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
P52395 UniProt NPD GO	E13B_SOYBN	Glucan endo-1,3-beta-glucosidase (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase) ((1->3)-beta-gluca ...	0.09	-	cyt	0					255
P52409 UniProt NPD GO	E13B_WHEAT	Glucan endo-1,3-beta-glucosidase precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase) ((1->3)- ...	0.09	-	exc	0					461
Q75KH3 UniProt NPD GO	GRDH_ORYSA	Glucose and ribitol dehydrogenase homolog (EC 1.1.1.-)	0.09	-	cyt	0					300
P55239 UniProt NPD GO	GLGL2_HORVU	Glucose-1-phosphate adenylyltransferase large subunit 2 (EC 2.7.7.27) (ADP-glucose synthase) (ADP-gl ...	0.09	-	cyt	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				181
P55233 UniProt NPD GO	GLGL1_BETVU	Glucose-1-phosphate adenylyltransferase large subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.09	-	cyt	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				522
P08059 UniProt NPD GO	G6PI_PIG	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.09	-	cyt	0	Cytoplasm			1GZV	557
Q8VHN2 UniProt NPD GO	NMD3B_RAT	Glutamate [NMDA] receptor subunit 3B precursor (N-methyl-D-aspartate receptor subtype 3B) (NR3B) (NM ...	0.09	-	end	4	Cell membrane; multi-pass membrane protein (By similarity). Requires the presence of GRIN1 to be tar ...				1002
O77564 UniProt NPD GO	FOLH1_PIG	Glutamate carboxypeptidase 2 (EC 3.4.17.21) (Glutamate carboxypeptidase II) (Membrane glutamate carb ...	0.09	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity)				751
Q9P6I2 UniProt NPD GO	CPGL_SCHPO	Glutamate carboxypeptidase-like protein	0.09	-	cyt	0					474
Q4PRC2 UniProt NPD GO	DCE2_CANFA	Glutamate decarboxylase 2 (EC 4.1.1.15) (Glutamate decarboxylase, 65 kDa isoform) (GAD-65) (65 kDa g ...	0.09	-	cyt	0	Cytoplasm; cytosol (By similarity). Cytoplasmic vesicle (By similarity). Associated to cytoplasmic v ...				585
Q05329 UniProt NPD GO	DCE2_HUMAN	Glutamate decarboxylase 2 (EC 4.1.1.15) (Glutamate decarboxylase, 65 kDa isoform) (GAD-65) (65 kDa g ...	0.09	-	cyt	0	Cytoplasm; cytosol. Cytoplasmic vesicle. Associated to cytoplasmic vesicles. In neurons, cytosolic l ...		138275	1ES0	585
Q05683 UniProt NPD GO	DCE2_RAT	Glutamate decarboxylase 2 (EC 4.1.1.15) (Glutamate decarboxylase, 65 kDa isoform) (GAD-65) (65 kDa g ...	0.09	-	cyt	0	Cytoplasm; cytosol (By similarity). Cytoplasmic vesicle (By similarity). Associated to cytoplasmic v ...				585
P26443 UniProt NPD GO	DHE3_MOUSE	Glutamate dehydrogenase 1, mitochondrial precursor (EC 1.4.1.3) (GDH)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			558
Q9C5V5 UniProt NPD GO	GLR28_ARATH	Glutamate receptor 2.8 precursor (Ligand-gated ion channel 2.8)	0.09	-	end	3 *	Membrane; multi-pass membrane protein				947
P46309 UniProt NPD GO	GSH1_ARATH	Glutamate--cysteine ligase, chloroplast precursor (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) ( ...	0.09	-	cyt	0	Plastid; chloroplast (Probable)				522
O23736 UniProt NPD GO	GSH1_BRAJU	Glutamate--cysteine ligase, chloroplast precursor (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) ( ...	0.09	-	cyt	0	Plastid; chloroplast (By similarity)			2GWD	514
P31593 UniProt NPD GO	GSA_TOBAC	Glutamate-1-semialdehyde 2,1-aminomutase, chloroplast precursor (EC 5.4.3.8) (GSA) (Glutamate-1-semi ...	0.09	-	mit	0	Plastid; chloroplast				478
Q43127 UniProt NPD GO	GLNA2_ARATH	Glutamine synthetase, chloroplast/mitochondrial precursor (EC 6.3.1.2) (Glutamate--ammonia ligase) ( ...	0.09	-	mit	0	Plastid; chloroplast. Mitochondrion				430
P08263 UniProt NPD GO	GSTA1_HUMAN	Glutathione S-transferase A1 (EC 2.5.1.18) (GTH1) (HA subunit 1) (GST-epsilon) (GSTA1-1) (GST class- ...	0.09	-	cyt	0	Cytoplasm	cytoplasm [NAS]	138359	1YDK	221
P09488 UniProt NPD GO	GSTM1_HUMAN	Glutathione S-transferase Mu 1 (EC 2.5.1.18) (GSTM1-1) (GST class-mu 1) (GSTM1a-1a) (GSTM1b-1b) (HB ...	0.09	-	cyt	0	Cytoplasm		138350	2F3M	217
Q28514 UniProt NPD GO	GSTP1_MACMU	Glutathione S-transferase P (EC 2.5.1.18) (GST class-pi)	0.09	-	cyt	0				1LX2	209
Q5R8R5 UniProt NPD GO	GSTP1_PONPY	Glutathione S-transferase P (EC 2.5.1.18) (GST class-pi)	0.09	-	cyt	0					209
P51781 UniProt NPD GO	GSTA1_PIG	Glutathione S-transferase alpha M14 (EC 2.5.1.18) (GST class-alpha)	0.09	-	cyt	0	Cytoplasm (By similarity)				221
