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Conserved domains on  [gi|557798183|gb|ESS41772|]
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DNA primase [Burkholderia cenocepacia KC-01]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
16-494 0e+00

DNA primase (bacterial type) [Replication, recombination and repair];


:

Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 619.46  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  16 IPHSFLQDLLNRVDIVDVVGRYVQLKKGGANFMGLCPFHNEKSPSFTVSPTKQFYHCFGCGAHGTAIGFLMEHAGLTFPE 95
Cdd:COG0358    2 IPDEFIDEIRARVDIVDVIGEYVKLKKAGRNYKGLCPFHDEKTPSFTVSPEKQFYHCFGCGAGGDVISFLMEYEGLSFPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  96 AVQELAQSVGLTVPHEPSmrgggggggggggggggDYPAPVSKSVATALSDAMTAACDYYRKQLRG---ATVAIQYLKNR 172
Cdd:COG0358   82 AVEELAERAGIELPEEEG-----------------SPEEREEASERERLYEALELAAKFYQEQLKNtpeGKAARDYLKKR 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 173 GLTGEIAARFGLGYAPDGWQNLEAAFPD--YRDESLVEAGLVIVSEKTdaqgvaRRYDRFRERIMFPIRNVKGQVIGFGG 250
Cdd:COG0358  145 GLSDETIERFGLGYAPDGWDALLKHLKKkgFSEEELVEAGLVIEREDG------GYYDRFRGRIMFPIRDLRGRVIGFGG 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 251 RVLGSGEPKYLNSPETPLFNKGSELYGLFEARLAIRERKYVLVVEGYMDVVALAQLGFPNAVATLGTACTPIHVQKLLRQ 330
Cdd:COG0358  219 RVLDDGEPKYLNSPETPLFHKGRVLYGLDLARKAIRKEDRVIVVEGYMDVIALHQAGIKNAVATLGTALTEEHIKLLKRY 298

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 331 TDTVIFSFDGDSAGRRAARRALEACLphaGDNRTIRFLFLPTEHDPDSYVREFGADAFSEQVERAMPLSQFLLNEAIAGK 410
Cdd:COG0358  299 TDEVILCFDGDAAGQKAALRALELLL---KDGLQVRVLFLPDGEDPDELIRKEGAEAFRELLENAKPLIEFLIERLLEGY 375

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 411 ALDQPEGRAKALFDAKPLLQALPANALRAQIMHMFADRLDIPFEEVAAL-----SDVDTRIatppRQAPARSERRRVTDS 485
Cdd:COG0358  376 DLDTPEGRAALLREALPLLAKIPDPILRELYLRELAERLGLDEEALDALarlkrRALEKRI----EELKEELKEARGDEE 451


                 ....*....
gi 557798183 486 EKRALRTLV 494
Cdd:COG0358  452 EKKELRELL 460
DnaG_DnaB_bind super family cl07879
DNA primase DnaG DnaB-binding; Eubacterial DnaG primases interact with several factors to from ...
 486-632 1.23e-14

DNA primase DnaG DnaB-binding; Eubacterial DnaG primases interact with several factors to from the replisome. One of these factors in DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB.


The actual alignment was detected with superfamily member smart00766:

Pssm-ID: 447551  Cd Length: 125  Bit Score: 70.75  E-value: 1.23e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   486 EKRALRTLVMHPRIASQLDDEQIATLRALPRIgELFAEVVDHARALGdgaefRLLSDVLRTSSNGATYEEIFREILDYDE 565
Cdd:smart00766   1 MRELIRLLLQNPELASLVPDLLPLELFTHPGL-ALLAELLALCRGAP-----GLTTGQLLEHWRDTPYRELLSELAVWDH 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   566 NVrdlllqnPEDETVperqreqeriagEELQAAVLKMRYDACCDRLDRL---ARQSTFTPEELAELTELN 632
Cdd:smart00766  75 LI-------DEENLE------------EEFQDALARLRKQLLERRIEELiakLRRSGLTVEEKKELQALL 125
 
Name Accession Description Interval E-value
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
16-494 0e+00

DNA primase (bacterial type) [Replication, recombination and repair];


