. 2018 Mar 1;9:361. doi: 10.3389/fmicb.2018.00361

Table 1.

ARG boxes detected in DNA fragments bound by ArgR in DNA band-shift assays.

					Chromosomal coordinates
Regulated gene(s)	Gene name	Product	ARG box identifier	Sequence	Left	Right	Distance to start codon	Ri (bit)
SCO0256 ^a^,^f		Short chain oxidoreductase-like	AB.SCO0256_1	GCCCGCACGCTGTTGGGCAG	245912	245931	55	5.8
SCO0256 ^a^,^f		Short chain oxidoreductase-like	AB.SCO0256_2	CACCGCACGAGAGCGCGGAG	245932	245951	35	7.7
SCO1086 ^a		Hypothetical protein	AB.SCO1086_1	CAGTCAATGACTTTTCAGGT	1146431	1146450	5	5.0
SCO1086		Hypothetical protein	AB.SCO1086_2	GAACGCATACCTATGCAGTG	1146451	1146470	25	15.7
SCO1236	ureA	Urease gamma subunit	AB.SCO1236_0	GATTGATTACCGATGCAGTC	1310778	1310797	183	7.4
SCO1483 ^c	pyrA	Carbamoylphosphate synthetase L chain	AB.SCO1483_0	GGTCGAACAGGTAGGCGGCG	1587621	1587640	209	5.6
SCO1487	pyrB	Aspartate carbamoyltransferase	AB.SCO1487_0	CTCCGTAAGGCGATTCATGC	1591396	1591415	9	9.3
SCO1488	pyrR	Pyrimidine operon regulatory protein	AB.SCO1488_0	TGTTGCTTGTCCATACGAAA	1592070	1592089	−13	7.4
SCO1489	bldD	BldD, transcriptional regulator	AB.SCO1489_0	CGCTGCGTAACCTCACAGTG	1592299	1592318	63	9.6
SCO1570 ^a	argH	Argininosuccinate lyase	AB.SCO1570_1	TCATGCATGAGTATGCAGAA	1681889	1681908	30	16.3
SCO1570	argH	Argininosuccinate lyase	AB.SCO1570_2	CTCTGCATGTTTCGTCAATC	1681909	1681928	50	4.4
SCO1580 ^c	argC	N-acetyl-γ-glutamyl-phosphate reductase	AB.SCO1580_A0	GCCCGCATACCCACTCGCTC	1691417	1691436	−44	9.5
SCO1580 ^a^,^d	argC	N-acetyll-γ-glutamyl-phosphate reductase	AB.SCO1580_B1	GAGAGCATGACTATACGTGC	1691479	1691498	18\|-3	9.1
SCO1580 ^d	argC	N-acetyl–γ-glutamyl-phosphate reductase	AB.SCO1580_B2	CGATGCACGTTTATGCAATG	1691499	1691518	38\|-23	13.3
SCO1864 ^c^,^e		Putative acetyltransferase	AB.SCO1864_0	ATTCGTAACCCCATCCGGCG	1998411	1998430	38	3.8
SCO2015		2′,3′-cyclic-nt 2′-phosphodiesterase-like	AB.SCO2015_0	CCACGCATGACCACTCAACA	2157812	2157831	159	11.4
SCO2055 ^b		Hypothetical protein	AB.SCO2055_1	GTTCGGACGGTCACGCAGTG	2202678	2202697	63	11.8
SCO2055		Hypothetical protein	AB.SCO2055_2	GCATGAACGGTTGTACGAAG	2202699	2202718	42	9.0
SCO2231-2 ^b	malE-R	Maltose-binding, transcriptional repressor	AB.SCO2231-2_A1	TGCTGCAAAAATGTGCAAGA	2400395	2400414	136\|237	10.7
SCO2231-2	malE-R	Maltose-binding, transcriptional repressor	AB.SCO2231-2_A2	ATCTCCGAAGTTATCCGGGC	2400416	2400435	157\|216	5.1
SCO2231-2	malE-R	Maltose-binding, transcriptional repressor	AB.SCO2231-2_B0	CTCTGCAAGCTCTTGCCGCC	2400507	2400526	248\|125	11.9
SCO2529	smpA	Metalloprotease	AB.SCO2529_0	GTCCGTATCAGTATGCGGGA	2727401	2727420	144	10.7
