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
O04707 UniProt NPD GO	GAO1A_WHEAT	Gibberellin 20 oxidase 1-A (EC 1.14.11.-) (Gibberellin C-20 oxidase 1-B) (GA 20-oxidase 1-A) (Ta20ox ...	0.20	-	cyt	0					365
Q39112 UniProt NPD GO	GAOX3_ARATH	Gibberellin 20 oxidase 3 (EC 1.14.11.-) (Gibberellin C-20 oxidase 3) (GA 20-oxidase 3)	0.20	-	cyt	0					380
P36364 UniProt NPD GO	FGF9_RAT	Glia-activating factor precursor (GAF) (Fibroblast growth factor 9) (FGF-9) (HBGF-9)	0.20	-	cyt	0	Secreted protein				208
P07093 UniProt NPD GO	GDN_HUMAN	Glia-derived nexin precursor (GDN) (Protease nexin I) (PN-1) (Protease inhibitor 7)	0.20	-	mit	0	Secreted protein; extracellular space	extracellular region [NAS]	177010		398
O95838 UniProt NPD GO	GLP2R_HUMAN	Glucagon-like peptide 2 receptor precursor (GLP-2 receptor) (GLP-2-R) (GLP-2R)	0.20	-	end	5	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	603659		553
O93939 UniProt NPD GO	EXG1_HANAN	Glucan 1,3-beta-glucosidase 1 precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase 1)	0.20	-	exc	0	Secreted protein (Potential)				498
P23535 UniProt NPD GO	E13B_PHAVU	Glucan endo-1,3-beta-glucosidase, basic isoform precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydr ...	0.20	-	cyt	0	Vacuole (By similarity)				348
P52416 UniProt NPD GO	GLGS1_VICFA	Glucose-1-phosphate adenylyltransferase small subunit 1, chloroplast precursor (EC 2.7.7.27) (ADP-gl ...	0.20	-	mit	0	Plastid; chloroplast (By similarity)				508
Q42521 UniProt NPD GO	DCE1_ARATH	Glutamate decarboxylase 1 (EC 4.1.1.15) (GAD 1)	0.20	-	cyt	0					502
Q99259 UniProt NPD GO	DCE1_HUMAN	Glutamate decarboxylase 1 (EC 4.1.1.15) (Glutamate decarboxylase, 67 kDa isoform) (GAD-67) (67 kDa g ...	0.20	-	cyt	0		intracellular [IDA] vesicle membrane [NAS]	605363		594
P19492 UniProt NPD GO	GRIA3_RAT	Glutamate receptor 3 precursor (GluR-3) (GluR-C) (GluR-K3) (Glutamate receptor ionotropic, AMPA 3) ( ...	0.20	-	end	3	Membrane; multi-pass membrane protein	dendritic spine [IDA] ionotropic glutamate receptor complex [TAS] postsynaptic density [IDA] protein complex [IPI]			888
Q9Z2W8 UniProt NPD GO	GRIA4_MOUSE	Glutamate receptor 4 precursor (GluR-4) (GluR4) (GluR-D) (Glutamate receptor ionotropic, AMPA 4) (AM ...	0.20	-	end	4 *	Membrane; multi-pass membrane protein				902
P42264 UniProt NPD GO	GRIK3_RAT	Glutamate receptor, ionotropic kainate 3 precursor (Glutamate receptor 7) (GluR-7) (GluR7)	0.20	-	end	3	Membrane; multi-pass membrane protein				919
O22493 UniProt NPD GO	GSH1_LYCES	Glutamate--cysteine ligase, chloroplast precursor (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) ( ...	0.20	-	cyt	0	Plastid; chloroplast (By similarity)				523
Q9UI32 UniProt NPD GO	GLSL_HUMAN	Glutaminase liver isoform, mitochondrial precursor (EC 3.5.1.2) (GLS) (L-glutamine amidohydrolase) ( ...	0.20	-	nuc	0	Mitochondrion	mitochondrion [TAS]	606365		602