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 619.46  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  16 IPHSFLQDLLNRVDIVDVVGRYVQLKKGGANFMGLCPFHNEKSPSFTVSPTKQFYHCFGCGAHGTAIGFLMEHAGLTFPE 95
Cdd:COG0358    2 IPDEFIDEIRARVDIVDVIGEYVKLKKAGRNYKGLCPFHDEKTPSFTVSPEKQFYHCFGCGAGGDVISFLMEYEGLSFPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  96 AVQELAQSVGLTVPHEPSmrgggggggggggggggDYPAPVSKSVATALSDAMTAACDYYRKQLRG---ATVAIQYLKNR 172
Cdd:COG0358   82 AVEELAERAGIELPEEEG-----------------SPEEREEASERERLYEALELAAKFYQEQLKNtpeGKAARDYLKKR 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 173 GLTGEIAARFGLGYAPDGWQNLEAAFPD--YRDESLVEAGLVIVSEKTdaqgvaRRYDRFRERIMFPIRNVKGQVIGFGG 250
Cdd:COG0358  145 GLSDETIERFGLGYAPDGWDALLKHLKKkgFSEEELVEAGLVIEREDG------GYYDRFRGRIMFPIRDLRGRVIGFGG 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 251 RVLGSGEPKYLNSPETPLFNKGSELYGLFEARLAIRERKYVLVVEGYMDVVALAQLGFPNAVATLGTACTPIHVQKLLRQ 330
Cdd:COG0358  219 RVLDDGEPKYLNSPETPLFHKGRVLYGLDLARKAIRKEDRVIVVEGYMDVIALHQAGIKNAVATLGTALTEEHIKLLKRY 298

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 331 TDTVIFSFDGDSAGRRAARRALEACLphaGDNRTIRFLFLPTEHDPDSYVREFGADAFSEQVERAMPLSQFLLNEAIAGK 410
Cdd:COG0358  299 TDEVILCFDGDAAGQKAALRALELLL---KDGLQVRVLFLPDGEDPDELIRKEGAEAFRELLENAKPLIEFLIERLLEGY 375

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 411 ALDQPEGRAKALFDAKPLLQALPANALRAQIMHMFADRLDIPFEEVAAL-----SDVDTRIatppRQAPARSERRRVTDS 485
Cdd:COG0358  376 DLDTPEGRAALLREALPLLAKIPDPILRELYLRELAERLGLDEEALDALarlkrRALEKRI----EELKEELKEARGDEE 451


                 ....*....
gi 557798183 486 EKRALRTLV 494
Cdd:COG0358  452 EKKELRELL 460
dnaG TIGR01391
DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria ...
 16-449 9.16e-171

DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria protein. Most members of this family contain nearly two hundred additional residues C-terminal to the region represented here, but conservation between species is poor and the C-terminal region was not included in the seed alignment. This protein contains a CHC2 zinc finger (pfam01807) and a Toprim domain (pfam01751). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273595 [Multi-domain]  Cd Length: 415  Bit Score: 492.89  E-value: 9.16e-171
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   16 IPHSFLQDLLNRVDIVDVVGRYVQLKKGGANFMGLCPFHNEKSPSFTVSPTKQFYHCFGCGAHGTAIGFLMEHAGLTFPE 95
Cdd:TIGR01391   2 IPEEFIDELKERVDIVDVISEYVKLKKKGRNYVGLCPFHHEKTPSFSVSPEKQFYHCFGCGAGGDAIKFLMEIEGISFVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   96 AVQELAQSVGLTVPHEPsmrggggggggggggggGDYPAPVSKSVATALSDAMTAACDYYRKQLR---GATVAIQYLKNR 172
Cdd:TIGR01391  82 AVEELAKRAGIDLPFEK-----------------DQQEKKEQKSKRKKLYELLELAAKFFKNQLKhtpENRAALDYLQSR 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  173 GLTGEIAARFGLGYAPDGWQNLEAAFPD---YRDESLVEAGLVIVSEKTdaqgvaRRYDRFRERIMFPIRNVKGQVIGFG 249
Cdd:TIGR01391 145 GLSDETIDRFELGYAPNNWDFLFDFLQNkkgFDLELLAEAGLLVKKENG------KYYDRFRNRIMFPIHDPKGRVVGFG 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  250 GRVLGSGEPKYLNSPETPLFNKGSELYGLFEARLAIRERKYVLVVEGYMDVVALAQLGFPNAVATLGTACTPIHVQKLLR 329
Cdd:TIGR01391 219 GRALGDEKPKYLNSPETPLFKKSELLYGLHKARKEIRKEKELILVEGYMDVIALHQAGIKNAVASLGTALTEEHIKLLKR 298

