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
Q4W9R7 UniProt NPD GO	MCD4_ASPFU	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-) (AfpigN)	0.14	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				1032
Q07830 UniProt NPD GO	GPI13_YEAST	GPI ethanolamine phosphate transferase 3 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.14	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				1017
Q8TEQ8 UniProt NPD GO	PIGO_HUMAN	GPI ethanolamine phosphate transferase 3 (EC 2.-.-.-) (Phosphatidylinositol-glycan biosynthesis clas ...	0.14	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS]			1089
Q7S4Z3 UniProt NPD GO	GPI14_NEUCR	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.14	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				487
Q9VZM5 UniProt NPD GO	PIGB_DROME	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III)	0.14	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				561
P70552 UniProt NPD GO	GFRP_RAT	GTP cyclohydrolase 1 feedback regulatory protein (GTP cyclohydrolase I feedback regulatory protein) ...	0.14	-	cyt	0				1WPL	83
P32835 UniProt NPD GO	GSP1_YEAST	GTP-binding nuclear protein GSP1/CNR1	0.14	+	cyt	0	Nucleus	cytoplasm [TAS] nucleus [IDA]			219
P42558 UniProt NPD GO	RAN_CHICK	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.14	+	cyt	0	Nucleus				216
P39110 UniProt NPD GO	CIN4_YEAST	GTP-binding protein CIN4 (Chromosome instability protein 4)	0.14	-	nuc	0		cytoplasm [IDA]			191
O94655 UniProt NPD GO	YPT7_SCHPO	GTP-binding protein ypt7	0.14	-	cyt	0	Vacuole (By similarity)				205
P29411 UniProt NPD GO	KAD3_RAT	GTP:AMP phosphotransferase mitochondrial (EC 2.7.4.10) (Adenylate kinase 3) (AK3) (Adenylate kinase ...	0.14	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [ISS]			226
P20171 UniProt NPD GO	RASH_RAT	GTPase HRas precursor (Transforming protein p21) (p21ras) (H-Ras-1) (c-H-ras)	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				189
P32883 UniProt NPD GO	RASK_MOUSE	GTPase KRas (K-Ras 2) (Ki-Ras) (c-K-ras) (c-Ki-ras)	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side	membrane fraction [IDA]			189
P08644 UniProt NPD GO	RASK_RAT	GTPase KRas (K-Ras 2) (Ki-Ras) (c-K-ras) (c-Ki-ras)	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side				189
Q91806 UniProt NPD GO	RASN_XENLA	GTPase NRas precursor (Transforming protein N-Ras)	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				189
Q8WWP7 UniProt NPD GO	GIMA1_HUMAN	GTPase, IMAP family member 1 (Immunity-associated protein 1) (hIMAP1)	0.14	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein		608084		306
O02791 UniProt NPD GO	GALC_MACMU	Galactocerebrosidase precursor (EC 3.2.1.46) (GALCERase) (Galactosylceramidase) (Galactosylceramide ...	0.14	-	exc	1 *	Lysosome (By similarity)				669
P04387 UniProt NPD GO	GAL80_YEAST	Galactose/lactose metabolism regulatory protein GAL80	0.14	-	mit	0		cytoplasm [IDA] nucleus [IDA]			435
Q9CQW5 UniProt NPD GO	LEG2_MOUSE	Galectin-2	0.14	-	nuc	0					130
P18505 UniProt NPD GO	GBRB1_HUMAN	Gamma-aminobutyric-acid receptor beta-1 subunit precursor (GABA(A) receptor)	0.14	-	mit	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137190		474
Q9UJ14 UniProt NPD GO	GGT4_HUMAN	Gamma-glutamyltransferase 4 precursor (EC 2.3.2.2) (Gamma-glutamyltranspeptidase 4) (Gamma-glutamylt ...	0.14	-	end	1	Membrane; single-pass type II membrane protein (By similarity)				666
P19440 UniProt NPD GO	GGT1_HUMAN	Gamma-glutamyltranspeptidase 1 precursor (EC 2.3.2.2) (Gamma-glutamyltransferase 1) (GGT 1) (CD224 a ...	0.14	-	end	3 *	Membrane; single-pass type II membrane protein	membrane [NAS]	231950		569
P30796 UniProt NPD GO	GASR_PRANA	Gastrin/cholecystokinin type B receptor (CCK-B receptor) (CCK-BR) (Cholecystokinin-2 receptor) (CCK2 ...	0.14	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS] plasma membrane [ISS]			450
P18729 UniProt NPD GO	ZG57_XENLA	Gastrula zinc finger protein XLCGF57.1 (Fragment)	0.14	-	nuc	0	Nucleus (Potential)				336
