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Conserved domains on  [gi|1154766566|ref|WP_078683224|]
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site-specific DNA-methyltransferase [Clostridium sp. USBA 49]

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];
170-391 9.23e-60

DNA modification methylase [Replication, recombination and repair];


:

Pssm-ID: 440623  Cd Length: 236  Bit Score: 194.37  E-value: 9.23e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 170 RLMCGDSTmlsDVQKLMNGQKARFVFTDPPWNVDYGSDTRHPSwkprqiLNDNMSTEEFGAFLLRAFKCMKEVSEAGCMT 249
Cdd:COG0863     1 RLICGDCL---EVLKELPDESVDLIVTDPPYNLGKKYGLGRRE------IGNELSFEEYLEFLREWLAECYRVLKPGGSL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 250 YVVMSAQEWGSLMNVMREAGYHWSSTIIWKKDS--LVLSRKDYHTQYEPIWYGWLEGTRL-------CPLKDRKQSDVWE 320
Cdd:COG0863    72 YVNIGDRYISRLIAALRDAGFKLRNEIIWRKPNgvPGPSKRRFRNSHEYILWFTKGKKYTfnvdavkSIEDGRNPSDVWD 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1154766566 321 IPRPKVSE--EHPTMKPVSLVAKAMLNSSHIGDLTLDLFGGSGTTMIAAQQTGRVCFMMELDSKYCDVIVKRY 391
Cdd:COG0863   152 IPGVTPKErkGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVARRRL 224
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 13-97 6.24e-53

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: 171.25  E-value: 6.24e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566  13 PSKYNPRKDLKPGDPEYEKLRRSIEEFGYVEPVIWNKRTGNIVGGHQRYKVLTALGYKEIDCVVVDLDEQREKALNVALN 92
Cdd:cd16401     1 PAPYNPRKDLKPGDKEYEKLKESIEEFGLVDPLIVNKRTNVLIGGHQRLKVLKELGYTEVPVVVVDLDEEKEKALNIALN 80


                  ....*
gi 1154766566  93 KISGE 97
Cdd:cd16401    81 KISGE 85
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
170-391 9.23e-60

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 194.37  E-value: 9.23e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 170 RLMCGDSTmlsDVQKLMNGQKARFVFTDPPWNVDYGSDTRHPSwkprqiLNDNMSTEEFGAFLLRAFKCMKEVSEAGCMT 249
Cdd:COG0863     1 RLICGDCL---EVLKELPDESVDLIVTDPPYNLGKKYGLGRRE------IGNELSFEEYLEFLREWLAECYRVLKPGGSL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 250 YVVMSAQEWGSLMNVMREAGYHWSSTIIWKKDS--LVLSRKDYHTQYEPIWYGWLEGTRL-------CPLKDRKQSDVWE 320
Cdd:COG0863    72 YVNIGDRYISRLIAALRDAGFKLRNEIIWRKPNgvPGPSKRRFRNSHEYILWFTKGKKYTfnvdavkSIEDGRNPSDVWD 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1154766566 321 IPRPKVSE--EHPTMKPVSLVAKAMLNSSHIGDLTLDLFGGSGTTMIAAQQTGRVCFMMELDSKYCDVIVKRY 391
Cdd:COG0863   152 IPGVTPKErkGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVARRRL 224
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 13-97 6.24e-53

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: 171.25  E-value: 6.24e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566  13 PSKYNPRKDLKPGDPEYEKLRRSIEEFGYVEPVIWNKRTGNIVGGHQRYKVLTALGYKEIDCVVVDLDEQREKALNVALN 92
Cdd:cd16401     1 PAPYNPRKDLKPGDKEYEKLKESIEEFGLVDPLIVNKRTNVLIGGHQRLKVLKELGYTEVPVVVVDLDEEKEKALNIALN 80


                  ....*
gi 1154766566  93 KISGE 97
Cdd:cd16401    81 KISGE 85
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 1-92 4.81e-21