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  330 QTDTVIFSFDGDSAGRRAARRALEACLPHagdNRTIRFLFLPTEHDPDSYVREFGADAFSEQVERAMPLSQFLLNEAIAG 409
Cdd:TIGR01391 299 YADEIILCFDGDKAGRKAALRAIELLLPL---GINVKVIKLPGGKDPDEYLRKEGVEALKKLLENSKSLIEFLIARLLSN 375

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|
gi 557798183  410 KALDQPEGRAKALFDAKPLLQALPANALRAQIMHMFADRL 449
Cdd:TIGR01391 376 YNLDTPEEKAKLVEELLPLIKKIPDPILRDYYLQKLAQLL 415
Toprim_N pfam08275
DNA primase catalytic core, N-terminal domain;
154-282 2.17e-55

DNA primase catalytic core, N-terminal domain;


Pssm-ID: 429892 [Multi-domain]  Cd Length: 128  Bit Score: 184.26  E-value: 2.17e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  154 YYRKQLRGAT--VAIQYLKNRGLTGEIAARFGLGYAPDGWQNLEAAFPD--YRDESLVEAGLVIVSEKTdaqgvaRRYDR 229
Cdd:pfam08275   1 FYQELLKTNEgaAALDYLKSRGLSDETIERFQIGYAPDGWDNLLKFLKKkgFSEEELLEAGLLSKNEDG------RYYDR 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 557798183  230 FRERIMFPIRNVKGQVIGFGGRVLGSGEP-KYLNSPETPLFNKGSELYGLFEAR 282
Cdd:pfam08275  75 FRNRIMFPIKDARGRVVGFGGRALDDDKPpKYLNSPETPLFKKSKLLYGLDEAK 128
ZnF_CHCC smart00400
zinc finger;
47-101 3.51e-29

zinc finger;


Pssm-ID: 128681 [Multi-domain]  Cd Length: 55  Bit Score: 109.69  E-value: 3.51e-29
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 557798183    47 FMGLCPFHNEKSPSFTVSPTKQFYHCFGCGAHGTAIGFLMEHAGLTFPEAVQELA 101
Cdd:smart00400   1 YKGLCPFHGEKTPSFSVSPDKQFFHCFGCGAGGNVISFLMKYDKLSFVEAVKKLA 55
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 289-370 3.02e-22

TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.


Pssm-ID: 173784 [Multi-domain]  Cd Length: 79  Bit Score: 91.04  E-value: 3.02e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 289 KYVLVVEGYMDVVALAQLGFPNAVATLGTACTPIHVQKLLRQTDTVIFSFDGDSAGRRAARRALEACLPHagdNRTIRFL 368
Cdd:cd03364    1 KKVILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALRALELLLKL---GLNVRVL 77


                 ..
gi 557798183 369 FL 370
Cdd:cd03364   78 TL 79
DnaG_DnaB_bind smart00766
DNA primase DnaG DnaB-binding; DnaG_DnaB_bind defines a domain of primase required for ...
 486-632 1.23e-14

DNA primase DnaG DnaB-binding; DnaG_DnaB_bind defines a domain of primase required for functional interaction with DnaB that attracts primase to the replication fork. DnaG_DnaB_bind is responsible for the interaction between DnaG and DnaB.


Pssm-ID: 197866  Cd Length: 125  Bit Score: 70.75  E-value: 1.23e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   486 EKRALRTLVMHPRIASQLDDEQIATLRALPRIgELFAEVVDHARALGdgaefRLLSDVLRTSSNGATYEEIFREILDYDE 565
Cdd:smart00766   1 MRELIRLLLQNPELASLVPDLLPLELFTHPGL-ALLAELLALCRGAP-----GLTTGQLLEHWRDTPYRELLSELAVWDH 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   566 NVrdlllqnPEDETVperqreqeriagEELQAAVLKMRYDACCDRLDRL---ARQSTFTPEELAELTELN 632
Cdd:smart00766  75 LI-------DEENLE------------EEFQDALARLRKQLLERRIEELiakLRRSGLTVEEKKELQALL 125
PRK08624 PRK08624
hypothetical protein; Provisional
 214-339 2.12e-08

hypothetical protein; Provisional


Pssm-ID: 236314 [Multi-domain]  Cd Length: 373  Bit Score: 56.48  E-value: 2.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 214 VSEKTDAQGVARRY-DRFRERIMFPIRNVKGQVIGFGGRVLGSGE-------PKYLNSPetpLFN--KGSELYGLFEARL 283
Cdd:PRK08624 163 ISEKTQKYWEIKFYlDVISQRIIIPHRDESGELIGIRGRLLDKELvdknkyfPIYVNDT---GYNhpKGKILYGLWQNKK 239

