NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P53740 UniProt NPD GO	YN8S_YEAST	Uncharacterized protein YNR048W	0.10	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				393
P40323 UniProt NPD GO	YP073_YEAST	Uncharacterized protein YPL073C	0.10	-	nuc	0					161
P80625 UniProt NPD GO	UC19_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 406) (Fragment)	0.10	-		0					15
Q9ZQ88 UniProt NPD GO	UPS4_ARATH	Ureide permease 4 (AtUPS4)	0.10	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				401
P25688 UniProt NPD GO	URIC_MOUSE	Uricase (EC 1.7.3.3) (Urate oxidase)	0.10	-	cyt	0	Peroxisome	mitochondrion [IDA] peroxisome [TAS]			302
P09118 UniProt NPD GO	URIC_RAT	Uricase (EC 1.7.3.3) (Urate oxidase)	0.10	-	cyt	0	Peroxisome	peroxisomal matrix [TAS]			302
Q80YF6 UniProt NPD GO	UPK3B_MOUSE	Uroplakin-3B precursor (Uroplakin IIIb) (UPIIIb) (p35)	0.10	-	end	1 *	Membrane; single-pass type I membrane protein (Potential). Heterodimer formation with Uroplakin Ib i ...				275
Q38681 UniProt NPD GO	VATB1_ACEAT	Vacuolar ATP synthase subunit B isoform 1 (EC 3.6.3.14) (V-ATPase B subunit 1) (Vacuolar proton pump ...	0.10	-	cyt	0					492
Q38680 UniProt NPD GO	VATB2_ACEAT	Vacuolar ATP synthase subunit B isoform 2 (EC 3.6.3.14) (V-ATPase B subunit 2) (Vacuolar proton pump ...	0.10	-	cyt	0					492
Q16864 UniProt NPD GO	VATF_HUMAN	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.10	-	cyt	0		membrane fraction [TAS] proton-transporting two-sector ATPase complex [TAS]	607160		119
P39111 UniProt NPD GO	VATF_YEAST	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.10	-	mit	0		hydrogen-transporting ATPase V1 domain [TAS] vacuolar membrane (sensu Fungi) [TAS]			118
Q5R6I1 UniProt NPD GO	VA0D_PONPY	Vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump subunit d)	0.10	-	cyt	0					351
P61420 UniProt NPD GO	VA0D_BOVIN	Vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump subunit d) ...	0.10	-	cyt	0					351
P61421 UniProt NPD GO	VA0D_HUMAN	Vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump subunit d) ...	0.10	-	cyt	0		hydrogen-translocating V-type ATPase complex [NAS]	607028		351
Q01294 UniProt NPD GO	CARP_NEUCR	Vacuolar protease A precursor (EC 3.4.23.-)	0.10	-	end	0	Vacuole. Lysosome-like vacuoles (Potential)				396
Q920R6 UniProt NPD GO	VPP4_MOUSE	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 4 (V-ATPase 116 kDa isoform a4) (Vacu ...	0.10	-	end	6	Cell membrane; multi-pass membrane protein. Apical immunostaining present in male genital tissue. Ac ...	hydrogen-translocating V-type ATPase complex [IPI]			833
Q5RK19 UniProt NPD GO	SNF8_RAT	Vacuolar sorting protein SNF8 (ELL-associated protein of 30 kDa)	0.10	-	mit	0	Cytoplasm (Probable). Nucleus (Probable)				258
Q8L7E3 UniProt NPD GO	VSR7_ARATH	Vacuolar sorting receptor 7 precursor (AtVSR7) (Epidermal growth factor receptor-like protein 3) (At ...	0.10	-	end	1 *					625
Q90X24 UniProt NPD GO	TXVE_BOTIN	Vascular endothelial growth factor toxin precursor (svVEGF)	0.10	-	end	1 *	Secreted protein				146
P30518 UniProt NPD GO	V2R_HUMAN	Vasopressin V2 receptor (Renal-type arginine vasopressin receptor) (Antidiuretic hormone receptor) ( ...	0.10	-	end	7 *	Membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] endosome [TAS] Golgi apparatus [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	304800		371
P25660 UniProt NPD GO	IVB1_BUNFA	Venom basic protease inhibitor IX [Contains: Venom basic protease inhibitor VIIIB]	0.10	-	nuc	0	Secreted protein			1JC6	65
O13063 UniProt NPD GO	VSP3_TRIGA	Venom serine proteinase 3 precursor (EC 3.4.21.-)	0.10	-	exc	0	Secreted protein				258
Q9DF68 UniProt NPD GO	VSP1_TRIJE	Venom serine proteinase-like protein precursor (SP1)	0.10	-	exc	0	Secreted protein				260
P39557 UniProt NPD GO	YAL7_YEAST	Very hypothetical protein YAR047C	0.10	-	mit	2 *					106
P97524 UniProt NPD GO	S27A2_RAT	Very-long-chain acyl-CoA synthetase (EC 6.2.1.-) (VLCS) (Very-long-chain-fatty-acid-CoA ligase) (VLA ...	0.10	+	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Peroxisome; pero ...	microsome [IMP] peroxisome [IMP]			620
