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Conserved domains on  [gi|383396724|gb|AFH21526|]
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DNA adenine methylase [environmental Halophage eHP-3]

Protein Classification

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];
294-514 1.44e-51

DNA modification methylase [Replication, recombination and repair];


:

Pssm-ID: 440623  Cd Length: 236  Bit Score: 175.50  E-value: 1.44e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 294 VGDASDL--PLENESVDLIITSPPYNLGhgdwKMGGEGRepreDGIGyyDDRDEREYQAWQLNVLQELYRVATKGASLFY 371
Cdd:COG0863    4 CGDCLEVlkELPDESVDLIVTDPPYNLG----KKYGLGR----REIG--NELSFEEYLEFLREWLAECYRVLKPGGSLYV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 372 NHKPRQAEGeVIHPLdwirdQDNPWTLRQEVVWDRQSTHNHSPNIFW-PVDERVYWLTKGDP--------DMPDDGTGME 442
Cdd:COG0863   74 NIGDRYISR-LIAAL-----RDAGFKLRNEIIWRKPNGVPGPSKRRFrNSHEYILWFTKGKKytfnvdavKSIEDGRNPS 147

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 383396724 443 SIWRFHGPKP--NTDHPAPFPDELPRRCIEAlATDE-DVILDPFGGSMTTCEVAAKLGYESVGVDINPDWVE--KKR 514
Cdd:COG0863  148 DVWDIPGVTPkeRKGHPTQKPVELLERLILA-SSNPgDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEvaRRR 223
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 20-85 1.18e-21

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: 88.49  E-value: 1.18e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 383396724  20 YQVMPELSTDEFQRLKNDIEQNGIEYPIIVDADGEIIDGHHRMRAWKELGNdpDEIPTRTVDDTSD 85
Cdd:cd16404    6 EFRTPNPTNEEFEELKESIRKNGIIVPIIVDQDGVIIDGHHRYRIAKELGI--KEVPVIVYDFDDE 69
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 19-185 1.67e-15

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: 76.18  E-value: 1.67e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  19 PYQVMPELSTDEFQRLKNDIEQNGIEYPIIV--DADG--EIIDGHHRMRAWKELGNdpDEIPTRTVDDTSDENYHRAYRS 94
Cdd:COG1475   19 PYNPRRTFDEEALEELAASIREHGLLQPILVrpLGDGryEIIAGERRLRAAKLLGL--ETVPAIVRDLDDEEALELALIE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  95 NLLRRDLSDGTKREVVKQYLLEHpdrvaEDTQEAIAEDLGVSRALVTQ---VAN-DPDVKD-VTPNELTtdekREQVRTY 169
Cdd:COG1475   97 NLQREDLNPLEEARAYQRLLEEF-----GLTQEEIAERLGKSRSEVSNllrLLKlPPEVQEaLREGKLS----LGHARAL 167

                        170
                 ....*....|....*.
gi 383396724 170 VENNPDASNREVAREV 185
Cdd:COG1475  168 AALSDPERQEELAEKI 183
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
294-514 1.44e-51

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 175.50  E-value: 1.44e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 294 VGDASDL--PLENESVDLIITSPPYNLGhgdwKMGGEGRepreDGIGyyDDRDEREYQAWQLNVLQELYRVATKGASLFY 371
Cdd:COG0863    4 CGDCLEVlkELPDESVDLIVTDPPYNLG----KKYGLGR----REIG--NELSFEEYLEFLREWLAECYRVLKPGGSLYV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 372 NHKPRQAEGeVIHPLdwirdQDNPWTLRQEVVWDRQSTHNHSPNIFW-PVDERVYWLTKGDP--------DMPDDGTGME 442
Cdd:COG0863   74 NIGDRYISR-LIAAL-----RDAGFKLRNEIIWRKPNGVPGPSKRRFrNSHEYILWFTKGKKytfnvdavKSIEDGRNPS 147

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 383396724 443 SIWRFHGPKP--NTDHPAPFPDELPRRCIEAlATDE-DVILDPFGGSMTTCEVAAKLGYESVGVDINPDWVE--KKR 514
Cdd:COG0863  148 DVWDIPGVTPkeRKGHPTQKPVELLERLILA-SSNPgDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEvaRRR 223
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 307-511 1.89e-31

