Table 2.

Percentage of CM hits covered by pHMM.

Family	Total hits(CM)	Total hits(pHMM)	Common hits	% of CM hits covered by pHMM I#	% of CM hits covered by pHMM II#
FMN	844	831	830	99.40%	100%
Cobalamin	1713	1807	1703	99.41%	99.59%
TPP	2245	2250	2242	99.95%	99.95%
Lysine	651	621	618	97.45%	98.25%
Glycine	1185	1260	1174	99.66%	100%
Purine	595	645	594	99.83%	99.83%
Sam	1262	1278	1255	99.44%	99.68%
Sam alpha	194	233	127	69.02%	75.14%
Glms	172	154	153	96.83%	97.45%
PreQ1	332	2387	267	90.94%	98.84%

I^# : percentage coverage was calculated after removing hits lying in gene, in AT repetitive region and those which were located far upstream of the genes. II^# : percentage coverage was calculated after removing hits lying in gene, in AT repetitive region, those which were far upstream of the genes, as well as those hits that were upstream of putative and hypothetical genes.