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
P14528 UniProt NPD GO	GLB2_CALSO	Globin-2 (Globin II) (Hb II)	0.08	-	cyt	0					136
Q5ZLK4 UniProt NPD GO	GBGT1_CHICK	Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (EC 2.4.1.-) (Forssman glycolipid synthetase ...	0.08	-	mit	1 *					343
P09686 UniProt NPD GO	GLUC_MYOSC	Glucagon precursor [Contains: Glicentin-related polypeptide (GRPP); Glucagon; Glucagon-like peptide] ...	0.08	-	cyt	0	Secreted protein				96
P49426 UniProt NPD GO	EXG1_COCCA	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-beta 1,3 glucanase) (1,3-beta-D-glucanohydr ...	0.08	-	mit	0					788
P48828 UniProt NPD GO	G6PD_KLULA	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.08	-	cyt	0					497
P11412 UniProt NPD GO	G6PD_YEAST	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.08	-	cyt	0		cytoplasm [IDA]			504
Q25019 UniProt NPD GO	G6PD_HYACE	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD) (Zwischenferment) (Fragment)	0.08	-	cyt	0					153
P50309 UniProt NPD GO	G6PI_CRIGR	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.08	-	cyt	0	Cytoplasm (By similarity)				558
P42861 UniProt NPD GO	G6PI_LEIME	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.08	-	cyt	0	Cytoplasm			1T10	605
P54243 UniProt NPD GO	G6PI_OENME	Glucose-6-phosphate isomerase, cytosolic (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosph ...	0.08	-	cyt	0	Cytoplasm (By similarity)				568
Q9BDT0 UniProt NPD GO	GLCM_PANTR	Glucosylceramidase precursor (EC 3.2.1.45) (Beta-glucocerebrosidase) (Acid beta-glucosidase) (D-gluc ...	0.08	-	nuc	0	Lysosome; peripheral membrane protein				536
P04062 UniProt NPD GO	GLCM_HUMAN	Glucosylceramidase precursor (EC 3.2.1.45) (Beta-glucocerebrosidase) (Acid beta-glucosidase) (D-gluc ...	0.08	-	nuc	0	Lysosome; peripheral membrane protein		230800	2F61	536
Q04609 UniProt NPD GO	FOLH1_HUMAN	Glutamate carboxypeptidase 2 (EC 3.4.17.21) (Glutamate carboxypeptidase II) (Membrane glutamate carb ...	0.08	-	cyt	1 *	Cell membrane; single-pass type II membrane protein. Isoform PSMA': Cytoplasm	integral to plasma membrane [TAS] membrane [NAS] membrane fraction [TAS]	600934	2C6P	750
P43616 UniProt NPD GO	CPGL_YEAST	Glutamate carboxypeptidase-like protein YFR044C	0.08	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			481
P48320 UniProt NPD GO	DCE2_MOUSE	Glutamate decarboxylase 2 (EC 4.1.1.15) (Glutamate decarboxylase, 65 kDa isoform) (GAD-65) (65 kDa g ...	0.08	-	cyt	0	Cytoplasm; cytosol (By similarity). Cytoplasmic vesicle (By similarity). Associated to cytoplasmic v ...	axon [IDA] synapse [IDA]			585
P00368 UniProt NPD GO	DHE3_CHICK	Glutamate dehydrogenase 1, mitochondrial (EC 1.4.1.3) (GDH)	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix				503
P28492 UniProt NPD GO	GLSL_RAT	Glutaminase liver isoform, mitochondrial precursor (EC 3.5.1.2) (GLS) (L-glutamine amidohydrolase) ( ...	0.08	-	nuc	0	Mitochondrion	mitochondrial matrix [TAS]			602
P11600 UniProt NPD GO	GLNA_DUNSA	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (Fragment)	0.08	-	cyt	0	Cytoplasm (By similarity)				234
Q86ZF9 UniProt NPD GO	GLNA_NEUCR	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.08	-	cyt	0	Cytoplasm (By similarity)				362
O82560 UniProt NPD GO	GLNA2_SOYBN	Glutamine synthetase cytosolic isozyme 2 (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS1-2)	0.08	-	cyt	0	Cytoplasm				356
P08281 UniProt NPD GO	GLNA2_PEA	Glutamine synthetase leaf isozyme, chloroplast precursor (EC 6.3.1.2) (Glutamate--ammonia ligase) (C ...	0.08	-	mit	0	Plastid; chloroplast				430
P32289 UniProt NPD GO	GLNA_VIGAC	Glutamine synthetase nodule isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.08	-	cyt	0	Cytoplasm				356
P79764 UniProt NPD GO	GLRX1_CHICK	Glutaredoxin-1 (Thioltransferase-1) (TTase-1)	0.08	-	cyt	0	Cytoplasm				101
Q80Y14 UniProt NPD GO	GLRX5_MOUSE	Glutaredoxin-related protein 5	0.08	-	cyt	0		mitochondrion [IDA]			152
