We present a genome assembly from an individual male
(the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Cameroon. The genome sequence is 271 megabases in span. ...The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.5 kilobases in length.
We present a genome assembly from an individual female
(the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the ...assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
Catalytic site structure is normally highly conserved between distantly related enzymes. As a consequence, templates representing catalytic sites have the potential to succeed at function prediction ...in cases where methods based on sequence or overall structure fail. There are many methods for searching protein structures for matches to structural templates, but few validated template libraries to use with these methods. We present a library of structural templates representing catalytic sites, based on information from the scientific literature. Furthermore, we analyse homologous template families to discover the diversity within families and the utility of templates for active site recognition. Templates representing the catalytic sites of homologous proteins mostly differ by less than 1
Å root mean square deviation, even when the sequence similarity between the two proteins is low. Within these sets of homologues there is usually no discernible relationship between catalytic site structure similarity and sequence similarity. Because of this structural conservation of catalytic sites, the templates can discriminate between matches to related proteins and random matches with over 85% sensitivity and predictive accuracy. Templates based on protein backbone positions are more discriminating than those based on side-chain atoms. These analyses show encouraging prospects for prediction of functional sites in structural genomics structures of unknown function, and will be of use in analyses of convergent evolution and exploring relationships between active site geometry and chemistry. The template library can be queried
via a web server at
www.ebi.ac.uk/thornton-srv/databases/CSS and is available for download.
We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. ...Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and is publicly available as a web-based data resource. This paper presents the first release ...of a web-based search tool to explore enzyme reaction mechanisms in MACiE. We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and is publicly available as a web-based data resource. This paper presents the first release ...of a web-based search tool to explore enzyme reaction mechanisms in MACiE. We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
The process of deducing the catalytic mechanism of an enzyme from its structure is highly complex and requires extensive experimental work to validate a proposed mechanism. As one step towards ...improving the reliability of this process, we have gathered statistics describing the typical geometry of catalytic residues with regard to the substrate and one another. In order to analyse residue-substrate interactions, we have assembled a dataset of structures of enzymes of known mechanism bound to substrate, product, or a substrate analogue. Despite the challenges presented in obtaining such experimental data, we were able to include 42 enzyme structures. We have also assembled a separate dataset of catalytic residues which act upon other catalytic residues, using a set of 60 enzyme structures. For both datasets, we have extracted the distances between residues with a given catalytic function and their target moieties. The geometry of residues whose function involves the transfer or sharing of hydrogens (either with substrate or another residue) was analysed more closely. The results showed that the geometry for such productive interactions (prior to the transition state) closely resembles that seen in non-catalytic hydrogen bonds, with distances and angles in the normal expected range. Such statistics provide limits on “expected geometries” for catalytic residues, which will help to identify these residues and elucidate enzyme mechanisms.
We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. ...Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
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