Q96SL4 UniProt NPD GO	GPX7_HUMAN	Glutathione peroxidase 7 precursor (EC 1.11.1.9) (CL683)	0.09	-	exc	0	Secreted protein (Potential)				187
P35669 UniProt NPD GO	GSHB_SCHPO	Glutathione synthetase large chain (EC 6.3.2.3) (Glutathione synthase large chain) (GSH synthetase l ...	0.09	-	cyt	0					498
Q9JHF7 UniProt NPD GO	PTGD2_MOUSE	Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) (Glutathione-dependent PGD synthetase) ...	0.09	-	cyt	0	Cytoplasm				198
O35543 UniProt NPD GO	PTGD2_RAT	Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) (Glutathione-dependent PGD synthetase) ...	0.09	-	cyt	0	Cytoplasm			1PD2	198
P29834 UniProt NPD GO	GRP2_ORYSA	Glycine-rich cell wall structural protein 2 precursor	0.09	-	vac	1 *	Cell wall (Potential)				185
P84064 UniProt NPD GO	GRP1_CUCME	Glycine-rich protein GWK precursor [Contains: Glycine-rich protein GWK isoform 1; Glycine-rich prote ...	0.09	+	cyt	0		striated muscle thin filament [NAS]			36
Q96T91 UniProt NPD GO	GPHA2_HUMAN	Glycoprotein hormone alpha-2 precursor (Thyrostimulin subunit alpha)	0.09	-	exc	0	Secreted protein	extracellular region [IDA]	609651		129
P01217 UniProt NPD GO	GLHA_BOVIN	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.09	-	exc	1 *	Secreted protein				120
Q9GL36 UniProt NPD GO	GLHA_BUBBU	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.09	-	exc	1 *	Secreted protein				120
P68242 UniProt NPD GO	GLHA_COTJA	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.09	-	exc	1 *	Secreted protein				120
P68241 UniProt NPD GO	GLHA_MELGA	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.09	-	exc	1 *	Secreted protein				120
Q9BEH3 UniProt NPD GO	GLHA_MACFA	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.09	-	exc	1 *	Secreted protein				120
P47744 UniProt NPD GO	GLHA_FUNHE	Glycoprotein hormones alpha chain precursor (Gonadotropin alpha chain) (GTH-alpha)	0.09	-	exc	1 *	Secreted protein				125
Q6BHK4 UniProt NPD GO	GPI11_DEBHA	Glycosylphosphatidylinositol anchor biosynthesis protein 11	0.09	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				236
P01235 UniProt NPD GO	GTHB2_CYPCA	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta) (Luteinizing hormon ...	0.09	-	exc	1 *	Secreted protein				144
O42329 UniProt NPD GO	GNRR2_CLAGA	Gonadotropin-releasing hormone II receptor (Type II GnRH receptor) (GnRH-II-R)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				379
Q60481 UniProt NPD GO	CSF2_CAVPO	Granulocyte-macrophage colony-stimulating factor precursor (GM-CSF) (Colony-stimulating factor) (CSF ...	0.09	-	vac	0	Secreted protein				140
Q01888 UniProt NPD GO	GDC_BOVIN	Grave disease carrier protein (GDC) (Mitochondrial solute carrier protein homolog) (Solute carrier f ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				330
P16261 UniProt NPD GO	GDC_RAT	Grave disease carrier protein (GDC) (Mitochondrial solute carrier protein homolog) (Solute carrier f ...	0.09	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				322
Q3ZBN6 UniProt NPD GO	GA45A_BOVIN	Growth arrest and DNA-damage-inducible protein GADD45 alpha	0.09	-	cyt	0					165
P24522 UniProt NPD GO	GA45A_HUMAN	Growth arrest and DNA-damage-inducible protein GADD45 alpha (DNA-damage-inducible transcript 1) (DDI ...	0.09	-	cyt	0		nucleus [TAS]	126335		165
Q5E9A5 UniProt NPD GO	GA45B_BOVIN	Growth arrest and DNA-damage-inducible protein GADD45 beta	0.09	-	cyt	0					160
Q92847 UniProt NPD GO	GHSR_HUMAN	Growth hormone secretagogue receptor type 1 (GHS-R) (GH-releasing peptide receptor) (GHRP) (Ghrelin ...	0.09	-	end	7 *	Membrane; multi-pass membrane protein	cell surface [TAS] integral to membrane [TAS] plasma membrane [TAS]	601898		366
Q5RA81 UniProt NPD GO	GRPE1_PONPY	GrpE protein homolog 1, mitochondrial precursor (Mt-GrpE#1)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				217
Q9HAV7 UniProt NPD GO	GRPE1_HUMAN	GrpE protein homolog 1, mitochondrial precursor (Mt-GrpE#1) (HMGE)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]	606173		217
Q9WTT6 UniProt NPD GO	GUAD_RAT	Guanine deaminase (EC 3.5.4.3) (Guanase) (Guanine aminase) (Guanine aminohydrolase) (GAH)	0.09	-	mit	0					454
O43057 UniProt NPD GO	MSS4_SCHPO	Guanine nucleotide exchange factor MSS4 homolog	0.09	-	nuc	0					100

You are viewing entries 66201 to 66250 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.