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Conserved domains on  [gi|499339060|ref|WP_011028768|]
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MULTISPECIES: N-6 DNA methylase [Streptomyces]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
168-391 3.80e-45

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


:

Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 161.12  E-value: 3.80e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 168 AYEFLLGRHLDANPR---QYtLTPDPLADLMAELAGPA--RTVLDPACGTGSLLRAAAA-------TTRPGQELYGQESD 235
Cdd:COG0286    6 AYEYLLRKFAEESGKkagEF-YTPREVVRLMVELLDPKpgETVYDPACGSGGFLVEAAEylkehggDERKKLSLYGQEIN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 236 PalaaltalrlalstdATVRIAA---------------GDSLRADARTGLRADAALCHPPFNeRNWGHDELAYD--PRWE 298
Cdd:COG0286   85 P---------------TTYRLAKmnlllhgigdpnielGDTLSNDGDELEKFDVVLANPPFG-GKWKKEELKDDllGRFG 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 299 YGFPARTESELAWVQHALARVRDGGTVVVLMPPAAASRRSGRRVRADLLRRGALHAVIALPVGAAPPYNLPLHLWVLRRp 378
Cdd:COG0286  149 YGLPPKSNADLLFLQHILSLLKPGGRAAVVLPDGVLFRGAEKEIRKKLLENDLLEAIIGLPSNLFYNTGIPTCILFLTK- 227

                        250
                 ....*....|...
gi 499339060 379 ERAPAQPGVLLAD 391
Cdd:COG0286  228 GKPERTGKVLFID 240
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 550-648 9.37e-04

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


The actual alignment was detected with superfamily member cd16961:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 178  Bit Score: 40.83  E-value: 9.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 550 LTEPGDVVVPVLGG-GSVARVIDADtaGAALGRNLVLLRPDPAaLDPWFLAGFLRGTANHRQASSYASTA----TRLDVR 624
Cdd:cd16961   59 ILPKGDILISRSGTiGKVAIVKEND--KALLNQAVIVIRPKDE-VDSEFLYYFLKSPFGKKLIEGSAGSTqpnlNKSDLK 135

                         90       100
                 ....*....|....*....|....
gi 499339060 625 RLQLPRLPLDAQRGYGDRFRALDE 648
Cdd:cd16961  136 NLKIPLPPLEEQKKIANILDKLDA 159
PksD super family cl43841
Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites ...
 400-666 2.21e-03

Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites biosynthesis, transport and catabolism];


The actual alignment was detected with superfamily member COG3321:

Pssm-ID: 442550 [Multi-domain]  Cd Length: 1386  Bit Score: 41.40  E-value: 2.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  400 RGGPDWRSVRDAVLDAWTA---FDRTGRLDDRPGLARCLPVI----ELLDDDVDLAPARHLPPPTATGGTERLTDVRERL 472
Cdd:COG3321   825 RGEDELAQLLTALAQLWVAgvpVDWSALYPGRGRRRVPLPTYpfqrEDAAAALLAAALAAALAAAAALGALLLAALAAAL 904

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  473 DETLRLTAELAPAAPGTGRAALRRPLTTVGELARGGALVLRTGTNGGHARVPLLTDHDVLTGTGPSGTLPEGDEEPVLTE 552
Cdd:COG3321   905 AAALLALAAAAAAALALAAAALAALLALVALAAAAAALLALAAAAAAAAAALAAAEAGALLLLAAAAAAAAAAAAAAAAA 984

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  553 PGDVVVPVLGGGSVARVIDADTAGAALGRNLVLLRPDPAALDPWFLAGFLRGTANHRQASSYASTATRLDVRRLQLPRLP 632
Cdd:COG3321   985 AAAAAAAAAAALAAAAALALLAAAALLLAAAAAAAALLALAALLAAAAAALAAAAAAAAAAAALAALAAAAAAAAALALA 1064

                         250       260       270
                  ....*....|....*....|....*....|....
gi 499339060  633 LDAQRGYGDRFRALDEFERALRLAGRLGEQLARG 666
Cdd:COG3321  1065 LAALLLLAALAELALAAAALALAAALAAAALALA 1098
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
1-63 7.95e-03

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


:

Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 35.29  E-value: 7.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499339060   1 MQEHGTE-VTAAGIARLAGVGRAAVSNWRRRHaDFPRPVGGTETSPSFALADVEAWLRAQGKLA 63
Cdd:COG3311    1 MSLPPDRlLRLKEVAELLGVSRSTIYRLIKKG-EFPKPVKLGGRSVRWRESEVEAWLAARIAAS 63
 
Name Accession Description Interval E-value
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
168-391 3.80e-45

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


Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 161.12  E-value: 3.80e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 168 AYEFLLGRHLDANPR---QYtLTPDPLADLMAELAGPA--RTVLDPACGTGSLLRAAAA-------TTRPGQELYGQESD 235
Cdd:COG0286    6 AYEYLLRKFAEESGKkagEF-YTPREVVRLMVELLDPKpgETVYDPACGSGGFLVEAAEylkehggDERKKLSLYGQEIN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 236 PalaaltalrlalstdATVRIAA---------------GDSLRADARTGLRADAALCHPPFNeRNWGHDELAYD--PRWE 298
Cdd:COG0286   85 P---------------TTYRLAKmnlllhgigdpnielGDTLSNDGDELEKFDVVLANPPFG-GKWKKEELKDDllGRFG 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 299 YGFPARTESELAWVQHALARVRDGGTVVVLMPPAAASRRSGRRVRADLLRRGALHAVIALPVGAAPPYNLPLHLWVLRRp 378
Cdd:COG0286  149 YGLPPKSNADLLFLQHILSLLKPGGRAAVVLPDGVLFRGAEKEIRKKLLENDLLEAIIGLPSNLFYNTGIPTCILFLTK- 227

                        250
                 ....*....|...
gi 499339060 379 ERAPAQPGVLLAD 391
Cdd:COG0286  228 GKPERTGKVLFID 240
N6_Mtase pfam02384
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ...
 168-457 7.30e-28

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: 114.34  E-value: 7.30e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  168 AYEFLLGRHLDA---NPRQYtLTPDPLADLMAELAGPA--RTVLDPACGTGSLLRAAA------ATTRPGQELYGQESDP 236
Cdd:pfam02384   8 AYEYLLRKFAPNagkSGGEF-FTPREVSKLIVELLDPKpgESIYDPACGSGGFLIQAEkfvkehDGDTNDLSIYGQEKNP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  237 ALAALTAL--RLALSTDATVRIAAGDSLRADARTGL-RADAALCHPPFNERNWGHDELAYDPRW--EYGFPARTESELAW 311
Cdd:pfam02384  87 TTYRLARMnmILHGIEYDDFHIRHGDTLTSPKFEDDkKFDVVVANPPFSDKWDANDTLENDPRFrpAYGVAPKSNADLAF 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  312 VQHALARVRDGGTVVVLMPPAAASR-RSGRRVRADLLRRGALHAVIALPVGAAPPYNLPLHLWVLRRpERAPAQPGVLLA 390
Cdd:pfam02384 167 LQHIIYYLAPGGRAAVVLPNGVLFRgGAEGKIRKALVDKDLVETVIALPPNLFYNTSIPTCILFLTK-NKAERKGKVLFI 245

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499339060  391 DTGQ-FAGEGRGGPDWRSVRDAVLDAWTAFdrtgrlDDRPGLARCLPVIELLDDDVDLAPARHLPPPT 457
Cdd:pfam02384 246 DASNeFKKEGKLNILTDEHIEKIIDTFGEF------KDVDGFSKSATLEEIAANDYNLNVGRYVGTEE 307
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 550-648 9.37e-04

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


Pssm-ID: 341131 [Multi-domain]  Cd Length: 178  Bit Score: 40.83  E-value: 9.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 550 LTEPGDVVVPVLGG-GSVARVIDADtaGAALGRNLVLLRPDPAaLDPWFLAGFLRGTANHRQASSYASTA----TRLDVR 624
Cdd:cd16961   59 ILPKGDILISRSGTiGKVAIVKEND--KALLNQAVIVIRPKDE-VDSEFLYYFLKSPFGKKLIEGSAGSTqpnlNKSDLK 135

                         90       100
                 ....*....|....*....|....
gi 499339060 625 RLQLPRLPLDAQRGYGDRFRALDE 648
Cdd:cd16961  136 NLKIPLPPLEEQKKIANILDKLDA 159
PksD COG3321
Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites ...
 400-666 2.21e-03

Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 442550 [Multi-domain]  Cd Length: 1386  Bit Score: 41.40  E-value: 2.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  400 RGGPDWRSVRDAVLDAWTA---FDRTGRLDDRPGLARCLPVI----ELLDDDVDLAPARHLPPPTATGGTERLTDVRERL 472
Cdd:COG3321   825 RGEDELAQLLTALAQLWVAgvpVDWSALYPGRGRRRVPLPTYpfqrEDAAAALLAAALAAALAAAAALGALLLAALAAAL 904

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  473 DETLRLTAELAPAAPGTGRAALRRPLTTVGELARGGALVLRTGTNGGHARVPLLTDHDVLTGTGPSGTLPEGDEEPVLTE 552
Cdd:COG3321   905 AAALLALAAAAAAALALAAAALAALLALVALAAAAAALLALAAAAAAAAAALAAAEAGALLLLAAAAAAAAAAAAAAAAA 984

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  553 PGDVVVPVLGGGSVARVIDADTAGAALGRNLVLLRPDPAALDPWFLAGFLRGTANHRQASSYASTATRLDVRRLQLPRLP 632
Cdd:COG3321   985 AAAAAAAAAAALAAAAALALLAAAALLLAAAAAAAALLALAALLAAAAAALAAAAAAAAAAAALAALAAAAAAAAALALA 1064

                         250       260       270
                  ....*....|....*....|....*....|....
gi 499339060  633 LDAQRGYGDRFRALDEFERALRLAGRLGEQLARG 666
Cdd:COG3321  1065 LAALLLLAALAELALAAAALALAAALAAAALALA 1098
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
1-63 7.95e-03

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 35.29  E-value: 7.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499339060   1 MQEHGTE-VTAAGIARLAGVGRAAVSNWRRRHaDFPRPVGGTETSPSFALADVEAWLRAQGKLA 63
Cdd:COG3311    1 MSLPPDRlLRLKEVAELLGVSRSTIYRLIKKG-EFPKPVKLGGRSVRWRESEVEAWLAARIAAS 63
 
Name Accession Description Interval E-value
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
168-391 3.80e-45

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


Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 161.12  E-value: 3.80e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 168 AYEFLLGRHLDANPR---QYtLTPDPLADLMAELAGPA--RTVLDPACGTGSLLRAAAA-------TTRPGQELYGQESD 235
Cdd:COG0286    6 AYEYLLRKFAEESGKkagEF-YTPREVVRLMVELLDPKpgETVYDPACGSGGFLVEAAEylkehggDERKKLSLYGQEIN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 236 PalaaltalrlalstdATVRIAA---------------GDSLRADARTGLRADAALCHPPFNeRNWGHDELAYD--PRWE 298
Cdd:COG0286   85 P---------------TTYRLAKmnlllhgigdpnielGDTLSNDGDELEKFDVVLANPPFG-GKWKKEELKDDllGRFG 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 299 YGFPARTESELAWVQHALARVRDGGTVVVLMPPAAASRRSGRRVRADLLRRGALHAVIALPVGAAPPYNLPLHLWVLRRp 378
Cdd:COG0286  149 YGLPPKSNADLLFLQHILSLLKPGGRAAVVLPDGVLFRGAEKEIRKKLLENDLLEAIIGLPSNLFYNTGIPTCILFLTK- 227

                        250
                 ....*....|...
gi 499339060 379 ERAPAQPGVLLAD 391
Cdd:COG0286  228 GKPERTGKVLFID 240
N6_Mtase pfam02384
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ...
 168-457 7.30e-28

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: 114.34  E-value: 7.30e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  168 AYEFLLGRHLDA---NPRQYtLTPDPLADLMAELAGPA--RTVLDPACGTGSLLRAAA------ATTRPGQELYGQESDP 236
Cdd:pfam02384   8 AYEYLLRKFAPNagkSGGEF-FTPREVSKLIVELLDPKpgESIYDPACGSGGFLIQAEkfvkehDGDTNDLSIYGQEKNP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  237 ALAALTAL--RLALSTDATVRIAAGDSLRADARTGL-RADAALCHPPFNERNWGHDELAYDPRW--EYGFPARTESELAW 311
Cdd:pfam02384  87 TTYRLARMnmILHGIEYDDFHIRHGDTLTSPKFEDDkKFDVVVANPPFSDKWDANDTLENDPRFrpAYGVAPKSNADLAF 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  312 VQHALARVRDGGTVVVLMPPAAASR-RSGRRVRADLLRRGALHAVIALPVGAAPPYNLPLHLWVLRRpERAPAQPGVLLA 390
Cdd:pfam02384 167 LQHIIYYLAPGGRAAVVLPNGVLFRgGAEGKIRKALVDKDLVETVIALPPNLFYNTSIPTCILFLTK-NKAERKGKVLFI 245

