Abstract:
Background: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional
functional information based on biological characterization and functions of sequence-similar
proteins has become available. On the basis of this new information, an updated version of the
annotated chromosome has been generated.
Results: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116
RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession
U00096 were used. Some protein-coding sequences are compound and encode multimodular
proteins. The coding sequences (CDSs) are represented by modules (protein elements of at
least 100 amino acids with biological activity and independent evolutionary history). There are
4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5%
have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only
7% of the modules appear unique to E. coli, and this number is expected to be reduced as more
genome data becomes available. The imputed functions were assigned on the basis of manual
evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome
annotation system.
Conclusions: Much knowledge has been gained about functions encoded by the E. coli K-12 genome
since the 1997 annotation was published. The data presented here should be useful for analysis of
E. coli gene products as well as gene products encoded by other genomes.
