NCBI Conserved Domain Search

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: 252.80 E-value: 1.19e-82

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  36 IKSIAEVKGGKRLPAGADFVDEITNHPYIRVSDFENGTINCDGLKYISQDIQSKISRYTISKDDVYISIAGTIGKCGIIP 115
Cdd:cd17256     1 LGEIARVKGGGRLPKGESLSDGPTGVPYIRVTDIKNGGIDLDNLKYISPEIHEKIKRYTLSKGDILISIVGTIGRVGIVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 116 DFLDGANLTENAAKITDIKYSTNRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLL 195
Cdd:cd17256    81 KELDGANLTENAARIRPKDSISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLD 160

                         170
                  ....*....|....*...
gi 2047298907 196 DKINQAKQLIDEAKATFE 213
Cdd:cd17256   161 AKIDALEKQLAKLEELKK 178

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: 218.94 E-value: 2.75e-69

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 259 WKWVRAEFLfDEFPRNGYSPKSTESSFITKTLKLGAITKGYYKNDEFKYVDERIEQDSYLWLKNGDFLIQRANSIEYVGT 338
Cdd:cd17261     1 WEWVRLGDL-IEGIRNGWSPKPPDDETGWPVLKLSAVTSGKFDPSENKYLPESLEPASEYWLKPGDLLISRANTSELVGR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 339 SAIFTGADNESIYPDLIMKGKVNETVVLNQYLVHWINSMYGKQYFRQNATGTAGNMPKINKSILQNLLVPIPPIEEQRVI 418
Cdd:cd17261    80 AALVDGDPDNLIYPDKLIRLRVNEELLLPEYLALALNSPSARRQIESRATGTAGSMPKISQSDLKSLPIPLPPLAEQKRI 159

                         170       180
                  ....*....|....*....|
gi 2047298907 419 MKVLDCVFnsdnDALNKLEN 438
Cdd:cd17261   160 VARVDELL----ALIDRLEA 175

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 188.55 E-value: 1.92e-54

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  26 EVPGNWVWVRIKSIAEVKGGKRLPAG-ADFVDEITNHPYIRVSDFENGTINCDGLKYISqDIQSKISRYTISKDDVYISI 104
Cdd:PRK09737    5 KLPEGWVTTHISEICSVIRGVKPPKGyATKSLTMGDLPFIRTTDITNGAVDLTTLPYCM-DAPEDVSKYQLQDRDIVISS 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 105 AGTIGKCGIIPD-FLDGANLTENAAKITDIKYSTNRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNE 183
Cdd:PRK09737   84 AGSIGFSFLAQNpLPSNVVFASFAIRLKPVNYFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAE 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 184 QKRIADKVERLLDKINQAKQLIDEAKATFELRRAAILDKVFRGELTKKWREENfikndlkteqnyayydskIPDSWKWVR 263
Cdd:PRK09737  164 QKIIAEKLDTLLAQVDSTKARLEQIPQILKRFRQAVLGAAVSGKLTEEWRWPD------------------LPSTWSVHK 225

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 264 AEFLFDEfPRNGYSPKSTESSFITKTLKLGAITKGYYKNDEFKYVD-ERIEQDSYLwLKNGDFLIQRANSIEYVGTSAIF 342
Cdd:PRK09737  226 YSELVDS-RLGGMSSKANNFGSATPYLRNINVRWGSFDLEDLQDILiSDIERRELK-LKLGDVLFCRGNEPLEVGRCAIW 303

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 343 TG-ADNESIYPDLIMKGKVNETvVLNQYLVHWINSMYGKQY-FRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMK 420
Cdd:PRK09737  304 KEpQDIPVIYQKALIRARVKDD-IIPEYLVYNLKSPDSRNIsLSQLFTGTT--QKHITGKALANYPIRVPPLEEQAEIVR 380

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*.
gi 2047298907 421 VLDCVF-------NSDNDALNKLENyqpeidlLINGMLMKAFSGVL 459
Cdd:PRK09737  381 RVEQLFayadtieKQVNNALARVNN-------LTQSILAKAFRGEL 419

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: 139.97 E-value: 3.46e-39

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAE--VKGGKRLPagaDFVDEitNHPYIRVSDFENGTINCDGLKYISQ-DIQSKISRYTISKDDVYISIAGT 107
Cdd:cd17246     1 WEWVKLGEISSdiTDGTHPTP---KYVES--GIPFITSKNIKNGKIDFSDVKYISEeDHNEILKRSKLKKGDILFSIIGT 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 108 IGKCGIIPDFLDgANLTENAAKI-TDIKYSTNRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKR 186
Cdd:cd17246    76 IGRVAIVPEDLP-ANINQAVALIrPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQKR 154

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2047298907 187 IADKVERLLDKINQAKQLIDEAKATFELRRAAILD 221
Cdd:cd17246   155 IAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLLT 189

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: 124.16 E-value: 2.84e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAEVKGG---KrlpaGADFVDEitNHPYIRVSDFENGTINCDGLKYISQDIQSKISRYTISKDDVYISI-AG 106
Cdd:cd17278     1 WEVVKLGDIADIQNGyafK----SSDFSDE--GIPVIRIGNIKNGGIDLDDNSKYPEEPLEKYEKFLLKKGDILIAMtGG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 107 TIGKCGIIPDFLDGANLTENAAKITDIKYSTNRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKR 186
Cdd:cd17278    75 TVGKVAIVPEDDEPALLNQRVGKFRPKDKIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKK 154

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2047298907 187 IADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17278   155 IAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLF 188

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: 120.72 E-value: 6.18e-32

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 259 WKWVRAEFLFDEfPRNGYSPKSTESSFITKTLKLGAITKGYY-KNDEFKYVD-ERIEQDSYLwLKNGDFLIQRANSI-EY 335
Cdd:cd17517     1 WEVVKLGDLLED-PRYGTSKKSSYDGSGTPVLRIPNIYDGGIdLDDLKKRVDlSEKELEKYL-LKKGDILFNRSNGSpEL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 336 VGTSAIFTGADNESIYPDLIMKGKVNETVVLNQYLVHWINSMYGKQYFRQNATGTAGNmPKINKSILQNLLVPIPPIEEQ 415
Cdd:cd17517    79 VGKCALVDEEDEPAIFASYLIRLRLDKKKILPEFLYYYLNSPLGRKQIEKIAKSAAGQ-ANINQKDLKKLPIPLPPLEEQ 157

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2047298907 416 RVIMKVLDCVFnsdnDALNKLENYQPEIDLLINGML 451
Cdd:cd17517   158 KEIVEILESLD----SKIDLLEKKLEKLEQLFKSLM 189

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: 113.02 E-value: 3.01e-29

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  45 GKRLPAGADFVDE-ItnhPYIRVSDFENGTINCDGLKYISQDIQSKISRYTISKDDVYISIAGTIGKCGIIPDFLDGANl 123
Cdd:cd17264    14 GKNYPSKSEFVDEgI---PFINAGHLEDGTIDLSNMNFISEEKYNSLGSGKLQKGDILYCLRGSLGKCAIVDNYDEGAI- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 124 tenAAKITDI---KYSTNRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQ 200
Cdd:cd17264    90 ---ASSLVIIrpfAKVDVRYLYYYLNSPLGKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDK 166

                         170
                  ....*....|....*...
gi 2047298907 201 AKQLIDEAKATFELRRAA 218
Cdd:cd17264   167 LKQALEKLEELLQSLFQS 184

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: 110.16 E-value: 3.00e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAEVKGGKRLPAGADFVDEITnHPYIRVSDFENGTINcDGLKYISQDIQSKISRYTISKDDVYISIAGTIGKCGI 113
Cdd:cd16961     1 KKLGEIAEIISGKTPSSSSEYWDNGI-IPWIRISDINNGGII-LTDEKITEEGAEKLKKKILPKGDILISRSGTIGKVAI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 114 IpDFLDGANLTENAAKITDIKYSTNRYIYYVLNTEILKNQIKNSMKSTsQPKLALHRIQDLKLPLPPLNEQKRIADKVER 193
Cdd:cd16961    79 V-KENDKALLNQAVIVIRPKDEVDSEFLYYFLKSPFGKKLIEGSAGST-QPNLNKSDLKNLKIPLPPLEEQKKIANILDK 156

                         170
                  ....*....|....*...
gi 2047298907 194 LLDKINQAKQLIDEAKAT 211
Cdd:cd16961   157 LDALIELLEQKLEKLEQL 174

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: 108.75 E-value: 1.50e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAEVKGGKRLPAgADFVDEitNHPYIRVSDFENGTINCDGLKYISQDIQSKISRYTISKDDVYISIAGTIGK 110
Cdd:cd17259     1 WEWVKLGDVADILSGYAFKS-SEFSES--GIRLLRGANVGVGEIRWDDTVYLPEEYLEEYEKYLLKEGDIVIALDRPIIS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 111 CG----IIPDFLDGANLTENAAKITDIKYSTNRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKR 186
Cdd:cd17259    78 GGlkvaRIPKSDLPALLVQRVARIRPKDELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEEQKK 157

                         170       180
                  ....*....|....*....|....*
gi 2047298907 187 IADKVERLLDKINQAKQLIDEAKAT 211
Cdd:cd17259   158 IAEFLSSLDALIDLLEQKLEKLQQL 182

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: 102.23 E-value: 2.98e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAE-VKGGKrlpaGADFVDEITNHPYIRVSDFENGTINCDGLKYISQDIqSKISRYTISKDDVYISIAGTI- 108
Cdd:cd17261     1 WEWVRLGDLIEgIRNGW----SPKPPDDETGWPVLKLSAVTSGKFDPSENKYLPESL-EPASEYWLKPGDLLISRANTSe 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 109 --GKCG---------IIPDFLDGANLTENAAkitdikysTNRYIYYVLNTEILKNQIKNSMKST--SQPKLALHRIQDLK 175
Cdd:cd17261    76 lvGRAAlvdgdpdnlIYPDKLIRLRVNEELL--------LPEYLALALNSPSARRQIESRATGTagSMPKISQSDLKSLP 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2047298907 176 LPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAI 219
Cdd:cd17261   148 IPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191

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: 99.64 E-value: 2.79e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAEVKGGKRLPAgADFVDEitNHPYIR---VSDFENGTINCDGLkYISQDIQSKI-SRY-TISKDDVYISIA 105
Cdd:cd17289     1 WEWKKLGDIAEITSSKRIFK-SEYVDS--GIPFYRskeIIELFNGEEISTEL-FISEERYEEIkSKYgVPKKGDILITSV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 106 GTIGKCGIIPD-----FLDGaNLTEnaakITDIKYSTNRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPP 180
Cdd:cd17289    77 GTIGIPYLVKNddpfyFKDG-NLTW----FKNIKDINSKFLYYWFQSSIFKNQINSITIGSTQKALTIEKLKKTKIPLPP 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2047298907 181 LNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17289   152 LEEQKKIVSILSALDEKIDLNKKQLQKLEELAKTLFQYWF 191

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: 98.38 E-value: 7.66e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAE-VKGGKRLPAGADfvdeITNHPYIRVSDFENGTINCDGLKYISQDIQSKISRYTISKDDVYI----SIA 105
Cdd:cd17517     1 WEVVKLGDLLEdPRYGTSKKSSYD----GSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKELEKYLLKKGDILFnrsnGSP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 106 GTIGKCGIIPDFLDGA----NLtenaakI---TDIKYSTNRYIYYVLNTEILKNQIKNSMKSTS-QPKLALHRIQDLKLP 177
Cdd:cd17517    77 ELVGKCALVDEEDEPAifasYL------IrlrLDKKKILPEFLYYYLNSPLGRKQIEKIAKSAAgQANINQKDLKKLPIP 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2047298907 178 LPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAI 219
Cdd:cd17517   151 LPPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192

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: 98.31 E-value: 8.68e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 290 LKLGAITKGYYKNDEFKYVD-ERIEQDSYLwLKNGDFLIQRANSIEYVGTSAIFTGaDNESIYPDLIMKGKVNETVVLNQ 368
Cdd:cd17524    31 LRMGNIQDGGIDDDDLKYVDlDEKEFEKYL-LKKGDVLFNRTNSPELVGKTAIFRG-DGPATFASYLIRIRLNEEKILPE 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 369 YLVHWINSMYGKQYFRQNATGtAGNMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNS 428
Cdd:cd17524   109 YLNYFLNSPYGRKQIKSVATQ-GVGQANINATKLKAIPIPLPPLEEQKEIVEKLDELDAL 167