Q9V8Y9 UniProt NPD GO	OB56H_DROME	General odorant-binding protein 56h precursor	0.14	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			134
Q9ZT84 UniProt NPD GO	G3OX2_ARATH	Gibberellin 3-beta-dioxygenase 2 (EC 1.14.11.15) (Gibberellin 3 beta-hydroxylase 2) (GA 3-oxidase 2) ...	0.14	-	cyt	0					347
Q56JZ9 UniProt NPD GO	GMFG_BOVIN	Glia maturation factor gamma (GMF-gamma)	0.14	+	cyt	0					142
Q80T18 UniProt NPD GO	GMFG_RAT	Glia maturation factor gamma (GMF-gamma)	0.14	+	cyt	0					142
Q9Z0W0 UniProt NPD GO	GLP2R_RAT	Glucagon-like peptide 2 receptor precursor (GLP-2 receptor) (GLP-2-R) (GLP-2R)	0.14	-	end	5	Membrane; multi-pass membrane protein				550
Q876J3 UniProt NPD GO	EXG_SACBA	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.14	-	exc	0	Secreted protein (Potential)				448
P52407 UniProt NPD GO	E13B_HEVBR	Glucan endo-1,3-beta-glucosidase, basic vacuolar isoform precursor (EC 3.2.1.39) ((1->3)-beta-glucan ...	0.14	-	exc	0	Vacuole (Potential)				374
P26989 UniProt NPD GO	AMYH_SACFI	Glucoamylase GLA1 precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohyd ...	0.14	-	exc	0					519
P69327 UniProt NPD GO	AMYG_ASPAW	Glucoamylase precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrolas ...	0.14	-	exc	0				3GLY	640
P69328 UniProt NPD GO	AMYG_ASPNG	Glucoamylase precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrolas ...	0.14	-	exc	0				1KUM	640
P35557 UniProt NPD GO	HXK4_HUMAN	Glucokinase (EC 2.7.1.2) (Hexokinase-4) (Hexokinase type IV) (HK IV) (HK4) (Hexokinase-D)	0.14	+	cyt	0			125851	1V4T	465
P55234 UniProt NPD GO	GLGL2_MAIZE	Glucose-1-phosphate adenylyltransferase large subunit 2, chloroplast precursor (EC 2.7.7.27) (ADP-gl ...	0.14	-	cyt	0	Plastid; chloroplast (By similarity). Found in the chloroplast in leaf. Plastid; amyloplast (By simi ...				521
P11413 UniProt NPD GO	G6PD_HUMAN	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.14	-	cyt	0			305900	1QKI	514
Q5WN23 UniProt NPD GO	GCP2_CAEBR	Glutamate carboxypeptidase 2 homolog (EC 3.4.17.21) (Glutamate carboxypeptidase II homolog)	0.14	-	nuc	1 *	Membrane; single-pass type II membrane protein	integral to membrane [ISS]			770
Q8LGN0 UniProt NPD GO	GLR27_ARATH	Glutamate receptor 2.7 precursor (Ligand-gated ion channel 2.7)	0.14	-	end	4 *	Membrane; multi-pass membrane protein				949
P42260 UniProt NPD GO	GRIK2_RAT	Glutamate receptor, ionotropic kainate 2 precursor (Glutamate receptor 6) (GluR-6) (GluR6)	0.14	-	end	3 *	Membrane; multi-pass membrane protein	plasma membrane [IMP]		1YAE	908
P39087 UniProt NPD GO	GRIK2_MOUSE	Glutamate receptor, ionotropic kainate 2 precursor (Glutamate receptor 6) (GluR-6) (GluR6) (Glutamat ...	0.14	-	end	3 *	Membrane; multi-pass membrane protein	ionotropic glutamate receptor complex [IC]			889
P16580 UniProt NPD GO	GLNA_CHICK	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.14	-	cyt	0	Cytoplasm				373
P15105 UniProt NPD GO	GLNA_MOUSE	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.14	-	cyt	0	Cytoplasm	mitochondrion [IDA]			372
P49295 UniProt NPD GO	HEM12_CUCSA	Glutamyl-tRNA reductase 2, chloroplast precursor (EC 1.2.1.70) (GluTR)	0.14	-	cyt	0	Plastid; chloroplast (By similarity)				542
P81140 UniProt NPD GO	GCDH_PIG	Glutaryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.7) (GCD) (Fragment)	0.14	-	nuc	0	Mitochondrion; mitochondrial matrix				408
P28338 UniProt NPD GO	GSTT1_MUSDO	Glutathione S-transferase 1 (EC 2.5.1.18) (GST class-theta)	0.14	-	cyt	0					208
P20432 UniProt NPD GO	GSTT1_DROME	Glutathione S-transferase 1-1 (EC 2.5.1.18) (GST class-theta)	0.14	-	cyt	0					209
P67804 UniProt NPD GO	GSTT1_DROMA	Glutathione S-transferase 1-1 (EC 2.5.1.18) (GST class-theta) (Fragment)	0.14	-	mit	0					200
P67805 UniProt NPD GO	GSTT1_DROSI	Glutathione S-transferase 1-1 (EC 2.5.1.18) (GST class-theta) (Fragment)	0.14	-	mit	0					200
P30107 UniProt NPD GO	GSTT1_DROTE	Glutathione S-transferase 1-1 (EC 2.5.1.18) (GST class-theta) (Fragment)	0.14	-	mit	0					200

You are viewing entries 58351 to 58400 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.