NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|496028878|ref|WP_008753385|]
View 

N-6 DNA methylase [Lachnoanaerobaculum saburreum]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
N6_Mtase super family cl37510
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ...
 118-374 2.33e-29

N-6 DNA Methylase; 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 R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.


The actual alignment was detected with superfamily member pfam02384:

Pssm-ID: 426749 [Multi-domain]  Cd Length: 310  Bit Score: 118.19  E-value: 2.33e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  118 TPRGILKLAAKILDVQKNESVLELCSGKGNFFVE-------LALLRENIKYTGIE-------LSMANNFIANIRASvler 183
Cdd:pfam02384  29 TPREVSKLIVELLDPKPGESIYDPACGSGGFLIQaekfvkeHDGDTNDLSIYGQEknpttyrLARMNMILHGIEYD---- 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  184 DISLVLNDAMTY---KAENKADKLFANYPFLINIPDMENIIK-----YMEMLPDNIKRassDWIFNLKLVEQMKSGGKAV 255
Cdd:pfam02384 105 DFHIRHGDTLTSpkfEDDKKFDVVVANPPFSDKWDANDTLENdprfrPAYGVAPKSNA---DLAFLQHIIYYLAPGGRAA 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  256 AVMANGTTWNS-TDRKIREYFVKSGFIEATILLPPKLFTGISVATTLVVFS----NLNSHIKMIDACEKFTKEGRRNILS 330
Cdd:pfam02384 182 VVLPNGVLFRGgAEGKIRKALVDKDLVETVIALPPNLFYNTSIPTCILFLTknkaERKGKVLFIDASNEFKKEGKLNILT 261

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 496028878  331 DNDISDILDLL---QKDGKNSITISIKEIEENDYIINASRYLEKAPE 374
Cdd:pfam02384 262 DEHIEKIIDTFgefKDVDGFSKSATLEEIAANDYNLNVGRYVGTEEE 308
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 403-565 3.74e-19

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


The actual alignment was detected with superfamily member cd17517:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 192  Bit Score: 85.67  E-value: 3.74e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 403 KSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPN-LKKFCVRNNSIILTKT-GSPDF--KSAVVHvKEGTEILATGNMF 478
Cdd:cd17517   21 SSYDGSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKeLEKYLLKKGDILFNRSnGSPELvgKCALVD-EEDEPAIFASYLI 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 479 ILEIDETKADPYYVQALFDSELGRALFKSIYVGSAI-PTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLE 557
Cdd:cd17517  100 RLRLDKKKILPEFLYYYLNSPLGRKQIEKIAKSAAGqANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLE 179


                 ....*...
gi 496028878 558 TSREKLKQ 565
Cdd:cd17517  180 KLEQLFKS 187
 
Name Accession Description Interval E-value
N6_Mtase pfam02384
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ...
 118-374 2.33e-29

N-6 DNA Methylase; 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 R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.


Pssm-ID: 426749 [Multi-domain]  Cd Length: 310  Bit Score: 118.19  E-value: 2.33e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  118 TPRGILKLAAKILDVQKNESVLELCSGKGNFFVE-------LALLRENIKYTGIE-------LSMANNFIANIRASvler 183
Cdd:pfam02384  29 TPREVSKLIVELLDPKPGESIYDPACGSGGFLIQaekfvkeHDGDTNDLSIYGQEknpttyrLARMNMILHGIEYD---- 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  184 DISLVLNDAMTY---KAENKADKLFANYPFLINIPDMENIIK-----YMEMLPDNIKRassDWIFNLKLVEQMKSGGKAV 255
Cdd:pfam02384 105 DFHIRHGDTLTSpkfEDDKKFDVVVANPPFSDKWDANDTLENdprfrPAYGVAPKSNA---DLAFLQHIIYYLAPGGRAA 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  256 AVMANGTTWNS-TDRKIREYFVKSGFIEATILLPPKLFTGISVATTLVVFS----NLNSHIKMIDACEKFTKEGRRNILS 330
Cdd:pfam02384 182 VVLPNGVLFRGgAEGKIRKALVDKDLVETVIALPPNLFYNTSIPTCILFLTknkaERKGKVLFIDASNEFKKEGKLNILT 261

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 496028878  331 DNDISDILDLL---QKDGKNSITISIKEIEENDYIINASRYLEKAPE 374
Cdd:pfam02384 262 DEHIEKIIDTFgefKDVDGFSKSATLEEIAANDYNLNVGRYVGTEEE 308
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
118-316 2.53e-21

Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];


Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 93.33  E-value: 2.53e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 118 TPRGILKLAAKILDVQKNESVLELCSGKGNFFVELA--------LLRENIKYTGIE-------LSMANNFIANIRASVLE 182
Cdd:COG0286   27 TPREVVRLMVELLDPKPGETVYDPACGSGGFLVEAAeylkehggDERKKLSLYGQEinpttyrLAKMNLLLHGIGDPNIE 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 183 RDISLvLNDamtYKAENKADKLFANYPFLINIPDMENIIKYMEMLPDNIKRASS-DWIFNLKLVEQMKSGGKAVAVMANG 261
Cdd:COG0286  107 LGDTL-SND---GDELEKFDVVLANPPFGGKWKKEELKDDLLGRFGYGLPPKSNaDLLFLQHILSLLKPGGRAAVVLPDG 182

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 496028878 262 TTWNSTDRKIREYFVKSGFIEATILLPPKLFTGISVATTLVVFSN----LNSHIKMIDA 316
Cdd:COG0286  183 VLFRGAEKEIRKKLLENDLLEAIIGLPSNLFYNTGIPTCILFLTKgkpeRTGKVLFIDA 241
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 403-565 3.74e-19

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


Pssm-ID: 341198 [Multi-domain]  Cd Length: 192  Bit Score: 85.67  E-value: 3.74e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 403 KSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPN-LKKFCVRNNSIILTKT-GSPDF--KSAVVHvKEGTEILATGNMF 478
Cdd:cd17517   21 SSYDGSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKeLEKYLLKKGDILFNRSnGSPELvgKCALVD-EEDEPAIFASYLI 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 479 ILEIDETKADPYYVQALFDSELGRALFKSIYVGSAI-PTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLE 557
Cdd:cd17517  100 RLRLDKKKILPEFLYYYLNSPLGRKQIEKIAKSAAGqANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLE 179


                 ....*...
gi 496028878 558 TSREKLKQ 565
Cdd:cd17517  180 KLEQLFKS 187
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
495-565 3.56e-11

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 59.69  E-value: 3.56e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496028878 495 LFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREkLKQ 565
Cdd:COG0732    5 YLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKE-LRD 74
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
403-565 3.26e-10

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 62.59  E-value: 3.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 403 KSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTKTGSPDFkSAVVHVKEGTEILATGNMFILEI 482
Cdd:PRK09737  34 KSLTMGDLPFIRTTDITNGAVDLTTLPYCMDAPEDVSKYQLQDRDIVISSAGSIGF-SFLAQNPLPSNVVFASFAIRLKP 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 483 dETKADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREK 562
Cdd:PRK09737 113 -VNYFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAEQKIIAEKLDTLLAQVDSTKARLEQIPQI 191