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: 120.97  E-value: 1.89e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  307 VDLIITSPPYNLGhgdwkmggegreprEDGIGYYDDRDEREYQAWQLNVLQELYRVATKGASLFYNHKPRQAEGEVIHpl 386
Cdd:pfam01555   1 VDLIVTDPPYNLG--------------KDYGQWDDKDSIEEYLEWLEEWLKEVRRVLKPGGSIFINIGDSNIKSLKAL-- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  387 dwIRDQDNPWTLRQEVVWDRQSTHNHSPNI-FWPVDERVYWLTKGDP----------------------DMPDDGTGMES 443
Cdd:pfam01555  65 --ALEILGIFKLLNDIIWRKPNGMPNSNGErFTPAHEYILWFSKTKKyktfnydaikvpydekdklkkrGSEPNGKPIGD 142

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 383396724  444 IWRF-------HGPKPNTDHPAPFPDELPRRCIEALATDEDVILDPFGGSMTTCEVAAKLGYESVGVDINPDWVE 511
Cdd:pfam01555 143 VWDFsrvqpseKESGGNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVE 217
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 20-85 1.18e-21

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: 88.49  E-value: 1.18e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 383396724  20 YQVMPELSTDEFQRLKNDIEQNGIEYPIIVDADGEIIDGHHRMRAWKELGNdpDEIPTRTVDDTSD 85
Cdd:cd16404    6 EFRTPNPTNEEFEELKESIRKNGIIVPIIVDQDGVIIDGHHRYRIAKELGI--KEVPVIVYDFDDE 69
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 19-185 1.67e-15

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: 76.18  E-value: 1.67e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  19 PYQVMPELSTDEFQRLKNDIEQNGIEYPIIV--DADG--EIIDGHHRMRAWKELGNdpDEIPTRTVDDTSDENYHRAYRS 94
Cdd:COG1475   19 PYNPRRTFDEEALEELAASIREHGLLQPILVrpLGDGryEIIAGERRLRAAKLLGL--ETVPAIVRDLDDEEALELALIE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  95 NLLRRDLSDGTKREVVKQYLLEHpdrvaEDTQEAIAEDLGVSRALVTQ---VAN-DPDVKD-VTPNELTtdekREQVRTY 169
Cdd:COG1475   97 NLQREDLNPLEEARAYQRLLEEF-----GLTQEEIAERLGKSRSEVSNllrLLKlPPEVQEaLREGKLS----LGHARAL 167

                        170
                 ....*....|....*.
gi 383396724 170 VENNPDASNREVAREV 185
Cdd:COG1475  168 AALSDPERQEELAEKI 183
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
295-510 2.29e-13

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 70.52  E-value: 2.29e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 295 GDASDL--PLENESVDLIITSPPYNLGhgdwkmggegreprEDGIGYYDDRDEREYQAWQLNVLQELYRVATKGASLFYn 372
Cdd:PRK11524  14 GDALTElkKIPSESVDLIFADPPYNIG--------------KNFDGLIEAWKEDLFIDWLYEWIDECHRVLKKQGTMYI- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 373 hkprQAEGEVIHPLD-WIRDQdnpWTLRQEVVWDRQSTHNHSPNIFWPVDERVYWLTK--------GDPDMPDDGTGMES 443
Cdd:PRK11524  79 ----MNSTENMPFIDlYCRKL---FTIKSRIVWSYDSSGVQAKKYFGSMYEPILMMVKdaknytfnGDAILVEAKTGAKR 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 444 I---WRFHGPKP-NT---------------------DHPAPFPDELPRRCIEALATDEDVILDPFGGSMTTCEVAAKLGY 498
Cdd:PRK11524 152 AlidYRKNPPQPyNTqkvpgnvwdfprvrylmdeyeNHPTQKPEALLKRIILASSNPGDIVLDPFAGSFTTGAVAKASGR 231

                        250
                 ....*....|..
gi 383396724 499 ESVGVDINPDWV 510
Cdd:PRK11524 232 KFIGIEINSEYI 243
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 16-142 8.22e-12

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: 63.94  E-value: 8.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724   16 TSEPYQVMPELSTDEFQRLKNDIEQNGIEYPIIV----DADG--EIIDGHHRMRAWKELGNDPdeIPTRTVDDTSDENYH 89
Cdd:TIGR00180  14 QPNPYQPRKDFSEESLAELIESIKEQGQLQPILVrkhpDQPGryEIIAGERRWRAAKLAGLKT--IPAIVRELDDEQMLA 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 383396724   90 RAYRSNLLRRDLsdgTKREVVKQY--LLEHPDRvaedTQEAIAEDLGVSRALVTQ 142
Cdd:TIGR00180  92 DALIENIQREDL---SPIEEAQAYkrLLEKFSM----TQEDLAKKIGKSRAHITN 139
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 19-86 5.80e-09

