Modular organization and reticulate evolution of the ORF1 of Jockey superfamily transposable elements

Table 1 Identification of ORF1 domains

^aLineage and subgroup identified by phylogenetic analysis based on a concatenation of the ORF2 apurinic endonuclease (APE) and reverse transcriptase (RT) domains. For further details please see the text.
^bAverage percent pairwise nucleotide identity of the RT domain for each subgroup, estimated using Geneious [25].
^cORF1 type (I-V) identified for each subgroup, based on ORF1 types described by Khazina and Weichenrieder [11]. Subtypes (A, B and C) are used to show the diversity of ORF1 structures within types identified in this paper.
^dDomains identified within the ORF1 by HMM-HMM comparision [26] or by Pcoils [23]. CC, coiled-coil domain; CCHC, gag-like Cys₂HisCys zinc-knuckle; lz, leucine zipper; PHD, plant homeodomain; RRM, RNA recognition motif; Tnp22, transposase 22, (RCSB Protein Data Bank entry 2yko_A and Pfam entry PF02994), which is the L1ORF1 protein composed of a coiled-coil, RRM and CTD domain [24]; zf, zinc finger.
^eMinimum length of the inferred amino acid sequence for each domain.
^fAverage percent pairwise inferred amino acid identity for each domain, estimated using Geneious [25].
^gTop hits starting with ‘PTHR’ are from the Panther Classification System, all other top hits are from the RCSB Protein Data Bank.
^hProbability reported by HHPred [26].

ISSN: 1759-8753