                 ...
gi 496028878 563 LKQ 565
Cdd:PRK09737 192 LKR 194
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 138-222 4.06e-04

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 40.11  E-value: 4.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 138 VLELCSGKGNFFVELAlLRENIKYTGIELS-MANNFIANIRASVLERDISLVLNDAMT--YKAENKADKLFANYPFLINI 214
Cdd:cd02440    2 VLDLGCGTGALALALA-SGPGARVTGVDISpVALELARKAAAALLADNVEVLKGDAEElpPEADESFDVIISDPPLHHLV 80


                 ....*...
gi 496028878 215 PDMENIIK 222
Cdd:cd02440   81 EDLARFLE 88
rADc smart00650
Ribosomal RNA adenine dimethylases;
122-224 3.34e-03

Ribosomal RNA adenine dimethylases;


Pssm-ID: 128898  Cd Length: 169  Bit Score: 38.65  E-value: 3.34e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878   122 ILKLAAKILDVQKNESVLELCSGKGNFfvELALLRENIKYTGIELSmaNNFIANIRASVLERD-ISLVLNDAMTYK-AEN 199
Cdd:smart00650   1 VIDKIVRAANLRPGDTVLEIGPGKGAL--TEELLERAKRVTAIEID--PRLAPRLREKFAAADnLTVIHGDALKFDlPKL 76

                           90       100
                   ....*....|....*....|....*
gi 496028878   200 KADKLFANYPFLINIPDMENIIKYM 224
Cdd:smart00650  77 QPYKVVGNLPYNISTPILFKLLEEP 101
trmB PRK00121
tRNA (guanine-N(7)-)-methyltransferase; Reviewed
 133-209 7.17e-03

tRNA (guanine-N(7)-)-methyltransferase; Reviewed


Pssm-ID: 234649  Cd Length: 202  Bit Score: 38.22  E-value: 7.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 133 QKNESVLELCSGKGNFFVELALLRENIKYTGIE-----LSMANNFIA-----NIRasVLERDISLVLNDAMtykAENKAD 202
Cdd:PRK00121  39 NDAPIHLEIGFGKGEFLVEMAKANPDINFIGIEvhepgVGKALKKIEeegltNLR--LLCGDAVEVLLDMF---PDGSLD 113


                 ....*..
gi 496028878 203 KLFANYP 209
Cdd:PRK00121 114 RIYLNFP 120
 
Name Accession Description Interval E-value
N6_Mtase pfam02384
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ...
 118-374 2.33e-29

N-6 DNA Methylase; 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 R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.


Pssm-ID: 426749 [Multi-domain]  Cd Length: 310  Bit Score: 118.19  E-value: 2.33e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  118 TPRGILKLAAKILDVQKNESVLELCSGKGNFFVE-------LALLRENIKYTGIE-------LSMANNFIANIRASvler 183
Cdd:pfam02384  29 TPREVSKLIVELLDPKPGESIYDPACGSGGFLIQaekfvkeHDGDTNDLSIYGQEknpttyrLARMNMILHGIEYD---- 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  184 DISLVLNDAMTY---KAENKADKLFANYPFLINIPDMENIIK-----YMEMLPDNIKRassDWIFNLKLVEQMKSGGKAV 255
Cdd:pfam02384 105 DFHIRHGDTLTSpkfEDDKKFDVVVANPPFSDKWDANDTLENdprfrPAYGVAPKSNA---DLAFLQHIIYYLAPGGRAA 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  256 AVMANGTTWNS-TDRKIREYFVKSGFIEATILLPPKLFTGISVATTLVVFS----NLNSHIKMIDACEKFTKEGRRNILS 330
Cdd:pfam02384 182 VVLPNGVLFRGgAEGKIRKALVDKDLVETVIALPPNLFYNTSIPTCILFLTknkaERKGKVLFIDASNEFKKEGKLNILT 261

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 496028878  331 DNDISDILDLL---QKDGKNSITISIKEIEENDYIINASRYLEKAPE 374
Cdd:pfam02384 262 DEHIEKIIDTFgefKDVDGFSKSATLEEIAANDYNLNVGRYVGTEEE 308
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
118-316 2.53e-21

Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];


Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 93.33  E-value: 2.53e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 118 TPRGILKLAAKILDVQKNESVLELCSGKGNFFVELA--------LLRENIKYTGIE-------LSMANNFIANIRASVLE 182
Cdd:COG0286   27 TPREVVRLMVELLDPKPGETVYDPACGSGGFLVEAAeylkehggDERKKLSLYGQEinpttyrLAKMNLLLHGIGDPNIE 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 183 RDISLvLNDamtYKAENKADKLFANYPFLINIPDMENIIKYMEMLPDNIKRASS-DWIFNLKLVEQMKSGGKAVAVMANG 261
Cdd:COG0286  107 LGDTL-SND---GDELEKFDVVLANPPFGGKWKKEELKDDLLGRFGYGLPPKSNaDLLFLQHILSLLKPGGRAAVVLPDG 182

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 496028878 262 TTWNSTDRKIREYFVKSGFIEATILLPPKLFTGISVATTLVVFSN----LNSHIKMIDA 316
Cdd:COG0286  183 VLFRGAEKEIRKKLLENDLLEAIIGLPSNLFYNTGIPTCILFLTKgkpeRTGKVLFIDA 241
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 403-565 3.74e-19

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


Pssm-ID: 341198 [Multi-domain]  Cd Length: 192  Bit Score: 85.67  E-value: 3.74e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 403 KSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPN-LKKFCVRNNSIILTKT-GSPDF--KSAVVHvKEGTEILATGNMF 478
Cdd:cd17517   21 SSYDGSGTPVLRIPNIYDGGIDLDDLKKRVDLSEKeLEKYLLKKGDILFNRSnGSPELvgKCALVD-EEDEPAIFASYLI 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 479 ILEIDETKADPYYVQALFDSELGRALFKSIYVGSAI-PTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLE 557
Cdd:cd17517  100 RLRLDKKKILPEFLYYYLNSPLGRKQIEKIAKSAAGqANINQKDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLE 179


                 ....*...
gi 496028878 558 TSREKLKQ 565
Cdd:cd17517  180 KLEQLFKS 187
RMtype1_S_EcoJA65PI-TRD1-CR1_like cd17256
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 401-567 3.25e-18

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: 82.55  E-value: 3.25e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 401 ENKSNEPTNYRYIMLSNINDGDIYFTDNQYL-KDIQPNLKKFCVRNNSIILTKTGS--------PDFKSAvvHVKEGTEI 471
Cdd:cd17256   17 ESLSDGPTGVPYIRVTDIKNGGIDLDNLKYIsPEIHEKIKRYTLSKGDILISIVGTigrvgivpKELDGA--NLTENAAR 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 472 LATGNmfileidetKADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAE 551
Cdd:cd17256   95 IRPKD---------SISPRYLYYYLRSPFGQSQIESETKGAAQPKLNLKRIRELPIPLPPLEEQKRIVAILDSLDAKIDA 165

                        170
                 ....*....|....*.
gi 496028878 552 LKEKLETSREKLKQVF 567
Cdd:cd17256  166 LEKQLAKLEELKKALM 181
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 410-565 1.06e-17

