NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2129718046|gb|UEG62291|]
View 

restriction endonuclease subunit S [Stutzerimonas chloritidismutans]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 356-534 1.39e-79

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: 247.41  E-value: 1.39e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 356 LGSLSQVKGGKRLPAGTAFAPAKTPHVYIQVTNMKDGTIIDENLKYIDEVTKAAIKQYTISKDDVYITIAGTIGDVGIVP 435
Cdd:cd17256     1 LGEIARVKGGGRLPKGESLSDGPTGVPYIRVTDIKNGGIDLDNLKYISPEIHEKIKRYTLSKGDILISIVGTIGRVGIVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 436 EHFDGMNLTENAAKIVF-QKIDRRWLQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQHRIVAKVDQLM 514
Cdd:cd17256    81 KELDGANLTENAARIRPkDSISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLD 160

                         170       180
                  ....*....|....*....|
gi 2129718046 515 ALCDQLKTRLTQARQLNEQL 534
Cdd:cd17256   161 AKIDALEKQLAKLEELKKAL 180
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 90-252 3.35e-57

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoAO83I TRD1-CR1 and S.AbaB8342I TRD2-CR2; Escherichia coli strain A0 34/86 S subunit (S.EcoAO83I) recognizes 5'... GGANNNNNNNNATGC ... 3, and Acinetobacter baumannii B8342 S subunit (S.AbaB8342I) recognizes 5'... TTCANNNNNNTCC ... 3. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example S.AbaB8342I-TRD1 recognizes TTCA/TGAA and S.AbaB8342I-TRD2 recognizes GGA/TCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Type IIG restriction enzyme/N6-adenine DNA methyltransferases from Thermus scotoductus RFL1 (RM.TstI) and Acinetobacter lwoffi Ks 4-8 (RM.AloI), as well as type I DNA methyltransferases such as Sideroxydans lithotrophicus ES-1 Type I N6-adenine DNA methyltransferase (M.SliESORF1090P). RM.TstI recognizes 5' ... CACNNNNNNTCC ... 3' and RM.AloI recognizes 5' ... GAACNNNNNNTCC ... 3'.


:

Pssm-ID: 341156 [Multi-domain]  Cd Length: 158  Bit Score: 187.99  E-value: 3.35e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  90 RRFGEVFSLEYGDNLPADKRSNtGEYPVYGSNGVVGTHSTCFVDSPCIVVGRKGSAGALNLClSRGCCVTDVAYYCIPPS 169
Cdd:cd17267     1 VKLGDVIELQYGKDLPKSRRIP-GPYPVYGSNGIVGYHNEALVKGPGIVVGRKGSIGKVHYS-EEDFWPIDTTLYVKDFK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 170 AFSLDYAFKLFHTLGLDSL--GKGIkPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQ 247
Cdd:cd17267    79 GNDPRFLYYLLKTLDLERLnsGSAV-PGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLE----ELAD 153


                  ....*
gi 2129718046 248 ALLDS 252
Cdd:cd17267   154 ALLPK 158
class_II_aaRS-like_core super family cl00268
Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA ...
 242-319 1.48e-03

Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ.


The actual alignment was detected with superfamily member PRK12294:

Pssm-ID: 444800  Cd Length: 272  Bit Score: 40.56  E-value: 1.48e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2129718046 242 HAQLVQALLDSLTQASDAEDFAQNwRRLAEHFHTLFTTEPSIDALKQ-TLLQLAVMGKLVpqdPNDEPASELLKRITEE 319
Cdd:PRK12294  141 HYQLLDALLDKSLQTPDILSMIEE-RNLSGLVTYLSTEHPIVQILKEnTQQQLNVLEHYI---PNDHPALVELKIWERW 215
 
Name Accession Description Interval E-value
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 356-534 1.39e-79

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: 247.41  E-value: 1.39e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 356 LGSLSQVKGGKRLPAGTAFAPAKTPHVYIQVTNMKDGTIIDENLKYIDEVTKAAIKQYTISKDDVYITIAGTIGDVGIVP 435
Cdd:cd17256     1 LGEIARVKGGGRLPKGESLSDGPTGVPYIRVTDIKNGGIDLDNLKYISPEIHEKIKRYTLSKGDILISIVGTIGRVGIVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 436 EHFDGMNLTENAAKIVF-QKIDRRWLQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQHRIVAKVDQLM 514
Cdd:cd17256    81 KELDGANLTENAARIRPkDSISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLD 160

                         170       180
                  ....*....|....*....|
gi 2129718046 515 ALCDQLKTRLTQARQLNEQL 534
Cdd:cd17256   161 AKIDALEKQLAKLEELKKAL 180
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 90-252 3.35e-57

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoAO83I TRD1-CR1 and S.AbaB8342I TRD2-CR2; Escherichia coli strain A0 34/86 S subunit (S.EcoAO83I) recognizes 5'... GGANNNNNNNNATGC ... 3, and Acinetobacter baumannii B8342 S subunit (S.AbaB8342I) recognizes 5'... TTCANNNNNNTCC ... 3. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example S.AbaB8342I-TRD1 recognizes TTCA/TGAA and S.AbaB8342I-TRD2 recognizes GGA/TCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Type IIG restriction enzyme/N6-adenine DNA methyltransferases from Thermus scotoductus RFL1 (RM.TstI) and Acinetobacter lwoffi Ks 4-8 (RM.AloI), as well as type I DNA methyltransferases such as Sideroxydans lithotrophicus ES-1 Type I N6-adenine DNA methyltransferase (M.SliESORF1090P). RM.TstI recognizes 5' ... CACNNNNNNTCC ... 3' and RM.AloI recognizes 5' ... GAACNNNNNNTCC ... 3'.


Pssm-ID: 341156 [Multi-domain]  Cd Length: 158  Bit Score: 187.99  E-value: 3.35e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  90 RRFGEVFSLEYGDNLPADKRSNtGEYPVYGSNGVVGTHSTCFVDSPCIVVGRKGSAGALNLClSRGCCVTDVAYYCIPPS 169
Cdd:cd17267     1 VKLGDVIELQYGKDLPKSRRIP-GPYPVYGSNGIVGYHNEALVKGPGIVVGRKGSIGKVHYS-EEDFWPIDTTLYVKDFK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 170 AFSLDYAFKLFHTLGLDSL--GKGIkPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQ 247
Cdd:cd17267    79 GNDPRFLYYLLKTLDLERLnsGSAV-PGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLE----ELAD 153


                  ....*
gi 2129718046 248 ALLDS 252
Cdd:cd17267   154 ALLPK 158
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
346-530 6.24e-25

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 107.66  E-value: 6.24e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 346 QLPAGWEWVRLGSLSQVKGGKRLPAGTAFAPAK-TPHVYIQVTNMKDGTIIDENLKYIDEVTKAaIKQYTISKDDVYITI 424
Cdd:PRK09737    5 KLPEGWVTTHISEICSVIRGVKPPKGYATKSLTmGDLPFIRTTDITNGAVDLTTLPYCMDAPED-VSKYQLQDRDIVISS 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 425 AGTIGDVGIVPEHF-DGMNLTENAAKIVFQK-IDRRWLQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAE 502
Cdd:PRK09737   84 AGSIGFSFLAQNPLpSNVVFASFAIRLKPVNyFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAE 163

                         170       180
                  ....*....|....*....|....*...
gi 2129718046 503 QHRIVAKVDQLMALCDQLKTRLTQARQL 530
Cdd:PRK09737  164 QKIIAEKLDTLLAQVDSTKARLEQIPQI 191
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 348-526 1.96e-12

Type I restriction modification DNA specificity domain; This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits.


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 65.45  E-value: 1.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 348 PAGWEWVRLGSLSQVKGGKRLPAGTAFAPAKTPhvYIQVTNMKDGTIIDENLkyidevtkaaIKQYTISKDDVYITIAGT 427
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELKNNGKYP--YIRAGDLNNVVKGGLGY----------IKKYILPKGDITISSRAT 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 428 IGDVGIVPEHF---DGMNLTENAAKIVFQKIDRRWLQkalssqFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQH 504
Cdd:pfam01420  69 IGYVFYRDKPYytnQHIIVLIPKNNIKITEFLYLYLL------LKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQK 142

                         170       180
                  ....*....|....*....|..
gi 2129718046 505 RIVAKVDQLMALCDQLKTRLTQ 526
Cdd:pfam01420 143 KIAKILSQLDNTIELEKGILNE 164
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
463-543 8.55e-08

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 50.06  E-value: 8.55e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 463 ALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQHRIVAKVDQLMalcDQLkTRLTQARQLNEQLANTLVEHA 542
Cdd:COG0732     5 YLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLF---DKI-AALEKEIEKLKELRDALLPKL 80


                  .
gi 2129718046 543 V 543
Cdd:COG0732    81 F 81
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
185-253 2.51e-06

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 45.82  E-value: 2.51e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 185 LDSLGKGIK-PGLNRNEAYELVVAAPPLAEQHRIVAKVDELMalcDRLEAQQADAEsAHAQLVQALLDSL 253
Cdd:COG0732    15 LRSLATGSTqPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLF---DKIAALEKEIE-KLKELRDALLPKL 80
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 84-234 6.52e-04

Type I restriction modification DNA specificity domain; This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits.


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 40.80  E-value: 6.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  84 PNGWVWRRFGEVFSLEYGDNLPADKRSNTGEYPVYGSN-------GVVGTHSTCFVDSPCIVVGRKGSAGALNLclsrgc 156
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELKNNGKYPYIRAGdlnnvvkGGLGYIKKYILPKGDITISSRATIGYVFY------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 157 cvTDVAYYC-------IPPSAFSLDYAFKLFHTLGLDSL-----GKGIkPGLN--RNEAYELVVaaPPLAEQHRIVAKVD 222
Cdd:pfam01420  75 --RDKPYYTnqhiivlIPKNNIKITEFLYLYLLLKLKKLkslkfGSTQ-PKLTkeRLKEIKIPL--PPLEEQKKIAKILS 149

                         170
                  ....*....|..
gi 2129718046 223 ELMAlCDRLEAQ 234
Cdd:pfam01420 150 QLDN-TIELEKG 160
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
189-286 7.20e-04

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 42.18  E-value: 7.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 189 GKGIKpGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALldsLTQASDAEDFAQnWRr 268
Cdd:PRK09737  351 GTTQK-HITGKALANYPIRVPPLEEQAEIVRRVEQLFAYADTIEKQVNNALARVNNLTQSI---LAKAFRGELTAQ-WR- 424

                          90
                  ....*....|....*...
gi 2129718046 269 lAEHfHTLFTTEPSIDAL 286
Cdd:PRK09737  425 -AEN-PSLISGENSAAAL 440
hisZ PRK12294
ATP phosphoribosyltransferase regulatory subunit; Provisional
 242-319 1.48e-03

ATP phosphoribosyltransferase regulatory subunit; Provisional


Pssm-ID: 237044  Cd Length: 272  Bit Score: 40.56  E-value: 1.48e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2129718046 242 HAQLVQALLDSLTQASDAEDFAQNwRRLAEHFHTLFTTEPSIDALKQ-TLLQLAVMGKLVpqdPNDEPASELLKRITEE 319
Cdd:PRK12294  141 HYQLLDALLDKSLQTPDILSMIEE-RNLSGLVTYLSTEHPIVQILKEnTQQQLNVLEHYI---PNDHPALVELKIWERW 215
 
Name Accession Description Interval E-value
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 356-534 1.39e-79

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: 247.41  E-value: 1.39e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 356 LGSLSQVKGGKRLPAGTAFAPAKTPHVYIQVTNMKDGTIIDENLKYIDEVTKAAIKQYTISKDDVYITIAGTIGDVGIVP 435
Cdd:cd17256     1 LGEIARVKGGGRLPKGESLSDGPTGVPYIRVTDIKNGGIDLDNLKYISPEIHEKIKRYTLSKGDILISIVGTIGRVGIVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 436 EHFDGMNLTENAAKIVF-QKIDRRWLQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQHRIVAKVDQLM 514
Cdd:cd17256    81 KELDGANLTENAARIRPkDSISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLD 160

                         170       180
                  ....*....|....*....|
gi 2129718046 515 ALCDQLKTRLTQARQLNEQL 534
Cdd:cd17256   161 AKIDALEKQLAKLEELKKAL 180
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 90-252 3.35e-57

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoAO83I TRD1-CR1 and S.AbaB8342I TRD2-CR2; Escherichia coli strain A0 34/86 S subunit (S.EcoAO83I) recognizes 5'... GGANNNNNNNNATGC ... 3, and Acinetobacter baumannii B8342 S subunit (S.AbaB8342I) recognizes 5'... TTCANNNNNNTCC ... 3. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example S.AbaB8342I-TRD1 recognizes TTCA/TGAA and S.AbaB8342I-TRD2 recognizes GGA/TCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Type IIG restriction enzyme/N6-adenine DNA methyltransferases from Thermus scotoductus RFL1 (RM.TstI) and Acinetobacter lwoffi Ks 4-8 (RM.AloI), as well as type I DNA methyltransferases such as Sideroxydans lithotrophicus ES-1 Type I N6-adenine DNA methyltransferase (M.SliESORF1090P). RM.TstI recognizes 5' ... CACNNNNNNTCC ... 3' and RM.AloI recognizes 5' ... GAACNNNNNNTCC ... 3'.


