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Conserved domains on  [gi|1480816582|ref|WP_119497962|]
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restriction endonuclease subunit S [Psittacicella melopsittaci]

Protein Classification

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

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

PubMed:  24068554

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-277 2.64e-67

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


The actual alignment was detected with superfamily member cd17286:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 179  Bit Score: 213.12  E-value: 2.64e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWSREddqrkHKWVTPSDI-NSPTIENTKRTLTDLGWEKARKVPANSLLITCIASIGKNTINT 176
Cdd:cd17286     5 DLGEIVTGNTPSTKNSEYYGGE-----ILFVTPTDIdGNKYIYKTEKKLSEKGFKKARILPKGSILVTCIGSIGKNAIAT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 177 VPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPKdYKEQQKIGKFFKEVDDKIT 256
Cdd:cd17286    80 EDCATNQQINAIIPNKNYDPEFLYYALENWSKKIKSLAGKQAVPIINKTEFSKIKILVPP-LEEQQKIANFLSKLDELIE 158

                         170       180
                  ....*....|....*....|.
gi 1480816582 257 SLQNALSKSKELKRTLIYKLL 277
Cdd:cd17286   159 LQQQKIEKLEELKKGLLQKLF 179
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 308-467 9.87e-32

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


The actual alignment was detected with superfamily member cd17255:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 166  Bit Score: 119.17  E-value: 9.87e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 308 FKIGKIDNISR---LSQEKTEEFR--YPVYSSKTSNNGICGYFDTYSF-ENSITWTTDGEYAGDVKYREGKFQASIHCGI 381
Cdd:cd17255     1 KKLGDLFEIGRgrvISKKYISENPgdYPVYSSQTKNNGIMGYINTYDFdGEYITWTTDGANAGTVFYRNGKFSVTNVCGV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 382 MISNRGFSC-VSIAEILNRIAYRYATRANIPRVGMGTLKQIVISYPQgTEELQKLNCLFTDINNLIYTYEATLKQHKKFK 460
Cdd:cd17255    81 LKVKNKNINnKFLYYALNLIAKKYVSFDGNPKLMNNVMAKIKIPLPP-LEEQEKIANILDKLDELINLLIAKLKKLIELR 159


                  ....*..
gi 1480816582 461 QALVQRM 467
Cdd:cd17255   160 KKQLEYY 166
 
Name Accession Description Interval E-value
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 98-277 2.64e-67

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


Pssm-ID: 341175 [Multi-domain]  Cd Length: 179  Bit Score: 213.12  E-value: 2.64e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWSREddqrkHKWVTPSDI-NSPTIENTKRTLTDLGWEKARKVPANSLLITCIASIGKNTINT 176
Cdd:cd17286     5 DLGEIVTGNTPSTKNSEYYGGE-----ILFVTPTDIdGNKYIYKTEKKLSEKGFKKARILPKGSILVTCIGSIGKNAIAT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 177 VPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPKdYKEQQKIGKFFKEVDDKIT 256
Cdd:cd17286    80 EDCATNQQINAIIPNKNYDPEFLYYALENWSKKIKSLAGKQAVPIINKTEFSKIKILVPP-LEEQQKIANFLSKLDELIE 158

                         170       180
                  ....*....|....*....|.
gi 1480816582 257 SLQNALSKSKELKRTLIYKLL 277
Cdd:cd17286   159 LQQQKIEKLEELKKGLLQKLF 179
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 308-467 9.87e-32

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


Pssm-ID: 341144 [Multi-domain]  Cd Length: 166  Bit Score: 119.17  E-value: 9.87e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 308 FKIGKIDNISR---LSQEKTEEFR--YPVYSSKTSNNGICGYFDTYSF-ENSITWTTDGEYAGDVKYREGKFQASIHCGI 381
Cdd:cd17255     1 KKLGDLFEIGRgrvISKKYISENPgdYPVYSSQTKNNGIMGYINTYDFdGEYITWTTDGANAGTVFYRNGKFSVTNVCGV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 382 MISNRGFSC-VSIAEILNRIAYRYATRANIPRVGMGTLKQIVISYPQgTEELQKLNCLFTDINNLIYTYEATLKQHKKFK 460
Cdd:cd17255    81 LKVKNKNINnKFLYYALNLIAKKYVSFDGNPKLMNNVMAKIKIPLPP-LEEQEKIANILDKLDELINLLIAKLKKLIELR 159


                  ....*..
gi 1480816582 461 QALVQRM 467
Cdd:cd17255   160 KKQLEYY 166
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 88-270 9.95e-13

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: 66.22  E-value: 9.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  88 NESYQFFEVNEIGKVQTGNTPSTKVKEywsredDQRKHKWVTPSDINSPTIENTKRTltdlgweKARKVPANSLLITCIA 167
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELK------NNGKYPYIRAGDLNNVVKGGLGYI-------KKYILPKGDITISSRA 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 168 SIGKNTINTVPTSFNQQINSLTAKKGFDV----YYLLTSFNKNTKKLIRAGAssiTNIVNKTQFESFTLRLPKDyKEQQK 243
Cdd:pfam01420  68 TIGYVFYRDKPYYTNQHIIVLIPKNNIKIteflYLYLLLKLKKLKSLKFGST---QPKLTKERLKEIKIPLPPL-EEQKK 143

                         170       180
                  ....*....|....*....|....*..
gi 1480816582 244 IGKFFKEVDDKITSLQNalsKSKELKR 270
Cdd:pfam01420 144 IAKILSQLDNTIELEKG---ILNELER 167
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
198-277 9.46e-10

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 55.06  E-value: 9.46e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 198 YLLTSFNKNTKKLIRAGASSITNIvNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:COG0732     4 YYLRSPSFREYLRSLATGSTQPNL-NKKDLKKLPIPLP-PLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 296-426 4.07e-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: 41.19  E-value: 4.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 296 WKKGELYSIFDYFKiGKIDNisrlSQEKTEEFRYPVYSSKTSNNGICGYFDTYSF----ENSITWTTDGeYAGDVKYREG 371
Cdd:pfam01420   4 WEVFKLGDVFEIKK-GKTPK----KKELKNNGKYPYIRAGDLNNVVKGGLGYIKKyilpKGDITISSRA-TIGYVFYRDK 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1480816582 372 KFQASIHCGIMIS--------NRGFSCVSIAEILNRIAYRYAtranIPRVGMGTLKQIVISYP 426
Cdd:pfam01420  78 PYYTNQHIIVLIPknnikiteFLYLYLLLKLKKLKSLKFGST----QPKLTKERLKEIKIPLP 136
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
394-468 3.65e-03

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 36.58  E-value: 3.65e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1480816582 394 AEILNRIAYRYATRANIPRVGMGTLKQIVISYPQgTEELQKLNCLFTDINNLIYTYEATLKQHKKFKQALVQRML 468
Cdd:COG0732     8 SPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPP-LEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
 
Name Accession Description Interval E-value
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 98-277 2.64e-67

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


Pssm-ID: 341175 [Multi-domain]  Cd Length: 179  Bit Score: 213.12  E-value: 2.64e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWSREddqrkHKWVTPSDI-NSPTIENTKRTLTDLGWEKARKVPANSLLITCIASIGKNTINT 176
Cdd:cd17286     5 DLGEIVTGNTPSTKNSEYYGGE-----ILFVTPTDIdGNKYIYKTEKKLSEKGFKKARILPKGSILVTCIGSIGKNAIAT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 177 VPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPKdYKEQQKIGKFFKEVDDKIT 256
Cdd:cd17286    80 EDCATNQQINAIIPNKNYDPEFLYYALENWSKKIKSLAGKQAVPIINKTEFSKIKILVPP-LEEQQKIANFLSKLDELIE 158

                         170       180
                  ....*....|....*....|.
gi 1480816582 257 SLQNALSKSKELKRTLIYKLL 277
Cdd:cd17286   159 LQQQKIEKLEELKKGLLQKLF 179
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 95-277 9.99e-48

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: 162.24  E-value: 9.99e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  95 EVNEIGKVQTGNTPSTKVKEYWSREddqrkHKWVTPSDINSPT-IENTKRTLTDLGWEKARKVPANSLLITCIA-SIGKN 172
Cdd:cd17293     2 KLGELGEVVTGNTPSKKNPEYYGGD-----IPFIKPDDLNNGGiILTSEEYLSEEGAKKARIVPKGSILVTCIGgSIGKV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 173 TINTVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPkDYKEQQKIGKFFKEVD 252
Cdd:cd17293    77 GIADREVAFNQQINAIIPNKSVDPKFLYYQLLSSKFQLQAIASSTTLPIINKSKFEKIEIPLP-PLEEQKRIVAKLDKLF 155

