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Conserved domains on  [gi|2170640448|ref|WP_232927216|]
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restriction endonuclease subunit S [Enterobacter roggenkampii]

Protein Classification

restriction endonuclease subunit S domain-containing protein; restriction endonuclease subunit S( domain architecture ID 13020920)

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| 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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-192 2.15e-83

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: 255.07  E-value: 2.15e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLRVTSLG-STNGTRLVPAETVLLLVRGGALHNKIPV 86
Cdd:cd17249     1 VRLGDLGKFLSGGTPSKSNPEYWGGDIPWVSPKDMKSDYISDSEDHITELAvEESGTKLVPAGSVLIVVRGMILAHTFPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  87 GITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKVENTGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKA 166
Cdd:cd17249    81 AITTRPVAFNQDIKALIPK-EGIDPEFLLYALKANEDRILSLVDKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDA 159

                         170       180
                  ....*....|....*....|....*.
gi 2170640448 167 LDDKIILNQNINHTLEQMAQALFKSW 192
Cdd:cd17249   160 LDALIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 268-454 4.21e-79

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: 243.85  E-value: 4.21e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 268 WTLSEIGAQIDIAGGATPSTKTPDFWdNGDIHWTTPKDLSNVKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPV 347
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKNPEYW-NGDIPWITPTDLTKLKGKYISDTERKITELGLKNSSAKLLPAGSVLLSSRAPI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 348 GYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSA 427
Cdd:cd17273    80 GYVAIATNPLATNQGFKSIIPNEEIDNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEIPLPPLEEQKKIAAILSK 159

                         170       180
                  ....*....|....*....|....*..
gi 2170640448 428 IYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17273   160 LDELIELLEKENEKLKELRDGLLPKLF 186
 
Name Accession Description Interval E-value
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-192 2.15e-83

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: 255.07  E-value: 2.15e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLRVTSLG-STNGTRLVPAETVLLLVRGGALHNKIPV 86
Cdd:cd17249     1 VRLGDLGKFLSGGTPSKSNPEYWGGDIPWVSPKDMKSDYISDSEDHITELAvEESGTKLVPAGSVLIVVRGMILAHTFPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  87 GITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKVENTGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKA 166
Cdd:cd17249    81 AITTRPVAFNQDIKALIPK-EGIDPEFLLYALKANEDRILSLVDKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDA 159

                         170       180
                  ....*....|....*....|....*.
gi 2170640448 167 LDDKIILNQNINHTLEQMAQALFKSW 192
Cdd:cd17249   160 LDALIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 268-454 4.21e-79

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: 243.85  E-value: 4.21e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 268 WTLSEIGAQIDIAGGATPSTKTPDFWdNGDIHWTTPKDLSNVKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPV 347
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKNPEYW-NGDIPWITPTDLTKLKGKYISDTERKITELGLKNSSAKLLPAGSVLLSSRAPI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 348 GYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSA 427
Cdd:cd17273    80 GYVAIATNPLATNQGFKSIIPNEEIDNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEIPLPPLEEQKKIAAILSK 159

                         170       180
                  ....*....|....*....|....*..
gi 2170640448 428 IYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17273   160 LDELIELLEKENEKLKELRDGLLPKLF 186
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 3-183 1.25e-17

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: 80.09  E-value: 1.25e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   3 SNWSVKKLGDLVTFLSGGTPSKSNKdYWNGEIPWISASSMQSTRYHDSDlrvtslgsTNGTRLVPAETVLLLVRGGAlhn 82
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPKKKEL-KNNGKYPYIRAGDLNNVVKGGLG--------YIKKYILPKGDITISSRATI--- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  83 kIPVGITTREVTFNQDVKALVPKSEDITPYYLLAWLISSRELLlgKVENTGIGAGKLDTKILQDLDVPVPPKAELLRLEL 162
Cdd:pfam01420  70 -GYVFYRDKPYYTNQHIIVLIPKNNIKITEFLYLYLLLKLKKL--KSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAK 146

                         170       180
                  ....*....|....*....|.
gi 2170640448 163 FSKALDDKIILNQNINHTLEQ 183
Cdd:pfam01420 147 ILSQLDNTIELEKGILNELER 167
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 265-444 4.46e-17

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: 78.55  E-value: 4.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 265 PEGWTLSEIGAQIDIAGGATPSTKtpDFWDNGDIHWTTPKDLSNVKDKILLHTERKItkaglgkissglLPVNTVLMSSR 344
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKK--ELKNNGKYPYIRAGDLNNVVKGGLGYIKKYI------------LPKGDITISSR 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 345 APVGYLAIAKVPVAINQGYIAMK-CNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTK 423
Cdd:pfam01420  67 ATIGYVFYRDKPYYTNQHIIVLIpKNNIKITEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAK 146

                         170       180
                  ....*....|....*....|.
gi 2170640448 424 QVSAIYSLIENTMRENNSLTE 444
Cdd:pfam01420 147 ILSQLDNTIELEKGILNELER 167
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
387-461 5.95e-15

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 70.09  E-value: 5.95e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2170640448 387 EIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLLSGEITLP 461
Cdd:COG0732    14 YLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFTGELRVR 88
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
262-415 6.04e-10

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 61.05  E-value: 6.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 262 GEIPEGWTLSEIGAQIDIAGGAT-PSTKTpdfwdngdIHWTTPKDLSNVKDKILLHTERKITKAGLGK-----ISSGLLP 335
Cdd:PRK09737    4 GKLPEGWVTTHISEICSVIRGVKpPKGYA--------TKSLTMGDLPFIRTTDITNGAVDLTTLPYCMdapedVSKYQLQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 336 VNTVLMSSRAPVGYLAIAKVPVAINQGY----IAMKCNKELSPEFVLQWCSANMP--EIISRASGTTFAEISKKNFNPIP 409
Cdd:PRK09737   76 DRDIVISSAGSIGFSFLAQNPLPSNVVFasfaIRLKPVNYFSEYFLKHFLESSDYrnQLSLMSAGNAVQNINAQSLSTLT 155


                  ....*.
gi 2170640448 410 LVKPPL 415
Cdd:PRK09737  156 FPIPPI 161
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
5-459 2.33e-05

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 46.80  E-value: 2.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGTPSKSNKDYWN--GEIPWISASSMQSTRYHDSDLRVTSLGSTNGTRLVPAETVLLLVRGGALhn 82
Cdd:PRK09737   10 WVTTHISEICSVIRGVKPPKGYATKSLtmGDLPFIRTTDITNGAVDLTTLPYCMDAPEDVSKYQLQDRDIVISSAGSI-- 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  83 kIPVGITTREVTFNQDVKALVPKSE---DITPYYLLAWLISSRELLLGKVENTGIGAGKLDTKILQDLDVPVPPKAEllr 159
Cdd:PRK09737   88 -GFSFLAQNPLPSNVVFASFAIRLKpvnYFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAE--- 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 160 LELFSKALDDKIILNQNINHTLEQMAQALfkswfvdfepVKAKIAVLEAggsqedatraamtAISGKDAHalavfEREHP 239
Cdd:PRK09737  164 QKIIAEKLDTLLAQVDSTKARLEQIPQIL----------KRFRQAVLGA-------------AVSGKLTE-----EWRWP 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 240 EQyaelkttaelfPSAMQDSELGEI---PEGWTLSEIGAQidiaGGATPstktpdFWDNGDIHWTTpKDLSNVKDKILLH 316
Cdd:PRK09737  216 DL-----------PSTWSVHKYSELvdsRLGGMSSKANNF----GSATP------YLRNINVRWGS-FDLEDLQDILISD 273

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 317 TERKITKaglgkissglLPVNTVLMS---SRAPVGYLAIAKVPVAIN---QGY-IAMKCNKELSPEFV---LQWCSANMP 386
Cdd:PRK09737  274 IERRELK----------LKLGDVLFCrgnEPLEVGRCAIWKEPQDIPviyQKAlIRARVKDDIIPEYLvynLKSPDSRNI 343

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 387 EIISRASGTTFAEISKKNFNPIPLVKPPL----ELVKNyTKQVSAIYSLIE----NTMRENNSLTElrdTLLPKLLSGEI 458
Cdd:PRK09737  344 SLSQLFTGTTQKHITGKALANYPIRVPPLeeqaEIVRR-VEQLFAYADTIEkqvnNALARVNNLTQ---SILAKAFRGEL 419


                  .
gi 2170640448 459 T 459
Cdd:PRK09737  420 T 420
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
132-193 3.77e-05

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 42.35  E-value: 3.77e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2170640448 132 TGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:COG0732    20 TGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
 
Name Accession Description Interval E-value
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-192 2.15e-83

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: 255.07  E-value: 2.15e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLRVTSLG-STNGTRLVPAETVLLLVRGGALHNKIPV 86
Cdd:cd17249     1 VRLGDLGKFLSGGTPSKSNPEYWGGDIPWVSPKDMKSDYISDSEDHITELAvEESGTKLVPAGSVLIVVRGMILAHTFPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  87 GITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKVENTGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKA 166
Cdd:cd17249    81 AITTRPVAFNQDIKALIPK-EGIDPEFLLYALKANEDRILSLVDKAGHGTGSLDTDDLKNLPIPLPPLEEQRRIAAILDA 159

                         170       180
                  ....*....|....*....|....*.
gi 2170640448 167 LDDKIILNQNINHTLEQMAQALFKSW 192
Cdd:cd17249   160 LDALIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 268-454 4.21e-79

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: 243.85  E-value: 4.21e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 268 WTLSEIGAQIDIAGGATPSTKTPDFWdNGDIHWTTPKDLSNVKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPV 347
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKNPEYW-NGDIPWITPTDLTKLKGKYISDTERKITELGLKNSSAKLLPAGSVLLSSRAPI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 348 GYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSA 427
Cdd:cd17273    80 GYVAIATNPLATNQGFKSIIPNEEIDNEFLYYLLKNNKPEIESLASGSTFKEISKSTFKKIEIPLPPLEEQKKIAAILSK 159

                         170       180
                  ....*....|....*....|....*..
gi 2170640448 428 IYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17273   160 LDELIELLEKENEKLKELRDGLLPKLF 186
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-452 4.83e-49

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: 166.09  E-value: 4.83e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIgaqIDIAGGATPSTKTPDFWdNGDIHWTTPKDLSNVkDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPVG 348
Cdd:cd17243     4 SLSDV---VDIIGGGTPKTSVPEYW-NGDIPWFSVKDVNND-SRFVLDTEKKITELGLKNSSTKLLPKGTTIISARGTVG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 349 YLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAI 428
Cdd:cd17243    79 KLALLGIPMAMNQSCYGLRGKDGLSNYFLYYLLKNLIEELKQKAHGSVFDTITRKTFDEIKVPLPPEELQKSFENIVSPL 158

                         170       180
                  ....*....|....*....|....
gi 2170640448 429 YSLIENTMRENNSLTELRDTLLPK 452
Cdd:cd17243   159 FDKILNNLKENQTLAQLRDTLLPK 182
RMtype1_S_Vch69ORF1407P_TRD2-CR2_like cd17501
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio ...
 264-455 5.53e-45

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: 155.41  E-value: 5.53e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 264 IPEGWTLSEI-GAQIDIAGGATPSTKTPDFWDNGDIHWTTPKDLsnvKDKILLHTERKITKAGLGKISSGLLPVNTVLMS 342
Cdd:cd17501     1 VPEGWEVGTIlDLCYKTQSGGTPSRKNPEYWDGGIIPWLKTGEL---RDNIILDTEEKITEEGLKNSSAKLFPKGTVLVA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 343 SRAP-VGYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNY 421
Cdd:cd17501    78 MYGAtAGKLGILAKEATTNQACCALIPKEEYSPFFLYLYLLNSRDYLANLASGSAQQNISQQIIKNTKVLIPPEDLLEIF 157

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2170640448 422 TKQVSAIYSLIENTMRENNSLTELRDTLLPKLLS 455
Cdd:cd17501   158 NKLVEPLFDKIINNLKENQKLAKLRDTLLPKLMS 191
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 278-416 2.57e-42