Pssm-ID: 341156 [Multi-domain]  Cd Length: 158  Bit Score: 187.99  E-value: 3.35e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  90 RRFGEVFSLEYGDNLPADKRSNtGEYPVYGSNGVVGTHSTCFVDSPCIVVGRKGSAGALNLClSRGCCVTDVAYYCIPPS 169
Cdd:cd17267     1 VKLGDVIELQYGKDLPKSRRIP-GPYPVYGSNGIVGYHNEALVKGPGIVVGRKGSIGKVHYS-EEDFWPIDTTLYVKDFK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 170 AFSLDYAFKLFHTLGLDSL--GKGIkPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQ 247
Cdd:cd17267    79 GNDPRFLYYLLKTLDLERLnsGSAV-PGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLE----ELAD 153


                  ....*
gi 2129718046 248 ALLDS 252
Cdd:cd17267   154 ALLPK 158
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-534 2.55e-37

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


Pssm-ID: 341135 [Multi-domain]  Cd Length: 189  Bit Score: 136.11  E-value: 2.55e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQ--VKGgkrlpagtafaPAKTPHV------YIQVTNMKDGTIIDENLKYIDEVT-KAAIKQYTISKDDVY 421
Cdd:cd17246     1 WEWVKLGEISSdiTDG-----------THPTPKYvesgipFITSKNIKNGKIDFSDVKYISEEDhNEILKRSKLKKGDIL 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 422 ITIAGTIGDVGIVPEHFDgMNLTENAAKIVF--QKIDRRWLQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPP 499
Cdd:cd17246    70 FSIIGTIGRVAIVPEDLP-ANINQAVALIRPkkEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPP 148

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2129718046 500 LAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17246   149 LEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGL 183
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 90-251 3.44e-30

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: 115.62  E-value: 3.44e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  90 RRFGEVFSLEYGDNLPADKRSNTGEYPVYGSNGVVGTHSTCFVDSPCIVVGRKGS-AGALNLCLSRgCCVTDVAYYCIPP 168
Cdd:cd17266     1 VKLGELCKIKSGKSITASKISEEGDYPVYGGNGIIGYTDEYNHEGEYILIGRVGAlCGNVHYVEGK-FWVTDNALVVTPK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 169 SAFSLDYAFKLFHTLGLDSL--GKGIkPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLV 246
Cdd:cd17266    80 KENNIKFLYYLLKSLNLNQYatGSAQ-PLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDLLEKKLEKLI----ELK 154


                  ....*
gi 2129718046 247 QALLD 251
Cdd:cd17266   155 KELMQ 159
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-534 9.09e-27

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: 107.21  E-value: 9.09e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQVKGGKrlpagtAFapaK------TPHVYIQVTNMKDGTIIDENLKYIDEVTKAAIKQYTISKDDvyITI 424
Cdd:cd17278     1 WEVVKLGDIADIQNGY------AF---KssdfsdEGIPVIRIGNIKNGGIDLDDNSKYPEEPLEKYEKFLLKKGD--ILI 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 425 A---GTIGDVGIVPEHFDGMNLTENAAKIVF-QKIDRRWLQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPL 500
Cdd:cd17278    70 AmtgGTVGKVAIVPEDDEPALLNQRVGKFRPkDKIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPL 149

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2129718046 501 AEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17278   150 EEQKKIAEILDSLDAKIDKLEQKLEKLRDLLKPL 183
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 351-538 3.39e-25

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Escherichia coli A58 S subunit (S.EcoEI) TRD2-CR2, and Aminomonas paucivorans S subunit (S.Apa12260I); Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3', Escherichia coli A58 S subunit (S.EcoEI) recognizes 5'... GAGNNNNNNNATGC ... 3', and Aminomonas paucivorans S subunit (S.Apa12260I) recognizes 5'... GCCNNNNNCTCC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 recognizes AAC/GTT and S.EcoKI-TRD2 recognizes GCAC/GTGC, S.EcoEI TRD1 recognizes GAG/CTC and S.EcoEI TRD2 recognizes GCAT/ATGC, and S.Apa12260I TRD1 recognizes GCC/GGC and S.Apa12260I TRD2 recognizes GGAG/CTCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341150 [Multi-domain]  Cd Length: 191  Bit Score: 102.61  E-value: 3.39e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSL-SQVKGGK--------------RLPAGTafapaktphvyiqvtnmkDGTIIDENLKYIDEVTKAAiKQYTI 415
Cdd:cd17261     1 WEWVRLGDLiEGIRNGWspkppddetgwpvlKLSAVT------------------SGKFDPSENKYLPESLEPA-SEYWL 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 416 SKDDVYITIAGTI---GDVGIVPEHFDG-------MNLtenaaKIVFQKIDRRWLQKALSSQFAQRQFSD--STNQLAQP 483
Cdd:cd17261    62 KPGDLLISRANTSelvGRAALVDGDPDNliypdklIRL-----RVNEELLLPEYLALALNSPSARRQIESraTGTAGSMP 136

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2129718046 484 KLALHRIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17261   137 KISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
346-530 6.24e-25

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 107.66  E-value: 6.24e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 346 QLPAGWEWVRLGSLSQVKGGKRLPAGTAFAPAK-TPHVYIQVTNMKDGTIIDENLKYIDEVTKAaIKQYTISKDDVYITI 424
Cdd:PRK09737    5 KLPEGWVTTHISEICSVIRGVKPPKGYATKSLTmGDLPFIRTTDITNGAVDLTTLPYCMDAPED-VSKYQLQDRDIVISS 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 425 AGTIGDVGIVPEHF-DGMNLTENAAKIVFQK-IDRRWLQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAE 502
Cdd:PRK09737   84 AGSIGFSFLAQNPLpSNVVFASFAIRLKPVNyFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAE 163

                         170       180
                  ....*....|....*....|....*...
gi 2129718046 503 QHRIVAKVDQLMALCDQLKTRLTQARQL 530
Cdd:PRK09737  164 QKIIAEKLDTLLAQVDSTKARLEQIPQI 191
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 354-530 4.19e-23

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: 96.30  E-value: 4.19e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 354 VRLGSLSQVKGGKRLPAGTAFAPAKTpHVYIQVTNMKDGTIIDENLkYIDEVTKAAIKQYTISKDDVYITIAGTIGDVGI 433
Cdd:cd16961     1 KKLGEIAEIISGKTPSSSSEYWDNGI-IPWIRISDINNGGIILTDE-KITEEGAEKLKKKILPKGDILISRSGTIGKVAI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 434 VPEHfDGMNLTENAAKIVFQK-IDRRWLQKALSSQFAQRQFSDSTNQlAQPKLALHRIAGSVLALPPLAEQHRIVAKVDQ 512
Cdd:cd16961    79 VKEN-DKALLNQAVIVIRPKDeVDSEFLYYFLKSPFGKKLIEGSAGS-TQPNLNKSDLKNLKIPLPPLEEQKKIANILDK 156

                         170
                  ....*....|....*...
gi 2129718046 513 LMALCDQLKTRLTQARQL 530
Cdd:cd16961   157 LDALIELLEQKLEKLEQL 174
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 365-535 2.02e-22

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O69:H11 07-3763 S subunit (S.Eco3763I) TRD2-CR2; Escherichia coli O69:H11 07-3763 S subunit (S.Eco3763I) recognizes 5'... TACNNNNNNNRTRTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341153 [Multi-domain]  Cd Length: 184  Bit Score: 94.53  E-value: 2.02e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 365 GKRLPAGTAFAPAKTPhvYIQVTNMKDGTIIDENLKYIDEVTKAAIKQYTISKDDVYITIAGTIGDVGIVPEHFDGMNlt 444
Cdd:cd17264    14 GKNYPSKSEFVDEGIP--FINAGHLEDGTIDLSNMNFISEEKYNSLGSGKLQKGDILYCLRGSLGKCAIVDNYDEGAI-- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 445 enAAKIV----FQKIDRRWLQKALSSQFAQRQFSDSTNQLAQPKLAlhriAGSV----LALPPLAEQHRIVAKVDQLMAL 516
Cdd:cd17264    90 --ASSLViirpFAKVDVRYLYYYLNSPLGKSQIKKYDNGSAQPNLS----AKSLkkflIPLPPLEEQKRIVAKLDELDAL 163

                         170
                  ....*....|....*....
gi 2129718046 517 CDQLKTRLTQARQLNEQLA 535
Cdd:cd17264   164 IDKLKQALEKLEELLQSLF 182
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 350-539 2.36e-21

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I), Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) TRD2-CR2, and Streptomyces species SirexAA-E S subu; Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I) recognizes 5'... CACNNNNNNNCTGG ... 3' and Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) recognizes 5'... RTCANNNNNNNNGTGG ... 3'. The recognition sequence of Streptomyces species SirexAA-E S subunit (S.SspAAEORF2129P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Eco2071ORF3585P TRD1 recognizes RTCA/TGAY and S.Eco2071ORF3585P TRD2 recognizes CCAC/GTGG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341142 [Multi-domain]  Cd Length: 193  Bit Score: 91.77  E-value: 2.36e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 350 GWEWVRLGSLSQVKGGKRLpaGTAFAPAKTPHVYIQVTNMKDGTIIDENLKYIdEVTKAAIKQYTISKDDVYITIAGTIG 429
Cdd:cd17253     1 GWEWVRLGDVAEVQSGITK--GKKRRGGELEVPYLRVANVQDGYLDLSEVKEI-EVTEEELERYRLRKGDLLVTEGGDSD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 430 DVG---IVPEHFDGMnltenaakiVFQK-----------IDRRWLQKALSSQFAQRQFSDSTNQ---LAqpklalH---- 488
Cdd:cd17253    78 KLGrgaIWRGEIPPC---------LHQNhlfrvrpkddlLLPEFLSYWLNSAYGRGYFLRAAKQttnLA------Sinst 142

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2129718046 489 RIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTLV 539
Cdd:cd17253   143 KLKALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-534 1.39e-19

