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
Q9D1M7 UniProt NPD GO	FKB11_MOUSE	FK506-binding protein 11 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rota ...	0.36	+	end	1					201
O74191 UniProt NPD GO	FKBP4_SCHPO	FK506-binding protein 39 kDa (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.36	+	nuc	0					361
O15130 UniProt NPD GO	NPFF_HUMAN	FMRFamide-related peptides precursor [Contains: Neuropeptide SF (NPSF); Neuropeptide FF (NPFF); Neur ...	0.36	-	exc	0	Secreted protein	soluble fraction [TAS]	604643		113
Q9VWA8 UniProt NPD GO	FRG1_DROME	FRG1 protein homolog	0.36	+	cyt	0	Nucleus; nucleoplasm; Cajal body (By similarity). Nucleus; nucleoplasm; nuclear speckle (By similari ...				262
P23610 UniProt NPD GO	F8I2_HUMAN	Factor VIII intron 22 protein (CpG island protein)	0.36	-	cyt	0			305423		371
Q00597 UniProt NPD GO	FANCC_HUMAN	Fanconi anemia group C protein (Protein FACC)	0.36	-	cyt	0	Nucleus. Major form. Cytoplasm. Minor form	cytoplasm [TAS] cytosol [IDA] nucleus [TAS]	227650		558
Q91WJ8 UniProt NPD GO	FUBP1_MOUSE	Far upstream element-binding protein 1 (FUSE-binding protein 1) (FBP)	0.36	-	nuc	0	Nucleus (Probable)			1X4N	651
P34082 UniProt NPD GO	FAS2_DROME	Fasciclin-2 precursor (Fasciclin II) (FAS II)	0.36	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Cell membrane; lipid-ancho ...	axon [TAS] cytoplasm [IDA] integral to membrane [TAS] plasma membrane [IDA] postsynaptic membrane [TAS] presynaptic membrane [TAS]			873
P19096 UniProt NPD GO	FAS_MOUSE	Fatty acid synthase (EC 2.3.1.85) [Includes: [Acyl-carrier-protein] S-acetyltransferase (EC 2.3.1.38 ...	0.36	-	nuc	0		glycogen granule [IDA]			2504
Q2MHN2 UniProt NPD GO	FRIH_FELCA	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.36	-	nuc	0					182
Q95LA0 UniProt NPD GO	FATE1_BOVIN	Fetal and adult testis-expressed transcript protein homolog	0.36	-	nuc	0					180
O35622 UniProt NPD GO	FGF15_MOUSE	Fibroblast growth factor 15 precursor (FGF-15)	0.36	-	mit	0	Secreted protein				218
Q9ESL8 UniProt NPD GO	FGF16_MOUSE	Fibroblast growth factor 16 (FGF-16)	0.36	-	cyt	0	Secreted protein (By similarity)				207
O54769 UniProt NPD GO	FGF16_RAT	Fibroblast growth factor 16 (FGF-16)	0.36	-	cyt	0	Secreted protein				207
O46378 UniProt NPD GO	FMOD_RABIT	Fibromodulin (FM) (Collagen-binding 59 kDa protein) (Keratan sulfate proteoglycan fibromodulin) (KSP ...	0.36	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				147
P04937 UniProt NPD GO	FINC_RAT	Fibronectin precursor (FN)	0.36	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [TAS]			2477
P35554 UniProt NPD GO	FTN_DROME	Flightin (Muscle protein 27)	0.36	-	nuc	0		myofibril [IDA] striated muscle thick filament [IDA]			182
P35846 UniProt NPD GO	FOLR1_MOUSE	Folate receptor alpha precursor (FR-alpha) (Folate receptor 1) (Folate-binding protein 1)	0.36	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	membrane fraction [TAS]			255
Q8HXX9 UniProt NPD GO	FRDA_MACFA	Frataxin, mitochondrial precursor (Fxn)	0.36	-	mit	0	Mitochondrion. Mitochondrial and extramitochondrial (By similarity)				210
Q24342 UniProt NPD GO	FNG_DROME	Fringe glycosyltransferase (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase)	0.36	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	endoplasmic reticulum [IDA] Golgi apparatus [IDA] Golgi stack [IDA]			412
O42579 UniProt NPD GO	FZD3_XENLA	Frizzled-3 precursor (Fz-3) (Xfz3)	0.36	-	end	7	Membrane; multi-pass membrane protein				664
Q13068 UniProt NPD GO	GAGE4_HUMAN	G antigen 4 (GAGE-4)	0.36	-	nuc	0			604246		117
O76087 UniProt NPD GO	GAGE7_HUMAN	G antigen 7 (GAGE-7) (GAGE-7B) (GAGE-8) (AL4)	0.36	-	nuc	0			604132		117
O97663 UniProt NPD GO	GPR15_MACMU	G-protein coupled receptor 15	0.36	-	end	7 *	Membrane; multi-pass membrane protein				360
P56412 UniProt NPD GO	GPR15_MACNE	G-protein coupled receptor 15	0.36	-	end	7 *	Membrane; multi-pass membrane protein				360