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: 148.09  E-value: 2.57e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 278 DIAGGATPSTKTPDFWDnGDIHWTTPKDLSNVKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPVGYLAIAKVPV 357
Cdd:cd17279     8 RIVNGSTPKSGEEDYWD-GDIPWVTPADLSKLDGKYISSSQRKITEAGLESCGTSLVPAGSIILSTRAPIGYVAIATVEL 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2170640448 358 AINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLE 416
Cdd:cd17279    87 CTNQGCKALVPNSDVDSRFLYYLLLAAKEELNSLGRGTTFLELSTDELANFKIPLPPLS 145
RMtype1_S_MmaGORF2198P_TRD1-CR1_like cd17500
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 9-194 9.91e-34

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: 125.48  E-value: 9.91e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   9 KLGDLVT-FLSGGTPSKSNKDYW-NGEIPWISASSMQSTRYHDSDLRVTSLGSTN-GTRLVPAETVLLLVRGgALHNKIP 85
Cdd:cd17500     1 KLEDICIkITSGGTPSRSNKEYYnGGNIPWLKTKELNFKRIYDTEEKITEEGLKNsSAKLIPENTVIIAMYG-AGKTAGR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  86 VGITTREVTFNQDVKALVPKSEDITPYYLLAWLISSRELLLGKveNTGIGAGKLDTKILQDLDVPVPPKAELLRLELFSK 165
Cdd:cd17500    80 VAINKIPLTTNQACCNLIIDNKKADYRFVYYSLKTQYEELVNL--ASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILS 157

                         170       180
                  ....*....|....*....|....*....
gi 2170640448 166 ALDDKIILNQNINHTLEQMAQALFKSWFV 194
Cdd:cd17500   158 SLDDKIELNNRQNETLEAMAETLFKEWFV 186
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-453 1.06e-33

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: 125.26  E-value: 1.06e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIGaqiDIAGGATPSTKTPDFWdNGDIHWTTPKDLsnvKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRA--- 345
Cdd:cd17249     2 RLGDLG---KFLSGGTPSKSNPEYW-GGDIPWVSPKDM---KSDYISDSEDHITELAVEESGTKLVPAGSVLIVVRGmil 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 346 ----PVgylAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIIS--RASGTTFAEISKKNFNPIPLVKPPLELVK 419
Cdd:cd17249    75 ahtfPV---AITTRPVAFNQDIKALIPKEGIDPEFLLYALKANEDRILSlvDKAGHGTGSLDTDDLKNLPIPLPPLEEQR 151

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2170640448 420 NYTKQVSAIYSLIENTMRENNSLTELRDTLLPKL 453
Cdd:cd17249   152 RIAAILDALDALIDLLERKLAKLEELLKALMQAL 185
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 7-193 1.46e-33

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: 124.97  E-value: 1.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   7 VKKLGDLVTflsGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLR-VTSLG-STNGTRLVPAETVLLLVRGGALHNki 84
Cdd:cd17516     3 IGDLGKVVT---GKTPSTKNPEYFGGDIPFITPSDMKGGKYIIKTERrLSSKGlEKVKNKLIPANSICVTCIGSDMGK-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  85 pVGITTREVTFNQDVKALVPKSEDITPYYLLAWLISSRELLLGkventgIGAGKLDTKIL-----QDLDVPVPPKAELLR 159
Cdd:cd17516    78 -VAITKEPSVTNQQINSIIVNKNKFDPDFVYYLLKNNSKYLKS------IAGGSTATPIInkstfSNIEIPLPPLPEQKK 150

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2170640448 160 LELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17516   151 IAAILSSLDDKIENNRRINKTLEEMAQALFKEWF 184
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 5-193 2.76e-33

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: 124.06  E-value: 2.76e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGTPSKSNKDYWNGEIPWISAS--SMQSTRY-HDSDLRVTSLGSTN-GTRLVPAETVLLLVRggAl 80
Cdd:cd17273     1 WEVVKLGDVAEIVGGGTPSTKNPEYWNGDIPWITPTdlTKLKGKYiSDTERKITELGLKNsSAKLLPAGSVLLSSR--A- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  81 hnkiPVG---ITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKventgiGAG----KLDTKILQDLDVPVPP 153
Cdd:cd17273    78 ----PIGyvaIATNPLATNQGFKSIIPN-EEIDNEFLYYLLKNNKPEIESL------ASGstfkEISKSTFKKIEIPLPP 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2170640448 154 KAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17273   147 LEEQKKIAAILSKLDELIELLEKENEKLKELRDGLLPKLF 186
RMtype1_S_AchA6I-TRD2-CR2_like cd17243
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 7-190 4.29e-32

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: 120.63  E-value: 4.29e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   7 VKKLGDLVTFLSGGTPSKSNKDYWNGEIPWISAS-SMQSTRY-HDSDLRVTSLGSTN-GTRLVPAETVLLLVRG--GAlh 81
Cdd:cd17243     2 VKSLSDVVDIIGGGTPKTSVPEYWNGDIPWFSVKdVNNDSRFvLDTEKKITELGLKNsSTKLLPKGTTIISARGtvGK-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  82 nkipVGITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGK----VENTgigagkLDTKILQDLDVPVPPKAEL 157
Cdd:cd17243    80 ----LALLGIPMAMNQSCYGLRGK-DGLSNYFLYYLLKNLIEELKQKahgsVFDT------ITRKTFDEIKVPLPPEELQ 148

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2170640448 158 LRLELFSKALDDKIILNQNINHTLEQMAQALFK 190
Cdd:cd17243   149 KSFENIVSPLFDKILNNLKENQTLAQLRDTLLP 181
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 277-454 1.50e-31

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: 119.15  E-value: 1.50e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 277 IDIAGGATPSTKTPDFWdNGDIHWTTPKDLsnvKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPVGYLAIAKVP 356
Cdd:cd17285     8 EKIVGGGTPSKSNPEYW-NGDIPWASVKDL---KGKYLTSTEDKITEEGLKNSSSNLIPKGTVIIATRMGLGKVAINKID 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 357 VAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFN--PIPLvkPPLELVKNYTKQVSAIYSLIEN 434
Cdd:cd17285    84 VAINQDLKALFPKDELDPEYLLYWFLSIEETIESLGTGTTVKGITLEDLKslKIPL--PPLEEQKRIVAILDELDELIDK 161

                         170       180
                  ....*....|....*....|
gi 2170640448 435 TMRENNSLTELRDTLLPKLL 454
Cdd:cd17285   162 LEAKLEKLKQLKKGLMQSLL 181
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-189 9.13e-30

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: 114.52  E-value: 9.13e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLV-TFLSGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLRVTSLGSTNG-TRLVPAETVLLLVRggalhnkIP 85
Cdd:cd17285     1 KKLGDLVeKIVGGGTPSKSNPEYWNGDIPWASVKDLKGKYLTSTEDKITEEGLKNSsSNLIPKGTVIIATR-------MG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  86 VG---ITTREVTFNQDVKALVPKSEdITPYYLLAWLISSRElllgKVENTGIGA---G-KLDTkiLQDLDVPVPPKAELL 158
Cdd:cd17285    74 LGkvaINKIDVAINQDLKALFPKDE-LDPEYLLYWFLSIEE----TIESLGTGTtvkGiTLED--LKSLKIPLPPLEEQK 146

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2170640448 159 R----LELFSKALDDKIILNQNINHTLEQMAQALF 189
Cdd:cd17285   147 RivaiLDELDELIDKLEAKLEKLKQLKKGLMQSLL 181
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-193 1.93e-29

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: 113.38  E-value: 1.93e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLR--VTSLGSTN-GTRLVPAETVLLLVRGGalhnki 84
Cdd:cd17513     1 VKLGELGKFIGGGTPSTKNPEYWNGNIPWITSSDLSEDDIFKINIRkfITEEAIKNsATKIIPANSILIVTRVG------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  85 pVG---ITTREVTFNQDVKALVPKSEDItPYYLLAWLISSRELLLGKVENT---GIgagkldTK-ILQDLDVPVPPKAEL 157
Cdd:cd17513    75 -VGkvaINPFDICTSQDFTSLIPIKEVN-PLFLAYLLYSLLQKLKSQLQGTsikGI------TKdDLKNLKIPLPPLEEQ 146

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2170640448 158 LRLELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17513   147 QKIAAILSKLDKLIEAHEKKLEKLKQLKKGLMQKLF 182
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 269-454 2.13e-28

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: 110.71  E-value: 2.13e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIgAQIDIAGGaTPSTKTPDFWdNGDIHWTTPKDLSNvKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPVG 348
Cdd:cd17275     4 KLGEL-CEKMKSGG-TPSTSNKEYY-GGDIPFVKISDMTK-SGKYIYSTEKYITEEGLKNSSAWIVPKGTILYAMYASVG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 349 YLAIAKVPVAINQGYIAMKCNKE-LSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSA 427
Cdd:cd17275    80 KVAINKIDVATNQAILGIIPKDEkLDFEFLYYWLLSLKNELKRLIRTGTQANLNAEIVKNLPIPLPPLEEQKKIAEILDK 159

                         170       180
                  ....*....|....*....|....*..
gi 2170640448 428 IYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17275   160 IDAEIDKLEEKIEKLRELKKGLLQKMF 186
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 5-193 3.23e-28

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: 110.27  E-value: 3.23e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGTPSKSNKDYWNGE-IPWISASSMQSTRYHDSDLRVTSLGSTN-GTRLVPAETVLLlvrggAL-- 80
Cdd:cd17294     1 WEWKTLGEIAKIFSGGTPSTSNPEYWDGGtIPWLSSGEVNFKEIYETEKRITEEGLKNsSAKWIPKNSVLI-----ALag 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  81 --HNKIPVGITTREVTFNQDVKALVPKSEDITPYYLLAWLISSRELLlgKVENTGIGAGKLDTKILQDLDVPVPPKAELL 158
Cdd:cd17294    76 qgKTRGTVAILKIPLTTNQSLAAIEPDEEIANSRFLYYNLSSRYEEL--RSLSGGGGRGGLNLKIIKSLPIPLPPLEEQK 153

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2170640448 159 RLELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17294   154 KIVAILDKFDALINDLKEGLPALLELRQKQYEYLR 188
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-454 6.12e-28

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: 109.45  E-value: 6.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIGaqiDIAGGATPSTKTPDFWdNGDIHWTTPKDLsnvKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSR-APV 347
Cdd:cd17515     2 KLGDIG---KWGSGGTPSRSNPEYY-GGGIPWIKSGEL---NDGYITSTEEKITEEGLKNSSAKLFPKGSVLIAMYgATA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 348 GYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISK---KNFnPIPLvkPPLELVKNYTKQ 424
Cdd:cd17515    75 GKVGILGIDAATNQAICAILPNEEIDNEFLFYFLKSQKEYLISLGKGGAQPNISQgiiKNI-EIPL--PPLAEQKRIVAK 151

                         170       180       190
                  ....*....|....*....|....*....|
gi 2170640448 425 VSAIYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17515   152 LDKLDKLIEKLEKALEKLEELKKALMQKLL 181
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-193 4.23e-27

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: 107.13  E-value: 4.23e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLRVTSLGSTN-GTRLVPAETVLLLVRG---GAlhnk 83
Cdd:cd17515     1 VKLGDIGKWGSGGTPSRSNPEYYGGGIPWIKSGELNDGYITSTEEKITEEGLKNsSAKLFPKGSVLIAMYGataGK---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  84 ipVGITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLgkveNTGIGAGK--LDTKILQDLDVPVPPKAELLRLE 161
Cdd:cd17515    77 --VGILGIDAATNQAICAILPN-EEIDNEFLFYFLKSQKEYLI----SLGKGGAQpnISQGIIKNIEIPLPPLAEQKRIV 149

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2170640448 162 LFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17515   150 AKLDKLDKLIEKLEKALEKLEELKKALMQKLL 181
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17516
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-453 1.62e-26