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR),similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Salmonella enterica subsp. enterica serovar Potsdam S sub; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3' and Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 both recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2.It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341198 [Multi-domain]  Cd Length: 192  Bit Score: 86.82  E-value: 1.39e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSL-SQVKGGKRLPAgtAFAPAKTPHVYIqvTNMKDGTIIDENLKYIDEVTKAAIKQYTISKDDVYIT----IA 425
Cdd:cd17517     1 WEVVKLGDLlEDPRYGTSKKS--SYDGSGTPVLRI--PNIYDGGIDLDDLKKRVDLSEKELEKYLLKKGDILFNrsngSP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 426 GTIGDVGIVPEHFDGM----NLTenaaKIVF--QKIDRRWLQKALSSQFAQRQFSDSTNQLA-QPKLALHRIAGSVLALP 498
Cdd:cd17517    77 ELVGKCALVDEEDEPAifasYLI----RLRLdkKKILPEFLYYYLNSPLGRKQIEKIAKSAAgQANINQKDLKKLPIPLP 152

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2129718046 499 PLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17517   153 PLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSL 188
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-534 2.27e-19

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: 86.03  E-value: 2.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQVKGGKrlpagtAFAPA---KTPHVYIQVTNMKDGTIIDENLKYIDEVTKAAIKQYTISKDDVYITIAGT 427
Cdd:cd17259     1 WEWVKLGDVADILSGY------AFKSSefsESGIRLLRGANVGVGEIRWDDTVYLPEEYLEEYEKYLLKEGDIVIALDRP 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 428 IGDVG----IVPEHFDGMNLTENAAKIVFQK-IDRRWLQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAE 502
Cdd:cd17259    75 IISGGlkvaRIPKSDLPALLVQRVARIRPKDeLNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEE 154

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2129718046 503 QHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17259   155 QKKIAEFLSSLDALIDLLEQKLEKLQQLKKGL 186
RMtype1_S_StySPI-TRD2-CR2_like cd17523
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Salmonella ...
 351-538 5.63e-19

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


Pssm-ID: 341204 [Multi-domain]  Cd Length: 190  Bit Score: 84.98  E-value: 5.63e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSL---SQVKGGKRLPAGtafapaKTPHVYIQVTNMKDGTIIDENLKYIDeVTKAAIKQYTISKDDVYIT---- 423
Cdd:cd17523     1 WEWVRLGDLipeFQNGLSKRGGSD------GEPIIVLRLADIKNNKISFENLRRIK-LTEKEIEKYSLSKGDLLIIrvng 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 424 ---IAG-TI----GDVGIVPEHFDGMnltenaaKIVFQKIDRRWLQKALSSQFAQRQFSD---ST------NQLAqpkla 486
Cdd:cd17523    74 spdLVGrFIlfkgYEDVAYCDHFIRM-------RLDQEKIDPEFLSYIFNSPLIRRKIERnfvTSagqktvNQGH----- 141

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2129718046 487 lhrIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17523   142 ---IKSLPIPLPPLKEQKKIVARVEELFALIDQLESSLDLAQQLQNKLAQSI 190
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-529 4.41e-18

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: 82.66  E-value: 4.41e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSL-SQVKGGkrlpagtAFAPAKtphvY-------IQVTNMKDGTIIDENLKYIDEVTKAAIKQYTISKDDVYI 422
Cdd:cd17512     1 WEEIRLGDIiDYQKGY-------AFKSKD----YqdsgiriVRVSDFTDDSIDINNLVYISEEKANKYKKYELKENDIII 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 423 TIAG--------TIGDVGIVPEHFDGMNLTENAAKIVFQK--IDRRWLQKALSS----QFAQRQFSDSTNQLAqpkLALH 488
Cdd:cd17512    70 TTVGswpsnpdsVVGKVVRVPKEADGALLNQNAVKIRPKKgiLDQSFLFYNLKSerfkNYIESIARGNANQAS---ITLG 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2129718046 489 RIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQ 529
Cdd:cd17512   147 DIKKFKFLLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQ 187
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-534 1.06e-17

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: 81.07  E-value: 1.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQVKGG---KrlPAGTAFAPAKTPHVYIQVTNMKDGTIIDENLKYIDEVTKAaiKQYTISKDDVYITIA-G 426
Cdd:cd17252     1 WEWVRLGEIAEIIRGvtyK--KSDASEEPSEGGIPVLRANNIQNGGLDFDDLVYVPKSKVK--EEQKLKKGDILICMSsG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 427 T---IGDVGIVPEHFDGmnlTENA--AKIVF-QKIDRRWLQKALSSQFAQRQFSDST-----NQLAqpKLALHRIAgsvL 495
Cdd:cd17252    77 SkelVGKAAFIDEDTDY---TFGAfcGVIRPkKEIDPRYLFYFLQSPSYREYIRSLAsgtniNNLS--NEHLENLK---I 148

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2129718046 496 ALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17252   149 PLPPLAEQKRIVAKLDKLDALIDKLKQALEKLDELLKSL 187
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 87-253 3.34e-15

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


Pssm-ID: 341177 [Multi-domain]  Cd Length: 163  Bit Score: 73.27  E-value: 3.34e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  87 WVWRRFGEVFSLEYGdnlpAD-KRSNTGEYPVYGSNGVVGTHSTCFVDSPCIVVGRKGSagaLN--LCLSRGCCVTDVAY 163
Cdd:cd17288     1 WEVKKLGDLLKIKNG----KDyKHLEDGNYPVYGSGGIMGYVNDYLYDGESVLIGRKGT---IDkpLYVNGPFWTVDTMF 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 164 YCIPPSAFSLDYAFKLFHTLGLDSL--GKGIkPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALcDRLEAQQADAESA 241
Cdd:cd17288    74 YTEIKKNNDPKFLYYLLKTIDFKKYneATGV-PSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAK-DALIELQEKLLEK 151

                         170
                  ....*....|..
gi 2129718046 242 HAQLVQALLDSL 253
Cdd:cd17288   152 LKQYKLALMQEL 163
RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like cd17289
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-541 9.48e-15

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus amyloliquefaciens JRS5 S subunit (S.BamJRS5ORF1993P) TRD1-CR1 and Bacillus pumilus Jo2 S subunit (S.BpuJo2I) TRD1-CR1; The recognition sequences of Bacillus amyloliquefaciens JRS5 S subunit (S.BamJRS5ORF1993P) and Bacillus pumilus Jo2 S subunit (S.BpuJo2I) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341178 [Multi-domain]  Cd Length: 191  Bit Score: 72.68  E-value: 9.48e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQVKGGKRLPA------GTAFAPAKtphvyiQVTNMKDGTIIDENLkYIDEVTKAAIK-QY-TISKDDVYI 422
Cdd:cd17289     1 WEWKKLGDIAEITSSKRIFKseyvdsGIPFYRSK------EIIELFNGEEISTEL-FISEERYEEIKsKYgVPKKGDILI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 423 TIAGTIGDVGIVP--EHF---DGmNLT--ENaakivFQKIDRRWLQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVL 495
Cdd:cd17289    74 TSVGTIGIPYLVKndDPFyfkDG-NLTwfKN-----IKDINSKFLYYWFQSSIFKNQINSITIGSTQKALTIEKLKKTKI 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2129718046 496 ALPPLAEQHRIVAKVDQLMALCDQLKTRLtqarQLNEQLANTLVEH 541
Cdd:cd17289   148 PLPPLEEQKKIVSILSALDEKIDLNKKQL----QKLEELAKTLFQY 189
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 388-539 2.78e-14

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) TRD1-CR1, Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) TRD1-CR1; The recognition sequences of Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) and Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341182 [Multi-domain]  Cd Length: 180  Bit Score: 70.95  E-value: 2.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 388 NMKDGTIIDENLKYIDEvtKAAIKQYTISKDDVYIT-IAGTIGDVGIVpehfdgmnlTE--------NAAkIVFQKIDRR 458
Cdd:cd17293    34 DLNNGGIILTSEEYLSE--EGAKKARIVPKGSILVTcIGGSIGKVGIA---------DRevafnqqiNAI-IPNKSVDPK 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 459 WLQKALSSQFAQRQFSDStnqlaqpklalhriaGSVLA-------------LPPLAEQHRIVAKVDQLMALCDQLKTRLT 525
Cdd:cd17293   102 FLYYQLLSSKFQLQAIAS---------------STTLPiinkskfekieipLPPLEEQKRIVAKLDKLFALIDKLEESLE 166

                         170
                  ....*....|....
gi 2129718046 526 QARQLNEQLANTLV 539
Cdd:cd17293   167 ELDELLKSLFQSAF 180
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 194-249 1.26e-13

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: 69.49  E-value: 1.26e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2129718046 194 PGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQAL 249
Cdd:cd17261   136 PKISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDRLEAQLAAALQLLDRLRQAL 191
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 90-249 1.59e-12

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: 65.86  E-value: 1.59e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  90 RRFGEVFSLEYGDNLPADKR-SNTGEYPVYGSNGVVGTH----------------STCFVDSPCIVVGRKGSAG------ 146
Cdd:cd16961     1 KKLGEIAEIISGKTPSSSSEyWDNGIIPWIRISDINNGGiiltdekiteegaeklKKKILPKGDILISRSGTIGkvaivk 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 147 -ALNLCLSRGCCVTdvayycIPPSAFSLDYAFKLFHTLG----LDSLGKGIKPGLNRNEAYELVVAAPPLAEQHRIVAKV 221
Cdd:cd16961    81 eNDKALLNQAVIVI------RPKDEVDSEFLYYFLKSPFgkklIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANIL 154

                         170       180
                  ....*....|....*....|....*...
gi 2129718046 222 DELMALCDRLEAQQADAEsahaQLVQAL 249
Cdd:cd16961   155 DKLDALIELLEQKLEKLE----QLKQAL 178
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 146-250 1.78e-12

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2; The recognition sequence is undetermined for Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P). The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.TteMORF1547P TRD1-CR1 does not belong to this subfamily.


Pssm-ID: 341188 [Multi-domain]  Cd Length: 174  Bit Score: 65.65  E-value: 1.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 146 GALNL-----CLSRG-CCVTdvayyciPPSAFSLDYAFKLFHTLG--LDSLGKG-----IkpglNRNEAYELVVAAPPLA 212
Cdd:cd17497    68 GPTNIadqeyCIGRGlAAIR-------PKKGLDKKYLLYYLKSIEneLSSLGTGstfkaI----SKEDLENLLIPLPPLA 136

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2129718046 213 EQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17497   137 EQKRIAAFLDELTAKIDQLIALLEKAIELLKEYRQAVL 174
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 348-526 1.96e-12

Type I restriction modification DNA specificity domain; This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits.