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 557798183 284 AIRERKYVLVVEGYMDVVALAQL-GFPNAVATLGTAC-TPIHVQKLLR-QTDTVIFSFD 339
Cdd:PRK08624 240 YIKEKKKVIIVESEKSVLFSDKFyGEGNFVVAICGSNiSEVQAEKLLRlGVEEVTIALD 298
 
Name Accession Description Interval E-value
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
16-494 0e+00

DNA primase (bacterial type) [Replication, recombination and repair];


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 619.46  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  16 IPHSFLQDLLNRVDIVDVVGRYVQLKKGGANFMGLCPFHNEKSPSFTVSPTKQFYHCFGCGAHGTAIGFLMEHAGLTFPE 95
Cdd:COG0358    2 IPDEFIDEIRARVDIVDVIGEYVKLKKAGRNYKGLCPFHDEKTPSFTVSPEKQFYHCFGCGAGGDVISFLMEYEGLSFPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  96 AVQELAQSVGLTVPHEPSmrgggggggggggggggDYPAPVSKSVATALSDAMTAACDYYRKQLRG---ATVAIQYLKNR 172
Cdd:COG0358   82 AVEELAERAGIELPEEEG-----------------SPEEREEASERERLYEALELAAKFYQEQLKNtpeGKAARDYLKKR 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 173 GLTGEIAARFGLGYAPDGWQNLEAAFPD--YRDESLVEAGLVIVSEKTdaqgvaRRYDRFRERIMFPIRNVKGQVIGFGG 250
Cdd:COG0358  145 GLSDETIERFGLGYAPDGWDALLKHLKKkgFSEEELVEAGLVIEREDG------GYYDRFRGRIMFPIRDLRGRVIGFGG 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 251 RVLGSGEPKYLNSPETPLFNKGSELYGLFEARLAIRERKYVLVVEGYMDVVALAQLGFPNAVATLGTACTPIHVQKLLRQ 330
Cdd:COG0358  219 RVLDDGEPKYLNSPETPLFHKGRVLYGLDLARKAIRKEDRVIVVEGYMDVIALHQAGIKNAVATLGTALTEEHIKLLKRY 298

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 331 TDTVIFSFDGDSAGRRAARRALEACLphaGDNRTIRFLFLPTEHDPDSYVREFGADAFSEQVERAMPLSQFLLNEAIAGK 410
Cdd:COG0358  299 TDEVILCFDGDAAGQKAALRALELLL---KDGLQVRVLFLPDGEDPDELIRKEGAEAFRELLENAKPLIEFLIERLLEGY 375

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 411 ALDQPEGRAKALFDAKPLLQALPANALRAQIMHMFADRLDIPFEEVAAL-----SDVDTRIatppRQAPARSERRRVTDS 485
Cdd:COG0358  376 DLDTPEGRAALLREALPLLAKIPDPILRELYLRELAERLGLDEEALDALarlkrRALEKRI----EELKEELKEARGDEE 451


                 ....*....
gi 557798183 486 EKRALRTLV 494
Cdd:COG0358  452 EKKELRELL 460
dnaG TIGR01391
DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria ...
 16-449 9.16e-171

DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria protein. Most members of this family contain nearly two hundred additional residues C-terminal to the region represented here, but conservation between species is poor and the C-terminal region was not included in the seed alignment. This protein contains a CHC2 zinc finger (pfam01807) and a Toprim domain (pfam01751). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273595 [Multi-domain]  Cd Length: 415  Bit Score: 492.89  E-value: 9.16e-171
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   16 IPHSFLQDLLNRVDIVDVVGRYVQLKKGGANFMGLCPFHNEKSPSFTVSPTKQFYHCFGCGAHGTAIGFLMEHAGLTFPE 95
Cdd:TIGR01391   2 IPEEFIDELKERVDIVDVISEYVKLKKKGRNYVGLCPFHHEKTPSFSVSPEKQFYHCFGCGAGGDAIKFLMEIEGISFVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   96 AVQELAQSVGLTVPHEPsmrggggggggggggggGDYPAPVSKSVATALSDAMTAACDYYRKQLR---GATVAIQYLKNR 172
Cdd:TIGR01391  82 AVEELAKRAGIDLPFEK-----------------DQQEKKEQKSKRKKLYELLELAAKFFKNQLKhtpENRAALDYLQSR 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  173 GLTGEIAARFGLGYAPDGWQNLEAAFPD---YRDESLVEAGLVIVSEKTdaqgvaRRYDRFRERIMFPIRNVKGQVIGFG 249
Cdd:TIGR01391 145 GLSDETIDRFELGYAPNNWDFLFDFLQNkkgFDLELLAEAGLLVKKENG------KYYDRFRNRIMFPIHDPKGRVVGFG 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  250 GRVLGSGEPKYLNSPETPLFNKGSELYGLFEARLAIRERKYVLVVEGYMDVVALAQLGFPNAVATLGTACTPIHVQKLLR 329
Cdd:TIGR01391 219 GRALGDEKPKYLNSPETPLFKKSELLYGLHKARKEIRKEKELILVEGYMDVIALHQAGIKNAVASLGTALTEEHIKLLKR 298

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  330 QTDTVIFSFDGDSAGRRAARRALEACLPHagdNRTIRFLFLPTEHDPDSYVREFGADAFSEQVERAMPLSQFLLNEAIAG 409
Cdd:TIGR01391 299 YADEIILCFDGDKAGRKAALRAIELLLPL---GINVKVIKLPGGKDPDEYLRKEGVEALKKLLENSKSLIEFLIARLLSN 375

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|
gi 557798183  410 KALDQPEGRAKALFDAKPLLQALPANALRAQIMHMFADRL 449
Cdd:TIGR01391 376 YNLDTPEEKAKLVEELLPLIKKIPDPILRDYYLQKLAQLL 415
Toprim_N pfam08275
DNA primase catalytic core, N-terminal domain;
154-282 2.17e-55

DNA primase catalytic core, N-terminal domain;


Pssm-ID: 429892 [Multi-domain]  Cd Length: 128  Bit Score: 184.26  E-value: 2.17e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  154 YYRKQLRGAT--VAIQYLKNRGLTGEIAARFGLGYAPDGWQNLEAAFPD--YRDESLVEAGLVIVSEKTdaqgvaRRYDR 229
Cdd:pfam08275   1 FYQELLKTNEgaAALDYLKSRGLSDETIERFQIGYAPDGWDNLLKFLKKkgFSEEELLEAGLLSKNEDG------RYYDR 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 557798183  230 FRERIMFPIRNVKGQVIGFGGRVLGSGEP-KYLNSPETPLFNKGSELYGLFEAR 282
Cdd:pfam08275  75 FRNRIMFPIKDARGRVVGFGGRALDDDKPpKYLNSPETPLFKKSKLLYGLDEAK 128
zf-CHC2 pfam01807
CHC2 zinc finger; This domain is principally involved in DNA binding in DNA primases.
 17-111 9.64e-51

CHC2 zinc finger; This domain is principally involved in DNA binding in DNA primases.


Pssm-ID: 426447 [Multi-domain]  Cd Length: 95  Bit Score: 170.51  E-value: 9.64e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   17 PHSFLQDLLNRVDIVDVVGRYVQLKKGGANFMGLCPFHNEKSPSFTVSPTKQFYHCFGCGAHGTAIGFLMEHAGLTFPEA 96
Cdd:pfam01807   1 PPEFIDDLKNRIDIVDVVGQYVKLKKRGKDYVGLCPFHHEKTPSFTVSPDKQFYHCFGCGAGGDVIKFLMKIEKLSFVEA 80

                          90
                  ....*....|....*
gi 557798183   97 VQELAQSVGLTVPHE 111
Cdd:pfam01807  81 VEKLADRYGIEIPYE 95
ZnF_CHCC smart00400
zinc finger;
47-101 3.51e-29

zinc finger;


Pssm-ID: 128681 [Multi-domain]  Cd Length: 55  Bit Score: 109.69  E-value: 3.51e-29
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 557798183    47 FMGLCPFHNEKSPSFTVSPTKQFYHCFGCGAHGTAIGFLMEHAGLTFPEAVQELA 101
Cdd:smart00400   1 YKGLCPFHGEKTPSFSVSPDKQFFHCFGCGAGGNVISFLMKYDKLSFVEAVKKLA 55
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 289-370 3.02e-22

TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.


