Table 3.

Genes annotation of K. variicola UC4115 and A. brasilense Sp7 genomes related to nitrogen fixation, phosphate solubilization, IAA production, siderophores synthesis, and biocontrol activity.

Trait	PGfams ID	Gene annotation	KO/Gene_ID	KEGG_GENE_NAME	UC 4115	Sp7
Nitrogenase complex	PGF_00025954	Nitrogenase iron protein	K02588	nifH	*	*
	PGF_00025951	Nitrogenase molybdenum-iron protein alpha chain	K02586	nifD	*	*
	PGF_00025953	Nitrogenase molybdenum-iron protein beta chain	K02591	nifK	*	*
	PGF_00120348	Putative nitrogen fixation protein FixT	K02593	nifT	*	*
	PGF_00025669	NifY protein	–	nifY	*	*
	PGF_00025964	Nitrogenase MoFe cofactor biosynthesis protein NifE	K02587	nifE	*	*
	PGF_00945843	Nitrogenase iron-molybdenum-cofactor biosynthesis protein NifN	K02592	nifN	*	*
	PGF_00025961/ PGF_00025962	Nitrogen fixation protein NifX	K02596	nifX	*	*
	PGF_00420050	Cysteine desulfurase NifS	K04487	nifS	*	*
	PGF_00072326	Homocitrate synthase	K02594	nifV	*	*
	PGF_01958698	Putative NifW protein	K02595	nifW	*	*
	PGF_00025671	Putative NifZ protein	K02597	nifZ	*	*
	PGF_01971790	Nitrogen fixation protein NifM	K03769	nifM	*
	PGF_00071382	Flavodoxin FldA	K03839	nifF	*
	PGF_00029105	Nitrogen fixation negative regulator NifL/PAS-PAC protein	K23916	nifL	*
	PGF_03973235	Nif-specific regulatory protein	K02584	nifA	*	*
	PGF_06674514	Nitrogenase cofactor biosynthesis protein NifB	K02585	nifB	*	*
	PGF_00025976	Nitrogen fixation protein NifQ	K15790	nifQ	*	*
	PGF_00046007	Putative pyruvate:ferredoxin (flavodoxin) oxidoreductase	K03737	nifJ	*
	PGF_00015530	Iron-sulfur cluster assembly scaffold protein	K04488	nifU	*	*
	PGF_00401722	Nitrogenase-associated protein NifO	–	nifO	*	*
Nitrogenase transport	PGF_00424131	Na(+)-translocating NADH-quinone reductase subunit E	K03617	rnfA	*
	PGF_10542033	Electron transport complex protein RnfB; Required for nitrogen fixation	K03616	rnfB	*
	PGF_04400591	Electron transport complex protein rnfC	K03615	rnfC	*
	PGF_01678333	Electron transport complex protein RnfD; Required for nitrogen fixation	K03614	rnfD	*
	PGF_01484108	NADH-ubiquinone oxidoreductase	K03613	rnfE	*
	PGF_00424141	Electron transport complex protein RnfG	K03612	rnfG	*
Electron transport	PGF_05015473	Ferredoxin-like protein FixX/4Fe-4S ferredoxin	K03855	FixX		*
	PGF_03136394	Electron transfer flavoprotein-quinone oxidoreductase FixC	K00313	FixC		*
	PGF_03134445	Electron transfer flavoprotein, alpha subunit FixB	K03522	FixB		*
	PGF_03098759	Electron transfer flavoprotein, beta subunit FixA	K03521	FixA		*
	PGF_00849787	Two-component system response regulator	K14987	FixJ		*
Gluconic acid	PGF_04577966	Quinoprotein glucose dehydrogenase/glucose dehydrogenase, PQQ-dependent	K00117	gcd	*
	PGF_01393943	Pyrroloquinoline-quinone synthase C	K06137	pqqC	*	*
	PGF_01084777	Coenzyme PQQ synthesis protein F	–	pqqF	*
	PGF_00418484	Coenzyme PQQ synthesis protein B	K06136	pqqB	*	*
