Genome-wide motif predictions of BCARR-box in the amino-acid repressed genes of Lactobacillus helveticus CM4

Yamamoto, Naoyuki; Wakai, Taketo

doi:10.1186/s12866-017-1125-0

BMC Microbiology

Table 1 BCARR-boxes observed in promoter regions of specific genes and repressed gene expression in presence of peptides

From: Genome-wide motif predictions of BCARR-box in the amino-acid repressed genes of Lactobacillus helveticus CM4

No	ORF No	Repression (%)	Strand	^a Score	Location (bp)	Gene	Function	BCARR-box sequence
1	464	97.0	–	35	−11	dapF	Diaminopimelate epimerase	AAAATCACTTTTTTA
2	1025	97.0	+	46	254	paaD	Predicted metal-sulfur biosynthetic enzyme	AAAAATGATATTATC
3	1029	95.0	+	56	7	hisM	ABC-type amino acid transportor	AATAAGACTATTATT
4	724	93.0	+	60	87	pepO2	Neutral endopeptidase	AAAAAATGCTTTTAT
5	726	93.0	+	37	−120	potE	Amino acid transporters	AAAAAATCATGTTTT
6	1032	93.0	+	37	−229	ddpA	ABC-type dipeptide transport system	AAAATTCTAAAATAT
7	765	91.0	–	33	116	himM	ABC-type amino acid transporter	AAAAGTATTGTCTTT
8	769	91.0	+	45	−116	putative	unknown	AAAAAATCTATTTTT
9	1099	91.0	–	37	−19	med	Uncharacterized ABC-type transport system	GAAAATAATGTTCTT
10	1104	91.0	+	42	150	putative	unknown	AAAAAAGCCATTCTT
11	513	90.0	+	42	24	nlpA	ABC-type metal ion transport	AGAAATACAATTATT
12	661	89.0	+	37	−16	pepD	Di- and tripeptidases	AATAGACTTTTTTAT
13	1113	87.0	+	42	41	purK	Phosphoribosylaminoimidazole carboxylase	AAAATACCTTGTATT
14	1621	87.0	–	33	92		Uncharacterized conserved protein	AATACAAGATATTGT
15	670	86.0	–	33	−11	putative	unknown	AGAAATAGATTTTTT
16	738	85.0	+	35	42	putative	unknown	AAAGTAAGCGTTTTA
17	1219	85.0	+	46	35	prtH, prtP	Protease P&H	AAAAAATTAAATGTA
18	123	85.0	–	38	−15	putative	unknown	ACAAAAATTATTCTT
19	1102	84.0	+	48	−254	putative	unknown	TAAAAAAATATTATT
20	737	83.0	–	36	74	hpt	Hypoxanthine-guanine phosphoribosyltransferase	TGAAAAAGTATTATT
21	1543	77.0	–	34	−104	guaA	GMP synthase	AACAAGAACTTTTTG
22	129	75.0	+	45	−14	putative	unknown	AAAAATCCGTTTTTT
23	1030	74.0	+	56	−47	putative	unknown	AATAATAGTCTTATT
24	576	72.0	–	36	−135	potE	Amino acid transporters	GAAGAATACTCTTTG
25	1216	72.0	–	55	−29	putative	unknown	AATAAAAGGTTTTTA
26	1634	70.0	+	47	−218		ABC-type transportor	AAAAAAACTTTCCTA
27	1586	69.0	+	35	−14	guaB	IMP dehydrogenase	AACAAGTCCTTTTTT
28	1212	69.0	+	51	64	pepN2	Aminopeptidase N2	AGAACAACACTTTTA
29	1541	68.0	+	33	−90	putative	unknown	AACAAAACGATCATT
30	536	68.0	+	46	−67	pepC2	Aminopeptidase C	AAAATGCCAATTATT
31	1585	67.0	+	38	−3	pepE	Aminopeptidase C	GAACCCGCTTTTATT
32	632	66.0	–	46	2	putative	unknown	AAAAAGTCCAATCTT
33	646	65.0	+	40	−89	putative	unknown	AAACGGACAACCTTT
34	1162	62.0	–	42	−135	baeS	Signal transduction histidine kinase	AATTAAAGGTTTTAT
35	950	62.0	+	44	10	ddpA	ABC-type dipeptide transportor	AAAACATGGTATTAT
36	668	62.0	–	37	−21	putative	unknown	AAAAAGCAGCTTAGT
37	691	59.0	+	31	−177	lytT	Response regulator	AAAATCTCGCTTTTT
38	665	59.0	–	33	−90	putative	unknown	AAATATGATATTTTT
39	296	59.0	+	33	−46	uup	ATPase components	AAAAAGTTTTAATTA
40	1070	59.0	–	46	60	putative	unknown	AATAACACTGTTTTT
41	1514	58.0	–	38	−29		GAF domain-containing protein	AATCAAACTTTTTTC
42	701	57.0	–	37	−30		Uncharacterized conserved protein	GAGAAAAGGTTTGTT
43	1529	56.0	–	40	−89		FOG: CBS domain-containing protein	AAGAGATGCTTTTTT
44	1340	56.0	–	46	39	pepQ	Xaa-Pro aminopeptidase	AAAAAGAGGCTATTT
45	579	56.0	+	42	125	uvrC	Nuclease subunit	AAAAACCGGGCTGTT
46	518	55.0	+	46	−29	putative	unknown	AAAAAAACAATTATA
47	755	53.0	–	39	99	folB	Dihydroneopterin aldolase	AATACGAGGAGTTTT
48	1051	52.0	+	40	49	putative	unknown	AATCAATGTATTATT
49	1406	51.0	–	49	−51	fatA	Acyl-ACP thioesterase	AATATAAGTCCTTTT
50	806	50.0	+	57	64	putative	unknown	AAAAGAAGCTTGTTT
51	807	49.0	+	40	27	putative	unknown	AACAATAGAATTATA
52	537	48.0	+	38	−1	citT	Di- and tricarboxylate transporters	AAAAATAACTTTATT
53	1208	47.0	–	34	64	hflC	Membrane protease subunits	AACAACAGGACTTTA
54	1151	46.0	+	43	−122	putative	unknown	AAAAAATTTTTTTGT
55	1254	46.0	+	49	95	putative	unknown	AAAATAACTATTAAT
56	669	44.0	–	34	−222	putative	unknown	ATGAAATCGCTTATT
57	1530	40.0	+	42	149	putative	unknown	AAAAAAGCTTTGCTT
58	921	38.0	+	44	−12	putative	unknown	AAAACATCTTTTTTG
59	763	35.0	+	35	55	putative	unknown	AAAAATGCTTGACTT
60	201	34.0	+	36	109	deoR	Transcriptional regulator	AAAAATACATTGTTA
61	825	34.0	–	47	−8		Uncharacterized protein	ATTAATAGGTTTTCT
62	954	34.0	+	49	59	dppD	ABC-type dipeptide transportor	AAAAAAGCTATAAAT
63	1593	32.0	+	46	124	lytR	Transcriptional regulator	AAAAAACGTCATATT
64	635	32.0	+	51	−19	mdlB. cydC, sunT	ATPase and permease components	AAAAACACTTTAATT
65	1590	32.0	+	40	−29	putative	unknown	AAAACAGTTTTCTTA
66	655	31.0	+	41	167	putative	unknown	AAAAAACGTTTTAGC
67	1535	30.0	–	36	114	putative	unknown	AAAAGTAGTTTTCAT

^a Waterman-Eggert score by LALIGN analysis

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