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Conserved domains on  [gi|511276923|ref|WP_016338740|]
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DNA primase [Spiroplasma chrysopicola]

Protein Classification

DNA primase( domain architecture ID 11417495)

DNA primase is a DNA-dependent RNA polymerase that synthesizes short RNA primers for DNA polymerase during DNA replication

CATH:  3.90.980.10|1.20.50.20
Gene Ontology:  GO:0003896|GO:0006269
PubMed:  16285921|29558114|33252731
SCOP:  4002843

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];
3-432 8.47e-177

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


:

Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 510.06  E-value: 8.47e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923   3 LISNEKIESIRSKVNIVEILSEYLQLEKRGRNFWAVCPFHQDSHPSMSISPEKQIYRCFACSAGGNVFTFLQEYKNISFI 82
Cdd:COG0358    1 RIPDEFIDEIRARVDIVDVIGEYVKLKKAGRNYKGLCPFHDEKTPSFTVSPEKQFYHCFGCGAGGDVISFLMEYEGLSFP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  83 EALKIVAEKANVSLTELQNYQEVSRYSEEDKKIFAINELTKTFFMNNL-QTKKGLPAKQYLEERDISNEDILAFDLGYAD 161
Cdd:COG0358   81 EAVEELAERAGIELPEEEGSPEEREEASERERLYEALELAAKFYQEQLkNTPEGKAARDYLKKRGLSDETIERFGLGYAP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 162 SNSQSLYNFLLKKGFTINEIEQAGLVNINGKGQIYDYFNDRVMFPIHDDENNIIGFSGRLVQEKTnlPKYLNTLETKVFK 241
Cdd:COG0358  161 DGWDALLKHLKKKGFSEEELVEAGLVIEREDGGYYDRFRGRIMFPIRDLRGRVIGFGGRVLDDGE--PKYLNSPETPLFH 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 242 KEQVMYNFYRAKPFIKKSGNLILLEGYMDIISLNRMGIKNTVALMGTNLSDYHITTIKKVTPECIIFLDGDLPGVKASLK 321
Cdd:COG0358  239 KGRVLYGLDLARKAIRKEDRVIVVEGYMDVIALHQAGIKNAVATLGTALTEEHIKLLKRYTDEVILCFDGDAAGQKAALR 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 322 AAAKLLVNNFKVKVVYNETGKDPDELVKA-GEEEFiKKIIVGANYPVNFAINYFMDKYNLEDANELAEFLTIVGNLVKVI 400
Cdd:COG0358  319 ALELLLKDGLQVRVLFLPDGEDPDELIRKeGAEAF-RELLENAKPLIEFLIERLLEGYDLDTPEGRAALLREALPLLAKI 397

                        410       420       430
                 ....*....|....*....|....*....|..
gi 511276923 401 PDPIEKELSINNLAKVTKLSPTAIATkIEHLK 432
Cdd:COG0358  398 PDPILRELYLRELAERLGLDEEALDA-LARLK 428
 
Name Accession Description Interval E-value
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
3-432 8.47e-177