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: 94.21 E-value: 2.17e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAE-VKGG--KrlpaGADFVDEitNHPYIRVSDFENGTINCDGLKYISQDIQSKISRYTISKDDVYISIAG- 106
Cdd:cd17512     1 WEEIRLGDIIDyQKGYafK----SKDYQDS--GIRIVRVSDFTDDSIDINNLVYISEEKANKYKKYELKENDIIITTVGs 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 107 -------TIGKCGIIPDFLDGANLTENAAKITDIK-YSTNRYIYYVLNTEILKNQIKNSMK-STSQPKLALHRIQDLKLP 177
Cdd:cd17512    75 wpsnpdsVVGKVVRVPKEADGALLNQNAVKIRPKKgILDQSFLFYNLKSERFKNYIESIARgNANQASITLGDIKKFKFL 154

                         170       180
                  ....*....|....*....|....*....
gi 2047298907 178 LPPLNEQKRIADKVERLLDKINQAKQLID 206
Cdd:cd17512   155 LPPLEEQKKIASILSAYDDLIENNEKRIK 183

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: 93.39 E-value: 4.41e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAEVKGG---KrlPAGADFVDEITNHPYIRVSDFENGTINCDGLKYISQDIQSKISRytISKDDVYISIA-G 106
Cdd:cd17252     1 WEWVRLGEIAEIIRGvtyK--KSDASEEPSEGGIPVLRANNIQNGGLDFDDLVYVPKSKVKEEQK--LKKGDILICMSsG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 107 T---IGKCGIIPDFLD---GANLtenaAKITDIKYSTNRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPP 180
Cdd:cd17252    77 SkelVGKAAFIDEDTDytfGAFC----GVIRPKKEIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPP 152

                         170       180       190
                  ....*....|....*....|....*....|
gi 2047298907 181 LNEQKRIADKVERLLDKINQAKQLIDEAKA 210
Cdd:cd17252   153 LAEQKRIVAKLDKLDALIDKLKQALEKLDE 182

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: 91.77 E-value: 1.64e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  30 NWVWVRIKSIAEVKGGKRLpaGADFVDEITNHPYIRVSDFENGTINCDGLKYIsqDI-QSKISRYTISKDDVYISIAG-- 106
Cdd:cd17253     1 GWEWVRLGDVAEVQSGITK--GKKRRGGELEVPYLRVANVQDGYLDLSEVKEI--EVtEEELERYRLRKGDLLVTEGGds 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 107 -TIGKC----GIIPDFLdganlTEN---AAKITDIKYStNRYIYYVLNTEILKNQIKNSMKSTSQpkLAlH----RIQDL 174
Cdd:cd17253    77 dKLGRGaiwrGEIPPCL-----HQNhlfRVRPKDDLLL-PEFLSYWLNSAYGRGYFLRAAKQTTN--LA-SinstKLKAL 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2047298907 175 KLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17253   148 PVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193

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: 87.94 E-value: 2.88e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAEVKGGKRlPAGADFVDEITN--HPYIRVSDFENGTINcdglKYISQDIQSKIsrytISKDDVYI----SIAGT 107
Cdd:cd17263     1 VKLGEVCKFSKGKQ-PPISERFDEPKEgsVRYIQIEDLRNNNEK----KYIENPKKSVI----CNEDDILIvrdgANAGE 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 108 I--GKCGIIpdfldgANlteNAAKIT-DIKYSTNRYIYYVLNTEILKNQIKNSMKSTsQPKLALHRIQDLKLPLPPLNEQ 184
Cdd:cd17263    72 VgtGLEGAI------AS---TLFKIIpDKNIIDKDYLYYFLKSKEIQLNILTKAGST-IPHVNKKDLENLKIPLPSLEEQ 141

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2047298907 185 KRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17263   142 KKIAEILDKLDALIDKLKELIEKLIELKKGLFQELL 177

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: 87.54 E-value: 4.09e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAE-VKGGkrlpAGADFVDEITNHPYIRVSDFENGTINCDGLKYISQDiQSKISRYTISKDDvyISIA---G 106
Cdd:cd17521     1 WEVKKLGELSEkIQYG----YTASAAYEDGGPRYLRITDIQDDGVLWDTVPYCSIS-EEDAEKYLLKDGD--ILFArtgA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 107 TIGKCGIIPdfldgaNLTENA--------AKITDIKYStNRYIYYVLNTEILKNQIKNSMKSTSQP-----KLAlhriqD 173
Cdd:cd17521    74 TVGKSYLYK------EDDGKAvfasylirFRPNKKKVL-PKYLFYFTQSSLYWKQIKSISSGSAQPninaeKLK-----S 141

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2047298907 174 LKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAI 219
Cdd:cd17521   142 LKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLKELLQSL 187

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: 85.61 E-value: 2.81e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 303 DEFKYVD-ERIEQDSYLwLKNGDFLIQRANSIEYVGTSAIFTGADNESIYPDLIMKGKVNETVVLNQYLVHWINSMYGKQ 381
Cdd:cd17253    46 SEVKEIEvTEEELERYR-LRKGDLLVTEGGDSDKLGRGAIWRGEIPPCLHQNHLFRVRPKDDLLLPEFLSYWLNSAYGRG 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2047298907 382 YFRQNATGTaGNMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNsdndALNKLEN 438
Cdd:cd17253   125 YFLRAAKQT-TNLASINSTKLKALPVPLPPLEEQRRIVERLDELLA----LIDALEA 176

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: 84.33 E-value: 4.79e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  28 PGNWVWVRIKSIAEVKGGKRLPAGADfvDEITNHPYIRVSDFENGTIncdglkyisqDIQSKISRYTISKDDVYISIAGT 107
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKEL--KNNGKYPYIRAGDLNNVVK----------GGLGYIKKYILPKGDITISSRAT 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 108 IGKCGIIP-DFLDGANLTENAAKITDIkysTNRYIYYVLNTeiLKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKR 186
Cdd:pfam01420  69 IGYVFYRDkPYYTNQHIIVLIPKNNIK---ITEFLYLYLLL--KLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKK 143

                         170       180
                  ....*....|....*....|....
gi 2047298907 187 IADKVERLLDKINQAKQLIDEAKA 210
Cdd:pfam01420 144 IAKILSQLDNTIELEKGILNELER 167

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 79.72 E-value: 2.15e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 143 YVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKAtfelRRAAILDK 222
Cdd:COG0732     4 YYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKE----LRDALLPK 79


                  ....*.
gi 2047298907 223 VFRGEL 228
Cdd:COG0732    80 LFTGEL 85

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: 80.96 E-value: 8.86e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAEVKGGKRLPAG--ADFVDEItnhPYIRVSDFENGTINCDGLKYISQDIqSKISRyTISKDDVYIS-IAGTIGK 110
Cdd:cd17293     1 VKLGELGEVVTGNTPSKKnpEYYGGDI---PFIKPDDLNNGGIILTSEEYLSEEG-AKKAR-IVPKGSILVTcIGGSIGK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 111 CGIipdfldganltenaakiTDIKYSTN--------------RYIYYVLNTEILKNQIKNSM-------KStsqpklalh 169
Cdd:cd17293    76 VGI-----------------ADREVAFNqqinaiipnksvdpKFLYYQLLSSKFQLQAIASSttlpiinKS--------- 129

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2047298907 170 RIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17293   130 KFEKIEIPLPPLEEQKRIVAKLDKLFALIDKLEESLEELDELLKSLFQSAF 180

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: 81.03 E-value: 9.96e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 259 WKWVR----AEFLFD-EFPrngySPKSTES--SFITKTlklgAITKGYYKNDEFKYVDErieQDSYLWLKN-----GDFL 326
Cdd:cd17246     1 WEWVKlgeiSSDITDgTHP----TPKYVESgiPFITSK----NIKNGKIDFSDVKYISE---EDHNEILKRsklkkGDIL 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 327 IQRANSIeyvGTSAIFTGADNESIYPDLIMKgKVNETVVLNQYLVHWINSMYGKQYFRQNATGTAgnMPKINKSILQNLL 406
Cdd:cd17246    70 FSIIGTI---GRVAIVPEDLPANINQAVALI-RPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGT--QKNLSLGDLKNLK 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2047298907 407 VPIPPIEEQRVIMKVLDcvfnsdnDALNKLENYQPEIDLLIN 448
Cdd:cd17246   144 IPLPPLEEQKRIAAILD-------SLDALIDKLEQKLEKLED 178

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: 77.51 E-value: 1.68e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIA-EVKGGkrLPAGADfvDEITNHPYIRVSDFENGTINCDGLKYISQDiQSKISRYTISKDDVYI----SIA 105
Cdd:cd17524     1 WEWVTIGDLVtSVQYG--TSEKKS--EDEGGYPVLRMGNIQDGGIDDDDLKYVDLD-EKEFEKYLLKKGDVLFnrtnSPE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 106 gTIGKCGIIpdfldgaNLTENAA------KI-TDIKYSTNRYIYYVLNTEILKNQIKN-SMKSTSQ----PKlalhRIQD 173
Cdd:cd17524    76 -LVGKTAIF-------RGDGPATfasyliRIrLNEEKILPEYLNYFLNSPYGRKQIKSvATQGVGQaninAT----KLKA 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2047298907 174 LKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAI 219
Cdd:cd17524   144 IPIPLPPLEEQKEIVEKLDELDALIDRLEALLEEAEELLESLLQSL 189

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: 77.10 E-value: 1.96e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAEVKGGK---------RLPAGadfvdeitNHPYI----------RVSDFENgTINCDGLKyisqdiQSKIs 91
Cdd:cd17282     1 WEVKKLSDLGSLERGKfkhrprndpRLYGG--------DYPFIqtgdvarangYITSYSQ-TLNEKGLA------QSKL- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  92 rytISKDDVYISIAGTIGKCGII------PDFLDGANLTENAAkitdikysTNRYIYYVLNTeiLKNQIKNSMKSTSQPK 165
Cdd:cd17282    65 ---FPKGTLCITIAANIGDTAILgfdacfPDSVVGFIPNEEKI--------DVEFLEYYLRT--LKKELEAIAPQSAQKN 131

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2047298907 166 LALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKAtfelRRAAILDKVF 224
Cdd:cd17282   132 INLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIAKLEE----LKQSLLQEAF 186

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: 75.21 E-value: 7.64e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAEVK-GGKRLPAGADFVDEITNHPYIRVSDfengtINCDGlKYISQDIQ------SKISRYtISKDDVYISIAG 106
Cdd:cd17283     1 KKLGDISEIVrGASPRPIGDPITFDGDGIPWIKIGD-----VTKDG-KYITKTKEkiteegAKKSRL-VKPGDLILSNSM 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 107 TIGKcgiiPDFL-------DGAnltenaAKITDIKYSTNR-YIYYVLNTEILKNQiKNSMKSTSQPKLALHRIQDLKLPL 178
Cdd:cd17283    74 SFGR----PYILkidgcihDGW------LVFSDLKKKLDKdFLYYLLSSITVQLQ-FSAQAGGGTKNLNTDIVKNLKIPL 142

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2047298907 179 PPLNEQKRIADKVERLLDKINQAKQLIDEAKATFE 213
Cdd:cd17283   143 PPLEEQKRIAEILDSLDALIDALEEKLEKLEELKK 177

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: 74.98 E-value: 1.28e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAEVKGGKRLPAGADFVDEiTNHPYIRVSDFENgtinCDGLKYISQdiqskiSRYTISKDDVYISIAGTIGKCGI 113
Cdd:cd17250     1 VRLGDVCDFKAGSGFPEKYQGKED-GEYPFYKVGDMNN----SGNEKYLST------AENYISEEIVKELKAKLFPKGTI 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 114 IPDFLDGANLTE-------------NAAKITDIKYSTNRYIYYVLNTEILKNQIKnsmkSTSQPKLALHRIQDLKLPLPP 180
Cdd:cd17250    70 IFAKIGEAIKLNrrailskdscidnNVMGLIPNEGIDSEYLYYWLKKVDLYKYSQ----ATTVPSIRKSTLESIPIPLPP 145

