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
P09803 UniProt NPD GO	CADH1_MOUSE	Epithelial-cadherin precursor (E-cadherin) (Uvomorulin) (Cadherin-1) (ARC-1) (CD324 antigen) [Contai ...	0.28	-	end	1	Cell membrane; cell-cell junction; single-pass type I membrane protein. Colocalizes with DLG7 at sit ...	apical part of cell [IDA] basolateral plasma membrane [IDA] cell-cell adherens junction [IDA] plasma membrane [IDA]		1SUH	884
P14753 UniProt NPD GO	EPOR_MOUSE	Erythropoietin receptor precursor (EPO-R)	0.28	-	exc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein				507
P47982 UniProt NPD GO	EST6_DROMA	Esterase 6 precursor (EC 3.1.1.1) (Est-6) (Carboxylic-ester hydrolase 6) (Carboxylesterase-6)	0.28	-	vac	0	Secreted protein				542
Q99447 UniProt NPD GO	PCY2_HUMAN	Ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14) (Phosphorylethanolamine transferase) (CTP: ...	0.28	-	cyt	0			602679		389
Q4R4X9 UniProt NPD GO	EIF1B_MACFA	Eukaryotic translation initiation factor 1b (eIF1b)	0.28	-	cyt	0					113
Q9CXU9 UniProt NPD GO	EIF1B_MOUSE	Eukaryotic translation initiation factor 1b (eIF1b)	0.28	-	cyt	0					113
O60739 UniProt NPD GO	EIF1B_HUMAN	Eukaryotic translation initiation factor 1b (eIF1b) (Protein translation factor SUI1 homolog GC20)	0.28	-	cyt	0					113
P61220 UniProt NPD GO	EIF1B_PIG	Eukaryotic translation initiation factor 1b (eIF1b) (Protein translation factor SUI1 homolog GC20)	0.28	-	cyt	0					113
P14918 UniProt NPD GO	EXTN_MAIZE	Extensin precursor (Proline-rich glycoprotein)	0.28	-	mit	0					267
P47756 UniProt NPD GO	CAPZB_HUMAN	F-actin capping protein subunit beta (CapZ beta)	0.28	-	nuc	0		F-actin capping protein complex [TAS]	601572		276
Q12347 UniProt NPD GO	HRT3_YEAST	F-box protein HRT3 (High level expression reduces Ty3 transposition protein 3)	0.28	-	cyt	0					344
Q969U6 UniProt NPD GO	FBXW5_HUMAN	F-box/WD repeat protein 5 (F-box and WD-40 domain protein 5)	0.28	-	nuc	0			609072		566
Q9VZW5 UniProt NPD GO	FMAR_DROME	FMRFamide receptor (Larval opioid receptor) (DFR) (DrmFMRFa-R)	0.28	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [NAS]			549
Q9QXW4 UniProt NPD GO	FSCN3_MOUSE	Fascin-3 (Testis fascin)	0.28	-	cyt	0		cytoplasm [IDA]			498
Q9TM25 UniProt NPD GO	FTRC_CYACA	Ferredoxin-thioredoxin reductase, catalytic chain (EC 1.18.-.-) (FTR-C) (Ferredoxin-thioredoxin redu ...	0.28	-	nuc	0	Plastid; chloroplast				111
Q5R8J7 UniProt NPD GO	FRIH_PONPY	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.28	-	nuc	0					182
P02794 UniProt NPD GO	FRIH_HUMAN	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit) (Proliferation-inducing gene 15 protein)	0.28	-	nuc	0		ferritin complex [TAS] plasma membrane [ISS]	134770	2FHA	182
P02680 UniProt NPD GO	FIBG_RAT	Fibrinogen gamma chain precursor	0.28	-	exc	0	Secreted protein				445
P70492 UniProt NPD GO	FGF10_RAT	Fibroblast growth factor 10 precursor (FGF-10)	0.28	-	exc	1 *	Secreted protein (Potential)	cell surface [ISS] nucleus [ISS]			215
Q9NP95 UniProt NPD GO	FGF20_HUMAN	Fibroblast growth factor 20 (FGF-20)	0.28	-	nuc	0	Secreted protein	extracellular region [TAS] soluble fraction [TAS]	605558		211
Q5MK86 UniProt NPD GO	FGF23_TETNG	Fibroblast growth factor 23 precursor (FGF-23)	0.28	-	exc	0	Secreted protein (Potential)				263
P22182 UniProt NPD GO	FGFR1_XENLA	Fibroblast growth factor receptor 1 precursor (EC 2.7.10.1) (FGFR-1)	0.28	-	end	1	Membrane; single-pass type I membrane protein				812
Q07407 UniProt NPD GO	FGFR1_DROME	Fibroblast growth factor receptor homolog 1 precursor (EC 2.7.10.1) (Protein heartless)	0.28	-	end	2 *	Membrane; single-pass type I membrane protein	integral to membrane [ISS]			729
Q28749 UniProt NPD GO	FINC_RABIT	Fibronectin (FN) (Fragment)	0.28	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				100
Q9TXA7 UniProt NPD GO	API_ACAVI	Filarial antigen Av33 precursor	0.28	-	nuc	0	Secreted protein				234
P70040 UniProt NPD GO	FEN1A_XENLA	Flap endonuclease 1-A (EC 3.1.-.-) (Flap structure-specific endonuclease 1-A) (FEN-1-A) (xFEN-1a)	0.28	-	nuc	0	Nucleus	nucleus [IDA]			382