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: 105.71  E-value: 1.62e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIGaqiDIAGGATPSTKTPDFWDNgDIHWTTPKDLSNVKDKILlhTERKITKAGLGKISSGLLPVNTVLMSSRAP-V 347
Cdd:cd17516     2 KIGDLG---KVVTGKTPSTKNPEYFGG-DIPFITPSDMKGGKYIIK--TERRLSSKGLEKVKNKLIPANSICVTCIGSdM 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 348 GYLAIAKVPVAINQGYIAMKCNKEL-SPEFVLQWCSANMPEIISRASGTTFAEI-SKKNFNPIPLVKPPLELVKNYTKQV 425
Cdd:cd17516    76 GKVAITKEPSVTNQQINSIIVNKNKfDPDFVYYLLKNNSKYLKSIAGGSTATPIiNKSTFSNIEIPLPPLPEQKKIAAIL 155

                         170       180
                  ....*....|....*....|....*...
gi 2170640448 426 SAIYSLIENTMRENNSLTELRDTLLPKL 453
Cdd:cd17516   156 SSLDDKIENNRRINKTLEEMAQALFKEW 183
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-193 6.22e-26

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: 103.83  E-value: 6.22e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYW-NGEIPWISASSMQSTRYHDSDLRVTSLGSTNG-TRLVPAETVLLLVRG--GAlhnk 83
Cdd:cd17296     1 KKLGEICSIQSGGTPSRSKKEYWnNGTIPWVKISDCKNKYVDETEEFITEEGLNNSsAKLLKKGTILIAIFAtiGK---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  84 ipVGITTREVTFNQDVKALVPKSEDITPYYLLAWLISsrelLLGKVENTGIGAGK--LDTKILQDLDVPVPPKAELLR-- 159
Cdd:cd17296    77 --VGILKIEATTNQAIAGIKPKNKSINPKYLYYYLKS----LYEKFLSLGRGVAQnnINLSILKNLKIPLPPLEEQQRiv 150

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2170640448 160 --LELFSKALDDKIILNQninhTLEQMAQALFKSWF 193
Cdd:cd17296   151 aiLDKFEKLINKRQEGLQ----LLDELVKSLFEEMF 182
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 265-461 1.99e-25

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: 102.99  E-value: 1.99e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 265 PEGWtlsEIGAQIDIA---GGATPSTKTPDFWdNGDIHWTTPKDLSNVKDKILLHTERKITKAGLGKISSGLLPVNTVLM 341
Cdd:cd17248     1 PAHW---EVVPLTDVAkleSGHTPSRSRPEYW-NGCIPWISLADVKQLRGDYIYETKEKISELGIANSSARLLPAGTVVL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 342 SSRAPVGYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTT-----FAEIskKNFNpIPLvkPPLE 416
Cdd:cd17248    77 SRTASVGKSAIMGRPMATSQDFANWVCGPELDPEYLLYVLRAMKPEFERLAMGSThktiyMPDF--KALR-IAL--PPLE 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2170640448 417 LVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLLSGEITLP 461
Cdd:cd17248   152 EQRKIVDRLEALDAKIDALERKLERLIELLKELRQALLTAAVTGK 196
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17251
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 266-454 2.71e-25

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: 102.20  E-value: 2.71e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 266 EGWTLSEIGaqiDIAGGATPSTKTPDFWdNGDIHW-TTPkDLSNvkdKI-LLHTERKITKAGLGKISSGLLPVNTVLMSS 343
Cdd:cd17251     2 EVKTLKDFG---KIITGKTPSTKNKEYY-GGDIPFiKIP-DMHG---NVfITKTEDYLSEEGANSQKNKTLPKNSICVSC 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 344 RAPVGYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRAS-GTTFAEISKKNFNPIPLVKPPLELVKNYT 422
Cdd:cd17251    74 IATVGLVSITTEESQTNQQINSIIPKKENYRYYLYFALKSLKELLEALGSgGSTTLNLNKGKFSKIKILLPSEDLLKKFH 153

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2170640448 423 KQVSAIYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17251   154 KIVSPLFDKILNNQKENQKLSQLRDTLLPKLM 185
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 3-188 6.71e-25

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: 101.45  E-value: 6.71e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   3 SNWSVKKLGDLVTFLSGGTPSKSNKDYWNGE-IPWISASSMQSTRYHDSDLRVTSLGSTN-GTRLVPAETVLllvrggal 80
Cdd:cd17247     2 EHWEVVRLGDVARVGNGSTPSRKNPDYWNGGtIPWVSSGEVNDNRITEADEFITELALKEcSLPLVPPGSVL-------- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  81 hnkipVGIT----TR--------EVTFNQDVKALVPKSEDITPYYLLAWLISSRELLlgkvENTGIGAGK--LDTKILQD 146
Cdd:cd17247    74 -----VAMIgqgkTRgqaailaiEATINQNLAAIRPNEERVLPEYLHYYLESQYDEL----RRIGSGGGQgaLNCGILKA 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2170640448 147 LDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQAL 188
Cdd:cd17247   145 FPIPLPPLDEQREIVAELEALLAKIDLLEEKIARLIELLKEL 186
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-454 1.97e-24

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: 99.90  E-value: 1.97e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIGaqiDIAGGATPSTKTPDFWdNGDIHWTTPKDLSnvKDKILLHT-ERKITKAGLGKISSGLLPVNTVLMSSRAPV 347
Cdd:cd17513     2 KLGELG---KFIGGGTPSTKNPEYW-NGNIPWITSSDLS--EDDIFKINiRKFITEEAIKNSATKIIPANSILIVTRVGV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 348 GYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSA 427
Cdd:cd17513    76 GKVAINPFDICTSQDFTSLIPIKEVNPLFLAYLLYSLLQKLKSQLQGTSIKGITKDDLKNLKIPLPPLEEQQKIAAILSK 155

                         170       180
                  ....*....|....*....|....*..
gi 2170640448 428 IYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17513   156 LDKLIEAHEKKLEKLKQLKKGLMQKLF 182
RMtype1_S_Cep9333ORF4827P-TRD2-CR2_like cd17495
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 339-454 2.49e-24

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Crinalium epipsammum S subunit (S.Cep9333ORF4827P) TRD2-CR2 and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) T; The recognition sequences for Crinalium epipsammum S subunit (S.Cep9333ORF4827P) and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) 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: 341186 [Multi-domain]  Cd Length: 174  Bit Score: 99.07  E-value: 2.49e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 339 VLMSSRAPVGYLAIAKVPVAINQGYIAMKCnKELSPEFVLQWCSANMPEI-ISRASGTTFAEISKKNFNPIPLVKPPLEL 417
Cdd:cd17495    59 ILFSVRAPVGDINIANEKCCIGRGLAAIRS-KSGSQSFLFYQLKSLFKEFdIFNGEGTVFGSINKKDLENLPIIIPSDEI 137

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2170640448 418 VKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17495   138 IEAFEKLVSPIDQKIENNEKENRTLAKLRDTLLPKLM 174
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-449 4.35e-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: 98.61  E-value: 4.35e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIgaqIDIAGGATPSTKtPDFWDNGDIHWTTPKDLSNVKDKIllhTERKITKAGLGKISSGLLPVNTVLMSSRAPVG 348
Cdd:cd16961     2 KLGEI---AEIISGKTPSSS-SEYWDNGIIPWIRISDINNGGIIL---TDEKITEEGAEKLKKKILPKGDILISRSGTIG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 349 YLAIAK--VPVAINQGYIAMKCNKELSPEFVLQWC-SANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQV 425
Cdd:cd16961    75 KVAIVKenDKALLNQAVIVIRPKDEVDSEFLYYFLkSPFGKKLIEGSAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANIL 154

                         170       180
                  ....*....|....*....|....
gi 2170640448 426 SAIYSLIENTMRENNSLTELRDTL 449
Cdd:cd16961   155 DKLDALIELLEQKLEKLEQLKQAL 178
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 270-454 4.42e-24

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: 98.72  E-value: 4.42e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 270 LSEIGaqiDIAGGATPSTKTPDFWdNGDIHWTTPKDLSNvkDKILLHTERKITKAGLGKisSGLLPVNTVLMSSRAPVGY 349
Cdd:cd17286     3 LGDLG---EIVTGNTPSTKNSEYY-GGEILFVTPTDIDG--NKYIYKTEKKLSEKGFKK--ARILPKGSILVTCIGSIGK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 350 LAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIY 429
Cdd:cd17286    75 NAIATEDCATNQQINAIIPNKNYDPEFLYYALENWSKKIKSLAGKQAVPIINKTEFSKIKILVPPLEEQQKIANFLSKLD 154

                         170       180
                  ....*....|....*....|....*
gi 2170640448 430 SLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17286   155 ELIELQQQKIEKLEELKKGLLQKLF 179
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 268-454 7.58e-24

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: 98.33  E-value: 7.58e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 268 WTLSEIGAQIDIAGGATPSTKTPDFWDNGDIHWttpkdLSN--VKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSR- 344
Cdd:cd17294     1 WEWKTLGEIAKIFSGGTPSTSNPEYWDGGTIPW-----LSSgeVNFKEIYETEKRITEEGLKNSSAKWIPKNSVLIALAg 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 345 --APVGYLAIAKVPVAINQGYIAMKCNKE-LSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNY 421
Cdd:cd17294    76 qgKTRGTVAILKIPLTTNQSLAAIEPDEEiANSRFLYYNLSSRYEELRSLSGGGGRGGLNLKIIKSLPIPLPPLEEQKKI 155

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2170640448 422 TKQVSAIYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17294   156 VAILDKFDALINDLKEGLPALLELRQKQYEYLR 188
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 278-456 2.62e-22

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: 93.69  E-value: 2.62e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 278 DIAGGATPSTKTPDFWDNGDIHWTTPKDLSnvKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPVGYLAIAKVPV 357
Cdd:cd17244     8 DIKIGKTPPRKEPEYWSGDNIPWVSISDMG--KGKYISDTKEYITDEAVKKFNVKLVPKGTLLMSFKLTIGRVAIAGKDL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 358 AINQGYIAMK-CNKELSPEF---VLQwcSANMPEIISRAS-GTTfaeISKKNFNPIPLVKPPLElvknYTKQVSAIYSLI 432
Cdd:cd17244    86 YTNEAIAHFIpKDKKIDTEYlyyYLK--SFDYSSLGSTASkGKT---LNSKKIKEIPIPLPPLE----EQKRIAPILDKI 156

                         170       180
                  ....*....|....*....|....
gi 2170640448 433 ENTMRENNSLTELRDTLLPKLLSG 456
Cdd:cd17244   157 DALIDQLETLIELLDELLPKLMSG 180
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 265-449 1.53e-21

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: 91.82  E-value: 1.53e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 265 PEGWTLSEIGAQIDIAGGATPSTKTPDFWDNGDIHWTTPkdlSNVKDKILLHTERKITKAGLGKISSGLLPVNTVLMS-- 342
Cdd:cd17247     1 PEHWEVVRLGDVARVGNGSTPSRKNPDYWNGGTIPWVSS---GEVNDNRITEADEFITELALKECSLPLVPPGSVLVAmi 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 343 ----SRAPVGYLAIakvPVAINQ--GYIAMKcNKELSPEFVLQWCSANMPEIISRASGTTFAEISK---KNFnPIPLvkP 413
Cdd:cd17247    78 gqgkTRGQAAILAI---EATINQnlAAIRPN-EERVLPEYLHYYLESQYDELRRIGSGGGQGALNCgilKAF-PIPL--P 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2170640448 414 PL----ELVKNYTKQVSAIYSLIENTMRENNSLTELRDTL 449
Cdd:cd17247   151 PLdeqrEIVAELEALLAKIDLLEEKIARLIELLKELRQAL 190
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 269-455 2.49e-21