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 65.45  E-value: 1.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 348 PAGWEWVRLGSLSQVKGGKRLPAGTAFAPAKTPhvYIQVTNMKDGTIIDENLkyidevtkaaIKQYTISKDDVYITIAGT 427
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELKNNGKYP--YIRAGDLNNVVKGGLGY----------IKKYILPKGDITISSRAT 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 428 IGDVGIVPEHF---DGMNLTENAAKIVFQKIDRRWLQkalssqFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQH 504
Cdd:pfam01420  69 IGYVFYRDKPYytnQHIIVLIPKNNIKITEFLYLYLL------LKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQK 142

                         170       180
                  ....*....|....*....|..
gi 2129718046 505 RIVAKVDQLMALCDQLKTRLTQ 526
Cdd:pfam01420 143 KIAKILSQLDNTIELEKGILNE 164
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 90-233 2.04e-12

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: 65.22  E-value: 2.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  90 RRFGEVFSLEYGDNLPADKRSNTGEYPVYgSNGVV--GTHSTCFVDSPCIVV-GRKGSAGALNLCLSR----GCCvtdva 162
Cdd:cd17291     1 KKLGEIAEIKKGKQITKKELIENGKYPVI-AGGIEpsGYHNEYNREGNTITIsASGASAGYVNYWKEPfwasDCC----- 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2129718046 163 YYCIPPSAFSLDYafkLFHTL-----GLDSLGKGI-KPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEA 233
Cdd:cd17291    75 YILSSKNELVNKF---LYYFLknkqeEIYSLQRGAgQPHIYKKDIEKLKIPIPPLEEQQKIVEILDKFTELTAELPA 148
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 87-251 3.87e-12

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: 65.24  E-value: 3.87e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  87 WVWRRFGEVFSL-EYGDNlPADKRSNTGeYPVYGS----NGVVGTHSTCFVDSPC--------------IVVGRKGSAGa 147
Cdd:cd17246     1 WEWVKLGEISSDiTDGTH-PTPKYVESG-IPFITSknikNGKIDFSDVKYISEEDhneilkrsklkkgdILFSIIGTIG- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 148 lNLCL----SRGCCVTDVAyyCIPPSAFSLDYAFkLFHTLG--------LDSLGKGIKPGLNRNEAYELVVAAPPLAEQH 215
Cdd:cd17246    78 -RVAIvpedLPANINQAVA--LIRPKKEKIDPKY-LLYYLNspiiqkqiEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQK 153

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2129718046 216 RIVAKVDELMALCDRLEAQQADAESAHAQLVQALLD 251
Cdd:cd17246   154 RIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLLT 189
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 395-534 6.23e-12

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) TRD2-CR2 and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) T; The recognition sequences of Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341172 [Multi-domain]  Cd Length: 181  Bit Score: 64.42  E-value: 6.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 395 IDENLKYIDE----VTKAAIKQ--YtISKDDVYITIAGTIG-------DVGIvpeHfDGMnltenaakIVFQ----KIDR 457
Cdd:cd17283    37 VTKDGKYITKtkekITEEGAKKsrL-VKPGDLILSNSMSFGrpyilkiDGCI---H-DGW--------LVFSdlkkKLDK 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2129718046 458 RWLQKALSSQFAQRQFSDSTNQlAQPKLALHRIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17283   104 DFLYYLLSSITVQLQFSAQAGG-GTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLEELKKGL 179
RMtype1_S_EcoUTORF5051P-TRD2-CR2_like cd17524
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 388-538 8.16e-12

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) TRD2-CR2 and Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) TRD2-CR2; Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) recognizes 5'... CCANNNNNNNCTTC ... 3' and the recognition sequence of Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341205 [Multi-domain]  Cd Length: 189  Bit Score: 64.02  E-value: 8.16e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 388 NMKDGTIIDENLKYIDeVTKAAIKQYTISKDDV---------YItiagtiGDVGIVpehfdgmNLTENAA------KIVF 452
Cdd:cd17524    35 NIQDGGIDDDDLKYVD-LDEKEFEKYLLKKGDVlfnrtnspeLV------GKTAIF-------RGDGPATfasyliRIRL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 453 --QKIDRRWLQKALSSQFAQRQ-FSDSTNQLAQ-----PKLALHRIAgsvlaLPPLAEQHRIVAKVDQLMALCDQLKTRL 524
Cdd:cd17524   101 neEKILPEYLNYFLNSPYGRKQiKSVATQGVGQaninaTKLKAIPIP-----LPPLEEQKEIVEKLDELDALIDRLEALL 175

                         170
                  ....*....|....
gi 2129718046 525 TQARQLNEQLANTL 538
Cdd:cd17524   176 EEAEELLESLLQSL 189
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-543 8.36e-12

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: 64.00  E-value: 8.36e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQVKGGK---RlpagtafaPAKTPHVY------IQ---VTNMKdgtiidenlKYIDEVTK----AAIKQyt 414
Cdd:cd17282     1 WEVKKLSDLGSLERGKfkhR--------PRNDPRLYggdypfIQtgdVARAN---------GYITSYSQtlneKGLAQ-- 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 415 iSK----DDVYITIAGTIGDVGIVpeHFD--------GMNLTENaakivfqKIDRRWLQKALssQFAQRQFSDSTNQLAQ 482
Cdd:cd17282    62 -SKlfpkGTLCITIAANIGDTAIL--GFDacfpdsvvGFIPNEE-------KIDVEFLEYYL--RTLKKELEAIAPQSAQ 129

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2129718046 483 PKLALHRIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQArqlnEQLANTLVEHAV 543
Cdd:cd17282   130 KNINLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIAKL----EELKQSLLQEAF 186
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 209-250 1.32e-11

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) TRD1-CR1, Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) TRD1-CR1; The recognition sequences of Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) and Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341182 [Multi-domain]  Cd Length: 180  Bit Score: 63.24  E-value: 1.32e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2129718046 209 PPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17293   139 PPLEEQKRIVAKLDKLFALIDKLEESLEELDELLKSLFQSAF 180
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 427-534 2.12e-11

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: 62.84  E-value: 2.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 427 TIGDVGIVpehfdGMNLTEN---AAKIVFQKIDRRWLQKALSSQfaQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQ 503
Cdd:cd17515    73 TAGKVGIL-----GIDAATNqaiCAILPNEEIDNEFLFYFLKSQ--KEYLISLGKGGAQPNISQGIIKNIEIPLPPLAEQ 145

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2129718046 504 HRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17515   146 KRIVAKLDKLDKLIEKLEKALEKLEELKKAL 176
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 166-250 2.27e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Campylobacter species RM1670 S subunit (S.Csp16704I) TRD2-CR2, Aeromonas media WS S subunit (S.AmeWSORF2351P) TRD1-CR1, and Clos; Campylobacter species RM16704 S subunit (S.Csp16704I ) recognizes 5'... ACANNNNNNNNTCG ... 3', and the recognition sequences of Aeromonas media WS TRD1-CR1 S subunit (S.AmeWSORF2351P) and Clostridium carboxidivorans P7 S subunit (S.CcaPORF573P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341174 [Multi-domain]  Cd Length: 181  Bit Score: 62.52  E-value: 2.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 166 IPPSAFSLDYAFKLF--HTLGLDSLGKG--IKpGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESA 241
Cdd:cd17285    94 FPKDELDPEYLLYWFlsIEETIESLGTGttVK-GITLEDLKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEKLKQL 172


                  ....*....
gi 2129718046 242 HAQLVQALL 250
Cdd:cd17285   173 KKGLMQSLL 181
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 351-534 2.61e-11

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: 62.50  E-value: 2.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLS-QVKGGkrlpAGTAFAPAKTPHVYIQVTNMKDGTIIDENLKYIDEVTKAaIKQYTISKDDvyITIA---G 426
Cdd:cd17521     1 WEVKKLGELSeKIQYG----YTASAAYEDGGPRYLRITDIQDDGVLWDTVPYCSISEED-AEKYLLKDGD--ILFArtgA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 427 TIGDVGIVPEhfdgmnLTENAA------KIVF--QKIDRRWLQKALSSQFAQRQFSDSTNQLAQP-----KLAlhriaGS 493
Cdd:cd17521    74 TVGKSYLYKE------DDGKAVfasyliRFRPnkKKVLPKYLFYFTQSSLYWKQIKSISSGSAQPninaeKLK-----SL 142

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2129718046 494 VLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17521   143 KIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLKEL 183
RMtype1_S_HpyCR35ORFAP-TRD1-CR1_like cd17519
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 352-532 3.43e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) TRD1-CR1 and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190; The recognition sequences of Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341200 [Multi-domain]  Cd Length: 183  Bit Score: 62.33  E-value: 3.43e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 352 EWVRLGSLSQVKggkrlpAGTAFAPAK---TPHVYIQVTNMKDGTIIDENLKYIDEVT-KAAIKQYTISKDDVYITIAG- 426
Cdd:cd17519     1 EYKTLGEVCKFQ------NGFAFKSSKyreSGFPIIRITNIQNGKIDTDNLKYFDLNDyKENLDKYIVRPGDIVIAMSGa 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 427 TIGDVGIvpehfdgmNLTENAAKI---VFQ------KIDRRWLQKALSSQfaqRQFSDSTNQLAQPKLALHRIAGSVLAL 497
Cdd:cd17519    75 TTGKVGI--------NLTDQEFYLnqrVGKfipneeILNNRYLYHFLLSK---QNEKYILAGGSQPNLSSEKLKKIKIPI 143

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2129718046 498 PPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNE 532
Cdd:cd17519   144 PSLEVQEEIVSILDKFRELTNELESELNLRLKQYE 178
RMtype1_S_Eco2747II-TRD2-CR2-like cd17272
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-529 4.30e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Eco2747II TRD2-CR2 and S.Eco2747AII TRD2-CR2; Escherichia coli ST2747 S subunit (S.Eco2747II) and Escherichia coli ST2747A s SUBUNIT (S.Eco2747AII) recognize 5'... GAANNNNNNNTAAA ... 3'. Generally The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains mainly TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341161 [Multi-domain]  Cd Length: 189  Bit Score: 62.06  E-value: 4.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLsqvkggkrLPAGTAFAPA-----KTPHVYIQVTNMKDGTIIDENLKYIDEVTKAAIKqytISKDDVYITIA 425
Cdd:cd17272     1 VEEKTLGDI--------AVDGFQNGPApnfdeKGEIPVITSKNISNGKIDFEYVKYDFLSISKNRK---INKGDILITMI 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 426 GTIGDVGIVPEHfDGMNLTENAAKIVFQ--KIDRRWLQKALSSQfaQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQ 503
Cdd:cd17272    70 GTIGETAIVKCL-DPKFYTLNLYLIRLKkeKLLPSYLKYFLDSE--KFLNKSISATSGQGYLKANQIDKLEIPLPPLEEQ 146

                         170       180
                  ....*....|....*....|....*....
gi 2129718046 504 HRIVAKVDQLMALCDQLKTRL---TQARQ 529
Cdd:cd17272   147 QRIVKILDKFDTLCNDITEGLpaeIEARQ 175
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 354-530 6.49e-11

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: 61.36  E-value: 6.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 354 VRLGSLSQVKGGKRLPAGTAFA-PAKTPHVYIQVTNMKDgtiiDENLKYIDEVTKAAIkqytISKDDVYITIAG-TIGDV 431
Cdd:cd17263     1 VKLGEVCKFSKGKQPPISERFDePKEGSVRYIQIEDLRN----NNEKKYIENPKKSVI----CNEDDILIVRDGaNAGEV 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 432 GIVPEHFDGMNLtenaAKIVFQK--IDRRWLQKALSSQFAQRqFSDSTNQLAQP---KLALHRIagsVLALPPLAEQHRI 506
Cdd:cd17263    73 GTGLEGAIASTL----FKIIPDKniIDKDYLYYFLKSKEIQL-NILTKAGSTIPhvnKKDLENL---KIPLPSLEEQKKI 144

                         170       180
                  ....*....|....*....|....
gi 2129718046 507 VAKVDQLMALCDQLKTRLTQARQL 530
Cdd:cd17263   145 AEILDKLDALIDKLKELIEKLIEL 168
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 143-250 9.25e-11

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) TRD2-CR2 and Shewanella oneidensis MR-1 S subunit (S.SonIV) TRD1-CR1; Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) recognizes 5'... TACNNNNNNNRTRTC ... 3 while Shewanella oneidensis MR-1 S subunit (S.SonIV) recognizes 5'... TACNNNNNNGTNGT ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.SonIV-TRD1 recognizes TAC/GTA and S.SonIV-TRD2 recognizes ACNAC/GTNGT. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341139 [Multi-domain]  Cd Length: 185  Bit Score: 61.11  E-value: 9.25e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 143 GSAGALN--LCLSRGCCVTDVAYYCIPPSAFSLDYAFKLFHTLGLDSL-GKGIKPGLNRNEAYELVVAAPPLAEQHRIVA 219
Cdd:cd17250    75 GEAIKLNrrAILSKDSCIDNNVMGLIPNEGIDSEYLYYWLKKVDLYKYsQATTVPSIRKSTLESIPIPLPPLEEQKRIAA 154

