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Conserved domains on  [gi|1574302554|ref|WP_129719499|]
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restriction endonuclease subunit S [Mesomycoplasma neurolyticum]

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 ...
 227-367 1.06e-09

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 cd17521:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 187  Bit Score: 57.49  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 227 KNNNLNDKMTFY---DEKLESFFANKNDVFFTR---FPEPSFGIQNIYEEnsAVFDSSLVKLNIDETKIQKDFFKYFNYS 300
Cdd:cd17521    38 DDGVLWDTVPYCsisEEDAEKYLLKDGDILFARtgaTVGKSYLYKEDDGK--AVFASYLIRFRPNKKKVLPKYLFYFTQS 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1574302554 301 NFWLNWKQKNKTSTLLGGINFLTILNLTLSLPTLANQQKmilIINKLEKLIKILTNIQNKIQKIILI 367
Cdd:cd17521   116 SLYWKQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKR---IVAILDALDAKIDALEELLEKLEEL 179
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 11-146 4.13e-09

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 cd17266:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 159  Bit Score: 55.15  E-value: 4.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554  11 KLEEIAKFYLGK-ILKKPTESKGEYPLISSTskndGIIGKVETFNFQncitlprlgiEDNIFIT----------LRKYKF 79
Cdd:cd17266     2 KLGELCKIKSGKsITASKISEEGDYPVYGGN----GIIGYTDEYNHE----------GEYILIGrvgalcgnvhYVEGKF 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1574302554  80 SATSHLIIVKPNKNIvILDFLYLLLKSLNakISQYA-------IEGDLIKRLSLKklkslklsIPELSIQKEIV 146
Cdd:cd17266    68 WVTDNALVVTPKKEN-NIKFLYYLLKSLN--LNQYAtgsaqplITVSKLKKLKIP--------LPPLEEQKKIA 130
 
Name Accession Description Interval E-value
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 227-367 1.06e-09

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: 57.49  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 227 KNNNLNDKMTFY---DEKLESFFANKNDVFFTR---FPEPSFGIQNIYEEnsAVFDSSLVKLNIDETKIQKDFFKYFNYS 300
Cdd:cd17521    38 DDGVLWDTVPYCsisEEDAEKYLLKDGDILFARtgaTVGKSYLYKEDDGK--AVFASYLIRFRPNKKKVLPKYLFYFTQS 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1574302554 301 NFWLNWKQKNKTSTLLGGINFLTILNLTLSLPTLANQQKmilIINKLEKLIKILTNIQNKIQKIILI 367
Cdd:cd17521   116 SLYWKQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKR---IVAILDALDAKIDALEELLEKLEEL 179
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 11-146 4.13e-09

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


Pssm-ID: 341155 [Multi-domain]  Cd Length: 159  Bit Score: 55.15  E-value: 4.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554  11 KLEEIAKFYLGK-ILKKPTESKGEYPLISSTskndGIIGKVETFNFQncitlprlgiEDNIFIT----------LRKYKF 79
Cdd:cd17266     2 KLGELCKIKSGKsITASKISEEGDYPVYGGN----GIIGYTDEYNHE----------GEYILIGrvgalcgnvhYVEGKF 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1574302554  80 SATSHLIIVKPNKNIvILDFLYLLLKSLNakISQYA-------IEGDLIKRLSLKklkslklsIPELSIQKEIV 146
Cdd:cd17266    68 WVTDNALVVTPKKEN-NIKFLYYLLKSLN--LNQYAtgsaqplITVSKLKKLKIP--------LPPLEEQKKIA 130
 
Name Accession Description Interval E-value
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 227-367 1.06e-09

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: 57.49  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 227 KNNNLNDKMTFY---DEKLESFFANKNDVFFTR---FPEPSFGIQNIYEEnsAVFDSSLVKLNIDETKIQKDFFKYFNYS 300
Cdd:cd17521    38 DDGVLWDTVPYCsisEEDAEKYLLKDGDILFARtgaTVGKSYLYKEDDGK--AVFASYLIRFRPNKKKVLPKYLFYFTQS 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1574302554 301 NFWLNWKQKNKTSTLLGGINFLTILNLTLSLPTLANQQKmilIINKLEKLIKILTNIQNKIQKIILI 367
Cdd:cd17521   116 SLYWKQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKR---IVAILDALDAKIDALEELLEKLEEL 179
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 11-146 4.13e-09

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


Pssm-ID: 341155 [Multi-domain]  Cd Length: 159  Bit Score: 55.15  E-value: 4.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554  11 KLEEIAKFYLGK-ILKKPTESKGEYPLISSTskndGIIGKVETFNFQncitlprlgiEDNIFIT----------LRKYKF 79
Cdd:cd17266     2 KLGELCKIKSGKsITASKISEEGDYPVYGGN----GIIGYTDEYNHE----------GEYILIGrvgalcgnvhYVEGKF 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1574302554  80 SATSHLIIVKPNKNIvILDFLYLLLKSLNakISQYA-------IEGDLIKRLSLKklkslklsIPELSIQKEIV 146
Cdd:cd17266    68 WVTDNALVVTPKKEN-NIKFLYYLLKSLN--LNQYAtgsaqplITVSKLKKLKIP--------LPPLEEQKKIA 130
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 10-110 8.59e-08

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: 51.37  E-value: 8.59e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554  10 FKLEEIAKFYLGKIL--KKPTESKGEYPLISSTSKNDGIIGKVETFNF-QNCITLPRLGIEDNiFITLRKYKFSATSHLI 86
Cdd:cd17255     1 KKLGDLFEIGRGRVIskKYISENPGDYPVYSSQTKNNGIMGYINTYDFdGEYITWTTDGANAG-TVFYRNGKFSVTNVCG 79

