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
Q9VV73 UniProt NPD GO	NXF2_DROME	Nuclear RNA export factor 2	0.26	-	cyt	0	Cytoplasm. Nucleus; nucleoplasm. Localized in both the nucleoplasm and the cytoplasm. Not detected a ...	cytoplasm [IDA] nucleoplasm [IDA]			841
Q9ES54 UniProt NPD GO	NPL4_RAT	Nuclear protein localization protein 4 homolog (Protein NPL4)	0.26	-	cyt	0	Cytoplasm. Endoplasmic reticulum. Nucleus. Associated with the endoplasmic reticulum and nuclear			1Q5W	607
Q9BVI4 UniProt NPD GO	NOC4L_HUMAN	Nucleolar complex protein 4 homolog (NOC4 protein homolog) (NOC4-like protein) (Nucleolar complex-as ...	0.26	-	nuc	0	Nucleus; nuclear membrane; multi-pass membrane protein. Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [ISS]			516
Q4V9P9 UniProt NPD GO	NOL11_BRARE	Nucleolar protein 11-like	0.26	-	mit	0	Nucleus; nucleolus (By similarity)				708
P16039 UniProt NPD GO	NPM_CHICK	Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Numatrin) (Nucleolar protein NO38)	0.26	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleoplasm (By similarity). Nucleus; nucleolus (By similarity). ...	centrosome [ISS] cytoplasm [ISS] nucleus [ISS]			294
P49686 UniProt NPD GO	NUP42_YEAST	Nucleoporin NUP42 (Nuclear pore protein NUP42)	0.26	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side	nuclear pore [IDA]			430
Q8VYR2 UniProt NPD GO	NUDT9_ARATH	Nudix hydrolase 9 (EC 3.6.1.-) (AtNUDT9)	0.26	-	nuc	0					311
P08523 UniProt NPD GO	OMP_RAT	Olfactory marker protein (Olfactory neuronal-specific protein)	0.26	-	cyt	0	Cytoplasm	cytosol [NAS]		1ZRI	162
Q8NH03 UniProt NPD GO	OR2T3_HUMAN	Olfactory receptor 2T3	0.26	-	end	7 *	Membrane; multi-pass membrane protein				318
Q9H2C8 UniProt NPD GO	O51V1_HUMAN	Olfactory receptor 51V1 (Odorant receptor HOR3'beta1) (Olfactory receptor OR11-36)	0.26	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			321
O44535 UniProt NPD GO	OAZ_DROVI	Ornithine decarboxylase antizyme (ODC-Az) (Protein gutfeeling) (Fragment)	0.26	-	nuc	0					130
P50700 UniProt NPD GO	OSL3_ARATH	Osmotin-like protein OSM34 precursor	0.26	-	exc	1 *					244
P34996 UniProt NPD GO	P2RY1_CHICK	P2Y purinoceptor 1 (ATP receptor) (P2Y1) (Purinergic receptor)	0.26	-	end	6 *	Membrane; multi-pass membrane protein			1DDD	362
P49652 UniProt NPD GO	P2RY1_MELGA	P2Y purinoceptor 1 (ATP receptor) (P2Y1) (Purinergic receptor) (6H1 orphan receptor)	0.26	-	end	6 *	Membrane; multi-pass membrane protein				362
Q8BFV2 UniProt NPD GO	PCID2_MOUSE	PCI domain-containing protein 2 (CSN12-like protein)	0.26	-	cyt	0					399
Q6NXB2 UniProt NPD GO	PDZ11_BRARE	PDZ domain-containing protein 11	0.26	-	cyt	0					142
Q9Z0G0 UniProt NPD GO	GIPC1_MOUSE	PDZ domain-containing protein GIPC1 (RGS19-interacting protein 1) (GAIP C-terminus-interacting prote ...	0.26	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytosol [IDA] membrane [IDA]			333
Q10051 UniProt NPD GO	PRP19_CAEEL	PRP19/PSO4 homolog	0.26	-	cyt	0	Nucleus; nucleolus (By similarity)				492
Q876A6 UniProt NPD GO	AKR1_SACCA	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1) (Fragments)	0.26	-	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				742
Q9JKR5 UniProt NPD GO	ZDHC2_RAT	Palmitoyltransferase ZDHHC2 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 2) (DHHC-2)	0.26	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)				366
Q9UIJ5 UniProt NPD GO	ZDHC2_HUMAN	Palmitoyltransferase ZDHHC2 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 2) (DHHC-2) (Zi ...	0.26	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				367
P06303 UniProt NPD GO	PAHO_RAT	Pancreatic prohormone precursor (Pancreatic polypeptide) (PP) [Contains: Pancreatic hormone; C-termi ...	0.26	-	exc	1 *	Secreted protein				98
Q9GMU3 UniProt NPD GO	PNMA2_MACFA	Paraneoplastic antigen Ma2 homolog	0.26	-	cyt	0	Nucleus; nucleolus (By similarity)				364
Q9GL67 UniProt NPD GO	PTHY_FELCA	Parathyroid hormone precursor (Parathyrin) (PTH)	0.26	-	mit	0	Secreted protein (By similarity)				115