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2129718046 220 KVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17250   155 KLDELFEKLDKLKQALEAAKEQLKGLRQSLL 185
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 348-538 1.45e-10

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2; The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341136 [Multi-domain]  Cd Length: 190  Bit Score: 60.62  E-value: 1.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 348 PAGWEWVRLGSLSQVKGG---KRlpagtafapaKTPHVYiqvtnmKDGTI--------IDENLKYIDE-VTKAAIKQYT- 414
Cdd:cd17247     1 PEHWEVVRLGDVARVGNGstpSR----------KNPDYW------NGGTIpwvssgevNDNRITEADEfITELALKECSl 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 415 --ISKDDVYITIAG---TIGDVGIVpeHFDGMNlTENAAKIVF--QKIDRRWLQKALSSQFAQ-RQFSDSTNQLAqpkLA 486
Cdd:cd17247    65 plVPPGSVLVAMIGqgkTRGQAAIL--AIEATI-NQNLAAIRPneERVLPEYLHYYLESQYDElRRIGSGGGQGA---LN 138

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2129718046 487 LHRIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17247   139 CGILKAFPIPLPPLDEQREIVAELEALLAKIDLLEEKIARLIELLKELRQAL 190
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 203-250 4.29e-10

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I), Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) TRD2-CR2, and Streptomyces species SirexAA-E S subu; Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I) recognizes 5'... CACNNNNNNNCTGG ... 3' and Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) recognizes 5'... RTCANNNNNNNNGTGG ... 3'. The recognition sequence of Streptomyces species SirexAA-E S subunit (S.SspAAEORF2129P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Eco2071ORF3585P TRD1 recognizes RTCA/TGAY and S.Eco2071ORF3585P TRD2 recognizes CCAC/GTGG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341142 [Multi-domain]  Cd Length: 193  Bit Score: 59.41  E-value: 4.29e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2129718046 203 ELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17253   146 ALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLEELLKALRQALL 193
RMtype1_S_PluTORF4319P-TRD2-CR2_like cd17269
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 418-542 7.37e-10

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


Pssm-ID: 341158 [Multi-domain]  Cd Length: 168  Bit Score: 57.99  E-value: 7.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 418 DDVYITIAGTIGDVGIVpEHFDG-MNLTENAAKIVFQKIDR--RWLQKALSSQFAqRQFSDSTNQLAQPKLALHRIAGSV 494
Cdd:cd17269    43 DEEAILIAGNGSGVGNV-KYYNGkFNAYQRTYVIHPFKEEIdpKFLYYYLKSYFK-KYIEKNSVGSSVPYIRLPMLENFK 120

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2129718046 495 LALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTLVEHA 542
Cdd:cd17269   121 IPLPPLEEQKRIVRILDKFDALTAELPAELEARKKQYEYYRDALLSFA 168
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-534 9.42e-10

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


Pssm-ID: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 57.83  E-value: 9.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQVKGGKRLP---------AGtafapaKTPhvYIQVTNmkdgtIIDenlkYIDEvtkaaikqYTIskDDVY 421
Cdd:cd17262     1 WEVKKLGEVVENLDSKRIPlsseererrQG------NYP--YYGASG-----IVD----YVDD--------YIF--DGEY 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 422 ITIAgtigdvgivpEhfDGMNLTENAAKIVF------------------QKIDRRWLQKALSsqfaQRQFSDSTNQLAQP 483
Cdd:cd17262    54 VLIG----------E--DGANLLSRGTPIAFyvsgkfwvnnhahvlkgkNGISTEFLYYYLN----SIDISPYVTGAAQP 117

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2129718046 484 KL---ALHRIAgsvLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17262   118 KLnqaNLNSIP---IPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKAL 168
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 165-250 1.24e-09

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: 57.44  E-value: 1.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 165 CIPPSAFSLDYafkLFHTL-----GLDSLGKGI-KPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADA 238
Cdd:cd17515    93 ILPNEEIDNEF---LFYFLksqkeYLISLGKGGaQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKLIEKLEKALEKL 169

                          90
                  ....*....|..
gi 2129718046 239 ESAHAQLVQALL 250
Cdd:cd17515   170 EELKKALMQKLL 181
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 354-530 1.55e-09

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


Pssm-ID: 341184 [Multi-domain]  Cd Length: 182  Bit Score: 57.22  E-value: 1.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 354 VRLGSLSQVKGGkrlpaGTafaPAKTPHVY--------IQVTNMKDGtIIDENLKYIdevTKAAIKQYT---ISKDDVYI 422
Cdd:cd17296     1 KKLGEICSIQSG-----GT---PSRSKKEYwnngtipwVKISDCKNK-YVDETEEFI---TEEGLNNSSaklLKKGTILI 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 423 TIAGTIGDVGIVPehFD--------GMNLTENaakivfqKIDRRWLQKALSSQFaqRQFSDSTNQLAQPKLALHRIAGSV 494
Cdd:cd17296    69 AIFATIGKVGILK--IEattnqaiaGIKPKNK-------SINPKYLYYYLKSLY--EKFLSLGRGVAQNNINLSILKNLK 137

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2129718046 495 LALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQL 530
Cdd:cd17296   138 IPLPPLEEQQRIVAILDKFEKLINKRQEGLQLLDEL 173
RMtype1_S_Eco15ORF14057P-TRD1-CR1_like cd17525
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 351-534 2.71e-09

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: 56.86  E-value: 2.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQ------VKGGKRLPAGTAfapaktphvYIQVTNM-KDGTIIDENLKYIDEvTKAAIKQYTISKDDVYIT 423
Cdd:cd17525     1 WEWVKLGDILSstqlglVRSNSEDPNGYP---------YIKMGNIgRGGINLLKVETYVDA-TELEVEKYLLEDGDLLFN 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 424 IAGT---IGDVGIVPEHFDGMNLTENAAKIVFQKIdrrwlqkaLSSQFAQRQFSdSTNQLAQpklaLHRIAG---SVLA- 496
Cdd:cd17525    71 TRNTlelVGKVAIWRGELPKALFNNNILRIRFDDI--------VLPYFINYYLN-SPDGKKQ----LESIASgttSVAAi 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2129718046 497 -----------LPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17525   138 yqkdlkklklpLPPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKKAL 186
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 194-247 2.85e-09

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: 56.74  E-value: 2.85e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2129718046 194 PGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQ 247
Cdd:cd17256   129 PKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKALMQ 182
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 137-253 2.91e-09

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: 56.35  E-value: 2.91e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 137 IVVGRKGSA-GALNL-----CLSRGCCV--------TDVAYYCIppsAFSLDYafklfhtlgLDSLGKG-IKPGLNRNEA 201
Cdd:cd17496    59 ILFCVRGSTtGRLNIaddeyCIGRGVAAirpkngidTEFLYYLL---ESNLDY---------LLAAATGsTFPNISRDDL 126

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2129718046 202 YELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQALLDSL 253
Cdd:cd17496   127 LNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLE----ELRDTLLPKL 174
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 185-247 3.08e-09

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: 56.80  E-value: 3.08e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2129718046 185 LDSLGKGIkpGLN--RNEA-YELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQ 247
Cdd:cd17252   126 IRSLASGT--NINnlSNEHlENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQALEKLDELLKSLFQ 189
RMtype1_S_StySPI-TRD2-CR2_like cd17523
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Salmonella ...
 204-253 3.48e-09

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


Pssm-ID: 341204 [Multi-domain]  Cd Length: 190  Bit Score: 56.48  E-value: 3.48e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2129718046 204 LVVAAPPLAEQHRIVAKVDELMALCDRLEAQQadaeSAHAQLVQALLDSL 253
Cdd:cd17523   145 LPIPLPPLKEQKKIVARVEELFALIDQLESSL----DLAQQLQNKLAQSI 190
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 87-253 4.42e-09

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


Pssm-ID: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 55.90  E-value: 4.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  87 WVWRRFGEVFSLEygDNL--P--ADKRSN-TGEYPVYGSNGVVGthstcFVDS-----PCIVVGRKGSagalNLcLSRGc 156
Cdd:cd17262     1 WEVKKLGEVVENL--DSKriPlsSEERERrQGNYPYYGASGIVD-----YVDDyifdgEYVLIGEDGA----NL-LSRG- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 157 cvTDVAYYcI--------------PPSAFSLDYAFKLFHTLGLDSL--GkGIKPGLNRNEAYELVVAAPPLAEQHRIVAK 220
Cdd:cd17262    68 --TPIAFY-VsgkfwvnnhahvlkGKNGISTEFLYYYLNSIDISPYvtG-AAQPKLNQANLNSIPIPLPPLEEQKKIVAI 143

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2129718046 221 VDELMALCDRLEAQQADAEsahaQLVQALLDSL 253
Cdd:cd17262   144 LDKLDALIDLLEEELEKLI----ELKKALLQKL 172
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 354-539 6.48e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) TRD2-CR2 and Shewanella oneidensis MR-1 S subunit (S.SonIV) TRD1-CR1; Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) recognizes 5'... TACNNNNNNNRTRTC ... 3 while Shewanella oneidensis MR-1 S subunit (S.SonIV) recognizes 5'... TACNNNNNNGTNGT ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.SonIV-TRD1 recognizes TAC/GTA and S.SonIV-TRD2 recognizes ACNAC/GTNGT. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341139 [Multi-domain]  Cd Length: 185  Bit Score: 55.72  E-value: 6.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 354 VRLGSLSQVKggkrlpAGTAFapaktPHVY----------IQVTNMK---DGTIIDENLKYIDEVTKAAIKQYTISKDDV 420
Cdd:cd17250     1 VRLGDVCDFK------AGSGF-----PEKYqgkedgeypfYKVGDMNnsgNEKYLSTAENYISEEIVKELKAKLFPKGTI 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 421 YIT-IAGTI--GDVGI--VPEHFDGmNLtenAAKIVFQKIDRRWLQKALSSQ-FAQrqFSDSTN--QLAQPKLALHRIAg 492
Cdd:cd17250    70 IFAkIGEAIklNRRAIlsKDSCIDN-NV---MGLIPNEGIDSEYLYYWLKKVdLYK--YSQATTvpSIRKSTLESIPIP- 142

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2129718046 493 svlaLPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTLV 539
Cdd:cd17250   143 ----LPPLEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGLRQSLL 185
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 497-538 7.71e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Campylobacter species RM1670 S subunit (S.Csp16704I) TRD2-CR2, Aeromonas media WS S subunit (S.AmeWSORF2351P) TRD1-CR1, and Clos; Campylobacter species RM16704 S subunit (S.Csp16704I ) recognizes 5'... ACANNNNNNNNTCG ... 3', and the recognition sequences of Aeromonas media WS TRD1-CR1 S subunit (S.AmeWSORF2351P) and Clostridium carboxidivorans P7 S subunit (S.CcaPORF573P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341174 [Multi-domain]  Cd Length: 181  Bit Score: 55.20  E-value: 7.71e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2129718046 497 LPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17285   139 LPPLEEQKRIVAILDELDELIDKLEAKLEKLKQLKKGLMQSL 180
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
82-544 8.67e-09