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2047298907 181 LNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17250   146 LEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGLRQSLL 185

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: 74.55 E-value: 2.08e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 306 KYVDERIEQDSYlWLKNGDFLIQRANSIEYVGTSAIFTGaDNESIYPDLIMKGKVNETVVLNQYLVHWINSMYGKQYFRQ 385
Cdd:cd17526    50 KIVPSPKERKRY-LLQKGDVLFNNTNSQELVGKTALFDG-EEPYVFSNHMTRIRVKKSKINPEFLARYLHLLWRSGYFKK 127

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2047298907 386 NAT---GTAGnmpkINKSILQNLLVPIPPIEEQRVIMKVLDCVFN 427
Cdd:cd17526   128 LCTnwvNQAG----INSDTLANLKIPLPPLPEQKRIAEILDQIDR 168

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 70.47 E-value: 4.41e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 372 HWINSMYGKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFnsdnDALNKLENyqpEIDLLIN--- 448
Cdd:COG0732     4 YYLRSPSFREYLRSLATGST--QPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLF----DKIAALEK---EIEKLKElrd 74


                  ....*....
gi 2047298907 449 GMLMKAFSG 457
Cdd:COG0732    75 ALLPKLFTG 83

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: 72.18 E-value: 1.32e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAE-VKGGKrlpaGADFVDEITNHPYIRVSDFENGTINCDGLKYISQDiQSKISRYTISKDDVYIS-IAGT- 107
Cdd:cd17522     1 WKVVKLGDVLEeIRNGT----TVKQNKEGGGYPVTRIETISNGTIDLNRVGYAITN-EEKIEKYKLQKGDILFShINSIe 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 108 -IGKCGIIPD----FLDGANL---TENAAKITdikystNRYIYYVLNTEILKNQIKNSMK-STSQPKLALHRIQDLKLPL 178
Cdd:cd17522    76 hIGKTAIYDGdpepLIHGMNLlrlRPNKNIVD------PKYLYYLLKSDRFRNQFRSIAKkAVNQASINQTELKKIKIPL 149

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2047298907 179 PPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAI 219
Cdd:cd17522   150 PPLEEQQKIASILEKLDKKIEKRKEKIEKLKELKKGLFQKL 190

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: 71.49 E-value: 2.00e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 259 WKWVRAEFLFDEFpRNGYSPKSTESSFITKTLKLGAITKGYYKNDE-FKYVDE-RIEQDSYLwLKNGDFLIQRANSIEYV 336
Cdd:cd17525     1 WEWVKLGDILSST-QLGLVRSNSEDPNGYPYIKMGNIGRGGINLLKvETYVDAtELEVEKYL-LEDGDLLFNTRNTLELV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 337 GTSAIFTGADNESIYPDLIMKGKVNEtVVLNQYLVHWINSMYGKQYFRQNATGTAgNMPKINKSILQNLLVPIPPIEEQR 416
Cdd:cd17525    79 GKVAIWRGELPKALFNNNILRIRFDD-IVLPYFINYYLNSPDGKKQLESIASGTT-SVAAIYQKDLKKLKLPLPPLDEQR 156

                         170       180
                  ....*....|....*....|....
gi 2047298907 417 VIMKVLDCVFNSDNDALNKLENYQ 440
Cdd:cd17525   157 EIVSFLSELDAKIDQLEQKLEKLL 180

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: 70.32 E-value: 4.54e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  62 PYIRVSDFENGTINcDGLKYISQDIQSKISRYTISKDDVYISIAGTIGKCGIIpDFLDGANLTENAAKITDIKYSTnRYI 141
Cdd:cd17296    29 PWVKISDCKNKYVD-ETEEFITEEGLNNSSAKLLKKGTILIAIFATIGKVGIL-KIEATTNQAIAGIKPKNKSINP-KYL 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2047298907 142 YYVLNTeiLKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIA---DKVERLLDKINQAKQLIDE-AKATFE 213
Cdd:cd17296   106 YYYLKS--LYEKFLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVailDKFEKLINKRQEGLQLLDElVKSLFE 179

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: 70.28 E-value: 5.44e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 276 YSPKSTESSFITKTLKL---GAITKGYYKNDEFKYVDERIEQDSYlWLKNGDFLIQRAN-SIEYVGTSAIFTGADNES-- 349
Cdd:cd17252    18 YKKSDASEEPSEGGIPVlraNNIQNGGLDFDDLVYVPKSKVKEEQ-KLKKGDILICMSSgSKELVGKAAFIDEDTDYTfg 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 350 -----IYPDlimkgkvneTVVLNQYLVHWINSMYGKQYFRQNATGTAGNmpKINKSILQNLLVPIPPIEEQRVIMKVLDC 424
Cdd:cd17252    97 afcgvIRPK---------KEIDPRYLFYFLQSPSYREYIRSLASGTNIN--NLSNEHLENLKIPLPPLAEQKRIVAKLDK 165

                         170       180
                  ....*....|....*....|..
gi 2047298907 425 VFNSDNDALNKLENYQPEIDLL 446
Cdd:cd17252   166 LDALIDKLKQALEKLDELLKSL 187

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) TRD2-CR2; 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.StySPI-TRD1 recognizes AAC/GTT 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341204 [Multi-domain] Cd Length: 190 Bit Score: 69.96 E-value: 7.48e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 259 WKWVRAEFLFDEFpRNGYSPKSTESSFITKTLKLGAItkgyyKNDEFKYVDER------IEQDSYLwLKNGDFLIQRAN- 331
Cdd:cd17523     1 WEWVRLGDLIPEF-QNGLSKRGGSDGEPIIVLRLADI-----KNNKISFENLRriklteKEIEKYS-LSKGDLLIIRVNg 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 332 SIEYVGTSAIFTGaDNESIYPDLIMKGKVNETVVLNQYLVHWINSMYGKQYFRQNATGTAGNMpKINKSILQNLLVPIPP 411
Cdd:cd17523    74 SPDLVGRFILFKG-YEDVAYCDHFIRMRLDQEKIDPEFLSYIFNSPLIRRKIERNFVTSAGQK-TVNQGHIKSLPIPLPP 151

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2047298907 412 IEEQRVIMKVLDCVFNSDNDALNKLENYQPEIDLLING 449
Cdd:cd17523   152 LKEQKKIVARVEELFALIDQLESSLDLAQQLQNKLAQS 189

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: 69.33 E-value: 8.93e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 273 RNGYSPKSTESSF---ITKTLKLGAITKGYYKNDEFKYVDERIEQDSYLWLKNGDFLIQRANSIeyvGTSAIFTGADNES 349
Cdd:cd16961    10 ISGKTPSSSSEYWdngIIPWIRISDINNGGIILTDEKITEEGAEKLKKKILPKGDILISRSGTI---GKVAIVKENDKAL 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2047298907 350 IYPDlIMKGKVNETVvLNQYLVHWINSMYGKQYFRQNATGTagnMPKINKSILQNLLVPIPPIEEQRVIMKVLD 423
Cdd:cd16961    87 LNQA-VIVIRPKDEV-DSEFLYYFLKSPFGKKLIEGSAGST---QPNLNKSDLKNLKIPLPPLEEQKKIANILD 155

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: 69.00 E-value: 9.02e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 138 NRYIYYVLNTEILKNQIKNSMKSTS--Q--PKlalHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFE 213
Cdd:cd17260    82 PEFLYYLLRSPSFRKEAIKSMTGSSgrQrvPK---DFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLD 158


                  ....*..
gi 2047298907 214 LRRAAIL 220
Cdd:cd17260   159 ALLPKLL 165

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: 68.24 E-value: 1.47e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  91 SRYTISKDdvYISIA------GTI----GKCGIipdfldganlTENAAKITDIKYSTNRYIYYVLNTEILkNQIKNSmks 160
Cdd:cd17266    39 DEYNHEGE--YILIGrvgalcGNVhyveGKFWV----------TDNALVVTPKKENNIKFLYYLLKSLNL-NQYATG--- 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2047298907 161 TSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRR 216
Cdd:cd17266   103 SAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKELM 158

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: 68.30 E-value: 1.92e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  65 RVSDFENGTINCDGLKYISQDIQSKISrytISKDDVYI-----SIAgTIGKCGIIPDfldganLTENA---AKITDIKYS 136
Cdd:cd17265    29 RSSNIQNGKLDFDDNVYVNSKIPEKLI---VKEGDILIcvrngSRA-LIGKNALIDK------EAEGMtfgAFMTVFRSE 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 137 TNRYIYYVLNTEILKNQIKNSMKST-SQpkLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELR 215
Cdd:cd17265    99 YNDYLFHLFNSDLFKKQIGSFLTATiNQ--ITNGNLNNFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKEL 176


                  ....*
gi 2047298907 216 RAAIL 220
Cdd:cd17265   177 MQQLI 181

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) TRD2-CR2; 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.StySPI-TRD1 recognizes AAC/GTT 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341204 [Multi-domain] Cd Length: 190 Bit Score: 68.42 E-value: 2.50e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKS-IAEVKGG--KRlpAGADFVDEITnhpyIRVSDFENGTINCDGLKYISQDiQSKISRYTISKDDVYI----- 102
Cdd:cd17523     1 WEWVRLGDlIPEFQNGlsKR--GGSDGEPIIV----LRLADIKNNKISFENLRRIKLT-EKEIEKYSLSKGDLLIirvng 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 103 --SIAGTIGKCgiipdfldgaNLTENAA--------KItDIKYSTNRYIYYVLNTEILKNQIKNSMKSTS-QPKLALHRI 171
Cdd:cd17523    74 spDLVGRFILF----------KGYEDVAycdhfirmRL-DQEKIDPEFLSYIFNSPLIRRKIERNFVTSAgQKTVNQGHI 142

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2047298907 172 QDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAI 219
Cdd:cd17523   143 KSLPIPLPPLKEQKKIVARVEELFALIDQLESSLDLAQQLQNKLAQSI 190

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: 67.52 E-value: 3.59e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAEVKGGKRlPAGADFVDEITNHPYIR-VSDFENGTINcdglkyisqdiqskISRYTIS------KDDVYISIAG 106
Cdd:cd17496     1 VKLGDIAEIIMGQS-PKGESYNTEGIGIPLLNgPADFGDGYPI--------------PKKWTTKptklckKGDILFCVRG 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 107 -TIGKcgiiPDFLDGanltENA-----AKITDIKYSTNRYIYYVLNTEIlkNQIKNSMKSTSQPKLALHRIQDLKLPLPP 180
Cdd:cd17496    66 sTTGR----LNIADD----EYCigrgvAAIRPKNGIDTEFLYYLLESNL--DYLLAAATGSTFPNISRDDLLNLKIPLPP 135

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2047298907 181 LNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17496   136 LEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTLLPKLL 175

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: 67.39 E-value: 4.16e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  64 IRVSDFENGTINCDGL-KYISQD-IQSKISRYTISKDDVYISIAGTI-GKCGIIPDflDGANLTENAAKI---TDIKYST 137
Cdd:cd17518    28 LNVTNIVNGSLDLDKTdRYISTEeYNGKYKHFLIDEGDILIASSGNSwGKVAIVEK--DHLPLMLNTSTIrfkFIDGLLD 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2047298907 138 NRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAK 209
Cdd:cd17518   106 NNFLKYFLNSDYFKEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEAALEALRKKK 177

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: 67.56 E-value: 4.28e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 259 WKWVRAEFLFDEFpRNGYSPKSTESSFITKTLKLGAITKGYYKNDEFKYVDERIEQDSYLWLKNGDFLIQRANSIEYVGT 338
Cdd:cd17522     1 WKVVKLGDVLEEI-RNGTTVKQNKEGGGYPVTRIETISNGTIDLNRVGYAITNEEKIEKYKLQKGDILFSHINSIEHIGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 339 SAIFTGaDNESIYPDL-IMKGKVNETVVLNQYLVHWINSMYGKQYFRQNAtGTAGNMPKINKSILQNLLVPIPPIEEQRV 417
Cdd:cd17522    80 TAIYDG-DPEPLIHGMnLLRLRPNKNIVDPKYLYYLLKSDRFRNQFRSIA-KKAVNQASINQTELKKIKIPLPPLEEQQK 157

