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Conserved domains on  [gi|2059656015|tpg|DAV66451|]
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MAG TPA: adenine specific DNA methyltransferase [Caudoviricetes sp.]

Protein Classification

site-specific DNA-methyltransferase( domain architecture ID 11611662)

site-specific DNA-methyltransferase catalyzes specific methylation on cytosine or adenine on both strands and protects the DNA from cleavage by endonuclease

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
166-388 1.67e-69

DNA modification methylase [Replication, recombination and repair];


:

Pssm-ID: 440623  Cd Length: 236  Bit Score: 219.41  E-value: 1.67e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 166 RLVCGDSTkaetyDLL--MGSTKANLVITDPPYNVNYEGSAG-KIKNDNMADDAFYNFLLAAYTQMHSAMADDASIYVFH 242
Cdd:COG0863     1 RLICGDCL-----EVLkeLPDESVDLIVTDPPYNLGKKYGLGrREIGNELSFEEYLEFLREWLAECYRVLKPGGSLYVNI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 243 ADTEGLNFRRAFADAGFYLSGCCIWKKQSLVLGRSP--YQWQHEPCLYGWKkNGKHQW--------YTGRKETTIWEFD- 311
Cdd:COG0863    76 GDRYISRLIAALRDAGFKLRNEIIWRKPNGVPGPSKrrFRNSHEYILWFTK-GKKYTFnvdavksiEDGRNPSDVWDIPg 154

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2059656015 312 -KPKKNGDHPTMKPIPLLAYPIMNSTMSNAVVLDPFGGSGSTLIACEQTDRICYTVELDEKFCDVIVKRYIEQIGSSD 388
Cdd:COG0863   155 vTPKERKGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVARRRLEEATGLEF 232
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 13-97 1.11e-52

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci.


:

Pssm-ID: 319258 [Multi-domain]  Cd Length: 85  Bit Score: 170.48  E-value: 1.11e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015  13 PADYNPRKDLKPGDAEYEKLKRSIEQFGYVEPVIWNKTTGRVVGGHQRLKVLIDMGMTEVDCVVVELTEEKEKALNIALN 92
Cdd:cd16401     1 PAPYNPRKDLKPGDKEYEKLKESIEEFGLVDPLIVNKRTNVLIGGHQRLKVLKELGYTEVPVVVVDLDEEKEKALNIALN 80


                  ....*
gi 2059656015  93 KISGE 97
Cdd:cd16401    81 KISGE 85
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
166-388 1.67e-69

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 219.41  E-value: 1.67e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 166 RLVCGDSTkaetyDLL--MGSTKANLVITDPPYNVNYEGSAG-KIKNDNMADDAFYNFLLAAYTQMHSAMADDASIYVFH 242
Cdd:COG0863     1 RLICGDCL-----EVLkeLPDESVDLIVTDPPYNLGKKYGLGrREIGNELSFEEYLEFLREWLAECYRVLKPGGSLYVNI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 243 ADTEGLNFRRAFADAGFYLSGCCIWKKQSLVLGRSP--YQWQHEPCLYGWKkNGKHQW--------YTGRKETTIWEFD- 311
Cdd:COG0863    76 GDRYISRLIAALRDAGFKLRNEIIWRKPNGVPGPSKrrFRNSHEYILWFTK-GKKYTFnvdavksiEDGRNPSDVWDIPg 154

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2059656015 312 -KPKKNGDHPTMKPIPLLAYPIMNSTMSNAVVLDPFGGSGSTLIACEQTDRICYTVELDEKFCDVIVKRYIEQIGSSD 388
Cdd:COG0863   155 vTPKERKGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVARRRLEEATGLEF 232
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 13-97 1.11e-52

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci.