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: 91.20  E-value: 4.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   1 MDILKIPTEKLKPSKYNPRKDLkpGDPEYEKLRRSIEEFGYVEPVIWNKRTGN---IVGGHQRYKVLTALGYKEIDCVVV 77
Cdd:COG1475     5 EEIREIPIDKIVPSPYNPRRTF--DEEALEELAASIREHGLLQPILVRPLGDGryeIIAGERRLRAAKLLGLETVPAIVR 82

                          90
                  ....*....|....*
gi 1154766566  78 DLDEQREKALNVALN 92
Cdd:COG1475    83 DLDDEEALELALIEN 97
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 194-389 1.85e-16

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: 77.83  E-value: 1.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 194 VFTDPPWNVdygsdtrhpsWKPRQILNDNMSTEEFGAFLLRAFKCMKEV-SEAGCMtYVVMSAQEWGSLMNVMRE-AGYH 271
Cdd:pfam01555   4 IVTDPPYNL----------GKDYGQWDDKDSIEEYLEWLEEWLKEVRRVlKPGGSI-FINIGDSNIKSLKALALEiLGIF 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 272 W-SSTIIWKKDSLVLSRKDYH--TQYEPIWygWLEGT-----------------------RLCPLKDRKQSDVWEIPR-- 323
Cdd:pfam01555  73 KlLNDIIWRKPNGMPNSNGERftPAHEYIL--WFSKTkkyktfnydaikvpydekdklkkRGSEPNGKPIGDVWDFSRvq 150

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1154766566 324 -----PKVSEEHPTMKPVSLVAKAMLNSSHIGDLTLDLFGGSGTTMIAAQQTGRVCFMMELDSKYCDVIVK 389
Cdd:pfam01555 151 psekeSGGNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVEIAKE 221
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 5-92 6.13e-16

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: 72.72  E-value: 6.13e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566    5 KIPTEKLKPSKYNPRKDlkpGDPEYEKLRRSIEEFGYVEPVIWNKRTGN--IVGGHQRYKVLTALGYKEIDCVVVDLDEQ 82
Cdd:smart00470   2 EVPIEKLRPNPDQPRLT---SEESLEELAESIKENGLLQPIIVRPNDGRyeIIDGERRLRAAKLLGLKEVPVIVRDLDDE 78

                           90
                   ....*....|
gi 1154766566   83 REKALNVALN 92
Cdd:smart00470  79 EAIALSLEEN 88
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
167-390 3.49e-15

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 75.53  E-value: 3.49e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 167 GSHRLMCGDStmLSDVQKLMNgQKARFVFTDPPWNVDYGSDTRHPSWKprqilndnmstEEfgAFLLRAFK----CMKEV 242
Cdd:PRK11524    7 EAKTIIHGDA--LTELKKIPS-ESVDLIFADPPYNIGKNFDGLIEAWK-----------ED--LFIDWLYEwideCHRVL 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 243 SEAGCMtYVVMSAQEWGSLMNVMREAgYHWSSTIIWKKDSL-VLSRKDYHTQYEPIWYGwlegtrlcpLKDRKQ------ 315
Cdd:PRK11524   71 KKQGTM-YIMNSTENMPFIDLYCRKL-FTIKSRIVWSYDSSgVQAKKYFGSMYEPILMM---------VKDAKNytfngd 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 316 -------------------------------SDVWEIPRPKVS----EEHPTMKPVSLVAKAMLNSSHIGDLTLDLFGGS 360
Cdd:PRK11524  140 ailveaktgakralidyrknppqpyntqkvpGNVWDFPRVRYLmdeyENHPTQKPEALLKRIILASSNPGDIVLDPFAGS 219

                         250       260       270
                  ....*....|....*....|....*....|
gi 1154766566 361 GTTMIAAQQTGRVCFMMELDSKYCDVIVKR 390
Cdd:PRK11524  220 FTTGAVAKASGRKFIGIEINSEYIKMGLRR 249
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 4-92 3.90e-13