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: 91.01  E-value: 2.49e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIGaqiDIAGGATPSTKTPDFWdNGDIHW-TTpkdlSNVKDKILLHTERKITKAGLGKISSGLLPVNTVLMS----- 342
Cdd:cd17287     2 KLGEIA---KVSSGGTPSRSNPEYW-NGGIPWvKT----GEVNFNEITDTEEKITEEGLKNSSAKLFPKGTLLMAmygqg 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 343 -SRAPVGYLaiaKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTtfaeiSKKNFN-------PIPLvkPP 414
Cdd:cd17287    74 kTRGRVAIL---GIEAATNQACAAILPNDGINPDFLFYYLQSSYEELRDLSNGG-----GQPNLNagliksiEIPV--PP 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2170640448 415 LELVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLLS 455
Cdd:cd17287   144 LDEQQKIAAFLSAIDAKIDALEQKLELLQELKKSLMQQLFT 184
RMtype1_S_MjaORF132P-TRD1-CR1_like cd17275
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S. ...
 7-189 2.85e-21

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: 91.07  E-value: 2.85e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   7 VKKLGDLVTFL-SGGTPSKSNKDYWNGEIPWISASSM-QSTRY-HDSDLRVTSLGSTN-GTRLVPAETVLLLVRG--GAl 80
Cdd:cd17275     2 QVKLGELCEKMkSGGTPSTSNKEYYGGDIPFVKISDMtKSGKYiYSTEKYITEEGLKNsSAWIVPKGTILYAMYAsvGK- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  81 hnkipVGITTREVTFNQDVKALVPKSEDITPYYLLAWLISSRELLLgKVENTGIGAgKLDTKILQDLDVPVPPKAELLRL 160
Cdd:cd17275    81 -----VAINKIDVATNQAILGIIPKDEKLDFEFLYYWLLSLKNELK-RLIRTGTQA-NLNAEIVKNLPIPLPPLEEQKKI 153

                         170       180       190
                  ....*....|....*....|....*....|
gi 2170640448 161 -ELFSKAlDDKIILNQNINHTLEQMAQALF 189
Cdd:cd17275   154 aEILDKI-DAEIDKLEEKIEKLRELKKGLL 182
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 5-200 4.11e-21

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: 90.67  E-value: 4.11e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGTPSKSNKDYWNGEIPWIS---ASSMQSTRYHDSDLRVTSLGSTN-GTRLVPAETVLLLVRGGal 80
Cdd:cd17248     4 WEVVPLTDVAKLESGHTPSRSRPEYWNGCIPWISladVKQLRGDYIYETKEKISELGIANsSARLLPAGTVVLSRTAS-- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  81 hnkipVG---ITTREVTFNQDVKALVPkSEDITPYYLLAWLISSRELLL----GKVENTgIGagkLDTkiLQDLDVPVPP 153
Cdd:cd17248    82 -----VGksaIMGRPMATSQDFANWVC-GPELDPEYLLYVLRAMKPEFErlamGSTHKT-IY---MPD--FKALRIALPP 149

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2170640448 154 KAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKSWFVDFEPVK 200
Cdd:cd17248   150 LEEQRKIVDRLEALDAKIDALERKLERLIELLKELRQALLTAAVTGK 196
RMtype1_S_MmaGORF2198P_TRD1-CR1_like cd17500
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 277-449 4.18e-21

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: 90.42  E-value: 4.18e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 277 IDIAGGATPSTKTPDFWDNGDIHWTTPKDLSnvkDKILLHTERKITKAGLGKISSGLLPVNTVLMS---SRAPVGYLAIA 353
Cdd:cd17500     7 IKITSGGTPSRSNKEYYNGGNIPWLKTKELN---FKRIYDTEEKITEEGLKNSSAKLIPENTVIIAmygAGKTAGRVAIN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 354 KVPVAINQGYIAMKCNKELS-PEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLI 432
Cdd:cd17500    84 KIPLTTNQACCNLIIDNKKAdYRFVYYSLKTQYEELVNLASGAAQQNLNSKLIKNFEIPLPPLPEQKRIASILSSLDDKI 163

                         170
                  ....*....|....*..
gi 2170640448 433 ENTMRENNSLTELRDTL 449
Cdd:cd17500   164 ELNNRQNETLEAMAETL 180
RMtype1_M_Cni19672ORF1405P_RMtype11G_Hci611ORFHP_T cd17277
Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 ...
 268-438 5.71e-21

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: 90.16  E-value: 5.71e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 268 WTLSEIGAQIDIAGGATPSTKTPDFWDNGDIHWTTPKDLSNvKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPV 347
Cdd:cd17277     1 WPIVKLGEVCEIINGSTPSKKNEEYWNNGTIKWLTIPDIDE-RGLIISSTKQFITEKALEEKKVKLVPKNSVLLSCTATI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 348 GYLAIAKVPVAINQGYIAMKCNKE-LSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKnytKQVS 426
Cdd:cd17277    80 GKVAIAKIELTTNQQINALICKDSkILPEYLFYALKHIKQVLERLTTNPGVKHVNLSMLSNLQIPLPPLEVQK---KIVA 156

                         170
                  ....*....|....
gi 2170640448 427 AI--YSLIENTMRE 438
Cdd:cd17277   157 EIekVEKVIQGLRQ 170
RMtype1_M_Cni19672ORF1405P_RMtype11G_Hci611ORFHP_T cd17277
Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 ...
 5-176 6.88e-21

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: 89.77  E-value: 6.88e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGTPSKSNKDYW-NGEIPWISAS-------SMQSTRYHDSDlrvTSLGSTNgTRLVPAETVLLLVR 76
Cdd:cd17277     1 WPIVKLGEVCEIINGSTPSKKNEEYWnNGTIKWLTIPdiderglIISSTKQFITE---KALEEKK-VKLVPKNSVLLSCT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  77 ggALHNKipVGITTREVTFNQDVKALVPKSEDITPYYLLAWLISSRELLLGKVENTGIgaGKLDTKILQDLDVPVPPK-- 154
Cdd:cd17277    77 --ATIGK--VAIAKIELTTNQQINALICKDSKILPEYLFYALKHIKQVLERLTTNPGV--KHVNLSMLSNLQIPLPPLev 150

                         170       180
                  ....*....|....*....|....*..
gi 2170640448 155 -----AELLRLELFSKALDDKIILNQN 176
Cdd:cd17277   151 qkkivAEIEKVEKVIQGLRQKIDEYQP 177
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 282-416 1.04e-20

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: 89.18  E-value: 1.04e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 282 GATPSTKTPDFWDNGDIHWTTPKDLSNvkDKILLHTERKITKAGLGKISSGLLPVNTVLMSS-RAPVGYLAIAKVPVAIN 360
Cdd:cd17290    13 GTTPPSENEEYYDGGIIPWFTPGDFNG--DLILSESKRKLSELAIEDGEARLFPKNSVLVVGiGATIGKVGYSDKESSSN 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2170640448 361 QGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLE 416
Cdd:cd17290    91 QQITGIIFNKDINPKFLFYWLSSSKEELENLANGATLPILNQEKLKNIKLPVPPLN 146
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-188 2.00e-20

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: 88.21  E-value: 2.00e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLRVTSLGSTNGTR-LVPAETVLLLVRGGAlhnkIPV 86
Cdd:cd16961     1 KKLGEIAEIISGKTPSSSSEYWDNGIIPWIRISDINNGGIILTDEKITEEGAEKLKKkILPKGDILISRSGTI----GKV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  87 GITTRE--VTFNQDVKALVPKsEDITPYYLLAWLISSRELLlgKVENTGIGAGK-LDTKILQDLDVPVPPKAELLRLELF 163
Cdd:cd16961    77 AIVKENdkALLNQAVIVIRPK-DEVDSEFLYYFLKSPFGKK--LIEGSAGSTQPnLNKSDLKNLKIPLPPLEEQKKIANI 153

                         170       180
                  ....*....|....*....|....*
gi 2170640448 164 SKALDDKIILNQNINHTLEQMAQAL 188
Cdd:cd16961   154 LDKLDALIELLEQKLEKLEQLKQAL 178
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 8-191 2.92e-20

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: 87.93  E-value: 2.92e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLRVTSLGSTN-GTRLVPAETVLL------LVRGgal 80
Cdd:cd17287     1 KKLGEIAKVSSGGTPSRSNPEYWNGGIPWVKTGEVNFNEITDTEEKITEEGLKNsSAKLFPKGTLLMamygqgKTRG--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  81 hnkiPVGITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLlgkvENTGIGAGK--LDTKILQDLDVPVPPKAELL 158
Cdd:cd17287    78 ----RVAILGIEAATNQACAAILPN-DGINPDFLFYYLQSSYEEL----RDLSNGGGQpnLNAGLIKSIEIPVPPLDEQQ 148

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2170640448 159 RLELFSKALDDKIILNQninhTLEQMAQALFKS 191
Cdd:cd17287   149 KIAAFLSAIDAKIDALE----QKLELLQELKKS 177
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 269-454 3.82e-20

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: 87.51  E-value: 3.82e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIGaqiDIAGGATPSTKTPDFWdNGDIHWTTPKDLSNvkDKILLHTERKITKAGLGKisSGLLPVNTVLMSSRAP-V 347
Cdd:cd17293     2 KLGELG---EVVTGNTPSKKNPEYY-GGDIPFIKPDDLNN--GGIILTSEEYLSEEGAKK--ARIVPKGSILVTCIGGsI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 348 GYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSA 427
Cdd:cd17293    74 GKVGIADREVAFNQQINAIIPNKSVDPKFLYYQLLSSKFQLQAIASSTTLPIINKSKFEKIEIPLPPLEEQKRIVAKLDK 153

                         170       180
                  ....*....|....*....|....*..
gi 2170640448 428 IYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17293   154 LFALIDKLEESLEELDELLKSLFQSAF 180
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 265-454 4.38e-20

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: 87.65  E-value: 4.38e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 265 PEGWTLSEIGaqiDIAGGATPSTKTP-DFwdNGDIHWTTPKDLSNVK----DKILLHTERKITKAGLgKIssglLPVNTV 339
Cdd:cd17284     1 PEGWEVKRVG---DVCDCIVPGRDKPkSF--DGNIPWITIEDIKGKYisssKSGLGVSEEEIKEMNL-KV----IPKGSV 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 340 LMSSRAPVGYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVK 419
Cdd:cd17284    71 IMSCVGDFGIVAIATNELVINQQLHAFVPSKKINPEYLMYLLSLQKKYMEKIATGTTIPYLNKTNCESIPIPLPPIEEQN 150

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2170640448 420 NYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17284   151 KIAKILDSIDKKIDLLIAKLEKLQQLKKGLMQQLF 185
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 6-191 1.07e-19

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: 86.36  E-value: 1.07e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   6 SVKKLGDLVTflsGGTPSKSNKDYWNGEIPWISASSM-QSTRYHDSDLRVTSLGSTNGtRLVPAETVLLLVRGGALHNki 84
Cdd:cd17293     2 KLGELGEVVT---GNTPSKKNPEYYGGDIPFIKPDDLnNGGIILTSEEYLSEEGAKKA-RIVPKGSILVTCIGGSIGK-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  85 pVGITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKVENTGIGagkldtkIL-----QDLDVPVPPKAELLR 159
Cdd:cd17293    76 -VGIADREVAFNQQINAIIPN-KSVDPKFLYYQLLSSKFQLQAIASSTTLP-------IInkskfEKIEIPLPPLEEQKR 146

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2170640448 160 lelFSKALDDKIILNQNINHTLEQmAQALFKS 191
Cdd:cd17293   147 ---IVAKLDKLFALIDKLEESLEE-LDELLKS 174
RMtype1_S_Vch69ORF1407P_TRD2-CR2_like cd17501
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio ...
 5-183 1.61e-19

