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 (1,018) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,783 3,365 6
Proteins 1,776 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 2.491e-06 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 2.898e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 5.44e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.265e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 5.097e-05 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0004876 Least Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 2.794e-05 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.005693 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.006172 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.006522 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.01098 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.0177 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 4.376e-11 Informative Direct
Biological Process (BP) DNA replication 2.1e-07 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 2.436e-08 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 3.071e-15 Informative Direct
Molecular Function (MF) RNA polymerase activity 0.001052 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.002547 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.00189 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.06154 Least Informative Inherited
Cellular Component (CC) protein complex 0.00185 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1.879e-05 Moderately Informative Direct
Cellular Component (CC) nuclear part 2.88e-05 Moderately Informative Direct
Cellular Component (CC) chromosome 2.991e-07 Informative Direct
Cellular Component (CC) replisome 3.132e-15 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 1.134e-05 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 functionZinc0.0009852Least 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 ]