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Conserved domains on  [gi|240254185|ref|NP_174354|]
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nucleic acid binding protein [Arabidopsis thaliana]

Protein Classification

TOPRIM_primases domain-containing protein( domain architecture ID 10615257)

TOPRIM_primases domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 205-292 1.83e-13

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: 65.00  E-value: 1.83e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185  205 SEIIIVEGEPDKLAMEEAGFFNCVSVPDGAPET---VSSKEIPSESkdtafkyiwncndyLKKASRIVIATDGDGPGQAL 281
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVAVLGGALSPldgIGPEDLNIDS--------------LGGIKEVILALDGDVAGEKT 66

                          90
                  ....*....|.
gi 240254185  282 AEELARRLGKE 292
Cdd:pfam13662  67 ALYLAEALLEE 77
COG4643 super family cl26703
Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons] ...
 265-330 4.33e-04

Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons];


The actual alignment was detected with superfamily member COG4643:

Pssm-ID: 443681 [Multi-domain]  Cd Length: 435  Bit Score: 41.77  E-value: 4.33e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 240254185 265 ASRIVIATDGD-----GPGQALAEELARRLGkerCWLVkWPkKSEDEHFKDANEVLMSKGPHLLKEAILNA 330
Cdd:COG4643  258 VAELIIAADNDrntdgNPGQAAAEEAARAVG---GLVA-LP-PFPPKKGTDFNDLHQARGLEAVRAAFEAA 323
 
Name Accession Description Interval E-value
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 205-292 1.83e-13

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: 65.00  E-value: 1.83e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185  205 SEIIIVEGEPDKLAMEEAGFFNCVSVPDGAPET---VSSKEIPSESkdtafkyiwncndyLKKASRIVIATDGDGPGQAL 281
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVAVLGGALSPldgIGPEDLNIDS--------------LGGIKEVILALDGDVAGEKT 66

                          90
                  ....*....|.
gi 240254185  282 AEELARRLGKE 292
Cdd:pfam13662  67 ALYLAEALLEE 77
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
205-291 2.91e-10

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 55.73  E-value: 2.91e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185   205 SEIIIVEGEPDKLAMEEAGFFNCVSVPDGApeTVSSKEIPSESKDtafkyiwncndyLKKASRIVIATDGDGPGQALAEE 284
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGG--HLLSKEQIKLLKK------------LAKKAEVILATDPDREGEAIAWE 66


                   ....*..
gi 240254185   285 LARRLGK 291
Cdd:smart00493  67 LAELLKP 73
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 206-297 2.65e-09

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: 53.04  E-value: 2.65e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185 206 EIIIVEGEPDKLAMEEAGFFNCVSVPDGApetvsskeipseSKDTAFKYIWncndylKKASRIVIATDGDGPGQALAEEL 285
Cdd:cd01029    2 EVIIVEGYMDVLALHQAGIKNVVAALGTA------------NTEEQLRLLK------RFARTVILAFDNDEAGKKAAARA 63

                         90
                 ....*....|..
gi 240254185 286 ARRLGKERCWLV 297
Cdd:cd01029   64 LELLLALGGRVR 75
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
192-333 1.49e-05

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 46.28  E-value: 1.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185 192 RKILYGLD----DIEETSEIIIVEGEPDKLAMEEAGFFNCVSvPDGapetvsskeipseskdTAF-----KYIWncndyl 262
Cdd:COG0358  240 GRVLYGLDlarkAIRKEDRVIVVEGYMDVIALHQAGIKNAVA-TLG----------------TALteehiKLLK------ 296

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 240254185 263 KKASRIVIATDGDGPGQALAE---ELARRLGKErCWLVKWPKKsedehfKDANEVLMSKGPHLLKEAILNAEPY 333
Cdd:COG0358  297 RYTDEVILCFDGDAAGQKAALralELLLKDGLQ-VRVLFLPDG------EDPDELIRKEGAEAFRELLENAKPL 363
COG4643 COG4643
Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons] ...
 265-330 4.33e-04

Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons];


Pssm-ID: 443681 [Multi-domain]  Cd Length: 435  Bit Score: 41.77  E-value: 4.33e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 240254185 265 ASRIVIATDGD-----GPGQALAEELARRLGkerCWLVkWPkKSEDEHFKDANEVLMSKGPHLLKEAILNA 330
Cdd:COG4643  258 VAELIIAADNDrntdgNPGQAAAEEAARAVG---GLVA-LP-PFPPKKGTDFNDLHQARGLEAVRAAFEAA 323
 
Name Accession Description Interval E-value
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 205-292 1.83e-13

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: 65.00  E-value: 1.83e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185  205 SEIIIVEGEPDKLAMEEAGFFNCVSVPDGAPET---VSSKEIPSESkdtafkyiwncndyLKKASRIVIATDGDGPGQAL 281
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVAVLGGALSPldgIGPEDLNIDS--------------LGGIKEVILALDGDVAGEKT 66

                          90
                  ....*....|.
gi 240254185  282 AEELARRLGKE 292
Cdd:pfam13662  67 ALYLAEALLEE 77
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
205-291 2.91e-10

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 55.73  E-value: 2.91e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185   205 SEIIIVEGEPDKLAMEEAGFFNCVSVPDGApeTVSSKEIPSESKDtafkyiwncndyLKKASRIVIATDGDGPGQALAEE 284
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGG--HLLSKEQIKLLKK------------LAKKAEVILATDPDREGEAIAWE 66


                   ....*..
gi 240254185   285 LARRLGK 291
Cdd:smart00493  67 LAELLKP 73
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 206-297 2.65e-09