P39712 UniProt NPD GO	FLO9_YEAST	Flocculation protein FLO9 precursor	0.28	-	exc	1 *	Membrane; multi-pass membrane protein (Potential)				1322
Q96SL8 UniProt NPD GO	FIZ1_HUMAN	Flt3-interacting zinc finger protein 1	0.28	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]	609133		496
Q9WTJ4 UniProt NPD GO	FIZ1_MOUSE	Flt3-interacting zinc finger protein 1	0.28	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			500
Q5M7Q1 UniProt NPD GO	FLCN_XENTR	Folliculin	0.28	-	cyt	0					579
Q9R059 UniProt NPD GO	FHL3_MOUSE	Four and a half LIM domains protein 3 (FHL-3) (Skeletal muscle LIM-protein 2) (SLIM 2)	0.28	-	nuc	0		nucleus [IDA] stress fiber [IDA] Z disc [IDA]			289
Q28193 UniProt NPD GO	FURIN_BOVIN	Furin precursor (EC 3.4.21.75) (Paired basic amino acid residue-cleaving enzyme) (PACE) (Dibasic-pro ...	0.28	-	end	2 *	Golgi apparatus; trans-Golgi network. Seems to be localized intracellularly to the trans Golgi netwo ...				797
P39948 UniProt NPD GO	CCND1_RAT	G1/S-specific cyclin-D1	0.28	-	cyt	0					295
Q99L27 UniProt NPD GO	GMPR2_MOUSE	GMP reductase 2 (EC 1.7.1.7) (Guanosine 5'-monophosphate oxidoreductase 2) (Guanosine monophosphate ...	0.28	-	cyt	0					348
Q09782 UniProt NPD GO	GPI7_SCHPO	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.28	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				758
Q4IB63 UniProt NPD GO	GPI10_GIBZE	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.28	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				613
P47026 UniProt NPD GO	GWT1_YEAST	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.28	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	nuclear envelope-endoplasmic reticulum network [IDA]			498
Q8VEL9 UniProt NPD GO	REM2_MOUSE	GTP-binding protein REM 2 (Rad and Gem-like GTP-binding protein 2)	0.28	-	nuc	0	Cell membrane (By similarity)				272
Q9WTY2 UniProt NPD GO	REM2_RAT	GTP-binding protein REM 2 (Rad and Gem-like GTP-binding protein 2)	0.28	-	mit	0	Cell membrane				272
P06780 UniProt NPD GO	RHO1_YEAST	GTP-binding protein RHO1 (Rho-type GTPase 1)	0.28	-	cyt	0	Cell membrane; lipid anchor. Plasma membrane-associated at sites of polarized growth such as incipie ...	1,3-beta-glucan synthase complex [IDA] bud neck [IDA] bud tip [IDA] mating projection tip [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA] peroxisome [IDA]			208
P20790 UniProt NPD GO	SAS1_DICDI	GTP-binding protein SAS1	0.28	-	nuc	0					208
Q05147 UniProt NPD GO	RASK_XENLA	GTPase KRas (Ki-Ras) (K-ras)	0.28	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				187
Q9SWH5 UniProt NPD GO	FUT1_ARATH	Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) (Xyloglucan alpha-(1,2)-fucosyltransferase) ( ...	0.28	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				558
O35789 UniProt NPD GO	B3GA1_RAT	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.28	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi lumen [TAS]			334
Q02862 UniProt NPD GO	CASG_MOUSE	Gamma-casein precursor (PP22)	0.28	-	exc	0	Secreted protein				184
Q40901 UniProt NPD GO	THG_PETIN	Gamma-thionin homolog PPT precursor	0.28	-	mit	1 *					78
Q9UKL4 UniProt NPD GO	CXA9_HUMAN	Gap junction alpha-9 protein (Connexin-36) (Cx36)	0.28	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [NAS]	607058		321
P18738 UniProt NPD GO	ZG9_XENLA	Gastrula zinc finger protein XLCGF9.1 (Fragment)	0.28	-	nuc	0	Nucleus (Potential)				112
Q9P885 UniProt NPD GO	GGPPS_RHIRA	Geranylgeranyl pyrophosphate synthetase (GGPP synthetase) (GGPPSase) (Geranylgeranyl diphosphate syn ...	0.28	-	cyt	0	Cytoplasm	soluble fraction [ISS]			303
Q8VI38 UniProt NPD GO	GBGT1_MOUSE	Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (EC 2.4.1.88) (Forssman glycolipid synthetas ...	0.28	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	membrane [TAS]			347

You are viewing entries 42251 to 42300 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.