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Conserved domains on  [gi|916786761|ref|WP_051393817|]
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restriction endonuclease subunit S [Fructilactobacillus florum]

Protein Classification

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

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

PubMed:  24068554

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 9-181 8.12e-19

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


The actual alignment was detected with superfamily member cd17252:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 189  Bit Score: 80.30  E-value: 8.12e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGESYSGLSGKTKD---DFGIGNSKFITYKNIFDNEMISEsqmEKVLINSS--EKQNKVNIGDAFFTISSET 83
Cdd:cd17252    1 WEWVRLGEIAEIIRGVTYKKSDaseEPSEGGIPVLRANNIQNGGLDFD---DLVYVPKSkvKEEQKLKKGDILICMSSGS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  84 PNEVGMSSVLnFKHENLYLNSFSFGFRTNINIDNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQ 163
Cdd:cd17252   78 KELVGKAAFI-DEDTDYTFGAFCGVIRPKKEIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPLAEQ 156

                        170       180
                 ....*....|....*....|..
gi 916786761 164 ----TKVGLIFKSINKSIAANE 181
Cdd:cd17252  157 krivAKLDKLDALIDKLKQALE 178
 
Name Accession Description Interval E-value
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 9-181 8.12e-19

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: 80.30  E-value: 8.12e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGESYSGLSGKTKD---DFGIGNSKFITYKNIFDNEMISEsqmEKVLINSS--EKQNKVNIGDAFFTISSET 83
Cdd:cd17252    1 WEWVRLGEIAEIIRGVTYKKSDaseEPSEGGIPVLRANNIQNGGLDFD---DLVYVPKSkvKEEQKLKKGDILICMSSGS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  84 PNEVGMSSVLnFKHENLYLNSFSFGFRTNINIDNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQ 163
Cdd:cd17252   78 KELVGKAAFI-DEDTDYTFGAFCGVIRPKKEIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPLAEQ 156

                        170       180
                 ....*....|....*....|..
gi 916786761 164 ----TKVGLIFKSINKSIAANE 181
Cdd:cd17252  157 krivAKLDKLDALIDKLKQALE 178
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
124-181 3.35e-08

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 49.29  E-value: 3.35e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 916786761 124 FRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:COG0732    6 LRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALE 63
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
58-163 5.31e-03

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 37.17  E-value: 5.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  58 KVLINSSEKQNKVNIGDAFFTISSETPNEVGmSSVLNFKHENLYLNSFSFGFRTNINIDNYFLANSFRSEYFRNNIVKLA 137
Cdd:PRK09737  60 PYCMDAPEDVSKYQLQDRDIVISSAGSIGFS-FLAQNPLPSNVVFASFAIRLKPVNYFSEYFLKHFLESSDYRNQLSLMS 138

                         90       100
                 ....*....|....*....|....*.
gi 916786761 138 QGISRYNISKNKVLNLSIKIPDFCEQ 163
Cdd:PRK09737 139 AGNAVQNINAQSLSTLTFPIPPIAEQ 164
 
Name Accession Description Interval E-value
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 9-181 8.12e-19

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: 80.30  E-value: 8.12e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGESYSGLSGKTKD---DFGIGNSKFITYKNIFDNEMISEsqmEKVLINSS--EKQNKVNIGDAFFTISSET 83
Cdd:cd17252    1 WEWVRLGEIAEIIRGVTYKKSDaseEPSEGGIPVLRANNIQNGGLDFD---DLVYVPKSkvKEEQKLKKGDILICMSSGS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  84 PNEVGMSSVLnFKHENLYLNSFSFGFRTNINIDNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQ 163
Cdd:cd17252   78 KELVGKAAFI-DEDTDYTFGAFCGVIRPKKEIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPLAEQ 156

                        170       180
                 ....*....|....*....|..
gi 916786761 164 ----TKVGLIFKSINKSIAANE 181
Cdd:cd17252  157 krivAKLDKLDALIDKLKQALE 178
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 9-181 3.44e-17

