Functional genomics and enzyme evolution
http://www.bio-computing.org/showabstract.php?pmid=10710722
This summary page highlights the major points contained within a review article dealing with the impact of genome sequencing on understanding microbial enzyme evolution.
Evolution of a microbial nitrilase family
http://www.biomedcentral.com/1471-2148/5/42
This webpage contains a paper dealing with the distribution and comparative sequence analysis of nitrilases in bacteria. Both single organism and metagenomic sequences were analyzed.
Thesis: Evolution of bacterial catabolic enzymes
http://dspace1.lib.utexas.edu/handle/2152/769
This webpage contains a link to a thesis on bacterial catabolic enzyme evolution. It describes original research and a thorough review of the literature on this topic.
Evolution of bacterial enzymes acting on environmental chemicals
http://www.jbc.org/cgi/content/full/279/40/41259
This review article describes numerous examples of likely recent evolutionary adaptions for new enzyme functions to handle new chemical inputs into the environment.
Directed enzyme evolution
http://www.che.caltech.edu/groups/fha/Enzyme/directed.html
This webpage describes research on directed evolution in the laboratory with a focus on microbial enzymes that are of interest in the context of biosynthesis and biodegradation.
Molecular evolution of protein atomic composition
http://www.sciencemag.org/cgi/content/full/293/5528/297
This paper explores the connection between enzyme composition and adaption to nutrient availability. For example, enzymes expressed under conditions of sulfur limitation have a lower than average sulfur content.
Enzyme mechanism and evolution
http://www.weizmann.ac.il/Biological_Chemistry/scientist/Tawfik/home.html
This website describes research on the evolution of protein folds and catalytic promiscuity. A particular focus is on microbial phosphotriesterase activities, enzymes that degrade pesticides and nerve agents.
Structure-Function Linkage Database
http://sfld.rbvi.ucsf.edu/
The SFLD functions to link enzyme sequences and structures to specific biochemical reactions catalyzed. The superfamilies covered consist largely of microbial enzymes.
Phylogenetic modules from microbial metabolic pathways
http://www.bio-computing.org/showabstract.php?pmid=15712127
This webpage highlights work to link specific metabolic networks to specific organisms, using metabolic reconstructions from genome sequencing data.
Network perspective on topological importance of enzymes
http://www.bio-computing.org/showabstract.php?pmid=17425808
The research described here investigates the connection between the prevalence of enzymes and their relative importance in the metabolic networks of the organisms in which they are found.
References in enzyme evolution
http://lib.bioinfo.pl/pmid:16188925
This page provides a set of references dealing with enzyme evolution, structure and mechanism and databases that catalog this information.
Homology-derived secondary structure of proteins
http://consurf-hssp.tau.ac.il/cgi-bin/consurf-hsspNew.cgi?TMPL=index
This database provides estimates of the degree of evolutionary conservation of amino acids at different positions within protein families.
FireDB database
http://firedb.bioinfo.cnio.es/
FireDB is a database of functionally important residues catalogued from proteins of known structure. It contains tools for predicting functionally important residues in proteins, an important consideration in evolutionary comparisons of proteins.
CATH Database
http://www.cathdb.info/latest/index.html
CATH is a database that consists of a hierarchical classification of protein domain structures.
Superfamily
http://supfam.org/SUPERFAMILY/
This database is a useful tool for detecting distantly related proteins at the superfamily level.
GeneTrees
http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D328
GeneTrees is a phylogenomics system developed to carry out genomic analysis looking at individual genes and enzymes from the perspective of gene phylogenies.
Microbial genome database for comparative analysis
http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D343
This database is a platform for comparative analysis of microbes for which complete genome sequences are available. Similarities between all genes are computed and form the basis of various data outputs.