Table 1.

Assignment of proteins to COGs

Category	A. pernix	P. abyssi
Proteins assigned by COGNITOR	1,123	1,421
Proteins included in COGs*	1,102	1,404
True positives	1,062	1,381
Pre-existing COGs	1,011	1,339
New COGs	27	3
Divided†	24	39
False positives	44	31
Not accepted	21	17
Reassigned to a related COG	21	14
Reassigned to an unrelated COG	2	0
False negatives‡	17	9

^*Includes true positives, reassigned false positives, and false negatives. ^†Not included in 'To preexisting COG' or 'To new COG' numbers. ^‡Proteins added during manual checking.