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: 76.04  E-value: 3.44e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGESY-SGLSgKTKDDFGIGNsKFITYKNIFDNEMISESQMEKVLINSSEKQN-KVNIGDAFFTISSETPNE 86
Cdd:cd17517    1 WEVVKLGDLLEDPrYGTS-KKSSYDGSGT-PVLRIPNIYDGGIDLDDLKKRVDLSEKELEKyLLKKGDILFNRSNGSPEL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  87 VGMSSVLNFKHENLYLNSFSFGFRTNIN-IDNYFLANSFRSEYFRNNIVKLAQGISR-YNISKNKVLNLSIKIPDFCEQT 164
Cdd:cd17517   79 VGKCALVDEEDEPAIFASYLIRLRLDKKkILPEFLYYYLNSPLGRKQIEKIAKSAAGqANINQKDLKKLPIPLPPLEEQK 158

                        170
                 ....*....|....*..
gi 916786761 165 KVGLIFKSINKSIAANE 181
Cdd:cd17517  159 EIVEILESLDSKIDLLE 175
RMtype1_S_Ara36733I_TRD1-CR1_like cd17268
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 9-181 1.88e-12

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: 62.85  E-value: 1.88e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGESYSGlSGKTKDDF---GIGnskFI------TYKNIFDNEMISesqmeKVLINSSEKQNKVNIGDAFFTI 79
Cdd:cd17268    1 VEWKTLGEIGEFIRG-KGITKKDFvesGVP---CIhygeiyTKYGIYTTKTKS-----FISEELAKKLRKAKPGDLLIAG 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  80 SSETPNEVGMSSV-LNfkHENLYLNSFSFGFRTNINIDnyFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIP 158
Cdd:cd17268   72 TGETIEDIGKAVAwLG--DEEVAAGGDIIIFRHSQNPK--YLSYLLNSPAFQKQKRKLGTGTKVVHISASDLAKIKIPVP 147

                        170       180
                 ....*....|....*....|...
gi 916786761 159 DFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17268  148 PLEEQERIVEILDKFDALIAGLP 170
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 12-181 1.47e-10

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: 57.78  E-value: 1.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  12 RKLKNFGESYSGLSGKTKDDF-GIGNSKFITYKNIFDNEMISESQMEKVLINSSEKQNKVNIGDAFFTISsetpNEVGMS 90
Cdd:cd16961    1 KKLGEIAEIISGKTPSSSSEYwDNGIIPWIRISDINNGGIILTDEKITEEGAEKLKKKILPKGDILISRS----GTIGKV 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  91 SVLNFKHeNLYLNSFSFGFRTNINIDNYFLANSFRSEyFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIF 170
Cdd:cd16961   77 AIVKEND-KALLNQAVIVIRPKDEVDSEFLYYFLKSP-FGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANIL 154

                        170
                 ....*....|.
gi 916786761 171 KSINKSIAANE 181
Cdd:cd16961  155 DKLDALIELLE 165
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 9-181 3.13e-10

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: 57.13  E-value: 3.13e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGESYSGLSGKTKDdFGIGNSKFITYKNIFDNEMISESQMeKVLINSSEKQNK--VNIGDAFFTISSETpne 86
Cdd:cd17278    1 WEVVKLGDIADIQNGYAFKSSD-FSDEGIPVIRIGNIKNGGIDLDDNS-KYPEEPLEKYEKflLKKGDILIAMTGGT--- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  87 VGMSSVLNFKHENLYLNSFSFGFRTNINIDNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKV 166
Cdd:cd17278   76 VGKVAIVPEDDEPALLNQRVGKFRPKDKIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKI 155

                        170
                 ....*....|....*
gi 916786761 167 GLIFKSINKSIAANE 181
Cdd:cd17278  156 AEILDSLDAKIDKLE 170
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
124-181 3.35e-08

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 49.29  E-value: 3.35e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 916786761 124 FRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:COG0732    6 LRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALE 63
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 9-181 4.13e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2; This model contains Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2 and similar TRD-CR's. S.SonII recognizes 5'... GTCANNNNNNRTCA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.SonII TRD1-CR1 does not belong to this subfamily.