                         170       180
                  ....*....|....*....|....*....
gi 2047298907 418 IMKVLDcvfnsdnDALNKLENYQPEIDLL 446
Cdd:cd17522   158 IASILE-------KLDKKIEKRKEKIEKL 179

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: 65.92 E-value: 1.34e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 107 TIGKCGIIpdfldGANLTEN---AAKITDIKYStNRYIYYVLntEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNE 183
Cdd:cd17515    73 TAGKVGIL-----GIDAATNqaiCAILPNEEID-NEFLFYFL--KSQKEYLISLGKGGAQPNISQGIIKNIEIPLPPLAE 144

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2047298907 184 QKRIADKVERLLDKINQAKQLIDEAKATFElrraAILDKVF 224
Cdd:cd17515   145 QKRIVAKLDKLDKLIEKLEKALEKLEELKK----ALMQKLL 181

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: 66.40 E-value: 1.44e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  28 PGNWVWVRIKSIAEVKGGkrlpagadfvdeitnH-PYIRVSDFENGTIncdglKYIS-QDIqSKISRYTISKDDVYISIA 105
Cdd:cd17248     1 PAHWEVVPLTDVAKLESG---------------HtPSRSRPEYWNGCI-----PWISlADV-KQLRGDYIYETKEKISEL 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 106 G--------------------TIGKCGIIP-------DFldganltenAAKITDIKYStNRYIYYVLNTEilKNQIKNSM 158
Cdd:cd17248    60 GianssarllpagtvvlsrtaSVGKSAIMGrpmatsqDF---------ANWVCGPELD-PEYLLYVLRAM--KPEFERLA 127

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2047298907 159 KSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAILDKVFRGE 227
Cdd:cd17248   128 MGSTHKTIYMPDFKALRIALPPLEEQRKIVDRLEALDAKIDALERKLERLIELLKELRQALLTAAVTGK 196

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: 65.14 E-value: 3.46e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAeVKGGKRLPAGAdfVDEITNHPYIRVSDFENGTINcdgLKYISQDIQSKISRYTISKDDVYISIAGTIGK 110
Cdd:cd17272     1 VEEKTLGDIA-VDGFQNGPAPN--FDEKGEIPVITSKNISNGKID---FEYVKYDFLSISKNRKINKGDILITMIGTIGE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 111 CGIIpDFLDGANLTENAAKI-TDIKYSTNRYIYYVLNTEILKNQIKNsmKSTSQPKLALHRIQDLKLPLPPLNEQKRIA- 188
Cdd:cd17272    75 TAIV-KCLDPKFYTLNLYLIrLKKEKLLPSYLKYFLDSEKFLNKSIS--ATSGQGYLKANQIDKLEIPLPPLEEQQRIVk 151

                         170
                  ....*....|....
gi 2047298907 189 --DKVERLLDKINQ 200
Cdd:cd17272   152 ilDKFDTLCNDITE 165

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: 64.11 E-value: 5.48e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  88 SKISRytisKDDVYISIAGTIG-------KCGIipdfldGANLtenaAKITDIKYSTNRYIYYVLNteILKNQIknSMKS 160
Cdd:cd17497    51 KKIAE----KGDILLSVRAPVGptniadqEYCI------GRGL----AAIRPKKGLDKKYLLYYLK--SIENEL--SSLG 112

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2047298907 161 TSQPKLALHR--IQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17497   113 TGSTFKAISKedLENLLIPLPPLAEQKRIAAFLDELTAKIDQLIALLEKAIELLKEYRQAVL 174

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 67.21 E-value: 6.54e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  61 HPYIRVSDFENGTINCDGLKYISQDiQSKISRYTISKDDVYISIAG---TIGKCGIIPDFLDGANLTENAAKITDIKYST 137
Cdd:PRK09737  248 TPYLRNINVRWGSFDLEDLQDILIS-DIERRELKLKLGDVLFCRGNeplEVGRCAIWKEPQDIPVIYQKALIRARVKDDI 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 138 N-RYIYYVLNTeILKNQIKNSMKST--SQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFEL 214
Cdd:PRK09737  327 IpEYLVYNLKS-PDSRNISLSQLFTgtTQKHITGKALANYPIRVPPLEEQAEIVRRVEQLFAYADTIEKQVNNALARVNN 405

                         170       180
                  ....*....|....*....|..
gi 2047298907 215 RRAAILDKVFRGELTKKWREEN 236
Cdd:PRK09737  406 LTQSILAKAFRGELTAQWRAEN 427

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: 63.29 E-value: 1.17e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 295 ITKGYYKNDEFKYVDERIEQ--DSYLwLKNGDFLIQRANSIEYVGtsaiftgadnesIYPDLIMKGKVNETVV------- 365
Cdd:cd17256    34 IKNGGIDLDNLKYISPEIHEkiKRYT-LSKGDILISIVGTIGRVG------------IVPKELDGANLTENAArirpkds 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2047298907 366 -LNQYLVHWINSMYGKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQ 440
Cdd:cd17256   101 iSPRYLYYYLRSPFGQSQIESETKGAA--QPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLE 174

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: 63.10 E-value: 1.24e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  61 HPYIRVSDFENGTINCDGLKYIS-QDIQSKISRYTISKDDVYISIAG-TIGKCGIipdfldgaNLTENA--------AKI 130
Cdd:cd17519    27 FPIIRITNIQNGKIDTDNLKYFDlNDYKENLDKYIVRPGDIVIAMSGaTTGKVGI--------NLTDQEfylnqrvgKFI 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 131 TDIKYSTNRYIYYVLnteILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKverlLDKINqakQLIDEAKA 210
Cdd:cd17519    99 PNEEILNNRYLYHFL---LSKQNEKYILAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSI----LDKFR---ELTNELES 168


                  ....*.
gi 2047298907 211 TFELRR 216
Cdd:cd17519   169 ELNLRL 174

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

Pssm-ID: 341158 [Multi-domain] Cd Length: 168 Bit Score: 61.07 E-value: 5.54e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 139 RYIYYVLNTEILKNQIKNSMKSTSqPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAA 218
Cdd:cd17269    85 KFLYYYLKSYFKKYIEKNSVGSSV-PYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAELPAELEARKKQYEYYRDA 163


                  ..
gi 2047298907 219 IL 220
Cdd:cd17269   164 LL 165

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: 60.95 E-value: 6.26e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  60 NHPYIRVSDFENGTINCDGLKYISQDIQSKISRYTISKDDVYISIAGTIGKCGIIpdfldGANLTENAA----KITDIKY 135
Cdd:cd17244    27 NIPWVSISDMGKGKYISDTKEYITDEAVKKFNVKLVPKGTLLMSFKLTIGRVAIA-----GKDLYTNEAiahfIPKDKKI 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2047298907 136 STNrYIYYVLNTEILKNQIKNSMKSTsqpklALH--RIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKA 210
Cdd:cd17244   102 DTE-YLYYYLKSFDYSSLGSTASKGK-----TLNskKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDE 172

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

Pssm-ID: 341147 [Multi-domain] Cd Length: 173 Bit Score: 60.88 E-value: 6.45e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  69 FENGTI--NC------DGLKYISQDIQSKI---SRYTISKDDVYISIAGTIGKCGIIPDFlDGANLTENAAKITDIKYST 137
Cdd:cd17258    12 FCNGNIklVCikneliNSLKVKIVEPDYKIglkQSKIFKKGDVLITRHGTIGRVSIILSE-EACLSSHVAGFNSKEGISD 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2047298907 138 NRYIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIAdKVERLLDK-INQAKQLIDEAK 209
Cdd:cd17258    91 NKFIKYLFNSKKIKNRLMSYGASSTQPALNLSRLLKIKFPNPPLEEQQKIG-KILSTWDRaIELTEQKLELLQ 162

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: 60.25 E-value: 1.23e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  60 NHPYIRVSDFEN--GTINcDGLKYISQDIQSKISRYTISKDDVYISIAGTIGKCGI--IPdfldganLTENAAkITDIKY 135
Cdd:cd17275    29 DIPFVKISDMTKsgKYIY-STEKYITEEGLKNSSAWIVPKGTILYAMYASVGKVAInkID-------VATNQA-ILGIIP 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 136 STNR--YIYYVLNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADkverLLDKINQAKQLIDEAKATFE 213
Cdd:cd17275   100 KDEKldFEFLYYWLLSLKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIAE----ILDKIDAEIDKLEEKIEKLR 175

                         170
                  ....*....|.
gi 2047298907 214 LRRAAILDKVF 224
Cdd:cd17275   176 ELKKGLLQKMF 186

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: 60.19 E-value: 1.42e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 298 GYYKNDEFKYVDERIEQDSYLwLKNGDFLIQRANSIeyVGTSAIFTGADNESIYPD-LImKGKVNETVVLNQYLVHWINS 376
Cdd:cd17521    40 GVLWDTVPYCSISEEDAEKYL-LKDGDILFARTGAT--VGKSYLYKEDDGKAVFASyLI-RFRPNKKKVLPKYLFYFTQS 115

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2047298907 377 MYGKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDcvfnsdnDALNKLENYQPEIDLLIN 448
Cdd:cd17521   116 SLYWKQIKSISSGSA--QPNINAEKLKSLKIPLPPLEEQKRIVAILD-------ALDAKIDALEELLEKLEE 178

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: 60.29 E-value: 1.47e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAE-VKGGKRLPAGADFVDEITNHPYIRVSDFENGTINCDGLKYISQD-IQSKISRYtISKDDVYI-SIAGTIGK 110
Cdd:cd17290     1 KKLKRLAKsIKTGTTPPSENEEYYDGGIIPWFTPGDFNGDLILSESKRKLSELaIEDGEARL-FPKNSVLVvGIGATIGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 111 CGIipdfldganLTENAA---KITDIKYS---TNRYIYYVLNTeiLKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQ 184
Cdd:cd17290    80 VGY---------SDKESSsnqQITGIIFNkdiNPKFLFYWLSS--SKEELENLANGATLPILNQEKLKNIKLPVPPLNEQ 148

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2047298907 185 KRIADKVERLLDKINQ----AKQLIDEAKatfELRRAAI 219
Cdd:cd17290   149 QKIVEFLDKKTAKIDAliakKEQLIELLK---EYRQALI 184

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: 60.26 E-value: 1.60e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  62 PYIRVSDFENGTINCDGLKYISQDIQSKISRYTISKDDVYISIAGTIGKCGIIPDFLDGANLTENAAKITDIKYSTNRYI 141
Cdd:cd17514    30 PWLTSGETDDNFINNTSEKITTKNGLEDSSIRIVPKGTILIACTGQGYTRGQVAVLQIDASTNQAIAAIRCKENVNPKYL 109

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2047298907 142 YYVLNTEilKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDE 207
Cdd:cd17514   110 YYYLKTQ--KNNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNILETLEFFEKDSLRKIKE 173

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: 59.81 E-value: 2.35e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAEVK-GGKrlPAgadfvdeiTNHP-YirvsdFENGTIN--------------CDglKYISQDIQSKISRYT 94
Cdd:cd17294     1 WEWKTLGEIAKIFsGGT--PS--------TSNPeY-----WDGGTIPwlssgevnfkeiyeTE--KRITEEGLKNSSAKW 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  95 ISKDDVYISIAG---TIGKCGI--IPdfldganLTEN---AAKITDIKYSTNRYIYYVLNTEIlkNQIKNSMKSTSQPKL 166
Cdd:cd17294    64 IPKNSVLIALAGqgkTRGTVAIlkIP-------LTTNqslAAIEPDEEIANSRFLYYNLSSRY--EELRSLSGGGGRGGL 134

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2047298907 167 ALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKatfELRRAAI 219
Cdd:cd17294   135 NLKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLPALL---ELRQKQY 184

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: 59.53 E-value: 2.55e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  28 PGNWVWVRIKSIAEV--------KggkrlpagaDFVDEItnhPYIRVSDFENGTINCDGLK-YISQDIQSKISRYTISKD 98
Cdd:cd17284     1 PEGWEVKRVGDVCDCivpgrdkpK---------SFDGNI---PWITIEDIKGKYISSSKSGlGVSEEEIKEMNLKVIPKG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  99 DVYISIAGTIGKCGIIpdfldGANLTENAAKITDI--KYSTNRYIYYVLNTEilKNQIKNSMKSTSQPKLALHRIQDLKL 176
Cdd:cd17284    69 SVIMSCVGDFGIVAIA-----TNELVINQQLHAFVpsKKINPEYLMYLLSLQ--KKYMEKIATGTTIPYLNKTNCESIPI 141

