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: 245.10 E-value: 7.91e-80

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  38 LGKLGRVKGGKRLPPGHVLQEEVTSRPYIRVTDIEHNSVNYEKVKYVSEDTFNKIRNYTISKNDLFISIAGTIGRVGMIP 117
Cdd:cd17256    1 LGEIARVKGGGRLPKGESLSDGPTGVPYIRVTDIKNGGIDLDNLKYISPEIHEKIKRYTLSKGDILISIVGTIGRVGIVP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 118 ESLNGANLTENAAKITEFNSLEQKYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLF 197
Cdd:cd17256   81 KELDGANLTENAARIRPKDSISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLD 160

                        170       180
                 ....*....|....*....|.
gi 522109379 198 AKLDQAKELAQNALDSFDTRK 218
Cdd:cd17256  161 AKIDALEKQLAKLEELKKALM 181

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 153.11 E-value: 1.75e-41

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  28 EVPGNWVWTRLGKLGRVKGGKRLPPGH-VLQEEVTSRPYIRVTDIEHNSVNYEKVKYVSeDTFNKIRNYTISKNDLFISI 106
Cdd:PRK09737   5 KLPEGWVTTHISEICSVIRGVKPPKGYaTKSLTMGDLPFIRTTDITNGAVDLTTLPYCM-DAPEDVSKYQLQDRDIVISS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 107 AGTIGRVGMIPESL-NGANLTENAAKITEFNSLEQKYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAE 185
Cdd:PRK09737  84 AGSIGFSFLAQNPLpSNVVFASFAIRLKPVNYFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAE 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 186 QQRIVDRIESLFAKLDQAK---ELAQNALDSFdtrKAAILHKAFTGELTAKWREEHgvGMDSWVKKTFNQVADIKSN-LV 261
Cdd:PRK09737 164 QKIIAEKLDTLLAQVDSTKarlEQIPQILKRF---RQAVLGAAVSGKLTEEWRWPD--LPSTWSVHKYSELVDSRLGgMS 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 262 DPSSYMDNPHIAPDNIERRTGR--LLEYRTIREDGVTSGKHKFSKGQILYSKI-RPYLSKVVLV-----DFNGLCSADMY 333
Cdd:PRK09737 239 SKANNFGSATPYLRNINVRWGSfdLEDLQDILISDIERRELKLKLGDVLFCRGnEPLEVGRCAIwkepqDIPVIYQKALI 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 334 PIEAKEDT--KYLWYYMLSDEFLEQASSAGSRSVLPK-INQKELSAVKVMIPSWNEQREVVRILDNLL--AREIEtKDLA 408
Cdd:PRK09737 319 RARVKDDIipEYLVYNLKSPDSRNISLSQLFTGTTQKhITGKALANYPIRVPPLEEQAEIVRRVEQLFayADTIE-KQVN 397

                        410       420
                 ....*....|....*....|..
gi 522109379 409 NVIDHIEVMKKSILARAFRGVL 430
Cdd:PRK09737 398 NALARVNNLTQSILAKAFRGEL 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: 136.50 E-value: 5.31e-38

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLGKL------GRVKGGKRLPPGHvlqeevtsrPYIRVTDIEHNSVNYEKVKYVSEDTFNKIR-NYTISKNDLFIS 105
Cdd:cd17246    1 WEWVKLGEIssditdGTHPTPKYVESGI---------PFITSKNIKNGKIDFSDVKYISEEDHNEILkRSKLKKGDILFS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 106 IAGTIGRVGMIPESLNgANLTENAAKITEFNS-LEQKYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIA 184
Cdd:cd17246   72 IIGTIGRVAIVPEDLP-ANINQAVALIRPKKEkIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLE 150

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 522109379 185 EQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17246  151 EQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLL 188

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: 123.00 E-value: 6.97e-33

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLGKLGRVKGG---KRlppghvlqEEVTSRPY--IRVTDIEHNSVNYEKVKYVSEDTFNKIRNYTISKNDLFISI- 106
Cdd:cd17278    1 WEVVKLGDIADIQNGyafKS--------SDFSDEGIpvIRIGNIKNGGIDLDDNSKYPEEPLEKYEKFLLKKGDILIAMt 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 107 AGTIGRVGMIPESLNGANLTENAAKITEFNSLEQKYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQ 186
Cdd:cd17278   73 GGTVGKVAIVPEDDEPALLNQRVGKFRPKDKIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQ 152

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 522109379 187 QRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17278  153 KKIAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLF 188

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: 107.08 E-value: 3.89e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  37 RLGKLGRVKGGKRLPPGHVLQEEVTsRPYIRVTDIEHNSVNYEKVkYVSEDTFNKIRNYTISKNDLFISIAGTIGRVGMI 116
Cdd:cd16961    2 KLGEIAEIISGKTPSSSSEYWDNGI-IPWIRISDINNGGIILTDE-KITEEGAEKLKKKILPKGDILISRSGTIGKVAIV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 117 PESLNGAnLTENAAKITEFNSLEQKYLMYLLLSNDLQNQIKqSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESL 196
Cdd:cd16961   80 KENDKAL-LNQAVIVIRPKDEVDSEFLYYFLKSPFGKKLIE-GSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKL 157

                        170
                 ....*....|....*.
gi 522109379 197 FAKLDQAKELAQNALD 212
Cdd:cd16961  158 DALIELLEQKLEKLEQ 173

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: 100.71 E-value: 8.84e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLGKLGRVKGGKRLPPGHVLQEEVTSR-PYIRVTDIEHNSVNYEKVKYVSEDTFNKirNYTISKNDLFISIA-GT- 109
Cdd:cd17252    1 WEWVRLGEIAEIIRGVTYKKSDASEEPSEGGiPVLRANNIQNGGLDFDDLVYVPKSKVKE--EQKLKKGDILICMSsGSk 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 110 --IGRVGMIPESLN---GANLtenaAKITEFNSLEQKYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIA 184
Cdd:cd17252   79 elVGKAAFIDEDTDytfGAFC----GVIRPKKEIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPLA 154

                        170       180
                 ....*....|....*....|....*...
gi 522109379 185 EQQRIVDRIESLFAKLDQAKELAQNALD 212
Cdd:cd17252  155 EQKRIVAKLDKLDALIDKLKQALEKLDE 182

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: 100.41 E-value: 1.40e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLGKLGRVKGGKRlppghVLQEEVTSR--PYIRVTDIEHNSvNYEKVK---YVSEDTFNKIRNY--TISKNDLFIS 105
Cdd:cd17289    1 WEWKKLGDIAEITSSKR-----IFKSEYVDSgiPFYRSKEIIELF-NGEEIStelFISEERYEEIKSKygVPKKGDILIT 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 106 IAGTIGRVGMIPES----LNGANLTEnaakITEFNSLEQKYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLP 181
Cdd:cd17289   75 SVGTIGIPYLVKNDdpfyFKDGNLTW----FKNIKDINSKFLYYWFQSSIFKNQINSITIGSTQKALTIEKLKKTKIPLP 150

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 522109379 182 PIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTR 217
Cdd:cd17289  151 PLEEQKKIVSILSALDEKIDLNKKQLQKLEELAKTL 186

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: 97.53 E-value: 1.09e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  36 TRLGKLGRVKGGKRlPP--------GHVlqeevtsrPYIRVTDIEHNSVNYEKVKYVSEDTFNKIRnyTISKNDLFIS-I 106
Cdd:cd17293    1 VKLGELGEVVTGNT-PSkknpeyygGDI--------PFIKPDDLNNGGIILTSEEYLSEEGAKKAR--IVPKGSILVTcI 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 107 AGTIGRVGMIPESLnGANLTENAakITEFNSLEQKYLMYLLLSNDLQNQIKQStiATTQAKLALNRIENLVLPLPPIAEQ 186
Cdd:cd17293   70 GGSIGKVGIADREV-AFNQQINA--IIPNKSVDPKFLYYQLLSSKFQLQAIAS--STTLPIINKSKFEKIEIPLPPLEEQ 144

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 522109379 187 QRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17293  145 KRIVAKLDKLFALIDKLEESLEELDELLKSLFQSAF 180

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: 96.07 E-value: 3.51e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNYEKVKYVSEDTFNKIRNYTISKNDLFISIAGTIGRVGMIPESLNGANltenAAK---ITEFNSLEQ 140
Cdd:cd17264   29 PFINAGHLEDGTIDLSNMNFISEEKYNSLGSGKLQKGDILYCLRGSLGKCAIVDNYDEGAI----ASSlviIRPFAKVDV 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 141 KYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAA 220
Cdd:cd17264  105 RYLYYYLNSPLGKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQSLFQS 184

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: 94.14 E-value: 2.26e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLGKL-GRVKGGKRLPPghvlQEEVTSRPYIRVTDIEHNSVNYEKVKYVSEDTfNKIRNYTISKNDLFISIAGTIG 111
Cdd:cd17261    1 WEWVRLGDLiEGIRNGWSPKP----PDDETGWPVLKLSAVTSGKFDPSENKYLPESL-EPASEYWLKPGDLLISRANTSE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 112 RVG------------MIPESLNGANLTENAAKitefnsleQKYLMYLLLSNDLQNQIKQ--STIATTQAKLALNRIENLV 177
Cdd:cd17261   76 LVGraalvdgdpdnlIYPDKLIRLRVNEELLL--------PEYLALALNSPSARRQIESraTGTAGSMPKISQSDLKSLP 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 522109379 178 LPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAI 221
Cdd:cd17261  148 IPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191

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: 92.96 E-value: 4.88e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLGKLGRVKGGKRLPPGHVLQEEVtsrPYIRVTDIEHNSVNYEKVKYVSEDTFNKIRNYTISKNDLFISIAGTIG- 111
Cdd:cd17259    1 WEWVKLGDVADILSGYAFKSSEFSESGI---RLLRGANVGVGEIRWDDTVYLPEEYLEEYEKYLLKEGDIVIALDRPIIs 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 112 ---RVGMIPESLNGANLTENAAKITEFNSLEQKYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQR 188
Cdd:cd17259   78 gglKVARIPKSDLPALLVQRVARIRPKDELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEEQKK 157

                        170       180
                 ....*....|....*....|....
gi 522109379 189 IVDRIESLFAKLDQAKELAQNALD 212
Cdd:cd17259  158 IAEFLSSLDALIDLLEQKLEKLQQ 181