Pssm-ID: 341135 [Multi-domain]  Cd Length: 189  Bit Score: 48.29  E-value: 4.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGES---YSGLSGKTKDDfGIgnsKFITYKNIFDN-------EMISESQMEKVLINSsekqnKVNIGDAFFT 78
Cdd:cd17246    1 WEWVKLGEISSDitdGTHPTPKYVES-GI---PFITSKNIKNGkidfsdvKYISEEDHNEILKRS-----KLKKGDILFS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  79 ISSEtpneVGMSSVLNfKHENLYLNSFSFGFRTNI-NIDNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKI 157
Cdd:cd17246   72 IIGT----IGRVAIVP-EDLPANINQAVALIRPKKeKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPL 146

                        170       180
                 ....*....|....*....|....
gi 916786761 158 PDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17246  147 PPLEEQKRIAAILDSLDALIDKLE 170
RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like cd17258
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 41-177 1.14e-05

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: 43.93  E-value: 1.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  41 TYKNIFDNEMISESQ---MEKVLINSSEKQNK-VNIGDAFFTIssetPNEVGMSSVLNFkhENLYLNSFSFGFRTNINI- 115
Cdd:cd17258   16 NIKLVCIKNELINSLkvkIVEPDYKIGLKQSKiFKKGDVLITR----HGTIGRVSIILS--EEACLSSHVAGFNSKEGIs 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 916786761 116 DNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSI 177
Cdd:cd17258   90 DNKFIKYLFNSKKIKNRLMSYGASSTQPALNLSRLLKIKFPNPPLEEQQKIGKILSTWDRAI 151
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 109-181 1.18e-05

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


Pssm-ID: 341148 [Multi-domain]  Cd Length: 189  Bit Score: 44.04  E-value: 1.18e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 916786761 109 FRTNINIDNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17259  101 IRPKDELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLE 173
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 109-183 2.12e-05

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: 43.30  E-value: 2.12e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 916786761 109 FRTNINIDNYFLANSFRseYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANEFK 183
Cdd:cd17245   86 IRANKDIDNLFLYYYLK--YNKPELEKLGTGSTFKAINKKDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKAL 158
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 108-181 3.81e-05

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: 42.42  E-value: 3.81e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 916786761 108 GFRTNINIDNYFLANSFRSEyfRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17515   92 AILPNEEIDNEFLFYFLKSQ--KEYLISLGKGGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKLIEKLE 163
RMtype1_S_Eco15ORF14057P-TRD1-CR1_like cd17525
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 9-184 1.65e-04

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: 40.68  E-value: 1.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGESYS--GLSGKTKDDFGIgnsKFITYKNIFDNEMISESQMEKVLINSSEK-QNKVNIGDAFFTiSSETPN 85
Cdd:cd17525    1 WEWVKLGDILSSTQlgLVRSNSEDPNGY---PYIKMGNIGRGGINLLKVETYVDATELEVeKYLLEDGDLLFN-TRNTLE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  86 EVGMSSVLNFKHENLYLNSFSFGFRTNINIDNYFLANSFRSEYFRNNIVKLAQG-ISRYNISKNKVLNLSIKIPDFCEQT 164
Cdd:cd17525   77 LVGKVAIWRGELPKALFNNNILRIRFDDIVLPYFINYYLNSPDGKKQLESIASGtTSVAAIYQKDLKKLKLPLPPLDEQR 156

                        170       180
                 ....*....|....*....|
gi 916786761 165 KVGLIFKSINKSIAANEFKH 184
Cdd:cd17525  157 EIVSFLSELDAKIDQLEQKL 176
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 87-181 2.52e-04

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: 40.28  E-value: 2.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  87 VGMSSVLNFKHENLYLNSFSFGFRT-NINIDNYFLANSFRSEYFRNNIVKLAQG-ISRYNISKNKVLNLSIKIPDFCEQT 164
Cdd:cd17512   83 VGKVVRVPKEADGALLNQNAVKIRPkKGILDQSFLFYNLKSERFKNYIESIARGnANQASITLGDIKKFKFLLPPLEEQK 162