                         170       180
                  ....*....|....*....|....*
gi 1480816582 253 DKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17293   156 ALIDKLEESLEELDELLKSLFQSAF 180
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-278 1.50e-42

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.HinAWORF1578P TRD2-CR2; Haemophilus influenzae RdAW S subunit (S.HinAWORF1578P) recognizes 5'... CTANNNNNGTTY ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341197 [Multi-domain]  Cd Length: 184  Bit Score: 148.85  E-value: 1.50e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWSREddqrkHKWVTPSDI-NSPTIENTKRTLTDLGWE--KARKVPANSLLITCIAS-IGKNT 173
Cdd:cd17516     5 DLGKVVTGKTPSTKNPEYFGGD-----IPFITPSDMkGGKYIIKTERRLSSKGLEkvKNKLIPANSICVTCIGSdMGKVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 174 INTVPTSFNQQINSLTA-KKGFD---VYYLLtsfnKNTKKLIR--AGASSITNIVNKTQFESFTLRLPKdYKEQQKIGKF 247
Cdd:cd17516    80 ITKEPSVTNQQINSIIVnKNKFDpdfVYYLL----KNNSKYLKsiAGGSTATPIINKSTFSNIEIPLPP-LPEQKKIAAI 154

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1480816582 248 FKEVDDKITSLQNALSKSKELKRTLiYKLLF 278
Cdd:cd17516   155 LSSLDDKIENNRRINKTLEEMAQAL-FKEWF 184
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-277 1.53e-37

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: 135.61  E-value: 1.53e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWsrEDDqrkHKWVTPSDI---NSPTIENTKRTLTDLGWEK--ARKVPANSLLITCIASIGKN 172
Cdd:cd17273     8 DVAEIVGGGTPSTKNPEYW--NGD---IPWITPTDLtklKGKYISDTERKITELGLKNssAKLLPAGSVLLSSRAPIGYV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 173 TINTVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPkDYKEQQKIGKFFKEVD 252
Cdd:cd17273    83 AIATNPLATNQGFKSIIPNEEIDNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEIPLP-PLEEQKKIAAILSKLD 161

                         170       180
                  ....*....|....*....|....*
gi 1480816582 253 DKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17273   162 ELIELLEKENEKLKELRDGLLPKLF 186
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 308-467 9.87e-32

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


Pssm-ID: 341144 [Multi-domain]  Cd Length: 166  Bit Score: 119.17  E-value: 9.87e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 308 FKIGKIDNISR---LSQEKTEEFR--YPVYSSKTSNNGICGYFDTYSF-ENSITWTTDGEYAGDVKYREGKFQASIHCGI 381
Cdd:cd17255     1 KKLGDLFEIGRgrvISKKYISENPgdYPVYSSQTKNNGIMGYINTYDFdGEYITWTTDGANAGTVFYRNGKFSVTNVCGV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 382 MISNRGFSC-VSIAEILNRIAYRYATRANIPRVGMGTLKQIVISYPQgTEELQKLNCLFTDINNLIYTYEATLKQHKKFK 460
Cdd:cd17255    81 LKVKNKNINnKFLYYALNLIAKKYVSFDGNPKLMNNVMAKIKIPLPP-LEEQEKIANILDKLDELINLLIAKLKKLIELR 159


                  ....*..
gi 1480816582 461 QALVQRM 467
Cdd:cd17255   160 KKQLEYY 166
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 101-273 2.14e-30

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Algibacter lectus S subunit (S.AleSS8ORF2795P) TRD1-CR1 and Vibrio parahaemolyticus O1:K33 CDC_K4557 S subunit (S.Vpa4557ORF2259; The recognition sequences of Algibacter lectus S subunit (S.AleSS8ORF2795P) and Vibrio parahaemolyticus O1:K33 CDC_K4557 S subunit (S.Vpa4557ORF22590P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341179 [Multi-domain]  Cd Length: 184  Bit Score: 116.15  E-value: 2.14e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 101 KVQTGNTPSTKVKEYWSREDDQrkhkWVTPSDINSP-TIENTKRTLTDLGWE--KARKVPANSLLITCI-ASIGKNTINT 176
Cdd:cd17290     9 SIKTGTTPPSENEEYYDGGIIP----WFTPGDFNGDlILSESKRKLSELAIEdgEARLFPKNSVLVVGIgATIGKVGYSD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 177 VPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPkDYKEQQKIGKFF----KEVD 252
Cdd:cd17290    85 KESSSNQQITGIIFNKDINPKFLFYWLSSSKEELENLANGATLPILNQEKLKNIKLPVP-PLNEQQKIVEFLdkktAKID 163

                         170       180
                  ....*....|....*....|.
gi 1480816582 253 DKITSLQNALSKSKELKRTLI 273
Cdd:cd17290   164 ALIAKKEQLIELLKEYRQALI 184
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-276 7.02e-30

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: 114.86  E-value: 7.02e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWSREddqrkHKWVTPSDINSPTIENTKRTLTDLGWEK--ARKVPANSLLITCIASIGKNT-- 173
Cdd:cd17249     5 DLGKFLSGGTPSKSNPEYWGGD-----IPWVSPKDMKSDYISDSEDHITELAVEEsgTKLVPAGSVLIVVRGMILAHTfp 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 174 --INTVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIR------AGASSI-TNivnktQFESFTLRLPKDyKEQQKI 244
Cdd:cd17249    80 vaITTRPVAFNQDIKALIPKEGIDPEFLLYALKANEDRILSlvdkagHGTGSLdTD-----DLKNLPIPLPPL-EEQRRI 153

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1480816582 245 GKFFKEVDDKITSLQNALSKSKELKRTLIYKL 276
Cdd:cd17249   154 AAILDALDALIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17251
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 96-277 1.79e-27

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S.HinAWORF1578P TRD2-CR2; Haemophilus influenzae RdAW S subunit (S.HinAWORF1578P) recognizes 5'... CTANNNNNGTTY ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains mostly TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341140 [Multi-domain]  Cd Length: 185  Bit Score: 108.36  E-value: 1.79e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  96 VNEIGKVQTGNTPSTKVKEYWsrEDDQrkhKWVTPSDI-NSPTIENTKRTLTDLGWEKARK--VPANSLLITCIASIGKN 172
Cdd:cd17251     6 LKDFGKIITGKTPSTKNKEYY--GGDI---PFIKIPDMhGNVFITKTEDYLSEEGANSQKNktLPKNSICVSCIATVGLV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 173 TINTVPTSFNQQINSLTAKKGFDVYYLLTSFnKNTKKLIRAGASS---ITNiVNKTQFESFTLRLPkdykEQQKIGKFFK 249
Cdd:cd17251    81 SITTEESQTNQQINSIIPKKENYRYYLYFAL-KSLKELLEALGSGgstTLN-LNKGKFSKIKILLP----SEDLLKKFHK 154

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1480816582 250 EVD---DKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17251   155 IVSplfDKILNNQKENQKLSQLRDTLLPKLM 185
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 95-277 5.48e-27

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) TRD2-CR2 and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) TRD; The recognition sequences of Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341194 [Multi-domain]  Cd Length: 182  Bit Score: 106.83  E-value: 5.48e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  95 EVNEIGKVQTGNTPSTKVKEYWSREDdqrkhKWVTPSDI--NSPTIENTKRTLTDLGWEK--ARKVPANSLLITCIASIG 170
Cdd:cd17513     2 KLGELGKFIGGGTPSTKNPEYWNGNI-----PWITSSDLseDDIFKINIRKFITEEAIKNsaTKIIPANSILIVTRVGVG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 171 KNTINTVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLI-RAGASSITNIVnKTQFESFTLRLPKDyKEQQKIGKFFK 249
Cdd:cd17513    77 KVAINPFDICTSQDFTSLIPIKEVNPLFLAYLLYSLLQKLKsQLQGTSIKGIT-KDDLKNLKIPLPPL-EEQQKIAAILS 154

                         170       180
                  ....*....|....*....|....*...
gi 1480816582 250 EVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17513   155 KLDKLIEAHEKKLEKLKQLKKGLMQKLF 182
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 101-277 4.25e-25

