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
P13020 UniProt NPD GO	GELS_MOUSE	Gelsolin precursor (Actin-depolymerizing factor) (ADF) (Brevin)	0.10	-	exc	0	Isoform 2: Cytoplasm. Isoform 1: Secreted protein	actin cytoskeleton [ISS] cytosol [ISS] extracellular region [ISS] lamellipodium [IDA]		1NPH	780
Q43133 UniProt NPD GO	GGPPS_SINAL	Geranylgeranyl pyrophosphate synthetase, chloroplast precursor (GGPP synthetase) (GGPS) [Includes: D ...	0.10	-	mit	0	Plastid; chloroplast; chloroplast stroma (Probable). Plastid; chromoplast (Probable)				366
Q39103 UniProt NPD GO	G3OX1_ARATH	Gibberellin 3-beta-dioxygenase 1 (EC 1.14.11.15) (Gibberellin 3 beta-hydroxylase 1) (GA 3-oxidase 1) ...	0.10	-	mit	0		cytoplasm [TAS]			358
P81026 UniProt NPD GO	GLUC1_ORENI	Glucagon-1 (Glucagon I)	0.10	-	nuc	0	Secreted protein				36
P23776 UniProt NPD GO	EXG1_YEAST	Glucan 1,3-beta-glucosidase I/II precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase I/II) (Soluble cell ...	0.10	-	exc	0	Cell wall. Secreted protein	cell wall (sensu Fungi) [IDA]		1H4P	448
P52397 UniProt NPD GO	E13J_TOBAC	Glucan endo-1,3-beta-glucosidase, acidic isoform PR-O (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolas ...	0.10	-	cyt	0	Secreted protein; extracellular space				160
P36914 UniProt NPD GO	AMYG_ASPOR	Glucoamylase precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrolas ...	0.10	-	nuc	0					612
P17712 UniProt NPD GO	HXK4_RAT	Glucokinase (EC 2.7.1.2) (Hexokinase-4) (Hexokinase type IV) (HK IV) (HK4) (Hexokinase-D)	0.10	-	cyt	0					465
Q6BUZ2 UniProt NPD GO	GNT1_DEBHA	Glucose N-acetyltransferase 1 (EC 2.4.1.-) (N-acetylglucosaminyltransferase)	0.10	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity). Vacuole; vacu ...				464
P53403 UniProt NPD GO	GTR3_DROME	Glucose transporter type 3 (Glucose transporter-like protein)	0.10	-	end	10	Membrane; multi-pass membrane protein				507
Q24625 UniProt NPD GO	G6PD_DROSI	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD) (Zwischenferment) (Fragment)	0.10	-	cyt	0					153
Q5R4E3 UniProt NPD GO	G6PI_PONPY	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.10	-	cyt	0	Cytoplasm (By similarity)				557
Q91ZU9 UniProt NPD GO	NMD3B_MOUSE	Glutamate [NMDA] receptor subunit 3B precursor (N-methyl-D-aspartate receptor subunit NR3B) (NR3B) ( ...	0.10	-	end	4	Cell membrane; multi-pass membrane protein. Requires the presence of GRIN1 to be targeted at the pla ...	cell soma [IDA] N-methyl-D-aspartate selective glutamate re... [IMP]			1003
P48321 UniProt NPD GO	DCE2_PIG	Glutamate decarboxylase 2 (EC 4.1.1.15) (Glutamate decarboxylase, 65 kDa isoform) (GAD-65) (65 kDa g ...	0.10	-	cyt	0	Cytoplasm; cytosol (By similarity). Cytoplasmic vesicle (By similarity). Associated to cytoplasmic v ...				585
Q64I00 UniProt NPD GO	DHE4_PONPY	Glutamate dehydrogenase 2, mitochondrial precursor (EC 1.4.1.3) (GDH)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				558
O04660 UniProt NPD GO	GLR21_ARATH	Glutamate receptor 2.1 precursor (Ligand-gated ion channel 2.1) (AtGLR3)	0.10	-	end	4 *	Membrane; multi-pass membrane protein				901
Q91755 UniProt NPD GO	GRIK2_XENLA	Glutamate receptor, ionotropic kainate 2 (Glutamate receptor 6) (GluR-6) (GluR6) (Fragment)	0.10	-	mit	2 *	Membrane; multi-pass membrane protein				285
P42799 UniProt NPD GO	GSA1_ARATH	Glutamate-1-semialdehyde 2,1-aminomutase 1, chloroplast precursor (EC 5.4.3.8) (GSA 1) (Glutamate-1- ...	0.10	-	mit	0	Plastid; chloroplast				474
Q810D6 UniProt NPD GO	GRWD1_MOUSE	Glutamate-rich WD repeat-containing protein 1 (Protein A301)	0.10	-	cyt	0	Nucleus; nucleolus (By similarity)				446
Q571F8 UniProt NPD GO	GLSL_MOUSE	Glutaminase liver isoform, mitochondrial precursor (EC 3.5.1.2) (GLS) (L-glutamine amidohydrolase) ( ...	0.10	-	nuc	0	Mitochondrion (By similarity)				602
P00965 UniProt NPD GO	GLNA3_PHAVU	Glutamine synthetase N-1 (EC 6.3.1.2) (Gln isozyme gamma) (Glutamate--ammonia ligase)	0.10	-	cyt	0	Cytoplasm				356
Q9XQ94 UniProt NPD GO	GLNA2_MEDSA	Glutamine synthetase leaf isozyme, chloroplast precursor (EC 6.3.1.2) (Glutamate--ammonia ligase) (C ...	0.10	-	mit	0	Plastid; chloroplast				428
O22506 UniProt NPD GO	GLNA2_DAUCA	Glutamine synthetase, chloroplast precursor (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS2)	0.10	-	cyt	0	Plastid; chloroplast (By similarity)				432
