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DNA binding

This subsection of the ‘Function’ section specifies the position and type of each DNA-binding domain present within the protein.

We annotate experimentally defined DNA-binding domains and conserved DNA-binding domains defined by the InterPro resources PROSITE, Pfam and SMART; examples include the AP2/ERF domain, the ETS domain, the Fork-Head domain, the HMG box and the Myb domain.

1. Predicted DNA-binding domains

As with other domain types predicted using InterPro resources, the number and type of each protein domain is explicitly stated in the ‘Sequence similarities’ subsection of the ‘Family and Domains’ section.
Examples: P10103, P46200, Q9SGJ6, P14921, P55317, P30658

Special types of DNA-binding domain

a. bHLH and bZIP proteins

In the case of basic helix-loop-helix (bHLH) and basic leucine-zipper (bZIP) domains, we describe the C-terminal HLH and leucine zipper motifs separately in the ‘Domain’ subsection of the ‘Family and Domains’ section. The N-terminal basic region of these domains is described in the ‘DNA-binding’ subsection.

For bHLH proteins, the basic region is usually directly followed by the HLH domain in the sequence.
Example: P35869

In bZIP proteins, the basic region is followed by the leucine-zipper domain, characterized by an LXXXXXXL motif, and begins with the first Leu/Ile and stops with the last Leu/Ile residues.
Examples: P18289, P15407

b. Homeobox proteins

Homeobox proteins constitute a large family which contains several subtypes. When a homeobox belongs to a subtype, it is indicated in the ‘Description’ field after ‘Homeobox’ preceded by a semicolon.
Examples: Q9H2P0, O81788, Q90655, P20823

When a particular homeobox is incomplete or differs significantly from the consensus it may be annotated as either ‘partial’ or ‘atypical’.
Examples: Q6WRX8, Q8MJD5

2. Experimentally determined DNA-binding domains

When a DNA-binding domain has been identified experimentally but does not correspond to a domain modelled by an InterPro resource, then the simple fact of the existence of the domain is indicated but no particular description is provided.
Example: P13574

Such domains are transferred to close species using the ‘By similarity’ qualifier.
Example: Q08400

Related keywords: DNA-binding, Homeobox.