SUPERFAMILY 1.75 HMM library and genome assignments server


DNA primase core superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   DNA primase core [ 56730]
Superfamily:   DNA primase core [ 56731] (2)
Families:   DNA primase DnaG catalytic core [ 56732]
  Primase fragment of primase-helicase protein [ 90090]


Superfamily statistics
Genomes (2,828) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,552 0 4
Proteins 3,547 0 4


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 2.431e-08 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 2.851e-08 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 5.545e-08 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.36e-07 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 6.029e-07 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0004876 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.4897 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.002392 Least Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 2.794e-05 Moderately Informative Direct
Biological Process (BP) organelle organization 4.226e-05 Moderately Informative Direct
Biological Process (BP) DNA metabolic process 3.092e-13 Informative Direct
Biological Process (BP) mitochondrion organization 2.99e-10 Informative Direct
Biological Process (BP) DNA replication 2.1e-07 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.0007112 Least Informative Direct
Molecular Function (MF) binding 0.02013 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 8.655e-06 Moderately Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 6.779e-12 Informative Direct
Molecular Function (MF) DNA binding 9.408e-07 Informative Direct
Molecular Function (MF) structure-specific DNA binding 2.032e-11 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.03537 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0337 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.006874 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.00189 Least Informative Inherited
Cellular Component (CC) mitochondrial part 2.617e-07 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 2.351e-05 Moderately Informative Direct
Cellular Component (CC) mitochondrial matrix 4.42e-11 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA replication0InformativeDirect
Cellular componentDNA-directed RNA polymerase0Highly InformativeDirect
Cellular componentPrimosome0Highly InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 2 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a DNA primase core domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 2 hidden Markov models representing the DNA primase core superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]