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: 86.08  E-value: 1.61e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVK-KLGDLVTFLSGGTPSKSNKDYWNGE-IPWISASSMQSTRYHDSDLRVTSLGSTNGT-RLVPAETVLLLVRGGAlh 81
Cdd:cd17501     5 WEVGtILDLCYKTQSGGTPSRKNPEYWDGGiIPWLKTGELRDNIILDTEEKITEEGLKNSSaKLFPKGTVLVAMYGAT-- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  82 nkIP-VGITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKventGIGAGK--LDTKILQDLDVPVPPKAELL 158
Cdd:cd17501    83 --AGkLGILAKEATTNQACCALIPK-EEYSPFFLYLYLLNSRDYLANL----ASGSAQqnISQQIIKNTKVLIPPEDLLE 155

                         170       180
                  ....*....|....*....|....*
gi 2170640448 159 RLELFSKALDDKIILNQNINHTLEQ 183
Cdd:cd17501   156 IFNKLVEPLFDKIINNLKENQKLAK 180
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-156 2.42e-19

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: 85.30  E-value: 2.42e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYWNGEIPWISA---SSMQSTRYHDSDLRVTSLGSTN-GTRLVPAETVLLLVRGgalhnk 83
Cdd:cd17279     1 VPLKRIFRIVNGSTPKSGEEDYWDGDIPWVTPadlSKLDGKYISSSQRKITEAGLEScGTSLVPAGSIILSTRA------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  84 iPVG---ITTREVTFNQDVKALVPKSEDITPYYLLAWLISSREL-LLGK----VEntgigagkLDTKILQDLDVPVPPKA 155
Cdd:cd17279    75 -PIGyvaIATVELCTNQGCKALVPNSDVDSRFLYYLLLAAKEELnSLGRgttfLE--------LSTDELANFKIPLPPLS 145


                  .
gi 2170640448 156 E 156
Cdd:cd17279   146 E 146
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-453 2.67e-18

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: 82.26  E-value: 2.67e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIGaqiDIAGGATPSTKTPDFWDNGDIHWTTPKDLsnvKDKILLHTERKITKAGLGKISSGLLPVNTVLMSSRAPVG 348
Cdd:cd17296     2 KLGEIC---SIQSGGTPSRSKKEYWNNGTIPWVKISDC---KNKYVDETEEFITEEGLNNSSAKLLKKGTILIAIFATIG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 349 YLAIAKVPVAINQGYIAMK-CNKELSPEFVLQWCSANMPEIISRASGTTFAEISK---KNFnPIPLvkPPLELvknyTKQ 424
Cdd:cd17296    76 KVGILKIEATTNQAIAGIKpKNKSINPKYLYYYLKSLYEKFLSLGRGVAQNNINLsilKNL-KIPL--PPLEE----QQR 148

                         170       180
                  ....*....|....*....|....*....
gi 2170640448 425 VSAIYSLIENTMRENNSLTELRDTLLPKL 453
Cdd:cd17296   149 IVAILDKFEKLINKRQEGLQLLDELVKSL 177
RMtype1_S_Lla161ORF747P_TRD1-CR1_like cd17286
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus ...
 8-188 3.38e-18

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: 82.16  E-value: 3.38e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRY-HDSDLRVTSLGsTNGTRLVPAETVLLLVRG--GalhnKi 84
Cdd:cd17286     1 KKLGDLGEIVTGNTPSTKNSEYYGGEILFVTPTDIDGNKYiYKTEKKLSEKG-FKKARILPKGSILVTCIGsiG----K- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  85 pVGITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKventgigAGKLDTKIL-----QDLDVPVPPKAELLR 159
Cdd:cd17286    75 -NAIATEDCATNQQINAIIPN-KNYDPEFLYYALENWSKKIKSL-------AGKQAVPIInktefSKIKILVPPLEEQQK 145

                         170       180
                  ....*....|....*....|....*....
gi 2170640448 160 LELFSKALDDKIILNQNINHTLEQMAQAL 188
Cdd:cd17286   146 IANFLSKLDELIELQQQKIEKLEELKKGL 174
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 3-183 1.25e-17

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: 80.09  E-value: 1.25e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   3 SNWSVKKLGDLVTFLSGGTPSKSNKdYWNGEIPWISASSMQSTRYHDSDlrvtslgsTNGTRLVPAETVLLLVRGGAlhn 82
Cdd:pfam01420   2 EDWEVFKLGDVFEIKKGKTPKKKEL-KNNGKYPYIRAGDLNNVVKGGLG--------YIKKYILPKGDITISSRATI--- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  83 kIPVGITTREVTFNQDVKALVPKSEDITPYYLLAWLISSRELLlgKVENTGIGAGKLDTKILQDLDVPVPPKAELLRLEL 162
Cdd:pfam01420  70 -GYVFYRDKPYYTNQHIIVLIPKNNIKITEFLYLYLLLKLKKL--KSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAK 146

                         170       180
                  ....*....|....*....|.
gi 2170640448 163 FSKALDDKIILNQNINHTLEQ 183
Cdd:pfam01420 147 ILSQLDNTIELEKGILNELER 167
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-156 3.21e-17

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: 79.55  E-value: 3.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLS-GGTPSKSNKDYW-NGEIPWISASSMQSTRY-HDSDLRVTSLG-STNGTRLVPAETVLLLVRGGALHNk 83
Cdd:cd17290     1 KKLKRLAKSIKtGTTPPSENEEYYdGGIIPWFTPGDFNGDLIlSESKRKLSELAiEDGEARLFPKNSVLVVGIGATIGK- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2170640448  84 ipVGITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKVENTGIGAgkLDTKILQDLDVPVPPKAE 156
Cdd:cd17290    80 --VGYSDKESSSNQQITGIIFN-KDINPKFLFYWLSSSKEELENLANGATLPI--LNQEKLKNIKLPVPPLNE 147
Methylase_S pfam01420
Type I restriction modification DNA specificity domain; This domain is also known as the ...
 265-444 4.46e-17

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: 78.55  E-value: 4.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 265 PEGWTLSEIGAQIDIAGGATPSTKtpDFWDNGDIHWTTPKDLSNVKDKILLHTERKItkaglgkissglLPVNTVLMSSR 344
Cdd:pfam01420   1 PEDWEVFKLGDVFEIKKGKTPKKK--ELKNNGKYPYIRAGDLNNVVKGGLGYIKKYI------------LPKGDITISSR 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 345 APVGYLAIAKVPVAINQGYIAMK-CNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTK 423
Cdd:pfam01420  67 ATIGYVFYRDKPYYTNQHIIVLIpKNNIKITEFLYLYLLLKLKKLKSLKFGSTQPKLTKERLKEIKIPLPPLEEQKKIAK 146

                         170       180
                  ....*....|....*....|.
gi 2170640448 424 QVSAIYSLIENTMRENNSLTE 444
Cdd:pfam01420 147 ILSQLDNTIELEKGILNELER 167
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-189 4.96e-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: 78.67  E-value: 4.96e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYW-NGEIPWISASSMQSTRY-HDSDLRVTSLGSTN-GTRLVPAETVLL---LVRGgalh 81
Cdd:cd17244     1 VKLGDIFDIKIGKTPPRKEPEYWsGDNIPWVSISDMGKGKYiSDTKEYITDEAVKKfNVKLVPKGTLLMsfkLTIG---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  82 nKipVGITTREVTFNQDVKALVPKSEDITPYYLLAWLissRELLLGKVENTGIGAGKLDTKILQDLDVPVPPKAELLRLE 161
Cdd:cd17244    77 -R--VAIAGKDLYTNEAIAHFIPKDKKIDTEYLYYYL---KSFDYSSLGSTASKGKTLNSKKIKEIPIPLPPLEEQKRIA 150

                         170       180
                  ....*....|....*....|....*...
gi 2170640448 162 LFSKALDDKIILNQNINHTLEQMAQALF 189
Cdd:cd17244   151 PILDKIDALIDQLETLIELLDELLPKLM 178
RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like cd17280
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter ...
 268-449 1.02e-16

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: 77.98  E-value: 1.02e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 268 WTLSEIGaqIDIAGGATPSTKTPDFWDnGDIHWTTPKDLsnvKDKILLHTERKITKAGLGKISSG-LLPVNTVLMSSR-A 345
Cdd:cd17280     1 WKISHLF--GLIGSGTTPKSDNEDYYD-GGIPWVTTGDL---RDGIITETSKKITDKALDDYSALkIYPAGSLVIAMYgA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 346 PVGYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISK---KNFnPIPLvkPPLE----LV 418
Cdd:cd17280    75 TIGRLGILGIDATTNQACCVLSGSNKIDIKFLFYWLLANRDELISLASGGGQPNISQeliKSL-RIPV--PPLEeqkqIA 151

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2170640448 419 KNYTKQVSAIYSLIENTMRENNSLTELRDTL 449
Cdd:cd17280   152 AFLDKKTAKIDSLIEKKERLIELLKERRQAL 182
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 337-454 1.18e-16

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: 77.58  E-value: 1.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 337 NTVLMSSRAPVGYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLE 416
Cdd:cd17245    57 GDILISVRAPVGDVNIADEKCCIGRGLAAIRANKDIDNLFLYYYLKYNKPELEKLGTGSTFKAINKKDLEELKIPLPPLE 136

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2170640448 417 LVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17245   137 EQQKIAEILSTVDEAIEKTKALIEKLDELKKGLMQELF 174
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 337-450 1.77e-16

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: 76.95  E-value: 1.77e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 337 NTVLMSSRAPVGYLAIAKVPVAINQGY--IAMKCNKELSPEFVLQwcsANMPEIISRASGTTFAEISKKNFNPIPLVKPP 414
Cdd:cd17498    57 GDILMSVRAPVGDLNIANKDICIGRGLcsIRMKNGNNSFLYYLLK---NNIKNLINKSSGTVFGSINKDDIENLEVDIPE 133

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2170640448 415 LELVKNYTKQVSAIYSLIENTMRENNSLTELRDTLL 450
Cdd:cd17498   134 DEEQKRIANILSKIDDKIEINNQINKNLEELAQAIF 169
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 358-454 3.23e-16

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: 76.38  E-value: 3.23e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 358 AINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMR 437
Cdd:cd17496    79 CIGRGVAAIRPKNGIDTEFLYYLLESNLDYLLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQ 158

                          90
                  ....*....|....*..
gi 2170640448 438 ENNSLTELRDTLLPKLL 454
Cdd:cd17496   159 EIEKLEELRDTLLPKLL 175
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-193 1.06e-15

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: 74.90  E-value: 1.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDL-VTFLSGGTPSKSNKDYWN-GEIPWISASSMQSTRYHDSDLRVTSLG--STNGTRLVPAETVLLLVRGGAlHNK 83
Cdd:cd17514     1 VKIQDIaFEIINGGTPSRNEPEYWNnGDIPWLTSGETDDNFINNTSEKITTKNglEDSSIRIVPKGTILIACTGQG-YTR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  84 IPVGITTREVTFNQDVKALVPKSEDItPYYLLAWLISSRELLLGKveNTGIGAGKLDTKILQDLDVPVPPKAELLRLELF 163
Cdd:cd17514    80 GQVAVLQIDASTNQAIAAIRCKENVN-PKYLYYYLKTQKNNLRNL--TSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNI 156

                         170       180       190
                  ....*....|....*....|....*....|
gi 2170640448 164 SKALDDKiilNQNINHTLEQMAQALFKSWF 193
Cdd:cd17514   157 LETLEFF---EKDSLRKIKETAQDINLMIN 183
RMtype1_S_NmaSCMORF606P_TRD2-CR2_like cd17271
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 273-455 1.27e-15

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: 75.00  E-value: 1.27e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 273 IGAQIDIAGGATPSTKTPDFWdNGDIHWTTPKDLsnvKDKILLHTERKITKAGLGKISSGLLPVNTVLMS--------SR 344
Cdd:cd17271     2 GEVLKGLSSGATPSRGNPEYF-NGDIPWITSGEL---NYNYITDTNEKITEEAVKNTNLKIHPKGTFLIAitgleaagTR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 345 apvGYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISR-ASGTT----FAEISKKnfnpIPLVKPPLELVK 419
Cdd:cd17271    78 ---GKCAITGIPATTNQSCMAFYPTKKLTTEFLFYWYKKYGNYLGFKyAQGTKqqsyTADIVKK----LPILLPTLKEQK 150