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: 53.04  E-value: 2.65e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185 206 EIIIVEGEPDKLAMEEAGFFNCVSVPDGApetvsskeipseSKDTAFKYIWncndylKKASRIVIATDGDGPGQALAEEL 285
Cdd:cd01029    2 EVIIVEGYMDVLALHQAGIKNVVAALGTA------------NTEEQLRLLK------RFARTVILAFDNDEAGKKAAARA 63

                         90
                 ....*....|..
gi 240254185 286 ARRLGKERCWLV 297
Cdd:cd01029   64 LELLLALGGRVR 75
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 205-300 3.54e-07

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: 47.42  E-value: 3.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185 205 SEIIIVEGEPDKLAMEEAGFFNC-VSVPDGAPETVSSKEIPSEskdtafkyiwncndyLKKASRIVIATDGDGPGQALAE 283
Cdd:cd00188    1 KKLIIVEGPSDALALAQAGGYGGaVVALGGHALNKTRELLKRL---------------LGEAKEVIIATDADREGEAIAL 65

                         90
                 ....*....|....*..
gi 240254185 284 ELARRLGKERCWlVKWP 300
Cdd:cd00188   66 RLLELLKSLGKK-VRRL 81
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 206-286 2.22e-06

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: 45.43  E-value: 2.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185  206 EIIIVEGEPDKLAMEEAGFFNCVSVpdgapeTVSSKEIPSESKDTAFKYIWNCNDYLKKASRIVIATDGDGPGQALAEEL 285
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAV------VAVLGHLLSLEKGPKKKALKALKELALKAKEVILATDPDREGEAIALKL 74


                  .
gi 240254185  286 A 286
Cdd:pfam01751  75 L 75
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 206-294 1.44e-05

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: 42.50  E-value: 1.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185 206 EIIIVEGEPDKLAMEEAGFFNCVSVPdGapeTVSSKEIpseskdtaFKYIWNCNDylkkasRIVIATDGDGPGQALAEEL 285
Cdd:cd03364    2 KVILVEGYMDVIALHQAGIKNVVASL-G---TALTEEQ--------AELLKRLAK------EVILAFDGDEAGQKAALRA 63


                 ....*....
gi 240254185 286 ARRLGKERC 294
Cdd:cd03364   64 LELLLKLGL 72
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
192-333 1.49e-05

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 46.28  E-value: 1.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185 192 RKILYGLD----DIEETSEIIIVEGEPDKLAMEEAGFFNCVSvPDGapetvsskeipseskdTAF-----KYIWncndyl 262
Cdd:COG0358  240 GRVLYGLDlarkAIRKEDRVIVVEGYMDVIALHQAGIKNAVA-TLG----------------TALteehiKLLK------ 296

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 240254185 263 KKASRIVIATDGDGPGQALAE---ELARRLGKErCWLVKWPKKsedehfKDANEVLMSKGPHLLKEAILNAEPY 333
Cdd:COG0358  297 RYTDEVILCFDGDAAGQKAALralELLLKDGLQ-VRVLFLPDG------EDPDELIRKEGAEAFRELLENAKPL 363
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 208-315 2.07e-05

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


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 42.55  E-value: 2.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185  208 IIVEGEPDKLAMEEAGFFN--CVSvPDGAPETvsskeipseskDTAFKYIwncNDYLKKasrIVIATDGDGPGQALAEEL 285
Cdd:pfam13155   1 VVFEGYIDALSLAQAGIKNvlYVA-TLGTALT-----------EAQIKLL---KRYPKE---VILAFDNDEAGRKAAKRL 62

                          90       100       110
                  ....*....|....*....|....*....|..
gi 240254185  286 ARRLGKE--RCWLVKWPKKsedehfKDANEVL 315
Cdd:pfam13155  63 AELLKEAgvDVKIRLLPDG------KDWNEYL 88
COG4643 COG4643
Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons] ...
 265-330 4.33e-04

Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons];


Pssm-ID: 443681 [Multi-domain]  Cd Length: 435  Bit Score: 41.77  E-value: 4.33e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 240254185 265 ASRIVIATDGD-----GPGQALAEELARRLGkerCWLVkWPkKSEDEHFKDANEVLMSKGPHLLKEAILNA 330
Cdd:COG4643  258 VAELIIAADNDrntdgNPGQAAAEEAARAVG---GLVA-LP-PFPPKKGTDFNDLHQARGLEAVRAAFEAA 323
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 205-290 4.48e-03

TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). 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.


Pssm-ID: 173777  Cd Length: 81  Bit Score: 35.70  E-value: 4.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185 205 SEIIIVEGEPDKLAMEEAGFfncvsvpDGAPETVSSKEIPSESKDTAfkyiwncndyLKKASRIVIATDGDGPGQALAEE 284
Cdd:cd01027    2 GEVIIVEGKNDTESLKKLGI-------EAEIIETNGSIINKETIELI----------KKAYRGVIILTDPDRKGEKIRKK 64


                 ....*.
gi 240254185 285 LARRLG 290
Cdd:cd01027   65 LSEYLS 70
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 206-289 8.02e-03

5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 36.93  E-value: 8.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254185 206 EIIIVEGEPDKLAMEEAgffncvsvPDGAPETVSSKEIPSEskdtafkyiwnCNDYLKKASR---IVIATDGDGPGQALA 282
Cdd:COG1658    9 EVIVVEGKDDTAALKRA--------VDADIIETNGSAISEE-----------TLELIKVAAEkrgVIILTDPDRAGERIR 69


                 ....*..
gi 240254185 283 EELARRL 289
Cdd:COG1658   70 KRISEHL 76
 
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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