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 510.06  E-value: 8.47e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923   3 LISNEKIESIRSKVNIVEILSEYLQLEKRGRNFWAVCPFHQDSHPSMSISPEKQIYRCFACSAGGNVFTFLQEYKNISFI 82
Cdd:COG0358    1 RIPDEFIDEIRARVDIVDVIGEYVKLKKAGRNYKGLCPFHDEKTPSFTVSPEKQFYHCFGCGAGGDVISFLMEYEGLSFP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  83 EALKIVAEKANVSLTELQNYQEVSRYSEEDKKIFAINELTKTFFMNNL-QTKKGLPAKQYLEERDISNEDILAFDLGYAD 161
Cdd:COG0358   81 EAVEELAERAGIELPEEEGSPEEREEASERERLYEALELAAKFYQEQLkNTPEGKAARDYLKKRGLSDETIERFGLGYAP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 162 SNSQSLYNFLLKKGFTINEIEQAGLVNINGKGQIYDYFNDRVMFPIHDDENNIIGFSGRLVQEKTnlPKYLNTLETKVFK 241
Cdd:COG0358  161 DGWDALLKHLKKKGFSEEELVEAGLVIEREDGGYYDRFRGRIMFPIRDLRGRVIGFGGRVLDDGE--PKYLNSPETPLFH 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 242 KEQVMYNFYRAKPFIKKSGNLILLEGYMDIISLNRMGIKNTVALMGTNLSDYHITTIKKVTPECIIFLDGDLPGVKASLK 321
Cdd:COG0358  239 KGRVLYGLDLARKAIRKEDRVIVVEGYMDVIALHQAGIKNAVATLGTALTEEHIKLLKRYTDEVILCFDGDAAGQKAALR 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 322 AAAKLLVNNFKVKVVYNETGKDPDELVKA-GEEEFiKKIIVGANYPVNFAINYFMDKYNLEDANELAEFLTIVGNLVKVI 400
Cdd:COG0358  319 ALELLLKDGLQVRVLFLPDGEDPDELIRKeGAEAF-RELLENAKPLIEFLIERLLEGYDLDTPEGRAALLREALPLLAKI 397

                        410       420       430
                 ....*....|....*....|....*....|..
gi 511276923 401 PDPIEKELSINNLAKVTKLSPTAIATkIEHLK 432
Cdd:COG0358  398 PDPILRELYLRELAERLGLDEEALDA-LARLK 428
dnaG TIGR01391
DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria ...
 4-414 1.65e-143

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: 423.17  E-value: 1.65e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923    4 ISNEKIESIRSKVNIVEILSEYLQLEKRGRNFWAVCPFHQDSHPSMSISPEKQIYRCFACSAGGNVFTFLQEYKNISFIE 83
Cdd:TIGR01391   2 IPEEFIDELKERVDIVDVISEYVKLKKKGRNYVGLCPFHHEKTPSFSVSPEKQFYHCFGCGAGGDAIKFLMEIEGISFVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923   84 ALKIVAEKANVSLTELQNYQEVSRYSEEDKKIFAINELTKTFFMNNL-QTKKGLPAKQYLEERDISNEDILAFDLGYADS 162
Cdd:TIGR01391  82 AVEELAKRAGIDLPFEKDQQEKKEQKSKRKKLYELLELAAKFFKNQLkHTPENRAALDYLQSRGLSDETIDRFELGYAPN 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  163 NSQSLYNFLL-KKGFTINEIEQAGLVNINGKGQIYDYFNDRVMFPIHDDENNIIGFSGRLVQEKTnlPKYLNTLETKVFK 241
Cdd:TIGR01391 162 NWDFLFDFLQnKKGFDLELLAEAGLLVKKENGKYYDRFRNRIMFPIHDPKGRVVGFGGRALGDEK--PKYLNSPETPLFK 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  242 KEQVMYNFYRAKPFIKKSGNLILLEGYMDIISLNRMGIKNTVALMGTNLSDYHITTIKKVTPECIIFLDGDLPGVKASLK 321
Cdd:TIGR01391 240 KSELLYGLHKARKEIRKEKELILVEGYMDVIALHQAGIKNAVASLGTALTEEHIKLLKRYADEIILCFDGDKAGRKAALR 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  322 AAAKLLVNNFKVKVVYNETGKDPDELVKAGEEEFIKKIIVGANYPVNFAINYFMDKYNLEDANELAEFLTIVGNLVKVIP 401
Cdd:TIGR01391 320 AIELLLPLGINVKVIKLPGGKDPDEYLRKEGVEALKKLLENSKSLIEFLIARLLSNYNLDTPEEKAKLVEELLPLIKKIP 399

                         410
                  ....*....|...
gi 511276923  402 DPIEKELSINNLA 414
Cdd:TIGR01391 400 DPILRDYYLQKLA 412
Toprim_N pfam08275
DNA primase catalytic core, N-terminal domain;
125-253 4.92e-47

DNA primase catalytic core, N-terminal domain;