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2170640448 420 NYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLLS 455
Cdd:cd17271   151 KIANFLSDIDELIATLEKKIEKLKKIKKGLMQKLLT 186
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 269-450 1.77e-15

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: 74.54  E-value: 1.77e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIGaqiDIAGGATPSTKTPDFWDNGD-IHW--TTpkDLSNvkdKILLHTERKITKAGLGKISSGLLPVNTVL--MSS 343
Cdd:cd17276     2 KIGDIA---KTSSGGTPLRSNQEYYFNGGtIPWvkTT--DLNN---GVIYETEEKITEKALKETSCKLLPKGTVLvaMYG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 344 RA-PVGYLAIAKVPVAINQGYIAMKCN-KELSPEFVLQWCSANMPEIISRASGTTFA-EISKKNFNPIPLVKPPLELVKN 420
Cdd:cd17276    74 GFgQIGRTGLLGIPAAINQAICAILPNeKKVNPEFLLRYLNFNRPYWMRVAASSRKDpNITKDDVRNFPIPLPPLDEQRA 153

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2170640448 421 YTKQVSAIYSLIENTMRE----NNSLTELRDTLL 450
Cdd:cd17276   154 IVEFLSDVDALIDSLEALieklRELKKGLMQQLL 187
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 8-189 3.28e-15

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: 73.77  E-value: 3.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPSKSNKDYW--NGEIPWISASSMQSTRYHDSDLRVTS--LGSTNGtRLVPAETVLLLVRGGAlhNK 83
Cdd:cd17276     1 KKIGDIAKTSSGGTPLRSNQEYYfnGGTIPWVKTTDLNNGVIYETEEKITEkaLKETSC-KLLPKGTVLVAMYGGF--GQ 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  84 I-PVGITTREVTFNQDVKALVPKSEDITPYYLLAWLISSRElllgKVENTGIGAGKlDTKILQD----LDVPVPPKAELL 158
Cdd:cd17276    78 IgRTGLLGIPAAINQAICAILPNEKKVNPEFLLRYLNFNRP----YWMRVAASSRK-DPNITKDdvrnFPIPLPPLDEQR 152

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2170640448 159 RLELFSKALDDKII-LNQNINHTLEQ---MAQALF 189
Cdd:cd17276   153 AIVEFLSDVDALIDsLEALIEKLRELkkgLMQQLL 187
RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like cd17514
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 277-444 5.93e-15

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: 72.97  E-value: 5.93e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 277 IDIAGGATPSTKTPDFWDNGDIHWTTPKDlsnVKDKILLHTERKIT-KAGLGKISSGLLPVNTVLMSSRAP---VGYLAI 352
Cdd:cd17514     8 FEIINGGTPSRNEPEYWNNGDIPWLTSGE---TDDNFINNTSEKITtKNGLEDSSIRIVPKGTILIACTGQgytRGQVAV 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 353 AKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLI 432
Cdd:cd17514    85 LQIDASTNQAIAAIRCKENVNPKYLYYYLKTQKNNLRNLTSGVAQKNLNIEMLRNLQIPLPPKEEQQKIVNILETLEFFE 164

                         170
                  ....*....|..
gi 2170640448 433 ENTMRENNSLTE 444
Cdd:cd17514   165 KDSLRKIKETAQ 176
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
387-461 5.95e-15

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 70.09  E-value: 5.95e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2170640448 387 EIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLLSGEITLP 461
Cdd:COG0732    14 YLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLFTGELRVR 88
RMtype1_S_HpyAXIII_TRD1-CR1_like cd17281
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-451 5.36e-14

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: 70.32  E-value: 5.36e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIgaqIDIAGGATPSTKTPDFWDNGDIHWTTPKDLsNVKDKILLHTERKITKAGLGKisSGLLPVNTVLMSSRAPVG 348
Cdd:cd17281     6 KLGEI---FDIRNGYTPSKSNKEYWENGTIPWFRMEDI-RENGRILSDSIQHITPSAVKG--GKLFPANSIILSTTATIG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 349 YLAIAKVPVAINQGYIAM----KCNKELSPEFVL-------QWCSANmpeiisrASGTTFAEISKKNFN--PIPLvkPPL 415
Cdd:cd17281    80 EHALITVDSLANQRFTNFslkkSYKNKLDIKFLFyyffvlgEWCKKN-------INIGGFPSVDMNKLKkfKIPI--PPL 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2170640448 416 E----LVK---NYTKQVSAIYSLI--ENTMRENNsLTELRDTLLP 451
Cdd:cd17281   151 EeqekIVEildKFTKLTADLTAELpaELEARKKQ-YEYYRDKLLS 194
RMtype1_S_NmaSCMORF606P_TRD2-CR2_like cd17271
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 11-193 1.92e-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: 65.76  E-value: 1.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  11 GDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRYHDSDLRVTSLG--STNgTRLVPAETVLLL--------VRGGAl 80
Cdd:cd17271     3 EVLKGLSSGATPSRGNPEYFNGDIPWITSGELNYNYITDTNEKITEEAvkNTN-LKIHPKGTFLIAitgleaagTRGKC- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  81 hnkipvGITTREVTFNQDVKALVPKsEDITPYYLLAW-LISSRELLLGKVENTgigagK---LDTKILQDLDVPVPPKAE 156
Cdd:cd17271    81 ------AITGIPATTNQSCMAFYPT-KKLTTEFLFYWyKKYGNYLGFKYAQGT-----KqqsYTADIVKKLPILLPTLKE 148

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2170640448 157 LLRLELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17271   149 QKKIANFLSDIDELIATLEKKIEKLKKIKKGLMQKLL 185
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 337-444 1.93e-12

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


Pssm-ID: 341190 [Multi-domain]  Cd Length: 175  Bit Score: 65.33  E-value: 1.93e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 337 NTVLMSSRAPVGYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFN--PIPLvkPP 414
Cdd:cd17499    58 NDILMSVRAPVGDVNITTRKICIGRGLAAIRAKKNIDKKYLFYFLLSNKDYFKGKSGGSTFKSINKNQIKniKIPL--PP 135

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2170640448 415 LELVKNYTKQVSAIYSLI---ENTMRENNSLTE 444
Cdd:cd17499   136 LEEQKRIVSELDKLFKLIfeaKNNIEEALANAQ 168
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 367-454 2.30e-11

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: 62.09  E-value: 2.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 367 KCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTELR 446
Cdd:cd17254    86 VPDEEIDKDYLYYLLKALTEEIESQAHGSTMVHITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLEELR 165


                  ....*...
gi 2170640448 447 DTLLPKLL 454
Cdd:cd17254   166 KALLQSLL 173
RMtype1_S_Aco12261I-TRD1-CR1_like cd17498
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-193 2.73e-11

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: 61.93  E-value: 2.73e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTP-SKS-NKDywNGEIPWISASSMQSTRYHDSDLRvtslgSTNGTRLVPAETVLLLVRGgalhnkiP 85
Cdd:cd17498     1 VKLGEIAEITMGQSPkSEFyNED--GIGLPFLQGNRTFGDKYPYIDTY-----TTDIKKIAKKGDILMSVRA-------P 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  86 VG---ITTREVTFNQDVKALVPKSED-ITPYYLLAWLISsrelllgKVENTGIGA--GKLDTKILQDLDVPVPPKAELLR 159
Cdd:cd17498    67 VGdlnIANKDICIGRGLCSIRMKNGNnSFLYYLLKNNIK-------NLINKSSGTvfGSINKDDIENLEVDIPEDEEQKR 139

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2170640448 160 LELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17498   140 IANILSKIDDKIEINNQINKNLEELAQAIFKHWF 173
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 5-192 7.19e-11

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: 61.40  E-value: 7.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGTpSKSNKDYWNGeIPWISASSMQSTRYHDSDLRvtslgstngtRLVPAETV-----------LL 73
Cdd:cd17517     1 WEVVKLGDLLEDPRYGT-SKKSSYDGSG-TPVLRIPNIYDGGIDLDDLK----------KRVDLSEKelekyllkkgdIL 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  74 LVRGGALHNKipVGITT------REVTFnqdvkA-----LVPKSEDITPYYLLAWLISS--RELLLGKVENTGIGAGkLD 140
Cdd:cd17517    69 FNRSNGSPEL--VGKCAlvdeedEPAIF-----AsylirLRLDKKKILPEFLYYYLNSPlgRKQIEKIAKSAAGQAN-IN 140

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2170640448 141 TKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKSW 192
Cdd:cd17517   141 QKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSLMQSL 192
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 336-450 8.51e-11

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


Pssm-ID: 341188 [Multi-domain]  Cd Length: 174  Bit Score: 60.64  E-value: 8.51e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 336 VNTVLMSSRAPVGYLAIAKVPVAINQGYIAMKCNKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPL 415
Cdd:cd17497    56 KGDILLSVRAPVGPTNIADQEYCIGRGLAAIRPKKGLDKKYLLYYLKSIENELSSLGTGSTFKAISKEDLENLLIPLPPL 135

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2170640448 416 E----LVKNYTKQVSAIYSLIENTMRENNSLTELRDTLL 450
Cdd:cd17497   136 AeqkrIAAFLDELTAKIDQLIALLEKAIELLKEYRQAVL 174
RMtype1_S_HinAWORF1578P-TRD2-CR2_like cd17251
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 5-184 1.43e-10

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: 60.21  E-value: 1.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGTPSKSNKDYWNGEIPWISASSMQSTRY-HDSDLRVTSLG-STNGTRLVPAE--------TVLLl 74
Cdd:cd17251     1 WEVKTLKDFGKIITGKTPSTKNKEYYGGDIPFIKIPDMHGNVFiTKTEDYLSEEGaNSQKNKTLPKNsicvsciaTVGL- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  75 vrggalhnkipVGITTREVTFNQDVKALVPKSEdITPYYLLAWLISSRELLlgkvENTGIGA---GKLDTKILQDLDVPV 151
Cdd:cd17251    80 -----------VSITTEESQTNQQINSIIPKKE-NYRYYLYFALKSLKELL----EALGSGGsttLNLNKGKFSKIKILL 143

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2170640448 152 PPKAELLRLELFSKALDDKIILNQNINHTLEQM 184
Cdd:cd17251   144 PSEDLLKKFHKIVSPLFDKILNNQKENQKLSQL 176
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 5-193 2.08e-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: 59.84  E-value: 2.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGTPSKsnKDYWNGEIPWISASSMQSTRYHDSDLRVTSLGSTNG--TRLVPAETVLLLVRGGALHN 82
Cdd:cd17246     1 WEWVKLGEISSDITDGTHPT--PKYVESGIPFITSKNIKNGKIDFSDVKYISEEDHNEilKRSKLKKGDILFSIIGTIGR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  83 kipVGITTREVTF--NQDVKALVPKSEDITPYYLLAWLISS--RELLLGKveNTGIGAGKLDTKILQDLDVPVPPKAELL 158
Cdd:cd17246    79 ---VAIVPEDLPAniNQAVALIRPKKEKIDPKYLLYYLNSPiiQKQIEKN--AVGGTQKNLSLGDLKNLKIPLPPLEEQK 153

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2170640448 159 RL-ELFSKaLDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17246   154 RIaAILDS-LDALIDKLEQKLEKLEDLKKGLMQDLL 188
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-451 4.72e-10

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: 58.65  E-value: 4.72e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIgaqIDIAGGATPStktP--DF-WDNGD-IHWTTPKDLSNvKDKILLHTERKITKAGLGKisSGLLPVNTVLMSSR 344
Cdd:cd17283     2 KLGDI---SEIVRGASPR---PigDPiTFDGDgIPWIKIGDVTK-DGKYITKTKEKITEEGAKK--SRLVKPGDLILSNS 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 345 APVGYLAIAKVPVAINQGYIAMKC-NKELSPEFVLQWCSANMPEIISRASGTTFAeiskKNFN-------PIPLvkPPLE 416
Cdd:cd17283    73 MSFGRPYILKIDGCIHDGWLVFSDlKKKLDKDFLYYLLSSITVQLQFSAQAGGGT----KNLNtdivknlKIPL--PPLE 146