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: 91.39 E-value: 1.97e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  65 YIRVTDIEHNSVNYEKVKYVSEDTfNKIRNYTISKNDLFIS-IAGTIGRVGMIPESLnganltENA--------AKITEf 135
Cdd:cd17521   30 YLRITDIQDDGVLWDTVPYCSISE-EDAEKYLLKDGDILFArTGATVGKSYLYKEDD------GKAvfasylirFRPNK- 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 136 NSLEQKYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFD 215
Cdd:cd17521  102 KKVLPKYLFYFTQSSLYWKQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLK 181


                 ....*.
gi 522109379 216 TRKAAI 221
Cdd:cd17521  182 ELLQSL 187

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: 86.51 E-value: 1.09e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  63 RPYIRVTDIEHNSVNYEKVKYVSEDTFNKIRNYTISKNDLFISIAG--------TIGRVGMIPESLNGANLTENAAKITE 134
Cdd:cd17512   28 IRIVRVSDFTDDSIDINNLVYISEEKANKYKKYELKENDIIITTVGswpsnpdsVVGKVVRVPKEADGALLNQNAVKIRP 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 135 FNS-LEQKYLMYLLLSNDLQNQIkqSTIA---TTQAKLALNRIENLVLPLPPIAEQQRI------VDR-IESLFAKLDQA 203
Cdd:cd17512  108 KKGiLDQSFLFYNLKSERFKNYI--ESIArgnANQASITLGDIKKFKFLLPPLEEQKKIasilsaYDDlIENNEKRIKLL 185


                 ....*.
gi 522109379 204 KELAQN 209
Cdd:cd17512  186 EQMKQA 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: 86.05 E-value: 1.48e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLGKL-GRVKGGKRLPPGhvlqEEVTSRPYIRVTDIEHNSVNYEKVKYVSEDTFNKIRNYTISKNDLFI----SIA 107
Cdd:cd17517    1 WEVVKLGDLlEDPRYGTSKKSS----YDGSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKELEKYLLKKGDILFnrsnGSP 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 108 GTIGRVGMIPESLNGA----NLTenAAKITEfNSLEQKYLMYLLLSNDLQNQIKQ-STIATTQAKLALNRIENLVLPLPP 182
Cdd:cd17517   77 ELVGKCALVDEEDEPAifasYLI--RLRLDK-KKILPEFLYYYLNSPLGRKQIEKiAKSAAGQANINQKDLKKLPIPLPP 153

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 522109379 183 IAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAI 221
Cdd:cd17517  154 LEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192

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: 84.86 E-value: 3.43e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  36 TRLGKLGRVKGGKRlPPGHVLQEEVTSR--PYIRVTDIEHNSVNyekvKYVSEDTFNKIrnytISKNDLFI----SIAGT 109
Cdd:cd17263    1 VKLGEVCKFSKGKQ-PPISERFDEPKEGsvRYIQIEDLRNNNEK----KYIENPKKSVI----CNEDDILIvrdgANAGE 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 110 IGRvgmipeSLNGAnLTENAAKITEFNS-LEQKYLMYLLLSNDLQNQIkQSTIATTQAKLALNRIENLVLPLPPIAEQQR 188
Cdd:cd17263   72 VGT------GLEGA-IASTLFKIIPDKNiIDKDYLYYFLKSKEIQLNI-LTKAGSTIPHVNKKDLENLKIPLPSLEEQKK 143

                        170       180
                 ....*....|....*....|..
gi 522109379 189 IVDRIESLFAKLDQAKELAQNA 210
Cdd:cd17263  144 IAEILDKLDALIDKLKELIEKL 165

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 78.95 E-value: 3.90e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 145 YLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLdqakELAQNALDSFDTRKAAILHK 224
Cdd:COG0732    4 YYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKI----AALEKEIEKLKELRDALLPK 79


                 ....*.
gi 522109379 225 AFTGEL 230
Cdd:COG0732   80 LFTGEL 85

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: 81.75 E-value: 5.99e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  32 NWVWTRLGKLGRVKGGKRLPPGHVLQEevTSRPYIRVTDIEHNSVNYEKVKY--VSEDTFNKirnYTISKNDLFISIAG- 108
Cdd:cd17253    1 GWEWVRLGDVAEVQSGITKGKKRRGGE--LEVPYLRVANVQDGYLDLSEVKEieVTEEELER---YRLRKGDLLVTEGGd 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 109 --TIGRV----GMIPESLNganltEN---AAKITEfNSLEQKYLMYLLLSNDLQNQI----KQST-IATtqakLALNRIE 174
Cdd:cd17253   76 sdKLGRGaiwrGEIPPCLH-----QNhlfRVRPKD-DLLLPEFLSYWLNSAYGRGYFlraaKQTTnLAS----INSTKLK 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 522109379 175 NLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17253  146 ALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193

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: 76.13 E-value: 4.09e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  36 TRLGKLGRVKGGKRLPPGHVLQEEvTSRPYIRVTDIEhNSVNYEKVK----YVSEDTFNKIRNYTISKND-LFISIAGTI 110
Cdd:cd17250    1 VRLGDVCDFKAGSGFPEKYQGKED-GEYPFYKVGDMN-NSGNEKYLStaenYISEEIVKELKAKLFPKGTiIFAKIGEAI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 111 --GRVGMIPESLNGANlteNAAKITEFNSLEQKYLMYLLLSNDLqnqiKQSTIATTQAKLALNRIENLVLPLPPIAEQQR 188
Cdd:cd17250   79 klNRRAILSKDSCIDN---NVMGLIPNEGIDSEYLYYWLKKVDL----YKYSQATTVPSIRKSTLESIPIPLPPLEEQKR 151

                        170       180       190
                 ....*....|....*....|....*....|....
gi 522109379 189 IVDRIESLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17250  152 IAAKLDELFEKLDKLKQALEAAKEQLKGLRQSLL 185

type I restriction-modification system specificity subunit;

Pssm-ID: 236619 [Multi-domain] Cd Length: 461 Bit Score: 79.54 E-value: 6.64e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNYEKVKYVSEDTFnKIRNYTISKNDLFISIAG---TIGRVGMIPESLNGANLTENA---AKITEfnS 137
Cdd:PRK09737 249 PYLRNINVRWGSFDLEDLQDILISDI-ERRELKLKLGDVLFCRGNeplEVGRCAIWKEPQDIPVIYQKAlirARVKD--D 325

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 138 LEQKYLMYLLlSNDLQNQIKQSTIAT--TQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFD 215
Cdd:PRK09737 326 IIPEYLVYNL-KSPDSRNISLSQLFTgtTQKHITGKALANYPIRVPPLEEQAEIVRRVEQLFAYADTIEKQVNNALARVN 404

                        170       180
                 ....*....|....*....|..
gi 522109379 216 TRKAAILHKAFTGELTAKWREE 237
Cdd:PRK09737 405 NLTQSILAKAFRGELTAQWRAE 426

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: 75.33 E-value: 7.74e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNyEKVKYVSEDTFNKIRNYTISKNDLFISIAGTIGRVGM--IPESLNganltENAAKITEFN-SLEQ 140
Cdd:cd17296   29 PWVKISDCKNKYVD-ETEEFITEEGLNNSSAKLLKKGTILIAIFATIGKVGIlkIEATTN-----QAIAGIKPKNkSINP 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 141 KYLMYLLLSndLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAA 220
Cdd:cd17296  103 KYLYYYLKS--LYEKFLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKFEKLINKRQEGLQLLDELVKSLFEE 180


                 ..
gi 522109379 221 IL 222
Cdd:cd17296  181 MF 182

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: 74.40 E-value: 1.96e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  99 KNDLFISIAGTIGRVGMI------PESLNGANLTENAAKItefnsleqKYLMYLLLSndLQNQIKQSTIATTQAKLALNR 172
Cdd:cd17282   67 KGTLCITIAANIGDTAILgfdacfPDSVVGFIPNEEKIDV--------EFLEYYLRT--LKKELEAIAPQSAQKNINLEI 136

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 522109379 173 IENLVLPLPPIAEQQRIVDRIEslfaKLDQAKELAQNALDSFDTRKAAILHKAF 226
Cdd:cd17282  137 LRPLKIPVPPLEEQKKIVEILD----ALDDLIDNLEKRIAKLEELKQSLLQEAF 186

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: 73.33 E-value: 4.39e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 136 NSLEQKYLMYLLLS--NDLQNQIKQSTIATtqakLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDS 213
Cdd:cd17248  105 PELDPEYLLYVLRAmkPEFERLAMGSTHKT----IYMPDFKALRIALPPLEEQRKIVDRLEALDAKIDALERKLERLIEL 180

                         90
                 ....*....|....*.
gi 522109379 214 FDTRKAAILHKAFTGE 229
Cdd:cd17248  181 LKELRQALLTAAVTGK 196

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: 72.39 E-value: 6.37e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379   30 PGNWVWTRLGKLGRVKGGKRLPPGHVLQEEVTsrPYIRVTDIEHNSVNYEkvkyvsedtfNKIRNYTISKNDLFISIAGT 109
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELKNNGKY--PYIRAGDLNNVVKGGL----------GYIKKYILPKGDITISSRAT 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  110 IGRVGMIPESLNGAN-LTENAAKItefNSLEQKYLMYLLLSndLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQR 188
Cdd:pfam01420  69 IGYVFYRDKPYYTNQhIIVLIPKN---NIKITEFLYLYLLL--KLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKK 143

                         170
                  ....*....|...
gi 522109379  189 IVDRIESLFAKLD 201
Cdd:pfam01420 144 IAKILSQLDNTIE 156

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: 72.58 E-value: 6.37e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEH-NSVNYEKVKYVSEDTFNKIRNYTISKNDLFISIAGTIGRVgmipeSLNGANLTENAA---KITEFNSLE 139
Cdd:cd17275   31 PFVKISDMTKsGKYIYSTEKYITEEGLKNSSAWIVPKGTILYAMYASVGKV-----AINKIDVATNQAilgIIPKDEKLD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 140 QKYLMYLLLSndLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDriesLFAKLDQAKELAQNALDSFDTRKA 219
Cdd:cd17275  106 FEFLYYWLLS--LKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIAE----ILDKIDAEIDKLEEKIEKLRELKK 179