                          90       100
                  ....*....|....*....|....
gi 1574302554  87 IVKPNKNIVILDFLYLLLKSLNAK 110
Cdd:cd17255    80 VLKVKNKNINNKFLYYALNLIAKK 103
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 192-364 2.27e-07

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: 50.19  E-value: 2.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 192 LSDLLDKQKPYKMGKINFESDDKKNNLYILTYKSFKNNNLNdkmTFYDEKLESFFANKNDVFFTRFPEPSFGIQNIYEen 271
Cdd:cd17263     3 LGEVCKFSKGKQPPISERFDEPKEGSVRYIQIEDLRNNNEK---KYIENPKKSVICNEDDILIVRDGANAGEVGTGLE-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 272 sAVFDSSLVKLNIDETKIQKDFFKYFNYSNFWLNWKQKNKTSTLlGGINFLTILNLTLSLPTLANQQKMILIINKLEKLI 351
Cdd:cd17263    78 -GAIASTLFKIIPDKNIIDKDYLYYFLKSKEIQLNILTKAGSTI-PHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALI 155

                         170
                  ....*....|...
gi 1574302554 352 KILTNIQNKIQKI 364
Cdd:cd17263   156 DKLKELIEKLIEL 168
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 219-371 1.86e-04

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: 42.13  E-value: 1.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 219 YILTYKSFKNNNLN-DKMTF-----YDEKLESFFANKNDVFFTRfpEPSFGIQNIYEENS-AVFDSSLVKLNIDETKIQK 291
Cdd:cd17246    29 PFITSKNIKNGKIDfSDVKYiseedHNEILKRSKLKKGDILFSI--IGTIGRVAIVPEDLpANINQAVALIRPKKEKIDP 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 292 DFFKYFNYSNFWLNWKQKNKTSTLLGGINFLTILNLTLSLPTLANQQKmilIINKLEKLIKILTNIQNKIQKIILINNQI 371
Cdd:cd17246   107 KYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQKR---IAAILDSLDALIDKLEQKLEKLEDLKKGL 183
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 207-363 2.54e-04

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: 41.75  E-value: 2.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 207 INFESDDKKNNLYILTYKSFKNN--NLNDKMTFYD---EKLESFFANKNDVFFTRfpepSFGIQN------IYEEN--SA 273
Cdd:cd17517    17 TSKKSSYDGSGTPVLRIPNIYDGgiDLDDLKKRVDlseKELEKYLLKKGDILFNR----SNGSPElvgkcaLVDEEdePA 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 274 VFDSSLVKLNIDETKIQKDFFKYFNYSNFWLNWKQKN-KTSTLLGGINFLTILNLTLSLPTLANQQKmilIINKLEKLIK 352
Cdd:cd17517    93 IFASYLIRLRLDKKKILPEFLYYYLNSPLGRKQIEKIaKSAAGQANINQKDLKKLPIPLPPLEEQKE---IVEILESLDS 169

                         170
                  ....*....|.
gi 1574302554 353 ILTNIQNKIQK 363
Cdd:cd17517   170 KIDLLEKKLEK 180
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 267-367 2.97e-04

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: 40.60  E-value: 2.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 267 IYEENSAVF-DSSLVKLNIDETKIQKDFFKYFnYSNFwlNWKQKNKTStllggINFL---TILNLTLSLPTLANQQKMIL 342
Cdd:cd17292    47 IYDGEDAYFqDSNIVWLDNDESKVLNKFLYYF-YQII--KWKKTEGST-----IKRLyndNLLNTKIPVPSLDEQRKIAE 118

                          90       100
                  ....*....|....*....|....*
gi 1574302554 343 IINKLEKLIkilTNIQNKIQKIILI 367
Cdd:cd17292   119 FLSLLDALI---ALLQKKLEKLIAL 140
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 192-364 3.56e-04

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: 40.83  E-value: 3.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 192 LSDLLDKQKPYKMGKINFESDDKKNNlyILTYKSFKNNNLNDKMTF----YDEKLESFFANKNDVFFTRfpEPSFGIQNI 267
Cdd:cd16961     3 LGEIAEIISGKTPSSSSEYWDNGIIP--WIRISDINNGGIILTDEKiteeGAEKLKKKILPKGDILISR--SGTIGKVAI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554 268 YEENS-AVFDSSLVKLNIDETKIQKdFFKYFNYSNFWLNWKQKNKTSTLLGgINFLTILNLTLSLPTLANQQKMILIINK 346
Cdd:cd16961    79 VKENDkALLNQAVIVIRPKDEVDSE-FLYYFLKSPFGKKLIEGSAGSTQPN-LNKSDLKNLKIPLPPLEEQKKIANILDK 156

                         170
                  ....*....|....*...
gi 1574302554 347 LEKLIKILTNIQNKIQKI 364
Cdd:cd16961   157 LDALIELLEQKLEKLEQL 174
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 11-147 2.68e-03

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: 38.26  E-value: 2.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554  11 KLEEIAKFYLGK-ILKKPTESKGEYPLISSTSKNdgiIGKVETFN-FQNCITLPRLGIedNI-FITLRKYKFSATSHLII 87
Cdd:cd17291     2 KLGEIAEIKKGKqITKKELIENGKYPVIAGGIEP---SGYHNEYNrEGNTITISASGA--SAgYVNYWKEPFWASDCCYI 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1574302554  88 VKPNKNIVILdFLYLLLKSLNAKISQYAIEGDlIKRLSLKKLKSLKLSIPELSIQKEIVQ 147
Cdd:cd17291    77 LSSKNELVNK-FLYYFLKNKQEEIYSLQRGAG-QPHIYKKDIEKLKIPIPPLEEQQKIVE 134
 
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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