                         90
                 ....*....|....*..
gi 916786761 165 KVGLIFKSINKSIAANE 181
Cdd:cd17512  163 KIASILSAYDDLIENNE 179
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 112-179 2.94e-04

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: 40.22  E-value: 2.94e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 916786761 112 NINIDNYFLAnsFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAA 179
Cdd:cd17275  101 DEKLDFEFLY--YWLLSLKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIAEILDKIDAEIDK 166
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 112-181 6.67e-04

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) TRD1-CR1, and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) TRD2-CR2; The recognition sequences of Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341175 [Multi-domain]  Cd Length: 179  Bit Score: 39.01  E-value: 6.67e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 916786761 112 NINIDNYFL--ANSFRSEYFRNNIVKLAQGIsrynISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17286   94 NKNYDPEFLyyALENWSKKIKSLAGKQAVPI----INKTEFSKIKILVPPLEEQQKIANFLSKLDELIELQQ 161
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 112-181 6.91e-04

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: 39.04  E-value: 6.91e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761 112 NINIDNYFLANSFRSEyfRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17513   97 IKEVNPLFLAYLLYSL--LQKLKSQLQGTSIKGITKDDLKNLKIPLPPLEEQQKIAAILSKLDKLIEAHE 164
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 9-181 1.01e-03

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: 38.62  E-value: 1.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGES--YsGLSGKTKDDFGigNSKF--ITykNIFDNEMISESQMEKVLINSSEKQNKVNIGDAFFtisSETP 84
Cdd:cd17521    1 WEVKKLGELSEKiqY-GYTASAAYEDG--GPRYlrIT--DIQDDGVLWDTVPYCSISEEDAEKYLLKDGDILF---ARTG 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  85 NEVGMSSVLNFKHENLYLNSFSFGFRTNIN-IDNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQ 163
Cdd:cd17521   73 ATVGKSYLYKEDDGKAVFASYLIRFRPNKKkVLPKYLFYFTQSSLYWKQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQ 152

                        170
                 ....*....|....*...
gi 916786761 164 TKVGLIFKSINKSIAANE 181
Cdd:cd17521  153 KRIVAILDALDAKIDALE 170
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 108-181 1.93e-03

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: 37.48  E-value: 1.93e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 916786761 108 GFRTNINIDNYFLANSFrsEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17496   86 AIRPKNGIDTEFLYYLL--ESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNK 157
RMtype1_S_Asp27244ORF1181P-TRD1-CR1_like cd17518
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 38-179 2.83e-03

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: 37.34  E-value: 2.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  38 KFITYKNIFDNEMISES-----QMEKVliNSSEKQNKVNIGDAFFTISSetpNEVGMSSVLNFKHENLYLNSFSFGFRT- 111
Cdd:cd17518   26 KLLNVTNIVNGSLDLDKtdryiSTEEY--NGKYKHFLIDEGDILIASSG---NSWGKVAIVEKDHLPLMLNTSTIRFKFi 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 916786761 112 NINIDNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAA 179
Cdd:cd17518  101 DGLLDNNFLKYFLNSDYFKEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEA 168
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 69-181 3.07e-03

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: 37.13  E-value: 3.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  69 KVNIGDAFFT-ISSETpnEVGMSSVLNFKHENLY--LNSFSFGFRTNInIDNYFLANSFRSEYFRNNIVKLAQ-GISRYN 144
Cdd:cd17522   60 KLQKGDILFShINSIE--HIGKTAIYDGDPEPLIhgMNLLRLRPNKNI-VDPKYLYYLLKSDRFRNQFRSIAKkAVNQAS 136

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 916786761 145 ISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17522  137 INQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRK 173
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 108-181 3.31e-03

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: 37.00  E-value: 3.31e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 916786761 108 GFRT---NINIDNYFLAnsFRSEYFRNNIVKLAQGiSRYN-ISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17273   94 GFKSiipNEEIDNEFLY--YLLKNNKPEIESLASG-STFKeISKSTFKKIEIPLPPLEEQKKIAAILSKLDELIELLE 168
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 112-181 3.94e-03