                 ....*..
gi 522109379 220 AILHKAF 226
Cdd:cd17275  180 GLLQKMF 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: 71.36 E-value: 1.61e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNYEKVK-YVSEDTFNKIRnyTISKNDLFISIAGTIGRvgmipeslnganltenaAKITEF------- 135
Cdd:cd17283   30 PWIKIGDVTKDGKYITKTKeKITEEGAKKSR--LVKPGDLILSNSMSFGR-----------------PYILKIdgcihdg 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 136 --------NSLEQKYLMYLLLSNDLQNQiKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELA 207
Cdd:cd17283   91 wlvfsdlkKKLDKDFLYYLLSSITVQLQ-FSAQAGGGTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKL 169


                 ..
gi 522109379 208 QN 209
Cdd:cd17283  170 EK 171

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: 70.54 E-value: 3.96e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNYekvKYVSEDTFNKIRNYTISKNDLFISIAGTIGRVGMIPEsLNGANLTENAA--KITEfNSLEQK 141
Cdd:cd17272   29 PVITSKNISNGKIDF---EYVKYDFLSISKNRKINKGDILITMIGTIGETAIVKC-LDPKFYTLNLYliRLKK-EKLLPS 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 522109379 142 YLMYLLLSNDLQNqiKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIV---DRIESL 196
Cdd:cd17272  104 YLKYFLDSEKFLN--KSISATSGQGYLKANQIDKLEIPLPPLEEQQRIVkilDKFDTL 159

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: 70.32 E-value: 3.97e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNYEK-VKYVSEDTFNKIRNYTISKNDLFISIAGTIGRVgmipeSLNGANLTENAAKI--TEFNSLEQ 140
Cdd:cd17284   31 PWITIEDIKGKYISSSKsGLGVSEEEIKEMNLKVIPKGSVIMSCVGDFGIV-----AIATNELVINQQLHafVPSKKINP 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 141 KYLMYLL--LSNDLQNQIKQSTIattqakLALNR--IENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDT 216
Cdd:cd17284  106 EYLMYLLslQKKYMEKIATGTTI------PYLNKtnCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKG 179


                 ....*.
gi 522109379 217 RKAAIL 222
Cdd:cd17284  180 LMQQLF 185

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: 70.27 E-value: 4.12e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 130 AKITEFNSLEQKYLMYLLLSndLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQN 209
Cdd:cd17497   84 AAIRPKKGLDKKYLLYYLKS--IENELSSLGTGSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDELTAKIDQLIALLEK 161

                         90
                 ....*....|...
gi 522109379 210 ALDSFDTRKAAIL 222
Cdd:cd17497  162 AIELLKEYRQAVL 174

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: 68.67 E-value: 1.54e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  69 TDIEHNSVNYEKVKYVSEDTFNKIRnyTISKND-LFISIaGTIGRVGMIPESLnGANLTENAakITEFNSLEQKYLMYLL 147
Cdd:cd17286   33 TDIDGNKYIYKTEKKLSEKGFKKAR--ILPKGSiLVTCI-GSIGKNAIATEDC-ATNQQINA--IIPNKNYDPEFLYYAL 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 148 LSNdlQNQIKqsTIATTQAKLALNR--IENLVLPLPPIAEQQRIVDriesLFAKLDQAKELAQNALDSFDTRKAAILHKA 225
Cdd:cd17286  107 ENW--SKKIK--SLAGKQAVPIINKteFSKIKILVPPLEEQQKIAN----FLSKLDELIELQQQKIEKLEELKKGLLQKL 178


                 .
gi 522109379 226 F 226
Cdd:cd17286  179 F 179

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: 68.20 E-value: 2.05e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNYEKVKYVSEdtFNKIRNYTISKNDLFISIAGTIGRVGMIpeSLNGANLTENAAKITEF-NSLEQKY 142
Cdd:cd17258   18 KLVCIKNELINSLKVKIVEPDYK--IGLKQSKIFKKGDVLITRHGTIGRVSII--LSEEACLSSHVAGFNSKeGISDNKF 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 143 LMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDriesLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17258   94 IKYLFNSKKIKNRLMSYGASSTQPALNLSRLLKIKFPNPPLEEQQKIGK----ILSTWDRAIELTEQKLELLQQQKKGLM 169


                 ....
gi 522109379 223 HKAF 226
Cdd:cd17258  170 QQLF 173

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: 68.41 E-value: 2.19e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLG------KLGRVKGGkrlppghvlQEEVTSRPYIRVTDIEHNSVNYEKV-KYVSEdTFNKIRNYTISKNDLFIS 105
Cdd:cd17525    1 WEWVKLGdilsstQLGLVRSN---------SEDPNGYPYIKMGNIGRGGINLLKVeTYVDA-TELEVEKYLLEDGDLLFN 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 106 IAGT---IGRVGMIPESLNGANLTENAAKITEFNSLEQKYLMYLLLSNDLQNQIKQSTIATTQ-AKLALNRIENLVLPLP 181
Cdd:cd17525   71 TRNTlelVGKVAIWRGELPKALFNNNILRIRFDDIVLPYFINYYLNSPDGKKQLESIASGTTSvAAIYQKDLKKLKLPLP 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 522109379 182 PIAEQQRIVDRIESLFAKLDQAKELAQNALDsfdtRKAAILHKA 225
Cdd:cd17525  151 PLDEQREIVSFLSELDAKIDQLEQKLEKLLQ----IKKALMQQL 190

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: 68.33 E-value: 2.62e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLGK-LGRVKGGKrlppgHVLQEEvtSRPYIRVTDIE---HNSVNYEKVKYVsEDTFNKIRNYTISKNDLFIS-IA 107
Cdd:cd17522    1 WKVVKLGDvLEEIRNGT-----TVKQNK--EGGGYPVTRIEtisNGTIDLNRVGYA-ITNEEKIEKYKLQKGDILFShIN 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 108 GT--IGRVGMI---PESL-NGANLTENAAKITEFNSleqKYLMYLLLSNDLQNQIKQ-STIATTQAKLALNRIENLVLPL 180
Cdd:cd17522   73 SIehIGKTAIYdgdPEPLiHGMNLLRLRPNKNIVDP---KYLYYLLKSDRFRNQFRSiAKKAVNQASINQTELKKIKIPL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 522109379 181 PPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAI 221
Cdd:cd17522  150 PPLEEQQKIASILEKLDKKIEKRKEKIEKLKELKKGLFQKL 190

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: 67.09 E-value: 3.43e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 110 IGRVG-------MIPESlngANLTENAAKITEFNSLEQKYLMYLLLSNDLqNQIKQSTiatTQAKLALNRIENLVLPLPP 182
Cdd:cd17266   50 IGRVGalcgnvhYVEGK---FWVTDNALVVTPKKENNIKFLYYLLKSLNL-NQYATGS---AQPLITVSKLKKLKIPLPP 122

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 522109379 183 IAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRK 218
Cdd:cd17266  123 LEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKELM 158

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: 67.33 E-value: 5.15e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNYEKVKYVSEDTFNK-IRNYTISKNDLFISIAG-TIGRVGMipeslngaNLTENA----AKITEF-- 135
Cdd:cd17519   28 PIIRITNIQNGKIDTDNLKYFDLNDYKEnLDKYIVRPGDIVIAMSGaTTGKVGI--------NLTDQEfylnQRVGKFip 99

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 522109379 136 --NSLEQKYLMYLLLSNDLqnqIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESL 196
Cdd:cd17519  100 neEILNNRYLYHFLLSKQN---EKYILAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILDKF 159

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: 67.07 E-value: 5.48e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  97 ISKNDLFISIAG-TIGRVGM--IPESLNGAnltenAAKITEFNSLEQKYLMYLLLS--NDLQNQIKQSTiattQAKLALN 171
Cdd:cd17515   60 FPKGSVLIAMYGaTAGKVGIlgIDAATNQA-----ICAILPNEEIDNEFLFYFLKSqkEYLISLGKGGA----QPNISQG 130

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 522109379 172 RIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKElaqnALDSFDTRKAAILHKAF 226
Cdd:cd17515  131 IIKNIEIPLPPLAEQKRIVAKLDKLDKLIEKLEK----ALEKLEELKKALMQKLL 181

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: 66.62 E-value: 7.04e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  66 IRVTDIEHNSVNYEKV-KYVSEDTFN-KIRNYTISKNDLFISIAGTI-GRVGMIPESLNGANLTENAAKITEFNS-LEQK 141
Cdd:cd17518   28 LNVTNIVNGSLDLDKTdRYISTEEYNgKYKHFLIDEGDILIASSGNSwGKVAIVEKDHLPLMLNTSTIRFKFIDGlLDNN 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 522109379 142 YLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALD 212
Cdd:cd17518  108 FLKYFLNSDYFKEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEAALEALRKKKQ 178

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: 65.60 E-value: 1.34e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  99 KNDLFISIAG-TIGRvgmipesLNGANlTENA-----AKITEFNSLEQKYLMYLLLSNdlQNQIKQSTIATTQAKLALNR 172
Cdd:cd17496   56 KGDILFCVRGsTTGR-------LNIAD-DEYCigrgvAAIRPKNGIDTEFLYYLLESN--LDYLLAAATGSTFPNISRDD 125

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 522109379 173 IENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17496  126 LLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTLLPKLL 175

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: 63.94 E-value: 6.36e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 248 KTFNQVADIKS--NLVDPSSYMDN---PHIAPDNIERRTGRLLEYRTIREDGVTSGKHKFSKGQILYSKIRPyLSKVVLV 322
Cdd:cd16961    1 KKLGEIAEIISgkTPSSSSEYWDNgiiPWIRISDINNGGIILTDEKITEEGAEKLKKKILPKGDILISRSGT-IGKVAIV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 323 DFN--GLCSADMYPIEAKE--DTKYLWYYMLSDEFLEQASSAGSrSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLL 398
Cdd:cd16961   80 KENdkALLNQAVIVIRPKDevDSEFLYYFLKSPFGKKLIEGSAG-STQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLD 158


                 ..
gi 522109379 399 AR 400
Cdd:cd16961  159 AL 160

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: 63.63 E-value: 6.61e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 131 KITEFNSLEQKYLMYLLLsNDLQNQIKQSTIAT----TQAKLalnriENLVLPLPPIAEQQRIVDRIESLFAKLDQAKEL 206
Cdd:cd17254   84 KVVPDEEIDKDYLYYLLK-ALTEEIESQAHGSTmvhiTKGDL-----ENIKVPLPPLEEQKRIAAILDELDALIDALEEQ 157

                         90
                 ....*....|....*.
gi 522109379 207 AQNALDSFDTRKAAIL 222
Cdd:cd17254  158 LKKLEELRKALLQSLL 173

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: 64.01 E-value: 7.32e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 142 YLMYLLLSNdlQNQIKQ--STIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKA 219
Cdd:cd17249  106 FLLYALKAN--EDRILSlvDKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEELLKALMQ 183