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: 80.89  E-value: 1.06e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 410 YRYIMLSNINDGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTKTGSPDfksAVVHVKEGTEILATGNMFILEIDETkADP 489
Cdd:cd16961   27 IPWIRISDINNGGIILTDEKITEEGAEKLKKKILPKGDILISRSGTIG---KVAIVKENDKALLNQAVIVIRPKDE-VDS 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496028878 490 YYVQALFDSELGRALFKSiYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSrEKLKQ 565
Cdd:cd16961  103 EFLYYFLKSPFGKKLIEG-SAGSTQPNLNKSDLKNLKIPLPPLEEQKKIANILDKLDALIELLEQKLEKL-EQLKQ 176
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 410-567 2.88e-16

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: 77.18  E-value: 2.88e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 410 YRYIMLSNINDGDIYFTDNQYL--KDIQPNLKKFCVRNNSIILTKTGSPDfKSAVVhvKEGTEILATGNMFILEIDETKA 487
Cdd:cd17246   28 IPFITSKNIKNGKIDFSDVKYIseEDHNEILKRSKLKKGDILFSIIGTIG-RVAIV--PEDLPANINQAVALIRPKKEKI 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 488 DPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17246  105 DPKYLLYYLNSPIIQKQIEKNAVGGTQKNLSLGDLKNLKIPLPPLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLM 184
RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like cd17521
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 401-567 1.31e-15

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: 75.21  E-value: 1.31e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 401 ENKSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTKTGSPDFKSAVVHVKEGTEILAtGNMFIL 480
Cdd:cd17521   19 ASAAYEDGGPRYLRITDIQDDGVLWDTVPYCSISEEDAEKYLLKDGDILFARTGATVGKSYLYKEDDGKAVFA-SYLIRF 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 481 EIDETKADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSR 560
Cdd:cd17521   98 RPNKKKVLPKYLFYFTQSSLYWKQIKSISSGSAQPNINAEKLKSLKIPLPPLEEQKRIVAILDALDAKIDALEELLEKLE 177


                 ....*..
gi 496028878 561 EKLKQVF 567
Cdd:cd17521  178 ELLKELL 184
RMtype1_S_HmoORF3075P-TRD1-CR1_like cd17520
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 403-563 1.84e-15

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Heliobacterium modesticaldum Ice1 S subunit (S1.HmoORF3075P) TRD1-CR1; The recognition sequence of Heliobacterium modesticaldum Ice1 S subunit (S1.HmoORF3075P) 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 subfamily also includes the TRD-CR-like sequence-recognition domain of type I N6-adenine DNA methyltransferase (M) subunit of Clostridium intestinale URNW (M2.CinURNWORF2828P). The recognition sequence of M2.CinURNWORF2828P is undetermined. Type I methyltransferases included in this group include two domains: one for methylation, and another (TRD-CR-like) for sequence-recognition.


Pssm-ID: 341201 [Multi-domain]  Cd Length: 180  Bit Score: 74.80  E-value: 1.84e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 403 KSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTKTGSPdFKSAVVHvKEGTEILATGNMFILEI 482
Cdd:cd17520   18 KDIKPGSISVLNISNIEDGEIDYSGMDTIEEEERKVKRYELRDGDLVLSCRGTA-IKVAVFR-EQKKIVIASANIIVIRP 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 483 DEtKADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEEL----EKIAELKEKLET 558
Cdd:cd17520   96 NE-KVLSEYLKIFLESPVGTALIKSFQRGTTVMNINHSDIAEMEIPLLPLEEQKKIAEEYRKERslyrETVRKAEKRWTE 174


                 ....*
gi 496028878 559 SREKL 563
Cdd:cd17520  175 EKEKI 179
RMtype1_S_EcoKI-TRD2-CR2_like cd17261
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 402-565 4.11e-14

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


Pssm-ID: 341150 [Multi-domain]  Cd Length: 191  Bit Score: 71.03  E-value: 4.11e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 402 NKSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTKTGSPDFKSAVVHVKEGTEILA---TgnMF 478
Cdd:cd17261   20 KPPDDETGWPVLKLSAVTSGKFDPSENKYLPESLEPASEYWLKPGDLLISRANTSELVGRAALVDGDPDNLIypdK--LI 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 479 ILEIDETKADPYYVQALFDSELGRALFKSIYVGSA--IPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKL 556
Cdd:cd17261   98 RLRVNEELLLPEYLALALNSPSARRQIESRATGTAgsMPKISQSDLKSLPIPLPPLAEQKRIVARVDELLALIDRLEAQL 177


                 ....*....
gi 496028878 557 ETSREKLKQ 565
Cdd:cd17261  178 AAALQLLDR 186
RMtype1_S_AbaB8300I-TRD1-CR1_like cd17263
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 401-567 1.25e-13

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) TRD1-CR1; Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) recognizes 5'... GAYNNNNNNNTCYC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341152 [Multi-domain]  Cd Length: 177  Bit Score: 69.07  E-value: 1.25e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 401 ENKSNEPTNYRYIMLSNIndgdiYFTDNQYLKDIQPNLKKFCVRNNSIILTKTGSPDFKsaVVHVKEGteILATgNMFIL 480
Cdd:cd17263   18 SERFDEPKEGSVRYIQIE-----DLRNNNEKKYIENPKKSVICNEDDILIVRDGANAGE--VGTGLEG--AIAS-TLFKI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 481 EIDETKADPYYVQALFDSELgRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSR 560
Cdd:cd17263   88 IPDKNIIDKDYLYYFLKSKE-IQLNILTKAGSTIPHVNKKDLENLKIPLPSLEEQKKIAEILDKLDALIDKLKELIEKLI 166


                 ....*..
gi 496028878 561 EKLKQVF 567
Cdd:cd17263  167 ELKKGLF 173
RMtype1_S_EcoKI-TRD1-CR1_like cd17252
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 400-568 1.47e-13

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: 69.51  E-value: 1.47e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 400 DENKSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPNLKKFcVRNNSI-ILTKTGSPDF--KSAVVhvKEGTEILATGN 476
Cdd:cd17252   22 DASEEPSEGGIPVLRANNIQNGGLDFDDLVYVPKSKVKEEQK-LKKGDIlICMSSGSKELvgKAAFI--DEDTDYTFGAF 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 477 MFILEIDEtKADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKL 556
Cdd:cd17252   99 CGVIRPKK-EIDPRYLFYFLQSPSYREYIRSLASGTNINNLSNEHLENLKIPLPPLAEQKRIVAKLDKLDALIDKLKQAL 177

                        170
                 ....*....|..
gi 496028878 557 ETSREKLKQVFN 568
Cdd:cd17252  178 EKLDELLKSLFQ 189
RMtype1_S_EcoUTORF5051P-TRD2-CR2_like cd17524
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 401-568 2.73e-13

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


Pssm-ID: 341205 [Multi-domain]  Cd Length: 189  Bit Score: 68.65  E-value: 2.73e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 401 ENKSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTKTGSPDF--KSAVVHvKEGTEILAtGNMF 478
Cdd:cd17524   19 EKKSEDEGGYPVLRMGNIQDGGIDDDDLKYVDLDEKEFEKYLLKKGDVLFNRTNSPELvgKTAIFR-GDGPATFA-SYLI 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 479 ILEIDETKADPYYVQALFDSELGRALFKSIY---VGSAipTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEK 555
Cdd:cd17524   97 RIRLNEEKILPEYLNYFLNSPYGRKQIKSVAtqgVGQA--NINATKLKAIPIPLPPLEEQKEIVEKLDELDALIDRLEAL 174

