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).



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

Genbank accession: 20152573
Clade: Ty (Pseudovirus)
Cluster or genus: Pseudovirus
Branch or class: Branch 1
Family: Ty1/Copia
System: LTR retroelements
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Kluyveromyces marxianus.jpg
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
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Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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