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 57.97  E-value: 8.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  82 ELPNGWVWRRFGEVFSLEYGDNLP---ADKRSNTGEYPVYG----SNGVVGTHSTCFV-DSPC-----------IVVGRK 142
Cdd:PRK09737    5 KLPEGWVTTHISEICSVIRGVKPPkgyATKSLTMGDLPFIRttdiTNGAVDLTTLPYCmDAPEdvskyqlqdrdIVISSA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 143 GSAGALNLCLSRGCCVTDVAYYCIPPSAFSLDYAFKLFHTLG-------LDSLGKGIK-PGLNRNEAYELVVAAPPLAEQ 214
Cdd:PRK09737   85 GSIGFSFLAQNPLPSNVVFASFAIRLKPVNYFSEYFLKHFLEssdyrnqLSLMSAGNAvQNINAQSLSTLTFPIPPIAEQ 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 215 HRIVAKVDELMALCDrleaqqadaeSAHAQLvqalldsltqasdaEDFAQNWRRLaehfhtlfttepsidalKQTLLQLA 294
Cdd:PRK09737  165 KIIAEKLDTLLAQVD----------STKARL--------------EQIPQILKRF-----------------RQAVLGAA 203

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 295 VMGKLvpqdpndepasellkriTEEKarlvaegklkkQKPSpeigeeekpfqLPAGWEWVRLGSLSQVKGGKRLPAGTAF 374
Cdd:PRK09737  204 VSGKL-----------------TEEW-----------RWPD-----------LPSTWSVHKYSELVDSRLGGMSSKANNF 244

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 375 APAktpHVYIQVTNMKDGTIIDENLKYIdEVTKAAIKQYTISKDDVYITIAGTIGDVGIV-----PEHfdgMNLTENAAK 449
Cdd:PRK09737  245 GSA---TPYLRNINVRWGSFDLEDLQDI-LISDIERRELKLKLGDVLFCRGNEPLEVGRCaiwkePQD---IPVIYQKAL 317

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 450 I---VFQKIDRRWLQKALSS----QFAQRQFSDSTnqlAQPKLALHRIAGSVLALPPLAEQHRIVAKVDQLMALCDqlkt 522
Cdd:PRK09737  318 IrarVKDDIIPEYLVYNLKSpdsrNISLSQLFTGT---TQKHITGKALANYPIRVPPLEEQAEIVRRVEQLFAYAD---- 390

                         490       500
                  ....*....|....*....|....
gi 2129718046 523 rlTQARQLNEQLA--NTLVEHAVA 544
Cdd:PRK09737  391 --TIEKQVNNALArvNNLTQSILA 412
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 348-538 1.45e-08

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) TRD2-CR2 and Shewanella xiamenensis BC01 S subunit (S.SxiBC01OR; The recognition sequences of Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) and Shewanella xiamenensis BC01 S subunit (S.SxiBC01ORF77P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341173 [Multi-domain]  Cd Length: 185  Bit Score: 54.53  E-value: 1.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 348 PAGWEWVRLGSLSQVkggkrlpagtaFAPaktphvyiqvtnMKD------G-----TIIDENLKYIDE------VTKAAI 410
Cdd:cd17284     1 PEGWEVKRVGDVCDC-----------IVP------------GRDkpksfdGnipwiTIEDIKGKYISSsksglgVSEEEI 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 411 KQY---TISKDDVYITIAGTIGDVGIVpehfdGMNLTENA---AKIVFQKIDRRWLQKALSSQfaQRQFSDSTNQLAQPK 484
Cdd:cd17284    58 KEMnlkVIPKGSVIMSCVGDFGIVAIA-----TNELVINQqlhAFVPSKKINPEYLMYLLSLQ--KKYMEKIATGTTIPY 130

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2129718046 485 LALHRIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17284   131 LNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQQL 184
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 203-249 1.69e-08

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


Pssm-ID: 341138 [Multi-domain]  Cd Length: 185  Bit Score: 54.38  E-value: 1.69e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2129718046 203 ELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQAL 249
Cdd:cd17249   139 NLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 209-248 1.92e-08

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O69:H11 07-3763 S subunit (S.Eco3763I) TRD2-CR2; Escherichia coli O69:H11 07-3763 S subunit (S.Eco3763I) recognizes 5'... TACNNNNNNNRTRTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341153 [Multi-domain]  Cd Length: 184  Bit Score: 54.08  E-value: 1.92e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2129718046 209 PPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQA 248
Cdd:cd17264   145 PPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQSLFQS 184
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 497-539 2.07e-08

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2; The recognition sequence is undetermined for Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P). The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.TteMORF1547P TRD1-CR1 does not belong to this subfamily.


Pssm-ID: 341188 [Multi-domain]  Cd Length: 174  Bit Score: 54.09  E-value: 2.07e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2129718046 497 LPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTLV 539
Cdd:cd17497   132 LPPLAEQKRIAAFLDELTAKIDQLIALLEKAIELLKEYRQAVL 174
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 389-534 2.57e-08

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acetobacter pasteurianus S subunit (S.Apa101655I) TRD2-CR2; The S. Apa101655I S subunit recognizes 5'... TTAGNNNNNNTTC... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341133 [Multi-domain]  Cd Length: 180  Bit Score: 53.63  E-value: 2.57e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 389 MKDGTIIDENLKYIdevTKAAIKqytisKDDVYITIAGT--------IGDVGIVPEhfdgmNLTENAAKIVFQ----KID 456
Cdd:cd17244    36 MGKGKYISDTKEYI---TDEAVK-----KFNVKLVPKGTllmsfkltIGRVAIAGK-----DLYTNEAIAHFIpkdkKID 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 457 RRWLQKALSsQFAQRQFSDST------NQlaqpKLalhrIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQL 530
Cdd:cd17244   103 TEYLYYYLK-SFDYSSLGSTAskgktlNS----KK----IKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDEL 173


                  ....
gi 2129718046 531 NEQL 534
Cdd:cd17244   174 LPKL 177
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 490-530 2.96e-08

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoBI TRD1-CR1, S.EcoSanI TRD1-CR1, and S.EcoVR50I TRD1-CR1; Escherichia coli B S subunit (S.EcoBI) and Escherichia coli VR50 S subunit (S.EcoVR50I) recognize 5'... TGANNNNNNNNTGCT ... 3', while Escherichia coli Sanji S subunit (S.EcoSanI) recognizes 5'... TGANNNNNNCTTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341146 [Multi-domain]  Cd Length: 176  Bit Score: 53.68  E-value: 2.96e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2129718046 490 IAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQL 530
Cdd:cd17257   129 IDEIELPLPPLEEQRRIAEILDELDALIDKLIAKLEKLRDL 169
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 171-250 3.17e-08

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) TRD2-CR2 and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) T; The recognition sequences of Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341172 [Multi-domain]  Cd Length: 181  Bit Score: 53.64  E-value: 3.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 171 FSLDYAFKLFHT----LGLDSLGKGIKPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLV 246
Cdd:cd17283   101 LDKDFLYYLLSSitvqLQFSAQAGGGTKNLNTDIVKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLE----ELK 176


                  ....
gi 2129718046 247 QALL 250
Cdd:cd17283   177 KGLM 180
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 194-249 4.17e-08

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: 53.25  E-value: 4.17e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2129718046 194 PGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQAL 249
Cdd:cd17521   132 PNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLEELLKELLQSL 187
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 429-534 5.87e-08

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: 52.06  E-value: 5.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 429 GDVGIVPEHFDgmnLTENAAKI-VFQKIDRRWLQKALSSqFAQRQFSDSTnqlAQPKLALHRIAGSVLALPPLAEQHRIV 507
Cdd:cd17266    58 GNVHYVEGKFW---VTDNALVVtPKKENNIKFLYYLLKS-LNLNQYATGS---AQPLITVSKLKKLKIPLPPLEEQKKIA 130

                          90       100
                  ....*....|....*....|....*..
gi 2129718046 508 AKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17266   131 AILDSLDAKIDLLEKKLEKLIELKKEL 157
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 490-539 6.47e-08

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: 52.50  E-value: 6.47e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2129718046 490 IAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTLV 539
Cdd:cd17496   126 LLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTLLPKLL 175
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-534 8.25e-08

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: 52.49  E-value: 8.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQVKGGkrlpaGTafaPAKTPHVYIqvtnmkDGTII------DENLKYIDEV----TKAAIKQYT---ISK 417
Cdd:cd17294     1 WEWKTLGEIAKIFSG-----GT---PSTSNPEYW------DGGTIpwlssgEVNFKEIYETekriTEEGLKNSSakwIPK 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 418 DDVYITIAG---TIGDVGIVpehfdGMNLTEN---AAkIVFQK--IDRRWLQKALSSQFAQ-RQFSDSTnqlAQPKLALH 488
Cdd:cd17294    67 NSVLIALAGqgkTRGTVAIL-----KIPLTTNqslAA-IEPDEeiANSRFLYYNLSSRYEElRSLSGGG---GRGGLNLK 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2129718046 489 RIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17294   138 IIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLPALLELRQKQ 183
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
463-543 8.55e-08

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 50.06  E-value: 8.55e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 463 ALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQHRIVAKVDQLMalcDQLkTRLTQARQLNEQLANTLVEHA 542
Cdd:COG0732     5 YLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLF---DKI-AALEKEIEKLKELRDALLPKL 80


                  .
gi 2129718046 543 V 543
Cdd:COG0732    81 F 81
RMtype1_S_EcoUTORF5051P-TRD2-CR2_like cd17524
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 203-253 8.93e-08

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) TRD2-CR2 and Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) TRD2-CR2; Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) recognizes 5'... CCANNNNNNNCTTC ... 3' and the recognition sequence of Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341205 [Multi-domain]  Cd Length: 189  Bit Score: 52.47  E-value: 8.93e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2129718046 203 ELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQALLDSL 253
Cdd:cd17524   143 AIPIPLPPLEEQKEIVEKLDELDALIDRLEALLEEAE----ELLESLLQSL 189
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 203-250 9.03e-08

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.FclI TRD1-CR1; The recognition sequence of Flavobacterium columnare G4 S subunit (S.FclI) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also contains TRD-CR-like sequence-recognition domains of type I DNA methyltransferases, such as putative Type I N6-adenine DNA methyltransferases from Microbacterium ketosireducens (M.Msp12510ORF408P) and Treponema primitia ZAS-2 (M.TprZAS2ORF3630P). It may also include various type II restriction enzymes and methyltransferases.


Pssm-ID: 341143 [Multi-domain]  Cd Length: 173  Bit Score: 52.08  E-value: 9.03e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2129718046 203 ELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17254   126 NIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLEELRKALLQSLL 173
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 192-253 1.05e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR),similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Salmonella enterica subsp. enterica serovar Potsdam S sub; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3' and Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 both recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2.It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341198 [Multi-domain]  Cd Length: 192  Bit Score: 52.15  E-value: 1.05e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2129718046 192 IKPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQALLDSL 253
Cdd:cd17517   135 GQANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLEKLE----QLFKSLMQSL 192
RMtype1_S_Cje2232P-TRD2-CR2_like cd17526
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 351-538 1.16e-07

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) TRD2-CR2 and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) TRD1-CR1; The recognition sequences of Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. Also included in this subfamily is the C-terminal TRD-CR-like sequence-recognition domain of Microcystis aeruginosa putative type I N6-adenine DNA methyltransferase M subunit (M.Mae7806ORF3969P). The recognition sequence of M.Mae7806ORF3969P is undetermined.