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499339060  391 DTGQ-FAGEGRGGPDWRSVRDAVLDAWTAFdrtgrlDDRPGLARCLPVIELLDDDVDLAPARHLPPPT 457
Cdd:pfam02384 246 DASNeFKKEGKLNILTDEHIEKIIDTFGEF------KDVDGFSKSATLEEIAANDYNLNVGRYVGTEE 307
YtxK COG0827
Adenine-specific DNA N6-methylase [Replication, recombination and repair];
166-391 3.38e-07

Adenine-specific DNA N6-methylase [Replication, recombination and repair];


Pssm-ID: 440589 [Multi-domain]  Cd Length: 327  Bit Score: 52.64  E-value: 3.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 166 RKAYEFLLGRHLDANPR-QYTLTPDPLADLMAELAGPAR-----TVLDPACGTGSLLRAAAATTRPGQELYGQESDPALa 239
Cdd:COG0827   74 RKALQLALLKGMKESVQpNHQMTPDAIGLLIGYLVEKFTkkeglRILDPAVGTGNLLTTVLNQLKKKVNAYGVEVDDLL- 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 240 altalrlalstdatVRIAA--GDSLR-------ADARTGLR---ADAALCHPPfnernWGhdelaYDPRWE--YGFPART 305
Cdd:COG0827  153 --------------IRLAAvlANLQGhpvelfhQDALQPLLidpVDVVISDLP-----VG-----YYPNDEraKRFKLKA 208

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 306 ESELAWVQH-----ALARVRDGGTVVVLMPPAAASRRSGRRVRADLLRRGALHAVIALPVGAappYNLPLH---LWVLRR 377
Cdd:COG0827  209 DEGHSYAHHlfieqSLNYLKPGGYLFFLVPSNLFESDQAAQLREFLKEKAHIQGLIQLPESL---FKNEAAaksILILQK 285

                        250
                 ....*....|....*
gi 499339060 378 PERAPAQPG-VLLAD 391
Cdd:COG0827  286 KGEGTKQPKeVLLAQ 300
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
183-289 7.85e-05

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 44.12  E-value: 7.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 183 QYTlTPDPLADLMAELAG-----PARTVLDPACGTGSLLRAAAAttRPGQELYGQESDPALAALTALRLAlstDATVRIa 257
Cdd:COG2263   23 QYP-TPAELAAELLHLAYlrgdiEGKTVLDLGCGTGMLAIGAAL--LGAKKVVGVDIDPEALEIARENAE---RLGVRV- 95

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 499339060 258 agDSLRADART---GLRADAALCHPPFNERNWGHD 289
Cdd:COG2263   96 --DFIRADVTRiplGGSVDTVVMNPPFGAQRRHAD 128
RMtype1_S_TRD-CR_like cd16961
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 550-648 9.37e-04

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


Pssm-ID: 341131 [Multi-domain]  Cd Length: 178  Bit Score: 40.83  E-value: 9.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 550 LTEPGDVVVPVLGG-GSVARVIDADtaGAALGRNLVLLRPDPAaLDPWFLAGFLRGTANHRQASSYASTA----TRLDVR 624
Cdd:cd16961   59 ILPKGDILISRSGTiGKVAIVKEND--KALLNQAVIVIRPKDE-VDSEFLYYFLKSPFGKKLIEGSAGSTqpnlNKSDLK 135

                         90       100
                 ....*....|....*....|....
gi 499339060 625 RLQLPRLPLDAQRGYGDRFRALDE 648
Cdd:cd16961  136 NLKIPLPPLEEQKKIANILDKLDA 159
RMtype1_S_EcoR124I-TRD2-CR2_like cd17249
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 593-671 2.03e-03

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: 39.74  E-value: 2.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 593 LDPWFLAGFLRGTANH--RQASSYASTATRLDVRRLQ---LPRLPLDAQRGYGDRFRALDEFERALRLAGRLGEQLARGM 667
Cdd:cd17249  102 IDPEFLLYALKANEDRilSLVDKAGHGTGSLDTDDLKnlpIPLPPLEEQRRIAAILDALDALIDLLERKLAKLEELLKAL 181