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


Pssm-ID: 341164 [Multi-domain]  Cd Length: 186  Bit Score: 101.85  E-value: 4.25e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 101 KVQTGNTPSTKVKEYWSREddqrkHKWVTPSDINS--PTIENTKRTLTDLGWEK--ARKVPANSLLITCIASIGKNTINT 176
Cdd:cd17275    11 KMKSGGTPSTSNKEYYGGD-----IPFVKISDMTKsgKYIYSTEKYITEEGLKNssAWIVPKGTILYAMYASVGKVAINK 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 177 VPTSFNQQINSLTAKKG-----FdVYYLLTSFNKNTKKLIRAGASSitNIvNKTQFESFTLRLPkDYKEQQKIGKFFKEV 251
Cdd:cd17275    86 IDVATNQAILGIIPKDEkldfeF-LYYWLLSLKNELKRLIRTGTQA--NL-NAEIVKNLPIPLP-PLEEQKKIAEILDKI 160

                         170       180
                  ....*....|....*....|....*.
gi 1480816582 252 DDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17275   161 DAEIDKLEEKIEKLRELKKGLLQKMF 186
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-272 1.86e-24

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: 99.76  E-value: 1.86e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKvKEYWSREddqrKHKWVTPSDINSPTIENTKRTLTDLGWE--KARKVPANSLLITCIASIGKNTIN 175
Cdd:cd16961     5 EIAEIISGKTPSSS-SEYWDNG----IIPWIRISDINNGGIILTDEKITEEGAEklKKKILPKGDILISRSGTIGKVAIV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 176 T--VPTSFNQQINSLTAKKGFDVYYLLTSFN-KNTKKLIRAGASSITNIVNKTQFESFTLRLPkDYKEQQKIGKFFKEVD 252
Cdd:cd16961    80 KenDKALLNQAVIVIRPKDEVDSEFLYYFLKsPFGKKLIEGSAGSTQPNLNKSDLKNLKIPLP-PLEEQKKIANILDKLD 158

                         170       180
                  ....*....|....*....|
gi 1480816582 253 DKITSLQNALSKSKELKRTL 272
Cdd:cd16961   159 ALIELLEQKLEKLEQLKQAL 178
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 99-273 1.29e-23

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Burkholderia multivorans CF2 S subunit (S.BmuCF2ORF3362P) TRD1-CR1 and and Halomonas campaniensis LS21 S subunit (S.HcaLS21ORF99; The recognition sequences of Burkholderia multivorans CF2 S subunit (S.BmuCF2ORF3362P) and Halomonas campaniensis LS21 S subunit (S.HcaLS21ORF9970P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341168 [Multi-domain]  Cd Length: 184  Bit Score: 97.63  E-value: 1.29e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  99 IGKVQTGNTPSTKVKEYWsrEDDqrkHKWVTPSDIN---SPTIENTKRTLTDLGWEK--ARKVPANSLLITCIASIGKNT 173
Cdd:cd17279     6 IFRIVNGSTPKSGEEDYW--DGD---IPWVTPADLSkldGKYISSSQRKITEAGLEScgTSLVPAGSIILSTRAPIGYVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 174 INTVPTSFNQQINSLTAKKGFDV---YYLLTSfnkNTKKLIRAGASSITNIVNKTQFESFTLRLPkDYKEQQKIGKFF-- 248
Cdd:cd17279    81 IATVELCTNQGCKALVPNSDVDSrflYYLLLA---AKEELNSLGRGTTFLELSTDELANFKIPLP-PLSEQRAIADFLdr 156

                         170       180
                  ....*....|....*....|....*..
gi 1480816582 249 --KEVDDKITSLQNALSKSKELKRTLI 273
Cdd:cd17279   157 etAKIDALIAKKQQLIELLKEKRQALI 183
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 127-277 4.80e-23

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: 96.13  E-value: 4.80e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 127 WVTPSDINSPTIENTKR----TLTDLGWEKARKVPANSLLITCIASIGKNTINTVPTSFNQQINSLTAKKGFDVYYLLTS 202
Cdd:cd17284    32 WITIEDIKGKYISSSKSglgvSEEEIKEMNLKVIPKGSVIMSCVGDFGIVAIATNELVINQQLHAFVPSKKINPEYLMYL 111

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1480816582 203 FNKNTKKLIRAGASSITNIVNKTQFESFTLRLPKdYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17284   112 LSLQKKYMEKIATGTTIPYLNKTNCESIPIPLPP-IEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQQLF 185
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 95-277 1.83e-22

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: 94.04  E-value: 1.83e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  95 EVNEIGKVQTGNTPSTKVKEYWSREDdqrkhKWVTPSDINSPTIENTKRTLTDLGWEK--ARKVPANSLLITCI-ASIGK 171
Cdd:cd17515     2 KLGDIGKWGSGGTPSRSNPEYYGGGI-----PWIKSGELNDGYITSTEEKITEEGLKNssAKLFPKGSVLIAMYgATAGK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 172 NTINTVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSIT-NIvNKTQFESFTLRLPkDYKEQQKIGKFFKE 250
Cdd:cd17515    77 VGILGIDAATNQAICAILPNEEIDNEFLFYFLKSQKEYLISLGKGGAQpNI-SQGIIKNIEIPLP-PLAEQKRIVAKLDK 154

                         170       180
                  ....*....|....*....|....*..
gi 1480816582 251 VDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17515   155 LDKLIEKLEKALEKLEELKKALMQKLL 181
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 99-277 1.18e-17

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: 80.63  E-value: 1.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  99 IGKVQTGNTPSTKVKEYWSREDdqrkhKWVTPSDINSPTIENTKRTLTDLGWEK--ARKVPANSLLI-TCIAsIGKNTIN 175
Cdd:cd17285     7 VEKIVGGGTPSKSNPEYWNGDI-----PWASVKDLKGKYLTSTEDKITEEGLKNssSNLIPKGTVIIaTRMG-LGKVAIN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 176 TVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKI 255
Cdd:cd17285    81 KIDVAINQDLKALFPKDELDPEYLLYWFLSIEETIESLGTGTTVKGITLEDLKSLKIPLP-PLEEQKRIVAILDELDELI 159

                         170       180
                  ....*....|....*....|..
gi 1480816582 256 TSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17285   160 DKLEAKLEKLKQLKKGLMQSLL 181
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 97-273 2.29e-17

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: 79.82  E-value: 2.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  97 NEIGKVQTGNTPSTKVKEYWSREDdqrkHKWVTPSDIN-SPTIENTKRTLTDLGWEK--ARKVPANSLLITCIASIGKNT 173
Cdd:cd17244     4 GDIFDIKIGKTPPRKEPEYWSGDN----IPWVSISDMGkGKYISDTKEYITDEAVKKfnVKLVPKGTLLMSFKLTIGRVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 174 INTVPTSFNQQINSLTAKKGFD----VYYLLTSFNKNTKklirAGASSITNIVNKTQFESFTLRLPkDYKEQQKIGKFFK 249
Cdd:cd17244    80 IAGKDLYTNEAIAHFIPKDKKIdteyLYYYLKSFDYSSL----GSTASKGKTLNSKKIKEIPIPLP-PLEEQKRIAPILD 154

                         170       180
                  ....*....|....*....|....
gi 1480816582 250 EVDDKITSLQNALSKSKELKRTLI 273
Cdd:cd17244   155 KIDALIDQLETLIELLDELLPKLM 178
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 97-272 2.90e-17

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: 79.57  E-value: 2.90e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  97 NEIGKVQTGNTPSTKVKEYWSREDDqrkhKWVTPSDINSPTIENTKRTLTDLGWEK--ARKVPANSLLITCIASIGKNTI 174
Cdd:cd17296     4 GEICSIQSGGTPSRSKKEYWNNGTI----PWVKISDCKNKYVDETEEFITEEGLNNssAKLLKKGTILIAIFATIGKVGI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 175 NTVPTSFNQQINSLTAK-----KGFdVYYLLTSFNKNTKKLIRAGASsitNIVNKTQFESFTLRLPkDYKEQQKIGKFFK 249
Cdd:cd17296    80 LKIEATTNQAIAGIKPKnksinPKY-LYYYLKSLYEKFLSLGRGVAQ---NNINLSILKNLKIPLP-PLEEQQRIVAILD 154

                         170       180
                  ....*....|....*....|...
gi 1480816582 250 EVDDKITSLQNALSKSKELKRTL 272
Cdd:cd17296   155 KFEKLINKRQEGLQLLDELVKSL 177
RMtype1_M_Cni19672ORF1405P_RMtype11G_Hci611ORFHP_T cd17277
Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 ...
 91-260 3.66e-17

Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 Calditerrivibrio nitroreducens M.Cni19672ORF1405P TRD1-CR1 and RMtype11G Helicobacter cinaedi PAGU611 RM.Hci611ORFHP TRD1-CR1; The recognition sequence of Calditerrivibrio nitroreducens M.Cni19672ORF1405P is undetermined, and the predicted recognition sequence of RM.Hci611ORFHP is 5'... GAGNNNNNGT ... 3'. M.Cni19672ORF1405P is a putative type I N6-adenine DNA methyltransferase. RM.Hci611ORFHP is a type II subtype gamma (also called type IIG and type IIC) N6-adenine DNA methyltransferase. Both are DNA methyltransferase-specificity subunit fusion proteins, they each have a domain corresponding to a HsdM methylation (M) subunit followed by a C-terminal, TRD-CR-like domain for sequence-recognition, which corresponds to the HsdS specificty (S) subunit. The latter consists of two variable TRDs, and two CRs which separate the TRDs; the TRDs each bind to different specific sequences in the DNA. RM.Hci611ORFHP has an additional N-terminal HSDR_N domain. Restriction-modification (RM) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit, two modification (M) subunits, and two restriction (R) subunits.