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: 64.61  E-value: 3.90e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   4 LKIPTEKLKPSKYNPRKDlkpGDPEYEKLRRSIEEFGYVEPVIWNKRTGN---IVGGHQRYKVLTALGYKEIDCVVVDLD 80
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKD---SEESLEELAASIKKRGLLQPIIVRKTPDGryeIIAGERRLRAAKLLGLKEVPVIVREID 77

                          90
                  ....*....|..
gi 1154766566  81 EQREKALNVALN 92
Cdd:pfam02195  78 DEEAIALSLIEN 89
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 6-93 1.21e-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: 39.67  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   6 IPTEKLKPSKYNPRKDLKPGDpeYEKLRRSIEEFGYVEPVIWNKRTGN-----IVGGHQRYKVLTALGYKEIDCVVVDLD 80
Cdd:TIGR00180   8 IDIDLLQPNPYQPRKDFSEES--LAELIESIKEQGQLQPILVRKHPDQpgryeIIAGERRWRAAKLAGLKTIPAIVRELD 85

                          90
                  ....*....|...
gi 1154766566  81 EQREKALNVALNK 93
Cdd:TIGR00180  86 DEQMLADALIENI 98
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
170-391 9.23e-60

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 194.37  E-value: 9.23e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 170 RLMCGDSTmlsDVQKLMNGQKARFVFTDPPWNVDYGSDTRHPSwkprqiLNDNMSTEEFGAFLLRAFKCMKEVSEAGCMT 249
Cdd:COG0863     1 RLICGDCL---EVLKELPDESVDLIVTDPPYNLGKKYGLGRRE------IGNELSFEEYLEFLREWLAECYRVLKPGGSL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 250 YVVMSAQEWGSLMNVMREAGYHWSSTIIWKKDS--LVLSRKDYHTQYEPIWYGWLEGTRL-------CPLKDRKQSDVWE 320
Cdd:COG0863    72 YVNIGDRYISRLIAALRDAGFKLRNEIIWRKPNgvPGPSKRRFRNSHEYILWFTKGKKYTfnvdavkSIEDGRNPSDVWD 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1154766566 321 IPRPKVSE--EHPTMKPVSLVAKAMLNSSHIGDLTLDLFGGSGTTMIAAQQTGRVCFMMELDSKYCDVIVKRY 391
Cdd:COG0863   152 IPGVTPKErkGHPTQKPVELLERLILASSNPGDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEVARRRL 224
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 13-97 6.24e-53

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: 171.25  E-value: 6.24e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566  13 PSKYNPRKDLKPGDPEYEKLRRSIEEFGYVEPVIWNKRTGNIVGGHQRYKVLTALGYKEIDCVVVDLDEQREKALNVALN 92
Cdd:cd16401     1 PAPYNPRKDLKPGDKEYEKLKESIEEFGLVDPLIVNKRTNVLIGGHQRLKVLKELGYTEVPVVVVDLDEEKEKALNIALN 80


                  ....*
gi 1154766566  93 KISGE 97
Cdd:cd16401    81 KISGE 85
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 1-92 4.81e-21

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: 91.20  E-value: 4.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   1 MDILKIPTEKLKPSKYNPRKDLkpGDPEYEKLRRSIEEFGYVEPVIWNKRTGN---IVGGHQRYKVLTALGYKEIDCVVV 77
Cdd:COG1475     5 EEIREIPIDKIVPSPYNPRRTF--DEEALEELAASIREHGLLQPILVRPLGDGryeIIAGERRLRAAKLLGLETVPAIVR 82

                          90
                  ....*....|....*
gi 1154766566  78 DLDEQREKALNVALN 92
Cdd:COG1475    83 DLDDEEALELALIEN 97
ParB_N_like_MT cd16402
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 7-98 7.70e-17