                 ..
gi 522109379 220 AI 221
Cdd:cd17249  184 AL 185

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: 63.40 E-value: 1.02e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  97 ISKNDLFISIAGTIGRVGMIPESLN-GANLtenaAKITEFNSLEQKYLMYLLLSNdlQNQIKQSTIATTQAKLALNRIEN 175
Cdd:cd17499   55 AEKNDILMSVRAPVGDVNITTRKICiGRGL----AAIRAKKNIDKKYLFYFLLSN--KDYFKGKSGGSTFKSINKNQIKN 128

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 522109379 176 LVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNAL 211
Cdd:cd17499  129 IKIPLPPLEEQKRIVSELDKLFKLIFEAKNNIEEAL 164

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: 62.07 E-value: 1.92e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 133 TEF------NSLEQKYLMYLLLSNDLQNQIKQSTIATT-QAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKE 205
Cdd:cd17260   69 TEFhvlrpkEGILPEFLYYLLRSPSFRKEAIKSMTGSSgRQRVPKDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEA 148

                         90
                 ....*....|....*..
gi 522109379 206 LAQNALDSFDTRKAAIL 222
Cdd:cd17260  149 EIETLEELLDALLPKLL 165

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: 62.12 E-value: 2.69e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 109 TIGRVGM--IPESLNGANltenaAKITEFNSLEQKYLMYLLLSNdlQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQ 186
Cdd:cd17287   75 TRGRVAIlgIEAATNQAC-----AAILPNDGINPDFLFYYLQSS--YEELRDLSNGGGQPNLNAGLIKSIEIPVPPLDEQ 147

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 522109379 187 QRIVDRIESLFAKLDQAKElaqnALDSFDTRKAAILHKAFT 227
Cdd:cd17287  148 QKIAAFLSAIDAKIDALEQ----KLELLQELKKSLMQQLFT 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; 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: 61.78 E-value: 4.79e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 129 AAKITEFNSLEQKYLMYLLLSN-DLQNQIKQSTiattqAKLALN--RIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKE 205
Cdd:cd17247  100 AAIRPNEERVLPEYLHYYLESQyDELRRIGSGG-----GQGALNcgILKAFPIPLPPLDEQREIVAELEALLAKIDLLEE 174

                         90
                 ....*....|....*.
gi 522109379 206 LAQNALDSFDTRKAAI 221
Cdd:cd17247  175 KIARLIELLKELRQAL 190

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: 61.33 E-value: 4.94e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  82 KYVSEDTFNKIRNYTISKNDLFISIAGTIGRVGMIpeslnGANLTENAAkITEF----NSLEQKYLMYLLLSNDLQNQIK 157
Cdd:cd17244   47 EYITDEAVKKFNVKLVPKGTLLMSFKLTIGRVAIA-----GKDLYTNEA-IAHFipkdKKIDTEYLYYYLKSFDYSSLGS 120

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 522109379 158 QSTIATTqaklaLN--RIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQ 208
Cdd:cd17244  121 TASKGKT-----LNskKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIE 168

Restriction endonuclease S subunit [Defense mechanisms];

Pssm-ID: 440496 [Multi-domain] Cd Length: 88 Bit Score: 58.53 E-value: 5.66e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 346 YYMLSDEFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAReieTKDLANVIDHIEVMKKSILARA 425
Cdd:COG0732    4 YYLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDK---IAALEKEIEKLKELRDALLPKL 80


                 ...
gi 522109379 426 FRG 428
Cdd:COG0732   81 FTG 83

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: 61.31 E-value: 6.36e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  33 WVWTRLGKLGRVKGGKRLPPGHVLQEEVtsrPYIRVTDI--EHNSVNYEKVKYVSEDTFNKIRnyTISKNDLFISIAG-T 109
Cdd:cd17268    1 VEWKTLGEIGEFIRGKGITKKDFVESGV---PCIHYGEIytKYGIYTTKTKSFISEELAKKLR--KAKPGDLLIAGTGeT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 110 IGRVGMipeslNGANL-TENAA---KITEF-NSLEQKYLMYLLLSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIA 184
Cdd:cd17268   76 IEDIGK-----AVAWLgDEEVAaggDIIIFrHSQNPKYLSYLLNSPAFQKQKRKLGTGTKVVHISASDLAKIKIPVPPLE 150

                        170       180
                 ....*....|....*....|....*.
gi 522109379 185 EQQRIV---DRIESLFAKLDqaKELA 207
Cdd:cd17268  151 EQERIVeilDKFDALIAGLP--AEIE 174

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: 60.73 E-value: 9.51e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 289 TIREDGVTSGKHK-FSKGQILYSKI--------RPYLSKVVLVDFNglCSAdMYPIEaKEDTKYLWYYMLSDEFLEQASS 359
Cdd:cd17250   50 YISEEIVKELKAKlFPKGTIIFAKIgeaiklnrRAILSKDSCIDNN--VMG-LIPNE-GIDSEYLYYWLKKVDLYKYSQA 125

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 522109379 360 agsrSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAR-EIETKDLANVIDHIEVMKKSIL 422
Cdd:cd17250  126 ----TTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKlDKLKQALEAAKEQLKGLRQSLL 185

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: 58.95 E-value: 2.20e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 132 ITEFNSLEQKYLMYLLLSNDLQNQIKQSTIATtqaklaLNR--IENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQN 209
Cdd:cd17267   74 VKDFKGNDPRFLYYLLKTLDLERLNSGSAVPG------LNRndVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQT 147


                 ....*..
gi 522109379 210 ALDSFDT 216
Cdd:cd17267  148 LEELADA 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, 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: 59.49 E-value: 2.35e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNYEKVKYVSEDTFNKIRNYTISKNDLFISIAGTIGRVGMIPESLNGANLTENAAKITEFNSLEQKYL 143
Cdd:cd17514   30 PWLTSGETDDNFINNTSEKITTKNGLEDSSIRIVPKGTILIACTGQGYTRGQVAVLQIDASTNQAIAAIRCKENVNPKYL 109

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 522109379 144 MYLLLSndLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESL-FAKLDQAKELAQNALDSF 214
Cdd:cd17514  110 YYYLKT--QKNNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNILETLeFFEKDSLRKIKETAQDIN 179

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: 59.56 E-value: 2.84e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  66 IRVTDIEHNSVNYEKVKYVSEDTfNKIRNYTISKND-LFISIAGTIGRVGmipeSLNGANLTENAAKITEF-------NS 137
Cdd:cd17523   31 LRLADIKNNKISFENLRRIKLTE-KEIEKYSLSKGDlLIIRVNGSPDLVG----RFILFKGYEDVAYCDHFirmrldqEK 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 522109379 138 LEQKYLMYLLLSNDLQNQIKQSTIATT-QAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNAL 211
Cdd:cd17523  106 IDPEFLSYIFNSPLIRRKIERNFVTSAgQKTVNQGHIKSLPIPLPPLKEQKKIVARVEELFALIDQLESSLDLAQ 180

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: 59.06 E-value: 3.13e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 136 NSLEQKYLMYLLLSNDlQNQIKQSTIATTQAkLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFD 215
Cdd:cd17285   97 DELDPEYLLYWFLSIE-ETIESLGTGTTVKG-ITLEDLKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEKLKQLKK 174


                 ....*..
gi 522109379 216 TRKAAIL 222
Cdd:cd17285  175 GLMQSLL 181

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: 59.10 E-value: 3.85e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  86 EDTFNKIRNYTIS---------KNDLFISIAG-TIGRVGM--IPESLNGAnltenAAKITEFNSLEQKYLMYLLLSNdlQ 153
Cdd:cd17280   42 TETSKKITDKALDdysalkiypAGSLVIAMYGaTIGRLGIlgIDATTNQA-----CCVLSGSNKIDIKFLFYWLLAN--R 114

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 522109379 154 NQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAILHKA 225
Cdd:cd17280  115 DELISLASGGGQPNISQELIKSLRIPVPPLEEQKQIAAFLDKKTAKIDSLIEKKERLIELLKERRQALISEA 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: 58.65 E-value: 4.31e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 334 PIEAKEDTKYLWYYMLSDEFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAreiETKDLANVIDH 413
Cdd:cd17521   99 PNKKKVLPKYLFYFTQSSLYWKQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDA---KIDALEELLEK 175


                 ....*....
gi 522109379 414 IEVMKKSIL 422
Cdd:cd17521  176 LEELLKELL 184

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: 58.68 E-value: 4.32e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDI-EHNSVNYEKVKYVSEDTfnkIRNYT---ISKNdlfiSIA-GTigRVGMIPESLNGANLTENA--AKITEFN 136
Cdd:cd17513   28 PWITSSDLsEDDIFKINIRKFITEEA---IKNSAtkiIPAN----SILiVT--RVGVGKVAINPFDICTSQdfTSLIPIK 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 137 SLEQKYLMYLLLSndLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDriesLFAKLDQAKELAQNALDSFDT 216
Cdd:cd17513   99 EVNPLFLAYLLYS--LLQKLKSQLQGTSIKGITKDDLKNLKIPLPPLEEQQKIAA----ILSKLDKLIEAHEKKLEKLKQ 172

                        170
                 ....*....|
gi 522109379 217 RKAAILHKAF 226
Cdd:cd17513  173 LKKGLMQKLF 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: 58.65 E-value: 4.80e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIeHNSVNYEKVKYVSEDTFN----KIrnytISKNDLFISIAG---TIGRVgmipeSLNGANLTEN---AAKIT 133
Cdd:cd17294   32 PWLSSGEV-NFKEIYETEKRITEEGLKnssaKW----IPKNSVLIALAGqgkTRGTV-----AILKIPLTTNqslAAIEP 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 134 EFNSLEQKYLMYLLLSNdlQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVD-------RIESLFAKLDQAKEL 206
Cdd:cd17294  102 DEEIANSRFLYYNLSSR--YEELRSLSGGGGRGGLNLKIIKSLPIPLPPLEEQKKIVAildkfdaLINDLKEGLPALLEL 179


                 ....*...
gi 522109379 207 AQNALDSF 214
Cdd:cd17294  180 RQKQYEYL 187

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: 57.60 E-value: 1.04e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  90 NKIRNYTISKND---------LFISIAGTIGRVGmipeslnganLTENAA----KIT--EFNS-LEQKYLMYLLLSNdlQ 153
Cdd:cd17290   48 RKLSELAIEDGEarlfpknsvLVVGIGATIGKVG----------YSDKESssnqQITgiIFNKdINPKFLFYWLSSS--K 115

