In recent years, metagenome-based approaches have led to the accumulation of an increasing number of gene sequences from the uncultured microbes from different environments. Using the metagenome sequences to fully understand how complex microbial communities function and how microbes interact within these niches represents a major challenge for microbiologists today. A large percent of predicted metagenomic genes are expected to be transporters, which play crucial roles in fundamental cellular processes and functions in all prokaryotic and eukaryotic organisms. Systematic annotation and analyses of these transporter genes are of great value to increase our knowledge on microbial ecology and physiology of these microbes. 

The transporter annotation of metagenomic sequence data is challenging. The source organism of a sequence is typically unknown. Due to the ÒcosmopolitanÓ nature of metagenomic samples, a large fraction of the protein sequences predicted in the metagenomic data will be fragmentary. We significantly improved our transporter annotation pipeline (TransAAP), a web-based transporter annotation tool, to handle the volume, complexity, heterogeneity and fragmentary nature of the metagenomic data. We employed various sequence-based, domain-based, and cluster-based bioinformatics searches to maximize the possibility of predicting all the potential candidates of transporter genes out of metagenomic samples. We plan to include information such as transporter type and family classification, substrate prediction, the confidence levels, Pfam/TIGRfam hits and evalues, COG hits and evalue, the top hit to the non-redundant protein database and the top hit species, as well as a pre-computed phylogenetic tree with known transporters in the same family. A comparative analysis of the transporter profiles of metagenomic samples from the different environment, for example the various sample sites in the Global Ocean Sampling project, will illustrate the relationship between the transporter features and organismÕs physiology and living environment.