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: 74.96  E-value: 7.70e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   7 PTEKLKPSKYNPRKDlkpgDPEYEKLRRSIEEFGYVEPVIWNKrTGNIVGGHQRYKVLTALGYKEIDCVVVD-LDEQREK 85
Cdd:cd16402     1 KISELKPYENNPRNN----DKAVEKVAESIKEFGFLVPIVVDK-NNVIVAGHTRYKAAKRLGLEEVPCIVADdLTEEQIK 75

                          90
                  ....*....|...
gi 1154766566  86 ALNVALNKISgEF 98
Cdd:cd16402    76 AFRLADNKTS-EF 87
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 194-389 1.85e-16

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: 77.83  E-value: 1.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 194 VFTDPPWNVdygsdtrhpsWKPRQILNDNMSTEEFGAFLLRAFKCMKEV-SEAGCMtYVVMSAQEWGSLMNVMRE-AGYH 271
Cdd:pfam01555   4 IVTDPPYNL----------GKDYGQWDDKDSIEEYLEWLEEWLKEVRRVlKPGGSI-FINIGDSNIKSLKALALEiLGIF 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 272 W-SSTIIWKKDSLVLSRKDYH--TQYEPIWygWLEGT-----------------------RLCPLKDRKQSDVWEIPR-- 323
Cdd:pfam01555  73 KlLNDIIWRKPNGMPNSNGERftPAHEYIL--WFSKTkkyktfnydaikvpydekdklkkRGSEPNGKPIGDVWDFSRvq 150

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1154766566 324 -----PKVSEEHPTMKPVSLVAKAMLNSSHIGDLTLDLFGGSGTTMIAAQQTGRVCFMMELDSKYCDVIVK 389
Cdd:pfam01555 151 psekeSGGNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVEIAKE 221
ParB_N_like_MT cd16403
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 7-95 3.00e-16

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: 73.26  E-value: 3.00e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   7 PTEKLKPSKYNPRKDlkpgDPEY-EKLRRSIEEFGYVEPVIWNKRtGNIVGGHQRYKVLTALGYKEIDCVVVD-LDEQRE 84
Cdd:cd16403     1 PIDDLKPYPRNARTH----SEKQiEQLAASIREFGFTNPILVDED-GVIIAGHGRLLAAKLLGLKEVPVIRLDhLSEAQK 75

                          90
                  ....*....|.
gi 1154766566  85 KALNVALNKIS 95
Cdd:cd16403    76 RAYRIADNRLA 86
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 5-92 6.13e-16

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: 72.72  E-value: 6.13e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566    5 KIPTEKLKPSKYNPRKDlkpGDPEYEKLRRSIEEFGYVEPVIWNKRTGN--IVGGHQRYKVLTALGYKEIDCVVVDLDEQ 82
Cdd:smart00470   2 EVPIEKLRPNPDQPRLT---SEESLEELAESIKENGLLQPIIVRPNDGRyeIIDGERRLRAAKLLGLKEVPVIVRDLDDE 78

                           90
                   ....*....|
gi 1154766566   83 REKALNVALN 92
Cdd:smart00470  79 EAIALSLEEN 88
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
167-390 3.49e-15

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 75.53  E-value: 3.49e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 167 GSHRLMCGDStmLSDVQKLMNgQKARFVFTDPPWNVDYGSDTRHPSWKprqilndnmstEEfgAFLLRAFK----CMKEV 242
Cdd:PRK11524    7 EAKTIIHGDA--LTELKKIPS-ESVDLIFADPPYNIGKNFDGLIEAWK-----------ED--LFIDWLYEwideCHRVL 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 243 SEAGCMtYVVMSAQEWGSLMNVMREAgYHWSSTIIWKKDSL-VLSRKDYHTQYEPIWYGwlegtrlcpLKDRKQ------ 315
Cdd:PRK11524   71 KKQGTM-YIMNSTENMPFIDLYCRKL-FTIKSRIVWSYDSSgVQAKKYFGSMYEPILMM---------VKDAKNytfngd 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 316 -------------------------------SDVWEIPRPKVS----EEHPTMKPVSLVAKAMLNSSHIGDLTLDLFGGS 360
Cdd:PRK11524  140 ailveaktgakralidyrknppqpyntqkvpGNVWDFPRVRYLmdeyENHPTQKPEALLKRIILASSNPGDIVLDPFAGS 219

