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Conserved domains on  [gi|1826332662|ref|WP_167096016|]
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DNA methyltransferase [Parvibaculum indicum]

Protein Classification

site-specific DNA-methyltransferase( domain architecture ID 11611687)

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];
174-418 1.40e-64

DNA modification methylase [Replication, recombination and repair];


:

Pssm-ID: 440623  Cd Length: 236  Bit Score: 207.08  E-value: 1.40e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 174 RLLCADARDgqaWARLMDGETAEMVFTDPPYNVPVEGHVSGlgahhhaefAMASGEMSREAFQAFLTEVLGNMAAQARDG 253
Cdd:COG0863     1 RLICGDCLE---VLKELPDESVDLIVTDPPYNLGKKYGLGR---------REIGNELSFEEYLEFLREWLAECYRVLKPG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 254 SLHYVCMDWRHLGELLDAGKEVYREMKNLCVWTKSNGGMG---SLYRSQHELVGVFKKGKaPHINNVELGK---HGRYRS 327
Cdd:COG0863    69 GSLYVNIGDRYISRLIAALRDAGFKLRNEIIWRKPNGVPGpskRRFRNSHEYILWFTKGK-KYTFNVDAVKsieDGRNPS 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 328 NVWayagmnSFGGDRDEALAMHPTVKPVALVEDAILDATTRGGVVIDGFAGAGTTLMAAERAGRRAFCLEIEPRYMDVTL 407
Cdd:COG0863   148 DVW------DIPGVTPKERKGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVAR 221

                         250
                  ....*....|.
gi 1826332662 408 RRFRKATGIEP 418
Cdd:COG0863   222 RRLEEATGLEF 232
ParB_N_like_MT cd16403
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 12-99 3.47e-53

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: 172.26  E-value: 3.47e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  12 AIAALKPYARNPRTHSKKQLKQIEDSIRRFGWTNPVLIDSDGGVIAGHGRLEAAKAMGLREVPAIRFDHMSEAEKRAYVV 91
Cdd:cd16403     1 PIDDLKPYPRNARTHSEKQIEQLAASIREFGFTNPILVDEDGVIIAGHGRLLAAKLLGLKEVPVIRLDHLSEAQKRAYRI 80


                  ....*...
gi 1826332662  92 ADNRLAEN 99
Cdd:cd16403    81 ADNRLAEN 88
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
174-418 1.40e-64

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 207.08  E-value: 1.40e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 174 RLLCADARDgqaWARLMDGETAEMVFTDPPYNVPVEGHVSGlgahhhaefAMASGEMSREAFQAFLTEVLGNMAAQARDG 253
Cdd:COG0863     1 RLICGDCLE---VLKELPDESVDLIVTDPPYNLGKKYGLGR---------REIGNELSFEEYLEFLREWLAECYRVLKPG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 254 SLHYVCMDWRHLGELLDAGKEVYREMKNLCVWTKSNGGMG---SLYRSQHELVGVFKKGKaPHINNVELGK---HGRYRS 327
Cdd:COG0863    69 GSLYVNIGDRYISRLIAALRDAGFKLRNEIIWRKPNGVPGpskRRFRNSHEYILWFTKGK-KYTFNVDAVKsieDGRNPS 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 328 NVWayagmnSFGGDRDEALAMHPTVKPVALVEDAILDATTRGGVVIDGFAGAGTTLMAAERAGRRAFCLEIEPRYMDVTL 407
Cdd:COG0863   148 DVW------DIPGVTPKERKGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVAR 221

                         250
                  ....*....|.
gi 1826332662 408 RRFRKATGIEP 418
Cdd:COG0863   222 RRLEEATGLEF 232
ParB_N_like_MT cd16403
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 12-99 3.47e-53

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: 172.26  E-value: 3.47e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  12 AIAALKPYARNPRTHSKKQLKQIEDSIRRFGWTNPVLIDSDGGVIAGHGRLEAAKAMGLREVPAIRFDHMSEAEKRAYVV 91
Cdd:cd16403     1 PIDDLKPYPRNARTHSEKQIEQLAASIREFGFTNPILVDEDGVIIAGHGRLLAAKLLGLKEVPVIRLDHLSEAQKRAYRI 80


                  ....*...
gi 1826332662  92 ADNRLAEN 99
Cdd:cd16403    81 ADNRLAEN 88
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 197-408 5.65e-27

