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Saraswathi Abhiman (NCBI, 8600 Rockville Pike, Bethesda MD, 20894 USA)
These networks are derived from domain architectures and gene neighborhoods. The direction of the arrows shows the order of genes in operons from 5′ to 3′, or order of domains from N-terminal to C-terminal. The top panel shows domains and genes related to amidoligases of the ATP-grasp, glutamine synthetase-like and acetyltransferase folds. Grey arrows indicate information from gene neighborhoods and blue arrows indicate information derived from domain architectures. Domains that share the same fold are shown in the same shape and color. The shape of the domains corresponds to their functional role. The bottom panels show network graph of domains related to DNA methylation. The meta-network on the right is used to highlight the overall trends of associations between different functional types of domains involved in DNA methylation. The edge thickness is proportional to the relative frequency with which linkages between two domains or meta-nodes reoccur in distinct polypeptides and gene neighborhoods. Standard abbreviations are used for domain/gene names.