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2170640448 417 LVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLP 451
Cdd:cd17283   147 EQKRIAEILDSLDALIDALEEKLEKLEELKKGLMQ 181
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
262-415 6.04e-10

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 61.05  E-value: 6.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 262 GEIPEGWTLSEIGAQIDIAGGAT-PSTKTpdfwdngdIHWTTPKDLSNVKDKILLHTERKITKAGLGK-----ISSGLLP 335
Cdd:PRK09737    4 GKLPEGWVTTHISEICSVIRGVKpPKGYA--------TKSLTMGDLPFIRTTDITNGAVDLTTLPYCMdapedVSKYQLQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 336 VNTVLMSSRAPVGYLAIAKVPVAINQGY----IAMKCNKELSPEFVLQWCSANMP--EIISRASGTTFAEISKKNFNPIP 409
Cdd:PRK09737   76 DRDIVISSAGSIGFSFLAQNPLPSNVVFasfaIRLKPVNYFSEYFLKHFLESSDYrnQLSLMSAGNAVQNINAQSLSTLT 155


                  ....*.
gi 2170640448 410 LVKPPL 415
Cdd:PRK09737  156 FPIPPI 161
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 86-193 1.84e-09

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: 57.07  E-value: 1.84e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  86 VGITTREVTFNQDVKALVPKSEDITPYYLLAWLISSRELLlgkvENTGIGAGK--LDTKILQDLDVPVPPKAELLRLELF 163
Cdd:cd17282    81 TAILGFDACFPDSVVGFIPNEEKIDVEFLEYYLRTLKKEL----EAIAPQSAQknINLEILRPLKIPVPPLEEQKKIVEI 156

                          90       100       110
                  ....*....|....*....|....*....|
gi 2170640448 164 SKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17282   157 LDALDDLIDNLEKRIAKLEELKQSLLQEAF 186
RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like cd17280
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter ...
 5-188 2.79e-09

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: 56.40  E-value: 2.79e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTflSGGTPSKSNKDYWNGEIPWIsassmQStryhdSDLRVTSLGSTNGT------------RLVPAETVL 72
Cdd:cd17280     1 WKISHLFGLIG--SGTTPKSDNEDYYDGGIPWV-----TT-----GDLRDGIITETSKKitdkalddysalKIYPAGSLV 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  73 LLVRGGALHNkipVGITTREVTFNQDVKALVPkSEDITPYYLLAWLISSRELLLgkveNTGIGAGK--LDTKILQDLDVP 150
Cdd:cd17280    69 IAMYGATIGR---LGILGIDATTNQACCVLSG-SNKIDIKFLFYWLLANRDELI----SLASGGGQpnISQELIKSLRIP 140

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2170640448 151 VPPKAELLR----LELFSKALDDKIILNQNINHTLEQMAQAL 188
Cdd:cd17280   141 VPPLEEQKQiaafLDKKTAKIDSLIEKKERLIELLKERRQAL 182
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 269-455 5.75e-09

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: 55.61  E-value: 5.75e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 269 TLSEIGAQIdIAGgatpSTKTPDFWDNGdIHWTTPKDLSNvkDKILLHTERKITKAGLGKISS-GLLPVNTVLMSSRAPV 347
Cdd:cd17246     5 KLGEISSDI-TDG----THPTPKYVESG-IPFITSKNIKN--GKIDFSDVKYISEEDHNEILKrSKLKKGDILFSIIGTI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 348 GYLAIAK--VPVAINQGYIAMKCNKE-LSPEFVLQWCSANM--PEIISRASGTTFAEISKKNFN--PIPLvkPPLELVKN 420
Cdd:cd17246    77 GRVAIVPedLPANINQAVALIRPKKEkIDPKYLLYYLNSPIiqKQIEKNAVGGTQKNLSLGDLKnlKIPL--PPLEEQKR 154

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2170640448 421 YTKQVSAIYSLIENTMRENNSLTELRDTLLPKLLS 455
Cdd:cd17246   155 IAAILDSLDALIDKLEQKLEKLEDLKKGLMQDLLT 189
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 307-458 1.07e-08

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: 54.82  E-value: 1.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 307 SNVKDKILLHTERKITKAGLGKISSG-LLPVNTVLMS-SRAPVGYLAIAK---VPVAINQ--GYIamKCNKELSPEFVLQ 379
Cdd:cd17278    34 GNIKNGGIDLDDNSKYPEEPLEKYEKfLLKKGDILIAmTGGTVGKVAIVPeddEPALLNQrvGKF--RPKDKIDKEFLYY 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 380 WCSAN--MPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENtmrENNSLTELRDTLLPKLLSGE 457
Cdd:cd17278   112 LLRSDsfRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDK---LEQKLEKLRDLLKPLLQSLF 188


                  .
gi 2170640448 458 I 458
Cdd:cd17278   189 T 189
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 146-191 1.49e-08

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: 53.56  E-value: 1.49e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2170640448 146 DLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKS 191
Cdd:cd17267   113 SLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADALLPK 158
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 107-193 2.19e-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: 53.65  E-value: 2.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 107 EDITPYYLLAWLISSRELLLGKVenTGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQ 186
Cdd:cd17496    91 NGIDTEFLYYLLESNLDYLLAAA--TGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRD 168


                  ....*..
gi 2170640448 187 ALFKSWF 193
Cdd:cd17496   169 TLLPKLL 175
RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like cd17289
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 105-193 4.63e-08

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


Pssm-ID: 341178 [Multi-domain]  Cd Length: 191  Bit Score: 53.03  E-value: 4.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 105 KSEDITPYYLLAWLISS--RELLLGKVENTGIGAgkLDTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLE 182
Cdd:cd17289   103 NIKDINSKFLYYWFQSSifKNQINSITIGSTQKA--LTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLE 180

                          90
                  ....*....|.
gi 2170640448 183 QMAQALFKSWF 193
Cdd:cd17289   181 ELAKTLFQYWF 191
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 393-453 6.08e-08

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: 52.43  E-value: 6.08e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2170640448 393 SGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPKL 453
Cdd:cd17262   112 TGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQKL 172
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 8-190 1.48e-07

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: 51.33  E-value: 1.48e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   8 KKLGDLVTFLSGGTPS-KSNKDYWNG-EIPWI-----SASSM--QSTRYHdsdlrVTSLGSTNgTRLVPAETVLLlvrgg 78
Cdd:cd17283     1 KKLGDISEIVRGASPRpIGDPITFDGdGIPWIkigdvTKDGKyiTKTKEK-----ITEEGAKK-SRLVKPGDLIL----- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  79 alHNKIPVG---ITTREVTFNQDVKALVPKSEDITPYYLLaWLISSRELLLGKVENTGIGAGKLDTKILQDLDVPVPPKA 155
Cdd:cd17283    70 --SNSMSFGrpyILKIDGCIHDGWLVFSDLKKKLDKDFLY-YLLSSITVQLQFSAQAGGGTKNLNTDIVKNLKIPLPPLE 146

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2170640448 156 ELLRLELFSKALDDKIILNQNINHTLEQMAQALFK 190
Cdd:cd17283   147 EQKRIAEILDSLDALIDALEEKLEKLEELKKGLMQ 181
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 96-190 2.32e-07

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: 50.96  E-value: 2.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  96 NQDVKALVPKsEDITPYYLLAWLISS--RELLLGKVenTGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKALDDKIIL 173
Cdd:cd17256    89 TENAARIRPK-DSISPRYLYYYLRSPfgQSQIESET--KGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDA 165

                          90
                  ....*....|....*..
gi 2170640448 174 NQNINHTLEQMAQALFK 190
Cdd:cd17256   166 LEKQLAKLEELKKALMQ 182
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 5-191 2.40e-07

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: 51.07  E-value: 2.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGtPSKSnKDYWNGEIPWISASSMQSTRYHDSDLRVTSLGSTNGTrlvpaETVLLLvrggalHNKI 84
Cdd:cd17512     1 WEEIRLGDIIDYQKGY-AFKS-KDYQDSGIRIVRVSDFTDDSIDINNLVYISEEKANKY-----KKYELK------ENDI 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  85 --------P------VGITTR------EVTFNQDVKALVPKSEDITPYYLLAWLISSRelLLGKVENTGIGAGKLDTKIL 144
Cdd:cd17512    68 iittvgswPsnpdsvVGKVVRvpkeadGALLNQNAVKIRPKKGILDQSFLFYNLKSER--FKNYIESIARGNANQASITL 145

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170640448 145 QDL---DVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKS 191
Cdd:cd17512   146 GDIkkfKFLLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQALYQE 195
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 3-189 2.87e-07

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: 50.67  E-value: 2.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   3 SNWSVKKLGDLVTFLSGG--TPsKSNkdywNGEIPWISASSMQSTRYHDSDLrvtSLGSTN------GTRLVPAETVLLL 74
Cdd:cd17284     2 EGWEVKRVGDVCDCIVPGrdKP-KSF----DGNIPWITIEDIKGKYISSSKS---GLGVSEeeikemNLKVIPKGSVIMS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  75 VRG--GAlhnkipVGITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKVENTGIGAgkLDTKILQDLDVPVP 152
Cdd:cd17284    74 CVGdfGI------VAIATNELVINQQLHAFVPS-KKINPEYLMYLLSLQKKYMEKIATGTTIPY--LNKTNCESIPIPLP 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2170640448 153 PKAELLRLELFSKALDDKIILNQNINHTLEQ----MAQALF 189
Cdd:cd17284   145 PIEEQNKIAKILDSIDKKIDLLIAKLEKLQQlkkgLMQQLF 185
RMtype1_S_Sma198ORF994P-TRD2-CR2_like cd17494
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 305-454 4.21e-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: 49.83  E-value: 4.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 305 DLSNVKDKILLHTeRKITKagLGKIssgllpvNTVLMSSRAPVGYLAIAKVPVAINQGYIAMKCNKELspeFVLQWCSAN 384
Cdd:cd17494    35 DIKNGKVIPRIWT-SEITK--TANK-------GDIILSVRAPVGEVAKTNFDACIGRGVCAIKGNEFI---FLYLYLLNI 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 385 MPEIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17494   102 EGYWSKISQGSTFESINSNDIKNLKISIPSLEEQQKIATFLSTLDAEITLLEKKLEKLKQLKKGLLQKLF 171
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 96-194 6.54e-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: 49.43  E-value: 6.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  96 NQDVKALVPKSeDITPYYLLaWLISSRELLLgKVENTGIGA--GKLDTKILQDLDVPVPPKAELLRLELFSKALDDKIIL 173
Cdd:cd17278    92 NQRVGKFRPKD-KIDKEFLY-YLLRSDSFRN-QIKSSATGTaqPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDK 168

                          90       100
                  ....*....|....*....|.
gi 2170640448 174 NQNINHTLEQMAQALFKSWFV 194
Cdd:cd17278   169 LEQKLEKLRDLLKPLLQSLFT 189
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 331-454 1.65e-06

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: 48.21  E-value: 1.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 331 SGLLPVNTVLMSSRAPVGYLAIAKVPVAINQGYIAMKCNKE-LSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIP 409
Cdd:cd17282    62 SKLFPKGTLCITIAANIGDTAILGFDACFPDSVVGFIPNEEkIDVEFLEYYLRTLKKELEAIAPQSAQKNINLEILRPLK 141

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2170640448 410 LVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17282   142 IPVPPLEEQKKIVEILDALDDLIDNLEKRIAKLEELKQSLLQEAF 186
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 96-191 1.96e-06

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: 48.28  E-value: 1.96e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  96 NQDVKALVPKsEDITPYYLLAWLISSRELLLGKVENTGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQ 175
Cdd:cd17259    95 VQRVARIRPK-DELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLE 173

