Table 2. Signaling and regulatory domains or genes that are absent in P. marinus SS120 (Pma) or in lower copy number than in the freshwater cyanobacteria Thermosynechococcus elongatus (Tel), Synechocystis sp. PCC6803 (Syn), and Anabaena sp. PCC7120 (Ana).

			No. of genes/genome
Signaling system component or domain	Gene name	COG no.	Pma	Tel	Syn	Ana
Signal transduction mechanisms
Histidine kinases	—	0642	5	16	42	124
Response regulators	—	2197	6	26	41	84
PAS domains	—	2202	1	13	23	57
GAF domains	—	2203	0	15	28	62
HPt domains	—	2198	0	4	7	9
GGDEF domains	—	2199	0	10	23	14
EAL domains	—	2200	0	5	13	7
HD-GYP domains	—	2206	0	1	2	2
Ser/Thr protein kinase	—	0515	0	10	9	35
Ser/Thr protein	—	0631	0	3	3	4
Phosphatase 1
Ser/Thr protein	—	0639	0	1	1	2
Phosphatase 2
Adenylate cyclase	cyaA	2114	0	1	2	7
cAMP-binding domains	crp	0664	2	3	12	14
Phototaxis*
Hybrid histidine kinase	taxAY	0643/2198/0784	0	3	3	3
Photoreceptor for positive phototaxis	taxD	2203/0840	0	3	3	3
Putative phototaxis protein	taxP	0784	0	3	3	3
CheW-like signal transducer	taxW	0835	0	3	3	3
CheY-like signal transducer	taxY	0784	0	3	3	3
Regulation of RNA polymerase
Alternative σ28	fliA	1191	0	1	1	2
Alternative σ24	rpoE	1592	0	3	3	2
Anti-sigma factor	rsbW	2172	1	2	2	5
Serine phosphatase regulator of σ	rsbU	2208	1	2	5	5
Others
Phycobilisome degradation proteins	nblA	—	0	1	2	2
	nblB	—	0	2	1	1
Universal stress protein	uspA	0589	0	4	4	7
Drought-induced stress protein	CDS P34	—	0	1	2	2
Ankyrin repeats	—	0666	0	1	1	2
Forkhead domains	—	1716	0	2	2	2

COG, clusters of orthologous groups.

^*Gene designations after ref. 54.