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33  structures 1048  species 0  interactions 63042  sequences 3257  architectures

Clan: GAG-polyprotein (CL0523)


LTR-copia-type polyprotein segment Add an annotation

This superfamily is characterised by family members that are derived from retrotransposons of the copia-type.

This clan contains 10 families and the total number of domains in the clan is 63042. The clan was built by P Coggill.


This clan contains the following 10 member families:

DUF1759 DUF4219 DUF4939 PNMA Retrotran_gag_2 Retrotran_gag_3 Retrotran_gag_4 Retrotrans_gag Ty3_capsid TYA

Domain organisation

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

Loading domain graphics...


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

Pfam family Num. domains Alignment
Retrotrans_gag (PF03732) 23306 (37.0%) View
Retrotran_gag_2 (PF14223) 23222 (36.8%) View
DUF1759 (PF03564) 5937 (9.4%) View
Retrotran_gag_3 (PF14244) 3248 (5.2%) View
DUF4219 (PF13961) 2079 (3.3%) View
Ty3_capsid (PF19259) 2030 (3.2%) View
PNMA (PF14893) 1549 (2.5%) View
DUF4939 (PF16297) 1457 (2.3%) View
TYA (PF01021) 122 (0.2%) View
Retrotran_gag_4 (PF17241) 92 (0.1%) View
Total: 10 Total: 63042 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...



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...