Based on gene content and organization, it may be surmised that the psl gene cluster was involved in LPS and/or exopolysaccharide (EPS) biosynthesis.
Phylogenetic analysis of COG1518 combined with gene neighborhood comparisons yields a clear classification of CASS based on gene composition and (predicted) operon organization (Fig. 2a) which is, generally, in agreement with the recent study of Haft et al [ 24].
Second, we propose a different interpretation of results of some popular methods based on gene randomization, which does not violate the organization of the biological experiment, but gives up the concepts of significance or P-values.
A third estimate, from Dr. John Quackenbush and colleagues at the Institute for Genomic Research, also based on gene transcripts, puts the number of genes at about 120,000.
Gaps in the genome were filled by PCR, based on predicted gene organization in red-lineage plastids.
Further work is needed to verify the actual functions and relationships of Type 1 and 2 E. coli-like clusters, which will serve strengthen the confidence of predictions based on percent gene identity, gene cluster organization and mechanistic similarities reflected in protein organization.
Expand the genes based on the gene-gene interaction.
The 53 genera were arbitrarily grouped into 14 based on (1) their gene organization and (2) the existence of the C3 operon (Fig. 4).
Based on domain organization, R gene products can be categorized into five major types: TNL (TIR-NBS-LRR), CNL (CC-NBS-LRR), RLK (Receptor like kinases), RLP (Receptor like proteins) and Pto (a Ser/Thr kinase protein) [ 1, 5, 6].
Types of IR-LSC junction are based on the organization of genes flanking JLB and JLA in angiosperms.