Pssm-ID: 319258 [Multi-domain]  Cd Length: 85  Bit Score: 170.48  E-value: 1.11e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015  13 PADYNPRKDLKPGDAEYEKLKRSIEQFGYVEPVIWNKTTGRVVGGHQRLKVLIDMGMTEVDCVVVELTEEKEKALNIALN 92
Cdd:cd16401     1 PAPYNPRKDLKPGDKEYEKLKESIEEFGLVDPLIVNKRTNVLIGGHQRLKVLKELGYTEVPVVVVDLDEEKEKALNIALN 80


                  ....*
gi 2059656015  93 KISGE 97
Cdd:cd16401    81 KISGE 85
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 188-378 2.81e-21

DNA methylase; Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases.


Pssm-ID: 396230 [Multi-domain]  Cd Length: 221  Bit Score: 91.31  E-value: 2.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 188 NLVITDPPYNVnyeGSAGKIKNDNMADDAFYNFLLAAYTQMHSAMADDASIYVFhADTEGLNFRRAFADA---GFYLSGC 264
Cdd:pfam01555   2 DLIVTDPPYNL---GKDYGQWDDKDSIEEYLEWLEEWLKEVRRVLKPGGSIFIN-IGDSNIKSLKALALEilgIFKLLND 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 265 CIWKKQS-----------------LVLGRS----PYQWQHEPCLYGWKKNGKHQWYT--GRKETTIWEFD-------KPK 314
Cdd:pfam01555  78 IIWRKPNgmpnsngerftpaheyiLWFSKTkkykTFNYDAIKVPYDEKDKLKKRGSEpnGKPIGDVWDFSrvqpsekESG 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2059656015 315 KNGDHPTMKPIPLLAYPIMNSTMSNAVVLDPFGGSGSTLIACEQTDRICYTVELDEKFCDVIVK 378
Cdd:pfam01555 158 GNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVEIAKE 221
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 3-139 2.69e-17

Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441084 [Multi-domain]  Cd Length: 241  Bit Score: 80.80  E-value: 2.69e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015   3 IEKKNTADLLPADYNPRKDLkpGDAEYEKLKRSIEQFGYVEPVIWNKT-TGR--VVGGHQRLKVLIDMGMTEVDCVVVEL 79
Cdd:COG1475     7 IREIPIDKIVPSPYNPRRTF--DEEALEELAASIREHGLLQPILVRPLgDGRyeIIAGERRLRAAKLLGLETVPAIVRDL 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2059656015  80 TEEKEKALNIALNKISGEWDKDKLALLIADLQgADFDVS------LTGFDPAELDD---LLDVGADAKD 139
Cdd:COG1475    85 DDEEALELALIENLQREDLNPLEEARAYQRLL-EEFGLTqeeiaeRLGKSRSEVSNllrLLKLPPEVQE 152
PRK13699 PRK13699
putative methylase; Provisional
 188-372 9.18e-17

putative methylase; Provisional


Pssm-ID: 184255  Cd Length: 227  Bit Score: 78.72  E-value: 9.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 188 NLVITDPPYNVNYEGSAGK-IKNDNMADdafynFLLAAYTQMHSAMADDASIYVFHADTEGLNFRRAFADAGFYLSGCCI 266
Cdd:PRK13699   22 DFILTDPPYLVGFRDRQGRtIAGDKTDE-----WLQPACNEMYRVLKKDALMVSFYGWNRVDRFMAAWKNAGFSVVGHLV 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 267 WKKQS----------------LVLGRSPYQWQHEPCLYGWKkngkhqwYTGrkettiwefdkpkkNGDHPTMKPIPLLAY 330
Cdd:PRK13699   97 FTKNYtskaayvgyrhecayiLAKGRPALPQNPLPDVLGWK-------YSG--------------NRHHPTEKPVTSLQP 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2059656015 331 PIMNSTMSNAVVLDPFGGSGSTLIACEQTDRICYTVELDEKF 372
Cdd:PRK13699  156 LIESFTHPNAIVLDPFAGSGSTCVAALQSGRRYIGIELLEQY 197
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 4-92 8.24e-14

ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5-->3 exonuclease activity.


