. 2016 Aug 3;17:539. doi: 10.1186/s12864-016-2840-x

Table 4.

Genes predicted to contain a CcpA- binding motif^a in the upstream regions

Gene locus_tag	Gene function/name	Log₂FC, 20 h^b			Motif start coordinate^c	Motif sequence	Co-transcribed genes
Gene locus_tag	Gene function/name	G/R	G/X	X/R	Motif start coordinate^c	Motif sequence	Co-transcribed genes
Genes, upregulated on glucose and xylose
LACOL_0264	Fructokinase gmuE	1.46	−0.4	1.86	−88	ATTAAAACGGTTACAA
LACOL_0353	PTS system mannose-specific EIIAB component manX	2.47	0.49	1.98	−97	ATGAAAGCGTATTCAA	manXYZ
LACOL_0639	Mannose-6-phosphate isomerase pmi	1.54	−0.52	2.06	−58	TAGGAAGGGCTTACAT
LACOL_0566	Gluconokinase gntK	2.03	0.84	1.19	−112	ATGGAATCGGTTGCTA	LACOL_0567 ^d
LACOL_0566	Gluconokinase gntK	2.03	0.84	1.19	−95	TTGTAACCGATTTCCA	LACOL_0567 ^d
LACOL_1326	Gluconate permease gntP2	1.81	−0.21	2.02	−155	TTGTTAACGGTTACAA	LACOL_1325 ^d
LACOL_0266	Putative xylose-proton symporter xylP2	1.6	0.78	0.82	−130	TTGCAAGCGTTTACAA	LACOL_0265 ^d
LACOL_0399	Aldose 1-epimerase xylM	1.09	−0.39	1.47	−144	ATACAAGCGCTTTCAT	xylR ^d
LACOL_0399	Aldose 1-epimerase xylM	1.09	−0.39	1.47	−46	ATTTAATCGCTTACAT	xylR ^d
LACOL_0400	Transcriptional xylose repressor xylR	1.19	−0.43	1.62	−239	ATGTAAGCGATTAAAT	xylM ^d
LACOL_0400	Transcriptional xylose repressor xylR	1.19	−0.43	1.62	−141	ATGAAAGCGCTTGTAT	xylM ^d
LACOL_0401	Xylose isomerase xylA	2.33	−2.3	4.63	−90	GTGAAAGGGGTTGCAA	xylA-xylB
LACOL_0401	Xylose isomerase xylA	2.33	−2.3	4.63	−68	ATGTAAGCGTTATACT	xylA-xylB
LACOL_1587	D-xylose-proton symporter xylT	3.23	−0.9	4.13	−139	TTGGCAGCGGTTTCAT
LACOL_1587	D-xylose-proton symporter xylT	3.23	−0.9	4.13	−72	CTGAAAGCGGTTACGC
LACOL_0614	Phosphocarrier protein Hpr ptsH	1.61	0.26	1.36	−126	AATAAAACGTTTACAT	ptsH-ptsI
LACOL_1153	Pyruvate dehydrogenase E1 component alpha subunit pdhA	2.54	0.26	2.28	−60	AATAAAGCGCTTACAT	pdhA-pdhB-pdhC-pdhD
LACOL_0222	1,3-propanediol dehydrogenase dhaT	3.81	2.11	1.7	−41	TTGTAATCGCTTTAAT	LACOL_0223 ^d
Genes, upregulated on ribose
LACOL_0444	D-ribose pyranase rbsD1	−2.32	0.55	−2.87	−77	TTGAAAGCGGTTACTA	rbsD1-rbsA-rbsC-rbsB
LACOL_0616	Putative (deoxy)ribose permease deoP	−4.59	0.04	−4.63	−50	TTGTAAGCGGATTATT
LACOL_0617	D-ribose pyranase rbsD2	−4.57	0.34	−4.9	−108	TTGCAATCGTTTCCAA
LACOL_0618	Ribokinase rbsK2	−5.55	0.59	−6.13	−258	TTGGAAACGATTGCAA	rbsK2-rpiA2
Genes, upregulated on glucose
LACOL_0233	Glucose-6-phosphate dehydrogenase zwf	1.37	1.19	0.18	−107	GTGTAACCGGTTTATT
LACOL_0255	Aldehyde-alcohol dehydrogenase adhE	5.69	6.37	−0.68	−220	ATGTAAGCGATTACAA
LACOL_0923	Sugar (maltose):cation symporter	7.66	7.46	0.2	−53	CTGTAATCGGTTACAT	LACOL_0923-mdxK-pgmB
Other genes (mostly equally expressed)
LACOL_0188	CRISPR-associated protein cas9	0.56	−0.52	1.09	−67	ATGAAAGCGTTTAACC
LACOL_0275	L-arabinose isomerase araA	0.81	−0.19	1	−79	TTGTAAGCGATTAACA
LACOL_1004	N-acetylmannosamine-6-phosphate epimerase nanE	0.48	−0.13	0.61	−263	ATGTAAACGTTTTCTT	nanE-nanA-nanR, nanK ^d
LACOL_1005	N-acetylmannosamine kinase nanK	0.6	−0.55	1.14	−36	AAGAAAACGTTTACAT	nanE ^d
LACOL_0104	PTS system sugar-specific enzyme IIA component	0.4	0.3	0.1	−63	TTGTAAGCCTTTGCAA	LACOL_0104-LACOL_0106
LACOL_0218	Galactokinase galK	0.21	0.33	−0.12	−133	AATTAACCGTTTTCAT	galK-galT-galR
LACOL_0521	Beta-galactosidase large subunit lacL	0.39	−0.57	0.97	−63	TTGAAAGCGCTTTAAC	lacL-lacM
LACOL_1707	Beta-galactosidase lacZ	0.06	0.58	−0.52	−38	AAGAAAGCGCTTTCTA	LacZ-LACOL_1706-LACOL_1705

^a CcpA- binding motifs were found by scanning all upstream regions in the genome with the Lactobacillaceae-specific CcpA TFBS profile built using RegPrecise database

^b For the designations, such as G/R, see Table 2. Statistically significant changes are marked in bold

^c Motif start coordinate is given in relation to the predicted translational start site

^d The gene/operon upstream region is overlapped with the upstream region of the adjacent divergently oriented gene