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 522109379 154 NQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQ 208
Cdd:cd17290  116 EELENLANGATLPILNQEKLKNIKLPVPPLNEQQKIVEFLDKKTAKIDALIAKKE 170

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: 57.06 E-value: 1.34e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 136 NSLEQKYLMYLLlsndlqNQIKQSTIAT--TQAKL---ALNRIEnlvLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNA 210
Cdd:cd17262   91 NGISTEFLYYYL------NSIDISPYVTgaAQPKLnqaNLNSIP---IPLPPLEEQKKIVAILDKLDALIDLLEEELEKL 161

                         90
                 ....*....|.
gi 522109379 211 LDSFDTRKAAI 221
Cdd:cd17262  162 IELKKALLQKL 172

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: 57.47 E-value: 1.45e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 142 YLMYLLLSNDLQNQIKQ-STIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAA 220
Cdd:cd17524  109 YLNYFLNSPYGRKQIKSvATQGVGQANINATKLKAIPIPLPPLEEQKEIVEKLDELDALIDRLEALLEEAEELLESLLQS 188


                 .
gi 522109379 221 I 221
Cdd:cd17524  189 L 189

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: 56.98 E-value: 1.47e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  242 MDSWVKKTFNQVADIKSNLVDPSS----YMDNPHIapdnierRTGRLleYRTIREDGVTSGKHKFSKGQILYSkIRPYLS 317
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKelknNGKYPYI-------RAGDL--NNVVKGGLGYIKKYILPKGDITIS-SRATIG 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  318 KVVLVDFNGLCSADMYPIEAK---EDTKYLWYYMLSdeFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRIL 394
Cdd:pfam01420  71 YVFYRDKPYYTNQHIIVLIPKnniKITEFLYLYLLL--KLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAKIL 148

                         170
                  ....*....|....*..
gi 522109379  395 DNLLAREIETKDLANVI 411
Cdd:pfam01420 149 SQLDNTIELEKGILNEL 165

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: 56.79 E-value: 2.29e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  36 TRLGKLGRVKGGKRlPPGHVLQ---EEVtsrPYIRVTDIEHNSVNYEKVKYVSEDTFNKIRNYTISKND-LFISIAGTIG 111
Cdd:cd17516    1 VKIGDLGKVVTGKT-PSTKNPEyfgGDI---PFITPSDMKGGKYIIKTERRLSSKGLEKVKNKLIPANSiCVTCIGSDMG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 112 RVGMIPESLnganltenaakIT--EFNSL-------EQKYLMYLLLSNdlQNQIKQstIA-TTQAKLALNR--IENLVLP 179
Cdd:cd17516   77 KVAITKEPS-----------VTnqQINSIivnknkfDPDFVYYLLKNN--SKYLKS--IAgGSTATPIINKstFSNIEIP 141

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 522109379 180 LPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTR 217
Cdd:cd17516  142 LPPLPEQKKIAAILSSLDDKIENNRRINKTLEEMAQAL 179

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: 56.31 E-value: 2.47e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 340 DTKYLWYYMLSDEFLEQASSAGSrsVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAreiETKDLANVIDHIEVMKK 419
Cdd:cd17293   99 DPKFLYYQLLSSKFQLQAIASST--TLPIINKSKFEKIEIPLPPLEEQKRIVAKLDKLFA---LIDKLEESLEELDELLK 173


                 ....*..
gi 522109379 420 SILARAF 426
Cdd:cd17293  174 SLFQSAF 180

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: 55.22 E-value: 5.47e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 136 NSLEQKYLMYLLlsndlQNQIK---QSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALD 212
Cdd:cd17257   94 EELDKRFLYYAL-----PPPLKaieDTTSSTTVKHLSSKDIDEIELPLPPLEEQRRIAEILDELDALIDKLIAKLEKLRD 168

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: 54.85 E-value: 8.91e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 299 KHKFSKGQILYSKIRP--YLSKVVLVDfngLCSADMY---------PIEAKEDTKYLWYYMLSDEFLEQASSAGSRSV-L 366
Cdd:cd17522   58 KYKLQKGDILFSHINSieHIGKTAIYD---GDPEPLIhgmnllrlrPNKNIVDPKYLYYLLKSDRFRNQFRSIAKKAVnQ 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 522109379 367 PKINQKELSAVKVMIPSWNEQREVVRILDNLLArEIETkdLANVIDHIEVMKKSILA 423
Cdd:cd17522  135 ASINQTELKKIKIPLPPLEEQQKIASILEKLDK-KIEK--RKEKIEKLKELKKGLFQ 188

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: 54.04 E-value: 1.58e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 326 GLCSadmypIEAKE--DTKYLWYYMLS--DEFLEQASSagsrSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLARE 401
Cdd:cd17496   83 GVAA-----IRPKNgiDTEFLYYLLESnlDYLLAAATG----STFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKI 153

                         90       100
                 ....*....|....*....|....*
gi 522109379 402 IETKDLanvIDHIEVMKKSILARAF 426
Cdd:cd17496  154 DKNKQE---IEKLEELRDTLLPKLL 175

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: 53.95 E-value: 2.08e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNSVNYEKVK-YVSEDTFNKIRNYTISKNDLFISIAGTIGRVGmipesLNGANLTENA---AKITEFNSLE 139
Cdd:cd17277   32 KWLTIPDIDERGLIISSTKqFITEKALEEKKVKLVPKNSVLLSCTATIGKVA-----IAKIELTTNQqinALICKDSKIL 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 522109379 140 QKYLMYLLLSNdlQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIE 194
Cdd:cd17277  107 PEYLFYALKHI--KQVLERLTTNPGVKHVNLSMLSNLQIPLPPLEVQKKIVAEIE 159

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: 53.74 E-value: 2.29e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 288 RTIREDGVTSGKHK-FSKGQILYSKIRPYLSKVVLVD--------FNGL-CSADMYPieakedtKYLWYYMLS--DEFLE 355
Cdd:cd17290   48 RKLSELAIEDGEARlFPKNSVLVVGIGATIGKVGYSDkesssnqqITGIiFNKDINP-------KFLFYWLSSskEELEN 120

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 522109379 356 QASSAgsrsVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAR 400
Cdd:cd17290  121 LANGA----TLPILNQEKLKNIKLPVPPLNEQQKIVEFLDKKTAK 161

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: 53.60 E-value: 2.29e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 321 LVDFNGLCSADMYPIEAKEDTKYLWYYMLSDEFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNL--- 397
Cdd:cd17268   86 LGDEEVAAGGDIIIFRHSQNPKYLSYLLNSPAFQKQKRKLGTGTKVVHISASDLAKIKIPVPPLEEQERIVEILDKFdal 165


                 ....*....
gi 522109379 398 ---LAREIE 403
Cdd:cd17268  166 iagLPAEIE 174

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: 53.69 E-value: 2.45e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 522109379 334 PIEAKEDTKYLWYYMLSDEFLEQ--ASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAR 400
Cdd:cd17261  101 VNEELLLPEYLALALNSPSARRQieSRATGTAGSMPKISQSDLKSLPIPLPPLAEQKRIVARVDELLAL 169

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: 53.31 E-value: 3.02e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  99 KNDLFISIAGTIGRVGMIP-ESLNGANLtenaAKITEFNSLEQKYLMYLLL--SNDLQNQIKQSTIAttqaklALNR--I 173
Cdd:cd17245   56 KGDILISVRAPVGDVNIADeKCCIGRGL----AAIRANKDIDNLFLYYYLKynKPELEKLGTGSTFK------AINKkdL 125

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 522109379 174 ENLVLPLPPIAEQQRIVDRIEslfaKLDQAKELAQNALDSFDTRKAAILHKAF 226
Cdd:cd17245  126 EELKIPLPPLEEQQKIAEILS----TVDEAIEKTKALIEKLDELKKGLMQELF 174

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: 52.15 E-value: 7.77e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 334 PIEAKEDTKYLWYYMLSDEFLEQASSAGSRSV-LPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKDLanvID 412
Cdd:cd17517  103 LDKKKILPEFLYYYLNSPLGRKQIEKIAKSAAgQANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKK---LE 179

                         90
                 ....*....|...
gi 522109379 413 HIEVMKKSILARA 425
Cdd:cd17517  180 KLEQLFKSLMQSL 192

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: 51.77 E-value: 8.52e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 326 GLCSadmypIEAKE--DTKYLWYYMLSDEFLEQASSAGSrsVLPKINQKELSAVKVMIPSWNEQREVVRILDnLLAREIE 403
Cdd:cd17245   82 GLAA-----IRANKdiDNLFLYYYLKYNKPELEKLGTGS--TFKAINKKDLEELKIPLPPLEEQQKIAEILS-TVDEAIE 153

                         90       100
                 ....*....|....*....|...
gi 522109379 404 TKDlaNVIDHIEVMKKSILARAF 426
Cdd:cd17245  154 KTK--ALIEKLDELKKGLMQELF 174

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: 51.36 E-value: 1.01e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 522109379 136 NSLEQKYLMYLLLSNdlQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIV---DRIESLFAKLDQAKELAQN 209
Cdd:cd17291   81 NELVNKFLYYFLKNK--QEEIYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVeilDKFTELTAELPAELEARKK 155

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: 51.76 E-value: 1.23e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 304 KGQILYSKIRPyLSKVVLVD--FNGLCSADMY---PIEAKEDTKYLWYYMLSDEFLEQASSAGSRSVLPKINQKELSAVK 378
Cdd:cd17246   65 KGDILFSIIGT-IGRVAIVPedLPANINQAVAlirPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLK 143

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 522109379 379 VMIPSWNEQREVVRILDNLLA-REIETKDLANVIDHIEVMKKSIL 422
Cdd:cd17246  144 IPLPPLEEQKRIAAILDSLDAlIDKLEQKLEKLEDLKKGLMQDLL 188

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: 50.97 E-value: 1.32e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 328 CSADMYPIEAKED--TKYLWYYMLS--DEFLEQASSAGsrsvLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIE 403
Cdd:cd17291   70 ASDCCYILSSKNElvNKFLYYFLKNkqEEIYSLQRGAG----QPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFTELTAE 145