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: 53.08  E-value: 5.80e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 383396724    19 PYQVmPELSTDEFQRLKNDIEQNGIEYPIIVDADG---EIIDGHHRMRAWKELGndPDEIPTRTVDDTSDE 86
Cdd:smart00470  12 PDQP-RLTSEESLEELAESIKENGLLQPIIVRPNDgryEIIDGERRLRAAKLLG--LKEVPVIVRDLDDEE 79
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 19-86 4.57e-08

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: 50.74  E-value: 4.57e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 383396724   19 PYQVMpELSTDEFQRLKNDIEQNGIEYPIIVD--ADG--EIIDGHHRMRAWKELGndPDEIPTRTVDDTSDE 86
Cdd:pfam02195  12 PDQPR-KDSEESLEELAASIKKRGLLQPIIVRktPDGryEIIAGERRLRAAKLLG--LKEVPVIVREIDDEE 80
 
Name Accession Description Interval E-value
YhdJ COG0863
DNA modification methylase [Replication, recombination and repair];
294-514 1.44e-51

DNA modification methylase [Replication, recombination and repair];


Pssm-ID: 440623  Cd Length: 236  Bit Score: 175.50  E-value: 1.44e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 294 VGDASDL--PLENESVDLIITSPPYNLGhgdwKMGGEGRepreDGIGyyDDRDEREYQAWQLNVLQELYRVATKGASLFY 371
Cdd:COG0863    4 CGDCLEVlkELPDESVDLIVTDPPYNLG----KKYGLGR----REIG--NELSFEEYLEFLREWLAECYRVLKPGGSLYV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 372 NHKPRQAEGeVIHPLdwirdQDNPWTLRQEVVWDRQSTHNHSPNIFW-PVDERVYWLTKGDP--------DMPDDGTGME 442
Cdd:COG0863   74 NIGDRYISR-LIAAL-----RDAGFKLRNEIIWRKPNGVPGPSKRRFrNSHEYILWFTKGKKytfnvdavKSIEDGRNPS 147

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 383396724 443 SIWRFHGPKP--NTDHPAPFPDELPRRCIEAlATDE-DVILDPFGGSMTTCEVAAKLGYESVGVDINPDWVE--KKR 514
Cdd:COG0863  148 DVWDIPGVTPkeRKGHPTQKPVELLERLILA-SSNPgDIVLDPFAGSGTTLVAAERLGRRFIGIEIDPEYVEvaRRR 223
N6_N4_Mtase pfam01555
DNA methylase; Members of this family are DNA methylases. The family contains both N-4 ...
 307-511 1.89e-31

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: 120.97  E-value: 1.89e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  307 VDLIITSPPYNLGhgdwkmggegreprEDGIGYYDDRDEREYQAWQLNVLQELYRVATKGASLFYNHKPRQAEGEVIHpl 386
Cdd:pfam01555   1 VDLIVTDPPYNLG--------------KDYGQWDDKDSIEEYLEWLEEWLKEVRRVLKPGGSIFINIGDSNIKSLKAL-- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  387 dwIRDQDNPWTLRQEVVWDRQSTHNHSPNI-FWPVDERVYWLTKGDP----------------------DMPDDGTGMES 443
Cdd:pfam01555  65 --ALEILGIFKLLNDIIWRKPNGMPNSNGErFTPAHEYILWFSKTKKyktfnydaikvpydekdklkkrGSEPNGKPIGD 142

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 383396724  444 IWRF-------HGPKPNTDHPAPFPDELPRRCIEALATDEDVILDPFGGSMTTCEVAAKLGYESVGVDINPDWVE 511
Cdd:pfam01555 143 VWDFsrvqpseKESGGNGKHPTQKPEALLERLILASTNPGDIVLDPFAGSGTTGAAAKELGRNFIGIEIEEEYVE 217
pNOB8_ParB_N_like cd16404
pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain; archaeal pNOB8 ...
 20-85 1.18e-21