SCO2686 ^b^,^c^,^f		Putative luxR-family transcriptional regulator	AB.SCO2686_A1	TATTGAGCGTCCTTTCAAAA	2930741	2930760	−98	5.5
SCO2686 ^c^,^f		Putative luxR-family transcriptional regulator	AB.SCO2686_A2	TCGCGCATAGAAGTGCAGTC	2930762	2930781	−77	7.3
SCO2686 ^f		Putative luxR-family transcriptional regulator	AB.SCO2686_B0	CAATGCATGATCATGCCACA	2930862	2930881	23	12.6
SCO3034^f	whiB	Sporulation regulatory protein	AB.SCO3034_0	GGAACCAAGCCCATGCAGTA	3321156	3321175	140	9.4
SCO3067 ^f	arsI\|sigI	Anti anti sigma factor\|sigma factor SigI	AB.SCO3067_0	CACAGAACACACTTGCGGTC	3360549	3360568	108\|126	7.6
SCO3943 ^b^,^f	rstP	Putative transcriptional regulator	AB.SCO3943_A0	GGACGCATATGCACGCGTTG	4339185	4339204	39	10.2
SCO3943 ^b^,^f	rstP	Putative transcriptional regulator	AB.SCO3943_B0	TTCTGCAAGATCATTAATGC	4339215	4339234	69	9.4
SCO3978-9 ^f		Oxidoreductase\|TetR-like regulator	AB.SCO3978-9_0	TAACGGATAGCTTTTCATAA	4381976	4381995	27\|35	9.2
SCO4158^f		LacI-family regulatory protein-like	AB.SCO4158_0	CCTTGGATGACCTTGCGCCC	4576182	4576201	48	11.3
SCO4293^f		Putative threonine synthase	AB.SCO4293_0	GCCTCCATGGCTGTGCAGAC	4708595	4708614	−7	14.5
SCO4425	afsS	Sigma-like protein	AB.SCO4425_0	TGCCGGACGGGCGCGCGGAG	4842637	4842656	64	8.8
SCO4426 ^c^,^f	afsR	Regulatory protein	AB.SCO4426_0	TTTGCCTTGTTCATGCCGAC	4845804	4845823	36	1.2
SCO5226^f	nrdA	Ribonucleotide-diphosphate reductase	AB.SCO5226_0	GACTGGACAGGCGTGCGCGC	5688301	5688320	158	9.2
SCO5326-7^f		Hypothetical protein	AB.SCO5326-7_0	GCCTCGTTGGTCATGCATCC	5796724	5796743	146\|-7	8.9
SCO5583	amtB	Ammonium transporter	AB.SCO5583_0	CCATGCCAGGTCATTCGGAG	6085777	6085796	235	10.2
SCO5864^f		Conserved hypothetical protein	AB.SCO5864_0	CTCTCCGTGATCATGCACCC	6421332	6421351	267	11.8
SCO5896 ^c	redH	Phosphoenolpyruvate-utilizing enzyme	AB.SCO5896_0	GACGGCGTGGGCCTGCAGAA	6461067	6461086	−1669	6.3
SCO5976 ^a	arcB	Ornithine carbamoyltransferase	AB.SCO5976_1	CGCTGTATAGAAATTCAGAA	6550325	6550344	55	8.2
SCO5976	arcB	Ornithine carbamoyltransferase	AB.SCO5976_2	GTTCGTATAGACTTCCAGAA	6550345	6550364	35	9.6
SCO7036 ^a	argG	Argininosuccinate synthase	AB.SCO7036_1	CTTTGCATGGTCATGCGTAA	7824734	7824753	18	17.2
SCO7036	argG	Argininosuccinate synthase	AB.SCO7036_2	TGATGCATACTCTTCCTATG	7824754	7824773	−2	8.1
SCO7314	sigM	Probable RNA polymerase sigma factor	AB.SCO7314_0	ATCCGCATGCTCATAGAAAC	8120535	8120554	−13	9.5

, No separation between the ARG boxes;

, One nucleotide separation between ARG boxes;

, Not included in the model;

, Binding site “A” might to control both SCO1580 and SCO1581 genes;

, Alternative box located 27 nt before;

, Differential transcription not observed.