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. 2017 Jan 12;119(5):775–789. doi: 10.1093/aob/mcw260

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).