P10575 UniProt NPD GO	GLRX1_BOVIN	Glutaredoxin-1 (Thioltransferase) (TTase)	0.20	-	cyt	0	Cytoplasm				105
Q9NS18 UniProt NPD GO	GLRX2_HUMAN	Glutaredoxin-2, mitochondrial precursor	0.20	-	mit	0	Isoform 1: Mitochondrion. Isoform 2: Nucleus	mitochondrion [IDA] nucleus [IEP]	606820	2FLS	164
P56598 UniProt NPD GO	GST29_FASHE	Glutathione S-transferase 26 kDa 1 (EC 2.5.1.18) (GST1) (FH1) (GST class-mu)	0.20	-	cyt	0				2FHE	220
P16413 UniProt NPD GO	GSTMU_CAVPO	Glutathione S-transferase B (EC 2.5.1.18) (GST B) (GST class-mu)	0.20	-	cyt	0	Cytoplasm				217
Q9BEA9 UniProt NPD GO	GSTM3_MACFU	Glutathione S-transferase Mu 3 (EC 2.5.1.18) (GSTM3-3) (GST class-mu 3)	0.20	-	cyt	0	Cytoplasm (By similarity)				224
Q9TTY8 UniProt NPD GO	GSTP1_CAPHI	Glutathione S-transferase P (EC 2.5.1.18) (GST class-pi)	0.20	-	cyt	0					209
P20135 UniProt NPD GO	GSTT1_CHICK	Glutathione S-transferase theta-1 (EC 2.5.1.18) (GST-CL1) (GST class-theta)	0.20	-	cyt	0	Cytoplasm				260
P35668 UniProt NPD GO	GSHB_XENLA	Glutathione synthetase (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) (GSH-S)	0.20	-	cyt	0					474
P50440 UniProt NPD GO	GATM_HUMAN	Glycine amidinotransferase, mitochondrial precursor (EC 2.1.4.1) (L-arginine:glycine amidinotransfer ...	0.20	-	mit	0	Mitochondrion. Cytoplasm. The mitochondrial form is found in the intermembrane space probably attach ...	mitochondrial intermembrane space [IDA]	602360	9JDW	423
P20781 UniProt NPD GO	GLRB_RAT	Glycine receptor beta chain precursor (Glycine receptor 58 kDa subunit)	0.20	+	end	4	Membrane; multi-pass membrane protein			2FTS	496
P49840 UniProt NPD GO	GSK3A_HUMAN	Glycogen synthase kinase-3 alpha (EC 2.7.11.26) (GSK-3 alpha)	0.20	-	cyt	0			606784		483
P18265 UniProt NPD GO	GSK3A_RAT	Glycogen synthase kinase-3 alpha (EC 2.7.11.26) (GSK-3 alpha) (Factor A) (FA)	0.20	-	cyt	0					483
Q00310 UniProt NPD GO	KRE2_CANAL	Glycolipid 2-alpha-mannosyltransferase (EC 2.4.1.131) (Alpha-1,2-mannosyltransferase)	0.20	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				431
Q8TFN1 UniProt NPD GO	NMT_EMENI	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.20	-	cyt	0	Cytoplasm				492
Q9HD26 UniProt NPD GO	GOPC_HUMAN	Golgi-associated PDZ and coiled-coil motif-containing protein (PDZ protein interacting specifically ...	0.20	-	cyt	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. Golgi apparatus; trans-Golg ...	cytoplasm [ISS] Golgi apparatus [ISS] membrane fraction [ISS] plasma membrane [ISS]	606845		462
Q43847 UniProt NPD GO	SSY2_SOLTU	Granule-bound starch synthase 2, chloroplast precursor (EC 2.4.1.21) (Granule-bound starch synthase ...	0.20	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Soluble and granule-bound (By similarity)				767
O02708 UniProt NPD GO	CSF3_FELCA	Granulocyte colony-stimulating factor precursor (G-CSF) (Fragment)	0.20	-	cyt	0	Secreted protein				194
