Figure 5

Prediction of gene functions in archaea by genomic context analysis. (a) The superoperon coding for the predicted archaeal exosome (see [88]). (b) The partially conserved gene neighborhood coding for the predicted repair system found in archaeal and bacterial thermophiles (see [59] for details). (c-e) Predicted operons containing uncharacterized genes in the neighborhood of genes from the following COGs: COG1594, DNA-directed RNA polymerase, subunit M, and transcription elongation factor TFIIS (RPB9); COG0592, encoding a DNA polymerase sliding clamp subunit (PCNA ortholog); COG1631, ribosomal protein L44E; COG1095, DNA-directed RNA polymerase, subunit E' (RPB7); COG2093, DNA-directed RNA polymerase, subunit E" (RPE2); COG2004, ribosomal protein S24E; COG1709, transcriptional regulator; COG3425, 3-hydroxy-3-methylglutaryl CoA synthase (PksG); COG0183, acetyl-CoA acetyltransferase (Fad A/PaaJ orthologs). UC, uncharacterized, shown by white arrows. Species abbreviations are as in Table 1. Genes are shown not to scale and are denoted by their respective genes names (some are discussed further in the text); arrows indicate the direction of transcription. A solid line connects genes in a predicted operon. Species that have the same operon organization as the listed species are indicated in parentheses. Orthologous genes are aligned. Genes with similar general functions are shown by the same shading. Broken lines show that genes are in the same predicted operon but are not adjacent. Small arrows indicate the presence of additional functionally related genes in the same predicted operon; these genes are not shown for lack of space.