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: 88.49  E-value: 1.18e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 383396724  20 YQVMPELSTDEFQRLKNDIEQNGIEYPIIVDADGEIIDGHHRMRAWKELGNdpDEIPTRTVDDTSD 85
Cdd:cd16404    6 EFRTPNPTNEEFEELKESIRKNGIIVPIIVDQDGVIIDGHHRYRIAKELGI--KEVPVIVYDFDDE 69
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
 19-185 1.67e-15

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: 76.18  E-value: 1.67e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  19 PYQVMPELSTDEFQRLKNDIEQNGIEYPIIV--DADG--EIIDGHHRMRAWKELGNdpDEIPTRTVDDTSDENYHRAYRS 94
Cdd:COG1475   19 PYNPRRTFDEEALEELAASIREHGLLQPILVrpLGDGryEIIAGERRLRAAKLLGL--ETVPAIVRDLDDEEALELALIE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  95 NLLRRDLSDGTKREVVKQYLLEHpdrvaEDTQEAIAEDLGVSRALVTQ---VAN-DPDVKD-VTPNELTtdekREQVRTY 169
Cdd:COG1475   97 NLQREDLNPLEEARAYQRLLEEF-----GLTQEEIAERLGKSRSEVSNllrLLKlPPEVQEaLREGKLS----LGHARAL 167

                        170
                 ....*....|....*.
gi 383396724 170 VENNPDASNREVAREV 185
Cdd:COG1475  168 AALSDPERQEELAEKI 183
PRK11524 PRK11524
adenine-specific DNA-methyltransferase;
295-510 2.29e-13

adenine-specific DNA-methyltransferase;


Pssm-ID: 183177 [Multi-domain]  Cd Length: 284  Bit Score: 70.52  E-value: 2.29e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 295 GDASDL--PLENESVDLIITSPPYNLGhgdwkmggegreprEDGIGYYDDRDEREYQAWQLNVLQELYRVATKGASLFYn 372
Cdd:PRK11524  14 GDALTElkKIPSESVDLIFADPPYNIG--------------KNFDGLIEAWKEDLFIDWLYEWIDECHRVLKKQGTMYI- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 373 hkprQAEGEVIHPLD-WIRDQdnpWTLRQEVVWDRQSTHNHSPNIFWPVDERVYWLTK--------GDPDMPDDGTGMES 443
Cdd:PRK11524  79 ----MNSTENMPFIDlYCRKL---FTIKSRIVWSYDSSGVQAKKYFGSMYEPILMMVKdaknytfnGDAILVEAKTGAKR 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 444 I---WRFHGPKP-NT---------------------DHPAPFPDELPRRCIEALATDEDVILDPFGGSMTTCEVAAKLGY 498
Cdd:PRK11524 152 AlidYRKNPPQPyNTqkvpgnvwdfprvrylmdeyeNHPTQKPEALLKRIILASSNPGDIVLDPFAGSFTTGAVAKASGR 231

                        250
                 ....*....|..
gi 383396724 499 ESVGVDINPDWV 510
Cdd:PRK11524 232 KFIGIEINSEYI 243
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 16-142 8.22e-12

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: 63.94  E-value: 8.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724   16 TSEPYQVMPELSTDEFQRLKNDIEQNGIEYPIIV----DADG--EIIDGHHRMRAWKELGNDPdeIPTRTVDDTSDENYH 89
Cdd:TIGR00180  14 QPNPYQPRKDFSEESLAELIESIKEQGQLQPILVrkhpDQPGryEIIAGERRWRAAKLAGLKT--IPAIVRELDDEQMLA 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 383396724   90 RAYRSNLLRRDLsdgTKREVVKQY--LLEHPDRvaedTQEAIAEDLGVSRALVTQ 142
Cdd:TIGR00180  92 DALIENIQREDL---SPIEEAQAYkrLLEKFSM----TQEDLAKKIGKSRAHITN 139
ParB_N_like_MT cd16402
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 19-93 3.14e-09

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


Pssm-ID: 319259 [Multi-domain]  Cd Length: 87  Bit Score: 53.77  E-value: 3.14e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 383396724  19 PYQVMPELSTDEFQRLKNDIEQNGIEYPIIVDADGEIIDGHHRMRAWKELGNdpDEIPTRTVDDTSDENYhRAYR 93
Cdd:cd16402    7 PYENNPRNNDKAVEKVAESIKEFGFLVPIVVDKNNVIVAGHTRYKAAKRLGL--EEVPCIVADDLTEEQI-KAFR 78
ParB smart00470
ParB-like nuclease domain; Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB ...
 19-86 5.80e-09