Pssm-ID: 429892 [Multi-domain]  Cd Length: 128  Bit Score: 161.53  E-value: 4.92e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  125 FFMNNLQTKKGLPAKQYLEERDISNEDILAFDLGYADSNSQSLYNFLLKKGFTINEIEQAGLVNINGKGQIYDYFNDRVM 204
Cdd:pfam08275   1 FYQELLKTNEGAAALDYLKSRGLSDETIERFQIGYAPDGWDNLLKFLKKKGFSEEELLEAGLLSKNEDGRYYDRFRNRIM 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 511276923  205 FPIHDDENNIIGFSGRLVqEKTNLPKYLNTLETKVFKKEQVMYNFYRAK 253
Cdd:pfam08275  81 FPIKDARGRVVGFGGRAL-DDDKPPKYLNSPETPLFKKSKLLYGLDEAK 128
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 262-336 4.49e-26

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: 101.82  E-value: 4.49e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 511276923 262 LILLEGYMDIISLNRMGIKNTVALMGTNLSDYHITTIKKVTPECIIFLDGDLPGVKASLKAAAKLLVNNFKVKVV 336
Cdd:cd03364    3 VILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALRALELLLKLGLNVRVL 77
ZnF_CHCC smart00400
zinc finger;
37-89 1.56e-23

zinc finger;


Pssm-ID: 128681 [Multi-domain]  Cd Length: 55  Bit Score: 93.90  E-value: 1.56e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 511276923    37 AVCPFHQDSHPSMSISPEKQIYRCFACSAGGNVFTFLQEYKNISFIEALKIVA 89
Cdd:smart00400   3 GLCPFHGEKTPSFSVSPDKQFFHCFGCGAGGNVISFLMKYDKLSFVEAVKKLA 55
PRK08624 PRK08624
hypothetical protein; Provisional
 7-294 1.55e-07

hypothetical protein; Provisional


Pssm-ID: 236314 [Multi-domain]  Cd Length: 373  Bit Score: 53.78  E-value: 1.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923   7 EKIESIRSKVNIVEILSEYLQLEKRGRN----FWAVCpfHQDSHPSMSIS--PEKQIYRCFA-CSAGGNVFTFL-----Q 74
Cdd:PRK08624   5 DELKESLTPEDIIKILEEVGCENVRGKDgntiAETAC--HNDGGGSTKLYyyIENDNFHCYTrCGDIFDVFELLckrlkM 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  75 EYKNISFIEALKIVAEKANVSLtelqNYQEVSRYSEED-KKIFAINEltktffMNNLQTKKGLPAkqyleERDISNEDIL 153
Cdd:PRK08624  83 EGKALSFSKAIRKITKILGLSY----FYEPKQQGIKPSfLKILDWVW------TGKKEKKEKIQP-----QLKSFNENIL 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 154 AFDLGYadsnsqslYNFL-LKKGFTINEIEQAGLvningkGQIYDYFNDRVMFPIHDDENNIIGFSGR-LVQEKTNLPKY 231
Cdd:PRK08624 148 NQFVKI--------PNRKwLDEGISEKTQKYWEI------KFYLDVISQRIIIPHRDESGELIGIRGRlLDKELVDKNKY 213

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 511276923 232 LNTLETKVFKKEQVMYNFYRA---KPFIKKSGNLILLEGYMDIISLNRM-GI-KNTVALMGTNLSDYH 294
Cdd:PRK08624 214 FPIYVNDTGYNHPKGKILYGLwqnKKYIKEKKKVIIVESEKSVLFSDKFyGEgNFVVAICGSNISEVQ 281
 
Name Accession Description Interval E-value
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
3-432 8.47e-177