P28773 UniProt NPD GO	CSF2_SHEEP	Granulocyte-macrophage colony-stimulating factor precursor (GM-CSF) (Colony-stimulating factor) (CSF ...	0.20	-	exc	0	Secreted protein				144
P08884 UniProt NPD GO	GRAE_MOUSE	Granzyme E precursor (EC 3.4.21.-) (Cytotoxic cell protease 3) (CCP3) (CTL serine protease 2) (D12) ...	0.20	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes				248
Q9WVF6 UniProt NPD GO	PA2GD_MOUSE	Group IID secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GII ...	0.20	-	nuc	0	Isoform 1: Secreted protein (Potential). Isoform 2: Cytoplasm (Potential)				144
Q9BZM1 UniProt NPD GO	PG12A_HUMAN	Group XIIA secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GX ...	0.20	-	exc	0	Secreted protein	extracellular region [NAS]			189
Q28300 UniProt NPD GO	GNAT1_CANFA	Guanine nucleotide-binding protein G(t), alpha-1 subunit (Transducin alpha-1 chain)	0.20	-	gol	0					349
P20612 UniProt NPD GO	GNAT1_MOUSE	Guanine nucleotide-binding protein G(t), alpha-1 subunit (Transducin alpha-1 chain)	0.20	-	gol	0		heterotrimeric G-protein complex [TAS] membrane fraction [TAS]			349
Q08706 UniProt NPD GO	GBB_LYMST	Guanine nucleotide-binding protein subunit beta	0.20	-	cyt	0					341
Q9NDM2 UniProt NPD GO	GUTR1_DROME	Gustatory receptor trehalose 1 (Trehalose receptor 1)	0.20	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			392
P03991 UniProt NPD GO	HA1W_MOUSE	H-2 class I histocompatibility antigen, K-W28 alpha chain precursor	0.20	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			368
P14429 UniProt NPD GO	HA17_MOUSE	H-2 class I histocompatibility antigen, Q7 alpha chain precursor (QA-2 antigen)	0.20	-	exc	1	Membrane; single-pass type I membrane protein			1K8D	334
P30447 UniProt NPD GO	1A23_HUMAN	HLA class I histocompatibility antigen, A-23 alpha chain precursor (MHC class I antigen A*23) (A-9)	0.20	-	end	1	Membrane; single-pass type I membrane protein		142800		365
Q05944 UniProt NPD GO	HSP70_HYDMA	Heat shock 70 kDa protein	0.20	-	cyt	0					654
P29845 UniProt NPD GO	HSP7E_DROME	Heat shock 70 kDa protein cognate 5	0.20	-	mit	0					686
Q01899 UniProt NPD GO	HSP7M_PHAVU	Heat shock 70 kDa protein, mitochondrial precursor	0.20	-	mit	0	Mitochondrion				675
P91902 UniProt NPD GO	HSP70_CERCA	Heat shock protein 70 (HSP70)	0.20	-	cyt	0					638
Q5GFD5 UniProt NPD GO	OST6_MOUSE	Heparan sulfate glucosamine 3-O-sulfotransferase 6 (EC 2.8.2.23) (Heparan sulfate D-glucosaminyl 3-O ...	0.20	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				342
Q9MYY0 UniProt NPD GO	HPSE_BOVIN	Heparanase precursor (EC 3.2.-.-) [Contains: Heparanase 8 kDa subunit; Heparanase 50 kDa subunit]	0.20	-	exc	0	Lysosome; lysosomal membrane; peripheral membrane protein (By similarity). Secreted protein (By simi ...				545
Q64268 UniProt NPD GO	HEP2_RAT	Heparin cofactor 2 precursor (Heparin cofactor II) (HC-II) (Protease inhibitor leuserpin 2)	0.20	-	end	0					479

You are viewing entries 50651 to 50700 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.