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Conserved domains on  [gi|1954872939|gb|QQM89235|]
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toprim domain-containing protein (plasmid) [Klebsiella variicola]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG4643 super family cl26703
Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons] ...
 2-68 2.49e-13

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: 62.95  E-value: 2.49e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954872939   2 ALTEGIETGLAVMAGSKLPVWACYSSALLESVIIP----DEVEKVIIFADNDYN--GGQGLTSAEVLATRLRA 68
Cdd:COG4643   217 LIAEGYATALSVHEATGLPVVAALDAGNLLPVAQAlrerYPVAELIIAADNDRNtdGNPGQAAAEEAARAVGG 289
 
Name Accession Description Interval E-value
COG4643 COG4643
Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons] ...
 2-68 2.49e-13

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


Pssm-ID: 443681 [Multi-domain]  Cd Length: 435  Bit Score: 62.95  E-value: 2.49e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954872939   2 ALTEGIETGLAVMAGSKLPVWACYSSALLESVIIP----DEVEKVIIFADNDYN--GGQGLTSAEVLATRLRA 68
Cdd:COG4643   217 LIAEGYATALSVHEATGLPVVAALDAGNLLPVAQAlrerYPVAELIIAADNDRNtdGNPGQAAAEEAARAVGG 289
Toprim_3 pfam13362
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 1-75 6.65e-11

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: 53.17  E-value: 6.65e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1954872939  1 MALTEGIETGLAVMAG---SKLPVWACYSSALLESVIIPDEVEKVIIFADNDyNGGQGLTSAEVLATRLRAAGKCVHL 75
Cdd:pfam13362  2 LIIGEGIETALSLTQRlnpPGTPVIALLSAANLKAVAWPERVKRVYIAADND-AANDGQAAAEKLAERLEAAGIEAVL 78
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 3-63 2.10e-04

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: 36.09  E-value: 2.10e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954872939  3 LTEGIETGLAVMAGSKLPVWACYSSALLESVI--IPDEVEKVIIFADNDYNGGQGLTSAEVLA 63
Cdd:cd01029    5 IVEGYMDVLALHQAGIKNVVAALGTANTEEQLrlLKRFARTVILAFDNDEAGKKAAARALELL 67
 
Name Accession Description Interval E-value
COG4643 COG4643
Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons] ...
 2-68 2.49e-13

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


Pssm-ID: 443681 [Multi-domain]  Cd Length: 435  Bit Score: 62.95  E-value: 2.49e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954872939   2 ALTEGIETGLAVMAGSKLPVWACYSSALLESVIIP----DEVEKVIIFADNDYN--GGQGLTSAEVLATRLRA 68
Cdd:COG4643   217 LIAEGYATALSVHEATGLPVVAALDAGNLLPVAQAlrerYPVAELIIAADNDRNtdGNPGQAAAEEAARAVGG 289
Toprim_3 pfam13362
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 1-75 6.65e-11

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: 53.17  E-value: 6.65e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1954872939  1 MALTEGIETGLAVMAG---SKLPVWACYSSALLESVIIPDEVEKVIIFADNDyNGGQGLTSAEVLATRLRAAGKCVHL 75
Cdd:pfam13362  2 LIIGEGIETALSLTQRlnpPGTPVIALLSAANLKAVAWPERVKRVYIAADND-AANDGQAAAEKLAERLEAAGIEAVL 78
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 3-63 2.10e-04

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: 36.09  E-value: 2.10e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954872939  3 LTEGIETGLAVMAGSKLPVWACYSSALLESVI--IPDEVEKVIIFADNDYNGGQGLTSAEVLA 63
Cdd:cd01029    5 IVEGYMDVLALHQAGIKNVVAALGTANTEEQLrlLKRFARTVILAFDNDEAGKKAAARALELL 67
 
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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