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2047298907 177 PLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17284   142 PLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQQLF 185

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: 58.99 E-value: 3.95e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 352 PDLIMKGKVNETVVLNQYLVHWINSMygKQYFRQNATGTA-GNmpkINKSILQNLLVPIPPIEEQRVIMKVLDCVFnsdn 430
Cdd:cd17282    91 PDSVVGFIPNEEKIDVEFLEYYLRTL--KKELEAIAPQSAqKN---INLEILRPLKIPVPPLEEQKKIVEILDALD---- 161

                          90
                  ....*....|....*.
gi 2047298907 431 dalNKLENYQPEIDLL 446
Cdd:cd17282   162 ---DLIDNLEKRIAKL 174

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: 58.24 E-value: 4.94e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 139 RYIYYVLNtEILKNQIKNSMKSTSQpklalH----RIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFEL 214
Cdd:cd17254    94 DYLYYLLK-ALTEEIESQAHGSTMV-----HitkgDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLEELRKA 167


                  ....*.
gi 2047298907 215 RRAAIL 220
Cdd:cd17254   168 LLQSLL 173

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: 58.01 E-value: 6.13e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 128 AKITDIKYSTNRYIYYVLNTeiLKNQIK-NSMKSTSqpkLALHR--IQDLKLPLPPLNEQKRIADKVERLLDKINQAKQL 204
Cdd:cd17499    85 AAIRAKKNIDKKYLFYFLLS--NKDYFKgKSGGSTF---KSINKnqIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNN 159

                          90
                  ....*....|....*.
gi 2047298907 205 IDEAKATFELRRAAIL 220
Cdd:cd17499   160 IEEALANAQQLFKSIL 175

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: 58.40 E-value: 6.89e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAE--VKGGKRLPAGADfvdeiTNHPYIRVSDFENGTINCDG-LKYISQDIQSKiSRYTISKDDVYISIAGT 107
Cdd:cd17525     1 WEWVKLGDILSstQLGLVRSNSEDP-----NGYPYIKMGNIGRGGINLLKvETYVDATELEV-EKYLLEDGDLLFNTRNT 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 108 ---IGKCGIIPDFLDGANLTENAAKITDIKYSTNRYIYYVLNTEILKNQIKNSMKSTS------QPKLALhriqdLKLPL 178
Cdd:cd17525    75 lelVGKVAIWRGELPKALFNNNILRIRFDDIVLPYFINYYLNSPDGKKQLESIASGTTsvaaiyQKDLKK-----LKLPL 149

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2047298907 179 PPLNEQKRIADKVERLLDKINQAKQLIDEAKATFE 213
Cdd:cd17525   150 PPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKK 184

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: 58.29 E-value: 6.90e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 259 WKWVR----AEFLfdefprNGYSPKSteSSFI---TKTLKLGAITKGYYKNDEFKYVDE--RIEQDSYLwLKNGDFLIqr 329
Cdd:cd17278     1 WEVVKlgdiADIQ------NGYAFKS--SDFSdegIPVIRIGNIKNGGIDLDDNSKYPEepLEKYEKFL-LKKGDILI-- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 330 ANSIEYVGTSAIFTgadnesiypdlimkgKVNETVVLNQ--------------YLVHWINSMYGKQYFRQNATGTA-GNm 394
Cdd:cd17278    70 AMTGGTVGKVAIVP---------------EDDEPALLNQrvgkfrpkdkidkeFLYYLLRSDSFRNQIKSSATGTAqPN- 133

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2047298907 395 pkINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQpeidLLINGMLMKAFS 456
Cdd:cd17278   134 --ISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKLEQKLEKLR----DLLKPLLQSLFT 189

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: 57.42 E-value: 1.41e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  62 PYIRVSDF-ENGTINCDGLKYISQDIQSKISRYTISKDDVYISIAGTIGKCGIIPDFLdGANLTENAAKITDIKYsTNRY 140
Cdd:cd17277    32 KWLTIPDIdERGLIISSTKQFITEKALEEKKVKLVPKNSVLLSCTATIGKVAIAKIEL-TTNQQINALICKDSKI-LPEY 109

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2047298907 141 IYYVLNTeiLKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAK 209
Cdd:cd17277   110 LFYALKH--IKQVLERLTTNPGVKHVNLSMLSNLQIPLPPLEVQKKIVAEIEKVEKVIQGLRQKIDEYQ 176

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: 57.46 E-value: 1.45e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 137 TNRYIYYVLntEILKNQIKNSMKSTSQP--KLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFEL 214
Cdd:cd17249   103 DPEFLLYAL--KANEDRILSLVDKAGHGtgSLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEELLKA 180


                  ....*
gi 2047298907 215 RRAAI 219
Cdd:cd17249   181 LMQAL 185

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: 57.15 E-value: 1.48e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAEVKGGKrlP-AGADFVDEITNHPYIRVSDFENGTINCdglkYISQDIQSKisrYTISKDDVYISIAGtig 109
Cdd:cd17257     1 WEVVRLGDVADVQNGF--PfKSKLFNDEGGGLPLIRIRDLKSGDTET----YYTGEYDEK---YLVKNGDILIGMDG--- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 110 kcgiipDFldganlteNAAK---------------ITDIKYSTNRYIYYVLNTEILKnqIKNSMKSTSQPKLALHRIQDL 174
Cdd:cd17257    69 ------DF--------NAAIwkggdallnqrvcriRPKSEELDKRFLYYALPPPLKA--IEDTTSSTTVKHLSSKDIDEI 132

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2047298907 175 KLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKAT 211
Cdd:cd17257   133 ELPLPPLEEQRRIAEILDELDALIDKLIAKLEKLRDL 169

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

Pssm-ID: 341165 [Multi-domain] Cd Length: 187 Bit Score: 56.82 E-value: 1.96e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAEVK-GGKRLPAGADFVDEITNHPYIRVSDFENGTINcdglkyisqDIQSKISRYTIS--------KDDVYISI 104
Cdd:cd17276     1 KKIGDIAKTSsGGTPLRSNQEYYFNGGTIPWVKTTDLNNGVIY---------ETEEKITEKALKetsckllpKGTVLVAM 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 105 ---AGTIGKCGIIpdfldGANLTENAA--KITDIKYSTN-RYIYYVLNTeiLKNQIKNSMKSTSQ-PKLALHRIQDLKLP 177
Cdd:cd17276    72 yggFGQIGRTGLL-----GIPAAINQAicAILPNEKKVNpEFLLRYLNF--NRPYWMRVAASSRKdPNITKDDVRNFPIP 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2047298907 178 LPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17276   145 LPPLDEQRAIVEFLSDVDALIDSLEALIEKLRELKKGLMQQLL 187

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: 56.45 E-value: 2.63e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 359 KVNETVVLNQYLVHWINSMYGKqyFRQNATGTAGNMpkINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLEN 438
Cdd:cd17296    94 KPKNKSINPKYLYYYLKSLYEK--FLSLGRGVAQNN--INLSILKNLKIPLPPLEEQQRIVAILDKFEKLINKRQEGLQL 169

                          90
                  ....*....|...
gi 2047298907 439 YQPEIDLLINGML 451
Cdd:cd17296   170 LDELVKSLFEEMF 182

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: 55.24 E-value: 3.37e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  69 FENGTIncdGLK---YISQDI-QSKISRYTI-SKDDVYISIAGTIGKCGIipdfLDGanltENA----AKI----TDIKY 135
Cdd:cd17292     1 YKIGTF---GKEpdaYISRELfEEYKSKYSYpKKGDILISASGTIGRTVI----YDG----EDAyfqdSNIvwldNDESK 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 136 STNRYIYYVLNTeilknqIK-NSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKAtfel 214
Cdd:cd17292    70 VLNKFLYYFYQI------IKwKKTEGSTIKRLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALIALLQKKLEKLIA---- 139

                         170
                  ....*....|
gi 2047298907 215 RRAAILDKVF 224
Cdd:cd17292   140 LKKGLMQYLF 149

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

Pssm-ID: 341151 [Multi-domain] Cd Length: 172 Bit Score: 55.90 E-value: 3.43e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 119 DGANLTEN----AAKIT-------------DIKYSTNRYIYYVLNTeilKNqIKNSMKSTSQPKL---ALHRIqdlKLPL 178
Cdd:cd17262    59 DGANLLSRgtpiAFYVSgkfwvnnhahvlkGKNGISTEFLYYYLNS---ID-ISPYVTGAAQPKLnqaNLNSI---PIPL 131

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2047298907 179 PPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAI 219
Cdd:cd17262   132 PPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQKL 172

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: 55.70 E-value: 4.21e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 367 NQYLVHWINSMygKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQPEIDLL 446
Cdd:cd17499    95 KKYLFYFLLSN--KDYFKGKSGGST--FKSINKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNNIEEALANAQQL 170


                  ....*
gi 2047298907 447 INGML 451
Cdd:cd17499   171 FKSIL 175

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: 55.23 E-value: 5.06e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2047298907 134 KYSTNRYIYYVLNteilkNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLID 206
Cdd:cd17255    86 KNINNKFLYYALN-----LIAKKYVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIAKLK 153

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: 55.51 E-value: 7.37e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 295 ITKGYYKNDEFKYVDERIEQDSYLwlKNGDFLIQRANSIeyvGTSAIFTGADNESIYPDLIMkGKVNETVVLNQYLVHWI 374
Cdd:cd17272    36 ISNGKIDFEYVKYDFLSISKNRKI--NKGDILITMIGTI---GETAIVKCLDPKFYTLNLYL-IRLKKEKLLPSYLKYFL 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2047298907 375 NSmyGKQYFRQNaTGTAGnMPKINKSILQNLLVPIPPIEEQRVIMKVLDC 424
Cdd:cd17272   110 DS--EKFLNKSI-SATSG-QGYLKANQIDKLEIPLPPLEEQQRIVKILDK 155

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: 54.82 E-value: 9.61e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 295 ITKGYYKND-EFKYVDErieQDSYLWLKNGDFLIQR--ANsieyVGTsaIFTGAdnESIYPDLIMKGKVNETVVLNQYLV 371
Cdd:cd17263    32 IQIEDLRNNnEKKYIEN---PKKSVICNEDDILIVRdgAN----AGE--VGTGL--EGAIASTLFKIIPDKNIIDKDYLY 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2047298907 372 HWINSMYgkQYFRQNATGTAGnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFN 427
Cdd:cd17263   101 YFLKSKE--IQLNILTKAGST-IPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDA 153

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: 54.44 E-value: 9.94e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 130 ITDIKYSTNRYIYYVLNTeiLKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIAdkveRLLDKINqakQLIDEAK 209
Cdd:cd17291    77 LSSKNELVNKFLYYFLKN--KQEEIYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIV----EILDKFT---ELTAELP 147


                  ....*..
gi 2047298907 210 ATFELRR 216
Cdd:cd17291   148 AELEARK 154

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: 1.59e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2047298907 163 QPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAI 219
Cdd:cd17247   134 QGALNCGILKAFPIPLPPLDEQREIVAELEALLAKIDLLEEKIARLIELLKELRQAL 190

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

Pssm-ID: 341157 [Multi-domain] Cd Length: 185 Bit Score: 53.99 E-value: 1.82e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIAEVKGGKRLPAgADFVD---------EItnhpYIRVSDFENGTIncdglKYISQDIqSKISRYtISKDDVY 101
Cdd:cd17268     1 VEWKTLGEIGEFIRGKGITK-KDFVEsgvpcihygEI----YTKYGIYTTKTK-----SFISEEL-AKKLRK-AKPGDLL 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 102 ISIAGT----IGKC----GiipdfldganlTENAA---KITDIKYSTN-RYIYYVLNTEILKNQIK-----NSMKSTSQP 164
Cdd:cd17268    69 IAGTGEtiedIGKAvawlG-----------DEEVAaggDIIIFRHSQNpKYLSYLLNSPAFQKQKRklgtgTKVVHISAS 137

