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Conserved domains on  [gi|52697348|gb|AAU86411|]
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primase, partial [Escherichia coli]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaG super family cl43116
DNA primase (bacterial type) [Replication, recombination and repair];
1-134 6.50e-61

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


The actual alignment was detected with superfamily member COG0358:

Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 194.97  E-value: 6.50e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52697348   1 DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALpymTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAF 80
Cdd:COG0358 290 EHIKLLKRYTDEVILCFDGDAAGQKAALRALELLL---KDGLQVRVLFLPDGEDPDELIRKEGAEAFRELLENAKPLIEF 366

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 52697348  81 LFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDS 134
Cdd:COG0358 367 LIERLLEGYDLDTPEGRAALLREALPLLAKIPDPILRELYLRELAERLGLDEEA 420
 
Name Accession Description Interval E-value
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
1-134 6.50e-61

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 194.97  E-value: 6.50e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52697348   1 DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALpymTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAF 80
Cdd:COG0358 290 EHIKLLKRYTDEVILCFDGDAAGQKAALRALELLL---KDGLQVRVLFLPDGEDPDELIRKEGAEAFRELLENAKPLIEF 366

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 52697348  81 LFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDS 134
Cdd:COG0358 367 LIERLLEGYDLDTPEGRAALLREALPLLAKIPDPILRELYLRELAERLGLDEEA 420
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 1-49 1.39e-14

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: 64.84  E-value: 1.39e-14
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 52697348   1 DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYmtdGRQLRFMFL 49
Cdd:cd03364  34 EQAELLKRLAKEVILAFDGDEAGQKAALRALELLLKL---GLNVRVLTL 79
DnaB_bind pfam10410
DnaB-helicase binding domain of primase; This domain is the C-terminal region three-helical ...
 78-130 4.75e-13

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: 60.16  E-value: 4.75e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 52697348    78 SAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGI 130
Cdd:pfam10410   1 SEFLIRRLLKGYDLDTPEGRAAALREAAPLLAKIPDPVERDLYLRRLAEELGI 53
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
1-38 2.17e-06

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 43.40  E-value: 2.17e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 52697348      1 DHIQLLFRATNN--VICCYDGDRAGRDAAWRALETALPYM 38
Cdd:smart00493  36 EQIKLLKKLAKKaeVILATDPDREGEAIAWELAELLKPAG 75
PHA02031 PHA02031
putative DnaG-like primase
 5-71 1.30e-04

putative DnaG-like primase


Pssm-ID: 222844 [Multi-domain]  Cd Length: 266  Bit Score: 40.95  E-value: 1.30e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 52697348    5 LLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGrqlRFMFLPDGEDPDTLVRKEGKEAFEARM 71
Cdd:PHA02031 201 LLQQTCPRVLIFLDGDPAGVDGSAGAMRRLRPLLIEG---QVIITPDGFDPKDLEREQIRELLIGRI 264
 
Name Accession Description Interval E-value
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
1-134 6.50e-61

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 194.97  E-value: 6.50e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52697348   1 DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALpymTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAF 80
Cdd:COG0358 290 EHIKLLKRYTDEVILCFDGDAAGQKAALRALELLL---KDGLQVRVLFLPDGEDPDELIRKEGAEAFRELLENAKPLIEF 366

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 52697348  81 LFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDS 134
Cdd:COG0358 367 LIERLLEGYDLDTPEGRAALLREALPLLAKIPDPILRELYLRELAERLGLDEEA 420
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 1-49 1.39e-14

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: 64.84  E-value: 1.39e-14
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 52697348   1 DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYmtdGRQLRFMFL 49
Cdd:cd03364  34 EQAELLKRLAKEVILAFDGDEAGQKAALRALELLLKL---GLNVRVLTL 79
DnaB_bind pfam10410
DnaB-helicase binding domain of primase; This domain is the C-terminal region three-helical ...
 78-130 4.75e-13

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: 60.16  E-value: 4.75e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 52697348    78 SAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGI 130
Cdd:pfam10410   1 SEFLIRRLLKGYDLDTPEGRAAALREAAPLLAKIPDPVERDLYLRRLAEELGI 53
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 1-49 6.53e-10

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: 52.66  E-value: 6.53e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 52697348   1 DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYmtdGRQLRFMFL 49
Cdd:cd01029  34 EQLRLLKRFARTVILAFDNDEAGKKAAARALELLLAL---GGRVRVPPL 79
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 1-56 6.91e-10

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


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 52.95  E-value: 6.91e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 52697348     1 DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPymtDGRQLRFMFLPDGEDPD 56
Cdd:pfam13155  33 AQIKLLKRYPKEVILAFDNDEAGRKAAKRLAELLKE---AGVDVKIRLLPDGKDWN 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
1-38 2.17e-06

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 43.40  E-value: 2.17e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 52697348      1 DHIQLLFRATNN--VICCYDGDRAGRDAAWRALETALPYM 38
Cdd:smart00493  36 EQIKLLKKLAKKaeVILATDPDREGEAIAWELAELLKPAG 75
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 1-49 2.18e-05

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: 40.87  E-value: 2.18e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 52697348   1 DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYmtdGRQLRFMFL 49
Cdd:cd00188  38 ELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSL---GKKVRRLLL 83
PHA02031 PHA02031
putative DnaG-like primase
 5-71 1.30e-04

putative DnaG-like primase


Pssm-ID: 222844 [Multi-domain]  Cd Length: 266  Bit Score: 40.95  E-value: 1.30e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 52697348    5 LLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGrqlRFMFLPDGEDPDTLVRKEGKEAFEARM 71
Cdd:PHA02031 201 LLQQTCPRVLIFLDGDPAGVDGSAGAMRRLRPLLIEG---QVIITPDGFDPKDLEREQIRELLIGRI 264
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 1-32 4.48e-04

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: 37.72  E-value: 4.48e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 52697348     1 DHIQLLFRATNNVICCYDGDRAGRDAAWRALE 32
Cdd:pfam01751  45 KALKELALKAKEVILATDPDREGEAIALKLLE 76
Toprim_3 pfam13362
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 11-65 5.90e-03

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


Pssm-ID: 433146 [Multi-domain]  Cd Length: 97  Bit Score: 34.68  E-value: 5.90e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 52697348    11 NNVICCYDGD--RAGRDAAWRALETALPymtDGRQLRFMFLPDGEDPDTLVRKEGKE 65
Cdd:pfam13362  44 KRVYIAADNDaaNDGQAAAEKLAERLEA---AGIEAVLLEPEAGEDWNDDLQQTGAA 97
 
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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