P35661 UniProt NPD GO	GST27_SCHMA	Glutathione S-transferase 26 kDa (EC 2.5.1.18) (GST 26) (SM26/2 antigen) (GST class-mu)	0.10	-	cyt	0					218
P24472 UniProt NPD GO	GSTA4_MOUSE	Glutathione S-transferase 5.7 (EC 2.5.1.18) (GST 5.7) (GST class-alpha) (GST A4-4) (GSTA4-4)	0.10	-	cyt	0	Cytoplasm			1GUK	222
P10648 UniProt NPD GO	GSTA2_MOUSE	Glutathione S-transferase GT41A (EC 2.5.1.18) (GST class-alpha)	0.10	-	nuc	0				1ML6	221
Q9TSM5 UniProt NPD GO	GSTM1_MACFA	Glutathione S-transferase Mu 1 (EC 2.5.1.18) (GSTM1-1) (GST class-mu 1)	0.10	-	cyt	0	Cytoplasm (By similarity)				217
Q03013 UniProt NPD GO	GSTM4_HUMAN	Glutathione S-transferase Mu 4 (EC 2.5.1.18) (GSTM4-4) (GST class-mu 4) (GTS-Mu2)	0.10	-	cyt	0	Cytoplasm		138333	4GTU	217
P81942 UniProt NPD GO	GSTP1_BUFBU	Glutathione S-transferase P 1 (EC 2.5.1.18) (BBGSTP1-1) (GST class-pi)	0.10	-	cyt	0					210
Q01579 UniProt NPD GO	GSTT1_RAT	Glutathione S-transferase theta-1 (EC 2.5.1.18) (GST class-theta-1) (Glutathione S-transferase 5) (G ...	0.10	-	mit	0	Cytoplasm				239
Q8K2Q2 UniProt NPD GO	GSTO2_MOUSE	Glutathione transferase omega-2 (EC 2.5.1.18)	0.10	-	cyt	0					248
Q9NJP9 UniProt NPD GO	GLPK_TRYBB	Glycerol kinase, glycosomal (EC 2.7.1.30) (ATP:glycerol 3-phosphotransferase) (Glycerokinase) (GK)	0.10	-	pox	0	Glycosome	glycosome [NAS]			512
Q9CAY3 UniProt NPD GO	GPAT5_ARATH	Glycerol-3-phosphate acyltransferase 5 (EC 2.3.1.15) (AtGPAT5)	0.10	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				502
P50441 UniProt NPD GO	GATM_PIG	Glycine amidinotransferase (EC 2.1.4.1) (L-arginine:glycine amidinotransferase) (Transamidinase) (AT ...	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane				386
Q99070 UniProt NPD GO	GRP2_SORBI	Glycine-rich RNA-binding protein 2	0.10	+	cyt	0					168
P25074 UniProt NPD GO	GRP1_ORYSA	Glycine-rich cell wall structural protein 1 precursor	0.10	-	exc	0	Cell wall (Potential)				166
Q7Z2C4 UniProt NPD GO	SELG_DROME	Glycine-rich selenoprotein (G-rich selenoprotein) (dSelG)	0.10	-	cyt	1 *					110
P22146 UniProt NPD GO	GAS1_YEAST	Glycolipid-anchored surface protein 1 precursor (Glycoprotein GP115)	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	cell wall (sensu Fungi) [IDA] mitochondrion [IDA] plasma membrane [IDA]			559
P25329 UniProt NPD GO	GLHA_PHYCA	Glycoprotein hormones alpha chain (Anterior pituitary glycoprotein hormones common subunit alpha) (F ...	0.10	-	mit	0	Secreted protein				96
Q9JK68 UniProt NPD GO	GLHA_CAVPO	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.10	-	exc	0	Secreted protein				120
P01215 UniProt NPD GO	GLHA_HUMAN	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.10	-	exc	0	Secreted protein	soluble fraction [TAS]	118850	1XWD	116
Q91119 UniProt NPD GO	GLHA_MORSA	Glycoprotein hormones alpha chain precursor (Gonadotropin alpha chain) (GTH-alpha)	0.10	-	exc	0	Secreted protein				117
Q5AFT2 UniProt NPD GO	GPI11_CANAL	Glycosylphosphatidylinositol anchor biosynthesis protein 11	0.10	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				265
Q6C7G2 UniProt NPD GO	NMT_YARLI	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.10	-	cyt	0	Cytoplasm (By similarity)				443
P37038 UniProt NPD GO	GTHB2_HYPMO	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta) (Luteinizing hormon ...	0.10	-	exc	1 *	Secreted protein				141
Q95MG6 UniProt NPD GO	GNRR2_CALJA	Gonadotropin-releasing hormone II receptor (Type II GnRH receptor) (GnRH-II-R)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				380
P01587 UniProt NPD GO	CSF2_MOUSE	Granulocyte-macrophage colony-stimulating factor precursor (GM-CSF) (Colony-stimulating factor) (CSF ...	0.10	-	mit	0	Secreted protein				141
P08882 UniProt NPD GO	GRAC_MOUSE	Granzyme C precursor (EC 3.4.21.-) (Cytotoxic cell protease 2) (CCP2) (B10)	0.10	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes				248
Q07883 UniProt NPD GO	GRB2_CHICK	Growth factor receptor-bound protein 2 (Adapter protein GRB2) (SH2/SH3 adapter GRB2)	0.10	-	cyt	0					217
P50153 UniProt NPD GO	GBG4_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-4 subunit precursor	0.10	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				75

You are viewing entries 64401 to 64450 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.