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: 107.49  E-value: 5.65e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 197 MVFTDPPYNVPVEGHvsglgahhhaefaMASGEMSREAFQAFLTEVLGNMAAQ-ARDGSLhYVCMDWRHLGELLDAGKEV 275
Cdd:pfam01555   3 LIVTDPPYNLGKDYG-------------QWDDKDSIEEYLEWLEEWLKEVRRVlKPGGSI-FINIGDSNIKSLKALALEI 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 276 YREMK--NLCVWTKSNGgMGSL----YRSQHELVGVFKKGKAPHINNVELGKH----------------GRYRSNVWAYA 333
Cdd:pfam01555  69 LGIFKllNDIIWRKPNG-MPNSngerFTPAHEYILWFSKTKKYKTFNYDAIKVpydekdklkkrgsepnGKPIGDVWDFS 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1826332662 334 GMNSfGGDRDEALAMHPTVKPVALVEDAILDATTRGGVVIDGFAGAGTTLMAAERAGRRAFCLEIEPRYMDVTLR 408
Cdd:pfam01555 148 RVQP-SEKESGGNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVEIAKE 221
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 3-108 2.28e-19

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: 86.58  E-value: 2.28e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662   3 KQDLQIENVAIAALKPYARNPRTH-SKKQLKQIEDSIRRFGWTNPVLI--DSDGG--VIAGHGRLEAAKAMGLREVPAIR 77
Cdd:COG1475     2 KEGEEIREIPIDKIVPSPYNPRRTfDEEALEELAASIREHGLLQPILVrpLGDGRyeIIAGERRLRAAKLLGLETVPAIV 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1826332662  78 FDhMSEAEKRAYVVADN----------------RLAENAGWDPELLA 108
Cdd:COG1475    82 RD-LDDEEALELALIENlqredlnpleearayqRLLEEFGLTQEEIA 127
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 11-76 6.72e-13

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: 64.25  E-value: 6.72e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1826332662   11 VAIAALKPYARNPRTHSKKQLKQIEDSIRRFGWTNPVLIDSDGG---VIAGHGRLEAAKAMGLREVPAI 76
Cdd:smart00470   3 VPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIVRPNDGryeIIDGERRLRAAKLLGLKEVPVI 71
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 11-76 5.26e-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: 58.83  E-value: 5.26e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  11 VAIAALKPYARNPRTHSKKQLKQIEDSIRRFGWTNPVLID-SDGG---VIAGHGRLEAAKAMGLREVPAI 76
Cdd:pfam02195   3 VPISKLRPNPDQPRKDSEESLEELAASIKKRGLLQPIIVRkTPDGryeIIAGERRLRAAKLLGLKEVPVI 72
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
349-414 2.06e-10

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 61.28  E-value: 2.06e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826332662 349 HPTVKPVALVEDAILDATTRGGVVIDGFAGAGTTLMAAERAGRRAFCLEIEPRYMDVTLRRFRKAT 414
Cdd:PRK11524  189 HPTQKPEALLKRIILASSNPGDIVLDPFAGSFTTGAVAKASGRKFIGIEINSEYIKMGLRRLDVAS 254
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 11-99 5.67e-03

ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.


Pssm-ID: 272946 [Multi-domain]  Cd Length: 187  Bit Score: 37.74  E-value: 5.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  11 VAIAALKPYARNPRTH-SKKQLKQIEDSIRRFGWTNPVLI----DSDGG--VIAGHGRLEAAKAMGLREVPAIrFDHMSE 83
Cdd:TIGR00180   8 IDIDLLQPNPYQPRKDfSEESLAELIESIKEQGQLQPILVrkhpDQPGRyeIIAGERRWRAAKLAGLKTIPAI-VRELDD 86

                          90
                  ....*....|....*.
gi 1826332662  84 AEKRAYVVADNRLAEN 99
Cdd:TIGR00180  87 EQMLADALIENIQRED 102
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
174-418 1.40e-64