Pssm-ID: 341166 [Multi-domain]  Cd Length: 184  Bit Score: 79.37  E-value: 3.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  91 YQFFEVNEIGKVQTGNTPSTKVKEYWSREDDqrkhKWVTPSDI--NSPTIENTKRTLTDLGWE--KARKVPANSLLITCI 166
Cdd:cd17277     1 WPIVKLGEVCEIINGSTPSKKNEEYWNNGTI----KWLTIPDIdeRGLIISSTKQFITEKALEekKVKLVPKNSVLLSCT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 167 ASIGKNTINTVPTSFNQQINSLTAKKG-FDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLP------KDYK 239
Cdd:cd17277    77 ATIGKVAIAKIELTTNQQINALICKDSkILPEYLFYALKHIKQVLERLTTNPGVKHVNLSMLSNLQIPLPplevqkKIVA 156

                         170       180
                  ....*....|....*....|.
gi 1480816582 240 EQQKIGKFFKEVDDKITSLQN 260
Cdd:cd17277   157 EIEKVEKVIQGLRQKIDEYQP 177
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 98-277 7.53e-17

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: 78.40  E-value: 7.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWsreDDQRKHKWVTPSDINSPTIENTKRTLTDLGWEKA--RKVPANSLlitCIA------SI 169
Cdd:cd17276     5 DIAKTSSGGTPLRSNQEYY---FNGGTIPWVKTTDLNNGVIYETEEKITEKALKETscKLLPKGTV---LVAmyggfgQI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 170 GKNTINTVPTSFNQQINSLTAK-KGFDVYYLLTSFNKNTKKLIRAGASSIT--NIvNKTQFESFTLRLPkDYKEQQKIGK 246
Cdd:cd17276    79 GRTGLLGIPAAINQAICAILPNeKKVNPEFLLRYLNFNRPYWMRVAASSRKdpNI-TKDDVRNFPIPLP-PLDEQRAIVE 156

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1480816582 247 FFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17276   157 FLSDVDALIDSLEALIEKLRELKKGLMQQLL 187
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-277 8.55e-17

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: 78.30  E-value: 8.55e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWSREDdqrkHKWVTPSDINSPTIENTKRTLTDLGWEK--ARKVPANSLLItciASI------ 169
Cdd:cd17294     8 EIAKIFSGGTPSTSNPEYWDGGT----IPWLSSGEVNFKEIYETEKRITEEGLKNssAKWIPKNSVLI---ALAgqgktr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 170 GKNTINTVPTSFNQQINSLTAKKGFD----VYYLLTSFNKNTKKL----IRAGassitniVNKTQFESFTLRLPkDYKEQ 241
Cdd:cd17294    81 GTVAILKIPLTTNQSLAAIEPDEEIAnsrfLYYNLSSRYEELRSLsgggGRGG-------LNLKIIKSLPIPLP-PLEEQ 152

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1480816582 242 QKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17294   153 KKIVAILDKFDALINDLKEGLPALLELRQKQYEYLR 188
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 96-272 5.31e-16

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Arthrobacter chlorophenolicus A6 S subunit (S.AchA6I) TRD2-CR2; The S.AchA6I S subunit recognizes 5'... TGAANNNNNTCG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.AchA6I-TRD1 recognizes TGAA/TTCA, and TRD2 recognizes CGA/TCG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341132 [Multi-domain]  Cd Length: 182  Bit Score: 75.95  E-value: 5.31e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  96 VNEIGKVQTGNTPSTKVKEYWSREddqrkHKWVTPSDINSPT--IENTKRTLTDLGWEK--ARKVPANSLLITCIASIGK 171
Cdd:cd17243     5 LSDVVDIIGGGTPKTSVPEYWNGD-----IPWFSVKDVNNDSrfVLDTEKKITELGLKNssTKLLPKGTTIISARGTVGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 172 NTINTVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPKDyKEQQKIGKFFKEV 251
Cdd:cd17243    80 LALLGIPMAMNQSCYGLRGKDGLSNYFLYYLLKNLIEELKQKAHGSVFDTITRKTFDEIKVPLPPE-ELQKSFENIVSPL 158

                         170       180
                  ....*....|....*....|.
gi 1480816582 252 DDKITSLQNALSKSKELKRTL 272
Cdd:cd17243   159 FDKILNNLKENQTLAQLRDTL 179
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 96-277 4.93e-15

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


Pssm-ID: 341137 [Multi-domain]  Cd Length: 196  Bit Score: 73.33  E-value: 4.93e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  96 VNEIGKVQTGNTPSTKVKEYWsrEDDQrkhKWVTPSDIN---SPTIENTKRTLTDLGWEK--ARKVPANSLLITCIASIG 170
Cdd:cd17248     9 LTDVAKLESGHTPSRSRPEYW--NGCI---PWISLADVKqlrGDYIYETKEKISELGIANssARLLPAGTVVLSRTASVG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 171 KNTINTVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSitniVNKT----QFESFTLRLPkDYKEQQKIGK 246
Cdd:cd17248    84 KSAIMGRPMATSQDFANWVCGPELDPEYLLYVLRAMKPEFERLAMGS----THKTiympDFKALRIALP-PLEEQRKIVD 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1480816582 247 FFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17248   159 RLEALDAKIDALERKLERLIELLKELRQALL 189
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 98-277 1.14e-14

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: 72.14  E-value: 1.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWsrEDDQrkhKWVTPSDINSPTIENTKRTLTDLGWEK--ARKVPANSLLITCI---ASIGKN 172
Cdd:cd17287     5 EIAKVSSGGTPSRSNPEYW--NGGI---PWVKTGEVNFNEITDTEEKITEEGLKNssAKLFPKGTLLMAMYgqgKTRGRV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 173 TINTVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKlIRAGASSIT--NIvNKTQFESFTLRLPKdYKEQQKIGKFFKE 250
Cdd:cd17287    80 AILGIEAATNQACAAILPNDGINPDFLFYYLQSSYEE-LRDLSNGGGqpNL-NAGLIKSIEIPVPP-LDEQQKIAAFLSA 156

                         170       180
                  ....*....|....*....|....*..
gi 1480816582 251 VDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17287   157 IDAKIDALEQKLELLQELKKSLMQQLF 183
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 127-272 1.31e-14

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


Pssm-ID: 341172 [Multi-domain]  Cd Length: 181  Bit Score: 71.74  E-value: 1.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 127 WVTPSDI--NSPTIENTKRTLTDLGWEKARKVPANSLLITCIASIGKNTINTVPT----------SFNQQINsltakKGF 194
Cdd:cd17283    31 WIKIGDVtkDGKYITKTKEKITEEGAKKSRLVKPGDLILSNSMSFGRPYILKIDGcihdgwlvfsDLKKKLD-----KDF 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1480816582 195 dVYYLLTSfNKNTKKLIRAGASSITNIvNKTQFESFTLRLPKDyKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTL 272
Cdd:cd17283   106 -LYYLLSS-ITVQLQFSAQAGGGTKNL-NTDIVKNLKIPLPPL-EEQKRIAEILDSLDALIDALEEKLEKLEELKKGL 179
RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like cd17280
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter ...
 105-274 3.57e-13