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2047298907 165 KLAlhriqDLKLPLPPLNEQKRIAdkveRLLDKinqAKQLIDEAKATFELRR 216
Cdd:cd17268   138 DLA-----KIKIPVPPLEEQERIV----EILDK---FDALIAGLPAEIEARR 177

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

Pssm-ID: 341169 [Multi-domain] Cd Length: 187 Bit Score: 54.09 E-value: 1.85e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  60 NHPYIRVSDFENGTINCDGlKYISQDIQSKISRYTI-SKDDVYISIAG-TIGKCGIIpdfldGANLTENAA--KITDIKY 135
Cdd:cd17280    27 GIPWVTTGDLRDGIITETS-KKITDKALDDYSALKIyPAGSLVIAMYGaTIGRLGIL-----GIDATTNQAccVLSGSNK 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 136 STNRYIYYVLNteILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIAD----KVERLLDKINQAKQLIDEAKat 211
Cdd:cd17280   101 IDIKFLFYWLL--ANRDELISLASGGGQPNISQELIKSLRIPVPPLEEQKQIAAfldkKTAKIDSLIEKKERLIELLK-- 176

                         170
                  ....*....|..
gi 2047298907 212 fELRRAAILDKV 223
Cdd:cd17280   177 -ERRQALISEAV 187

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: 53.17 E-value: 1.98e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 130 ITDIKYSTNRYIYYVLnteilKNQIKNSMKS-TSQPKL---ALHRiqdLKLPLPPLNEQKRIADKVERLLDKINQAKQLI 205
Cdd:cd17267    74 VKDFKGNDPRFLYYLL-----KTLDLERLNSgSAVPGLnrnDVYS---LKVPLPPLEEQKAIAAILDALDDKIELNRRQN 145


                  ....*....
gi 2047298907 206 DEAKATFEL 214
Cdd:cd17267   146 QTLEELADA 154

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: 53.64 E-value: 2.15e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2047298907 362 ETVVLNQYLVHWINSMYGKQYFRQNATGTAGNmpkINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQ 440
Cdd:cd17283    98 KKKLDKDFLYYLLSSITVQLQFSAQAGGGTKN---LNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLE 173

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: 54.07 E-value: 2.28e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2047298907 359 KVNETVVLNQYLVHWINSMYgkQYFRQNATGtaGNMPKINKSILQNLLVPIPPIEEQRVIMKVLD 423
Cdd:cd17247   103 RPNEERVLPEYLHYYLESQY--DELRRIGSG--GGQGALNCGILKAFPIPLPPLDEQREIVAELE 163

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: 52.89 E-value: 4.26e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2047298907 171 IQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEAKATFELRRAAIL 220
Cdd:cd17285   132 LKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEKLKQLKKGLMQSLL 181

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Heliobacterium modesticaldum Ice1 S subunit (S1.HmoORF3075P) TRD1-CR1; The recognition sequence of Heliobacterium modesticaldum Ice1 S subunit (S1.HmoORF3075P) 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 subfamily also includes the TRD-CR-like sequence-recognition domain of type I N6-adenine DNA methyltransferase (M) subunit of Clostridium intestinale URNW (M2.CinURNWORF2828P). The recognition sequence of M2.CinURNWORF2828P is undetermined. Type I methyltransferases included in this group include two domains: one for methylation, and another (TRD-CR-like) for sequence-recognition.

Pssm-ID: 341201 [Multi-domain] Cd Length: 180 Bit Score: 52.84 E-value: 4.72e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAEVKGGKRLPAGADFVDEITnhpYIRVSDFENGTINCDGLKYISQDiQSKISRYTISKDDVYISIAGTIGKCGI 113
Cdd:cd17520     1 VKLKEVAEVFRGKSILKKDIKPGSIS---VLNISNIEDGEIDYSGMDTIEEE-ERKVKRYELRDGDLVLSCRGTAIKVAV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 114 ipdFLDGANLTENAAKITDIKYSTNRYIYYV---LNTEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADK 190
Cdd:cd17520    77 ---FREQKKIVIASANIIVIRPNEKVLSEYLkifLESPVGTALIKSFQRGTTVMNINHSDIAEMEIPLLPLEEQKKIAEE 153


                  ...
gi 2047298907 191 VER 193
Cdd:cd17520   154 YRK 156

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: 52.68 E-value: 4.91e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  81 YISQDIQSKISRYTISKDDVYISIAG---TIGKCGIIpdfldGANLTENAA---KITDIKYSTNRYIYYVLNTEilKNQI 154
Cdd:cd17500    47 KITEEGLKNSSAKLIPENTVIIAMYGagkTAGRVAIN-----KIPLTTNQAccnLIIDNKKADYRFVYYSLKTQ--YEEL 119

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2047298907 155 KNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKI---NQAKQLIDE-AKATF 212
Cdd:cd17500   120 VNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLDDKIelnNRQNETLEAmAETLF 181

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: 52.88 E-value: 5.26e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 128 AKITDIKYSTNRYIYYVLntEILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDE 207
Cdd:cd17287    93 AAILPNDGINPDFLFYYL--QSSYEELRDLSNGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAKIDALEQKLEL 170

                          90
                  ....*....|....*..
gi 2047298907 208 akatFELRRAAILDKVF 224
Cdd:cd17287   171 ----LQELKKSLMQQLF 183

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: 51.01 E-value: 1.95e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  34 VRIKSIAEVKGGKRLPAG--ADFVDEItnhPYIRVSDFENGTINCDGLKYISQDIQSKISRYTISKDDVYIS-IAGTIGK 110
Cdd:cd17516     1 VKIGDLGKVVTGKTPSTKnpEYFGGDI---PFITPSDMKGGKYIIKTERRLSSKGLEKVKNKLIPANSICVTcIGSDMGK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 111 CGIIPDflDGA-NLTENAakITDIKYSTN-RYIYYVLNTeiLKNQIKN-SMKSTSQPKLALHRIQDLKLPLPPLNEQKRI 187
Cdd:cd17516    78 VAITKE--PSVtNQQINS--IIVNKNKFDpDFVYYLLKN--NSKYLKSiAGGSTATPIINKSTFSNIEIPLPPLPEQKKI 151

                         170       180
                  ....*....|....*....|....*...
gi 2047298907 188 ADKVERLLDKINQAKQLIDEAKATFELR 215
Cdd:cd17516   152 AAILSSLDDKIENNRRINKTLEEMAQAL 179

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: 50.98 E-value: 2.06e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  62 PYIRVSDFENGTINC-DGLKYISQD-IQ---SKIsrytISKDdvyiSIA-GT---IGKCGIIP-------DFLDganlte 125
Cdd:cd17513    28 PWITSSDLSEDDIFKiNIRKFITEEaIKnsaTKI----IPAN----SILiVTrvgVGKVAINPfdictsqDFTS------ 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 126 naakITDIKYSTNRYIYYVL--NTEILKNQ-----IKNSMKSTsqpklalhrIQDLKLPLPPLNEQKRIADKVERLLDKI 198
Cdd:cd17513    94 ----LIPIKEVNPLFLAYLLysLLQKLKSQlqgtsIKGITKDD---------LKNLKIPLPPLEEQQKIAAILSKLDKLI 160

                         170       180
                  ....*....|....*....|....*.
gi 2047298907 199 NQAKQLIDEAKATFelrrAAILDKVF 224
Cdd:cd17513   161 EAHEKKLEKLKQLK----KGLMQKLF 182

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: 50.95 E-value: 2.49e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2047298907 360 VNETVVLNQYLVHWINSMYgkQYFRQNATGTA-GNmpkINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLE 437
Cdd:cd17294   101 PDEEIANSRFLYYNLSSRY--EELRSLSGGGGrGG---LNLKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLP 174

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: 50.57 E-value: 2.60e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2047298907 369 YLVHWINSMygKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDcvfnsdnDALNKLENYQPEIDLL 446
Cdd:cd17496    97 FLYYLLESN--LDYLLAAATGST--FPNISRDDLLNLKIPLPPLEEQKRIVAILD-------PLDEKIDKNKQEIEKL 163

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: 50.00 E-value: 4.11e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 273 RNGYSPKST---ESSFitKTLKLGAITKGYYKNDEFKYVDE---RIEQDSYLwLKNGDFLIqrANSIEYVGTSAIFTgAD 346
Cdd:cd17519    12 QNGFAFKSSkyrESGF--PIIRITNIQNGKIDTDNLKYFDLndyKENLDKYI-VRPGDIVI--AMSGATTGKVGINL-TD 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2047298907 347 NESIYPDLIMKGKVNETVVLNQYLVHWINSMYGKQYfrqnaTGTAGNMPKINKSILQNLLVPIPPIEEQRVIMKVLD 423
Cdd:cd17519    86 QEFYLNQRVGKFIPNEEILNNRYLYHFLLSKQNEKY-----ILAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILD 157

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: 50.12 E-value: 4.15e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 365 VLNQYLVHWInsMYGKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSdndaLNKLENYQPEID 444
Cdd:cd17515    99 IDNEFLFYFL--KSQKEYLISLGKGGA--QPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKL----IEKLEKALEKLE 170

                          90
                  ....*....|.
gi 2047298907 445 LLINGMLMKAF 455
Cdd:cd17515   171 ELKKALMQKLL 181

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: 50.25 E-value: 4.20e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 138 NRYIYYVLNteILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQA----KQLIDEAKatfE 213
Cdd:cd17279   103 SRFLYYLLL--AAKEELNSLGRGTTFLELSTDELANFKIPLPPLSEQRAIADFLDRETAKIDALiakkQQLIELLK---E 177


                  ....*.
gi 2047298907 214 LRRAAI 219
Cdd:cd17279   178 KRQALI 183

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: 49.38 E-value: 5.31e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 362 ETVVLNQ--------------YLVHWINSMygKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDcvfn 427
Cdd:cd17254    74 GKAILNQhifkvvpdeeidkdYLYYLLKAL--TEEIESQAHGST--MVHITKGDLENIKVPLPPLEEQKRIAAILD---- 145

                          90       100
                  ....*....|....*....|.
gi 2047298907 428 sdnDALNKLENYQPEIDLLIN 448
Cdd:cd17254   146 ---ELDALIDALEEQLKKLEE 163

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: 49.56 E-value: 5.85e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2047298907 355 IMKGKVNETVvLNQYLVHWINSMYGKQYFRqnatgtAGNMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFN 427
Cdd:cd17250    96 VMGLIPNEGI-DSEYLYYWLKKVDLYKYSQ------ATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFE 161

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: 49.52 E-value: 6.86e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 367 NQYLVHWINSMygKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQpeidLL 446
Cdd:cd17284   105 PEYLMYLLSLQ--KKYMEKIATGTT--IPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQ----QL 176


                  ....*....
gi 2047298907 447 INGMLMKAF 455
Cdd:cd17284   177 KKGLMQQLF 185

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: 49.29 E-value: 7.76e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 287 TKTLKLGAITKGYY---KNDEFKYVDERIEQDSYLWLKNGDFLIqrANSIEYVGTSAIFTGADNESIYPDLIMKGKVNET 363
Cdd:cd17518    25 IKLLNVTNIVNGSLdldKTDRYISTEEYNGKYKHFLIDEGDILI--ASSGNSWGKVAIVEKDHLPLMLNTSTIRFKFIDG 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 364 VVLNQYLVHWINSmygkQYFRQNATG--TAGNMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQP 441
Cdd:cd17518   103 LLDNNFLKYFLNS----DYFKEQLDLliTGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEAALEALRKKKQ 178


                  .
gi 2047298907 442 E 442
Cdd:cd17518   179 A 179

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: 49.07 E-value: 8.85e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 367 NQYLVHWInsMYGKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVfnsdNDALNKLENYQPEIDLL 446
Cdd:cd17245    94 NLFLYYYL--KYNKPELEKLGTGST--FKAINKKDLEELKIPLPPLEEQQKIAEILSTV----DEAIEKTKALIEKLDEL 165