                         250       260       270
                  ....*....|....*....|....*....|
gi 1154766566 361 GTTMIAAQQTGRVCFMMELDSKYCDVIVKR 390
Cdd:PRK11524  220 FTTGAVAKASGRKFIGIEINSEYIKMGLRR 249
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 4-92 3.90e-13

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: 64.61  E-value: 3.90e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   4 LKIPTEKLKPSKYNPRKDlkpGDPEYEKLRRSIEEFGYVEPVIWNKRTGN---IVGGHQRYKVLTALGYKEIDCVVVDLD 80
Cdd:pfam02195   1 EEVPISKLRPNPDQPRKD---SEESLEELAASIKKRGLLQPIIVRKTPDGryeIIAGERRLRAAKLLGLKEVPVIVREID 77

                          90
                  ....*....|..
gi 1154766566  81 EQREKALNVALN 92
Cdd:pfam02195  78 DEEAIALSLIEN 89
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
 1-91 7.85e-12

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: 61.08  E-value: 7.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   1 MDILKIPTEKLKPSKYNPRKdlKPGDPEYEKLRRSIEEFGYVEPVIWNKRTGN---IVGGHQRYKVLTALGYKEIDCVVV 77
Cdd:cd16396     1 GEVLEIPVADIIPNPYQPRK--EFDEEEIEELAESIKEHGLLQPIVVRKTKDGgyeIVAGERRWRAAKLLGWEKIPAIIR 78

                          90
                  ....*....|....
gi 1154766566  78 DLDEQRekALNVAL 91
Cdd:cd16396    79 DLSDKE--ALEIAL 90
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 11-82 8.98e-10

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: 54.59  E-value: 8.98e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1154766566  11 LKPSKYNPRkdLKPGDPEYEKLRRSIEEFGYVEPVIWNkRTGNIVGGHQRYKVLTALGYKEIDCVVVDLDEQ 82
Cdd:cd16404     1 LKEDEEFRT--PNPTNEEFEELKESIRKNGIIVPIIVD-QDGVIIDGHHRYRIAKELGIKEVPVIVYDFDDE 69
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 9-81 1.64e-08

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: 51.36  E-value: 1.64e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1154766566   9 EKLKPSKYNP--RKDlkpgDPEYEKLRRSIEEFGYVEPVIWNKRTGN---IVGGHQRYKVLTALGYKEIDCVVVDLDE 81
Cdd:cd16407     2 SELHPFPNHPfkVRD----DEEMEELVESIKENGVLTPIIVRPREDGgyeIISGHRRKRACELAGLETIPVIVREMDD 75
ParB_N_like_MT cd16844
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 26-78 5.51e-08

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: 49.19  E-value: 5.51e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1154766566  26 DPEYEKLRRSIEEFGYVEPVIWNKRtGNIVGGHQRYKVLTALGYKEIDCVVVD 78
Cdd:cd16844     3 DAQIERVAASIREFGFRVPVLIDKD-GEIVDGHLRLEAARRLGLETVPVIRVD 54
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 3-87 2.16e-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: 48.63  E-value: 2.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   3 ILKIPTEKLKPSKYNPRKDLkpgDPE-YEKLRRSIEEFGYVEPVIWNKRTGN---IVGGHQRYKVLTALGYKEIDCVVVD 78
Cdd:cd16393     1 VQEIPIDKIRPNPYQPRKEF---DEEaLKELAESIKEHGLLQPIVVRKVGDGryeIIAGERRWRAAKLAGLTEIPAIVRD 77

