Functional category          H. influenzae   M.pneumoniae  M.genitalium
    
Amino acid metabolism                 68  (4.0)       n.d.            n.d.           
Biosynthesis of cofactors             69  (4.0)        8  (1.2)        8  (1.7)      
Cell envelope                        105  (6.2)       54  (8.0)       30+ (6.3)      
Cellular processes                    54  (3.2)       20  (2.9)       20  (4.2)      
        * Chaperones                   6  (0.4)        7  (1.0)        7  (1.5)     
        * Secretion                   15  (0.9)        9  (1.3)        9  (1.9)     
Central intermediate metabolism       30  (1.7)        6  (0.9)        5  (1.0)      
Energy metabolism                    112  (6.6)       39  (5.7)       32  (6.7)      
Fatty acid and phospholipid           40  (2.3)        9  (1.3)        8  (1.7)      
metabolism                                                                           
Nucleotide metabolism                 73  (4.3)       19  (2.8)       19  (4.0)      
Regulatory functions                  64  (3.7)        8  (1.2)        8  (1.7)      
Replication, modification,            87  (5.1)       46  (6.8)       32  (6.7)     
restriction, recombination and                                                       
repair                                                                               
Transcription                         27  (1.6)       13  (1.9)       13  (2.7)      
Translation                          125  (7.3)       99 (14.6)       99 (20.6)      
Transport                            123  (7.2)       44  (6.5)       34  (7.1)      
Other categories (and general        331 (19.4)      191 (28.2)      176*(36.7)      
function                                                                             
 prediction only)                                                                    
Repetitive DNA sequence derived       n.a.            46  (6.8)       n.a.           
ORFs                                                                                 
No functional prediction or          295 (17.3)       74 (10.9)       11*(2.3)       
database match                                                                       
Total number of proteins             1703            677             479+            

Legend: Comparison of functional classification of proteins based on sequence similarity.

Abbreviations: n.d. = not detected, n.a. = not annotated, + = according to our calculations, * = as a result of our study, numbers are different from those published by Fraser et al. (2), numbers in brackets = percentage of total ORFs. For comparison between H.influenzae and M.genitalium see http://www.ncbi.nlm.nih.gov./cgi-bin/complete_genomes.