A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration

Kampers, Linde F. C.; Koehorst, Jasper J.; van Heck, Ruben J. A.; Suarez-Diez, Maria; Stams, Alfons J. M.; Schaap, Peter J.

doi:10.1186/s12866-020-02058-1

BMC Microbiology

Table 2 Respiratory design of a facultative anaerobic P. putida KT2440. Genes related to nitrogen metabolism

From: A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration

InterPro Entry	PFAM	Name	Abbreviation	Function	Source
	PF00491	ureohydrolases		Ammonia to urea conversion	PDC
		Arginase	ArgI	L-arginine + H(2) O < => L-ornithine + urea	PDC
		Agmatinase	SpeB	Agmatine + H(2) O < => putrescine + urea	PDC
		Formimidoylglutaminase	HutG	N-formimidoyl-L-glutamate + H(2) O < => L-glutamate + formamide	PDC
IPR015868	PF04960	Glutaminase		Glutamine + H2O → Glutamate + NH3	PDC, T
IPR000292	PF01226	Formate/nitrite transporter		Transporter	PDC, T
IPR025736	PF13556	PucR C-terminal helix-turn-helix domain	PucR	PucR-like transcriptional regulator	PDC, T
IPR000825	PF01458	Uncharacterized protein family (UPF0051)		Chaperone proteins for nitrogenase production	PDC, T
			NifS	Metallocluster formation Nitrogenase	PDC, T
			NifU	Metallocluster formation Nitrogenase	PDC, T
IPR005346	PF03658	Ubiquitin	RnfH family	Electron transport	PDC, T
	PF02508	Rnf-Nqr subunit, membrane protein	Rnf-Nqr	Nitrogen fixation	PDC, T
	PF03116	Nqr2 family	Nqr2	Nitrogen fixation	PDC, T
		RnfD family	RnfD	Nitrogen fixation	PDC, T
		RnfE family	RnfE	Nitrogen fixation	PDC, T
	PF03060	Nitronate monooxygenase		Nitrogen metabolism	PDC, T
IPR010349	PF06089	L-asparaginase II		Hydrolysis of L-asparagine to L-aspartate and ammonium.	PDC, T
PA3862	PF02423		DauB	NAD(P)H-dependent anabolic L-arginine dehydrogenase	PDC, T, Steen et al., 2012
PA3863	PF01266		DauA	FAD-dependent catabolic D-arginine dehydrogenase	PDC, T, Steen et al., 2012
PA3864	PF08348		DauR	Transcriptional regulator of the dauBAR operon	PDC, T, Steen et al., 2012
PA3864	PF13309				PDC, T, Steen et al., 2012
PA14_13750	PF07690	Nitrite extrusion protein (putative)	NarK2	Membrane protein; Transport of small molecules	PDC, T, Steen et al., 2012
PA14_13770	PF07690	Nitrite extrusion protein	NarK1	Membrane protein; Transport of small molecules	PDC, T, Steen et al., 2012
PA3875	PF14710		NarG	Energy metabolism	PDC, T, Steen et al., 2012
	PF00384				PDC, T, Steen et al., 2012
	PF01568				PDC, T, Steen et al., 2012
PA14_13800	PF13247	Nitrate reductase	NarH	β-subunit, Energy metabolism	PDC, T, Steen et al., 2012
PA14_13800	PF14711				PDC, T, Steen et al., 2012
PA14_13810	PF02613	Nitrate reductase	NarJ	Δ-chain, Energy metabolism	PDC, T, Steen et al., 2012
PA14_13830	PF02665	Nitrate reductase	NarI	γ-chain, Energy metabolism	PDC, T, Steen et al., 2012
PA3878	PF02518	two-component sensor	NarX		PDC, T, Steen et al., 2012
	PF00672				PDC, T, Steen et al., 2012
	PF07730				PDC, T, Steen et al., 2012
	PF13675				PDC, T, Steen et al., 2012
PA3879	PF00072	two-component response regulator	NarL	Response regulator	PDC, T, Steen et al., 2012
PA3879	PF00196				PDC, T, Steen et al., 2012
PA14_13850	PF04055	Heme d1 biosynthesis protein	NirJ	Heme d1 Biosynthesis	PDC, T, Steen et al., 2012
PA0516	PF02239	Heme d1 biosynthesis protein	NirF	Heme d1 Biosynthesis	PDC, T, Steen et al., 2012
PA0514		Heme d1 biosynthesis protein	NirL	Heme d1 Biosynthesis	PDC, T, Steen et al., 2012
PA0520	PF07728		NirQ	Regulatory protein	PDC, T, Steen et al., 2012
PA0520	PF08406		CbbQ	post-translational activation of Rubisco -- photosynthesis	PDC, T, Steen et al., 2012
			NorQ,	Post-translational activation of Rubisco -- photosynthesis
PA14_06750	PF13442	nitrite reductase precursor	NirM	Cofactor biosynthesis, Energy metabolism	PDC, T, Steen et al., 2012
PA3870	PF00994	molybdopterin biosynthetic protein A1	MoaA1	Biosynthesis of cofactors, prosthetic groups and carriers	PDC, Steen et al. 2012
	PF03453				PDC, Steen et al. 2012
	PF03454				PDC, Steen et al. 2012
PA14_13260	PF00994	molybdopterin biosynthetic protein B1	MoaB1		PDC
	PF00394	Multicopper oxidase			PDC, T
PA0519	PF13442	Nitrate reductase	NirS	Energy metabolism	PDC, T, Steen et al., 2012
		Nitrate reductase	NirS	Energy metabolism	PDC, T, Steen et al., 2012
	PF02239	Nitrate reductase	NirS	Energy metabolism	PDC, T, Steen et al., 2012
	PF05940	NnrS protein			PDC, T
			NirK	Reduction of nitrite to nitrous oxide	PDC, T
			Nor	Reduction of nitrite to nitrous oxide	PDC, T
PA14_06810	PF00034	nitric-oxide reductase	NorB-NorC	Subunit B, C	PDC, T, Steen et al., 2012
PA14_06830	PF00115	nitric-oxide reductase	NorB-NorC	Subunit B, C	PDC, T, Steen et al., 2012
PA14_06840	PF00092		NorD	Putative dinitrification protein	PDC, T, Steen et al., 2012
PA14_20230	PF04205		NosR	Regulatory protein for N2O reductase	PDC, T

T Trancriptomics, PDC Protein Domain Comparisons, GSM Genome Scale Modelling [30, 31];. Printed in bold are classes of genes, the genes belonging to that class listed directly underneath

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ISSN: 1471-2180

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