                          90
                  ....*....|.
gi 1154766566  79 LDEQ--REKAL 87
Cdd:cd16393    78 LDDEeaLELAL 88
PRK13699 PRK13699
putative methylase; Provisional
 170-383 3.94e-07

putative methylase; Provisional


Pssm-ID: 184255  Cd Length: 227  Bit Score: 50.60  E-value: 3.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 170 RLMCGDSTmlsDVQKLMNGQKARFVFTDPPWNVDYGSDTrhpswkPRQILNDNmsTEEFgafLLRAFKCMKEVSEAGCMT 249
Cdd:PRK13699    3 RFILGNCI---DVMARFPDNAVDFILTDPPYLVGFRDRQ------GRTIAGDK--TDEW---LQPACNEMYRVLKKDALM 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566 250 YVVMSAQEWGSLMNVMREAGYHWSSTIIWKKDslVLSRKDYHTQYEPIWYGWLEGTRLCPLKdrkqsdvweiPRPKV--- 326
Cdd:PRK13699   69 VSFYGWNRVDRFMAAWKNAGFSVVGHLVFTKN--YTSKAAYVGYRHECAYILAKGRPALPQN----------PLPDVlgw 136

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1154766566 327 ----SEEHPTMKPVSLVAKAMLNSSHIGDLTLDLFGGSGTTMIAAQQTGRVCFMMELDSKY 383
Cdd:PRK13699  137 kysgNRHHPTEKPVTSLQPLIESFTHPNAIVLDPFAGSGSTCVAALQSGRRYIGIELLEQY 197
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 26-75 4.48e-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: 43.73  E-value: 4.48e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1154766566  26 DPEYEKLRRSIEEFGYVEPVIWNKRTGN---IVGGHQRYKVLTALGYKEIDCV 75
Cdd:cd16387     2 EEELEELAESIREHGVLQPIIVRPLPDGryeIIAGERRWRAAKLAGLTTIPVV 54
IbrB_like cd16397
immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates ...
 1-81 1.68e-05

immunoglobulin-binding regulator IbrB activates eib genes; IbrB (along with IbrA) activates immunoglobulin-binding eib genes in Escherichia coli. IbrB is related to the ParB N-terminal domain family, which includes DNA-binding proteins involved in chromosomal/plasmid segregation and transcriptional regulation, consistent with a possible mechanism for IbrB in DNA binding-related regulation of eib expression. The ParB like family is a diverse domain superfamily with structural and sequence similarity to ParB of bacterial chromosomes/plasmid parABS partitioning system and Sulfiredoxin (Srx), which is a reactivator of oxidatively inactivated 2-cys peroxiredoxins. Other families includes proteins related to StrR, a putative regulator in the biosynthetic gene cluster and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators SbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ) and EdeB (Brevibacillus brevis antimicrobial peptide edeine biosynthetic cluster). Nuclease activity has also been reported in arabidopsis Srx.


Pssm-ID: 319255 [Multi-domain]  Cd Length: 100  Bit Score: 43.33  E-value: 1.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   1 MDILKIPTEKLKPSKYNPRKdLKPgdPEYEKLRRSIEEFGYVEP--VIWNKRTGN--IVGGHQRYKVLT-------ALGY 69
Cdd:cd16397     3 DNVQWVPIEKVQANDYNPNK-VAP--PEMKLLKLSILEDGFTQPivVYYDEEDDKyvIVDGFHRYTLAKkkplierLKGY 79

                          90
                  ....*....|..
gi 1154766566  70 keIDCVVVDLDE 81
Cdd:cd16397    80 --LPVVVLDKDL 89
ParB_Srx_like_nuclease cd16400
ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family ...
 6-78 2.11e-05