P30279 UniProt NPD GO	CCND2_HUMAN	G1/S-specific cyclin-D2	0.36	-	cyt	0			123833		289
P24865 UniProt NPD GO	CG21_SCHPO	G2/mitotic-specific cyclin cig1	0.36	+	cyt	0					415
P51988 UniProt NPD GO	CCNB_HYDAT	G2/mitotic-specific cyclin-B (Fragment)	0.36	-	mit	0					361
Q00422 UniProt NPD GO	GABPA_MOUSE	GA-binding protein alpha chain (GABP-subunit alpha)	0.36	-	cyt	0	Nucleus	nucleus [IDA]		1SXD	454
Q92643 UniProt NPD GO	GPI8_HUMAN	GPI-anchor transamidase precursor (EC 3.-.-.-) (GPI transamidase) (Phosphatidylinositol-glycan biosy ...	0.36	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	GPI-anchor transamidase complex [IMP]	605087		395
Q18905 UniProt NPD GO	CGP1_CAEEL	GTP-binding protein cgp-1	0.36	-	cyt	0					613
Q03249 UniProt NPD GO	GALT_MOUSE	Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-glucose-- ...	0.36	-	cyt	0					379
Q8HYB6 UniProt NPD GO	GBRL1_BOVIN	Gamma-aminobutyric acid receptor-associated protein-like 1 (GABA(A) receptor-associated protein-like ...	0.36	-	nuc	0					111
Q02738 UniProt NPD GO	CXB4_MOUSE	Gap junction beta-4 protein (Connexin-30.3) (Cx30.3)	0.36	+	end	4 *	Membrane; multi-pass membrane protein				266
P04563 UniProt NPD GO	GAST_RAT	Gastrin precursor [Contains: Big gastrin (Gastrin 34) (G34); Gastrin]	0.36	-	nuc	0	Secreted protein				104
P18734 UniProt NPD GO	ZG67_XENLA	Gastrula zinc finger protein XLCGF67.1 (Fragment)	0.36	-	nuc	0	Nucleus (Potential)				139
O19908 UniProt NPD GO	GLMS_CYACA	Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] (EC 2.6.1.16) (Hexosephosphate amin ...	0.36	-	cyt	0	Plastid; chloroplast				620
Q4HVS2 UniProt NPD GO	GNT1_GIBZE	Glucose N-acetyltransferase 1 (EC 2.4.1.-) (N-acetylglucosaminyltransferase)	0.36	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity). Vacuole; vacu ...				431
P38138 UniProt NPD GO	GLU2A_YEAST	Glucosidase 2 subunit alpha precursor (EC 3.2.1.84) (Glucosidase II subunit alpha) (Alpha-glucosidas ...	0.36	-	cyt	0	Endoplasmic reticulum	endoplasmic reticulum lumen [IDA] mitochondrion [IDA]			954
Q03391 UniProt NPD GO	NMDE4_MOUSE	Glutamate [NMDA] receptor subunit epsilon 4 precursor (N-methyl D-aspartate receptor subtype 2D) (NR ...	0.36	-	end	4	Membrane; multi-pass membrane protein				1323
P23818 UniProt NPD GO	GRIA1_MOUSE	Glutamate receptor 1 precursor (GluR-1) (GluR-A) (GluR-K1) (Glutamate receptor ionotropic, AMPA 1) ( ...	0.36	-	end	3	Membrane; multi-pass membrane protein	postsynaptic density [IDA]			907
Q8LGN1 UniProt NPD GO	GLR14_ARATH	Glutamate receptor 1.4 precursor (Ligand-gated ion channel 1.4)	0.36	+	end	5 *	Membrane; multi-pass membrane protein				861
Q6P7A1 UniProt NPD GO	LARG2_RAT	Glycosyltransferase-like protein LARGE2 (EC 2.4.-.-) (Glycosyltransferase-like 1B)	0.36	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				690
Q8L785 UniProt NPD GO	SYGM2_ARATH	Glycyl-tRNA synthetase 2, chloroplast/mitochondrial precursor (EC 6.1.1.14) (Glycine--tRNA ligase 2) ...	0.36	-	mit	0	Plastid; chloroplast. Mitochondrion				1067
P32237 UniProt NPD GO	GNRHR_SHEEP	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R)	0.36	+	end	7 *	Membrane; multi-pass membrane protein				328
Q9WV56 UniProt NPD GO	GDF2_MOUSE	Growth/differentiation factor 2 precursor (GDF-2) (Bone morphogenetic protein 9) (BMP-9)	0.36	-	exc	0	Secreted protein				428
Q5USW0 UniProt NPD GO	GDF8_TAUDE	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.36	+	mit	0	Secreted protein (By similarity)				375
Q60MJ0 UniProt NPD GO	GPA1_CAEBR	Guanine nucleotide-binding protein alpha-1 subunit	0.36	-	cyt	0					357
P87032 UniProt NPD GO	GPA1_USTMA	Guanine nucleotide-binding protein alpha-1 subunit	0.36	-	nuc	0					353
P29387 UniProt NPD GO	GBB4_MOUSE	Guanine nucleotide-binding protein subunit beta 4 (Transducin beta chain 4)	0.36	-	cyt	0					339

You are viewing entries 34951 to 35000 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.