Pssm-ID: 341207 [Multi-domain]  Cd Length: 192  Bit Score: 52.21  E-value: 1.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQ-VKGGkrLPAGT-AFAPAKTPHvyIQVTNM-KDGTI-IDENLKYIDEVTKaaIKQYTISKDDVYitiag 426
Cdd:cd17526     1 WEVVRLGDIILdIQSG--FASGKqNEDEDGVPQ--LRPHNItTDGELdLDKLIKIVPSPKE--RKRYLLQKGDVL----- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 427 tigdvgivpehFDGMNLTENAAK---------IVF-----------QKIDRRWLQKALSSQFAQRQF-SDSTNQLAQPKL 485
Cdd:cd17526    70 -----------FNNTNSQELVGKtalfdgeepYVFsnhmtrirvkkSKINPEFLARYLHLLWRSGYFkKLCTNWVNQAGI 138

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2129718046 486 ALHRIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17526   139 NSDTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDL 191
RMtype1_S_Eco15ORF14057P-TRD1-CR1_like cd17525
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 209-249 1.41e-07

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: 51.85  E-value: 1.41e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2129718046 209 PPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQAL 249
Cdd:cd17525   150 PPLDEQREIVSFLSELDAKIDQLEQKLEKLLQIKKALMQQL 190
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 203-250 2.61e-07

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


Pssm-ID: 341149 [Multi-domain]  Cd Length: 165  Bit Score: 50.51  E-value: 2.61e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2129718046 203 ELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17260   118 NYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 194-248 2.63e-07

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: 50.97  E-value: 2.63e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2129718046 194 PGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQA 248
Cdd:cd17259   135 PHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKKGLMQS 189
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 393-539 2.80e-07

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


Pssm-ID: 341190 [Multi-domain]  Cd Length: 175  Bit Score: 50.69  E-value: 2.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 393 TIIDENLKYIDEVTKAAIKqytiskDDVYITIAGTIGDVGIVPEHFD-GMNLtenAAKIVFQKIDRRWL---QKALSSQF 468
Cdd:cd17499    39 KYIKEPNTWTTSPTKIAEK------NDILMSVRAPVGDVNITTRKICiGRGL---AAIRAKKNIDKKYLfyfLLSNKDYF 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2129718046 469 AQRQ-----FSDSTNQLAQPKLALhriagsvlalPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTLV 539
Cdd:cd17499   110 KGKSggstfKSINKNQIKNIKIPL----------PPLEEQKRIVSELDKLFKLIFEAKNNIEEALANAQQLFKSIL 175
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 200-250 4.26e-07

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: 50.20  E-value: 4.26e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2129718046 200 EAYELVVaaPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17278   140 ESIKIPL--PPLEEQKKIAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLF 188
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 495-538 4.32e-07

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


Pssm-ID: 341149 [Multi-domain]  Cd Length: 165  Bit Score: 49.74  E-value: 4.32e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2129718046 495 LALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17260   121 IPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKL 164
RMtype1_S_PluTORF4319P-TRD2-CR2_like cd17269
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 203-248 4.35e-07

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


Pssm-ID: 341158 [Multi-domain]  Cd Length: 168  Bit Score: 49.90  E-value: 4.35e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2129718046 203 ELVVAAPPLAEQHRIVAKVDELMALCDR----LEAQQADAESAHAQLVQA 248
Cdd:cd17269   118 NFKIPLPPLEEQKRIVRILDKFDALTAElpaeLEARKKQYEYYRDALLSF 167
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 351-534 4.80e-07

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: 50.23  E-value: 4.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLS----------QVKGGKRLPagtafapaktphvyiqVTNMK---DGTIIDENLKYIDEVTKAaIKQYTISK 417
Cdd:cd17522     1 WKVVKLGDVLeeirngttvkQNKEGGGYP----------------VTRIEtisNGTIDLNRVGYAITNEEK-IEKYKLQK 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 418 DDV---YITIAGTIGDVGIVPE------HfdGMNL----TENaakivfQKIDRRWLQKALSSQFAQRQFSD----STNQ- 479
Cdd:cd17522    64 GDIlfsHINSIEHIGKTAIYDGdpepliH--GMNLlrlrPNK------NIVDPKYLYYLLKSDRFRNQFRSiakkAVNQa 135

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2129718046 480 -LAQPKLALHRIAgsvlaLPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17522   136 sINQTELKKIKIP-----LPPLEEQQKIASILEKLDKKIEKRKEKIEKLKELKKGL 186
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 484-534 5.39e-07

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


Pssm-ID: 341138 [Multi-domain]  Cd Length: 185  Bit Score: 50.14  E-value: 5.39e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2129718046 484 KLALHRIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17249   131 SLDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEELLKAL 181
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 166-248 5.90e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acetobacter pasteurianus S subunit (S.Apa101655I) TRD2-CR2; The S. Apa101655I S subunit recognizes 5'... TTAGNNNNNNTTC... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341133 [Multi-domain]  Cd Length: 180  Bit Score: 49.78  E-value: 5.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 166 IPPSAFSLDYAFKLFHTLGLDSLGKG--IKPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHA 243
Cdd:cd17244    96 PKDKKIDTEYLYYYLKSFDYSSLGSTasKGKTLNSKKIKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDELLP 175


                  ....*
gi 2129718046 244 QLVQA 248
Cdd:cd17244   176 KLMSG 180
RMtype1_S_Cje2232P-TRD2-CR2_like cd17526
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 209-250 6.61e-07

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) TRD2-CR2 and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) TRD1-CR1; The recognition sequences of Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. Also included in this subfamily is the C-terminal TRD-CR-like sequence-recognition domain of Microcystis aeruginosa putative type I N6-adenine DNA methyltransferase M subunit (M.Mae7806ORF3969P). The recognition sequence of M.Mae7806ORF3969P is undetermined.


Pssm-ID: 341207 [Multi-domain]  Cd Length: 192  Bit Score: 49.90  E-value: 6.61e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2129718046 209 PPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17526   151 PPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFEDLL 192
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 203-248 1.29e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoBI TRD1-CR1, S.EcoSanI TRD1-CR1, and S.EcoVR50I TRD1-CR1; Escherichia coli B S subunit (S.EcoBI) and Escherichia coli VR50 S subunit (S.EcoVR50I) recognize 5'... TGANNNNNNNNTGCT ... 3', while Escherichia coli Sanji S subunit (S.EcoSanI) recognizes 5'... TGANNNNNNCTTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341146 [Multi-domain]  Cd Length: 176  Bit Score: 48.68  E-value: 1.29e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2129718046 203 ELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQA 248
Cdd:cd17257   131 EIELPLPPLEEQRRIAEILDELDALIDKLIAKLEKLRDLLLPLLQS 176
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 495-538 2.01e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.FclI TRD1-CR1; The recognition sequence of Flavobacterium columnare G4 S subunit (S.FclI) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also contains TRD-CR-like sequence-recognition domains of type I DNA methyltransferases, such as putative Type I N6-adenine DNA methyltransferases from Microbacterium ketosireducens (M.Msp12510ORF408P) and Treponema primitia ZAS-2 (M.TprZAS2ORF3630P). It may also include various type II restriction enzymes and methyltransferases.


Pssm-ID: 341143 [Multi-domain]  Cd Length: 173  Bit Score: 48.22  E-value: 2.01e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2129718046 495 LALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17254   129 VPLPPLEEQKRIAAILDELDALIDALEEQLKKLEELRKALLQSL 172
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
185-253 2.51e-06

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 45.82  E-value: 2.51e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 185 LDSLGKGIK-PGLNRNEAYELVVAAPPLAEQHRIVAKVDELMalcDRLEAQQADAEsAHAQLVQALLDSL 253
Cdd:COG0732    15 LRSLATGSTqPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLF---DKIAALEKEIE-KLKELRDALLPKL 80
RMtype1_S_Asp27244ORF1181P-TRD1-CR1_like cd17518
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 384-529 2.52e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter sp. S subunit (S.Asp27244ORF1181P) TRD1-CR1; The recognition sequence of Acinetobacter sp. S subunit (S.Asp27244ORF1181P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341199 [Multi-domain]  Cd Length: 180  Bit Score: 48.13  E-value: 2.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 384 IQVTNMKDGTII-DENLKYI--DEVtKAAIKQYTISKDDVYITIAGTI-GDVGIVPEhfDGMNLTENAAKIVFQ----KI 455
Cdd:cd17518    28 LNVTNIVNGSLDlDKTDRYIstEEY-NGKYKHFLIDEGDILIASSGNSwGKVAIVEK--DHLPLMLNTSTIRFKfidgLL 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2129718046 456 DRRWLQKALSSQFAQRQFSDSTNQLAQPKLA---LHRIAgsvLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQ 529
Cdd:cd17518   105 DNNFLKYFLNSDYFKEQLDLLITGGAQPNFGpshLKKIK---IPLPPLEEQKRIAEILDDADDAIEAALEALRKKKQ 178
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 189-253 2.81e-06

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: 47.88  E-value: 2.81e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2129718046 189 GKGIkPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQALLDSL 253
Cdd:cd17263   117 GSTI-PHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALIDKLKELIEKLI----ELKKGLFQEL 176
RMtype1_S_Ara36733I_TRD1-CR1_like cd17268
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 351-529 3.96e-06

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


Pssm-ID: 341157 [Multi-domain]  Cd Length: 185  Bit Score: 47.44  E-value: 3.96e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 351 WEWVRLGSLSQVKGGKRLPAgTAFAPAKTP-----HVYiqvTnmKDGTIIDENLKYIDEvTKAAIKQYtISKDDVYITIA 425
Cdd:cd17268     1 VEWKTLGEIGEFIRGKGITK-KDFVESGVPcihygEIY---T--KYGIYTTKTKSFISE-ELAKKLRK-AKPGDLLIAGT 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 426 G-TIGDVG--IVpehFDGmnlTENAAK----IVF-QKIDRRWLQKALSSQFAQRQfsdsTNQLAQpKLALHRIAGSVLA- 496
Cdd:cd17268    73 GeTIEDIGkaVA---WLG---DEEVAAggdiIIFrHSQNPKYLSYLLNSPAFQKQ----KRKLGT-GTKVVHISASDLAk 141

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2129718046 497 ----LPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQ 529
Cdd:cd17268   142 ikipVPPLEEQERIVEILDKFDALIAGLPAEIEARRK 178
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 193-253 4.11e-06

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2; The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341136 [Multi-domain]  Cd Length: 190  Bit Score: 47.52  E-value: 4.11e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2129718046 193 KPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQALLDSL 253
Cdd:cd17247   134 QGALNCGILKAFPIPLPPLDEQREIVAELEALLAKIDLLEEKIARLI----ELLKELRQAL 190
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 146-250 4.66e-06

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


Pssm-ID: 341190 [Multi-domain]  Cd Length: 175  Bit Score: 47.22  E-value: 4.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 146 GALNL-----CLSRGCCVtdvayycIPPSAfSLDYAFKLFHTLGLDSLGKGIKPG-----LNRNEAYELVVAAPPLAEQH 215
Cdd:cd17499    69 GDVNIttrkiCIGRGLAA-------IRAKK-NIDKKYLFYFLLSNKDYFKGKSGGstfksINKNQIKNIKIPLPPLEEQK 140

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2129718046 216 RIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17499   141 RIVSELDKLFKLIFEAKNNIEEALANAQQLFKSIL 175
RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like cd17280
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter ...
 380-543 6.78e-06

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


Pssm-ID: 341169 [Multi-domain]  Cd Length: 187  Bit Score: 46.77  E-value: 6.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 380 PHVYIQVTNMKDGTIIDENlKYIdevTKAAIKQYTISKddVY----ITIA---GTIGDVGIVpehfdGMNLTENAAKIVF 452
Cdd:cd17280    27 GIPWVTTGDLRDGIITETS-KKI---TDKALDDYSALK--IYpagsLVIAmygATIGRLGIL-----GIDATTNQACCVL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 453 QKIdrrwlqKALSSQFAQRQFSDSTNQL-------AQPKLALHRIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLT 525
Cdd:cd17280    96 SGS------NKIDIKFLFYWLLANRDELislasggGQPNISQELIKSLRIPVPPLEEQKQIAAFLDKKTAKIDSLIEKKE 169