                        170
                 ....*....|...
gi 496028878 556 LETSREKLKQVFN 568
Cdd:cd17524  175 LEEAEELLESLLQ 187
RMtype1_S_LdeBORF1052P-TRD2-CR2 cd17278
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 403-568 3.95e-13

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: 67.92  E-value: 3.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 403 KSNE--PTNYRYIMLSNINDGDIYFTDNQYLKDIQPN-LKKFCVRNNSIILTKTGSPDFKSAVVhvKEGTEILA----TG 475
Cdd:cd17278   19 KSSDfsDEGIPVIRIGNIKNGGIDLDDNSKYPEEPLEkYEKFLLKKGDILIAMTGGTVGKVAIV--PEDDEPALlnqrVG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 476 NMFILEidetKADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEK 555
Cdd:cd17278   97 KFRPKD----KIDKEFLYYLLRSDSFRNQIKSSATGTAQPNISPKDIESIKIPLPPLEEQKKIAEILDSLDAKIDKLEQK 172

                        170
                 ....*....|...
gi 496028878 556 LETSREKLKQVFN 568
Cdd:cd17278  173 LEKLRDLLKPLLQ 185
RMtype1_S_Eco933I-TRD2-CR2_like cd17253
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 482-564 4.21e-13

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: 68.27  E-value: 4.21e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 482 IDETKADPYYVQALFDSELGRALFKSIYVGSA-IPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSR 560
Cdd:cd17253  103 PKDDLLLPEFLSYWLNSAYGRGYFLRAAKQTTnLASINSTKLKALPVPLPPLEEQRRIVERLDELLALIDALEASLAKLE 182


                 ....
gi 496028878 561 EKLK 564
Cdd:cd17253  183 ELLK 186
RMtype1_S_Cje2232P-TRD2-CR2_like cd17526
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 417-568 8.68e-12

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


Pssm-ID: 341207 [Multi-domain]  Cd Length: 192  Bit Score: 64.15  E-value: 8.68e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 417 NIN-DGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTKTGSPDF--KSAVVhvkEGTEILATGN-MFILEIDETKADPYYV 492
Cdd:cd17526   36 NITtDGELDLDKLIKIVPSPKERKRYLLQKGDVLFNNTNSQELvgKTALF---DGEEPYVFSNhMTRIRVKKSKINPEFL 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496028878 493 QALFDSELGRALFKSI---YVGSAipTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVFN 568
Cdd:cd17526  113 ARYLHLLWRSGYFKKLctnWVNQA--GINSDTLANLKIPLPPLPEQKRIAEILDQIDRLAKALRAEAEALLELAKSLFE 189
RMtype1_S_HpyCR35ORFAP-TRD1-CR1_like cd17519
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 413-565 2.67e-11

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


Pssm-ID: 341200 [Multi-domain]  Cd Length: 183  Bit Score: 62.71  E-value: 2.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 413 IMLSNINDGDIYFTDNQY--LKDIQPNLKKFCVRNNSIILTKTGSPDFKSAVVhvKEGTEILATGNMFILEIDETKADPY 490
Cdd:cd17519   30 IRITNIQNGKIDTDNLKYfdLNDYKENLDKYIVRPGDIVIAMSGATTGKVGIN--LTDQEFYLNQRVGKFIPNEEILNNR 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496028878 491 YvqaLFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLEtsrEKLKQ 565
Cdd:cd17519  108 Y---LYHFLLSKQNEKYILAGGSQPNLSSEKLKKIKIPIPSLEVQEEIVSILDKFRELTNELESELN---LRLKQ 176
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
495-565 3.56e-11

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 59.69  E-value: 3.56e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496028878 495 LFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREkLKQ 565
Cdd:COG0732    5 YLRSPSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKE-LRD 74
RMtype1_S_Eco4255III-TRD2-CR2_like cd17265
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 416-565 3.12e-10

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


Pssm-ID: 341154 [Multi-domain]  Cd Length: 181  Bit Score: 59.44  E-value: 3.12e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 416 SNINDGDIYFTDNQYLK-DIQPNLKkfcVRNNSI-ILTKTGSPDF--KSAVVhvKEGTEILATGN-MFILEidetKADPY 490
Cdd:cd17265   31 SNIQNGKLDFDDNVYVNsKIPEKLI---VKEGDIlICVRNGSRALigKNALI--DKEAEGMTFGAfMTVFR----SEYND 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496028878 491 YVQALFDSELGRALFKSiYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQ 565
Cdd:cd17265  102 YLFHLFNSDLFKKQIGS-FLTATINQITNGNLNNFKIPLPPLEEQEKIAEFLSSLDAKIDKLIKKIEKLIELKKE 175
PRK09737 PRK09737
type I restriction-modification system specificity subunit;
403-565 3.26e-10

type I restriction-modification system specificity subunit;


Pssm-ID: 236619 [Multi-domain]  Cd Length: 461  Bit Score: 62.59  E-value: 3.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 403 KSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTKTGSPDFkSAVVHVKEGTEILATGNMFILEI 482
Cdd:PRK09737  34 KSLTMGDLPFIRTTDITNGAVDLTTLPYCMDAPEDVSKYQLQDRDIVISSAGSIGF-SFLAQNPLPSNVVFASFAIRLKP 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 483 dETKADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREK 562
Cdd:PRK09737 113 -VNYFSEYFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAEQKIIAEKLDTLLAQVDSTKARLEQIPQI 191


                 ...
gi 496028878 563 LKQ 565
Cdd:PRK09737 192 LKR 194
RMtype1_S_StySPI-TRD2-CR2_like cd17523
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Salmonella ...
 403-564 1.08e-09

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


Pssm-ID: 341204 [Multi-domain]  Cd Length: 190  Bit Score: 58.02  E-value: 1.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 403 KSNEPTNYryIMLSNINDGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTK-TGSPDFKSAVVhVKEGTEILATGNMFI-L 480
Cdd:cd17523   23 SDGEPIIV--LRLADIKNNKISFENLRRIKLTEKEIEKYSLSKGDLLIIRvNGSPDLVGRFI-LFKGYEDVAYCDHFIrM 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 481 EIDETKADPYYVQALFDSELGRALFKSIYVGSA-IPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETS 559
Cdd:cd17523  100 RLDQEKIDPEFLSYIFNSPLIRRKIERNFVTSAgQKTVNQGHIKSLPIPLPPLKEQKKIVARVEELFALIDQLESSLDLA 179


                 ....*
gi 496028878 560 REKLK 564
Cdd:cd17523  180 QQLQN 184
RMtype1_S_AmiI-TRD2-CR2_like cd17248
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 488-564 1.88e-09

