Table 3.

Proteins Annotated as ORF or unknown which Are Assigned to Proteins of Known Function

	μ-score	Synechocystis proteins				Chloroplasts proteins—ORF or unknown				PSI-BLAST
Prot. ID	Prot. function	Gene	aa	Prot. ID	Prot. function	Organism	aa	Hits	Prot. detected
1	17.10	6466376a	rubisco expression prot	cfxX/Q	301	1276694	ORF301	Porphyra purpurea	301	>1000	CFXQ_CYAME
2	12.00	sll1536	molybdopterin biosynthesis prot MoeB	moeB	392	1276801	ORF382	Porphyra purpurea	382	585	moeB_MYCTU
3	9.60	sll1536	molybdopterin biosynthesis prot MoeB	moeB	392	6466397	chlN (incorrect)	Cyanidium caldarium	395	574	moeB_MYCTU
4	7.60	sll0621	thiol:disulfide interchange prot DsbD	dsbD	248	1276830	ORF240	Porphyra purpurea	240	58	cycZ_ECOLI
5	5.40	sll1035	uracil phosphoribosyl transferase	upp	216	1276820	ORF198	Porphyra purpurea	198	88	UPP_STRSL
6	4.70	slr1365	BioY prot	bioY	217	1016197	ORF188	Cyanophora parado	188	26	BIOY_BACSH
7	3.90	slr0839	ferrochelatase	hemH	387	1276821	ORF48	Porphyra purpurea	48	47	HEMZ_SYNY3
8	3.60	slr1365	BioY prot	bioY	217	7259544	unknown	Mesostigma viride	223	2	bioY_SYNY3
9	2.50	11691a	cytochrome b6/f subunit VI (3.5kD)	petL	31	5881712	ORF31	Arabidopsis thaliano	31	2	PETL_BETVU
10	2.50	12005a	cytochrome b6/f subunit VI (3.5kD)	petL	31	1262631	ORF62b	Pinus thunbergii	62	2	PETL_BETVU
11	2.50	11809a	maturase K	matK	509	295955	ORF506	Euglena gracilis	506	994	mat_PSEAL

List of ORFs from different cpDNAs for which functional annotation has been possible. The results from PSI-BLAST are also shown, indicating the number of significant hits obtained (column 11), and the ortholog assigned (column 12). Proteins in column 12 are labeled according to SwissProt nomenclature. 

^aNot in Synechocystis.