Element:Tkm1

Description Tkm1 is a Ty1/Copia-like LTR retrotransposon, characterized in the genome of the yeast Kluyveromyces marxianus (the sexual form of Candida kefyr) (Neuvéglise et al. 2002), belonging to Ty (Pseudovirus) clade one of the three original genera on which the in-progrees Pseudoviridae classification is constituted (Boeke et al 2005). The genome of Tkm1 is about 6 Kb in size (5994 bp long), including two 385-bp LTRs. The internal region of this element presents a Primer Binding Site (PBS) complementary to a tRNAiMet, two overlapping Open Reading Frames (ORFs) and a final Polypurine Tract (PPT) (Neuvéglise et al. 2002). The first ORF, of 430 amino acids (aa), displays the gag domains, while the second larger ORF (1320 aa) presents the typical Ty1/Copia pol polyprotein structure: protease, integrase, reverse transcriptase and RNase H (Neuvéglise et al. 2002). Structure Figure not to scale. If present, long terminal repeats (LTRs) have been highlighted in blue. Amino acid motifs noted with lines indicate the conserved residues in each protein domain, abbreviations below mean: MA=matrix PR=protease DU or DUT=dUTPase TM=transmembrane TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein CA=capsid RT=reverse transcriptase INT=Integrase CHR=chromodomain NC=nucleocapsid RH=RNaseH SU=surface MOV=movement protein PPT=polypurine tract PBS=primer binding site ATF=aphid transmission factor VAP=virion associated protein Related literature Mobile DNA II. (Craig et al. 2002)

Genbank accession: 20152573 Clade: Ty (Pseudovirus) Cluster or genus: Pseudovirus Branch or class: Branch 1 Family: Ty1/Copia System: LTR retroelements Host: Explore the Tree Life Project kluyveromyces marxianus Courtesy of Dr. Duong Van Hop Curator of the Vietnam Type Culture Collection, Institute of Microbiology and Biotechnology of Vietnam National University, Hanoi Browse all elements