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: 57.54  E-value: 1.88e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496028878 488 DPYYVQALFDSElgRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLK 564
Cdd:cd17248  108 DPEYLLYVLRAM--KPEFERLAMGSTHKTIYMPDFKALRIALPPLEEQRKIVDRLEALDAKIDALERKLERLIELLK 182
RMtype1_S_StySKI-TRD2-CR2_like cd17259
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 485-565 1.88e-09

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: 57.52  E-value: 1.88e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 485 TKADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLK 564
Cdd:cd17259  105 DELNSDFLYYLLQSDFFLNYVEPVLTGTDVPHISTKQIKNFKIPLPPLEEQKKIAEFLSSLDALIDLLEQKLEKLQQLKK 184


                 .
gi 496028878 565 Q 565
Cdd:cd17259  185 G 185
RMtype1_S_Eco15ORF14057P-TRD1-CR1_like cd17525
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 399-566 3.08e-09

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli 541-15 S subunit (S.Eco15ORF14057P) TRD1-CR1 and Desulfotignum phosphitoxidans S subunit (S.Dph13687ORF2110P) TRD2-CR2; The recognition sequences of Escherichia coli 541-15 S subunit (S.Eco15ORF14057P) and Desulfotignum phosphitoxidans S subunit (S.Dph13687ORF2110P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341206 [Multi-domain]  Cd Length: 190  Bit Score: 56.86  E-value: 3.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 399 LDENKSNEPTNYRYIMLSNINDGDIYFTDNQ-YLKDIQPNLKKFCVRNNSIILTKTGSPDF--KSAVVHvKEGTEILATG 475
Cdd:cd17525   17 LVRSNSEDPNGYPYIKMGNIGRGGINLLKVEtYVDATELEVEKYLLEDGDLLFNTRNTLELvgKVAIWR-GELPKALFNN 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 476 NMFILEIDEtKADPYYVQALFDSELGRALFKSIYVGS----AIPTislENLRKLEILLPSIEEQNIIGEKYKEELEKIAE 551
Cdd:cd17525   96 NILRIRFDD-IVLPYFINYYLNSPDGKKQLESIASGTtsvaAIYQ---KDLKKLKLPLPPLDEQREIVSFLSELDAKIDQ 171

                        170
                 ....*....|....*
gi 496028878 552 LKEKLETSREKLKQV 566
Cdd:cd17525  172 LEQKLEKLLQIKKAL 186
RMtype1_S_Eco16444ORF1681_TRD1-CR1_like cd17282
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 483-565 3.16e-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: 56.68  E-value: 3.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 483 DETKADPYYVQALFDSElgRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSrEK 562
Cdd:cd17282  100 NEEKIDVEFLEYYLRTL--KKELEAIAPQSAQKNINLEILRPLKIPVPPLEEQKKIVEILDALDDLIDNLEKRIAKL-EE 176


                 ...
gi 496028878 563 LKQ 565
Cdd:cd17282  177 LKQ 179
RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like cd17266
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 473-567 3.56e-09

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


Pssm-ID: 341155 [Multi-domain]  Cd Length: 159  Bit Score: 55.92  E-value: 3.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 473 ATGNMFILEIDETKADPYYVQALFDSELGRalfksiYV-GSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAE 551
Cdd:cd17266   69 VTDNALVVTPKKENNIKFLYYLLKSLNLNQ------YAtGSAQPLITVSKLKKLKIPLPPLEEQKKIAAILDSLDAKIDL 142

                         90
                 ....*....|....*.
gi 496028878 552 LKEKLETSREKLKQVF 567
Cdd:cd17266  143 LEKKLEKLIELKKELM 158
RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like cd17289
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 483-568 5.44e-09

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: 56.11  E-value: 5.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 483 DETKADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREK 562
Cdd:cd17289  103 NIKDINSKFLYYWFQSSIFKNQINSITIGSTQKALTIEKLKKTKIPLPPLEEQKKIVSILSALDEKIDLNKKQLQKLEEL 182


                 ....*.
gi 496028878 563 LKQVFN 568
Cdd:cd17289  183 AKTLFQ 188
RMtype1_S_TteMORF1547P-TRD2-CR2_like cd17497
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 511-565 4.90e-08

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


Pssm-ID: 341188 [Multi-domain]  Cd Length: 174  Bit Score: 52.94  E-value: 4.90e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496028878 511 GSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQ 565
Cdd:cd17497  114 GSTFKAISKEDLENLLIPLPPLAEQKRIAAFLDELTAKIDQLIALLEKAIELLKE 168
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 507-567 1.03e-07

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: 52.05  E-value: 1.03e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496028878 507 SIYV-GSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17262  108 SPYVtGAAQPKLNQANLNSIPIPLPPLEEQKKIVAILDKLDALIDLLEEELEKLIELKKALL 169
RMtype1_S_BliBORF2384P-TRD1-CR1_like cd17496
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 488-568 1.24e-07

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: 51.73  E-value: 1.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 488 DPYYVQALFDSELGRalFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17496   94 DTEFLYYLLESNLDY--LLAAATGSTFPNISRDDLLNLKIPLPPLEEQKRIVAILDPLDEKIDKNKQEIEKLEELRDTLL 171


                 .
gi 496028878 568 N 568
Cdd:cd17496  172 P 172
RMtype1_S_Eco3763I-TRD2-CR2_like cd17264
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 486-567 2.04e-07

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


Pssm-ID: 341153 [Multi-domain]  Cd Length: 184  Bit Score: 51.38  E-value: 2.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 486 KADPYYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQ 565
Cdd:cd17264  101 KVDVRYLYYYLNSPLGKSQIKKYDNGSAQPNLSAKSLKKFLIPLPPLEEQKRIVAKLDELDALIDKLKQALEKLEELLQS 180


                 ..
gi 496028878 566 VF 567
Cdd:cd17264  181 LF 182
RMtype1_S_Csp16704I_TRD2-CR2_like cd17285
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 465-568 3.22e-07

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: 50.58  E-value: 3.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 465 VKEGTEILAT----GNMFILEIDET-----KA-------DPYYvqaLFDselgraLFKSIY-------VGSAIPTISLEN 521
Cdd:cd17285   61 IPKGTVIIATrmglGKVAINKIDVAinqdlKAlfpkdelDPEY---LLY------WFLSIEetieslgTGTTVKGITLED 131

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 496028878 522 LRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVFN 568
Cdd:cd17285  132 LKSLKIPLPPLEEQKRIVAILDELDELIDKLEAKLEKLKQLKKGLMQ 178
RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like cd17515
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 505-567 6.93e-07

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: 49.74  E-value: 6.93e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 496028878 505 FKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17515  115 LISLGKGGAQPNISQGIIKNIEIPLPPLAEQKRIVAKLDKLDKLIEKLEKALEKLEELKKALM 177
RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like cd17284
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 486-565 1.44e-06

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: 48.75  E-value: 1.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 486 KADPYYVqaLFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQ 565
Cdd:cd17284  102 KINPEYL--MYLLSLQKKYMEKIATGTTIPYLNKTNCESIPIPLPPIEEQNKIAKILDSIDKKIDLLIAKLEKLQQLKKG 179
RMtype1_S_EcoAO83I-TRD1-CR1_like cd17267
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 483-567 1.46e-06