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: 67.96  E-value: 3.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 105 GNTPSTKVKEYWSREddqrkHKWVTPSDINSPTIENTKRTLTDLGWEK--ARKV-PANSLLITCI-ASIGKNTINTVPTS 180
Cdd:cd17280    13 GTTPKSDNEDYYDGG-----IPWVTTGDLRDGIITETSKKITDKALDDysALKIyPAGSLVIAMYgATIGRLGILGIDAT 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 181 FNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGAS-SITNIvNKTQFESFTLRLPkDYKEQQKIGKF----FKEVDDKI 255
Cdd:cd17280    88 TNQACCVLSGSNKIDIKFLFYWLLANRDELISLASGgGQPNI-SQELIKSLRIPVP-PLEEQKQIAAFldkkTAKIDSLI 165

                         170
                  ....*....|....*....
gi 1480816582 256 TSLQNALSKSKELKRTLIY 274
Cdd:cd17280   166 EKKERLIELLKERRQALIS 184
RMtype1_S_HpyAXIII_TRD1-CR1_like cd17281
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 91-270 8.49e-13

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


Pssm-ID: 341170  Cd Length: 196  Bit Score: 66.85  E-value: 8.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  91 YQFFEVNEIGKVQTGNTPSTKVKEYWSREDDqrkhKWVTPSDI--NSPTIENTKRTLTDLGWEKARKVPANSLLITCIAS 168
Cdd:cd17281     2 VEWKKLGEIFDIRNGYTPSKSNKEYWENGTI----PWFRMEDIreNGRILSDSIQHITPSAVKGGKLFPANSIILSTTAT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 169 IGKNTINTVPTSFNQQINSLTAKKGFD-------VYYLLTSFNKNTKKLIRAGASSitnIVNKTQFESFTLRLPkDYKEQ 241
Cdd:cd17281    78 IGEHALITVDSLANQRFTNFSLKKSYKnkldikfLFYYFFVLGEWCKKNINIGGFP---SVDMNKLKKFKIPIP-PLEEQ 153

                         170       180
                  ....*....|....*....|....*....
gi 1480816582 242 QKIGKFFKEVDDKITSLQNALSKSKELKR 270
Cdd:cd17281   154 EKIVEILDKFTKLTADLTAELPAELEARK 182
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 88-270 9.95e-13

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: 66.22  E-value: 9.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  88 NESYQFFEVNEIGKVQTGNTPSTKVKEywsredDQRKHKWVTPSDINSPTIENTKRTltdlgweKARKVPANSLLITCIA 167
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKKELK------NNGKYPYIRAGDLNNVVKGGLGYI-------KKYILPKGDITISSRA 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 168 SIGKNTINTVPTSFNQQINSLTAKKGFDV----YYLLTSFNKNTKKLIRAGAssiTNIVNKTQFESFTLRLPKDyKEQQK 243
Cdd:pfam01420  68 TIGYVFYRDKPYYTNQHIIVLIPKNNIKIteflYLYLLLKLKKLKSLKFGST---QPKLTKERLKEIKIPLPPL-EEQKK 143

                         170       180
                  ....*....|....*....|....*..
gi 1480816582 244 IGKFFKEVDDKITSLQNalsKSKELKR 270
Cdd:pfam01420 144 IAKILSQLDNTIELEKG---ILNELER 167
RMtype1_S_NmaSCMORF606P_TRD2-CR2_like cd17271
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 104-277 1.34e-12

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Nitrosopumilus maritimus SCM1 S subunit (S2.NmaSCMORF606P) TRD2-CR2, Corynebacterium jeikeium K411 S subunit (S.CjeKORF1254P) TRD2-CR2 and Porphyromonas canoris COT-108 OH27; The recognition sequences of Nitrosopumilus maritimus SCM1 S subunit (S2.NmaSCMORF606P), Corynebacterium jeikeium K411 S subunit (S.CjeKORF1254P), and Porphyromonas canoris COT-108 OH2762 S subunit (S2.Pca2762ORF8685P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341160 [Multi-domain]  Cd Length: 186  Bit Score: 66.14  E-value: 1.34e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 104 TGNTPSTKVKEYWSREDDqrkhkWVTPSDINSPTIENTKRTLTDLGWEKA--RKVPANSLLITcIASI------GKNTIN 175
Cdd:cd17271    10 SGATPSRGNPEYFNGDIP-----WITSGELNYNYITDTNEKITEEAVKNTnlKIHPKGTFLIA-ITGLeaagtrGKCAIT 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 176 TVPTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLIragassiTNIVNKTQFESFT--------LRLPKdYKEQQKIGKF 247
Cdd:cd17271    84 GIPATTNQSCMAFYPTKKLTTEFLFYWYKKYGNYLG-------FKYAQGTKQQSYTadivkklpILLPT-LKEQKKIANF 155

                         170       180       190
                  ....*....|....*....|....*....|
gi 1480816582 248 FKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17271   156 LSDIDELIATLEKKIEKLKKIKKGLMQKLL 185
RMtype1_S_Sba223ORF3470P-TRD1-CR1_like cd17270
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 138-276 1.99e-12

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


Pssm-ID: 341159 [Multi-domain]  Cd Length: 183  Bit Score: 65.42  E-value: 1.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 138 IENTKRTLTDLGWEKARKVPANSLLITCIASIGKNTINTVP----------TSFNQQINsltakKGFDVYYLLTSFNKNT 207
Cdd:cd17270    45 VEKTKQKISKLAQPKSVFVPKGTVIVTLQGSIGRVAITQYDayvdrtllifESYKININ-----KKFFAYQLKLKFEIEK 119

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1480816582 208 KKlirAGASSITNIVnKTQFESFTLRLPKdYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKL 276
Cdd:cd17270   120 EK---APGGTIKTIT-KEELSKFEIPIPS-LEEQKEIVNILDKFDELITELQLRKKQLEYYKKALLSFM 183
RMtype1_S_MmaGORF2198P_TRD1-CR1_like cd17500
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 101-279 9.56e-12

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) TRD1-CR1, and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) TRD1-CR1; The recognition sequences of Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains TRD1-CR1. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341191 [Multi-domain]  Cd Length: 186  Bit Score: 63.85  E-value: 9.56e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 101 KVQTGNTPSTKVKEYWSREDdqrkHKWVTPSDINSPTIENTKRTLTDLGWEK--ARKVPANSLLITCI---ASIGKNTIN 175
Cdd:cd17500     8 KITSGGTPSRSNKEYYNGGN----IPWLKTKELNFKRIYDTEEKITEEGLKNssAKLIPENTVIIAMYgagKTAGRVAIN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 176 TVPTSFNQ-----QINSLTAKKGFDVYYLLTSFNKnTKKLIRAGASSitNIvNKTQFESFTLRLPKdYKEQQKIGKFFKE 250
Cdd:cd17500    84 KIPLTTNQaccnlIIDNKKADYRFVYYSLKTQYEE-LVNLASGAAQQ--NL-NSKLIKNFEIPLPP-LPEQKRIASILSS 158

                         170       180
                  ....*....|....*....|....*....
gi 1480816582 251 VDDKITSLQNALSKSKELKRTLiYKLLFV 279
Cdd:cd17500   159 LDDKIELNNRQNETLEAMAETL-FKEWFV 186
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 98-272 1.96e-11

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: 62.93  E-value: 1.96e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  98 EIGKVQTGNTPSTKVKEYWSREDdqrkHKWVTPSDINSPTIENTKRTLTDLGWEKA--RKVPANSLLitcIASIG----- 170
Cdd:cd17247    11 DVARVGNGSTPSRKNPDYWNGGT----IPWVSSGEVNDNRITEADEFITELALKECslPLVPPGSVL---VAMIGqgktr 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 171 -KNTINTVPTSFNQQINSLTAKKG-----FDVYYLLTSFNKntkklIRAGASSiTNI--VNKTQFESFTLRLPkDYKEQQ 242
Cdd:cd17247    84 gQAAILAIEATINQNLAAIRPNEErvlpeYLHYYLESQYDE-----LRRIGSG-GGQgaLNCGILKAFPIPLP-PLDEQR 156

                         170       180       190
                  ....*....|....*....|....*....|
gi 1480816582 243 KIGKFFKEVDDKITSLQNALSKSKELKRTL 272
Cdd:cd17247   157 EIVAELEALLAKIDLLEEKIARLIELLKEL 186
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 150-277 1.29e-10

