SUPERFAMILY 1.75 HMM library and genome assignments server

Prim-pol domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Prim-pol domain [ 56746]
Superfamily:   Prim-pol domain [ 56747] (3)
Families:   PriA-like [ 56748] (2)
  Bifunctional DNA primase/polymerase N-terminal domain [ 103305]
  HP0184-like [ 143897]


Superfamily statistics
Genomes (1,029) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,799 3,365 6
Proteins 1,790 3,360 6


Functional annotation
General category Other
Detailed category Unknown function

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 0.0000001677 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000001959 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000376 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000000923 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.000003456 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0004566 Least Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00002649 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.006367 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.01198 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.006882 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.007281 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.01822 Moderately Informative Inherited
Biological Process (BP) DNA replication 0.0000001382 Highly Informative Direct
Molecular Function (MF) transferase activity 0.000000431 Least Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.000000002163 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) RNA polymerase activity 0.001031 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.0004402 Least Informative Direct
Cellular Component (CC) protein complex 0.0004673 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.01382 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.00196 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000001467 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000002597 Moderately Informative Direct
Cellular Component (CC) chromosome 0.00000006636 Informative Direct
Cellular Component (CC) nuclear chromosome part 0.00001813 Highly Informative Direct

Document: GO 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
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately 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) · 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 5 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 Prim-pol domain 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 5 hidden Markov models representing the Prim-pol domain 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) · UniProtKB KeyWords (KW) · Internal database links ]