summary: We describe an extension to the Homologous Structure Alignment Database (HOMSTRAD; Mizuguchi et al., Protein Sci., 7, 2469-2471, 1998a) to include homologous sequences derived from the protein families database Pfam (Bateman et al., Nucleic Acids Res., 28, 263-266, 2000). HOMSTRAD is integrated with the server FUGUE (Shi et al., submitted, 2001)… (More)
We review some recent developments in single-ratio and generalized fractional programming. In the latter case we focus on the maximization of the smallest of several ratios. To introduce these newer results, we provide the necessary context by including some major existing results . In this concise survey we consider applications, theory and algorithms.
Previous studies have shown that the deletion of brnQ from the Corynebacterium glutamicum chromosome results in a significant reduction in l-isoleucine uptake rates, while overexpression of brnFE leads to enhanced l-isoleucine export rates. Given that net excretion rates would be an important factor for high titers of l-isoleucine accumulation, we have… (More)
One of the most difficult fractional programs encountered so far is the sum-of-ratios problem. Contrary to earlier expectations it is much more removed from convex programming than other multi-ratio problems analyzed before. It really should be viewed in the context of global optimization. It proves to be essentially N P-complete in spite of its special… (More)
This paper presents a novel approach, which is based on integrated ~automatic0interactive! knowledge acquisition, to rapidly develop knowledge-based systems. Linguistic rules compatible with heuristic expert knowledge are used to construct the knowledge base. A fuzzy inference mechanism is used to query the knowledge base for problem solving. Compared with… (More)
DnaJ is a 36-kD heat shock protein that functions together with Dnak (Hsp70) as a molecular chaperone in Escherichia coli. We have obtained a cDNA clone from the higher plant Atriplex nummularia that encodes a 46.6-kD polypeptide (ANJ1) with an overall 35.2% amino acid sequence identity with the E. coli DnaJ. ANJ1 has 43.4% overall sequence identity with… (More)
MOTIVATION Although many methods are available for the identification of structural domains from protein three-dimensional structures, accurate definition of protein domains and the curation of such data for a large number of proteins are often possible only after manual intervention. The availability of domain definitions for protein structural entries is… (More)
Acetate is a primary inhibitory metabolite in Escherichia coli cultivation which is detrimental to bacterial growth and the formation of desired products. It can be derived from acetyl coenzyme A by the phosphotransacetylase (Pta)–acetate kinase (AckA) pathway. In this study, the fermentation characteristics of Pta mutant strain E. coli TRTHΔpta were… (More)