We have cloned and overexpressed multidrug transporter CaMdr1p as a green fluorescent protein-tagged protein to show its capability to extrude drug substrates. The drug extrusion was sensitive to pH and energy inhibitors and displayed selective substrate specificity. CaMdr1p has a unique and conserved antiporter motif, also called motif C [G(X6)G(X3)GP(X2)GP(X2)G], in its transmembrane segment ...

New polyketides, termed veramycins, were isolated along with their known congeners NFAT-133 and TM-123. Total synthesis from a central building block was accomplished, the BGC identified biosynthetic pathway for this molecule class proposed.

MOTIVATION The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches. RESULTS We describe a novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction of cis-regulatory elements in eukaryotic promoters. The algorithm is tested on biologica...

An enhanced version of an existing motif search algorithm BMA is presented. Motif searching is a computationally expensive task which is frequently performed in DNA sequence analysis. The algorithm has been tailored to fit on the COPACOBANA architecture, which is a massively parallel machine consisting of 120 FPGA chips. The performance gained exceeds that of a standard PC by a factor of over 1...

This work describes a method for predicting DNA binding function from structure using 3-dimensional templates. Proteins that bind DNA using small contiguous helix±turn±helix (HTH) motifs comprise a signi®cant number of all DNA-binding proteins. A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in the Protein Data Bank. The templates were...

Characterizing the DNA-binding specificities of transcription factors is a key problem in computational biology that has been addressed by multiple algorithms. These usually take as input sequences that are putatively bound by the same factor and output one or more DNA motifs. A common practice is to apply several such algorithms simultaneously to improve coverage at the price of redundancy. In...

PLACE (http://www.dna.affrc.go.jp/htdocs/PLACE/) is a database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements. Motifs were extracted from previously published reports on genes in vascular plants. In addition to the motifs originally reported, their variations in other genes or in other plant species in later reports are also compiled. Documents for each motif in...