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: 51.36 E-value: 1.44e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 338 KEDTKYLWYYMLSDEFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLArEIETkdLANVIDHIEVM 417
Cdd:cd17259  106 ELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDA-LIDL--LEQKLEKLQQL 182


                 ....*
gi 522109379 418 KKSIL 422
Cdd:cd17259  183 KKGLM 187

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: 50.13 E-value: 2.59e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 286 EYRTIREdgVTSGKHKFSKGQILYSKIRPYL--SKVVLVDF--NGLC--SADMYPIEAKEDT--KYLWYYMLSDEFLEQA 357
Cdd:cd17260   21 ETRPLKE--VKKGYTYFRNGDVLLAKITPCFenGKTAIVDGlpNGIGfgSTEFHVLRPKEGIlpEFLYYLLRSPSFRKEA 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 522109379 358 S-----SAGSRSVlpkinQKE-LSAVKVMIPSWNEQREVVRILDNLLAReIETkdLANVIDHIEVMKKSILARAF 426
Cdd:cd17260   99 IksmtgSSGRQRV-----PKDfLENYKIPLPPLEEQKRIAAILDSLDAK-IDA--LEAEIETLEELLDALLPKLL 165

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

Pssm-ID: 341154 [Multi-domain] Cd Length: 181 Bit Score: 50.19 E-value: 3.65e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 141 KYLMYLLLSNDLQNQIKQSTIAT----TQAKLAlnrieNLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDT 216
Cdd:cd17265  101 DYLFHLFNSDLFKKQIGSFLTATinqiTNGNLN-----NFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKE 175


                 ....*.
gi 522109379 217 RKAAIL 222
Cdd:cd17265  176 LMQQLI 181

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: 50.13 E-value: 3.68e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 334 PIEAKEDTKYLWYYM--LSDEFLEQASSAGSRSvlpkINQKELSAVKVMIPSWNEQREVVRILDNLLAReIETkdLANVI 411
Cdd:cd17282   99 PNEEKIDVEFLEYYLrtLKKELEAIAPQSAQKN----INLEILRPLKIPVPPLEEQKKIVEILDALDDL-IDN--LEKRI 171

                         90
                 ....*....|....*
gi 522109379 412 DHIEVMKKSILARAF 426
Cdd:cd17282  172 AKLEELKQSLLQEAF 186

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: 49.90 E-value: 5.22e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 522109379 165 QAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17526  135 QAGINSDTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192

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: 49.09 E-value: 6.76e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 326 GLCSadmypIEAKE--DTKYLWYYMLSDEflEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAR--E 401
Cdd:cd17497   82 GLAA-----IRPKKglDKKYLLYYLKSIE--NELSSLGTGSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDELTAKidQ 154

                         90       100
                 ....*....|....*....|.
gi 522109379 402 IETKdLANVIDHIEVMKKSIL 422
Cdd:cd17497  155 LIAL-LEKAIELLKEYRQAVL 174

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

Pssm-ID: 341184 [Multi-domain] Cd Length: 182 Bit Score: 49.14 E-value: 7.02e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 245 WVKktfnqVADIKSNLVDPSSymdnphiapdnierrtgrllEYrtIREDGV-TSGKHKFSKGQILYSkIRPYLSKVVLVD 323
Cdd:cd17296   30 WVK-----ISDCKNKYVDETE--------------------EF--ITEEGLnNSSAKLLKKGTILIA-IFATIGKVGILK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 324 FNGLCS---ADMYPIEAKEDTKYLWYYMLS--DEFLeqasSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLl 398
Cdd:cd17296   82 IEATTNqaiAGIKPKNKSINPKYLYYYLKSlyEKFL----SLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAILDKF- 156

                        170       180
                 ....*....|....*....|....*...
gi 522109379 399 arEIETKDLANVIDHIEVMKKSILARAF 426
Cdd:cd17296  157 --EKLINKRQEGLQLLDELVKSLFEEMF 182

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: 48.90 E-value: 8.39e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 522109379 334 PIEAKEDTKYLWYYMLSDEFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETK 405
Cdd:cd17518   99 FIDGLLDNNFLKYFLNSDYFKEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEAAL 170

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: 48.94 E-value: 1.10e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 522109379 173 IENLVLPLPPIAEQQRIVDRIESLFAKLDQAKElaqnALDSFDTRKAAILHKAF 226
Cdd:cd17273  137 FKKIEIPLPPLEEQKKIAAILSKLDELIELLEK----ENEKLKELRDGLLPKLF 186

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: 48.24 E-value: 1.20e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 332 MYPIEAKEDT--KYLWYYMLSDEFlEQASSAgsrSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIEtkdLAN 409
Cdd:cd17288   72 MFYTEIKKNNdpKFLYYLLKTIDF-KKYNEA---TGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDAL---IEL 144

                         90
                 ....*....|....*....
gi 522109379 410 VIDHIEVMKKSILARAFRG 428
Cdd:cd17288  145 QEKLLEKLKQYKLALMQEL 163

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: 48.71 E-value: 1.31e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 141 KYLMYLLLSN--DLQNQIKqstiATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRK 218
Cdd:cd17279  104 RFLYYLLLAAkeELNSLGR----GTTFLELSTDELANFKIPLPPLSEQRAIADFLDRETAKIDALIAKKQQLIELLKEKR 179


                 ...
gi 522109379 219 AAI 221
Cdd:cd17279  180 QAL 182

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: 48.66 E-value: 1.32e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 245 WVKKTFNQVADI------KSnlvdpSSYMDNPH--IAPDNIERRTGRLLE-YRTIREDGVTSGKHKFSKGQILYSKIRPY 315
Cdd:cd17278    1 WEVVKLGDIADIqngyafKS-----SDFSDEGIpvIRIGNIKNGGIDLDDnSKYPEEPLEKYEKFLLKKGDILIAMTGGT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 316 LSKVVLVDFNGLCS------ADMYPIEaKEDTKYLWYYMLSDEFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQRE 389
Cdd:cd17278   76 VGKVAIVPEDDEPAllnqrvGKFRPKD-KIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKK 154

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 522109379 390 VVRILDNLLAREIETKD-LANVIDHIEVMKKSILA 423
Cdd:cd17278  155 IAEILDSLDAKIDKLEQkLEKLRDLLKPLLQSLFT 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: 47.53 E-value: 3.02e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 298 GKHKFSKGQILYSkIRPYLSKVVLVDFN--GLCSADMYPIEAKE--DTKYLWYYMLSDEFLEQASSAGSRSVLPKINQKE 373
Cdd:cd17264   58 GSGKLQKGDILYC-LRGSLGKCAIVDNYdeGAIASSLVIIRPFAkvDVRYLYYYLNSPLGKSQIKKYDNGSAQPNLSAKS 136

                         90       100
                 ....*....|....*....|....*..
gi 522109379 374 LSAVKVMIPSWNEQREVVRILDNLLAR 400
Cdd:cd17264  137 LKKFLIPLPPLEEQKRIVAKLDELDAL 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: 47.30 E-value: 3.05e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 299 KHKFSKGQILYSKIRPYLSKVV--LVDFNGLCSADMY---PIEAKEDTKYLWYYMLSDEfLEQASSAGSrsVLPKINQKE 373
Cdd:cd17519   59 KYIVRPGDIVIAMSGATTGKVGinLTDQEFYLNQRVGkfiPNEEILNNRYLYHFLLSKQ-NEKYILAGG--SQPNLSSEK 135

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 522109379 374 LSAVKVMIPSWNEQREVVRILDNL------LAREIETKD 406
Cdd:cd17519  136 LKKIKIPIPSLEVQEEIVSILDKFreltneLESELNLRL 174

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

Pssm-ID: 341196 [Multi-domain] Cd Length: 181 Bit Score: 47.04 E-value: 3.76e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 338 KEDTKYLWYYMLS--DEFLEQasSAGSRSvlPKINQKELSAVKVMIPSWNEQREVVRILDNLLArEIETkdLANVIDHIE 415
Cdd:cd17515   98 EIDNEFLFYFLKSqkEYLISL--GKGGAQ--PNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDK-LIEK--LEKALEKLE 170

                         90
                 ....*....|.
gi 522109379 416 VMKKSILARAF 426
Cdd:cd17515  171 ELKKALMQKLL 181

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: 46.00 E-value: 6.08e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  83 YVSEDTFNKIRN-YTI-SKNDLFISIAGTIGRV----GmIPESLNGAN---LTENAAKITefnsleQKYLMYLLLSNDLq 153
Cdd:cd17292   13 YISRELFEEYKSkYSYpKKGDILISASGTIGRTviydG-EDAYFQDSNivwLDNDESKVL------NKFLYYFYQIIKW- 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 522109379 154 NQIKQSTIAttqaKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLdqakELAQNALDSFDTRKAAILHKAF 226
Cdd:cd17292   85 KKTEGSTIK----RLYNDNLLNTKIPVPSLDEQRKIAEFLSLLDALI----ALLQKKLEKLIALKKGLMQYLF 149

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: 46.42 E-value: 8.15e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 522109379 171 NRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17276  136 DDVRNFPIPLPPLDEQRAIVEFLSDVDALIDSLEALIEKLRELKKGLMQQLL 187

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Flavobacterium columnare S subunit (S.Fco49512ORF2615P) TRD2-CR2; The recognition sequence of Flavobacterium columnare S subunit (S.Fco49512ORF2615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341144 [Multi-domain] Cd Length: 166 Bit Score: 45.60 E-value: 9.07e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 522109379 140 QKYLMYLLlsndlQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKE 205
Cdd:cd17255   90 NKFLYYAL-----NLIAKKYVSFDGNPKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIA 150

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: 45.98 E-value: 1.06e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 334 PIEAKEDTKYLWYYMLS--DEFLEQASSAGsrsvLPKINQKELSAVKVMIPSWNEQREVVRILDNLLARE 401
Cdd:cd17247  104 PNEERVLPEYLHYYLESqyDELRRIGSGGG----QGALNCGILKAFPIPLPPLDEQREIVAELEALLAKI 169

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: 45.37 E-value: 1.21e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 326 GLCSADMypieAKEDTKYLwYYMLSDeFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAReIEtk 405
Cdd:cd17498   82 GLCSIRM----KNGNNSFL-YYLLKN-NIKNLINKSSGTVFGSINKDDIENLEVDIPEDEEQKRIANILSKIDDK-IE-- 152

                         90       100
                 ....*....|....*....|.
gi 522109379 406 DLANVIDHIEVMKKSILARAF 426
Cdd:cd17498  153 INNQINKNLEELAQAIFKHWF 173

