TABLE 2.

Sequence analysis and G+C content of subtracted clones

Clone	Insert size (bp)	Homolog(s)b	G+C content (%)c	Scored	E valued
B1a	960	No significant match	38.0	NAe	NA
B2	1,129	Rd HI1494, hypothetical protein	37.5	199	6e-50
B3	558	Rd HI1467, hypothetical ABC transport protein	33.9	243	1e-63
D2	356	D. radiodurans hypothetical protein	43.8	59.0	2e-08
D3a	1,025	traE of plasmid RP4	38.2	262	9e-69
D5a	1,088	Rd HI0361, hypothetical fecE iron transport gene	39.3	601	1e-171
D11	506	Rd HI1265, conserved hypothetical protein	39.3	335	2e-91
D13	676	No significant match	39.6	NA	NA
E3	1,253	Carotovoricin Er	39.9
		Tail sheath protein		152	1e-35
		Tail core protein		147	4e-34
E8a	616	P22 phage antirepressor protein	37.8	189	4e-47
E9a	444	H. influenzae hmcD hemocin gene	22.0	178	7e-44
E10	423	Rd HI0873, glucose 4,6-dehydratase (rffG)	37.1	178	3e-44
F2a	1,151	Hypothetical genes	34.5
		N. meningitidis MC58 adhesin/invasin		73	8e-12
		HI0422, ATP-dependent RNA helicase (srmB)		153	5e-36
F5a	1,370	Rd hypothetical proteins	35.1
		HI1273, conserved hypothetical protein		148	3e-34
		HI1266, hypothetical protein		193	7e-42
		HI1265, conserved hypothetical protein		179	1e-43
F6a	296	Rd HI0291/HI0292 hypothetical Hg binding proteins	35.4	76	3e-13
F7	885	Carotovoricin Er baseplate protein	42.4	149	5e-34
F10	763	H. influenzae immunoglobulin A protease (iga)	35.9	534	1e-151
F17	590	Rd hypothetical proteins	33.4
		HI1466.1, hypothetical TonB-dependent receptor protein		228	6e-59
		HI1467, hypothetical ABC transport protein		132	8e-30
F20	556	Carotovoricin Er tail protein	43.3	410	1e-21
MU33	826	Rd HI1508, Mu-like prophage protein GP36	41.9	50	4e-05
MU34	1,384	Thermotoga maritima hypothetical protein	29.6	77	1e-12

^aClone containing DNA present in H. influenzae biogroup aegyptius strains F3031 and F1947. All clones without a superscript a contain DNA unique to strain F3031.

^bIdentification of homologs to subtracted clones is based on BLASTx analysis. The designation HI followed by a number corresponds to loci identified in the H. influenzae Rd KW20 genome (10).

^cG+C content was determined with Artemis (http://www.sanger.ac.uk) by using a window of 120 nucleotides.

^dThe score and E value of the BLASTx analysis are shown. Scores of less than 50 were not considered significant matches.

^eNA, not applicable.