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280  structures 8612  species 14  interactions 48885  sequences 523  architectures

Clan: Toprim-like (CL0413)


Toprim domain Add an annotation

This is families that have a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins [1].

This clan contains 7 families and the total number of domains in the clan is 48885. The clan was built by RD Finn.

Literature references

  1. Honda M, Inoue J, Yoshimasu M, Ito Y, Shibata T, Mikawa T;, J Biol Chem. 2006;281:18549-18559.: Identification of the RecR Toprim domain as the binding site for both RecF and RecO. A role of RecR in RecFOR assembly at double-stranded DNA-single-stranded DNA junctions. PUBMED:16675461 EPMC:16675461


This clan contains the following 7 member families:

DUF2220 DUF2399 DUF3854 Toprim Toprim_2 Toprim_3 Toprim_4

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
Toprim (PF01751) 27720 (56.7%) View
Toprim_4 (PF13662) 11520 (23.6%) View
Toprim_2 (PF13155) 6030 (12.3%) View
Toprim_3 (PF13362) 1781 (3.6%) View
DUF2220 (PF09983) 892 (1.8%) View
DUF2399 (PF09664) 513 (1.0%) View
DUF3854 (PF12965) 429 (0.9%) View
Total: 7 Total: 48885 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



There are 14 interactions for this clan. More...

Interacting families
DEAD Toprim
DNA_gyraseB_C Toprim
DNA_topoisoIV Toprim
DnaB_bind Toprim_4
RecR Toprim_4
Topoisom_bac Toprim
Toprim DNA_gyraseB_C
Toprim_4 DnaB_bind
Toprim_N Toprim_4


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

Loading structure mapping...