Pssm-ID: 214678 [Multi-domain]  Cd Length: 89  Bit Score: 66.56  E-value: 8.24e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015    4 EKKNTADLLPADYNPRKDlkpGDAEYEKLKRSIEQFGYVEPVIWNKTTGR--VVGGHQRLKVLIDMGMTEVDCVVVELTE 81
Cdd:smart00470   1 VEVPIEKLRPNPDQPRLT---SEESLEELAESIKENGLLQPIIVRPNDGRyeIIDGERRLRAAKLLGLKEVPVIVRDLDD 77

                           90
                   ....*....|.
gi 2059656015   82 EKEKALNIALN 92
Cdd:smart00470  78 EEAIALSLEEN 88
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 4-92 5.65e-11

ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid protein ParB and mammalian Sulfiredoxin-1. ParB is involved in chromosome partition. It localizes to both poles of the predivisional cell following completion of DNA replication. Sulfiredoxin-1 contributes to oxidative stress resistance by reducing cysteine-sulfinic acid formed under exposure to oxidants in the peroxiredoxins PRDX1, PRDX2, PRDX3 and PRDX4.


Pssm-ID: 426651 [Multi-domain]  Cd Length: 90  Bit Score: 58.44  E-value: 5.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015   4 EKKNTADLLPADYNPRKDLKPgdaEYEKLKRSIEQFGYVEPVIWNKT-TGR--VVGGHQRLKVLIDMGMTEVDCVVVELT 80
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKDSEE---SLEELAASIKKRGLLQPIIVRKTpDGRyeIIAGERRLRAAKLLGLKEVPVIVREID 77

                          90
                  ....*....|..
gi 2059656015  81 EEKEKALNIALN 92
Cdd:pfam02195  78 DEEAIALSLIEN 89
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
166-388 1.67e-69

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 219.41  E-value: 1.67e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 166 RLVCGDSTkaetyDLL--MGSTKANLVITDPPYNVNYEGSAG-KIKNDNMADDAFYNFLLAAYTQMHSAMADDASIYVFH 242
Cdd:COG0863     1 RLICGDCL-----EVLkeLPDESVDLIVTDPPYNLGKKYGLGrREIGNELSFEEYLEFLREWLAECYRVLKPGGSLYVNI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 243 ADTEGLNFRRAFADAGFYLSGCCIWKKQSLVLGRSP--YQWQHEPCLYGWKkNGKHQW--------YTGRKETTIWEFD- 311
Cdd:COG0863    76 GDRYISRLIAALRDAGFKLRNEIIWRKPNGVPGPSKrrFRNSHEYILWFTK-GKKYTFnvdavksiEDGRNPSDVWDIPg 154

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2059656015 312 -KPKKNGDHPTMKPIPLLAYPIMNSTMSNAVVLDPFGGSGSTLIACEQTDRICYTVELDEKFCDVIVKRYIEQIGSSD 388
Cdd:COG0863   155 vTPKERKGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVARRRLEEATGLEF 232
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 13-97 1.11e-52

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci.


Pssm-ID: 319258 [Multi-domain]  Cd Length: 85  Bit Score: 170.48  E-value: 1.11e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015  13 PADYNPRKDLKPGDAEYEKLKRSIEQFGYVEPVIWNKTTGRVVGGHQRLKVLIDMGMTEVDCVVVELTEEKEKALNIALN 92
Cdd:cd16401     1 PAPYNPRKDLKPGDKEYEKLKESIEEFGLVDPLIVNKRTNVLIGGHQRLKVLKELGYTEVPVVVVDLDEEKEKALNIALN 80


                  ....*
gi 2059656015  93 KISGE 97
Cdd:cd16401    81 KISGE 85
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 188-378 2.81e-21

DNA methylase; Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases.


