gut metagenome Genome sequencing and assembly

Table 11 is used for Bacteria, Archaea, prokaryotic viruses and chloroplast proteins. As in the standard code, initiation is most efficient at AUG. In addition, GUG and UUG starts are documented in Archaea and Bacteria (Kozak 1983, Fotheringham et al. 1986, Golderer et al. 1995, Nolling et al. 1995, Sazuka & Ohara 1996, Genser et al. 1998, Wang et al. 2003). In E. coli, UUG is estimated to serve as initiator for about 3% of the bacterium's proteins (Blattner et al. 1997). CUG is known to function as an initiator for one plasmid-encoded protein (RepA) in Escherichia coli (Spiers and Bergquist, 1992). In addition to the NUG initiations, in rare cases Bacteria can initiate translation from an AUU codon as e.g. in the case of poly(A) polymerase PcnB and the InfC gene that codes for translation initiation factor IF3 (Polard et al. 1991, Liveris et al. 1993, Sazuka & Ohara 1996, Binns & Masters 2002). The internal assignments are the same as in the standard code though UGA codes at low efficiency for Trp in Bacillus subtilis and, presumably, in Escherichia coli (Hatfiled and Diamond, 1993).