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: 48.17  E-value: 1.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 483 DETKADPYYVQALFDSeLGRALFKSiyvGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREK 562
Cdd:cd17267   76 DFKGNDPRFLYYLLKT-LDLERLNS---GSAVPGLNRNDVYSLKVPLPPLEEQKAIAAILDALDDKIELNRRQNQTLEEL 151


                 ....*
gi 496028878 563 LKQVF 567
Cdd:cd17267  152 ADALL 156
RMtype1_S_Eco2747II-TRD2-CR2-like cd17272
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 403-538 1.48e-06

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


Pssm-ID: 341161 [Multi-domain]  Cd Length: 189  Bit Score: 48.96  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 403 KSNEPTNYRYIMLSNINDGDIYFTDNQYLKDIQPNLKKFCVRNNSIILTKTgspdfKSAVVHVKEGTEILATGNMFILEI 482
Cdd:cd17272   21 NFDEKGEIPVITSKNISNGKIDFEYVKYDFLSISKNRKINKGDILITMIGT-----IGETAIVKCLDPKFYTLNLYLIRL 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 496028878 483 DETKADPYYVQALFDSElgRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNII 538
Cdd:cd17272   96 KKEKLLPSYLKYFLDSE--KFLNKSISATSGQGYLKANQIDKLEIPLPPLEEQQRI 149
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 418-567 1.85e-06

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: 48.76  E-value: 1.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 418 INDGDIYFTDNQYLKDiqpnLKKFCVRNNSIILTKTGS--PDFKSAVVHV----KEGTEILATGNMFILEIDETKADPYY 491
Cdd:cd17512   41 IDINNLVYISEEKANK----YKKYELKENDIIITTVGSwpSNPDSVVGKVvrvpKEADGALLNQNAVKIRPKKGILDQSF 116

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496028878 492 VQALFDSELGRALFKSIYVGSAI-PTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17512  117 LFYNLKSERFKNYIESIARGNANqASITLGDIKKFKFLLPPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQALY 193
RMtype1_S_PluTORF4319P-TRD2-CR2_like cd17269
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 490-565 2.04e-06

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


Pssm-ID: 341158 [Multi-domain]  Cd Length: 168  Bit Score: 47.97  E-value: 2.04e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496028878 490 YYVQALFdselgRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQ 565
Cdd:cd17269   89 YYLKSYF-----KKYIEKNSVGSSVPYIRLPMLENFKIPLPPLEEQKRIVRILDKFDALTAELPAELEARKKQYEY 159
RMtype1_S_Eco4255II_TRD2-CR2_like cd17250
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 505-567 3.66e-06

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


Pssm-ID: 341139 [Multi-domain]  Cd Length: 185  Bit Score: 47.63  E-value: 3.66e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 496028878 505 FKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17250  119 LYKYSQATTVPSIRKSTLESIPIPLPPLEEQKRIAAKLDELFEKLDKLKQALEAAKEQLKGLR 181
RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like cd17513
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 482-567 5.09e-06

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: 47.13  E-value: 5.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 482 IDETKADPYYVQALFDSELgrALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKykeeLEKIAELKEKLETSRE 561
Cdd:cd17513   95 IPIKEVNPLFLAYLLYSLL--QKLKSQLQGTSIKGITKDDLKNLKIPLPPLEEQQKIAAI----LSKLDKLIEAHEKKLE 168


                 ....*.
gi 496028878 562 KLKQVF 567
Cdd:cd17513  169 KLKQLK 174
RMtype1_S_MjaORF1531P-TRD1-CR1_like cd17522
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 476-564 8.24e-06

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P/MjaXIIP) TRD1-CR1; The recognition sequence of Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P, also called MjaXIIP) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341203 [Multi-domain]  Cd Length: 190  Bit Score: 46.76  E-value: 8.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 476 NMFILEIDETKADPYYVQALFDSELGRALFKSIY---VGSAipTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAEL 552
Cdd:cd17522   95 NLLRLRPNKNIVDPKYLYYLLKSDRFRNQFRSIAkkaVNQA--SINQTELKKIKIPLPPLEEQQKIASILEKLDKKIEKR 172

                         90
                 ....*....|..
gi 496028878 553 KEKLETSREKLK 564
Cdd:cd17522  173 KEKIEKLKELKK 184
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 517-567 2.69e-05

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: 45.14  E-value: 2.69e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 496028878 517 ISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17249  132 LDTDDLKNLPIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEELLKALM 182
RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like cd17288
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 477-564 2.95e-05

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: 44.38  E-value: 2.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 477 MFILEIDEtKADP---YYVQALFDselgralFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIG---EKYKEELEKIA 550
Cdd:cd17288   72 MFYTEIKK-NNDPkflYYLLKTID-------FKKYNEATGVPSLTQTTLNKIKIPIPPLEEQQKIAsilDKLDAKDALIE 143

                         90
                 ....*....|....
gi 496028878 551 ELKEKLETSREKLK 564
Cdd:cd17288  144 LQEKLLEKLKQYKL 157
RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like cd17276
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S. ...
 480-564 4.50e-05

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


Pssm-ID: 341165 [Multi-domain]  Cd Length: 187  Bit Score: 44.50  E-value: 4.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 480 LEIDETKADPYYVQALFdsELGRALFKSIYVGSAI-PTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLET 558
Cdd:cd17276   97 ILPNEKKVNPEFLLRYL--NFNRPYWMRVAASSRKdPNITKDDVRNFPIPLPPLDEQRAIVEFLSDVDALIDSLEALIEK 174


                 ....*.
gi 496028878 559 SREKLK 564
Cdd:cd17276  175 LRELKK 180
RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like cd17293
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to ...
 511-567 5.33e-05

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: 43.98  E-value: 5.33e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 496028878 511 GSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17293  120 STTLPIINKSKFEKIEIPLPPLEEQKRIVAKLDKLFALIDKLEESLEELDELLKSLF 176
RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like cd17499
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 504-568 6.32e-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: 43.76  E-value: 6.32e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496028878 504 LFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVFN 568
Cdd:cd17499  108 YFKGKSGGSTFKSINKNQIKNIKIPLPPLEEQKRIVSELDKLFKLIFEAKNNIEEALANAQQLFK 172
RMtype1_S_MgeORF438P-TRD-CR_like cd17291
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 505-565 8.04e-05

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.MgeORF438P TRD1-CR1 and TRD2-CR2, and to Escherichia coli G5 S subunit (S.Eco16445ORF5013P ) TRD2-CR2 and Acetobacter pasteuri; The recognition sequences of Mycoplasma genitalium G-37 S subunit (S.MgeORF438P), Escherichia coli G5 S subunit (S.Eco16445ORF5013P), and Acetobacter pasteurianus IFO 3283-01 S subunit (S2.Apa3283ORF14230P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341180 [Multi-domain]  Cd Length: 161  Bit Score: 43.27  E-value: 8.04e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496028878 505 FKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKykeeLEKIAELKEKLETSRE-KLKQ 565
Cdd:cd17291   99 IYSLQRGAGQPHIYKKDIEKLKIPIPPLEEQQKIVEI----LDKFTELTAELPAELEaRKKQ 156
RMtype1_S_EcoJA69PI-TRD1-CR1_like cd17273
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 517-565 9.86e-05

