Table 1. List of differentially regulated proteins containing both MAPK-specific phosphorylation site and MAPK docking site as predicted by GPS 3.0 software and Eukaryotic Linear Motif Resource (http://elm.eu.org/index.html) in the roots of the mpk4 mutant.

Accesion number	Protein name	Phosphopeptide sequences	Docking sequence	Fold change	Cell compartment
gi|145324054	arabinogalactan protein 31	EVNHKTQTPSLAPAP	KFNRSLVAV, 180–188 [A]	unique in wild type	cell wall72
		HPHPPAKSPVKPPVK	KKLGKSTVVV, 285–294 [A]
		PPVKAPVSPPAKPPV	KLGKSTVVV, 286–294 [A]
		PPVKPPVSPPAKPPV
		APVKPPVSPPTKPPV
		PPTKPPVTPPVYPPK
gi|15226573	Ferredoxin–nitrite reductase	SFSLTFTSPLLPSSS	KPKRSVLV, 19–26 [A]	unique in wild type	plastid (prediction)
			KIEREPMKL, 74–82 [A]
			KSSKDDIDVRL, 103–113 [A]
			RKWNVCV, 246–252 [A]
			KDGRFGFNLLV, 274–284 [A]
			KRCEEAIPL, 291–299 [A]
			RQKTRMMWL, 328–336 [A]
			KKGVRVTELVPL, 554–565 [A]
			KGVRVTELVPL, 555–565 [A]
gi|15233349	aconitate hydratase 1	RATIANMSPEYGATM	RIDKLPYSIRI, 35–45 [A]	unique in wild type	cytosol, mitochondria73
		YFKGMTMSPPGPHGV	KRPHDRVPL, 378–386 [A]
			KKACDLGL, 458–465 [A]
gi|18400212	dihydrolipoamide acetyltransferase, long form protein	TTSTKLSSPMAGPKL	RRDHAVAV, 20–27 [A]	unique in wild type	mitochondria74
		EIGMPSLSPTMTEGN
gi|22331076	Subtilase family protein	PLLLCFFSPSSSSSD	RRHPSVISV, 93–101 [A]	unique in wild type	extracellular (prediction)
		LLRSLPSSPQPATLL
		HGFSARLSPIQTAAL
		REIHTTHTPAFLGFS
		LGTLIGPSPPSPRVA
		LIGPSPPSPRVAAFS
		ANVEIDVSPSKLAFS
gi|240254562	uncharacterized protein	SSSGNVTTPTQTAST	KSRDIDLSF, 1264–1272 [A]	unique in wild type	nucleus (prediction)
gi|30682607	mRNA decapping complex VCS	PGISAQPSPVTQQQQ	RKAQPLVVL, 352–360 [A]	unique in wild type	cytoplasmic foci75
		TPPLNLQSPRSNHNP	KESKRLEVAL, 918–927 [A]
		TLPQLPLSPRLSSKL	KRLEVAL, 921–927 [A]
gi|15232845	probable mitochondrial-processing peptidase subunit beta	DSVPASASPTALSPP	RRSQRRLFL, 11–19 [A]	13.11	mitochondria
		SASPTALSPPPPHLM	RINRERDVIL, 210–219 [A]
gi|15221019	GDSL esterase/lipase	ITVAGQNSPVVALFT			extracellular (prediction)
		KFSDGLITPDFLAKF	KFMKIPLAI, 88–96 [A]	5.48
		REFWVPPTPATVHAS
gi|15232603	60S acidic ribosomal protein P0-2	KGTVEIITPVELIKQ	RKGLRGDSVVL, 44–54 [A]		ribosome
		YDNGSVFSPEVLDLT	KGLRGDSVVL, 45–54 [A]	4.61
			KINKGTVEI, 148–156 [A]
gi|186513287	argininosuccinate synthase	ALNGKALSPATLLAE	RGKLKKVVL, 93–101 [A]		plastid76
			KKHNVPVPV, 255–263 [A]	3.63
			KKDMYMMSV, 293–301 [A]
			KLYKGSVSV, 393–401 [A]
gi|15240765	voltage dependent anion channel 2	DITATLGSPVISFGA	KHPRFGLSLAL, 264–274 [A]	2.41	mitochondria, plasma membrane24
gi|15218090	putative mitochondrial-processing peptidase subunit alpha-1	VAETSSSTPAYLSWL			mitochondria
		LKIASETTPNPAASI	RKMKVEI, 196–202 [A]	2.31
		GYSGPLASPLYAPES
gi|334185190	heat shock protein 70-3	DLLLLDVTPLSLGLE	RARFEELNI, 305–313 [A]	0.57	nucleus, cytoplasm30
			RIPKVQQLLV, 348–357 [A]
gi|14532542	proteasome subunit alpha type-5-A	AVEKRITSPLLEPSS	KTKEGVVLAV, 41–50 [A]	0.32	peroxisome, cytoplasm (prediction)
gi|30691626	heat shock protein 70-1	GTSGTEQTPEAEFEE	KRSDNIDL, 289–296 [A]	0.32	cytosol77
			KKQLIDL, 573–579 [A]
gi|30696056	elongation factor EF-2	EEMQRPGTPLYNIKA	KRLAKSDPMVV, 509–519 [A]	0.08	cytoplasm78
		KGLKEAMTPLSEFED	RLAKSDPMVV, 510–519 [A]