TABLE 1.

Functional annotation of predicted proteins based on genome sequence analysis of B. pertussis strain Tohama I, B. parapertussis_hu strain 12822 and B. bronchiseptica strain RB50

Functional annotationa	No. of proteins with assigned COGs inb:
	B. pertussis (3,436)	B. parapertussishu (4,185)	B. bronchiseptica (4,994)
Information storage and processing
Translation, ribosomal structure, and biogenesis	162	191	201
Transcription	269	362	442
DNA replication, recombination, and repair	337	143	133
RNA processing		1	1
Chromatin structure and dynamics	4	4	5
Cellular processes
Cell division and chromosome partitioning	30	30	35
Posttranslational modification, protein turnover, chaperones	100	132	140
Cell envelope biogenesis, outer membrane	175	208	226
Cell motility and secretion	57	64	82
Inorganic ion transport and metabolism	176	203	249
Signal transduction mechanisms	73	102	116
Intracellular trafficking and secretion	52	59	64
Defense mechanisms	25	31	41
Metabolism
Energy production and conversion	212	284	352
Carbohydrate transport and metabolism	139	197	237
Amino acid transport and metabolism	352	475	556
Nucleotide transport and metabolism	50	59	60
Coenzyme metabolism	107	114	121
Lipid metabolism	141	200	253
Secondary metabolites biosynthesis, transport and catabolism	98	143	172
Poorly characterized
General function prediction only	275	350	402
Unknown function	286	432	516
Undetermined COGs	315	401	591
Total no. of proteins with assigned COGs	3,121	3,784	4,403

^aFunctional classifications are based on COG (Clusters of Orthologous Groups) categories. Additional annotated sequence information can be obtained from the Sanger Institute (http://www.sanger.ac.uk/Projects/Microbes/) and from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Complete.html).

^bNumbers of predicted proteins are given in parentheses.