Table 1. List of the 61 selected targets after data mining in the ChIP-Seq analysis.

The ID, annotation of the gene downstream the selected promoter region, fold enrichment of the peak, functional category and selected DNA fragments and peak coordinates in the P. putida KT2440 reference genome (GCF_000007565.1_ASM756v1) are shown. In bold, those genes whose expression was validated by RT-q PCR.

	ID	Annotation	Enrichment	Categories	DNA Fragment Coordinates		Peak Coordinates
1	PP0009	rpmH 50S ribosomal protein L34	2.33	Translation	8847	9524	8860	9424
2	PP0036	transcriptional regulator	2.74	Regulatory	38954	39371	38757	39399
3	PP0153	hypothetical protein	4.32	hypothetical	161866	162366	161930	162266
4	PP0167	paxB toxin secretion ATP-binding protein	3.06	transport	193553	194537	193652	194437
5	PP0168	putative surface adhesion protein	3.06	transport	193553	194537	193652	194437
6	PP0397	yeaG protein kinase	2.53	Regulatory	484338	484816	483915	484716
7	PP0640	hypothetical protein	3.08	hypothetical	750762	751127	748555	751027
8	PP0731	pcs phosphatidylcholine synthase	4.19	enzymatic	850001	850910	850100	850810
9	PP0876	AraC family transcriptional regulator	2.93	Regulatory	1017151	1018026	1017172	1017926
10	PP0952	rpoN RNA polymerase sigma-54 factor	2.70	Regulatory	1095959	1096333	1095946	1096355
11	PP1116	resolvase family site-specific recombinase	2.09	enzymatic	1277917	1278833	1278016	1278868
12	PP1117	hypothetical protein	2.13	hypothetical	1279998	1281314	1280097	1281388
13	PP1206	oprD basic amino acid specific porin OprD	3.45	transport	1386355	1387119	1386334	1387019
14	PP1288	algD GDP-mannose 6-dehydrogenase	2.30	enzymatic	1474119	1474995	1474152	1474895
15	PP1691	hypothetical protein	3.03	hypothetical	1883564	1884708	1883621	1884716
16	PP1796	aprDB (pseudogene)	2.44	transport	2016394	2017010	2016493	2016929
17	PP1795	hypothetical protein	2.44	hypothetical	2016394	2017009	2016493	2016929
18	PP1947	hypothetical protein	2.32	hypothetical	2202041	2202420	2202121	2202416
19	PP2062	hypothetical protein	3.79	hypothetical	2345245	2346642	2344373	2346596
20	PP2063	hypothetical protein	3.79	hypothetical	2345245	2346643	2344373	2346596
21	PP2265	folD-II bifunctional methylenetetrahydro- folate dehydrogenase/ cyclohydrolase	3.38	enzymatic	2585408	2585860	2585507	2586482
22	PPt50	tRNA	3.38	Translation	2585408	2585860	2585507	2586482
23	PP2509	hypothetical protein	3.14	hypothetical	2856629	2858405	2856721	2858305
24	PP2541	transcriptional factor-like protein	3.38	Regulatory	2885949	2887273	2886048	2887173
25	PP2810	hypothetical protein	2.98	hypothetical	3202675	3203315	3202705	3203215
26	PP2858	hypothetical protein	2.75	hypothetical	3261156	3261619	3261202	3261519
27	PP3009	hypothetical protein	2.61	hypothetical	3401602	3401909	3401381	3403370
28	PP3012	hypothetical protein	2.61	hypothetical	3402885	3403137	3401381	3403370
29	PP3026	tail length determination protein	2.49	enzymatic	3412722	3413087	3412295	3412987
30	PP3074	bhbP D-beta-hydroxybutyrate permease	7.52	transport	3458628	3459012	3458727	3459050
31	PP3110	hypothetical protein	3.08	hypothetical	3519365	3521861	3519464	3521761
32	PP3238	transcriptional regulator PyrR	5.68	Regulatory	3674453	3674883	3674528	3674923
33	PP3420	sensor histidine kinase	3.38	Regulatory	3872278	3872784	3872243	3872733
34	PP3441	hypothetical protein	3.06	hypothetical	3899036	3899523	3899048	3899562
35	PP3540b	crcY regulatory RNA	2.57	Regulatory	4013035	4013244	4013134	4013436
36	PP3656	aromatic compound-specific porin	2.62	transport	4153120	4153479	4152926	4153689
37	PP3791	site-specific recombinase	2.40	enzymatic	4320663	4321941	4320709	4321841
38	PP3929	hypothetical protein	2.52	hypothetical	4433801	4434112	4433900	4434166
39	PP4035	pydP NCS1 family transporter PydP	4,28	transport	4547243	4547785	4547294	4547771
40	PP4050	glgA glycogen synthase	2,56	enzymatic	4563758	4564712	4320709	4321841
41	PP4070	hypothetical protein	3,42	hypothetical	4594982	4595629	4595080	4595540
42	PP4095	hypothetical protein	3,06	hypothetical	4630123	4631174	4629477	4631074
43	PP4283	GntR family transcriptional regulator	2,52	Regulatory	4874432	4874908	4874476	4874808
44	PP4309	NCS1 family transporter	3,29	transport	4899939	4900526	4899956	4900426
45	PP4391	flgB flagellar basal-body rod protein FlgB	2,44	motility	4983449	4983813	4983435	4983713
46	PP4424	HTH-type transcriptional regulator	2,36	Regulatory	5020010	5020411	5019442	5020946
47	PP4451	hypothetical protein	2,12	hypothetical	5049257	5050611	5048284	5050511
48	PP4471	mgtE magnesium transporter	2,26	transport	5078705	5079252	5078804	5080022
49	PP4474	alaS alanine—tRNA ligase	2,60	enzymatic	5084164	5084605	5084244	5084505
50	PP4486	argT lysine /arginine /ornithine ABC transporter substrate-binding protein	2,48	transport	5096664	5097230	5096657	5097130
51	PP4520	hypothetical protein	4,01	transport	5132506	5133016	5132454	5133090
52	PP4643	xanthine/uracil permease family protein	2,70	transport	5267050	5267512	5267006	5267505
53	crcZ	CrcZ regulatory RNA	4,32	Regulatory	5338050	5338276	5338149	5338829
54	PP_t72	tRNA	2,87	Translation	5361078	5361701	5360562	5361611
55	PP4739	hypothetical protein	2,40	hypothetical	5391562	5392963	5391661	5392863
56	PP4925	hypothetical protein	3,05	hypothetical	5604183	5604622	5602819	5604793
57	PP5129	hypothetical protein	3,46	hypothetical	5852185	5852693	5851137	5852593
58	PP5184	spuI glutamylpolyamine synthetase	2,88	transport	5912049	5912822	5912040	5912970
59	PP5212	iron-sulfur-binding oxidoreductase	2,66	transport	5944133	5944664	5944232	5944589
60	PP5376	hypothetical protein	2,64	hypothetical	6127775	6128896	6127848	6128801
61	PP5375	LysR family transcriptional regulator	2,64	Regulatory	6127775	6128895	6127848	6128801