Q94999 UniProt NPD GO	GSTT1_ANOGA	Glutathione S-transferase 1-1 (EC 2.5.1.18) (GST class-theta)	0.08	-	nuc	0					209
P08515 UniProt NPD GO	GST26_SCHJA	Glutathione S-transferase 26 kDa (EC 2.5.1.18) (GST 26) (SJ26 antigen) (GST class-mu)	0.08	-	cyt	0				1Y6E	217
Q9N0V4 UniProt NPD GO	GSTM1_BOVIN	Glutathione S-transferase Mu 1 (EC 2.5.1.18) (GSTM1-1) (GST class-mu 1)	0.08	-	cyt	0	Cytoplasm (By similarity)				217
P14942 UniProt NPD GO	GSTA4_RAT	Glutathione S-transferase alpha-4 (EC 2.5.1.18) (Glutathione S-transferase Yk) (GST Yk) (GST 8-8) (G ...	0.08	-	cyt	0	Cytoplasm				222
Q4AEI2 UniProt NPD GO	GPX1_HYLLA	Glutathione peroxidase 1 (EC 1.11.1.9) (GSHPx-1) (GPx-1) (Cellular glutathione peroxidase)	0.08	-	mit	0	Cytoplasm (By similarity)				201
Q8MJ14 UniProt NPD GO	GPX1_PIG	Glutathione peroxidase 1 (EC 1.11.1.9) (GSHPx-1) (GPx-1) (Cellular glutathione peroxidase)	0.08	-	mit	0	Cytoplasm (By similarity)				206
P52033 UniProt NPD GO	GPXC_DIRIM	Glutathione peroxidase precursor (EC 1.11.1.9) (Di29)	0.08	-	mit	0	Secreted protein; extracellular space (By similarity)				221
Q6BPI1 UniProt NPD GO	GSHR_DEBHA	Glutathione reductase (EC 1.8.1.7) (GR) (GRase)	0.08	-	cyt	0	Cytoplasm (By similarity)				490
P48642 UniProt NPD GO	GSHRC_ORYSA	Glutathione reductase, cytosolic (EC 1.8.1.7) (GR) (GRase)	0.08	-	mit	0	Cytoplasm				496
P78417 UniProt NPD GO	GSTO1_HUMAN	Glutathione transferase omega-1 (EC 2.5.1.18) (GSTO 1-1)	0.08	-	cyt	0	Cytoplasm	cytoplasm [NAS]	605482	1EEM	241
Q6UGN0 UniProt NPD GO	GPD_TRIAT	Glycerol-3-phosphate dehydrogenase [NAD+] (EC 1.1.1.8)	0.08	-	cyt	0					427
Q6J5J3 UniProt NPD GO	GPD1_SACBA	Glycerol-3-phosphate dehydrogenase [NAD+] 1 (EC 1.1.1.8)	0.08	-	mit	0	Cytoplasm (Potential)				391
Q00055 UniProt NPD GO	GPD1_YEAST	Glycerol-3-phosphate dehydrogenase [NAD+] 1 (EC 1.1.1.8)	0.08	-	mit	0	Cytoplasm. Peroxisome	cytosol [IDA] peroxisome [IDA]			390
P41911 UniProt NPD GO	GPD2_YEAST	Glycerol-3-phosphate dehydrogenase [NAD+] 2, mitochondrial precursor (EC 1.1.1.8)	0.08	-	mit	0	Cytoplasm. Mitochondrion	cytosol [TAS] mitochondrion [IDA]			440
P57057 UniProt NPD GO	GLPT_HUMAN	Glycerol-3-phosphate transporter (G-3-P transporter) (G-3-P permease) (Solute carrier family 37 memb ...	0.08	-	end	12 *	Membrane; multi-pass membrane protein (Potential)		608094		533
P27869 UniProt NPD GO	G25L_CANFA	Glycoprotein 25L precursor (GP25L)	0.08	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				215
Q9D2R4 UniProt NPD GO	G25L_MOUSE	Glycoprotein 25L precursor (GP25L)	0.08	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				215
Q8WMW8 UniProt NPD GO	GLHA_CAPHI	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.08	-	exc	1 *	Secreted protein				120
Q8WMR3 UniProt NPD GO	GLHA_CERNI	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.08	-	exc	1 *	Secreted protein				120
Q39659 UniProt NPD GO	MFPA_CUCSA	Glyoxysomal fatty acid beta-oxidation multifunctional protein MFP-a [Includes: Enoyl-CoA hydratase ( ...	0.08	-	cyt	0	Glyoxysome	glyoxysome [NAS]			725
Q9YGH2 UniProt NPD GO	GTHB2_CLUPA	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.08	-	exc	0	Secreted protein				149
Q98849 UniProt NPD GO	GTHB2_CARAU	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta) (Luteinizing hormon ...	0.08	-	exc	1 *	Secreted protein				140
Q8C0K5 UniProt NPD GO	GDC_MOUSE	Grave disease carrier protein homolog (GDC) (Mitochondrial solute carrier protein homolog) (Solute c ...	0.08	-	exc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrion [IDA]			332
P35358 UniProt NPD GO	OPSG_GECGE	Green-sensitive opsin P521 (Green photoreceptor pigment)	0.08	-	end	7	Membrane; multi-pass membrane protein				365
Q9QUL3 UniProt NPD GO	PA2GE_MOUSE	Group IIE secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GII ...	0.08	-	exc	1 *	Secreted protein				142
O46677 UniProt NPD GO	GROB_BOVIN	Growth-regulated protein homolog beta precursor (GRO-beta)	0.08	-	nuc	0	Secreted protein				104

You are viewing entries 68101 to 68150 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.