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: 53.08  E-value: 5.80e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 383396724    19 PYQVmPELSTDEFQRLKNDIEQNGIEYPIIVDADG---EIIDGHHRMRAWKELGndPDEIPTRTVDDTSDE 86
Cdd:smart00470  12 PDQP-RLTSEESLEELAESIKENGLLQPIIVRPNDgryEIIDGERRLRAAKLLG--LKEVPVIVRDLDDEE 79
ParBc pfam02195
ParB/Sulfiredoxin domain; Proteins containing this domain include Escherichia coli plasmid ...
 19-86 4.57e-08

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: 50.74  E-value: 4.57e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 383396724   19 PYQVMpELSTDEFQRLKNDIEQNGIEYPIIVD--ADG--EIIDGHHRMRAWKELGndPDEIPTRTVDDTSDE 86
Cdd:pfam02195  12 PDQPR-KDSEESLEELAASIKKRGLLQPIIVRktPDGryEIIAGERRLRAAKLLG--LKEVPVIVREIDDEE 80
ParB_N_like_MT cd16403
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 32-93 6.46e-08

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: 50.15  E-value: 6.46e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 383396724  32 QRLKNDIEQNGIEYPIIVDADGEIIDGHHRMRAWKELGNdpDEIPTRTVDDTSDENyHRAYR 93
Cdd:cd16403   21 EQLAASIREFGFTNPILVDEDGVIIAGHGRLLAAKLLGL--KEVPVIRLDHLSEAQ-KRAYR 79
ParB_N_like_MT cd16844
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 27-81 7.79e-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: 48.80  E-value: 7.79e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 383396724  27 STDEFQRLKNDIEQNGIEYPIIVDADGEIIDGHHRMRAWKELGndPDEIPTRTVD 81
Cdd:cd16844    2 NDAQIERVAASIREFGFRVPVLIDKDGEIVDGHLRLEAARRLG--LETVPVIRVD 54
PRK13699 PRK13699
putative methylase; Provisional
 306-505 1.02e-07

putative methylase; Provisional


Pssm-ID: 184255  Cd Length: 227  Bit Score: 52.91  E-value: 1.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 306 SVDLIITSPPYNLGHGDwkmggegREPREDGigyYDDRDEreyqaWQLNVLQELYRVATKGASL--FY--NHKPR----- 376
Cdd:PRK13699  20 AVDFILTDPPYLVGFRD-------RQGRTIA---GDKTDE-----WLQPACNEMYRVLKKDALMvsFYgwNRVDRfmaaw 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 377 -QAEGEVIHPLDWIRDqdnpWTLRQEVVWDRQsthnhspnifwpvdERVYWLTKGDPDMPDDGTGMESIWRFHGpkpNTD 455
Cdd:PRK13699  85 kNAGFSVVGHLVFTKN----YTSKAAYVGYRH--------------ECAYILAKGRPALPQNPLPDVLGWKYSG---NRH 143

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 383396724 456 HPAPFPDELPRRCIEALATDEDVILDPFGGSMTTCEVAAKLGYESVGVDI 505
Cdd:PRK13699 144 HPTEKPVTSLQPLIESFTHPNAIVLDPFAGSGSTCVAALQSGRRYIGIEL 193
ParB_N_like cd16407
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 19-86 1.51e-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: 49.05  E-value: 1.51e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 383396724  19 PYQVmpeLSTDEFQRLKNDIEQNGIEYPIIV--DADG--EIIDGHHRMRAWKELGNdpDEIPTRTVDDTSDE 86
Cdd:cd16407   11 PFKV---RDDEEMEELVESIKENGVLTPIIVrpREDGgyEIISGHRRKRACELAGL--ETIPVIVREMDDDE 77
ParB_N_like cd16410
ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning ...
 34-86 4.53e-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: 319267 [Multi-domain]  Cd Length: 80  Bit Score: 47.58  E-value: 4.53e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 383396724  34 LKNDIEQNGIEYPIIVDADGEIIDGHHRMRAWKELGNdpDEIPTRTVDDTSDE 86
Cdd:cd16410   20 LAESIKRHGLLNPIVVTPDNELIAGERRLEAAKLLGW--ETIEVRVMDIEDEK 70
ParB_N_Srx cd16387
ParB N-terminal domain and sulfiredoxin protein-related families; The ParB N-terminal domain ...
 29-69 1.18e-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: 45.66  E-value: 1.18e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 383396724  29 DEFQRLKNDIEQNGIEYPIIV----DADGEIIDGHHRMRAWKELG 69
Cdd:cd16387    3 EELEELAESIREHGVLQPIIVrplpDGRYEIIAGERRWRAAKLAG 47
ParB_N_like_MT cd16401
ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent ...
 8-86 1.44e-06