Pssm-ID: 396230 [Multi-domain]  Cd Length: 221  Bit Score: 91.31  E-value: 2.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 188 NLVITDPPYNVnyeGSAGKIKNDNMADDAFYNFLLAAYTQMHSAMADDASIYVFhADTEGLNFRRAFADA---GFYLSGC 264
Cdd:pfam01555   2 DLIVTDPPYNL---GKDYGQWDDKDSIEEYLEWLEEWLKEVRRVLKPGGSIFIN-IGDSNIKSLKALALEilgIFKLLND 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 265 CIWKKQS-----------------LVLGRS----PYQWQHEPCLYGWKKNGKHQWYT--GRKETTIWEFD-------KPK 314
Cdd:pfam01555  78 IIWRKPNgmpnsngerftpaheyiLWFSKTkkykTFNYDAIKVPYDEKDKLKKRGSEpnGKPIGDVWDFSrvqpsekESG 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2059656015 315 KNGDHPTMKPIPLLAYPIMNSTMSNAVVLDPFGGSGSTLIACEQTDRICYTVELDEKFCDVIVK 378
Cdd:pfam01555 158 GNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVEIAKE 221
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 3-139 2.69e-17

Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441084 [Multi-domain]  Cd Length: 241  Bit Score: 80.80  E-value: 2.69e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015   3 IEKKNTADLLPADYNPRKDLkpGDAEYEKLKRSIEQFGYVEPVIWNKT-TGR--VVGGHQRLKVLIDMGMTEVDCVVVEL 79
Cdd:COG1475     7 IREIPIDKIVPSPYNPRRTF--DEEALEELAASIREHGLLQPILVRPLgDGRyeIIAGERRLRAAKLLGLETVPAIVRDL 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2059656015  80 TEEKEKALNIALNKISGEWDKDKLALLIADLQgADFDVS------LTGFDPAELDD---LLDVGADAKD 139
Cdd:COG1475    85 DDEEALELALIENLQREDLNPLEEARAYQRLL-EEFGLTqeeiaeRLGKSRSEVSNllrLLKLPPEVQE 152
ParB_N_like_MT cd16403
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 7-95 2.77e-17

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci.


Pssm-ID: 319260 [Multi-domain]  Cd Length: 88  Bit Score: 76.34  E-value: 2.77e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015   7 NTADLLPADYNPRKDlkpGDAEYEKLKRSIEQFGYVEPVIWNKTtGRVVGGHQRLKVLIDMGMTEVDCVVVE-LTEEKEK 85
Cdd:cd16403     1 PIDDLKPYPRNARTH---SEKQIEQLAASIREFGFTNPILVDED-GVIIAGHGRLLAAKLLGLKEVPVIRLDhLSEAQKR 76

                          90
                  ....*....|
gi 2059656015  86 ALNIALNKIS 95
Cdd:cd16403    77 AYRIADNRLA 86
PRK13699 PRK13699
putative methylase; Provisional
 188-372 9.18e-17

putative methylase; Provisional


Pssm-ID: 184255  Cd Length: 227  Bit Score: 78.72  E-value: 9.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 188 NLVITDPPYNVNYEGSAGK-IKNDNMADdafynFLLAAYTQMHSAMADDASIYVFHADTEGLNFRRAFADAGFYLSGCCI 266
Cdd:PRK13699   22 DFILTDPPYLVGFRDRQGRtIAGDKTDE-----WLQPACNEMYRVLKKDALMVSFYGWNRVDRFMAAWKNAGFSVVGHLV 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 267 WKKQS----------------LVLGRSPYQWQHEPCLYGWKkngkhqwYTGrkettiwefdkpkkNGDHPTMKPIPLLAY 330
Cdd:PRK13699   97 FTKNYtskaayvgyrhecayiLAKGRPALPQNPLPDVLGWK-------YSG--------------NRHHPTEKPVTSLQP 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2059656015 331 PIMNSTMSNAVVLDPFGGSGSTLIACEQTDRICYTVELDEKF 372
Cdd:PRK13699  156 LIESFTHPNAIVLDPFAGSGSTCVAALQSGRRYIGIELLEQY 197
ParB_N_like_MT cd16402
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 10-95 1.10e-16

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains and DUF4417. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci.


