Table 2.

Homology searches of SKN-1 in the phylum Nematoda for its core DNA-binding regions

Species	Nematode clade	Current annotation	Adjacent basic region	Core DNA binding region	Website/reference(s)
Caenorhabditis elegans	V	P34707	452QRKRGRQSKDEQL464	506RKIRRRGKNKVAARTCRQRR525	Rupert et al. (1998), Choe et al. (2012b)
Pristionchus pacificus	V	H3EVC1	PRRRGRQSKDEQL	RKIRRRGKNKVAARTCRQRR	Choe et al. (2012b)
Strongyloides stercoralis	IVa	SS01750	KKKAGRVSKDNEL	RNIRRRGRNKIAAKKVRINR	Nematode.net; Choe et al. (2012b)
Meloidogyne hapla	IVb	Contig1686.frz3.gene3	KGKRGRRSKDDSL	KKIRRRGRNKLAARKCRDRR	Nematode.net
Meloidogyne incognita	IVb	Minc09034 (MI04199)	KGKRGRRSKDDSL	KKIRRRGRNKLAARKCRDRR	Nematode.net; Choe et al. (2012b)
Globodera pallida	IVb	GPLIN_000599400	KCKRGRKSKDNSL	KKIRRRGRNKFAAQKCRERR	Gene DB
Heterodera schachtii	IVb	HS01483	KSKRGRKSKDNSL	KKIRRRGRNKLAAQKCRERR	Nematode.net; Choe et al., 2012b
Bursaphelenchus xylophilus	IVb	BUX.s01653·203	QRKRGRQSKDEQL	KKIRRRGRNKVAARKCRERR	Nematode net; Kikuchi et al. (2011)
			: ** ***:.*	::*****:**.**:. * .*

The predicted residues involved in direct contact with DNA are highlighted in bold according to a previous analysis of the Cap’n’collar (CNC) DNA-binding domain and adjacent basic region (BR) in SKN-1 (Rupert et al., 1998, Choe et al., 2012b; Blackwell et al., 2015). Protein BLAST searches were performed using C. elegans SKN-1 proteins as query sequences. Multiple amino acid alignments were performed with Clustal Omega (Sievers et al., 2011). The consensus symbols refer to fully conserved (*), strongly similar (:) and weakly similar (.) sequences. ‘Nematode clade’ refers to the five major phylogenetic groups within nematodes according to Blaxter (1998).