1371390 at Tubb2c Tubulin, beta 2c −0.838 −0.886 −0.136 −0.925 0.261 −0.756 −0.063 1371479 at Mettl7a Methyltransferase like 7A 0.810 0.451 0.000 0.914 0.609 0.698 0.514 1371942 at Gstt3 Glutathione S-transferase theta 3 1.278 0.605 −0.351 1.671 0.673 1.492 0.72

The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project principally funded by the Japanese Ministry of International Trade and Industry, and the clones were sequenced in the governmental New Energy and Industrial Technology Development Organization (NEDO) Human cDNA Sequencing Project. The HUNT database contains an extensive amount of annotation from advanced analysis and represents an essential bioinformatics contribution towards understanding of the gene function. The HRI human cDNA clones were obtained from full-length enriched cDNA libraries constructed with the oligo-capping method and have resulted in novel full-length cDNA sequences. A large fraction has little similarity to any proteins of known function and to obtain clues about possible function we have developed original analysis procedures. Any putative function deduced here can be validated or refuted by complementary analysis results. The user can also extract information from specific categories like PROSITE patterns, PFAM domains, PSORT localization, transmembrane helices and clones with GENIUS structure assignments. The HUNT database can be accessed at http://www.hri.co.jp/HUNT.

A new theoretical method has been developed for recognition and classification of membrane proteins. The method is based on computation of a polar energy surface that can reveal characteristic interaction patterns for individual helices even if crystal or NMR structure coordinates are not available. A protein with N transmembrane helices is described as a set of N vectors that are derived from a Fourier analysis of this polar energy surface computed for each helix. We then derive a polarity difference score (PDS) for any two proteins computed as the root mean square deviation between the respective vector coordinate sets. The score was found to correlate with the degree of structural similarity between the following three protein families for which tertiary structures have been determined: bacteriorhodopsin, rhodopsin, and the cytochrome c oxidase III subunit.

Identification of a novel mouse nuclear protein termed activator of basal transcription 1 (mABT1) that associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters is described. We also identify mABT1 homologous counterparts in Caenorhabditis elegans and Saccharomyces cerevisiae and show the homologous yeast gene to be essential for growth. The mABT1 associated with TBP in HeLa nuclear extracts and with purified mouse TBP in vitro. In addition, ectopically expressed mABT1 was coimmunoprecipitated with endogenous TBP in transfected cells. More importantly, mABT1 significantly enhanced transcription from an adenovirus major late promoter in a reconstituted cell-free system. We furthermore demonstrate that mABT1 consistently enhanced transcription from a reporter gene with a minimal core promoter as well as from reporter genes with various enhancer elements in a cotransfection assay. Taken together, these results suggest that mABT1 is a novel TBP-binding protein which can function as a basal transcription activator.

Several attempts to provide a completely automated procedure for genome analysis categorize the hits to globular domains into those matching a sequence of known three dimensional structure. Based only on standard sequence searching procedures such as FASTA, BLAST, complete genomes have currently been analyzed and 10-20% of the ORF sequences linked to a domain of known structure [1,2]. More Recently, many projects [3] joining sequence search and fold recognition components have been largely increased the fraction ratio to almost 40% [4,5,6]. On the contrary, our interest is to maximize the number of the relationships identified by the method based on sequence search alone, because sequence search is more sensitive and quick than the fold-recognition procedures, and then it can be immediately applied to all finished genomes. Our method is based on the high performance of MISS (Multiple Intermediate Sequence Search) method [7] in which the query and the target sequences are linked by multiple intermediate sequences which were gathered by iterative sequence search (PSIblast) [8]. The reliability of links between the query – the intermediate – the target sequence were already promised by safer threshold of sequence search algolisums with high sensitivity and specificity, evaluated in the previous work [8]. Using MISS method we can detect distance homologues although they share quite weak sequence similarity below twilight zone.