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: 60.61  E-value: 1.29e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 150 WEKARKVPANSLLITCIASIGKNTI--NTVPTSFNQQINSLTAKKG-----FDVYYLLTSFNKNTKKLIRAGaSSITNIv 222
Cdd:cd17246    57 ILKRSKLKKGDILFSIIGTIGRVAIvpEDLPANINQAVALIRPKKEkidpkYLLYYLNSPIIQKQIEKNAVG-GTQKNL- 134

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1480816582 223 NKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17246   135 SLGDLKNLKIPLP-PLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLL 188
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 138-277 1.79e-10

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: 59.76  E-value: 1.79e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 138 IENTKRTLTDLGWEKARKVPANSLLITCIASIGKNTINTVPTSFNQQINSLTAKK-GFDVYYLLTSFnKNTKKLIRAGAS 216
Cdd:cd17282    47 ITSYSQTLNEKGLAQSKLFPKGTLCITIAANIGDTAILGFDACFPDSVVGFIPNEeKIDVEFLEYYL-RTLKKELEAIAP 125

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1480816582 217 SIT--NIvNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17282   126 QSAqkNI-NLEILRPLKIPVP-PLEEQKKIVEILDALDDLIDNLEKRIAKLEELKQSLLQEAF 186
RMtype1_S_Vch69ORF1407P_TRD2-CR2_like cd17501
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio ...
 101-277 4.83e-10

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio cholerae 1311-69 S subunit (S.Vch69ORF1407P) TRD2-CR2, and Methanococcoides methylutens MM1 S subunit (S.MmeMM1ORF456P) TRD2-CR2; The recognition sequences of Vibrio cholerae 1311-69 S subunit (S.Vch69ORF1407P) and Methanococcoides methylutens MM1 S subunit (S.MmeMM1ORF456P) 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: 341192 [Multi-domain]  Cd Length: 191  Bit Score: 58.73  E-value: 4.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 101 KVQTGNTPSTKVKEYWSREDdqrkHKWVTPSDINSPTIENTKRTLTDLGWEK--ARKVPANSLLITCI-ASIGKNTINTV 177
Cdd:cd17501    16 KTQSGGTPSRKNPEYWDGGI----IPWLKTGELRDNIILDTEEKITEEGLKNssAKLFPKGTVLVAMYgATAGKLGILAK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 178 PTSFNQQINSLTAKKGFDVYYLLTSFNKNTKKLI-RAGASSITNIvNKTQFESFTLRLPKDykeqqKIGKFFKE----VD 252
Cdd:cd17501    92 EATTNQACCALIPKEEYSPFFLYLYLLNSRDYLAnLASGSAQQNI-SQQIIKNTKVLIPPE-----DLLEIFNKlvepLF 165

                         170       180
                  ....*....|....*....|....*
gi 1480816582 253 DKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17501   166 DKIINNLKENQKLAKLRDTLLPKLM 190
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
198-277 9.46e-10

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 55.06  E-value: 9.46e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 198 YLLTSFNKNTKKLIRAGASSITNIvNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:COG0732     4 YYLRSPSFREYLRSLATGSTQPNL-NKKDLKKLPIPLP-PLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 102-254 1.88e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2, Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1, and re; The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 3'. The recognition sequence of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. It also includes the TRD-CR-like domains of putative type II restriction enzymes and methyltransferases, such as Helicobacter cinaedi PAGU611 Hci611ORFHP which may recognize 5'... GAGNNNNNGT ... 3', and type I N6-adenine DNA methyltransferases, such as Calditerrivibrio nitroreducens M.Cni19672ORF1405P whose recognition sequence is undetermined.


Pssm-ID: 341195 [Multi-domain]  Cd Length: 183  Bit Score: 56.80  E-value: 1.88e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 102 VQTGNTPSTKVKEYWSREDDqrkhKWVTPSDINSPTIENTKRTLTD---LGWEKARKVPANSLLITCIA---SIGKNTIN 175
Cdd:cd17514    10 IINGGTPSRNEPEYWNNGDI----PWLTSGETDDNFINNTSEKITTkngLEDSSIRIVPKGTILIACTGqgyTRGQVAVL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 176 TVPTSFNQQINSLTAKKGFD---VYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFtlrLPKdYKEQQKIGKFFKEVD 252
Cdd:cd17514    86 QIDASTNQAIAAIRCKENVNpkyLYYYLKTQKNNLRNLTSGVAQKNLNIEMLRNLQIP---LPP-KEEQQKIVNILETLE 161


                  ..
gi 1480816582 253 DK 254
Cdd:cd17514   162 FF 163
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 187-277 1.99e-09

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2 and Aminobacterium colombiense DSM 12261 S subunit (S.Aco12; The S.Aco12261I S subunit recognizes 5'... GCANNNNNNTGT ... 3', while the recognition sequence is undetermined for S.TteMORF1547P TRD2-CR2. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. S.TteMORF1547P TRD1-CR1 and S.Aco12261I TRD2-CR2 do not belong to this family. This family may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341134 [Multi-domain]  Cd Length: 174  Bit Score: 56.78  E-value: 1.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 187 SLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPKDyKEQQKIGKFFKEVDDKITSLQNALSKSK 266
Cdd:cd17245    85 AIRANKDIDNLFLYYYLKYNKPELEKLGTGSTFKAINKKDLEELKIPLPPL-EEQQKIAEILSTVDEAIEKTKALIEKLD 163

                          90
                  ....*....|.
gi 1480816582 267 ELKRTLIYKLL 277
Cdd:cd17245   164 ELKKGLMQELF 174
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 306-465 2.93e-09

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


Pssm-ID: 341155 [Multi-domain]  Cd Length: 159  Bit Score: 55.92  E-value: 2.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 306 DYFKIGKIDNISrlSQEKTEEFRYPVYSSktsnNGICGYFDTYSFE-NSITWTTDGEYAGDVKYREGKFQASIHCGIMIS 384
Cdd:cd17266     5 ELCKIKSGKSIT--ASKISEEGDYPVYGG----NGIIGYTDEYNHEgEYILIGRVGALCGNVHYVEGKFWVTDNALVVTP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 385 NRGFSCVSIAEILNRIAY-RYATRANIPRVGMGTLKQIVISYPQgTEELQKLNCLFTDINNLIYTYEATLKQHKKFKQAL 463
Cdd:cd17266    79 KKENNIKFLYYLLKSLNLnQYATGSAQPLITVSKLKKLKIPLPP-LEEQKKIAAILDSLDAKIDLLEKKLEKLIELKKEL 157


                  ..
gi 1480816582 464 VQ 465
Cdd:cd17266   158 MQ 159
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 184-277 3.21e-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: 53.27  E-value: 3.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 184 QINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPKDyKEQQKIGKFFKEVDDKITSLQNALS 263
Cdd:cd17496    83 GVAAIRPKNGIDTEFLYYLLESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPL-EEQKRIVAILDPLDEKIDKNKQEIE 161

                          90
                  ....*....|....
gi 1480816582 264 KSKELKRTLIYKLL 277
Cdd:cd17496   162 KLEELRDTLLPKLL 175
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 182-273 4.33e-08

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: 52.90  E-value: 4.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 182 NQQINSLTAKKGFD---VYYLLTSFN-KNTKKLIRAGaSSITNIvNKTQFESFTLRLPKdYKEQQKIGKFFKEVDDKITS 257
Cdd:cd17259    95 VQRVARIRPKDELNsdfLYYLLQSDFfLNYVEPVLTG-TDVPHI-STKQIKNFKIPLPP-LEEQKKIAEFLSSLDALIDL 171

                          90
                  ....*....|....*.
gi 1480816582 258 LQNALSKSKELKRTLI 273
Cdd:cd17259   172 LEQKLEKLQQLKKGLM 187
RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like cd17258
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 147-277 1.16e-07

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: 51.64  E-value: 1.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 147 DLGWEKARKVPANSLLITCIASIGK-NTINTVPTSFNQQINSLTAKKGFD----VYYLLtSFNKNTKKLIRAGASSITNI 221
Cdd:cd17258    40 KIGLKQSKIFKKGDVLITRHGTIGRvSIILSEEACLSSHVAGFNSKEGISdnkfIKYLF-NSKKIKNRLMSYGASSTQPA 118

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1480816582 222 VNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17258   119 LNLSRLLKIKFPNP-PLEEQQKIGKILSTWDRAIELTEQKLELLQQQKKGLMQQLF 173
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 181-277 1.65e-07

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: 50.92  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 181 FNQQINSLTAKKGFDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQN 260
Cdd:cd17254    78 LNQHIFKVVPDEEIDKDYLYYLLKALTEEIESQAHGSTMVHITKGDLENIKVPLP-PLEEQKRIAAILDELDALIDALEE 156