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: 46.06  E-value: 1.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724   8 PAEGNPAGTSEPyqvmpelSTDEFQRLKNDIEQNGIEYPIIVD-ADGEIIDGHHRMRAWKELGndPDEIPTRTVD-DTSD 85
Cdd:cd16401    1 PAPYNPRKDLKP-------GDKEYEKLKESIEEFGLVDPLIVNkRTNVLIGGHQRLKVLKELG--YTEVPVVVVDlDEEK 71


                 .
gi 383396724  86 E 86
Cdd:cd16401   72 E 72
ParB_Srx_like_nuclease cd16400
ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI; This family ...
 25-69 3.61e-06

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: 44.85  E-value: 3.61e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 383396724  25 ELSTDEFQRLKNDIEQNGIEY-PIIVDAD-GEIIDGHHRMRAWKELG 69
Cdd:cd16400   12 EVDPDRVEELIEKILEEGVWTkPIIVDKNtGIILDGHHRLEAAKRLG 58
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 291-367 1.09e-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: 45.71  E-value: 1.09e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 383396724 291 TLEVGDASDLPLENESVDLIITSPPYnlghgdwkmggeGRepredGIGYYDDRDEREYQawqlNVLQELYRVATKGA 367
Cdd:COG1041   77 DVIRGDARDLPLADESVDAIVTDPPY------------GR-----SSKISGEELLELYE----KALEEAARVLKPGG 132
Mod COG2189
Adenine specific DNA methylase Mod [Replication, recombination and repair];
323-502 1.59e-05

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


Pssm-ID: 441792 [Multi-domain]  Cd Length: 491  Bit Score: 47.46  E-value: 1.59e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 323 WKMGGEGREprEDGIGYYDDRDEREYQAWQLNVLqelyRVATKGASLFY--NHKPRqaeGEVIHPldwirdqDNPWTLRQ 400
Cdd:COG2189  175 LKFNGLPRT--EEQLKRYKNPDNDPRGRWRSVPL----TAPGGRPNLFYpiEHPST---GKEVYP-------GRGWRWSK 238

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724 401 EVVWDRQSTHNhspnIFWPVDE-----RVYWLTKGDPDMPddgtgMESIWRFHGPkpNTDH-------------PAPFPD 462
Cdd:COG2189  239 ETMEELIADGR----IYFGKDGngvprRKRYLDEVKKGVV-----PTTIWDDIGT--NQNGtkelkelfggkvfDTPKPE 307

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 383396724 463 ELPRRCIEALATDEDVILDPFGGSMTTCEVAAKLGYESVG 502
Cdd:COG2189  308 KLLKRIIEIATNPGDLVLDFFAGSGTTAHAVMKLNAEDGG 347
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 456-515 1.78e-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: 45.32  E-value: 1.78e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 383396724 456 HPAPFPDELPRRCIE-ALATDEDVILDPFGGSMTTCEVAAKLGYESVGVDINPDWVEKKRE 515
Cdd:COG1041    6 YPGSLDPRLARALVNlAGAKEGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPKMVEGARE 66
Noc_N cd16396
nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning ...
 19-96 6.93e-05

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: 41.82  E-value: 6.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  19 PYQVMPELSTDEFQRLKNDIEQNGIEYPIIV--DADG--EIIDGHHRMRAWKELGNdpDEIPTRTVDDTSDENYHRAYRS 94
Cdd:cd16396   15 PYQPRKEFDEEEIEELAESIKEHGLLQPIVVrkTKDGgyEIVAGERRWRAAKLLGW--EKIPAIIRDLSDKEALEIALIE 92


                 ..
gi 383396724  95 NL 96
Cdd:cd16396   93 NL 94
RepB_like_N cd16405
plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on ...
 29-86 1.21e-04

plasmid segregation replication protein B like protein, N-terminal domain; RepB, found on plasmids and secondary chromosomes, works along with repA in directing plasmid segregation, and has been shown in Rhizobium etli to require the parS centromere-like sequence for full transcriptional repression of the repABC operon, inducing plasmid incompatibility. RepA is a Walker-type ATPase that complexes with RepB to form DNA-protein complexes in the presence of ATP/ADP. RepC is an initiator protein for the plasmid. repA and repB are homologous to the parA and ParB genes of the parABS partitioning system found on primary chromosomes.