Pssm-ID: 319259 [Multi-domain]  Cd Length: 87  Bit Score: 74.57  E-value: 1.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015  10 DLLPADYNPRKDlkpgDAEYEKLKRSIEQFGYVEPVIWNKTtGRVVGGHQRLKVLIDMGMTEVDCVVV-ELTEEKEKALN 88
Cdd:cd16402     4 ELKPYENNPRNN----DKAVEKVAESIKEFGFLVPIVVDKN-NVIVAGHTRYKAAKRLGLEEVPCIVAdDLTEEQIKAFR 78


                  ....*..
gi 2059656015  89 IALNKIS 95
Cdd:cd16402    79 LADNKTS 85
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 4-92 8.24e-14

ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5-->3 exonuclease activity.


Pssm-ID: 214678 [Multi-domain]  Cd Length: 89  Bit Score: 66.56  E-value: 8.24e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015    4 EKKNTADLLPADYNPRKDlkpGDAEYEKLKRSIEQFGYVEPVIWNKTTGR--VVGGHQRLKVLIDMGMTEVDCVVVELTE 81
Cdd:smart00470   1 VEVPIEKLRPNPDQPRLT---SEESLEELAESIKENGLLQPIIVRPNDGRyeIIDGERRLRAAKLLGLKEVPVIVRDLDD 77

                           90
                   ....*....|.
gi 2059656015   82 EKEKALNIALN 92
Cdd:smart00470  78 EEAIALSLEEN 88
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 4-92 5.65e-11

ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid protein ParB and mammalian Sulfiredoxin-1. ParB is involved in chromosome partition. It localizes to both poles of the predivisional cell following completion of DNA replication. Sulfiredoxin-1 contributes to oxidative stress resistance by reducing cysteine-sulfinic acid formed under exposure to oxidants in the peroxiredoxins PRDX1, PRDX2, PRDX3 and PRDX4.


Pssm-ID: 426651 [Multi-domain]  Cd Length: 90  Bit Score: 58.44  E-value: 5.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015   4 EKKNTADLLPADYNPRKDLKPgdaEYEKLKRSIEQFGYVEPVIWNKT-TGR--VVGGHQRLKVLIDMGMTEVDCVVVELT 80
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKDSEE---SLEELAASIKKRGLLQPIIVRKTpDGRyeIIAGERRLRAAKLLGLKEVPVIVREID 77

                          90
                  ....*....|..
gi 2059656015  81 EEKEKALNIALN 92
Cdd:pfam02195  78 DEEAIALSLIEN 89
ParB_N_like_MT cd16844
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 26-78 1.98e-09

ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain; This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains and DUF4417. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci.


Pssm-ID: 319272 [Multi-domain]  Cd Length: 54  Bit Score: 53.04  E-value: 1.98e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2059656015  26 DAEYEKLKRSIEQFGYVEPVIWNKTtGRVVGGHQRLKVLIDMGMTEVDCVVVE 78
Cdd:cd16844     3 DAQIERVAASIREFGFRVPVLIDKD-GEIVDGHLRLEAARRLGLETVPVIRVD 54
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 22-82 2.94e-08

pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ParB acts in a plasmid partitioning system made up of 3 parts: AspA, ParA motor protein, and ParB, which links ParA to the protein-DNA superhelix. As demonstrated in Sulfolobus, AspA spreads along DNA, which allows ParB binding, and links to the Walker-motif containing ParA motor protein. The Sulfolobus ParB C-terminal domain resembles eukaryotic segregation protein CenpA, and other histones. This family is related to the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system and related proteins.


Pssm-ID: 319261 [Multi-domain]  Cd Length: 69  Bit Score: 50.35  E-value: 2.94e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2059656015  22 LKPGDAEYEKLKRSIEQFGYVEPVIWNkTTGRVVGGHQRLKVLIDMGMTEVDCVVVELTEE 82
Cdd:cd16404    10 PNPTNEEFEELKESIRKNGIIVPIIVD-QDGVIIDGHHRYRIAKELGIKEVPVIVYDFDDE 69
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
184-379 2.91e-07