                          90
                  ....*....|....*.
gi 2170640448 176 NINHTLEQMAQALFKS 191
Cdd:cd17259   174 QKLEKLQQLKKGLMQS 189
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 60-193 3.72e-06

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: 47.15  E-value: 3.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  60 TNGTRLVPAETVLLLVRGgalhnkiPVG---ITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLlgkvENTGIGA 136
Cdd:cd17245    48 TKPTKIAEKGDILISVRA-------PVGdvnIADEKCCIGRGLAAIRAN-KDIDNLFLYYYLKYNKPEL----EKLGTGS 115

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2170640448 137 --GKLDTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17245   116 tfKAINKKDLEELKIPLPPLEEQQKIAEILSTVDEAIEKTKALIEKLDELKKGLMQELF 174
RMtype1_S_HpyAXIII_TRD1-CR1_like cd17281
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 5-36 7.26e-06

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: 46.82  E-value: 7.26e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2170640448   5 WSVKKLGDLVTFLSGGTPSKSNKDYW-NGEIPW 36
Cdd:cd17281     2 VEWKKLGEIFDIRNGYTPSKSNKEYWeNGTIPW 34
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 131-192 8.77e-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: 45.89  E-value: 8.77e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2170640448 131 NTGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKSW 192
Cdd:cd17262   111 VTGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALLQKL 172
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 63-193 1.06e-05

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


Pssm-ID: 341190 [Multi-domain]  Cd Length: 175  Bit Score: 45.68  E-value: 1.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  63 TRLVPAETVLLLVRGgalhnkiPVG---ITTREVTFNQDVKALVPKsEDITPYYLLAWLISSRELLLGKveNTGIGAGKL 139
Cdd:cd17499    52 TKIAEKNDILMSVRA-------PVGdvnITTRKICIGRGLAAIRAK-KNIDKKYLFYFLLSNKDYFKGK--SGGSTFKSI 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2170640448 140 DTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:cd17499   122 NKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNNIEEALANAQQLFKSIL 175
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 106-193 1.19e-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: 45.50  E-value: 1.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 106 SEDITPYYLLAWLISSRELLLGKVENTGiGAG--KLDTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQ 183
Cdd:cd17260    77 KEGILPEFLYYLLRSPSFRKEAIKSMTG-SSGrqRVPKDFLENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEE 155

                          90
                  ....*....|
gi 2170640448 184 MAQALFKSWF 193
Cdd:cd17260   156 LLDALLPKLL 165
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 102-192 1.22e-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: 45.94  E-value: 1.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 102 LVPKSEDITPYYLLAWLISSR-----ELLLGKVENTGIGAgkldtKILQDLDVPVPPKAELLRLELFSKALDDKIILNQN 176
Cdd:cd17521    97 FRPNKKKVLPKYLFYFTQSSLywkqiKSISSGSAQPNINA-----EKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEE 171

                          90
                  ....*....|....*.
gi 2170640448 177 INHTLEQMAQALFKSW 192
Cdd:cd17521   172 LLEKLEELLKELLQSL 187
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 369-455 1.26e-05

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


Pssm-ID: 341146 [Multi-domain]  Cd Length: 176  Bit Score: 45.59  E-value: 1.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 369 NKELSPEFVLQWCSANMPEIISRASGTTFAEISKKNFNPIPLVKPPLElvkNYTKQVSAIYSLIENTMRENNSLTELRDT 448
Cdd:cd17257    93 SEELDKRFLYYALPPPLKAIEDTTSSTTVKHLSSKDIDEIELPLPPLE---EQRRIAEILDELDALIDKLIAKLEKLRDL 169


                  ....*..
gi 2170640448 449 LLPKLLS 455
Cdd:cd17257   170 LLPLLQS 176
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
5-459 2.33e-05

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 46.80  E-value: 2.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   5 WSVKKLGDLVTFLSGGTPSKSNKDYWN--GEIPWISASSMQSTRYHDSDLRVTSLGSTNGTRLVPAETVLLLVRGGALhn 82
Cdd:PRK09737   10 WVTTHISEICSVIRGVKPPKGYATKSLtmGDLPFIRTTDITNGAVDLTTLPYCMDAPEDVSKYQLQDRDIVISSAGSI-- 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  83 kIPVGITTREVTFNQDVKALVPKSE---DITPYYLLAWLISSRELLLGKVENTGIGAGKLDTKILQDLDVPVPPKAEllr 159
Cdd:PRK09737   88 -GFSFLAQNPLPSNVVFASFAIRLKpvnYFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAE--- 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 160 LELFSKALDDKIILNQNINHTLEQMAQALfkswfvdfepVKAKIAVLEAggsqedatraamtAISGKDAHalavfEREHP 239
Cdd:PRK09737  164 QKIIAEKLDTLLAQVDSTKARLEQIPQIL----------KRFRQAVLGA-------------AVSGKLTE-----EWRWP 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 240 EQyaelkttaelfPSAMQDSELGEI---PEGWTLSEIGAQidiaGGATPstktpdFWDNGDIHWTTpKDLSNVKDKILLH 316
Cdd:PRK09737  216 DL-----------PSTWSVHKYSELvdsRLGGMSSKANNF----GSATP------YLRNINVRWGS-FDLEDLQDILISD 273

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 317 TERKITKaglgkissglLPVNTVLMS---SRAPVGYLAIAKVPVAIN---QGY-IAMKCNKELSPEFV---LQWCSANMP 386
Cdd:PRK09737  274 IERRELK----------LKLGDVLFCrgnEPLEVGRCAIWKEPQDIPviyQKAlIRARVKDDIIPEYLvynLKSPDSRNI 343

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 387 EIISRASGTTFAEISKKNFNPIPLVKPPL----ELVKNyTKQVSAIYSLIE----NTMRENNSLTElrdTLLPKLLSGEI 458
Cdd:PRK09737  344 SLSQLFTGTTQKHITGKALANYPIRVPPLeeqaEIVRR-VEQLFAYADTIEkqvnNALARVNNLTQ---SILAKAFRGEL 419


                  .
gi 2170640448 459 T 459
Cdd:PRK09737  420 T 420
RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like cd17289
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 367-454 2.52e-05

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


Pssm-ID: 341178 [Multi-domain]  Cd Length: 191  Bit Score: 44.94  E-value: 2.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 367 KCNKELSPEFVLQWCSANMP--EIISRASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTE 444
Cdd:cd17289   102 KNIKDINSKFLYYWFQSSIFknQINSITIGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEE 181

                          90
                  ....*....|
gi 2170640448 445 LRDTLLPKLL 454
Cdd:cd17289   182 LAKTLFQYWF 191
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
132-193 3.77e-05

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 42.35  E-value: 3.77e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2170640448 132 TGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKSWF 193
Cdd:COG0732    20 TGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDALLPKLF 81
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 400-452 4.36e-05

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


Pssm-ID: 341156 [Multi-domain]  Cd Length: 158  Bit Score: 43.54  E-value: 4.36e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2170640448 400 ISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTELRDTLLPK 452
Cdd:cd17267   106 LNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEELADALLPK 158
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 101-190 5.33e-05

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: 43.59  E-value: 5.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 101 ALV--PKSEDITPYylLAWLISSRELllgkventgigaGKLDT---------KILQDLDVPVPPKAELLRLELFSKALDD 169
Cdd:cd17266    73 ALVvtPKKENNIKF--LYYLLKSLNL------------NQYATgsaqplitvSKLKKLKIPLPPLEEQKKIAAILDSLDA 138

                          90       100
                  ....*....|....*....|.
gi 2170640448 170 KIILNQNINHTLEQMAQALFK 190
Cdd:cd17266   139 KIDLLEKKLEKLIELKKELMQ 159
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 363-454 7.09e-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: 43.19  E-value: 7.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 363 YIAMKCNKELSPEFVlqWCSANMPEIISRA----SGTT---------FAEIskknfnPIPLvkPPLELVKNYTKQVSAIY 429
Cdd:cd17260    71 FHVLRPKEGILPEFL--YYLLRSPSFRKEAiksmTGSSgrqrvpkdfLENY------KIPL--PPLEEQKRIAAILDSLD 140

                          90       100
                  ....*....|....*....|....*
gi 2170640448 430 SLIENTMRENNSLTELRDTLLPKLL 454
Cdd:cd17260   141 AKIDALEAEIETLEELLDALLPKLL 165
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
3-166 1.23e-04

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 44.49  E-value: 1.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448   3 SNWSVKKLGDLVTFLSGGTPSKSNKDywNGEIPWISASSMQSTRYHDSDLRVTSLGSTNGTRLVPAETVLLLVRGGALHN 82
Cdd:PRK09737  219 STWSVHKYSELVDSRLGGMSSKANNF--GSATPYLRNINVRWGSFDLEDLQDILISDIERRELKLKLGDVLFCRGNEPLE 296

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448  83 KIPVGITTREvtfnQDVKALVPKS-------EDITPYYLLAWL--ISSRELLLGKVEnTGIGAGKLDTKILQDLDVPVPP 153
Cdd:PRK09737  297 VGRCAIWKEP----QDIPVIYQKAlirarvkDDIIPEYLVYNLksPDSRNISLSQLF-TGTTQKHITGKALANYPIRVPP 371

                         170
                  ....*....|....*...
gi 2170640448 154 ---KAELLRL--ELFSKA 166
Cdd:PRK09737  372 leeQAEIVRRveQLFAYA 389
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 339-450 5.18e-04

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: 40.94  E-value: 5.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 339 VLMSSRAPVGYLAIakVP-----VAINQGyiAMK--CNKELSPEFVLQWCSANM--PEIISRASGTTFAEISK---KNFn 406
Cdd:cd17256    65 ILISIVGTIGRVGI--VPkeldgANLTEN--AARirPKDSISPRYLYYYLRSPFgqSQIESETKGAAQPKLNLkriREL- 139

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2170640448 407 PIPLvkPPLELVKNYTKQVSAIYSLIENTMRENNSLTELRDTLL 450
Cdd:cd17256   140 PIPL--PPLEEQKRIVAILDSLDAKIDALEKQLAKLEELKKALM 181
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 368-450 6.88e-04

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: 40.62  E-value: 6.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 368 CNKELSPEFVLQWCSAN-MPEIISR-ASGTTFAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTEL 445
Cdd:cd17252   104 PKKEIDPRYLFYFLQSPsYREYIRSlASGTNINNLSNEHLENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQALEKLDEL 183


                  ....*
gi 2170640448 446 RDTLL 450
Cdd:cd17252   184 LKSLF 188
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 106-193 1.52e-03

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: 39.37  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 106 SEDITPYYLLAWLissrELLLGKVENTGIGAG-----KldtKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHT 180
Cdd:cd17254    88 DEEIDKDYLYYLL----KALTEEIESQAHGSTmvhitK---GDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKK 160

                          90
                  ....*....|...
gi 2170640448 181 LEQMAQALFKSWF 193
Cdd:cd17254   161 LEELRKALLQSLL 173
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 131-195 1.61e-03

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


Pssm-ID: 341177 [Multi-domain]  Cd Length: 163  Bit Score: 38.99  E-value: 1.61e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2170640448 131 NTGIGAGKLDTKILQDLDVPVPPKAELLRLELFSKALDDKIILNQNINHTLEQMAQALFKSWFVD 195
Cdd:cd17288    99 NEATGVPSLTQTTLNKIKIPIPPLEEQQKIASILDKLDAKDALIELQEKLLEKLKQYKLALMQEL 163
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 369-454 6.99e-03

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: 37.84  E-value: 6.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170640448 369 NKELSPEFVLQWCSANM--PEIISRASGTT-FAEISKKNFNPIPLVKPPLELVKNYTKQVSAIYSLIENTMRENNSLTEL 445
Cdd:cd17253   105 DDLLLPEFLSYWLNSAYgrGYFLRAAKQTTnLASINSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLEEL 184


                  ....*....
gi 2170640448 446 RDTLLPKLL 454
Cdd:cd17253   185 LKALRQALL 193
 
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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