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 207.08  E-value: 1.40e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 174 RLLCADARDgqaWARLMDGETAEMVFTDPPYNVPVEGHVSGlgahhhaefAMASGEMSREAFQAFLTEVLGNMAAQARDG 253
Cdd:COG0863     1 RLICGDCLE---VLKELPDESVDLIVTDPPYNLGKKYGLGR---------REIGNELSFEEYLEFLREWLAECYRVLKPG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 254 SLHYVCMDWRHLGELLDAGKEVYREMKNLCVWTKSNGGMG---SLYRSQHELVGVFKKGKaPHINNVELGK---HGRYRS 327
Cdd:COG0863    69 GSLYVNIGDRYISRLIAALRDAGFKLRNEIIWRKPNGVPGpskRRFRNSHEYILWFTKGK-KYTFNVDAVKsieDGRNPS 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 328 NVWayagmnSFGGDRDEALAMHPTVKPVALVEDAILDATTRGGVVIDGFAGAGTTLMAAERAGRRAFCLEIEPRYMDVTL 407
Cdd:COG0863   148 DVW------DIPGVTPKERKGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVAR 221

                         250
                  ....*....|.
gi 1826332662 408 RRFRKATGIEP 418
Cdd:COG0863   222 RRLEEATGLEF 232
ParB_N_like_MT cd16403
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 12-99 3.47e-53

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: 172.26  E-value: 3.47e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  12 AIAALKPYARNPRTHSKKQLKQIEDSIRRFGWTNPVLIDSDGGVIAGHGRLEAAKAMGLREVPAIRFDHMSEAEKRAYVV 91
Cdd:cd16403     1 PIDDLKPYPRNARTHSEKQIEQLAASIREFGFTNPILVDEDGVIIAGHGRLLAAKLLGLKEVPVIRLDHLSEAQKRAYRI 80


                  ....*...
gi 1826332662  92 ADNRLAEN 99
Cdd:cd16403    81 ADNRLAEN 88
ParB_N_like_MT cd16402
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 12-98 1.05e-29

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: 110.40  E-value: 1.05e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  12 AIAALKPYARNPRtHSKKQLKQIEDSIRRFGWTNPVLIDSDGGVIAGHGRLEAAKAMGLREVPAIRFDHMSEAEKRAYVV 91
Cdd:cd16402     1 KISELKPYENNPR-NNDKAVEKVAESIKEFGFLVPIVVDKNNVIVAGHTRYKAAKRLGLEEVPCIVADDLTEEQIKAFRL 79


                  ....*..
gi 1826332662  92 ADNRLAE 98
Cdd:cd16402    80 ADNKTSE 86
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 197-408 5.65e-27

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: 107.49  E-value: 5.65e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 197 MVFTDPPYNVPVEGHvsglgahhhaefaMASGEMSREAFQAFLTEVLGNMAAQ-ARDGSLhYVCMDWRHLGELLDAGKEV 275
Cdd:pfam01555   3 LIVTDPPYNLGKDYG-------------QWDDKDSIEEYLEWLEEWLKEVRRVlKPGGSI-FINIGDSNIKSLKALALEI 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 276 YREMK--NLCVWTKSNGgMGSL----YRSQHELVGVFKKGKAPHINNVELGKH----------------GRYRSNVWAYA 333
Cdd:pfam01555  69 LGIFKllNDIIWRKPNG-MPNSngerFTPAHEYILWFSKTKKYKTFNYDAIKVpydekdklkkrgsepnGKPIGDVWDFS 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1826332662 334 GMNSfGGDRDEALAMHPTVKPVALVEDAILDATTRGGVVIDGFAGAGTTLMAAERAGRRAFCLEIEPRYMDVTLR 408
Cdd:pfam01555 148 RVQP-SEKESGGNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVEIAKE 221
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 3-108 2.28e-19

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: 86.58  E-value: 2.28e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662   3 KQDLQIENVAIAALKPYARNPRTH-SKKQLKQIEDSIRRFGWTNPVLI--DSDGG--VIAGHGRLEAAKAMGLREVPAIR 77
Cdd:COG1475     2 KEGEEIREIPIDKIVPSPYNPRRTfDEEALEELAASIREHGLLQPILVrpLGDGRyeIIAGERRLRAAKLLGLETVPAIV 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1826332662  78 FDhMSEAEKRAYVVADN----------------RLAENAGWDPELLA 108
Cdd:COG1475    82 RD-LDDEEALELALIENlqredlnpleearayqRLLEEFGLTQEEIA 127
ParB_N_like_MT cd16844
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 26-79 2.50e-15

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: 69.99  E-value: 2.50e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1826332662  26 HSKKQLKQIEDSIRRFGWTNPVLIDSDGGVIAGHGRLEAAKAMGLREVPAIRFD 79
Cdd:cd16844     1 KNDAQIERVAASIREFGFRVPVLIDKDGEIVDGHLRLEAARRLGLETVPVIRVD 54
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 18-96 4.07e-14

