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33  structures 1955  species 0  interactions 2420  sequences 36  architectures

Family: DNA_primase_S (PF01896)

Summary: DNA primase small subunit

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

DNA primase small subunit Provide feedback

DNA primase synthesises the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits. This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme [1]. The family also contains many bacterial DNA primases.

Literature references

  1. Francesconi S, Longhese MP, Piseri A, Santocanale C, Lucchini G, Plevani P; , Proc Natl Acad Sci U S A 1991;88:3877-3881.: Mutations in conserved yeast DNA primase domains impair DNA replication in vivo. PUBMED:2023935 EPMC:2023935

  2. Mikhailov VS, Rohrmann GF; , J Virol 2002;76:2287-2297.: Baculovirus replication factor LEF-1 is a DNA primase. PUBMED:11836407 EPMC:11836407

  3. Iyer LM, Koonin EV, Leipe DD, Aravind L; , Nucleic Acids Res. 2005;33:3875-3896.: Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. PUBMED:16027112 EPMC:16027112

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002755

This family represents the small subunit, and also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme [ PUBMED:11836407 ].

DNA primase synthesises the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits [ PUBMED:2023935 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan AEP (CL0243), which has the following description:

This clan includes the small subunit of 2 and eukaryotic DNA primase, and primase-helicase proteins from bacteriophages and plasmids. All known cellular life forms use primases to synthesis a short RNA primer which is extended during DNA replication by a polymerase. Bacterial DNA primase adopts a different fold to archaeal and eukaryotic primases and belongs to a different superfamily.

The clan contains the following 3 members:

DNA_primase_S PPL4 Replicase


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
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Representative proteomes UniProt

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Enright A
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman A
Number in seed: 37
Number in full: 2420
Average length of the domain: 200.20 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 47.67 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 26.8 26.8
Noise cut-off 26.7 26.7
Model length: 182
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DNA_primase_S domain has been found. There are 33 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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