	PGF_03579782	Coenzyme PQQ synthesis protein D	K06138	pqqD	*
	PGF_00418486	Coenzyme PQQ synthesis protein E	K06139	pqqE	*	*
Phosphonate transporter	PGF_12684827	Phosphonate ABC transporter, permease protein	K02042	phnE1	*
	PGF_00033841	Phosphonate ABC transporter, permease protein	K02042	phnE2	*
	PGF_00033852	Phosphate-binding protein of phosphonate ABC transporter	K02044	phnD	*
	PGF_00033832	Phosphonate transport system ATP-binding protein	K02041	PhnC	*
Phosphate transporter	PGF_07668761	Phosphate transport system substrate-binding protein	K02040	Pst S	*	*
	PGF_01072302	Phosphate transport system permease protein	K02038	Pst A	*	*
	PGF_02405545	Phosphate transport system permease protein	K02037	Pst C	*	*
	PGF_06213055	Phosphate transport system ATP-binding protein	K02036	Pst B	*	*
Indole-3-acetic acid (IAA) biosynthesis	PGF_05599542	Indole-3-pyruvate decarboxylase	K04103	ipdC	*	*
	PGF_00049805	Amidase	K01426	–	*
	PGF_07597988	Aldehyde dehydrogenase (NAD+) (EC 1.2.1.3)		aldh	*	*
	PGF_00418275	Nitrile hydratase, alpha subunit	K01721	nthA	*	*
	PGF_00418276	Nitrile hydratase, beta subunit	K20807	nthB	*	*
	PGF_03811905/ PGF_02254418	Histidinol-phosphate aminotransferase	K00817	hisC	*	*
Siderophore production	PGF_00015658/ PGF_00015659	Isochorismate/ Apo-aryl carrier protein	K01252	entB, dhbB, vibB, mxcF	*	*
	PGF_00025850/ PGF_07637567	2,3-dihydroxybenzoate-AMP ligase	K02363	entE, dhbE, vibE, mxcE	*	*
	PGF_05075091	Enterobactin synthetase component F	K02364	entF	*	*
	PGF_00424602	Enterobactin exporter	K08225	entS	*
	PGF_00023831/ PGF_08225224	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase	K00216	entA	*	*
	PGF_00015696	Isochorismate synthase	K02361	entC	*
	PGF_00422373	4′-phosphopantetheinyl transferase EntD	K02362	entD	*
	PGF_00037591	Proofreading thioesterase in enterobactin biosynthesis	K24147	entH	*
	PGF_07721642	MbtH-like protein	K05375	MbtH		*
	PGF_00004447	Ferric enterobactin-binding periplasmic protein	K23185	FepB	*
	PGF_00004441	Ferric enterobactin transport system permease protein	K23186	FepD	*
	PGF_00004444	Ferric enterobactin transport system permease protein	K23187	FepG	*
	PGF_00004439	Ferric enterobactin transport ATP-binding protein	K23188	FepC	*
	PGF_00424600/ PGF_08225224	Enterobactin esterase	K07214	Fes	*	*
	PGF_00057226	TonB-dependent receptor; Outer membrane receptor for ferric enterobactin and colicins B, D	K19611	FepA	*	*
	PGF_00052044	Alternative sigma factor	–	PvdS		*
	PGF_00045754	PvdE, pyoverdine ABC export system, fused ATPase and permease components	K06160	PvdE		*
4-hydroxybenzoate Production	PGF_00417843	Chorismate-pyruvate lyase	K03181	ubiC	*
GABA	PGF_07204877	Succinate-semialdehyde dehydrogenase	K00135	gabD	*	*
	PGF_04337880	4-aminobutyrate aminotransferase	K07250	gabT	*	*
Phenazine biosynthesis	PGF_10329977	Phenazine biosynthesis	-	phzF	*	*

The symbol * indicates that the gene is present in the genome.