                          90
                  ....*....|....*..
gi 1480816582 261 ALSKSKELKRTLIYKLL 277
Cdd:cd17254   157 QLKKLEELRKALLQSLL 173
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 167-277 2.12e-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: 50.97  E-value: 2.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 167 ASIGKNTIntVPTSF-----NQQINSLTAKKGFD---VYYLLTSfnKNTKKLIRAGASSIT--NIvNKTQFESFTLRLPk 236
Cdd:cd17278    74 GTVGKVAI--VPEDDepallNQRVGKFRPKDKIDkefLYYLLRS--DSFRNQIKSSATGTAqpNI-SPKDIESIKIPLP- 147

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1480816582 237 DYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17278   148 PLEEQKKIAEILDSLDAKIDKLEQKLEKLRDLLKPLLQSLF 188
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 192-277 6.36e-07

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) TRD2-CR2 and Lactobacillus amylovorus GRL 1112 S subunit (S1.L; The recognition sequences of Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) and Lactobacillus amylovorus GRL 1112 S subunit (S1.LamGRLORF5415P) 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: 341185 [Multi-domain]  Cd Length: 171  Bit Score: 49.44  E-value: 6.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 192 KGFDVYYLLTSFNKNTKKLIRAGaSSITNIvNKTQFESFTLRLPKDyKEQQKIGKFFKEVDDKITSLQNALSKSKELKRT 271
Cdd:cd17494    89 NEFIFLYLYLLNIEGYWSKISQG-STFESI-NSNDIKNLKISIPSL-EEQQKIATFLSTLDAEITLLEKKLEKLKQLKKG 165


                  ....*.
gi 1480816582 272 LIYKLL 277
Cdd:cd17494   166 LLQKLF 171
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 309-458 6.71e-07

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: 49.05  E-value: 6.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 309 KIGKIDNISR----LSQEKTEEFRYPVYssktsNNGIC--GYFDTYSFE-NSITWTTDGEYAGDVKYREGKFQASIHCgi 381
Cdd:cd17291     2 KLGEIAEIKKgkqiTKKELIENGKYPVI-----AGGIEpsGYHNEYNREgNTITISASGASAGYVNYWKEPFWASDCC-- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 382 misnrgFSCVSIAEILNRIAYRY-----------ATRANIPRVGMGTLKQIVISYPQgTEELQKLNCLFTDINNLIYTYE 450
Cdd:cd17291    75 ------YILSSKNELVNKFLYYFlknkqeeiyslQRGAGQPHIYKKDIEKLKIPIPP-LEEQQKIVEILDKFTELTAELP 147


                  ....*...
gi 1480816582 451 ATLKQHKK 458
Cdd:cd17291   148 AELEARKK 155
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 188-272 7.32e-07

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: 48.98  E-value: 7.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 188 LTAKKGFDV---YYLLTSFNKNtkKLIRAGA-SSITNivnkTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALS 263
Cdd:cd17266    76 VTPKKENNIkflYYLLKSLNLN--QYATGSAqPLITV----SKLKKLKIPLP-PLEEQKKIAAILDSLDAKIDLLEKKLE 148


                  ....*....
gi 1480816582 264 KSKELKRTL 272
Cdd:cd17266   149 KLIELKKEL 157
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 196-277 2.23e-06

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: 47.88  E-value: 2.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 196 VYYLLTS--FnkntKKLIRAGASSITNIVNKTQFESFTLRLPKdYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLI 273
Cdd:cd17265   103 LFHLFNSdlF----KKQIGSFLTATINQITNGNLNNFKIPLPP-LEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKELM 177


                  ....
gi 1480816582 274 YKLL 277
Cdd:cd17265   178 QQLI 181
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 197-276 2.72e-06

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: 47.92  E-value: 2.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 197 YYLLTSFNKNTKKLIRAGASSITNIvNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKL 276
Cdd:cd17517   115 YYLNSPLGRKQIEKIAKSAAGQANI-NQKDLKKLPIPLP-PLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 188-276 4.58e-06

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


Pssm-ID: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 46.66  E-value: 4.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 188 LTAKKGFDVYYLLTSFNkntkkliragASSITNIV--------NKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQ 259
Cdd:cd17262    87 LKGKNGISTEFLYYYLN----------SIDISPYVtgaaqpklNQANLNSIPIPLP-PLEEQKKIVAILDKLDALIDLLE 155

                          90
                  ....*....|....*..
gi 1480816582 260 NALSKSKELKRTLIYKL 276
Cdd:cd17262   156 EELEKLIELKKALLQKL 172
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 196-277 5.06e-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: 46.73  E-value: 5.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 196 VYYLLTSFNKNTKKLIRAGASsitnI--VNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLI 273
Cdd:cd17263    99 LYYFLKSKEIQLNILTKAGST----IphVNKKDLENLKIPLP-SLEEQKKIAEILDKLDALIDKLKELIEKLIELKKGLF 173


                  ....
gi 1480816582 274 YKLL 277
Cdd:cd17263   174 QELL 177
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 161-273 5.76e-06

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: 46.72  E-value: 5.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 161 LLITCIASIGKntINTVPTSFN-----QQINSLTAKKGFD---VYYLLTS------FNKNTKKLIRAGassitniVNKTQ 226
Cdd:cd17256    65 ILISIVGTIGR--VGIVPKELDganltENAARIRPKDSISpryLYYYLRSpfgqsqIESETKGAAQPK-------LNLKR 135

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1480816582 227 FESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLI 273
Cdd:cd17256   136 IRELPIPLP-PLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKALM 181
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 159-278 1.30e-05

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


Pssm-ID: 341189 [Multi-domain]  Cd Length: 173  Bit Score: 45.37  E-value: 1.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 159 NSLLITCIASIGKNTINTVPTSFNQQINSLTAKKGFD--VYYLLtsfNKNTKKLIRAGASSITNIVNKTQFESFTLRLPK 236
Cdd:cd17498    57 GDILMSVRAPVGDLNIANKDICIGRGLCSIRMKNGNNsfLYYLL---KNNIKNLINKSSGTVFGSINKDDIENLEVDIPE 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1480816582 237 DyKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTlIYKLLF 278
Cdd:cd17498   134 D-EEQKRIANILSKIDDKIEINNQINKNLEELAQA-IFKHWF 173
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 196-272 2.34e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoKI TRD1-CR1, S.StySPI TRD1-CR1, S.Ara36733II TRD1-CR1, and S.Eco3722I TRD1-CR1; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) and Escherichia coli NCM3722 S subunit (S.Eco3722I) recognize 5'... AACNNNNNNGTGC ... 3', Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3', and Actinomyces radicidentis S subunit (S.Ara36733II) recognizes 5'... CATCNNNNNNCTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC, and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Treponema pedis T A4 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.TpeTA4ORF2695P. It may also include type I DNA methyltransferases.


Pssm-ID: 341141 [Multi-domain]  Cd Length: 189  Bit Score: 44.86  E-value: 2.34e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1480816582 196 VYYLLTSfnKNTKKLIR--AGASSITNIvNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTL 272
Cdd:cd17252   113 LFYFLQS--PSYREYIRslASGTNINNL-SNEHLENLKIPLP-PLAEQKRIVAKLDKLDALIDKLKQALEKLDELLKSL 187
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 197-276 5.09e-05

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: 44.01  E-value: 5.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 197 YYLLTSFNKNTKKLIRAGaSSITNIvNKTQFESFTLRLPKDyKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKL 276
Cdd:cd17521   111 YFTQSSLYWKQIKSISSG-SAQPNI-NAEKLKSLKIPLPPL-EEQKRIVAILDALDAKIDALEELLEKLEELLKELLQSL 187
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 197-277 6.42e-05

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


Pssm-ID: 341142 [Multi-domain]  Cd Length: 193  Bit Score: 43.62  E-value: 6.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 197 YYLLTSFNKNT-KKLIRAGASSITNI--VNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLI 273
Cdd:cd17253   111 EFLSYWLNSAYgRGYFLRAAKQTTNLasINSTKLKALPVPLP-PLEEQRRIVERLDELLALIDALEASLAKLEELLKALR 189


                  ....
gi 1480816582 274 YKLL 277
Cdd:cd17253   190 QALL 193
RMtype1_S_Eco15ORF14057P-TRD1-CR1_like cd17525
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 181-276 6.65e-05