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


Pssm-ID: 341162 [Multi-domain]  Cd Length: 186  Bit Score: 43.55  E-value: 9.86e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 496028878 517 ISLENLRKLEILLPSIEEQNIIGEKykeeLEKIAELKEKLETSREKLKQ 565
Cdd:cd17273  132 ISKSTFKKIEIPLPPLEEQKKIAAI----LSKLDELIELLEKENEKLKE 176
RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like cd17296
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 469-568 1.35e-04

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: 42.97  E-value: 1.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 469 TEILATGNMFI--LEIDETKADP----YYVQALFDSelgralFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKY 542
Cdd:cd17296   80 LKIEATTNQAIagIKPKNKSINPkylyYYLKSLYEK------FLSLGRGVAQNNINLSILKNLKIPLPPLEEQQRIVAIL 153

                         90       100
                 ....*....|....*....|....*.
gi 496028878 543 KEELEKIAELKEKLETSREKLKQVFN 568
Cdd:cd17296  154 DKFEKLINKRQEGLQLLDELVKSLFE 179
RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like cd17290
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 511-567 1.60e-04

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: 42.96  E-value: 1.60e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 496028878 511 GSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17290  124 GATLPILNQEKLKNIKLPVPPLNEQQKIVEFLDKKTAKIDALIAKKEQLIELLKEYR 180
RMtype1_S_Sba223ORF3470P-TRD1-CR1_like cd17270
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 490-563 1.63e-04

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


Pssm-ID: 341159 [Multi-domain]  Cd Length: 183  Bit Score: 42.69  E-value: 1.63e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496028878 490 YYVQALFDSELGRAlfksiyVGSAIPTISLENLRKLEILLPSIEEQNIIG---EKYKEELEKIAELKEKLETSREKL 563
Cdd:cd17270  109 YQLKLKFEIEKEKA------PGGTIKTITKEELSKFEIPIPSLEEQKEIVnilDKFDELITELQLRKKQLEYYKKAL 179
RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like cd17280
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter ...
 507-564 1.64e-04

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: 42.92  E-value: 1.64e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 496028878 507 SIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLK 564
Cdd:cd17280  119 SLASGGGQPNISQELIKSLRIPVPPLEEQKQIAAFLDKKTAKIDSLIEKKERLIELLK 176
RMtype1_S_EcoEI-TRD1-CR1_like cd17260
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 522-567 1.93e-04

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


Pssm-ID: 341149 [Multi-domain]  Cd Length: 165  Bit Score: 42.04  E-value: 1.93e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 496028878 522 LRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17260  116 LENYKIPLPPLEEQKRIAAILDSLDAKIDALEAEIETLEELLDALL 161
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 130-280 2.14e-04

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 41.52  E-value: 2.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 130 LDVQKNESVLELCSGKGNFFVELAllRENIKYTGIELSMANNFIANIRASVLERDISLVLNDAMTYK-AENKADKLFANY 208
Cdd:COG2226   18 LGLRPGARVLDLGCGTGRLALALA--ERGARVTGVDISPEMLELARERAAEAGLNVEFVVGDAEDLPfPDGSFDLVISSF 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 496028878 209 pFLINIPDMENIIKymemlpdNIKRAssdwifnlklveqMKSGGKAVAVmangtTWNSTDRK-IREYFVKSGF 280
Cdd:COG2226   96 -VLHHLPDPERALA-------EIARV-------------LKPGGRLVVV-----DFSPPDLAeLEELLAEAGF 142
RMtype1_S_MmaC7ORF19P_TRD1-CR1_like cd17294
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 480-568 2.38e-04

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: 42.48  E-value: 2.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 480 LEIDETKADPYYVQALFDS---ELgralfKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKL 556
Cdd:cd17294   99 IEPDEEIANSRFLYYNLSSryeEL-----RSLSGGGGRGGLNLKIIKSLPIPLPPLEEQKKIVAILDKFDALINDLKEGL 173

                         90
                 ....*....|..
gi 496028878 557 ETSREKLKQVFN 568
Cdd:cd17294  174 PALLELRQKQYE 185
RMtype1_S_EcoBI-TRD1-CR1_like cd17257
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 522-567 2.84e-04

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: 41.74  E-value: 2.84e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 496028878 522 LRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17257  129 IDEIELPLPPLEEQRRIAEILDELDALIDKLIAKLEKLRDLLLPLL 174
RMtype1_S_FclI-TRD1-CR1_like cd17254
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 517-568 2.97e-04

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: 41.68  E-value: 2.97e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 496028878 517 ISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVFN 568
Cdd:cd17254  119 ITKGDLENIKVPLPPLEEQKRIAAILDELDALIDALEEQLKKLEELRKALLQ 170
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 138-222 4.06e-04

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 40.11  E-value: 4.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 138 VLELCSGKGNFFVELAlLRENIKYTGIELS-MANNFIANIRASVLERDISLVLNDAMT--YKAENKADKLFANYPFLINI 214
Cdd:cd02440    2 VLDLGCGTGALALALA-SGPGARVTGVDISpVALELARKAAAALLADNVEVLKGDAEElpPEADESFDVIISDPPLHHLV 80


                 ....*...
gi 496028878 215 PDMENIIK 222
Cdd:cd02440   81 EDLARFLE 88
RMtype1_S_Ara36733I_TRD1-CR1_like cd17268
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 432-565 4.27e-04

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


Pssm-ID: 341157 [Multi-domain]  Cd Length: 185  Bit Score: 41.66  E-value: 4.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 432 KDIQPNLKKfcVRNNSIILTKTGS--PDFKSAVVHVKEGtEILATGNMFILEideTKADPYYVQALFDSELGRALFKSIY 509
Cdd:cd17268   53 EELAKKLRK--AKPGDLLIAGTGEtiEDIGKAVAWLGDE-EVAAGGDIIIFR---HSQNPKYLSYLLNSPAFQKQKRKLG 126

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 496028878 510 VGSAIPTISLENLRKLEILLPSIEEQNIIGEKykeeLEKIAELKEKLETSREKLKQ 565
Cdd:cd17268  127 TGTKVVHISASDLAKIKIPVPPLEEQERIVEI----LDKFDALIAGLPAEIEARRK 178
RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like cd17255
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 515-568 6.09e-04

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


Pssm-ID: 341144 [Multi-domain]  Cd Length: 166  Bit Score: 40.59  E-value: 6.09e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 496028878 515 PTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVFN 568
Cdd:cd17255  111 PKLMNNVMAKIKIPLPPLEEQEKIANILDKLDELINLLIAKLKKLIELRKKQLE 164
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 108-206 7.38e-04

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 40.30  E-value: 7.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 108 DLEDSIKEASTPRgiLKLAAKILDVQKNESVLELCSGKGNFFVELAlLRENIKYTGIELS--MANNFIANIRASVLERDI 185
Cdd:COG2230   27 DPDDTLEEAQEAK--LDLILRKLGLKPGMRVLDIGCGWGGLALYLA-RRYGVRVTGVTLSpeQLEYARERAAEAGLADRV 103

                         90       100
                 ....*....|....*....|.
gi 496028878 186 SLVLNDAMTYKAENKADKLFA 206
Cdd:COG2230  104 EVRLADYRDLPADGQFDAIVS 124
RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like cd17283
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 504-564 7.72e-04