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: 36.70  E-value: 3.94e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761 112 NINIDNYFLANSFRSEYfrNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17287   98 NDGINPDFLFYYLQSSY--EELRDLSNGGGQPNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAKIDALE 165
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 58-166 4.30e-03

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: 36.75  E-value: 4.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  58 KVLINSSE--KQNKVNIGDAFFTISSeTPNEVGMSSVLNFKHENLY----LnsfsfgFRTNIN---IDNYFLANSFRSEY 128
Cdd:cd17261   47 KYLPESLEpaSEYWLKPGDLLISRAN-TSELVGRAALVDGDPDNLIypdkL------IRLRVNeelLLPEYLALALNSPS 119

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 916786761 129 FRNNIVKLAQGI--SRYNISKNKVLNLSIKIPDFCEQTKV 166
Cdd:cd17261  120 ARRQIESRATGTagSMPKISQSDLKSLPIPLPPLAEQKRI 159
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
58-163 5.31e-03

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 37.17  E-value: 5.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  58 KVLINSSEKQNKVNIGDAFFTISSETPNEVGmSSVLNFKHENLYLNSFSFGFRTNINIDNYFLANSFRSEYFRNNIVKLA 137
Cdd:PRK09737  60 PYCMDAPEDVSKYQLQDRDIVISSAGSIGFS-FLAQNPLPSNVVFASFAIRLKPVNYFSEYFLKHFLESSDYRNQLSLMS 138

                         90       100
                 ....*....|....*....|....*.
gi 916786761 138 QGISRYNISKNKVLNLSIKIPDFCEQ 163
Cdd:PRK09737 139 AGNAVQNINAQSLSTLTFPIPPIAEQ 164
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 109-181 6.07e-03

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: 36.32  E-value: 6.07e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 916786761 109 FRTNINIDNYFLANSFRSEYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17256   95 IRPKDSISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALE 167
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 108-181 6.35e-03

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: 36.27  E-value: 6.35e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 916786761 108 GFRTN-INIDNYFLANSFRseYFRNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17282   96 GFIPNeEKIDVEFLEYYLR--TLKKELEAIAPQSAQKNINLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLE 168
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 9-181 7.60e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1 and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) TRD2-CR; The recognition sequences of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341183 [Multi-domain]  Cd Length: 188  Bit Score: 35.93  E-value: 7.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761   9 WEQRKLKNFGESYSGlsG---KTKDDFGIGN------SKFITYKNIFDNE-MISESQMEkvliNSSEK---QNKVNIGDA 75
Cdd:cd17294    1 WEWKTLGEIAKIFSG--GtpsTSNPEYWDGGtipwlsSGEVNFKEIYETEkRITEEGLK----NSSAKwipKNSVLIALA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  76 FftiSSETpneVGMSSVLNFkheNLYLNSFSFGFRTNINIDNY-FLANSFRSEYfrNNIVKLAQGISRYNISKNKVLNLS 154
Cdd:cd17294   75 G---QGKT---RGTVAILKI---PLTTNQSLAAIEPDEEIANSrFLYYNLSSRY--EELRSLSGGGGRGGLNLKIIKSLP 143

                        170       180
                 ....*....|....*....|....*..
gi 916786761 155 IKIPDFCEQTKVGLIFKSINKSIAANE 181
Cdd:cd17294  144 IPLPPLEEQKKIVAILDKFDALINDLK 170
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 25-173 9.45e-03

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: 35.61  E-value: 9.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916786761  25 SGKTKDDFGIGNSKFITYKNIFDNEMISESQMEKVLINSsekqnkvnigdaffTISSETPNEVGMSSVlnfkheNLYLNS 104
Cdd:cd17514   34 SGETDDNFINNTSEKITTKNGLEDSSIRIVPKGTILIAC--------------TGQGYTRGQVAVLQI------DASTNQ 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 916786761 105 FSFGFRTNINIDNYFLANSFRSEYfrNNIVKLAQGISRYNISKNKVLNLSIKIPDFCEQTKVGLIFKSI 173
Cdd:cd17514   94 AIAAIRCKENVNPKYLYYYLKTQK--NNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNILETL 160
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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