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: 43.76  E-value: 6.65e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 181 FNQQINSLTAKKGFDVYYLLTSFN-KNTKKLIRAGASSITNIVNKTQFESFTLRLP-KDYKEQQKIGKFFKEVDDKITSL 258
Cdd:cd17525    93 FNNNILRIRFDDIVLPYFINYYLNsPDGKKQLESIASGTTSVAAIYQKDLKKLKLPlPPLDEQREIVSFLSELDAKIDQL 172

                          90
                  ....*....|....*...
gi 1480816582 259 QNALSKSKELKRTLIYKL 276
Cdd:cd17525   173 EQKLEKLLQIKKALMQQL 190
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 222-277 8.85e-05

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: 42.81  E-value: 8.85e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1480816582 222 VNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17260   111 VPKDFLENYKIPLP-PLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALLPKLL 165
RMtype1_S_Eco540ANI-TRD1-CR1_like cd17274
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 227-277 1.51e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Eco540ANI TRD1-CR1, S.Eco2747AII TRD1-CR1, S.Eco540AI TRD1-CR1, S.Eco2747II TRD1-CR1, and S.Eco540I TRD1-CR1; Escherichia coli ST540AN S subunit (S.Eco540ANI ), Escherichia coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540 S subunit (S.Eco540I) recognize 5'... GAANNNNNNRTCG ... 3'. Escherichia coli ST2747A S subunit (S.Eco2747AII) and Escherichia coli ST2747 S subunit (S.Eco2747II) recognize 5'... GAANNNNNNNTAAA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341163  Cd Length: 171  Bit Score: 42.48  E-value: 1.51e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1480816582 227 FESFTLRLPKdYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17274   121 YSKFKIPLPP-LEEQNKIVRILDKFDELIAELEAKLELLKKQKKYYLQKLF 170
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 86-272 3.52e-04

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: 41.47  E-value: 3.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582  86 GFNESYQFFEvneigkvqTGNTPSTKVkeywsreddqrkhkwvtpSDIN----SPTIENTKRTL--TDLGWEKARKVPAN 159
Cdd:cd17250    14 GFPEKYQGKE--------DGEYPFYKV------------------GDMNnsgnEKYLSTAENYIseEIVKELKAKLFPKG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 160 SLLITCI-ASIGKN--TINTVPTSFNQQINSLTAKKGFD---VYYLLTSFNknTKKLIRAgassiTNI--VNKTQFESFT 231
Cdd:cd17250    68 TIIFAKIgEAIKLNrrAILSKDSCIDNNVMGLIPNEGIDseyLYYWLKKVD--LYKYSQA-----TTVpsIRKSTLESIP 140

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1480816582 232 LRLPKdYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTL 272
Cdd:cd17250   141 IPLPP-LEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGL 180
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 189-272 4.03e-04

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: 40.85  E-value: 4.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 189 TAKKGFD---VYYLLTSFNKNTKKliraGASSI-TniVNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSK 264
Cdd:cd17267    75 KDFKGNDprfLYYLLKTLDLERLN----SGSAVpG--LNRNDVYSLKVPLP-PLEEQKAIAAILDALDDKIELNRRQNQT 147


                  ....*...
gi 1480816582 265 SKELKRTL 272
Cdd:cd17267   148 LEELADAL 155
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 296-426 4.07e-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: 41.19  E-value: 4.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 296 WKKGELYSIFDYFKiGKIDNisrlSQEKTEEFRYPVYSSKTSNNGICGYFDTYSF----ENSITWTTDGeYAGDVKYREG 371
Cdd:pfam01420   4 WEVFKLGDVFEIKK-GKTPK----KKELKNNGKYPYIRAGDLNNVVKGGLGYIKKyilpKGDITISSRA-TIGYVFYRDK 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1480816582 372 KFQASIHCGIMIS--------NRGFSCVSIAEILNRIAYRYAtranIPRVGMGTLKQIVISYP 426
Cdd:pfam01420  78 PYYTNQHIIVLIPknnikiteFLYLYLLLKLKKLKSLKFGST----QPKLTKERLKEIKIPLP 136
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 191-276 4.09e-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: 41.37  E-value: 4.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 191 KKGFDVYYLLTSFN-KNTKKLIRAGA------SSItnivNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALS 263
Cdd:cd17522   103 KNIVDPKYLYYLLKsDRFRNQFRSIAkkavnqASI----NQTELKKIKIPLP-PLEEQQKIASILEKLDKKIEKRKEKIE 177

                          90
                  ....*....|...
gi 1480816582 264 KSKELKRTLIYKL 276
Cdd:cd17522   178 KLKELKKGLFQKL 190
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 239-277 4.38e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to the S subunit TRD2-CR2 regions of Lactococcus lactis subsp. cremoris A17 (S.LlaA17I), Haemophilus influenzae Rd (S.HindORF215P) ; Lactococcus lactis subsp. cremoris A17 S subunit (S.LlaA17I) recognizes 5'... CAANNNNNNNNTAYG... 3', while the recognition sequences of Clostridium species ASF502 S subunit (S.Csp502ORF478P) and Haemophilus influenzae Rd S subunit (S.HindORF215P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Porphyromonas species COT-108 OH1349 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.Psp1349ORF730P) of unknown recognition sequence. It may also include type I DNA methyltransferases.


Pssm-ID: 341181 [Multi-domain]  Cd Length: 149  Bit Score: 40.60  E-value: 4.38e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1480816582 239 KEQQKIGKFFKEVDDKITSLQNALSKSKELKRTLIYKLL 277
Cdd:cd17292   111 DEQRKIAEFLSLLDALIALLQKKLEKLIALKKGLMQYLF 149
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 182-273 5.12e-04

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) TRD2-CR2; The recognition sequence of Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341193 [Multi-domain]  Cd Length: 195  Bit Score: 41.05  E-value: 5.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 182 NQQINSLTAKKG-----FDVYYLLTSFNKNTKKLIRAGASSITNIVNKTQFEsFTLRLPkDYKEQQKIGKFFKEVDDKIT 256
Cdd:cd17512    99 NQNAVKIRPKKGildqsFLFYNLKSERFKNYIESIARGNANQASITLGDIKK-FKFLLP-PLEEQKKIASILSAYDDLIE 176

                          90
                  ....*....|....*..
gi 1480816582 257 SLQNALSKSKELKRTLI 273
Cdd:cd17512   177 NNEKRIKLLEQMKQALY 193
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 197-272 7.82e-04

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


Pssm-ID: 341144 [Multi-domain]  Cd Length: 166  Bit Score: 40.20  E-value: 7.82e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1480816582 197 YYLLTSFNKNTKKLIRAGAssiTNIVNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTL 272
Cdd:cd17255    91 KFLYYALNLIAKKYVSFDG---NPKLMNNVMAKIKIPLP-PLEEQEKIANILDKLDELINLLIAKLKKLIELRKKQ 162
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 418-468 1.30e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) TRD2-CR2 and Lactobacillus amylovorus GRL 1112 S subunit (S1.L; The recognition sequences of Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) and Lactobacillus amylovorus GRL 1112 S subunit (S1.LamGRLORF5415P) 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: 341185 [Multi-domain]  Cd Length: 171  Bit Score: 39.43  E-value: 1.30e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1480816582 418 LKQIVISYPQgTEELQKLNCLFTDINNLIYTYEATLKQHKKFKQALVQRML 468
Cdd:cd17494   122 IKNLKISIPS-LEEQQKIATFLSTLDAEITLLEKKLEKLKQLKKGLLQKLF 171
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
394-468 3.65e-03

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 36.58  E-value: 3.65e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1480816582 394 AEILNRIAYRYATRANIPRVGMGTLKQIVISYPQgTEELQKLNCLFTDINNLIYTYEATLKQHKKFKQALVQRML 468
Cdd:COG0732     8 SPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPP-LEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
RMtype1_S_EcoUTORF5051P-TRD2-CR2_like cd17524
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 197-276 4.26e-03

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


Pssm-ID: 341205 [Multi-domain]  Cd Length: 189  Bit Score: 38.21  E-value: 4.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1480816582 197 YYLLTSFN-KNTKKLIRAGASSI---TNIvNKTQFESFTLRLPkDYKEQQKIGKFFKEVDDKITSLQNALSKSKELKRTL 272
Cdd:cd17524   108 EYLNYFLNsPYGRKQIKSVATQGvgqANI-NATKLKAIPIPLP-PLEEQKEIVEKLDELDALIDRLEALLEEAEELLESL 185


                  ....
gi 1480816582 273 IYKL 276
Cdd:cd17524   186 LQSL 189
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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