Q12907 UniProt NPD GO	LMAN2_HUMAN	Vesicular integral-membrane protein VIP36 precursor (GP36b glycoprotein) (Lectin, mannose-binding 2) ...	0.10	-	nuc	1	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...	ER-Golgi intermediate compartment [IDA]	609551		356
P49256 UniProt NPD GO	LMAN2_CANFA	Vesicular integral-membrane protein VIP36 precursor (Lectin, mannose-binding 2)	0.10	-	end	1	Golgi apparatus; Golgi membrane; single-pass type I membrane protein				356
Q9DBH5 UniProt NPD GO	LMAN2_MOUSE	Vesicular integral-membrane protein VIP36 precursor (Lectin, mannose-binding 2)	0.10	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type I membrane protein (By similarity)				358
Q62472 UniProt NPD GO	VNS2_MOUSE	Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) (Lipocalin-4) ...	0.10	-	exc	0	Secreted protein				185
Q5R7W0 UniProt NPD GO	WIPI3_PONPY	WD repeat domain phosphoinositide-interacting protein 3 (WIPI-3) (WD repeat protein 45-like) (WDR45- ...	0.10	-	cyt	0					344
Q640T2 UniProt NPD GO	WIPI3_XENTR	WD repeat domain phosphoinositide-interacting protein 3 (WIPI-3) (WD repeat protein 45-like) (WDR45- ...	0.10	-	cyt	0					344
Q9BRP4 UniProt NPD GO	WDR71_HUMAN	WD repeat protein 71 (Protein G-16)	0.10	-	nuc	0					392
O74184 UniProt NPD GO	POP3_SCHPO	WD repeat protein pop3 (WD repeat protein wat1)	0.10	-	cyt	0					314
Q8N6F8 UniProt NPD GO	WBS27_HUMAN	Williams-Beuren syndrome chromosome region 27 protein	0.10	+	cyt	0			194050		245
Q9LM66 UniProt NPD GO	XCP2_ARATH	Xylem cysteine proteinase 2 precursor (EC 3.4.22.-) (AtXCP2)	0.10	-	exc	0	Vacuole (By similarity). Predominantly. Cell membrane (By similarity). May be associated to plasma m ...				356
P58317 UniProt NPD GO	ZN121_HUMAN	Zinc finger protein 121 (Zinc finger protein 20) (Fragment)	0.10	-	nuc	0	Nucleus (Probable)		194628		295
Q60738 UniProt NPD GO	ZNT1_MOUSE	Zinc transporter 1 (ZnT-1) (Solute carrier family 30 member 1)	0.10	-	end	5 *	Cell membrane; multi-pass membrane protein (Probable)				503
O81123 UniProt NPD GO	ZIP1_ARATH	Zinc transporter 1 precursor (ZRT/IRT-like protein 1)	0.10	-	end	9 *	Cell membrane; multi-pass membrane protein (Potential)				355
O77726 UniProt NPD GO	ZP2_MACRA	Zona pellucida sperm-binding protein 2 precursor (Zona pellucida glycoprotein ZP2) (Zona pellucida p ...	0.10	-	nuc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				745
P10761 UniProt NPD GO	ZP3_MOUSE	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3) (Sperm receptor) ...	0.10	+	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				424
P05131 UniProt NPD GO	KAPB1_BOVIN	cAMP-dependent protein kinase, beta-1-catalytic subunit (EC 2.7.11.11) (PKA C-beta-1)	0.10	-	nuc	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm. Monomeric catalytic subunit: Nucleus. T ...				350
Q3SWS8 UniProt NPD GO	RAE1L_RAT	mRNA-associated protein mrnp 41 (Rae1 protein homolog)	0.10	-	exc	0	Cytoplasm (By similarity). Nucleus (By similarity)				368
Q59WV0 UniProt NPD GO	PALI_CANAL	pH-response regulator protein palI/RIM9	0.10	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				346
Q5BK68 UniProt NPD GO	SNPC3_RAT	snRNA-activating protein complex subunit 3 (SNAPc subunit 3) (snRNA-activating protein complex 50 kD ...	0.10	-	cyt	0	Nucleus (By similarity)				407
Q6CX53 UniProt NPD GO	GLGB_KLULA	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.09	-	cyt	0					719
P32775 UniProt NPD GO	GLGB_YEAST	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.09	-	cyt	0		cytoplasm [IDA]			704
O82782 UniProt NPD GO	HIS4_ARATH	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase, ...	0.09	-	mit	0	Plastid; chloroplast				304
Q9MB95 UniProt NPD GO	1A11_PRUMU	1-aminocyclopropane-1-carboxylate synthase 1 (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methionine m ...	0.09	-	cyt	0					492
Q8LAH7 UniProt NPD GO	OPR1_ARATH	12-oxophytodienoate reductase 1 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 1) (OPDA-reductas ...	0.09	-	cyt	0	Cytoplasm			1VJI	372
O49996 UniProt NPD GO	1433D_TOBAC	14-3-3-like protein D	0.09	-	cyt	0					249

You are viewing entries 65451 to 65500 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.