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 510.06  E-value: 8.47e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923   3 LISNEKIESIRSKVNIVEILSEYLQLEKRGRNFWAVCPFHQDSHPSMSISPEKQIYRCFACSAGGNVFTFLQEYKNISFI 82
Cdd:COG0358    1 RIPDEFIDEIRARVDIVDVIGEYVKLKKAGRNYKGLCPFHDEKTPSFTVSPEKQFYHCFGCGAGGDVISFLMEYEGLSFP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  83 EALKIVAEKANVSLTELQNYQEVSRYSEEDKKIFAINELTKTFFMNNL-QTKKGLPAKQYLEERDISNEDILAFDLGYAD 161
Cdd:COG0358   81 EAVEELAERAGIELPEEEGSPEEREEASERERLYEALELAAKFYQEQLkNTPEGKAARDYLKKRGLSDETIERFGLGYAP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 162 SNSQSLYNFLLKKGFTINEIEQAGLVNINGKGQIYDYFNDRVMFPIHDDENNIIGFSGRLVQEKTnlPKYLNTLETKVFK 241
Cdd:COG0358  161 DGWDALLKHLKKKGFSEEELVEAGLVIEREDGGYYDRFRGRIMFPIRDLRGRVIGFGGRVLDDGE--PKYLNSPETPLFH 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 242 KEQVMYNFYRAKPFIKKSGNLILLEGYMDIISLNRMGIKNTVALMGTNLSDYHITTIKKVTPECIIFLDGDLPGVKASLK 321
Cdd:COG0358  239 KGRVLYGLDLARKAIRKEDRVIVVEGYMDVIALHQAGIKNAVATLGTALTEEHIKLLKRYTDEVILCFDGDAAGQKAALR 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 322 AAAKLLVNNFKVKVVYNETGKDPDELVKA-GEEEFiKKIIVGANYPVNFAINYFMDKYNLEDANELAEFLTIVGNLVKVI 400
Cdd:COG0358  319 ALELLLKDGLQVRVLFLPDGEDPDELIRKeGAEAF-RELLENAKPLIEFLIERLLEGYDLDTPEGRAALLREALPLLAKI 397

                        410       420       430
                 ....*....|....*....|....*....|..
gi 511276923 401 PDPIEKELSINNLAKVTKLSPTAIATkIEHLK 432
Cdd:COG0358  398 PDPILRELYLRELAERLGLDEEALDA-LARLK 428
dnaG TIGR01391
DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria ...
 4-414 1.65e-143

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: 423.17  E-value: 1.65e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923    4 ISNEKIESIRSKVNIVEILSEYLQLEKRGRNFWAVCPFHQDSHPSMSISPEKQIYRCFACSAGGNVFTFLQEYKNISFIE 83
Cdd:TIGR01391   2 IPEEFIDELKERVDIVDVISEYVKLKKKGRNYVGLCPFHHEKTPSFSVSPEKQFYHCFGCGAGGDAIKFLMEIEGISFVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923   84 ALKIVAEKANVSLTELQNYQEVSRYSEEDKKIFAINELTKTFFMNNL-QTKKGLPAKQYLEERDISNEDILAFDLGYADS 162
Cdd:TIGR01391  82 AVEELAKRAGIDLPFEKDQQEKKEQKSKRKKLYELLELAAKFFKNQLkHTPENRAALDYLQSRGLSDETIDRFELGYAPN 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  163 NSQSLYNFLL-KKGFTINEIEQAGLVNINGKGQIYDYFNDRVMFPIHDDENNIIGFSGRLVQEKTnlPKYLNTLETKVFK 241
Cdd:TIGR01391 162 NWDFLFDFLQnKKGFDLELLAEAGLLVKKENGKYYDRFRNRIMFPIHDPKGRVVGFGGRALGDEK--PKYLNSPETPLFK 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  242 KEQVMYNFYRAKPFIKKSGNLILLEGYMDIISLNRMGIKNTVALMGTNLSDYHITTIKKVTPECIIFLDGDLPGVKASLK 321
Cdd:TIGR01391 240 KSELLYGLHKARKEIRKEKELILVEGYMDVIALHQAGIKNAVASLGTALTEEHIKLLKRYADEIILCFDGDKAGRKAALR 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  322 AAAKLLVNNFKVKVVYNETGKDPDELVKAGEEEFIKKIIVGANYPVNFAINYFMDKYNLEDANELAEFLTIVGNLVKVIP 401
Cdd:TIGR01391 320 AIELLLPLGINVKVIKLPGGKDPDEYLRKEGVEALKKLLENSKSLIEFLIARLLSNYNLDTPEEKAKLVEELLPLIKKIP 399