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: 67.25  E-value: 4.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  18 PYarNPRTH---SKKQLKQIEDSIRRFGWTNPVLIDS-DGGVIAGHGRLEAAKAMGLREVPAIRFDhMSEAEKRAYVVAD 93
Cdd:cd16401     3 PY--NPRKDlkpGDKEYEKLKESIEEFGLVDPLIVNKrTNVLIGGHQRLKVLKELGYTEVPVVVVD-LDEEKEKALNIAL 79


                  ...
gi 1826332662  94 NRL 96
Cdd:cd16401    80 NKI 82
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 11-76 6.72e-13

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: 64.25  E-value: 6.72e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1826332662   11 VAIAALKPYARNPRTHSKKQLKQIEDSIRRFGWTNPVLIDSDGG---VIAGHGRLEAAKAMGLREVPAI 76
Cdd:smart00470   3 VPIEKLRPNPDQPRLTSEESLEELAESIKENGLLQPIIVRPNDGryeIIDGERRLRAAKLLGLKEVPVI 71
ParB_N_like cd16410
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 28-87 1.61e-11

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: 319267 [Multi-domain]  Cd Length: 80  Bit Score: 59.91  E-value: 1.61e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1826332662  28 KKQLKQIE---DSIRRFGWTNPVLIDSDGGVIAGHGRLEAAKAMGLREVPAIRFDHMSEAEKR 87
Cdd:cd16410    11 RKDLGDIEalaESIKRHGLLNPIVVTPDNELIAGERRLEAAKLLGWETIEVRVMDIEDEKEKL 73
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 11-76 5.26e-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: 58.83  E-value: 5.26e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  11 VAIAALKPYARNPRTHSKKQLKQIEDSIRRFGWTNPVLID-SDGG---VIAGHGRLEAAKAMGLREVPAI 76
Cdd:pfam02195   3 VPISKLRPNPDQPRKDSEESLEELAASIKKRGLLQPIIVRkTPDGryeIIAGERRLRAAKLLGLKEVPVI 72
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
349-414 2.06e-10

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 61.28  E-value: 2.06e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1826332662 349 HPTVKPVALVEDAILDATTRGGVVIDGFAGAGTTLMAAERAGRRAFCLEIEPRYMDVTLRRFRKAT 414
Cdd:PRK11524  189 HPTQKPEALLKRIILASSNPGDIVLDPFAGSFTTGAVAKASGRKFIGIEINSEYIKMGLRRLDVAS 254
ParB_N_like cd16408
ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning ...
 16-94 4.37e-10

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: 319265 [Multi-domain]  Cd Length: 84  Bit Score: 56.10  E-value: 4.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  16 LKPYARNP-RTHSKKQLKQIEDSIRRFGWTNPVLID--SDGG--VIAGHGRLEAAKAMGLREVPAIRFDHMSEAEKRAYV 90
Cdd:cd16408     1 LVPFSDHPfKLYTGERLEDMVESIKENGVLQPIIVRpiEDGKyeILAGHNRVNAAKLAGLTTIPAIIKENLTDEEAKLIV 80


                  ....
gi 1826332662  91 VADN 94
Cdd:cd16408    81 VETN 84
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 27-79 2.47e-09

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: 53.43  E-value: 2.47e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1826332662  27 SKKQLKQIEDSIRRFGWTNPVLIDSDGGVIAGHGRLEAAKAMGLREVPAIRFD 79
Cdd:cd16404    13 TNEEFEELKESIRKNGIIVPIIVDQDGVIIDGHHRYRIAKELGIKEVPVIVYD 65
ParB_Srx_like_nuclease cd16400
ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family ...
 11-83 3.76e-09

ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family contains a Pyrococcus Furiosus enzyme reported to have DNA nuclease activity and resembles the N-terminal domain of ParB proteins of the parABS bacterial chromosome partitioning system. This sub-family also includes siderophore staphylobactin biosynthesis protein SbnI. 60% of the P. furiosus nuclease activity was retained at 90 degree C, suggesting a physiological role in the organism, which can grow in temperatures as high as 100 degrees Celsius. The protein has endo- and exo-nuclease activity vs. single- and double-stranded DNA, and nuclease activity was lost in methylated proteins prepared for structure solution. This family has a fairly well-conserved DGHHR motif that corresponds to the same structural position as the phosphorylation site (a portion of the ATP-Mg-binding site) of sulfiredoxin and the arginine-rich ParB BoxII of ParB.