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: 42.15  E-value: 2.11e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1154766566   6 IPTEKLKPS-KYNPRKdlkpgdpeYEKLRRSIEEFGYVE-PVIWNKRTGNIVGGHQRYKVLTALGYKEIDCVVVD 78
Cdd:cd16400     2 LPISDLRPHeEVDPDR--------VEELIEKILEEGVWTkPIIVDKNTGIILDGHHRLEAAKRLGLKRVPCVLLD 68
ParB_N_like cd16409
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ...
 26-94 3.73e-05

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: 41.52  E-value: 3.73e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1154766566  26 DPEY-EKLRRSIEEFGYVEPVIWNKRTGN----IVGGHqRYKVLTALGYKEIDCVVVDLDEQREKALNVALNKI 94
Cdd:cd16409     2 DPEHvEALAQSIAEHGLLTPITVRQDPGGrytlIAGAH-RLAAAKLLGWDTIDAIIVKADDLEAELLEIDENLI 74
Mod COG2189
Adenine specific DNA methylase Mod [Replication, recombination and repair];
331-390 2.18e-04

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


Pssm-ID: 441792 [Multi-domain]  Cd Length: 491  Bit Score: 43.22  E-value: 2.18e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1154766566 331 PTMKPVSLVAKAMLNSSHIGDLTLDLFGGSGTTMIAAQQTG------RVCFMMELDSKYCDVIVKR 390
Cdd:COG2189   302 DTPKPEKLLKRIIEIATNPGDLVLDFFAGSGTTAHAVMKLNaedggnRRFILVQLGEYADTVTKER 367
ParB_N_like cd16410
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 19-85 5.25e-04

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: 38.34  E-value: 5.25e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1154766566  19 RKDLkpGDpeYEKLRRSIEEFGYVEPVIWNKRtGNIVGGHQRYKVLTALGYKEIDCVVVDLDEQREK 85
Cdd:cd16410    11 RKDL--GD--IEALAESIKRHGLLNPIVVTPD-NELIAGERRLEAAKLLGWETIEVRVMDIEDEKEK 72
ParB_N_like cd16408
ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning ...
 11-90 5.54e-04

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: 38.76  E-value: 5.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566  11 LKPSKYNPRKdLKPGDpEYEKLRRSIEEFGYVEPVIWNKRTGN---IVGGHQRYKVLTALGYKEIDCVVVDLDEQREKAL 87
Cdd:cd16408     1 LVPFSDHPFK-LYTGE-RLEDMVESIKENGVLQPIIVRPIEDGkyeILAGHNRVNAAKLAGLTTIPAIIKENLTDEEAKL 78


                  ...
gi 1154766566  88 NVA 90
Cdd:cd16408    79 IVV 81
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 6-93 1.21e-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: 39.67  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   6 IPTEKLKPSKYNPRKDLKPGDpeYEKLRRSIEEFGYVEPVIWNKRTGN-----IVGGHQRYKVLTALGYKEIDCVVVDLD 80
Cdd:TIGR00180   8 IDIDLLQPNPYQPRKDFSEES--LAELIESIKEQGQLQPILVRKHPDQpgryeIIAGERRWRAAKLAGLKTIPAIVRELD 85

                          90
                  ....*....|...
gi 1154766566  81 EQREKALNVALNK 93
Cdd:TIGR00180  86 DEQMLADALIENI 98
ParB_N_like cd16411
ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems; ...
 6-87 2.62e-03

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: 36.81  E-value: 2.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154766566   6 IPTEKLK---PSKYNPRKdlkpgdpeYEKLRRSIEEFGYVEPVIWNKRTG-------NIVGGHQRYKVLTALGYKEIDCV 75
Cdd:cd16411     1 IPIDDIRvlnPRSRNRKI--------FREIVESIATVGLKRPITVRRRSSddggykyDLVCGQGRLEAFKALGETEIPAI 72

                          90
                  ....*....|..
gi 1154766566  76 VVDLDEqrEKAL 87
Cdd:cd16411    73 VVDVDE--EDAL 82
 
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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