                  ....*....
gi 2047298907 447 INGMLMKAF 455
Cdd:cd17245   166 KKGLMQELF 174

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: 48.74 E-value: 1.17e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  31 WVWVRIKSIA-EVKGGkrLPAGADFVDEiTNHPYIR---VSdfENGTINCDGLKYISQDIqSKISRYTISKDDVYISiaG 106
Cdd:cd17526     1 WEVVRLGDIIlDIQSG--FASGKQNEDE-DGVPQLRphnIT--TDGELDLDKLIKIVPSP-KERKRYLLQKGDVLFN--N 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 107 T-----IGKCGIIpdfldgaNLTENAA---KITDIKYSTNR----YIYYVLNteiLKNQIKNSMK-ST---SQPKLALHR 170
Cdd:cd17526    73 TnsqelVGKTALF-------DGEEPYVfsnHMTRIRVKKSKinpeFLARYLH---LLWRSGYFKKlCTnwvNQAGINSDT 142

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2047298907 171 IQDLKLPLPPLNEQKRIADKVERLLDKINQAKQlidEAKATFELRRAAILD 221
Cdd:cd17526   143 LANLKIPLPPLPEQKRIAEILDQIDRLAKALRA---EAEALLELAKSLFED 190

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: 48.56 E-value: 1.52e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 138 NRYIYYVLNTeiLKNQIKN----------SmKSTsqpklalhrIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDE 207
Cdd:cd17273   106 NEFLYYLLKN--NKPEIESlasgstfkeiS-KST---------FKKIEIPLPPLEEQKKIAAILSKLDELIELLEKENEK 173

                          90
                  ....*....|....*..
gi 2047298907 208 AKATfelrRAAILDKVF 224
Cdd:cd17273   174 LKEL----RDGLLPKLF 186

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: 48.56 E-value: 1.56e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 365 VLNQYLVHWINSMygKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFnsdndalNKLENYQPEID 444
Cdd:cd17273   104 IDNEFLYYLLKNN--KPEIESLASGST--FKEISKSTFKKIEIPLPPLEEQKKIAAILSKLD-------ELIELLEKENE 172


                  ..
gi 2047298907 445 LL 446
Cdd:cd17273   173 KL 174

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

Pssm-ID: 341157 [Multi-domain] Cd Length: 185 Bit Score: 47.82 E-value: 2.45e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 320 LKNGDFLIqrANS---IEYVGTSAIFTGadNESIYPD---LIMKGKVNetvvlNQYLVHWINSMYGKQYFRQNATGTAgn 393
Cdd:cd17268    62 AKPGDLLI--AGTgetIEDIGKAVAWLG--DEEVAAGgdiIIFRHSQN-----PKYLSYLLNSPAFQKQKRKLGTGTK-- 130

                          90       100       110
                  ....*....|....*....|....*....|
gi 2047298907 394 MPKINKSILQNLLVPIPPIEEQRVIMKVLD 423
Cdd:cd17268   131 VVHISASDLAKIKIPVPPLEEQERIVEILD 160

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: 47.45 E-value: 2.66e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 358 GKV---NETVVLNQ--------------YLVHWINSMYgkqyFRQNATGTAGNMPKINKSILQNLLVPIPPIEEQRVIMK 420
Cdd:cd17293    74 GKVgiaDREVAFNQqinaiipnksvdpkFLYYQLLSSK----FQLQAIASSTTLPIINKSKFEKIEIPLPPLEEQKRIVA 149


                  ....*..
gi 2047298907 421 VLDCVFN 427
Cdd:cd17293   150 KLDKLFA 156

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

Pssm-ID: 341169 [Multi-domain] Cd Length: 187 Bit Score: 47.16 E-value: 4.61e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 360 VNETVVLNQYLVHWINSMygKQYFRQNATGtaGNMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENy 439
Cdd:cd17280    96 SGSNKIDIKFLFYWLLAN--RDELISLASG--GGQPNISQELIKSLRIPVPPLEEQKQIAAFLDKKTAKIDSLIEKKER- 170


                  ....*..
gi 2047298907 440 qpEIDLL 446
Cdd:cd17280   171 --LIELL 175

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

Pssm-ID: 341149 [Multi-domain] Cd Length: 165 Bit Score: 46.66 E-value: 4.73e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2047298907 365 VLNQYLVHWINSmygkQYFRQNA----TGTAGNMpKINKSILQNLLVPIPPIEEQRVIMKVLDCVFN 427
Cdd:cd17260    80 ILPEFLYYLLRS----PSFRKEAiksmTGSSGRQ-RVPKDFLENYKIPLPPLEEQKRIAAILDSLDA 141

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

Pssm-ID: 341148 [Multi-domain] Cd Length: 189 Bit Score: 47.12 E-value: 4.86e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 259 WKWVRAEFLFDEFprNGYSPKSTESSFI-TKTLKLGAITKGYYKNDEFKY--VDERIEQDSYLwLKNGDFLIQRANSIEY 335
Cdd:cd17259     1 WEWVKLGDVADIL--SGYAFKSSEFSESgIRLLRGANVGVGEIRWDDTVYlpEEYLEEYEKYL-LKEGDIVIALDRPIIS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 336 VGTS-AIFTGADNESIypdlimkgkvnetvvLNQ--------------YLVHWINSMYGKQYFRQNATGTAgnMPKINKS 400
Cdd:cd17259    78 GGLKvARIPKSDLPAL---------------LVQrvarirpkdelnsdFLYYLLQSDFFLNYVEPVLTGTD--VPHISTK 140

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2047298907 401 ILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQ 440
Cdd:cd17259   141 QIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKLEKLQ 180

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: 46.78 E-value: 5.53e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 274 NGYSPKSTESSFITKT----LKLGAITKGYYKNDEFKYVDERIEQDSYLWL-KNGDFLIQRANSIEYVGTSAI--FTGAD 346
Cdd:cd17514    12 NGGTPSRNEPEYWNNGdipwLTSGETDDNFINNTSEKITTKNGLEDSSIRIvPKGTILIACTGQGYTRGQVAVlqIDAST 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 347 NESIYPdLIMKGKVNEtvvlnQYLVHWINSMygKQYFRqnATGTAGNMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVF 426
Cdd:cd17514    92 NQAIAA-IRCKENVNP-----KYLYYYLKTQ--KNNLR--NLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNILETLE 161

                         170       180
                  ....*....|....*....|..
gi 2047298907 427 NSDNDALNKLENYQPEIDLLIN 448
Cdd:cd17514   162 FFEKDSLRKIKETAQDINLMIN 183

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

Pssm-ID: 341170 Cd Length: 196 Bit Score: 46.82 E-value: 5.77e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2047298907 366 LNQYLVHWINSMYGKQYF-------RQNATgtAGNMPKINKSILQNLLVPIPPIEEQRVIMKVLD 423
Cdd:cd17281    99 LKKSYKNKLDIKFLFYYFfvlgewcKKNIN--IGGFPSVDMNKLKKFKIPIPPLEEQEKIVEILD 161

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: 46.68 E-value: 5.78e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  60 NHPYIRVSDFENGTINC-DGLKYISQDIQSKISRYTISKDDVYISIAGTIGKCGIIpdfldGANLTEN--AAKITDIKYS 136
Cdd:cd17243    28 DIPWFSVKDVNNDSRFVlDTEKKITELGLKNSSTKLLPKGTTIISARGTVGKLALL-----GIPMAMNqsCYGLRGKDGL 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2047298907 137 TNRYIYYVLNTEIlkNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKI----NQAKQL 204
Cdd:cd17243   103 SNYFLYYLLKNLI--EELKQKAHGSVFDTITRKTFDEIKVPLPPEELQKSFENIVSPLFDKIlnnlKENQTL 172

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: 46.27 E-value: 6.50e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 355 IMKGKVNetvVLNQYLVHWINSMYGKQYfrqnATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDcvfnsdnDALN 434
Cdd:cd17262    86 VLKGKNG---ISTEFLYYYLNSIDISPY----VTGAA--QPKLNQANLNSIPIPLPPLEEQKKIVAILD-------KLDA 149

                          90
                  ....*....|....
gi 2047298907 435 KLENYQPEIDLLIN 448
Cdd:cd17262   150 LIDLLEEELEKLIE 163

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) TRD2-CR2, and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) TRD2-CR2; The recognition sequences of Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341176 [Multi-domain] Cd Length: 184 Bit Score: 46.33 E-value: 7.33e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 365 VLNQYLVHWINSMYgkQYFRQNATGtaGNMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNsdndALNKLENYQPEID 444
Cdd:cd17287   101 INPDFLFYYLQSSY--EELRDLSNG--GGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDA----KIDALEQKLELLQ 172

                          90
                  ....*....|..
gi 2047298907 445 LLINGMLMKAFS 456
Cdd:cd17287   173 ELKKSLMQQLFT 184

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: 46.05 E-value: 8.00e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2047298907 360 VNETVVLNQYLVHWINSmYGKQYFRQNATGtaGNMPKINKSILQNLLVPIPPIEEQRVIMKVLD 423
Cdd:cd17269    77 PFKEEIDPKFLYYYLKS-YFKKYIEKNSVG--SSVPYIRLPMLENFKIPLPPLEEQKRIVRILD 137

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: 46.14 E-value: 8.25e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2047298907 134 KYSTNRYIYYVLNTeiLKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDE 207
Cdd:cd17498    89 KNGNNSFLYYLLKN--NIKNLINKSSGTVFGSINKDDIENLEVDIPEDEEQKRIANILSKIDDKIEINNQINKN 160

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: 45.62 E-value: 1.20e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 358 GKV---NETVVLNQ---------------YLVHWINSMYgkQYFRQNATGTAGnMPKINKSILQNLLVPIPPIEEQRVIM 419
Cdd:cd17516    76 GKVaitKEPSVTNQqinsiivnknkfdpdFVYYLLKNNS--KYLKSIAGGSTA-TPIINKSTFSNIEIPLPPLPEQKKIA 152

                          90       100
                  ....*....|....*....|....*..
gi 2047298907 420 KVLDCVFnsdndalNKLENYQPEIDLL 446
Cdd:cd17516   153 AILSSLD-------DKIENNRRINKTL 172

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

Pssm-ID: 341177 [Multi-domain] Cd Length: 163 Bit Score: 45.15 E-value: 1.32e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 131 TDIKYSTN-RYIYYVLNTEILKnqiknSM-KSTSQPKLALHRIQDLKLPLPPLNEQKRIADkverLLDKINQAKQLIDEA 208
Cdd:cd17288    75 TEIKKNNDpKFLYYLLKTIDFK-----KYnEATGVPSLTQTTLNKIKIPIPPLEEQQKIAS----ILDKLDAKDALIELQ 145

                          90
                  ....*....|....*...
gi 2047298907 209 KATFELRRAAILDKVFRG 226
Cdd:cd17288   146 EKLLEKLKQYKLALMQEL 163

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: 45.52 E-value: 1.40e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2047298907 365 VLNQYLVHWINSMygKQYFRQNATGTAGNMPKINKSILQNLLVPIPPIEEQRVIMKVLD 423
Cdd:cd17249   102 IDPEFLLYALKAN--EDRILSLVDKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILD 158

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: 45.59 E-value: 1.41e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 360 VNETVVLNQYLVHWINSMygKQYFRQNATGTA--GnmpkINKSILQNLLVPIPPIEEQRVIMKVLDCVFNsdndALNKLE 437
Cdd:cd17513    95 IPIKEVNPLFLAYLLYSL--LQKLKSQLQGTSikG----ITKDDLKNLKIPLPPLEEQQKIAAILSKLDK----LIEAHE 164

                          90
                  ....*....|....*...
gi 2047298907 438 NYQPEIDLLINGMLMKAF 455
Cdd:cd17513   165 KKLEKLKQLKKGLMQKLF 182

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: 45.18 E-value: 1.74e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 307 YVDERIEQDsyLWLKNGDFLI-QRANSIEYVGTSAIFTGADnesiyPDL----IMkgkvneTVV---LNQYLVHWINSMY 378
Cdd:cd17265    45 YVNSKIPEK--LIVKEGDILIcVRNGSRALIGKNALIDKEA-----EGMtfgaFM------TVFrseYNDYLFHLFNSDL 111

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 379 GKQYFRQNATGTaGNmpKINKSILQNLLVPIPPIEEQRVIMKVLDcvfnsdnDALNKLENYQPEIDLLIN 448
Cdd:cd17265   112 FKKQIGSFLTAT-IN--QITNGNLNNFKIPLPPLEEQEKIAEFLS-------SLDAKIDKLIKKIEKLIE 171