                 ....
gi 499339060 668 YDGL 671
Cdd:cd17249  182 MQAL 185
PksD COG3321
Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites ...
 400-666 2.21e-03

Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 442550 [Multi-domain]  Cd Length: 1386  Bit Score: 41.40  E-value: 2.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  400 RGGPDWRSVRDAVLDAWTA---FDRTGRLDDRPGLARCLPVI----ELLDDDVDLAPARHLPPPTATGGTERLTDVRERL 472
Cdd:COG3321   825 RGEDELAQLLTALAQLWVAgvpVDWSALYPGRGRRRVPLPTYpfqrEDAAAALLAAALAAALAAAAALGALLLAALAAAL 904

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  473 DETLRLTAELAPAAPGTGRAALRRPLTTVGELARGGALVLRTGTNGGHARVPLLTDHDVLTGTGPSGTLPEGDEEPVLTE 552
Cdd:COG3321   905 AAALLALAAAAAAALALAAAALAALLALVALAAAAAALLALAAAAAAAAAALAAAEAGALLLLAAAAAAAAAAAAAAAAA 984

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060  553 PGDVVVPVLGGGSVARVIDADTAGAALGRNLVLLRPDPAALDPWFLAGFLRGTANHRQASSYASTATRLDVRRLQLPRLP 632
Cdd:COG3321   985 AAAAAAAAAAALAAAAALALLAAAALLLAAAAAAAALLALAALLAAAAAALAAAAAAAAAAAALAALAAAAAAAAALALA 1064

                         250       260       270
                  ....*....|....*....|....*....|....
gi 499339060  633 LDAQRGYGDRFRALDEFERALRLAGRLGEQLARG 666
Cdd:COG3321  1065 LAALLLLAALAELALAAAALALAAALAAAALALA 1098
RMtype1_S_BceB55ORF5615P-TRD2-CR2_like cd17512
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 564-669 6.15e-03

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: 38.36  E-value: 6.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 564 GSVARVIDADtAGAALGRNLVLLRPDPAALDPWFLAGFL-------------RGTANhrQASsyastATRLDVRRLQLPR 630
Cdd:cd17512   84 GKVVRVPKEA-DGALLNQNAVKIRPKKGILDQSFLFYNLkserfknyiesiaRGNAN--QAS-----ITLGDIKKFKFLL 155

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 499339060 631 LPLDAQRGYGDRFRALDEFERALRLAGRLGEQLARGMYD 669
Cdd:cd17512  156 PPLEEQKKIASILSAYDDLIENNEKRIKLLEQMKQALYQ 194
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 191-216 6.76e-03

tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440663 [Multi-domain]  Cd Length: 172  Bit Score: 38.01  E-value: 6.76e-03
                         10        20
                 ....*....|....*....|....*...
gi 499339060 191 LADLMAELAG--PARTVLDPACGTGSLL 216
Cdd:COG1041   14 LARALVNLAGakEGDTVLDPFCGTGTIL 41
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
1-63 7.95e-03

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 35.29  E-value: 7.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499339060   1 MQEHGTE-VTAAGIARLAGVGRAAVSNWRRRHaDFPRPVGGTETSPSFALADVEAWLRAQGKLA 63
Cdd:COG3311    1 MSLPPDRlLRLKEVAELLGVSRSTIYRLIKKG-EFPKPVKLGGRSVRWRESEVEAWLAARIAAS 63
RMtype1_S_SonII-TRD2-CR2_like cd17246
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 552-669 9.97e-03

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: 37.89  E-value: 9.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499339060 552 EPGDVVVPVLGG-GSVArVIDADTaGAALGRNLVLLRPDPAALDPWFLAGFLRGTANHRQASSYASTATRL-----DVRR 625
Cdd:cd17246   64 KKGDILFSIIGTiGRVA-IVPEDL-PANINQAVALIRPKKEKIDPKYLLYYLNSPIIQKQIEKNAVGGTQKnlslgDLKN 141

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 499339060 626 LQLPRLPLDAQRGYGDRFRALDEFERALRLAGRLGEQLARGMYD 669
Cdd:cd17246  142 LKIPLPPLEEQKRIAAILDSLDALIDKLEQKLEKLEDLKKGLMQ 185
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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