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: 45.50 E-value: 1.22e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 340 DTKYLWYYMLS---DEFLeqassagSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKDLanvIDHIEV 416
Cdd:cd17262   94 STEFLYYYLNSidiSPYV-------TGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEE---LEKLIE 163


                 ....*.
gi 522109379 417 MKKSIL 422
Cdd:cd17262  164 LKKALL 169

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: 45.28 E-value: 1.32e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 141 KYLMYLLLSNdLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKAA 220
Cdd:cd17269   85 KFLYYYLKSY-FKKYIEKNSVGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAELPAELEARKKQYEYYRDA 163


                 ....*
gi 522109379 221 ILHKA 225
Cdd:cd17269  164 LLSFA 168

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: 45.28 E-value: 1.58e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 522109379 333 YPIEAKEDTKYLWYYMLS--DEFLEQASSAGSrsvLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIET 404
Cdd:cd17269   76 HPFKEEIDPKFLYYYLKSyfKKYIEKNSVGSS---VPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAEL 146

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: 44.47 E-value: 2.96e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 338 KEDTKYLWYYMLSDEFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKD-LANVIDHIEV 416
Cdd:cd17252  107 EIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQaLEKLDELLKS 186


                 ..
gi 522109379 417 MK 418
Cdd:cd17252  187 LF 188

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: 44.40 E-value: 3.10e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 332 MYPIEAKEDTKYLWYYMLSD-EFLEQASSAGSRSVLpkiNQKELSAVKVMIPSWNEQREVVRILDNLLAreiETKDLANV 410
Cdd:cd17294   99 IEPDEEIANSRFLYYNLSSRyEELRSLSGGGGRGGL---NLKIIKSLPIPLPPLEEQKKIVAILDKFDA---LINDLKEG 172

                         90
                 ....*....|..
gi 522109379 411 IDHIEVMKKSIL 422
Cdd:cd17294  173 LPALLELRQKQY 184

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: 44.00 E-value: 3.25e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 141 KYLMYLLLSNDLQNQIKQSTI-ATTQAklALNRIEnlvLPLPPIAEQQRIVDRIESLFAKLDQAKELAQNALDSFDTRKA 219
Cdd:cd17288   84 KFLYYLLKTIDFKKYNEATGVpSLTQT--TLNKIK---IPIPPLEEQQKIASILDKLDAKDALIELQEKLLEKLKQYKLA 158


                 ....
gi 522109379 220 AILH 223
Cdd:cd17288  159 LMQE 162

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: 44.51 E-value: 3.81e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 522109379 340 DTKYLWYYM-LSDEFLEQASSAGSrsvLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKD 406
Cdd:cd17281  108 DIKFLFYYFfVLGEWCKKNINIGG---FPSVDMNKLKKFKIPIPPLEEQEKIVEILDKFTKLTADLTA 172

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: 44.03 E-value: 4.20e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 334 PIEAKEDTKYLWYYMLSDEFLEQaSSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKDLanvIDH 413
Cdd:cd17263   89 PDKNIIDKDYLYYFLKSKEIQLN-ILTKAGSTIPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALIDKLKEL---IEK 164


                 ....*....
gi 522109379 414 IEVMKKSIL 422
Cdd:cd17263  165 LIELKKGLF 173

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: 43.62 E-value: 6.03e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 334 PIEAKEDTKYLWYYMLS----DEFLEQASSAgsrSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAR-EIETKDLA 408
Cdd:cd17253  103 PKDDLLLPEFLSYWLNSaygrGYFLRAAKQT---TNLASINSTKLKALPVPLPPLEEQRRIVERLDELLALiDALEASLA 179

                         90
                 ....*....|....
gi 522109379 409 NVIDHIEVMKKSIL 422
Cdd:cd17253  180 KLEELLKALRQALL 193

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: 43.25 E-value: 6.61e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 338 KEDTKYLwYYMLSDEFLEQASSAGSrSVLPKINQKELSAVKVMIPSWNEQREVVRILDNlLAREIETkdLANVIDHIEVM 417
Cdd:cd17286   96 NYDPEFL-YYALENWSKKIKSLAGK-QAVPIINKTEFSKIKILVPPLEEQQKIANFLSK-LDELIEL--QQQKIEKLEEL 170


                 ....*
gi 522109379 418 KKSIL 422
Cdd:cd17286  171 KKGLL 175

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: 43.55 E-value: 7.30e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 338 KEDTKYLWYYMLS--DEFLEQASSagsrSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLaREIETKDLANviDHIE 415
Cdd:cd17273  103 EIDNEFLYYLLKNnkPEIESLASG----STFKEISKSTFKKIEIPLPPLEEQKKIAAILSKLD-ELIELLEKEN--EKLK 175

                         90
                 ....*....|.
gi 522109379 416 VMKKSILARAF 426
Cdd:cd17273  176 ELRDGLLPKLF 186

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

Pssm-ID: 341165 [Multi-domain] Cd Length: 187 Bit Score: 43.34 E-value: 7.37e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 327 LCSadMYPIEAKEDTKYLWYYMLSDEFLEQASSAGSRSVlPKINQKELSAVKVMIPSWNEQREVVRILDNLLAR-EIETK 405
Cdd:cd17276   94 ICA--ILPNEKKVNPEFLLRYLNFNRPYWMRVAASSRKD-PNITKDDVRNFPIPLPPLDEQRAIVEFLSDVDALiDSLEA 170

                         90
                 ....*....|....*..
gi 522109379 406 DLANVIDHIEVMKKSIL 422
Cdd:cd17276  171 LIEKLRELKKGLMQQLL 187

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: 43.35 E-value: 8.02e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  64 PYIRVTDIEHNS-VNYEKVKYVSEDTFNKIRnyTISKNDLFISIAGTIGRVGMIP-ESLNGANLTeNAAKITEF-NSLEQ 140
Cdd:cd17281   33 PWFRMEDIRENGrILSDSIQHITPSAVKGGK--LFPANSIILSTTATIGEHALITvDSLANQRFT-NFSLKKSYkNKLDI 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 141 KYLMYL--LLSNDLQNQIKQSTIATTQaklaLNRIENLVLPLPPIAEQQRIVdRIeslfakldqakelaqnaLDSFDTrk 218
Cdd:cd17281  110 KFLFYYffVLGEWCKKNINIGGFPSVD----MNKLKKFKIPIPPLEEQEKIV-EI-----------------LDKFTK-- 165

                        170
                 ....*....|....*
gi 522109379 219 aaiLHKAFTGELTAK 233
Cdd:cd17281  166 ---LTADLTAELPAE 177

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: 43.08 E-value: 8.98e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  62 SRPYIRVTDIEHNSvnyeKVKyvsEDTFNKIRNYTIS------KNDLFISIAGTIGRVGMipeSLNGANLTENAAKITEF 135
Cdd:cd17270   29 SMPFVQVADVGDNF----KLV---EKTKQKISKLAQPksvfvpKGTVIVTLQGSIGRVAI---TQYDAYVDRTLLIFESY 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 136 N-SLEQKYLMYLLLSNDLQNQIKQ--STIAT-TQAKLalnriENLVLPLPPIAEQQRIVdrieSLFAKLDQAKELAQNAL 211
Cdd:cd17270   99 KiNINKKFFAYQLKLKFEIEKEKApgGTIKTiTKEEL-----SKFEIPIPSLEEQKEIV----NILDKFDELITELQLRK 169

                        170
                 ....*....|...
gi 522109379 212 DSFDTRKAAILHK 224
Cdd:cd17270  170 KQLEYYKKALLSF 182

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: 42.82 E-value: 1.08e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  97 ISKNDLFISIAGTIGRVGM--IPESLNGAN--LTENaakitefNSLEQKYLMYLLLSndLQNQIKQSTIATTQAKLALNR 172
Cdd:cd17243   64 LPKGTTIISARGTVGKLALlgIPMAMNQSCygLRGK-------DGLSNYFLYYLLKN--LIEELKQKAHGSVFDTITRKT 134

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 522109379 173 IENLVLPLPPIAEQQRIVDRIESLFAKLD----QAKELAQ 208
Cdd:cd17243  135 FDEIKVPLPPEELQKSFENIVSPLFDKILnnlkENQTLAQ 174

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: 42.66 E-value: 1.25e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  78 YEKVKYVSEDTFNKIRNYTISKNDLFISIAG---TIGRVGM--IPESLNGA--NLTENAaKITEFNsleqkYLMYLLLSN 150
Cdd:cd17500   42 YDTEEKITEEGLKNSSAKLIPENTVIIAMYGagkTAGRVAInkIPLTTNQAccNLIIDN-KKADYR-----FVYYSLKTQ 115

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 522109379 151 dlQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLD 201
Cdd:cd17500  116 --YEELVNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLDDKIE 164

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: 42.44 E-value: 1.70e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  68 VTDIEHNSVNYEKVKYVSEDtFNKIRNYTISKNDLFISIAGTIGRVGMIPESLNGANLTENAAKITEFNSLEQKYLMYLL 147
Cdd:cd17520   30 ISNIEDGEIDYSGMDTIEEE-ERKVKRYELRDGDLVLSCRGTAIKVAVFREQKKIVIASANIIVIRPNEKVLSEYLKIFL 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 522109379 148 LSNDLQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLDQAKELAQN 209
Cdd:cd17520  109 ESPVGTALIKSFQRGTTVMNINHSDIAEMEIPLLPLEEQKKIAEEYRKERSLYRETVRKAEK 170

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: 41.66 E-value: 2.13e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 338 KEDTKYLWYYMLSDEFLEQASSAGSrsvlPKINQKELSAVKVMIPSWNEQREVVRILDNLLArEIETkdLANVIDHIEVM 417
Cdd:cd17266   81 ENNIKFLYYLLKSLNLNQYATGSAQ----PLITVSKLKKLKIPLPPLEEQKKIAAILDSLDA-KIDL--LEKKLEKLIEL 153


                 ....*
gi 522109379 418 KKSIL 422
Cdd:cd17266  154 KKELM 158

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: 41.72 E-value: 2.34e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 340 DTKYLWYYMLSDEflEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKDLANVIDHI-EVMK 418
Cdd:cd17285  100 DPEYLLYWFLSIE--ETIESLGTGTTVKGITLEDLKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEKLKQLkKGLM 177