Pssm-ID: 173784 [Multi-domain]  Cd Length: 79  Bit Score: 91.04  E-value: 3.02e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 289 KYVLVVEGYMDVVALAQLGFPNAVATLGTACTPIHVQKLLRQTDTVIFSFDGDSAGRRAARRALEACLPHagdNRTIRFL 368
Cdd:cd03364    1 KKVILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALRALELLLKL---GLNVRVL 77


                 ..
gi 557798183 369 FL 370
Cdd:cd03364   78 TL 79
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 289-370 2.42e-18

TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.


Pssm-ID: 173779 [Multi-domain]  Cd Length: 79  Bit Score: 79.62  E-value: 2.42e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 289 KYVLVVEGYMDVVALAQLGFPNAVATLGTACTPIHVQKLLRQTDTVIFSFDGDSAGRRAARRALEACLPHagdNRTIRFL 368
Cdd:cd01029    1 DEVIIVEGYMDVLALHQAGIKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKAAARALELLLAL---GGRVRVP 77


                 ..
gi 557798183 369 FL 370
Cdd:cd01029   78 PL 79
DnaG_DnaB_bind smart00766
DNA primase DnaG DnaB-binding; DnaG_DnaB_bind defines a domain of primase required for ...
 486-632 1.23e-14

DNA primase DnaG DnaB-binding; DnaG_DnaB_bind defines a domain of primase required for functional interaction with DnaB that attracts primase to the replication fork. DnaG_DnaB_bind is responsible for the interaction between DnaG and DnaB.


Pssm-ID: 197866  Cd Length: 125  Bit Score: 70.75  E-value: 1.23e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   486 EKRALRTLVMHPRIASQLDDEQIATLRALPRIgELFAEVVDHARALGdgaefRLLSDVLRTSSNGATYEEIFREILDYDE 565
Cdd:smart00766   1 MRELIRLLLQNPELASLVPDLLPLELFTHPGL-ALLAELLALCRGAP-----GLTTGQLLEHWRDTPYRELLSELAVWDH 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183   566 NVrdlllqnPEDETVperqreqeriagEELQAAVLKMRYDACCDRLDRL---ARQSTFTPEELAELTELN 632
Cdd:smart00766  75 LI-------DEENLE------------EEFQDALARLRKQLLERRIEELiakLRRSGLTVEEKKELQALL 125
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 293-380 1.16e-13

Toprim-like; This is a family or Toprim-like proteins.


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 66.82  E-value: 1.16e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  293 VVEGYMDVVALAQLGFPNA--VATLGTACTPIHVQKLLRQTDTVIFSFDGDSAGRRAARRALEAcLPHAGDNRTIRflFL 370
Cdd:pfam13155   2 VFEGYIDALSLAQAGIKNVlyVATLGTALTEAQIKLLKRYPKEVILAFDNDEAGRKAAKRLAEL-LKEAGVDVKIR--LL 78

                          90
                  ....*....|
gi 557798183  371 PTEHDPDSYV 380
Cdd:pfam13155  79 PDGKDWNEYL 88
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 289-341 1.04e-10

Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.


Pssm-ID: 433387 [Multi-domain]  Cd Length: 85  Bit Score: 58.45  E-value: 1.04e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  289 KYVLVVEGYMDVVALAQLGFPNAVATLGTACTPI-HVQKLLRQTDT------VIFSFDGD 341
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVAVLGGALSPLdGIGPEDLNIDSlggikeVILALDGD 60
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 289-367 6.41e-10

Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 55.90  E-value: 6.41e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 289 KYVLVVEGYMDVVALAQLGFP--NAVATLGTAC--TPIHVQKLLRQTDTVIFSFDGDSAGRRAARRALEACLPHAGDNRT 364
Cdd:cd00188    1 KKLIIVEGPSDALALAQAGGYggAVVALGGHALnkTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSLGKKVRR 80


