Table 1.

Predicted core Crc regulon of Pseudomonas.

Gene name	Function	PAO1	PA14	PA7	LESB58	Pf0-1	Pf-5	SBW25	KT2440	F1	W619	B728a	DC3000
	Amino acid transport and metabolism
putP	Sodium/proline symporter	0783	54150	4736	45601	0453	0496	0452	4946	4818	0522	NM	NM
	Probable amino acid permease	0789	54040	4729	45531	4561	4906	1103	1059	1100	1089	NO	NO
phhA	Phenylalanine-4-hydroxylase	0872	52990	4644	44441	1499	1611	4458	4490	1424	3779	NM	NM	Y
gltI	Probable binding protein component of ABC transporter	1342	46910	4043	38391	4535	4871	1139	1071	1112	1100	NM	NM
	Probable sodium/alanine symporter	2252	35460	2989	30521	NM	NM	NM	0496	0530	0551	5052	5500
	Probable glutamine synthetase	2040	38140	3247	32821	5408	5930	5849	5184	5091	0279	4868	5310
	Carbohydrate transport and metabolism
mltE	Probable binding protein component of ABC maltose/mannitol transporter	2338	34420	2925	29651	2640	3070	2745	NO	NO	2041	2440	2707
oprB	Glucose/carbohydrate outer membrane porin precursor	3186	23030	1943	18821	4366	4613	4842	1019	1057	4205	1117	1296	Y
	Probable binding protein component of ABC sugar transporter	3190	22980	1939	18781	4370	4617	4846	1015	1053	4209	1113	1292	Y
lldP	L-lactate permease	4770	63080	5490	51551	0753	0817	5278	4735	4601	0696	NO	NO
fruA	PTS fructose IIC component	NM	NM	NM	NM	0795	0861	0806	0795	0818	4398	0823	0956	Y
glpF	Glycerol uptake facilitator protein	NM	NM	NM	NM	4531	4867	1143	1076	1117	1105	3904	4167
	Energy production and conservation
coxB	Cytochrome c oxidase, subunit II	0105	01290	0180	01061	0079	0061	0058	0103	0119	0122	NO	NO
pntB	Pyridine nucleotide transhydrogenase, beta subunit	0196	02470	0277	01971	0112	0113	0111	0155	0173	5072	NM	NO
acsA	Acetyl-coenzyme A synthetase	0887	52800	4627	44291	4293	4522	4766	4487	1428	3776	3572	1825
	Putative glycerate 2-kinase	1499	45030	3833	39131	1595	1698	1800	4300	1569	3625	NO	NO
	Probable D-beta-hydroxybutyrate permease	2004	38580	3285	33191	3078	3575	2629	3074	2650	2717	NO	NO
	Putative acetate transporter	3235	22340	1890	18321	1607	1711	1813	1742	3977	1292	3757	1623
cstA	Probable carbon starvation protein	4606	60950	5246	49911	4883	5352	5333	4641	4503	0798	4273	4638
phaC1	Poly(3-hydroxyalkanoic acid) synthase 1	5056	66820	5794	54461	0394	0434	0396	5003	4877	0461	NO	NO
phaF	polyhydroxyalkanoate synthesis protein PhaF	5060	66875	5799	54501	NM	NM	NM	5007	4881	0457	0391	5147
	Alginate metabolism
algP	Alginate regulatory protein	5253	69370	5998	56471	NM	NM	NM	0194	0215	0263	0054	0136
	Lipid metabolism
fadD2	Long-chain-fatty-acid--CoA ligase	3300	21340	1824	17661	4354	4599	4830	4550	1339	3845	3836	4098
estA	Esterase	5112	67510	5845	55021	NM	NM	NM	0418	0452	4784	4606	0569
	Polyamine metabolism
aphA	Acetylpolyamine aminohydrolase	1409	46230	3930	40041	5631	6145	6061	5340	5249	0133	NO	NO
	Xenobiotic degradation and transport
pcaK	Benzoate transport	NM	NM	NM	NM	1266	1316	1362	1376	4347	1016	2124	2340
	DNA replication, recombination and repair
recA	RecA protein	3617	17530	1523	14181	1175	1231	1189	1629	4088	4030	1378	4033
hupA	HU family DNA-binding protein	5348	70600	6125	57431	5600	6102	6032	5313	5222	0160	NM	NM	Y
	nucleotide transport and metabolism
	Probable transporter	1519	44800	3815	38911	1711	4364	4355	4284	1584	3610	NO	NO
xdhA	Xanthine dehydrogenase	1524	44710	3809	38041	1797	1889	4592	4278	1590	3604	NM	NM
	Translation
rplR	50S ribosomal protein L18	4247	09010	0853	06811	5063	5566	5511	0470	0503	4733	4532	0642
tufB	Elongation factor Tu	4277	08830	0835	06631	5081	5584	5529	0452	0485	4751	4550	0624
	Unknown function
	Hypothetical protein	0754	54540	4766	45891	NM	NM	NM	1418	4303	1058	3966	4232	Y
	Probable transporter	1507	44950	3824	39041	1701	4371	4364	4290	1578	3616	NO	NO
	Probable major facilitator superfamily (MFS) transporter	3709	16410	1427	12731	3359	2486	2159	0057	0073	0076	NO	NO
	Hypothetical protein	3923	13130	1184	10541	4708	5116	0923	0765	0792	4424	0991	1149
	Probable ATP-binding component of ABC transporter	4461	57930	5034	48401	0858	0916	0883	0953	0992	4262	4146	4452
	Hypothetical protein	4570	60480	5210	49531	4863	5332	5174	0685	0716	4500	NO	NO
	Hypothetical protein	5052	66760	5789	54421	0398	0438	0400	5090	4963	0375	NM	NM
	Phosphotransferase domain-containing protein	NM	NM	NM	NM	1487	1597	4880	4500	1412	3789	3586	1810

Loci with an A-rich motif in the upstream region in all strains tested for at least three species are shown. The numbers under strain names indicate the locus id, according to Genbank annotation, of the locus with the A-rich motif in the upstream region. NO (no ortholog) indicates that no orthologous locus was found. NM (no motif) indicates that the orthologous locus did not have the A-rich motif in the upstream region. Y indicates that the locus is has increased transcript and/or protein levels in a crc mutant of P. putida KT2442 (a spontaneous rifampicin resistant mutant of KT2440) [26].