Pssm-ID: 319262 [Multi-domain]  Cd Length: 91  Bit Score: 40.99  E-value: 1.21e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 383396724  29 DEFQRLKNDIEQNGIEYPIIV----DADG--EIIDGHHRMRAWKELGndpdeIPTR-TVDDTSDE 86
Cdd:cd16405   22 DEFEELKESIRESGQQVPILVrphpEEGGryEIVYGHRRLRACRELG-----LPVRaIVRELSDE 81
SPO0J_N cd16393
Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member; ...
 19-91 3.62e-04

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: 39.77  E-value: 3.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 383396724  19 PYQVMPELSTDEFQRLKNDIEQNGIEYPIIVDADG----EIIDGHHRMRAWKELGNdpDEIPTrTVDDTSD--------- 85
Cdd:cd16393   13 PYQPRKEFDEEALKELAESIKEHGLLQPIVVRKVGdgryEIIAGERRWRAAKLAGL--TEIPA-IVRDLDDeealelali 89


                 ....*.
gi 383396724  86 ENYHRA 91
Cdd:cd16393   90 ENIQRE 95
ParB_N_like cd16408
ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning ...
 29-86 1.04e-03

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: 37.99  E-value: 1.04e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 383396724  29 DEFQRLKNDIEQNGIEYPIIV----DADGEIIDGHHRMRAWKELGndPDEIPTRTVDDTSDE 86
Cdd:cd16408   15 ERLEDMVESIKENGVLQPIIVrpieDGKYEILAGHNRVNAAKLAG--LTTIPAIIKENLTDE 74
ParB_N_Srx_like cd16390
uncharacterized family distantly related to the N-terminal domain of the ParB/Srx superfamily; ...
 46-85 1.33e-03

uncharacterized family distantly related to the N-terminal domain of the ParB/Srx superfamily; Uncharacterized proteins distantly related to the N-terminal domain of the ParB superfamily, primarily involved in bacterial and plasmid parABS-related partitioning systems. A small minority of proteins in this family include a C-terminal inorganic pyrophosphatase domain. Also within the ParB superfamily is sulfiredoxin (Srx), which is a reactivator of oxidatively inactivated 2-cys peroxiredoxins. Other families includes 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: 319249  Cd Length: 162  Bit Score: 39.47  E-value: 1.33e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 383396724  46 PIIVDADGE--IIDGHHRMRAWKELGNDPDEIPTRTVDDTSD 85
Cdd:cd16390   46 PVVIGPGGRlyLTDGHHLLRALLELGVGGLKVPVRVVADLSD 87
ParB_N_like cd16409
ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems; This family ...
 34-86 2.92e-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: 36.51  E-value: 2.92e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 383396724  34 LKNDIEQNGIEYPIIVDADGE----IIDGHHRMRAWKELGNdpDEIPTRTVDDTSDE 86
Cdd:cd16409    9 LAQSIAEHGLLTPITVRQDPGgrytLIAGAHRLAAAKLLGW--DTIDAIIVKADDLE 63
RpiR COG1737
DNA-binding transcriptional regulator, MurR/RpiR family, contains HTH and SIS domains ...
 95-141 6.62e-03

DNA-binding transcriptional regulator, MurR/RpiR family, contains HTH and SIS domains [Transcription];


Pssm-ID: 441343 [Multi-domain]  Cd Length: 286  Bit Score: 38.76  E-value: 6.62e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 383396724  95 NLLRRDLSDGTKRE-VVKQYLLEHPDRVAEDTQEAIAEDLGVSRALVT 141
Cdd:COG1737    9 ERIRARYPSLSPSErRIADYILDNPEEVAFMSIAELAEAAGVSEATVV 56
UPF0020 pfam01170
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated ...
 291-316 7.96e-03

Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains.


Pssm-ID: 395932 [Multi-domain]  Cd Length: 184  Bit Score: 37.72  E-value: 7.96e-03
                          10        20
                  ....*....|....*....|....*.
gi 383396724  291 TLEVGDASDLPLENESVDLIITSPPY 316
Cdd:pfam01170  93 EFVQADAADLPLLEGSVDVIVTNPPY 118
 
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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