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: 44.07 E-value: 3.77e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 128 AKITDIKYSTNRYIYYVLNteILKNQI-KNSMKSTSQpklALHR--IQDLKLPLPPLNEQKRIA---DKVERLLDKINQA 201
Cdd:cd17245    84 AAIRANKDIDNLFLYYYLK--YNKPELeKLGTGSTFK---AINKkdLEELKIPLPPLEEQQKIAeilSTVDEAIEKTKAL 158


                  ....*...
gi 2047298907 202 KQLIDEAK 209
Cdd:cd17245   159 IEKLDELK 166

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: 44.32 E-value: 3.92e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 360 VNETVVLNQYLvhwinsMYGKQYFRQ---NATGTAGnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKL 436
Cdd:cd17277   100 CKDSKILPEYL------FYALKHIKQvleRLTTNPG-VKHVNLSMLSNLQIPLPPLEVQKKIVAEIEKVEKVIQGLRQKI 172

                          90
                  ....*....|..
gi 2047298907 437 ENYQPEIDLLIN 448
Cdd:cd17277   173 DEYQPLINAILD 184

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: 43.65 E-value: 3.97e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 327 IQRANSIEYVG--TSAIFTGADNESIYPDlimkgkvneTVVLNQYLVHWINSMygKQYFRQNATGTAgnMPKINKSILQN 404
Cdd:cd17291    52 SASGASAGYVNywKEPFWASDCCYILSSK---------NELVNKFLYYFLKNK--QEEIYSLQRGAG--QPHIYKKDIEK 118

                          90
                  ....*....|....*....
gi 2047298907 405 LLVPIPPIEEQRVIMKVLD 423
Cdd:cd17291   119 LKIPIPPLEEQQKIVEILD 137

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: 44.02 E-value: 4.16e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  77 DGLKYISQ------DIQSKISRyTISKDDVYISIAGTIGKCGIIpdFLDGA-NLTENAAkITDIKYSTNrYIYYVL--NT 147
Cdd:cd17286    36 DGNKYIYKtekklsEKGFKKAR-ILPKGSILVTCIGSIGKNAIA--TEDCAtNQQINAI-IPNKNYDPE-FLYYALenWS 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 148 EILKN-------QIKNsmKSTsqpklalhrIQDLKLPLPPLNEQKRIADKVERLLDKINQAKQLIDEakatFELRRAAIL 220
Cdd:cd17286   111 KKIKSlagkqavPIIN--KTE---------FSKIKILVPPLEEQQKIANFLSKLDELIELQQQKIEK----LEELKKGLL 175


                  ....
gi 2047298907 221 DKVF 224
Cdd:cd17286   176 QKLF 179

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: 44.07 E-value: 4.18e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2047298907 365 VLNQYLVHWINSMYGKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVF 426
Cdd:cd17264   102 VDVRYLYYYLNSPLGKSQIKKYDNGSA--QPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELD 161

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: 43.69 E-value: 5.41e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2047298907 365 VLNQYLVHWINSmyGKQYFRQNATGTAGNmpKINKSILQNLLVPIPPIEEQRVIMKVLD 423
Cdd:cd17497    92 LDKKYLLYYLKS--IENELSSLGTGSTFK--AISKEDLENLLIPLPPLAEQKRIAAFLD 146

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: 43.69 E-value: 5.43e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2047298907 360 VNETVVLNQYLVHWINSmYGKQYFRQNATGTAGNmpkINKSILQNLLVPIPPIEEQRVIMKVLD 423
Cdd:cd17275    99 PKDEKLDFEFLYYWLLS-LKNELKRLIRTGTQAN---LNAEIVKNLPIPLPPLEEQKKIAEILD 158

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

Pssm-ID: 341170 Cd Length: 196 Bit Score: 42.97 E-value: 1.31e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  62 PYIRVSDF-ENGTINCDGLKYISQDIQSKISryTISKDDVYISIAGTIGKCG-IIPDFLdgAN-------LTENAAKITD 132
Cdd:cd17281    33 PWFRMEDIrENGRILSDSIQHITPSAVKGGK--LFPANSIILSTTATIGEHAlITVDSL--ANqrftnfsLKKSYKNKLD 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 133 IKYstnryIYYVLNteILKNQIKNSMKSTSQPKLALHRIQDLKLPLPPLNEQKRIAdkveRLLDKI-NQAKQLIDEAKAT 211
Cdd:cd17281   109 IKF-----LFYYFF--VLGEWCKKNINIGGFPSVDMNKLKKFKIPIPPLEEQEKIV----EILDKFtKLTADLTAELPAE 177


                  ....*
gi 2047298907 212 FELRR 216
Cdd:cd17281   178 LEARK 182

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

Pssm-ID: 341165 [Multi-domain] Cd Length: 187 Bit Score: 42.57 E-value: 1.75e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 360 VNETVVLNQYLVHWINsmYGKQYFRQNATGTAGNmPKINKSILQNLLVPIPPIEEQRVIMKVLdcvfnsdNDALNKLENY 439
Cdd:cd17276    99 PNEKKVNPEFLLRYLN--FNRPYWMRVAASSRKD-PNITKDDVRNFPIPLPPLDEQRAIVEFL-------SDVDALIDSL 168


                  ....*...
gi 2047298907 440 QPEIDLLI 447
Cdd:cd17276   169 EALIEKLR 176

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

Pssm-ID: 341159 [Multi-domain] Cd Length: 183 Bit Score: 41.92 E-value: 2.48e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  62 PYIRVSDF-ENGTINCDGLKYISQDIQSKiSRYtISKDDVYISIAGTIGKCGI--IPDFLDganltENAAKITDIKYSTN 138
Cdd:cd17270    31 PFVQVADVgDNFKLVEKTKQKISKLAQPK-SVF-VPKGTVIVTLQGSIGRVAItqYDAYVD-----RTLLIFESYKININ 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 139 RYIY-YVLNTEILKNQIK---NSMKSTSQPKLAlhriqDLKLPLPPLNEQKRIAdkveRLLDKINQAKQLIDEAKATFEL 214
Cdd:cd17270   104 KKFFaYQLKLKFEIEKEKapgGTIKTITKEELS-----KFEIPIPSLEEQKEIV----NILDKFDELITELQLRKKQLEY 174


                  ....*...
gi 2047298907 215 RRAAILDK 222
Cdd:cd17270   175 YKKALLSF 182

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: 41.87 E-value: 2.68e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907  62 PYIRVSDFENGTIN------------CDGLKYISQDIQSKISRYTISKDDVYISI-----AGTIGKCGIIpdfldGANLT 124
Cdd:cd17271    14 PSRGNPEYFNGDIPwitsgelnynyiTDTNEKITEEAVKNTNLKIHPKGTFLIAItgleaAGTRGKCAIT-----GIPAT 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 125 ENAA--KITDIKYSTNRYIY--YVLNTEILKNQIknsMKSTSQPKLALHRIQDLKLPLPPLNEQKRIADKVERLLDKINQ 200
Cdd:cd17271    89 TNQScmAFYPTKKLTTEFLFywYKKYGNYLGFKY---AQGTKQQSYTADIVKKLPILLPTLKEQKKIANFLSDIDELIAT 165

                         170
                  ....*....|
gi 2047298907 201 AKQLIDEAKA 210
Cdd:cd17271   166 LEKKIEKLKK 175

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: 40.97 E-value: 4.53e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 359 KVNETVVLNQYLVHWINSmYGKQYFRQNATgtagnmPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLEN 438
Cdd:cd17255    82 KVKNKNINNKFLYYALNL-IAKKYVSFDGN------PKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIAKLKK 154


                  ..
gi 2047298907 439 YQ 440
Cdd:cd17255   155 LI 156

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: 41.03 E-value: 5.09e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 365 VLNQYLVHWINSMygKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVImkvldcvfnsdndaLNKLENYQPEID 444
Cdd:cd17290   102 INPKFLFYWLSSS--KEELENLANGAT--LPILNQEKLKNIKLPVPPLNEQQKI--------------VEFLDKKTAKID 163


                  ....
gi 2047298907 445 LLIN 448
Cdd:cd17290   164 ALIA 167

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: 40.70 E-value: 7.03e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2047298907 361 NETVVLNQYLVHWINSMYGKQYFRQNATGTAGNMPKINKsiLQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENY 439
Cdd:cd17289   103 NIKDINSKFLYYWFQSSIFKNQINSITIGSTQKALTIEK--LKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKL 179

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: 39.74 E-value: 9.36e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2047298907 383 FRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQ 440
Cdd:cd17266    96 LNQYATGSA--QPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLI 151

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: 39.65 E-value: 1.20e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 320 LKNGDFLIqraNSIEYVGTSAIFtgaDNESIYPDLIMKGKVNETVVLNQYLVHWINSMYGKQYFRQNATGTagnmPKINK 399
Cdd:pfam01420  56 LPKGDITI---SSRATIGYVFYR---DKPYYTNQHIIVLIPKNNIKITEFLYLYLLLKLKKLKSLKFGSTQ----PKLTK 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2047298907 400 SILQNLLVPIPPIEEQRVIMKVLDCVFNSD---NDALNKLEN 438
Cdd:pfam01420 126 ERLKEIKIPLPPLEEQKKIAKILSQLDNTIeleKGILNELER 167

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: 39.38 E-value: 1.25e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2047298907 383 FRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVFnsDNDALNKLEN 438
Cdd:cd17288    95 FKKYNEATG--VPSLTQTTLNKIKIPIPPLEEQQKIASILDKLD--AKDALIELQE 146

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: 39.82 E-value: 1.30e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 365 VLNQYLVHWINSMygKQYFRQNATG----TAGnMPKINKsilqnLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQ 440
Cdd:cd17248   107 LDPEYLLYVLRAM--KPEFERLAMGsthkTIY-MPDFKA-----LRIALPPLEEQRKIVDRLEALDAKIDALERKLERLI 178

                          90
                  ....*....|....*..
gi 2047298907 441 PEIDLLINGMLMKAFSG 457
Cdd:cd17248   179 ELLKELRQALLTAAVTG 195

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: 39.41 E-value: 1.60e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 365 VLNQYLVHWINSMYgkQYFRQNATGT--AGnmpkINKSILQNLLVPIPPIEEQRVIMKVLDCVFnsdnDALNKLENYQPE 442
Cdd:cd17285    99 LDPEYLLYWFLSIE--ETIESLGTGTtvKG----ITLEDLKSLKIPLPPLEEQKRIVAILDELD----ELIDKLEAKLEK 168


                  ....*....
gi 2047298907 443 IDLLINGML 451
Cdd:cd17285   169 LKQLKKGLM 177

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: 39.40 E-value: 1.73e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 376 SMYGKQYFRQNATGTAgnMPKINKSILQNLLVPIPPIEEQRVIMKVLDCVfnsDndalNKLENYQPEIDLLIN---GMLM 452
Cdd:cd17286   106 LENWSKKIKSLAGKQA--VPIINKTEFSKIKILVPPLEEQQKIANFLSKL---D----ELIELQQQKIEKLEElkkGLLQ 176


                  ...
gi 2047298907 453 KAF 455
Cdd:cd17286   177 KLF 179

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: 38.22 E-value: 4.26e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2047298907 397 INKSILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQPEIDLLING 449
Cdd:cd17244   128 LNSKKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDELLPKLMSG 180

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: 37.86 E-value: 5.15e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047298907 127 AAKITDIKYSTN--RYIYYVLNTeiLKNQIKNsmkstsqpklalHR------IQDLKLPLPPLNEQKRIAdkveRLLDKI 198
Cdd:cd17274    83 AMKILTPKNNNVnlKFVYEALQT--IKYVPGD------------HKrhwiseYSKFKIPLPPLEEQNKIV----RILDKF 144

                          90       100
                  ....*....|....*....|....*....
gi 2047298907 199 NqakQLIDEAKATFELRRA---AILDKVF 224
Cdd:cd17274   145 D---ELIAELEAKLELLKKqkkYYLQKLF 170

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: 37.47 E-value: 7.62e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2047298907 400 SILQNLLVPIPPIEEQRVIMKVLDCVFNSDNDALNKLENYQ 440
Cdd:cd17274   119 SEYSKFKIPLPPLEEQNKIVRILDKFDELIAELEAKLELLK 159