                         170
                  ....*....|....*...
gi 2129718046 526 QARQLNEQLANTLVEHAV 543
Cdd:cd17280   170 RLIELLKERRQALISEAV 187
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 489-538 1.15e-05

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


Pssm-ID: 341165 [Multi-domain]  Cd Length: 187  Bit Score: 46.04  E-value: 1.15e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2129718046 489 RIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17276   137 DVRNFPIPLPPLDEQRAIVEFLSDVDALIDSLEALIEKLRELKKGLMQQL 186
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 194-250 1.36e-05

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


Pssm-ID: 341165 [Multi-domain]  Cd Length: 187  Bit Score: 46.04  E-value: 1.36e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2129718046 194 PGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17276   131 PNITKDDVRNFPIPLPPLDEQRAIVEFLSDVDALIDSLEALIEKLRELKKGLMQQLL 187
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 447-534 2.83e-05

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: 44.79  E-value: 2.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 447 AAKIVFQKIDRRWLQKALSSQF-AQRQFSDSTNQlaqPKLALHRIAGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLT 525
Cdd:cd17287    93 AAILPNDGINPDFLFYYLQSSYeELRDLSNGGGQ---PNLNAGLIKSIEIPVPPLDEQQKIAAFLSAIDAKIDALEQKLE 169


                  ....*....
gi 2129718046 526 QARQLNEQL 534
Cdd:cd17287   170 LLQELKKSL 178
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 165-253 4.60e-05

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: 44.32  E-value: 4.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 165 CIPPSAFSLDYafkLFHTLgldslgKGIKPGLNRN--------------EAYELVVaaPPLAEQHRIVAKVDELMALCDR 230
Cdd:cd17273    98 IIPNEEIDNEF---LYYLL------KNNKPEIESLasgstfkeiskstfKKIEIPL--PPLEEQKKIAAILSKLDELIEL 166

                          90       100
                  ....*....|....*....|...
gi 2129718046 231 LEAQQADAEsahaQLVQALLDSL 253
Cdd:cd17273   167 LEKENEKLK----ELRDGLLPKL 185
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 388-538 4.83e-05

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


Pssm-ID: 341154 [Multi-domain]  Cd Length: 181  Bit Score: 44.03  E-value: 4.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 388 NMKDGTIIDENLKYIDevTKAAIKQYTiSKDDVYITI----AGTIGDVGIVPEHFDGMnlTENAAKIVFQKIDRRWLQKA 463
Cdd:cd17265    32 NIQNGKLDFDDNVYVN--SKIPEKLIV-KEGDILICVrngsRALIGKNALIDKEAEGM--TFGAFMTVFRSEYNDYLFHL 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2129718046 464 LSSQFAQRQ---FSDST-NQLAQPKLAlhriaGSVLALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTL 538
Cdd:cd17265   107 FNSDLFKKQigsFLTATiNQITNGNLN-----NFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKELMQQL 180
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 452-538 5.39e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoAO83I TRD1-CR1 and S.AbaB8342I TRD2-CR2; Escherichia coli strain A0 34/86 S subunit (S.EcoAO83I) recognizes 5'... GGANNNNNNNNATGC ... 3, and Acinetobacter baumannii B8342 S subunit (S.AbaB8342I) recognizes 5'... TTCANNNNNNTCC ... 3. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example S.AbaB8342I-TRD1 recognizes TTCA/TGAA and S.AbaB8342I-TRD2 recognizes GGA/TCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Type IIG restriction enzyme/N6-adenine DNA methyltransferases from Thermus scotoductus RFL1 (RM.TstI) and Acinetobacter lwoffi Ks 4-8 (RM.AloI), as well as type I DNA methyltransferases such as Sideroxydans lithotrophicus ES-1 Type I N6-adenine DNA methyltransferase (M.SliESORF1090P). RM.TstI recognizes 5' ... CACNNNNNNTCC ... 3' and RM.AloI recognizes 5' ... GAACNNNNNNTCC ... 3'.


Pssm-ID: 341156 [Multi-domain]  Cd Length: 158  Bit Score: 43.54  E-value: 5.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 452 FQKIDRRWLQKALSSQFAQRQFSDStnqlAQPKL---ALHRIagsVLALPPLAEQHRIVAKVDQLMALCDQLKTRLtqar 528
Cdd:cd17267    77 FKGNDPRFLYYLLKTLDLERLNSGS----AVPGLnrnDVYSL---KVPLPPLEEQKAIAAILDALDDKIELNRRQN---- 145

                          90
                  ....*....|
gi 2129718046 529 QLNEQLANTL 538
Cdd:cd17267   146 QTLEELADAL 155
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 490-534 7.84e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoJA69PI TRD1-CR1, MjaXIP/S.MjaORF132P TRD2-CR2, and S.HspDL1ORF16625P TRD2-CR2; Escherichia coli UCD_JA69_pb S subunit (S.EcoJA69PI) recognizes 5'... CCANNNNNNNCTTC ... 3'. The recognition sequences of Methanococcus jannaschii MjaXIP/S.MjaORF132P TRD2-CR2 and Halobacterium species DL1 S subunit (S.HspDL1ORF16625P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various putative type II restriction enzymes and methyltransferases and may also include type I DNA methyltransferases.


Pssm-ID: 341162 [Multi-domain]  Cd Length: 186  Bit Score: 43.55  E-value: 7.84e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2129718046 490 IAGSVLA-----LPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQL 534
Cdd:cd17273   132 ISKSTFKkieipLPPLEEQKKIAAILSKLDELIELLEKENEKLKELRDGL 181
RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like cd17258
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 385-526 7.90e-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: 43.55  E-value: 7.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 385 QVTNMKDGTIIDENLKYIDEVTKAAI---KQYTISKDDVYITIAGTIGDVGIvpEHFDGMNLTENAAKIV-FQKI-DRRW 459
Cdd:cd17258    16 NIKLVCIKNELINSLKVKIVEPDYKIglkQSKIFKKGDVLITRHGTIGRVSI--ILSEEACLSSHVAGFNsKEGIsDNKF 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2129718046 460 LQKALSSQFAQRQFSDSTNQLAQPKLALHRIAGSVLALPPLAEQHRIVA---KVD-------QLMALCDQLKTRLTQ 526
Cdd:cd17258    94 IKYLFNSKKIKNRLMSYGASSTQPALNLSRLLKIKFPNPPLEEQQKIGKilsTWDraielteQKLELLQQQKKGLMQ 170
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 203-256 1.08e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Actinosynnema mirum DSM 43827 S subunit (S. AmiI) TRD2-CR2; The S. AmiI S subunit recognizes 5'... CAGNNNNNNNTCGA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S. AmiI -TRD1 recognizes CAG/CTG, and TRD2 recognizes TCGA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341137 [Multi-domain]  Cd Length: 196  Bit Score: 43.29  E-value: 1.08e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2129718046 203 ELVVAAPPLAEQHRIVAKVDELMALCDRLEAQqadaesahAQLVQALLDSLTQA 256
Cdd:cd17248   142 ALRIALPPLEEQRKIVDRLEALDAKIDALERK--------LERLIELLKELRQA 187
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 204-253 1.53e-04

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: 42.82  E-value: 1.53e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2129718046 204 LVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQALLDSL 253
Cdd:cd17282   140 LKIPVPPLEEQKKIVEILDALDDLIDNLEKRIAKLE----ELKQSLLQEA 185
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 84-234 6.52e-04

Type I restriction modification DNA specificity domain; This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits.


Pssm-ID: 396139 [Multi-domain]  Cd Length: 167  Bit Score: 40.80  E-value: 6.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046  84 PNGWVWRRFGEVFSLEYGDNLPADKRSNTGEYPVYGSN-------GVVGTHSTCFVDSPCIVVGRKGSAGALNLclsrgc 156
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELKNNGKYPYIRAGdlnnvvkGGLGYIKKYILPKGDITISSRATIGYVFY------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 157 cvTDVAYYC-------IPPSAFSLDYAFKLFHTLGLDSL-----GKGIkPGLN--RNEAYELVVaaPPLAEQHRIVAKVD 222
Cdd:pfam01420  75 --RDKPYYTnqhiivlIPKNNIKITEFLYLYLLLKLKKLkslkfGSTQ-PKLTkeRLKEIKIPL--PPLEEQKKIAKILS 149

                         170
                  ....*....|..
gi 2129718046 223 ELMAlCDRLEAQ 234
Cdd:pfam01420 150 QLDN-TIELEKG 160
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
189-286 7.20e-04

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 42.18  E-value: 7.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 189 GKGIKpGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALldsLTQASDAEDFAQnWRr 268
Cdd:PRK09737  351 GTTQK-HITGKALANYPIRVPPLEEQAEIVRRVEQLFAYADTIEKQVNNALARVNNLTQSI---LAKAFRGELTAQ-WR- 424

                          90
                  ....*....|....*...
gi 2129718046 269 lAEHfHTLFTTEPSIDAL 286
Cdd:PRK09737  425 -AEN-PSLISGENSAAAL 440
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 196-253 8.69e-04

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: 40.60  E-value: 8.69e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2129718046 196 LNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAEsahaQLVQALLDSL 253
Cdd:cd17522   137 INQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKRKEKIEKLK----ELKKGLFQKL 190
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 495-543 9.62e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Actinosynnema mirum DSM 43827 S subunit (S. AmiI) TRD2-CR2; The S. AmiI S subunit recognizes 5'... CAGNNNNNNNTCGA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S. AmiI -TRD1 recognizes CAG/CTG, and TRD2 recognizes TCGA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341137 [Multi-domain]  Cd Length: 196  Bit Score: 40.59  E-value: 9.62e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2129718046 495 LALPPLAEQHRIVAKVDQLMALCDQLKTRLTQARQLNEQLANTLVEHAV 543
Cdd:cd17248   145 IALPPLEEQRKIVDRLEALDAKIDALERKLERLIELLKELRQALLTAAV 193
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 165-250 1.35e-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: 40.16  E-value: 1.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129718046 165 CIPPSAFSLDYAFkLFHTLG-----LDSLGKG-IKPGLNRNEAYELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADA 238
Cdd:cd17294    98 AIEPDEEIANSRF-LYYNLSsryeeLRSLSGGgGRGGLNLKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGLPAL 176

                          90
                  ....*....|..
gi 2129718046 239 ESAHAQLVQALL 250
Cdd:cd17294   177 LELRQKQYEYLR 188
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 203-250 1.40e-03

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


Pssm-ID: 341154 [Multi-domain]  Cd Length: 181  Bit Score: 39.79  E-value: 1.40e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2129718046 203 ELVVAAPPLAEQHRIVAKVDELMALCDRLEAQQADAESAHAQLVQALL 250
Cdd:cd17265   134 NFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKELMQQLI 181
hisZ PRK12294
ATP phosphoribosyltransferase regulatory subunit; Provisional
 242-319 1.48e-03

ATP phosphoribosyltransferase regulatory subunit; Provisional


Pssm-ID: 237044  Cd Length: 272  Bit Score: 40.56  E-value: 1.48e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2129718046 242 HAQLVQALLDSLTQASDAEDFAQNwRRLAEHFHTLFTTEPSIDALKQ-TLLQLAVMGKLVpqdPNDEPASELLKRITEE 319
Cdd:PRK12294  141 HYQLLDALLDKSLQTPDILSMIEE-RNLSGLVTYLSTEHPIVQILKEnTQQQLNVLEHYI---PNDHPALVELKIWERW 215
RMtype1_S_Ara36733I_TRD1-CR1_like cd17268
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 204-234 7.79e-03

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: 37.81  E-value: 7.79e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2129718046 204 LVVAAPPLAEQHRIVAKVDELMALCDRLEAQ 234
Cdd:cd17268   142 IKIPVPPLEEQERIVEILDKFDALIAGLPAE 172
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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