Pssm-ID: 319257 [Multi-domain]  Cd Length: 72  Bit Score: 52.94  E-value: 3.76e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1826332662  11 VAIAALKPYARnprtHSKKQLKQIEDSIRRFG-WTNPVLIDSDGGVIA-GHGRLEAAKAMGLREVPAIRFDHMSE 83
Cdd:cd16400     2 LPISDLRPHEE----VDPDRVEELIEKILEEGvWTKPIIVDKNTGIILdGHHRLEAAKRLGLKRVPCVLLDYDDD 72
ParB_N_like cd16411
ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems; ...
 22-99 6.69e-09

ParB N-terminal, parA -binding, 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: 319268 [Multi-domain]  Cd Length: 90  Bit Score: 52.60  E-value: 6.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  22 NPRTHSKKQLKQIEDSIRRFGWTNPV---LIDSDGG-----VIAGHGRLEAAKAMGLREVPAIRFDhMSEAEkrAYVVAd 93
Cdd:cd16411    10 NPRSRNRKIFREIVESIATVGLKRPItvrRRSSDDGgykydLVCGQGRLEAFKALGETEIPAIVVD-VDEED--ALLMS- 85


                  ....*.
gi 1826332662  94 nrLAEN 99
Cdd:cd16411    86 --LVEN 89
PRK13699 PRK13699
putative methylase; Provisional
 349-409 5.62e-08

putative methylase; Provisional


Pssm-ID: 184255  Cd Length: 227  Bit Score: 53.30  E-value: 5.62e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1826332662 349 HPTVKPVALVEDAILDATTRGGVVIDGFAGAGTTLMAAERAGRRAFCLEIEPRYMDVTLRR 409
Cdd:PRK13699  144 HPTEKPVTSLQPLIESFTHPNAIVLDPFAGSGSTCVAALQSGRRYIGIELLEQYHRAGQQR 204
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 8-99 3.68e-07

Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; Spo0J (stage 0 sporulation protein J) is a ParB family member, a critical component of the ParABS-type bacterial chromosome segregation system. The Spo0J N-terminal region acts in protein-protein interaction and is adjacent to the DNA-binding domain that binds to parS sites. Two Spo0J bind per parS site, and Spo0J interacts with neighbors via the N-terminal domain to form oligomers via an Arginine-rich patch (RRXR). This superfamily 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: 319251 [Multi-domain]  Cd Length: 97  Bit Score: 47.86  E-value: 3.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662   8 IENVAIAALKPYARNPRTH-SKKQLKQIEDSIRRFGWTNPVLIDSDGG----VIAGHGRLEAAKAMGLREVPAIrFDHMS 82
Cdd:cd16393     1 VQEIPIDKIRPNPYQPRKEfDEEALKELAESIKEHGLLQPIVVRKVGDgryeIIAGERRWRAAKLAGLTEIPAI-VRDLD 79

                          90
                  ....*....|....*..
gi 1826332662  83 EAEkrAYVVAdnrLAEN 99
Cdd:cd16393    80 DEE--ALELA---LIEN 91
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 13-76 4.90e-07

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: 47.13  E-value: 4.90e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1826332662  13 IAALKPYARNP-RTHSKKQLKQIEDSIRRFGWTNPVLI--DSDGG--VIAGHGRLEAAKAMGLREVPAI 76
Cdd:cd16407     1 LSELHPFPNHPfKVRDDEEMEELVESIKENGVLTPIIVrpREDGGyeIISGHRRKRACELAGLETIPVI 69
Mod COG2189
Adenine specific DNA methylase Mod [Replication, recombination and repair];
272-413 6.01e-07

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


Pssm-ID: 441792 [Multi-domain]  Cd Length: 491  Bit Score: 51.70  E-value: 6.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662 272 GKEVYREM--KNLCVWTKSNGGMGSLYRSQHElvgvFKKGKAPhinnvelgkhgryrSNVWAYAGMNSFGGDRDEALAMH 349
Cdd:COG2189   237 SKETMEELiaDGRIYFGKDGNGVPRRKRYLDE----VKKGVVP--------------TTIWDDIGTNQNGTKELKELFGG 298

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1826332662 350 ---PTVKPVALVEDAILDATTRGGVVIDGFAGAGTTLMAAER-----AGRRAFCL-EIEPRYMDVTLRRFRKA 413
Cdd:COG2189   299 kvfDTPKPEKLLKRIIEIATNPGDLVLDFFAGSGTTAHAVMKlnaedGGNRRFILvQLGEYADTVTKERLRRV 371
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
 7-99 7.23e-07

nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning protein family; Nucleoid occlusion protein has been shown in Bacillus subtilis to bind to specific DNA sequences on the chromosome (Noc-binding DNA sequences, NBS), inhibiting cell division near the nucleoid and thereby protecting the chromosome. This N-terminal domain is related to the N-terminal domain of ParB/repB partitioning system proteins.


