TABLE 2.

PhoP-dependent genes of Pve involved in pectin and arabinose degradation and utilisation.

Gene name(s)	Locus_tag(s)	Fold changea	Product(s)	Best operator	Scoreb
Polygalacturonic acid utilisation
pelI	OA04_11360	0.14	Pectate lyase PelI	AATTTTATTATTTATTTAT	12.2
pehA	OA04_11370	117.60	Endo-polygalacturonase	AATTTTATTATTTATTTAT	12.2
pehN	OA04_12450	2.15	Endo-polygalacturonase	ATTTTTTAGTGAGGTTAAG	8.1
pelP	OA04_21040	9.67	Endo-pectate lyase	ATCTTTTCATTTTATTTAC	7.5
pnl	OA04_29050	2.63	Pectin lyase	TTATTTGTTTTTGATTAAA	9
togT	OA04_08060	2.01	Oligogalacturonide transporter	TATTTGATCTTGCGTTTAT	8.2
–	OA04_21060-OA04_21050	25.51	KdgM-like porins	ATTTTTTGTAATCATTTCG	8.9
–	OA04_07070	2.00	Polygalacturonic acid binding protein	–	–
–	OA04_12400	2.02	Coagulation factor 5/8 type domain protein	TTATTTTAAAGCGCTTTAC	7.8
–	OA04_32560	2.04	Coagulation factor 5/8 type domain protein	GTATTTTAAAGCGGTTTAC	8.7
Arabinose transport and utilisation
araD	OA04_19040	0.08	L-ribulose-5-phosphate 4-epimerase	CTGTTTTTTTAGCGTTTCT	9.8
araC	OA04_22270	0.11	DNA-binding transcriptional regulator AraC	TATTTTATTTGCCATTTTG	9.1
araFGH	OA04_22300-OA04_22280	0.06	L-arabinose transporter subunits	GGTTTGTGCATACATTTAG	5.6
araBA	OA04_22310-OA04_22320	0.02	L-ribulokinase and L-arabinose isomerase	GGTTTGTGCATACATTTAG	5.6
–	OA04_38360-OA04_38370	0.19	Sugar (Glycoside-Pentoside-Hexuronide):cation symporter and exo-α-1,5-L-arabinofuranosidase	ATTTTTGCAACCGATTTCA	6.2
ytfQRT	OA04_43130-OA04_43110	0.14	Galactofuranose/arabinofuranose ABC transporter subunits	TGATTTTGTGCATATTTAC	7.3

^aWild type vs. phoP mutant ratio. For operons, the value for the first gene is shown. Supplementary Table 3 contains values for all genes.

^bChIPmunk score for the best operator.