                 ....
gi 522109379 419 KSIL 422
Cdd:cd17285  178 QSLL 181

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: 41.77 E-value: 3.09e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 522109379 340 DTKYLWYYMLS--DEFLEQASSAGSrsvlPKINQKELSAVKVMIPSWNEQREVVRILDNllareiETKDLANVIDHIE 415
Cdd:cd17280  102 DIKFLFYWLLAnrDELISLASGGGQ----PNISQELIKSLRIPVPPLEEQKQIAAFLDK------KTAKIDSLIEKKE 169

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

Pssm-ID: 341190 [Multi-domain] Cd Length: 175 Bit Score: 41.45 E-value: 3.14e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 326 GLCSadmypIEAKE--DTKYLWYYMLS--DEFLEQASSAGSRSvlpkINQKELSAVKVMIPSWNEQREVVRILDNLLARE 401
Cdd:cd17499   83 GLAA-----IRAKKniDKKYLFYFLLSnkDYFKGKSGGSTFKS----INKNQIKNIKIPLPPLEEQKRIVSELDKLFKLI 153


                 ....
gi 522109379 402 IETK 405
Cdd:cd17499  154 FEAK 157

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: 41.32 E-value: 3.63e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 328 CSAdMYPIEaKEDTKYLWYY-MLSDEFLEQASSAGsrsvlpkiNQKELSA-----VKVMIPSWNEQREVVRILDNLLaRE 401
Cdd:cd17287   92 CAA-ILPND-GINPDFLFYYlQSSYEELRDLSNGG--------GQPNLNAgliksIEIPVPPLDEQQKIAAFLSAID-AK 160

                         90       100
                 ....*....|....*....|....*
gi 522109379 402 IETkdLANVIDHIEVMKKSILARAF 426
Cdd:cd17287  161 IDA--LEQKLELLQELKKSLMQQLF 183

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: 41.04 E-value: 4.22e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 340 DTKYLWYYM-LSDEFLEQASSAGSrsvLPKINQKELSAVKVMIPSWNEQREVVRILDNLLA-REIETKDLANVIDHIEVM 417
Cdd:cd17284  104 NPEYLMYLLsLQKKYMEKIATGTT---IPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKkIDLLIAKLEKLQQLKKGL 180


                 ....*
gi 522109379 418 KKSIL 422
Cdd:cd17284  181 MQQLF 185

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: 40.93 E-value: 4.37e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 335 IEAKEDTKYLWYYMLSDEFLEQASSAGSRSVlPKINQKELSAVKVMIPSWNEQREVVRILDNLLArEIETkdLANVIDHI 414
Cdd:cd17283   97 LKKKLDKDFLYYLLSSITVQLQFSAQAGGGT-KNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDA-LIDA--LEEKLEKL 172


                 ....*...
gi 522109379 415 EVMKKSIL 422
Cdd:cd17283  173 EELKKGLM 180

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: 40.36 E-value: 6.07e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  82 KYVSEDTF----NKIRNytisKNDLFISIAGTIGRVGMIPE---------SLNGanltenaakitefNSLEQKYLMYLLL 148
Cdd:cd17498   39 KYPYIDTYttdiKKIAK----KGDILMSVRAPVGDLNIANKdicigrglcSIRM-------------KNGNNSFLYYLLK 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 522109379 149 SNdlQNQIKQSTIATTQAKLALNRIENLVLPLPPIAEQQRIVDRIESLFAKLdqakELAQNALDSFDTRKAAILHKAF 226
Cdd:cd17498  102 NN--IKNLINKSSGTVFGSINKDDIENLEVDIPEDEEQKRIANILSKIDDKI----EINNQINKNLEELAQAIFKHWF 173

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: 40.15 E-value: 9.53e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 330 ADMYPIEAKEDTKYLWYYMLSDEFleqaSSAGSRSVLPK-INQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKDLA 408
Cdd:cd17244   92 AHFIPKDKKIDTEYLYYYLKSFDY----SSLGSTASKGKtLNSKKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLI 167


                 .
gi 522109379 409 N 409
Cdd:cd17244  168 E 168

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoR124I TRD2-CR2, S.Eco540I TRD2-CR2, S.Eco540AI TRD2-CR2, and S.Eco540ANI TRD2-CR2; Escherichia coli (R124) S subunit (S.EcoR124I), E. coli ST540 S subunit (S.Eco540I), E. coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540AN S subunit (S.Eco540ANI) recognize the sequence 5'... GAANNNNNNRTCG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoR124I -TRD1 recognizes GAA/TTC, and -TRD2 recognizes CGAY/RTCG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.

Pssm-ID: 341138 [Multi-domain] Cd Length: 185 Bit Score: 40.13 E-value: 1.05e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 338 KEDTKYLWYYMLS--DEFLEQASSAGSrSVLpKINQKELSAVKVMIPSWNEQREVVRILDNLLAR-EIETKDLANVIDHI 414
Cdd:cd17249  101 GIDPEFLLYALKAneDRILSLVDKAGH-GTG-SLDTDDLKNLPIPLPPLEEQRRIAAILDALDALiDLLERKLAKLEELL 178


                 ....*..
gi 522109379 415 EVMKKSI 421
Cdd:cd17249  179 KALMQAL 185

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: 39.72 E-value: 1.25e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 522109379 340 DTKYLWYYMLSDEFLEQASSAgsRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNL----------LAREIE 403
Cdd:cd17272  101 LPSYLKYFLDSEKFLNKSISA--TSGQGYLKANQIDKLEIPLPPLEEQQRIVKILDKFdtlcnditegLPAEIE 172

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: 39.18 E-value: 1.91e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379  80 KVKYVSeDTFNKIR-------NYTI-SKNDLFISI-----AGTIGRVGM--IPESLNGANLTENAAK--ITEFnsLEQKY 142
Cdd:cd17271   35 NYNYIT-DTNEKITeeavkntNLKIhPKGTFLIAItgleaAGTRGKCAItgIPATTNQSCMAFYPTKklTTEF--LFYWY 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 143 LMYlllSNDLQNQIKQstiATTQAKLALNRIENLVLPLPPIAEQQRIVDriesLFAKLDQAKELAQNALDSFDTRKAAIL 222
Cdd:cd17271  112 KKY---GNYLGFKYAQ---GTKQQSYTADIVKKLPILLPTLKEQKKIAN----FLSDIDELIATLEKKIEKLKKIKKGLM 181


                 ....*
gi 522109379 223 HKAFT 227
Cdd:cd17271  182 QKLLT 186

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: 39.23 E-value: 1.97e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 522109379 342 KYLWYYMLSDEFLEQASSAGSrSVLPKINQKELSAVKVMIPSWNEQREVVRILDNL--LAREIETK 405
Cdd:cd17270  104 KKFFAYQLKLKFEIEKEKAPG-GTIKTITKEELSKFEIPIPSLEEQKEIVNILDKFdeLITELQLR 168

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: 38.93 E-value: 2.13e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 287 YRTIREDGVTSGKHK---FSKGQILYSKIRPyLSKVVLVDFNGLCSAD----MYPIEAKEDTKYLWYYMLSDEFLEQASS 359
Cdd:cd17258   31 KVKIVEPDYKIGLKQskiFKKGDVLITRHGT-IGRVSIILSEEACLSShvagFNSKEGISDNKFIKYLFNSKKIKNRLMS 109

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 522109379 360 AGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNL-LAREIETKDLANV 410
Cdd:cd17258  110 YGASSTQPALNLSRLLKIKFPNPPLEEQQKIGKILSTWdRAIELTEQKLELL 161

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: 38.99 E-value: 2.50e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 343 YLWYYMLSDEFLEQASSAGSRSV-LPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKDLanvIDHIEVMKKSI 421
Cdd:cd17524  109 YLNYFLNSPYGRKQIKSVATQGVgQANINATKLKAIPIPLPPLEEQKEIVEKLDELDALIDRLEAL---LEEAEELLESL 185


                 ....
gi 522109379 422 LARA 425
Cdd:cd17524  186 LQSL 189

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: 38.31 E-value: 4.18e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 522109379 337 AKEDTKYLWYYMLSDEflEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAR 400
Cdd:cd17279   99 SDVDSRFLYYLLLAAK--EELNSLGRGTTFLELSTDELANFKIPLPPLSEQRAIADFLDRETAK 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: 37.91 E-value: 4.54e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 334 PIEAKEDTKYLwYYMLSDEFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAReIETkdLANVIDH 413
Cdd:cd17516   96 VNKNKFDPDFV-YYLLKNNSKYLKSIAGGSTATPIINKSTFSNIEIPLPPLPEQKKIAAILSSLDDK-IEN--NRRINKT 171

                         90
                 ....*....|...
gi 522109379 414 IEVMKKSILARAF 426
Cdd:cd17516  172 LEEMAQALFKEWF 184

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: 37.48 E-value: 6.20e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 342 KYLWYYMLSDEFLEQASS-AGSRsvlpkINQ---KELSAVKVMIPSWNEQREVVRILDNLLAR-EIETKDLANVIDHIEV 416
Cdd:cd17265  101 DYLFHLFNSDLFKKQIGSfLTAT-----INQitnGNLNNFKIPLPPLEEQEKIAEFLSSLDAKiDKLIKKIEKLIELKKE 175


                 ....*.
gi 522109379 417 MKKSIL 422
Cdd:cd17265  176 LMQQLI 181

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: 37.44 E-value: 6.70e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 340 DTKYLwYYML---SDEFLEQASSAGsrsvLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKDLanvIDHIEV 416
Cdd:cd17254   92 DKDYL-YYLLkalTEEIESQAHGST----MVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQ---LKKLEE 163

                         90
                 ....*....|
gi 522109379 417 MKKSILARAF 426
Cdd:cd17254  164 LRKALLQSLL 173

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: 37.21 E-value: 8.12e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 522109379 336 EAKEDTKYLWYYMLSDEFLEQASS--AGSRSVlPKINQKELSAVKVMIPSWNEQREVVRILDNLLAR 400
Cdd:cd17525  103 DDIVLPYFINYYLNSPDGKKQLESiaSGTTSV-AAIYQKDLKKLKLPLPPLDEQREIVSFLSELDAK 168

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: 37.24 E-value: 8.12e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 522109379 340 DTKYLWYYMLSDEFLEQASSAGSRSVLPKINQKELSAVKVMIPSWNEQREVVRILDNLLAREIETKDLanvIDHIEVMKK 419
Cdd:cd17289  108 NSKFLYYWFQSSIFKNQINSITIGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQ---LQKLEELAK 184


                 ....*..
gi 522109379 420 SILARAF 426
Cdd:cd17289  185 TLFQYWF 191