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: 40.54  E-value: 7.72e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496028878 504 LFKSIYVG---SAIPTISLENL-----RKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLK 564
Cdd:cd17283  109 LLSSITVQlqfSAQAGGGTKNLntdivKNLKIPLPPLEEQKRIAEILDSLDALIDALEEKLEKLEELKK 177
RMtype1_S_LlaA17I_TRD2-CR2_like cd17292
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 511-565 1.31e-03

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


Pssm-ID: 341181 [Multi-domain]  Cd Length: 149  Bit Score: 39.45  E-value: 1.31e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 496028878 511 GSAIPTISLENLRKLEILLPSIEEQNIIGE---KYKEELEKIAELKEKLETSREKLKQ 565
Cdd:cd17292   89 GSTIKRLYNDNLLNTKIPVPSLDEQRKIAEflsLLDALIALLQKKLEKLIALKKGLMQ 146
RMtype1_S_Apa101655I-TRD2-CR2_like cd17244
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 522-567 1.32e-03

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: 40.15  E-value: 1.32e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 496028878 522 LRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQVF 567
Cdd:cd17244  133 IKEIPIPLPPLEEQKRIAPILDKIDALIDQLETLIELLDELLPKLM 178
RMtype1_S_EcoN10ORF171P_TRD2-CR2_like cd17287
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia ...
 479-568 1.32e-03

Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) TRD2-CR2, and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) TRD2-CR2; The recognition sequences of Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341176 [Multi-domain]  Cd Length: 184  Bit Score: 40.16  E-value: 1.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 479 ILEIDET------------KADPYYVQALFDS------ELGRalfksiyvGSAIPTISLENLRKLEILLPSIEEQNIIGE 540
Cdd:cd17287   81 ILGIEAAtnqacaailpndGINPDFLFYYLQSsyeelrDLSN--------GGGQPNLNAGLIKSIEIPVPPLDEQQKIAA 152

                         90       100
                 ....*....|....*....|....*...
gi 496028878 541 KykeeLEKIAELKEKLETSREKLKQVFN 568
Cdd:cd17287  153 F----LSAIDAKIDALEQKLELLQELKK 176
RMtype1_S_Asp27244ORF1181P-TRD1-CR1_like cd17518
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 413-557 1.56e-03

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


Pssm-ID: 341199 [Multi-domain]  Cd Length: 180  Bit Score: 39.66  E-value: 1.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 413 IMLSNINDGDIYF-TDNQYLKDIQPN--LKKFCVRNNSIILTKTGSPDFKSAVVHVKEGTEILATGNMFILEIDEtKADP 489
Cdd:cd17518   28 LNVTNIVNGSLDLdKTDRYISTEEYNgkYKHFLIDEGDILIASSGNSWGKVAIVEKDHLPLMLNTSTIRFKFIDG-LLDN 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496028878 490 YYVQALFDSELGRALFKSIYVGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLE 557
Cdd:cd17518  107 NFLKYFLNSDYFKEQLDLLITGGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEAALEALR 174
RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like cd17279
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 511-565 2.24e-03

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: 39.47  E-value: 2.24e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496028878 511 GSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETSREKLKQ 565
Cdd:cd17279  123 GTTFLELSTDELANFKIPLPPLSEQRAIADFLDRETAKIDALIAKKQQLIELLKE 177
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 138-224 2.24e-03

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 37.54  E-value: 2.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878  138 VLELCSGKGNFFVELAlLRENIKYTGIELSMANNFIANIRASVLERDISLVLNDAMTYK-AENKADKLFANYPF-LINIP 215
Cdd:pfam13649   1 VLDLGCGTGRLTLALA-RRGGARVTGVDLSPEMLERARERAAEAGLNVEFVQGDAEDLPfPDGSFDLVVSSGVLhHLPDP 79


                  ....*....
gi 496028878  216 DMENIIKYM 224
Cdd:pfam13649  80 DLEAALREI 88
RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1 cd17245
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 511-566 2.30e-03

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: 39.06  E-value: 2.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 496028878 511 GSAIPTISLENLRKLEILLPSIEEQNIIGEKykeeLEKIAELKEKLETSREKLKQV 566
Cdd:cd17245  114 GSTFKAINKKDLEELKIPLPPLEEQQKIAEI----LSTVDEAIEKTKALIEKLDEL 165
rADc smart00650
Ribosomal RNA adenine dimethylases;
122-224 3.34e-03

Ribosomal RNA adenine dimethylases;


Pssm-ID: 128898  Cd Length: 169  Bit Score: 38.65  E-value: 3.34e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878   122 ILKLAAKILDVQKNESVLELCSGKGNFfvELALLRENIKYTGIELSmaNNFIANIRASVLERD-ISLVLNDAMTYK-AEN 199
Cdd:smart00650   1 VIDKIVRAANLRPGDTVLEIGPGKGAL--TEELLERAKRVTAIEID--PRLAPRLREKFAAADnLTVIHGDALKFDlPKL 76

                           90       100
                   ....*....|....*....|....*
gi 496028878   200 KADKLFANYPFLINIPDMENIIKYM 224
Cdd:smart00650  77 QPYKVVGNLPYNISTPILFKLLEEP 101
RMtype1_S_Eco2747I-TRD2-CR2_like cd17247
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 480-565 3.76e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2; 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: 38.66  E-value: 3.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 480 LEIDETKADPYYVQALFDS------ELGRalfksiyvGSAIPTISLENLRKLEILLPSIEEQNIIGEKYKEELEKIAELK 553
Cdd:cd17247  102 IRPNEERVLPEYLHYYLESqydelrRIGS--------GGGQGALNCGILKAFPIPLPPLDEQREIVAELEALLAKIDLLE 173

                         90
                 ....*....|..
gi 496028878 554 EKLETSREKLKQ 565
Cdd:cd17247  174 EKIARLIELLKE 185
RMtype1_S_Eco540ANI-TRD1-CR1_like cd17274
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 524-565 4.29e-03

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


Pssm-ID: 341163  Cd Length: 171  Bit Score: 38.24  E-value: 4.29e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 496028878 524 KLEILLPSIEEQNIIGEKYKEELEKIAELKEKLETsREKLKQ 565
Cdd:cd17274  123 KFKIPLPPLEEQNKIVRILDKFDELIAELEAKLEL-LKKQKK 163
trmB PRK00121
tRNA (guanine-N(7)-)-methyltransferase; Reviewed
 133-209 7.17e-03

tRNA (guanine-N(7)-)-methyltransferase; Reviewed


Pssm-ID: 234649  Cd Length: 202  Bit Score: 38.22  E-value: 7.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496028878 133 QKNESVLELCSGKGNFFVELALLRENIKYTGIE-----LSMANNFIA-----NIRasVLERDISLVLNDAMtykAENKAD 202
Cdd:PRK00121  39 NDAPIHLEIGFGKGEFLVEMAKANPDINFIGIEvhepgVGKALKKIEeegltNLR--LLCGDAVEVLLDMF---PDGSLD 113


                 ....*..
gi 496028878 203 KLFANYP 209
Cdd:PRK00121 114 RIYLNFP 120
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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