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 51.65  E-value: 2.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 184 STKANLVITDPPYNVnyegsaGKiKNDNMAD----DAFYNFLLAAYTQMHSAMADDASIYVFhADTEGLNFRRAFADAGF 259
Cdd:PRK11524   25 SESVDLIFADPPYNI------GK-NFDGLIEawkeDLFIDWLYEWIDECHRVLKKQGTMYIM-NSTENMPFIDLYCRKLF 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 260 YLSGCCIWK-KQSLVLGRSPYQWQHEPCLYGwKKNGKHQWY----------TGRKETTI-------------------WE 309
Cdd:PRK11524   97 TIKSRIVWSyDSSGVQAKKYFGSMYEPILMM-VKDAKNYTFngdailveakTGAKRALIdyrknppqpyntqkvpgnvWD 175

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2059656015 310 FDKPKKNGD----HPTMKPIPLLAYPIMNSTMSNAVVLDPFGGSGSTLIACEQTDRICYTVELDEKFCDVIVKR 379
Cdd:PRK11524  176 FPRVRYLMDeyenHPTQKPEALLKRIILASSNPGDIVLDPFAGSFTTGAVAKASGRKFIGIEINSEYIKMGLRR 249
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 26-75 6.04e-06

ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain/Sulfiredoxin (Srx) superfamily contains proteins with diverse activities. Many of the families are involved in segregation and competition between plasmids and chromosomes. Several families share similar activities with the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system. Also within this superfamily is sulfiredoxin (Srx; reactivator of oxidatively inactivated 2-cys peroxiredoxins), RepB N-terminal domain (plasmid segregation replication protein B like protein), nucleoid occlusion protein, KorB N-terminal domain partition protein of low copy number plasmid RK2, irbB (immunoglobulin-binding regulator that activates eib genes), N-terminal domain of sopB protein (promotes proper partitioning of F1 plasmid), fertility inhibition factors OSA and FiwA,DNA sulfur modification protein DndB, and a ParB-like toxin domain. Other activities includes a StrR (regulator in the streptomycin biosynthetic gene cluster), and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators sbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ). Nuclease activity has also been reported in Arabidopsis Srx.


Pssm-ID: 319246 [Multi-domain]  Cd Length: 54  Bit Score: 43.35  E-value: 6.04e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2059656015  26 DAEYEKLKRSIEQFGYVEPVIWNKTTG---RVVGGHQRLKVLIDMGMTEVDCV 75
Cdd:cd16387     2 EEELEELAESIREHGVLQPIIVRPLPDgryEIIAGERRWRAAKLAGLTTIPVV 54
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 26-82 7.54e-06

ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning systems; This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA ("spreading", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci.


Pssm-ID: 319264 [Multi-domain]  Cd Length: 86  Bit Score: 44.05  E-value: 7.54e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015  26 DAEYEKLKRSIEQFGYVEPVIWNKTTGR---VVGGHQRLKVLIDMGMTEVDCVVVELTEE 82
Cdd:cd16407    17 DEEMEELVESIKENGVLTPIIVRPREDGgyeIISGHRRKRACELAGLETIPVIVREMDDD 76
Mod COG2189
Adenine specific DNA methylase Mod [Replication, recombination and repair];
290-408 1.92e-05

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


Pssm-ID: 441792 [Multi-domain]  Cd Length: 491  Bit Score: 46.69  E-value: 1.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059656015 290 WKKNGKHQWY---------TGRKETTIW-----------EFDKPKKNGDHPTMKPIPLLAYPIMNSTMSNAVVLDPFGGS 349
Cdd:COG2189   252 FGKDGNGVPRrkryldevkKGVVPTTIWddigtnqngtkELKELFGGKVFDTPKPEKLLKRIIEIATNPGDLVLDFFAGS 331

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2059656015 350 GSTLIACEQ------TDRICYTVELDEKFCDVIVKRyIEQIGSSDGVTVQRDGLTYKYSEVANEN 408
Cdd:COG2189   332 GTTAHAVMKlnaedgGNRRFILVQLGEYADTVTKER-LRRVIDGISKGVGQGGGGFRYYELATAL 395
 
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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