                         410
                  ....*....|...
gi 511276923  402 DPIEKELSINNLA 414
Cdd:TIGR01391 400 DPILRDYYLQKLA 412
Toprim_N pfam08275
DNA primase catalytic core, N-terminal domain;
125-253 4.92e-47

DNA primase catalytic core, N-terminal domain;


Pssm-ID: 429892 [Multi-domain]  Cd Length: 128  Bit Score: 161.53  E-value: 4.92e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  125 FFMNNLQTKKGLPAKQYLEERDISNEDILAFDLGYADSNSQSLYNFLLKKGFTINEIEQAGLVNINGKGQIYDYFNDRVM 204
Cdd:pfam08275   1 FYQELLKTNEGAAALDYLKSRGLSDETIERFQIGYAPDGWDNLLKFLKKKGFSEEELLEAGLLSKNEDGRYYDRFRNRIM 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 511276923  205 FPIHDDENNIIGFSGRLVqEKTNLPKYLNTLETKVFKKEQVMYNFYRAK 253
Cdd:pfam08275  81 FPIKDARGRVVGFGGRAL-DDDKPPKYLNSPETPLFKKSKLLYGLDEAK 128
zf-CHC2 pfam01807
CHC2 zinc finger; This domain is principally involved in DNA binding in DNA primases.
 5-96 2.06e-38

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


Pssm-ID: 426447 [Multi-domain]  Cd Length: 95  Bit Score: 137.00  E-value: 2.06e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923    5 SNEKIESIRSKVNIVEILSEYLQLEKRGRNFWAVCPFHQDSHPSMSISPEKQIYRCFACSAGGNVFTFLQEYKNISFIEA 84
Cdd:pfam01807   1 PPEFIDDLKNRIDIVDVVGQYVKLKKRGKDYVGLCPFHHEKTPSFTVSPDKQFYHCFGCGAGGDVIKFLMKIEKLSFVEA 80

                          90
                  ....*....|..
gi 511276923   85 LKIVAEKANVSL 96
Cdd:pfam01807  81 VEKLADRYGIEI 92
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 262-336 4.49e-26

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: 101.82  E-value: 4.49e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 511276923 262 LILLEGYMDIISLNRMGIKNTVALMGTNLSDYHITTIKKVTPECIIFLDGDLPGVKASLKAAAKLLVNNFKVKVV 336
Cdd:cd03364    3 VILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALRALELLLKLGLNVRVL 77
ZnF_CHCC smart00400
zinc finger;
37-89 1.56e-23

zinc finger;


Pssm-ID: 128681 [Multi-domain]  Cd Length: 55  Bit Score: 93.90  E-value: 1.56e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 511276923    37 AVCPFHQDSHPSMSISPEKQIYRCFACSAGGNVFTFLQEYKNISFIEALKIVA 89
Cdd:smart00400   3 GLCPFHGEKTPSFSVSPDKQFFHCFGCGAGGNVISFLMKYDKLSFVEAVKKLA 55
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 262-336 6.61e-21

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: 86.94  E-value: 6.61e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 511276923 262 LILLEGYMDIISLNRMGIKNTVALMGTNLSDYHITTIKKVTPECIIFLDGDLPGVKASLKAAAKLLVNNFKVKVV 336
Cdd:cd01029    3 VIIVEGYMDVLALHQAGIKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKAAARALELLLALGGRVRVP 77
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 263-348 1.06e-17

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


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 78.37  E-value: 1.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  263 ILLEGYMDIISLNRMGIKNT--VALMGTNLSDYHITTIKKVTPECIIFLDGDLPGVKASLKAAAKLLVNNFKVKVVYNET 340
Cdd:pfam13155   1 VVFEGYIDALSLAQAGIKNVlyVATLGTALTEAQIKLLKRYPKEVILAFDNDEAGRKAAKRLAELLKEAGVDVKIRLLPD 80