                 ...
gi 557798183 365 IRF 367
Cdd:cd00188   81 LLL 83
PRK08624 PRK08624
hypothetical protein; Provisional
 214-339 2.12e-08

hypothetical protein; Provisional


Pssm-ID: 236314 [Multi-domain]  Cd Length: 373  Bit Score: 56.48  E-value: 2.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 214 VSEKTDAQGVARRY-DRFRERIMFPIRNVKGQVIGFGGRVLGSGE-------PKYLNSPetpLFN--KGSELYGLFEARL 283
Cdd:PRK08624 163 ISEKTQKYWEIKFYlDVISQRIIIPHRDESGELIGIRGRLLDKELvdknkyfPIYVNDT---GYNhpKGKILYGLWQNKK 239

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 557798183 284 AIRERKYVLVVEGYMDVVALAQL-GFPNAVATLGTAC-TPIHVQKLLR-QTDTVIFSFD 339
Cdd:PRK08624 240 YIKEKKKVIIVESEKSVLFSDKFyGEGNFVVAICGSNiSEVQAEKLLRlGVEEVTIALD 298
DnaB_bind pfam10410
DnaB-helicase binding domain of primase; This domain is the C-terminal region three-helical ...
 399-452 4.57e-08

DnaB-helicase binding domain of primase; This domain is the C-terminal region three-helical domain of primase. Primases synthesize short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases, and this domain is the region of the primase which binds DnaB-helicase. It is associated with the Toprim domain (pfam01751) which is the central catalytic core.


Pssm-ID: 463082  Cd Length: 54  Bit Score: 49.76  E-value: 4.57e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 557798183  399 SQFLLNEAIAGKALDQPEGRAKALFDAKPLLQALPANALRAQIMHMFADRLDIP 452
Cdd:pfam10410   1 SEFLIRRLLKGYDLDTPEGRAAALREAAPLLAKIPDPVERDLYLRRLAEELGIS 54
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
289-341 6.99e-07

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 47.26  E-value: 6.99e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 557798183   289 KYVLVVEGYMDVVALAQLGF--PNAVATLGTACTPIHVQKLLRQTD--TVIFSFDGD 341
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGkrGNVVALGGHLLSKEQIKLLKKLAKkaEVILATDPD 57
61 PHA02540
DNA primase; Provisional
 70-316 2.36e-05

DNA primase; Provisional


Pssm-ID: 222863 [Multi-domain]  Cd Length: 337  Bit Score: 46.91  E-value: 2.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183  70 YHCFGCGAHGTAIGFLMEHAGLTFPEAVQELAQSVGLTVP-HEPSMRGGgggggggggggggdyPAPVSKSVATaLSDam 148
Cdd:PHA02540  56 FKCHNCGYHRPFGNFLKDYEPDLYREYIMERFKERGTGKGrPVPKPKFE---------------FKKEKKVIEK-LPF-- 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 149 taaCDYYRKqLRGATVAIQYLKNRGLTGEiaaRFGLGYAPDGWQNLEAAF-PDYRDESLVEAGLVIvsektdaqgvarry 227
Cdd:PHA02540 118 ---CERLDT-LPEDHPIIKYVENRCIPKD---KWKLLYFTREWQKLVNSIkPDTYKKEKPEPRLVI-------------- 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557798183 228 drfrerimfPIRNVKGQVIGFGGRVLGSGEP-KYLNSPETPLFNKgseLYGLFEarlaIRERKYVLVVEGYMDVVALaql 306
Cdd:PHA02540 177 ---------PIFNKDGKIESFQGRALRKDAPqKYITIKADEEATK---IYGLDR----IDPGKTVYVVEGPIDSLFL--- 237

                        250
                 ....*....|
gi 557798183 307 gfPNAVATLG 316
Cdd:PHA02540 238 --PNSIAITG 245
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 291-341 5.16e-05

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 42.34  E-value: 5.16e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 557798183  291 VLVVEGYMDVVALAQL---GFPNAVATLGTACTPIH---------VQKLLRQTDTVIFSFDGD 341
Cdd:pfam01751   2 LIIVEGPSDAIALEKAlggGFQAVVAVLGHLLSLEKgpkkkalkaLKELALKAKEVILATDPD 64
 
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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