN 194
Cdd:cd17244  101 IDTEYLYYYLKSFdyssLGSTASKGKT---LNSKKIKEIPIPLPP------LEEQKRiaPILDKIDALIDQLETLIELLD 171


                 ....*....
gi 497036889 195 TLLPRLMSG 203
Cdd:cd17244  172 ELLPKLMSG 180
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 149-199 3.82e-03

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: 36.61  E-value: 3.82e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 497036889 149 RDALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLSTLRNTLLPR 199
Cdd:cd17267  108 RNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADALLPK 158
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 150-200 5.67e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) 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: 36.26  E-value: 5.67e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 497036889 150 DALENARVLIPCSDDYLKIEEQLQPLYDAIIAHRVEIRKLSTLRNTLLPRL 200
Cdd:cd17262  122 ANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQKL 172
 
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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