                  ....*...
gi 511276923  341 GKDPDELV 348
Cdd:pfam13155  81 GKDWNEYL 88
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 262-337 1.63e-17

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: 77.71  E-value: 1.63e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  262 LILLEGYMDIISLNRMGIKNTVALMGTNLS--------DYHITTIKKVTpECIIFLDGDLPGVKASLKAAAKLLVNNFKV 333
Cdd:pfam13662   3 IIVVEGYADVIALEKAGYKGAVAVLGGALSpldgigpeDLNIDSLGGIK-EVILALDGDVAGEKTALYLAEALLEEGVKV 81


                  ....
gi 511276923  334 KVVY 337
Cdd:pfam13662  82 SRLA 85
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 262-337 2.77e-09

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: 53.97  E-value: 2.77e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 262 LILLEGYMDIISLNRMGIK--NTVALMGT--NLSDYHITTIKKVTPECIIFLDGDLPGVKASLKAAAKLLVNNFKVKVVY 337
Cdd:cd00188    3 LIIVEGPSDALALAQAGGYggAVVALGGHalNKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSLGKKVRRLL 82
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
262-330 4.94e-09

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 53.03  E-value: 4.94e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 511276923   262 LILLEGYMDIISLNRMGIK--NTVALMGTNLSDYHITTIKKVTPEC--IIFLDGDLPGVKASLKAAAKLLVNN 330
Cdd:smart00493   3 LIIVEGPADAIALEKAGGKrgNVVALGGHLLSKEQIKLLKKLAKKAevILATDPDREGEAIAWELAELLKPAG 75
PRK08624 PRK08624
hypothetical protein; Provisional
 7-294 1.55e-07

hypothetical protein; Provisional


Pssm-ID: 236314 [Multi-domain]  Cd Length: 373  Bit Score: 53.78  E-value: 1.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923   7 EKIESIRSKVNIVEILSEYLQLEKRGRN----FWAVCpfHQDSHPSMSIS--PEKQIYRCFA-CSAGGNVFTFL-----Q 74
Cdd:PRK08624   5 DELKESLTPEDIIKILEEVGCENVRGKDgntiAETAC--HNDGGGSTKLYyyIENDNFHCYTrCGDIFDVFELLckrlkM 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  75 EYKNISFIEALKIVAEKANVSLtelqNYQEVSRYSEED-KKIFAINEltktffMNNLQTKKGLPAkqyleERDISNEDIL 153
Cdd:PRK08624  83 EGKALSFSKAIRKITKILGLSY----FYEPKQQGIKPSfLKILDWVW------TGKKEKKEKIQP-----QLKSFNENIL 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 154 AFDLGYadsnsqslYNFL-LKKGFTINEIEQAGLvningkGQIYDYFNDRVMFPIHDDENNIIGFSGR-LVQEKTNLPKY 231
Cdd:PRK08624 148 NQFVKI--------PNRKwLDEGISEKTQKYWEI------KFYLDVISQRIIIPHRDESGELIGIRGRlLDKELVDKNKY 213

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 511276923 232 LNTLETKVFKKEQVMYNFYRA---KPFIKKSGNLILLEGYMDIISLNRM-GI-KNTVALMGTNLSDYH 294
Cdd:PRK08624 214 FPIYVNDTGYNHPKGKILYGLwqnKKYIKEKKKVIIVESEKSVLFSDKFyGEgNFVVAICGSNISEVQ 281
DnaB_bind pfam10410
DnaB-helicase binding domain of primase; This domain is the C-terminal region three-helical ...
 367-420 8.56e-07

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: 46.29  E-value: 8.56e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 511276923  367 VNFAINYFMDKYNLEDANELAEFLTIVGNLVKVIPDPIEKELSINNLAKVTKLS 420
Cdd:pfam10410   1 SEFLIRRLLKGYDLDTPEGRAAALREAAPLLAKIPDPVERDLYLRRLAEELGIS 54
PRK04031 PRK04031
DNA primase; Provisional
 252-312 1.75e-05