Pssm-ID: 319254 [Multi-domain]  Cd Length: 95  Bit Score: 47.22  E-value: 7.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662   7 QIENVAIAALKPYARNPR-THSKKQLKQIEDSIRRFGWTNPVLI--DSDGG--VIAGHGRLEAAKAMGLREVPAIRFDhM 81
Cdd:cd16396     2 EVLEIPVADIIPNPYQPRkEFDEEEIEELAESIKEHGLLQPIVVrkTKDGGyeIVAGERRWRAAKLLGWEKIPAIIRD-L 80

                          90
                  ....*....|....*...
gi 1826332662  82 SeaEKRAYVVAdnrLAEN 99
Cdd:cd16396    81 S--DKEALEIA---LIEN 93
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 31-76 8.48e-07

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: 45.66  E-value: 8.48e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1826332662  31 LKQIEDSIRRFGWTNPVLIDSDGG----VIAGHGRLEAAKAMGLREVPAI 76
Cdd:cd16387     5 LEELAESIREHGVLQPIIVRPLPDgryeIIAGERRWRAAKLAGLTTIPVV 54
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 347-401 2.19e-05

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: 44.55  E-value: 2.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1826332662 347 AMHPTVkPVALVEdaiLDATTRGGVVIDGFAGAGTTLMAAERAGRRAFCLEIEPR 401
Cdd:COG1041     9 SLDPRL-ARALVN---LAGAKEGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPK 59
KorB_N_like cd16398
ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related ...
 22-88 3.34e-04

ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related domains; KorB, a member of the ParB like family, is present on the low copy number, broad host range plasmid RK2. KorB encodes a gene product involved in segregation of RK2 and acts as a transcriptional regulator, down-regulating at least 6 RK2 operons. KorB binds RNA polymerase and acts cooperatively with several co-repressors in modulating transcription. KorB is comprised of 3 domains, including a beta-strand C-terminal domain similar to SH3 domains and an alpha helical central domain that interacts with operator DNA. In ParB of P1 and SopB of F, the N-terminal region is responsible for interaction with the parA component. However, korB interaction with the RK2 parA-equivalent IncC has been mapped to the central HTH motif. This family is related to 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: 319256 [Multi-domain]  Cd Length: 91  Bit Score: 39.56  E-value: 3.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  22 NPRTH-SKKQLKQIEDSIRRFGWTNPVLI----DSDGGVIAGHG--RLEAAKAMGLREVPAI------RFDHMSEAEKRA 88
Cdd:cd16398    10 NPRTEfDEEKIEELAASIKERGVKSPISVrphpEKPGKYIINHGarRYRASKWAGLKTIPAFidndhdDFDQVIENIQRE 89
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 11-99 5.67e-03

ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.


Pssm-ID: 272946 [Multi-domain]  Cd Length: 187  Bit Score: 37.74  E-value: 5.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1826332662  11 VAIAALKPYARNPRTH-SKKQLKQIEDSIRRFGWTNPVLI----DSDGG--VIAGHGRLEAAKAMGLREVPAIrFDHMSE 83
Cdd:TIGR00180   8 IDIDLLQPNPYQPRKDfSEESLAELIESIKEQGQLQPILVrkhpDQPGRyeIIAGERRWRAAKLAGLKTIPAI-VRELDD 86

                          90
                  ....*....|....*.
gi 1826332662  84 AEKRAYVVADNRLAEN 99
Cdd:TIGR00180  87 EQMLADALIENIQRED 102
ParB_N_like cd16409
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ...
 34-76 7.18e-03

ParB N-terminal-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: 319266 [Multi-domain]  Cd Length: 74  Bit Score: 35.35  E-value: 7.18e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1826332662  34 IEDSIRRFGWTNPVLIDSDGG----VIAGHGRLEAAKAMGLREVPAI 76
Cdd:cd16409     9 LAQSIAEHGLLTPITVRQDPGgrytLIAGAHRLAAAKLLGWDTIDAI 55
 
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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