Q9DAK2 UniProt NPD GO	PACRG_MOUSE	Parkin coregulated gene protein homolog (Hypertension-related protein 1-like protein)	0.26	-	nuc	0					241
P91607 UniProt NPD GO	PER_DROCP	Period circadian protein (Fragment)	0.26	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				375
Q99LL5 UniProt NPD GO	PWP1_MOUSE	Periodic tryptophan protein 1 homolog	0.26	+	mit	0	Nucleus (By similarity)				501
P36966 UniProt NPD GO	PEX6_YARLI	Peroxisomal biogenesis factor 6 (Peroxin-6) (Peroxisome biosynthesis protein PAY4)	0.26	-	cyt	0	Cytoplasm (Probable)				1024
Q43617 UniProt NPD GO	PHS2_PHALU	Phaseolin precursor (Fragment)	0.26	-	exc	1 *	Protein body (By similarity). Vacuole (By similarity). Cotyledonary membrane-bound vacuolar protein ...				423
P27991 UniProt NPD GO	PAL1_SOYBN	Phenylalanine ammonia-lyase 1 (EC 4.3.1.5)	0.26	-	nuc	0	Cytoplasm (Probable)				713
P46961 UniProt NPD GO	GPI2_YEAST	Phosphatidylinositol N-acetylglucosaminyltransferase GPI2 subunit (EC 2.4.1.198)	0.26	-	end	6	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] glycosylphosphatidylinositol-N-acetylglucos... [IPI]			280
Q6EX42 UniProt NPD GO	PI5K1_ORYSA	Phosphatidylinositol-4-phosphate 5-kinase 1 precursor (EC 2.7.1.68) (1-phosphatidylinositol-4-phosph ...	0.26	-	cyt	0					801
Q9P8L1 UniProt NPD GO	PLB1_CRYNE	Phospholipase B precursor (EC 3.1.1.5) (Lysophospholipase)	0.26	+	exc	0	Secreted protein (By similarity)				637
P07934 UniProt NPD GO	PHKG1_MOUSE	Phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (EC 2.7.11.19) (Phosphorylase ...	0.26	-	cyt	0					387
P13286 UniProt NPD GO	PHKG1_RAT	Phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (EC 2.7.11.19) (Phosphorylase ...	0.26	-	cyt	0		phosphorylase kinase complex [TAS]			387
P15735 UniProt NPD GO	PHKG2_HUMAN	Phosphorylase b kinase gamma catalytic chain, testis/liver isoform (EC 2.7.11.19) (PHK-gamma-T) (Pho ...	0.26	-	cyt	0			172471		406
P84743 UniProt NPD GO	PBLST_EUGGR	Photoactivated adenylate cyclase subunit beta-like protein ST-	0.26	-	mit	0	Flagellum	flagellum [IDA]			859
Q85C36 UniProt NPD GO	YCF3_ANTFO	Photosystem I assembly protein ycf3	0.26	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				170
Q8M9W1 UniProt NPD GO	YCF3_CHAGL	Photosystem I assembly protein ycf3	0.26	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				169
P12202 UniProt NPD GO	YCF3_MARPO	Photosystem I assembly protein ycf3	0.26	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
P25412 UniProt NPD GO	YCF4_AEGTA	Photosystem I assembly protein ycf4	0.26	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
Q31910 UniProt NPD GO	YCF4_BRAOL	Photosystem I assembly protein ycf4	0.26	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
P07038 UniProt NPD GO	PMA1_NEUCR	Plasma membrane ATPase (EC 3.6.3.6) (Proton pump)	0.26	+	end	9	Cell membrane; multi-pass membrane protein			1MHS	920
P30057 UniProt NPD GO	RR7_EPIVI	Plastid 30S ribosomal protein S7	0.26	-	nuc	0	Plastid				155
P19954 UniProt NPD GO	RR30_SPIOL	Plastid-specific 30S ribosomal protein 1, chloroplast precursor (CS-S5) (CS5) (S22) (Ribosomal prote ...	0.26	-	mit	0	Plastid; chloroplast; chloroplast stroma				302
P30035 UniProt NPD GO	PLF4_SHEEP	Platelet factor 4 (PF-4) (CXCL4)	0.26	-	exc	0	Secreted protein	extracellular region [ISS]			85
P25105 UniProt NPD GO	PTAFR_HUMAN	Platelet-activating factor receptor (PAF-R)	0.26	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane [IDA]	173393		342
P57722 UniProt NPD GO	PCBP3_MOUSE	Poly(rC)-binding protein 3 (Alpha-CP3)	0.26	-	nuc	0	Cytoplasm (By similarity)				339
P60047 UniProt NPD GO	PABP5_GORGO	Polyadenylate-binding protein 5 (Poly(A)-binding protein 5) (PABP 5)	0.26	-	nuc	0	Cytoplasm (By similarity)				382
Q96DU9 UniProt NPD GO	PABP5_HUMAN	Polyadenylate-binding protein 5 (Poly(A)-binding protein 5) (PABP 5)	0.26	-	nuc	0	Cytoplasm (By similarity)		300407		382

You are viewing entries 44451 to 44500 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.