DNA primase; Provisional


Pssm-ID: 235206  Cd Length: 408  Bit Score: 47.50  E-value: 1.75e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 511276923 252 AKPFIKKSGNLILLEGYMDIISLNRMGIKNTVALMGTNLSDyhitTIKKVTPE--CIIFLDGD 312
Cdd:PRK04031 162 AGPNVDDSDAIIVVEGRADVLNLLRYGIKNAIAVEGTNVPE----TIIELSKKktVTAFLDGD 220
61 PHA02540
DNA primase; Provisional
 58-291 3.17e-04

DNA primase; Provisional


Pssm-ID: 222863 [Multi-domain]  Cd Length: 337  Bit Score: 43.44  E-value: 3.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  58 YRCFACSAGGNVFTFLQEYKNISFIEALKivaEKANVSLTELQNYQEVSRySEEDKKIFAINELTktfFMNNLQT-KKGL 136
Cdd:PHA02540  56 FKCHNCGYHRPFGNFLKDYEPDLYREYIM---ERFKERGTGKGRPVPKPK-FEFKKEKKVIEKLP---FCERLDTlPEDH 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 137 PAKQYLEERDISNEdilAFDLGYADSNSQSLYNfLLKKGFTINEIEQAglvningkgqiydyfndRVMFPIHDDENNIIG 216
Cdd:PHA02540 129 PIIKYVENRCIPKD---KWKLLYFTREWQKLVN-SIKPDTYKKEKPEP-----------------RLVIPIFNKDGKIES 187

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 511276923 217 FSGRLVQEKTNLpKY----LNTLETKVFKKEQvmynfyrakpfIKKSGNLILLEGYMDiiSLNrmgIKNTVALMGTNLS 291
Cdd:PHA02540 188 FQGRALRKDAPQ-KYitikADEEATKIYGLDR-----------IDPGKTVYVVEGPID--SLF---LPNSIAITGGDLD 249
PHA02031 PHA02031
putative DnaG-like primase
 165-362 3.56e-04

putative DnaG-like primase


Pssm-ID: 222844 [Multi-domain]  Cd Length: 266  Bit Score: 42.87  E-value: 3.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 165 QSLYNFLLKKGFTINEIEQAGLVNINGKGQiydyfndRVMFPIHDdenniiGFSGRLVQEKTnlPKYlntletkvfkkeq 244
Cdd:PHA02031  88 QSLYGLLLSKGIDPNMMEPGLPLEYSERQG-------RLIFRTDA------GWLGRATADQQ--PKW------------- 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923 245 VMYNFYR-----AKPFIKKSGNLILLEGYMDIISLnRMGIKN----TVALMGTNLSDYHITTIKKVT-PECIIFLDGDLP 314
Cdd:PHA02031 140 VGYGYPApdyvgWPPELSMPRPVVLTEDYLSALKV-RWACNKpevfAVALLGTRLRDRLAAILLQQTcPRVLIFLDGDPA 218

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 511276923 315 GVKASLKAAAKLLVNNFKVKVVYNETGKDPDELvkagEEEFIKKIIVG 362
Cdd:PHA02031 219 GVDGSAGAMRRLRPLLIEGQVIITPDGFDPKDL----EREQIRELLIG 262
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 262-337 1.06e-03

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: 38.49  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511276923  262 LILLEGYMDIISLNRM---GIKNTVALMGTNLSDYHITTIKKVTP---------ECIIFLDGDLPGVKASLKAAAKLLVN 329
Cdd:pfam01751   2 LIIVEGPSDAIALEKAlggGFQAVVAVLGHLLSLEKGPKKKALKAlkelalkakEVILATDPDREGEAIALKLLELKELL 81


                  ....*...
gi 511276923  330 NFKVKVVY 337
Cdd:pfam01751  82 ENAGGRVE 89
 
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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