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
Q7M416 UniProt NPD GO	GLB1_LIOJA	Globin-1 (Myoglobin I)	0.01	-	cyt	0					145
P80721 UniProt NPD GO	GLB_PAREP	Globin-3 (Myoglobin)	0.01	-	cyt	0				1KFR	147
Q27302 UniProt NPD GO	GLBH_CAEBR	Globin-like protein	0.01	-	cyt	0	Cytoplasm (Potential)				160
Q9URU6 UniProt NPD GO	EXG1_SCHPO	Glucan 1,3-beta-glucosidase 1 precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.01	-	nuc	0	Secreted protein (Potential)				407
Q12700 UniProt NPD GO	EXG_DEBOC	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.01	-	exc	0	Secreted protein (Potential)				425
Q12725 UniProt NPD GO	EXG_YARLI	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.01	-	vac	0	Secreted protein (By similarity)				421
P34742 UniProt NPD GO	E13A_HORVU	Glucan endo-1,3-beta-glucosidase GI (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase GI) ((1->3)-beta ...	0.01	-	cyt	0					310
Q02437 UniProt NPD GO	E13D_HORVU	Glucan endo-1,3-beta-glucosidase GIV (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase GIV) ((1->3)-be ...	0.01	-	cyt	0	Vacuole (Probable)				327
P52401 UniProt NPD GO	E132_SOLTU	Glucan endo-1,3-beta-glucosidase, basic isoform 2 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohy ...	0.01	-	cyt	1 *	Vacuole (By similarity)				363
O93806 UniProt NPD GO	GNA1_CANAL	Glucosamine 6-phosphate N-acetyltransferase (EC 2.3.1.4) (Phosphoglucosamine transacetylase) (Phosph ...	0.01	-	nuc	0					149
P46926 UniProt NPD GO	GNPI_HUMAN	Glucosamine-6-phosphate isomerase (EC 3.5.99.6) (Glucosamine-6-phosphate deaminase) (GNPDA) (GlcN6P ...	0.01	-	cyt	0	Cytoplasm (By similarity)		601798	1NE7	289
Q5R8T8 UniProt NPD GO	GNPI_PONPY	Glucosamine-6-phosphate isomerase (EC 3.5.99.6) (Glucosamine-6-phosphate deaminase) (GNPDA) (GlcN6P ...	0.01	-	cyt	0	Cytoplasm (By similarity)				289
Q5KTS5 UniProt NPD GO	GRDH_DAUCA	Glucose and ribitol dehydrogenase (EC 1.1.1.-) (Carrot ABA-induced in somatic embryos 5 protein)	0.01	-	nuc	0					291
Q9FZ42 UniProt NPD GO	GRDH1_ARATH	Glucose and ribitol dehydrogenase homolog 1 (EC 1.1.1.-)	0.01	-	nuc	0					288
Q06222 UniProt NPD GO	TH2A_TRYBB	Glucose transporter 2A	0.01	-	end	12 *	Membrane; multi-pass membrane protein				529
P55236 UniProt NPD GO	GLGL1_SPIOL	Glucose-1-phosphate adenylyltransferase large subunit (EC 2.7.7.27) (ADP-glucose synthase) (ADP-gluc ...	0.01	-	nuc	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				21
P55240 UniProt NPD GO	GLGS_MAIZE	Glucose-1-phosphate adenylyltransferase small subunit (EC 2.7.7.27) (ADP-glucose synthase) (ADP-gluc ...	0.01	-	cyt	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				125
O42153 UniProt NPD GO	G6PT_HAPNU	Glucose-6-phosphatase (EC 3.1.3.9) (G6Pase) (G-6-Pase)	0.01	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				352
Q758L0 UniProt NPD GO	G6PI_ASHGO	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.01	-	cyt	0	Cytoplasm (By similarity)				555
P52029 UniProt NPD GO	G6PI_DROME	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.01	-	cyt	0	Cytoplasm (By similarity)				558
P52030 UniProt NPD GO	G6PI_DROSI	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.01	-	cyt	0	Cytoplasm (By similarity)				558
P52031 UniProt NPD GO	G6PI_DROYA	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.01	-	cyt	0	Cytoplasm (By similarity)				558
P12341 UniProt NPD GO	G6PI_KLULA	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.01	-	cyt	0	Cytoplasm				555
P78917 UniProt NPD GO	G6PI_SCHPO	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.01	-	cyt	0	Cytoplasm (By similarity)				550
P46479 UniProt NPD GO	G6PI_CALFI	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.01	-	cyt	0	Cytoplasm				304
P83780 UniProt NPD GO	G6PI_CANAL	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.01	-	cyt	0	Cytoplasm				23
P54236 UniProt NPD GO	G6PI1_CLAFR	Glucose-6-phosphate isomerase, cytosolic 1 (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phos ...	0.01	-	cyt	0	Cytoplasm (By similarity)				568
P54238 UniProt NPD GO	G6PI1_CLARO	Glucose-6-phosphate isomerase, cytosolic 1 (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phos ...	0.01	-	cyt	0	Cytoplasm (By similarity)				570
P54239 UniProt NPD GO	G6PI1_CLAWI	Glucose-6-phosphate isomerase, cytosolic 1 (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phos ...	0.01	-	cyt	0	Cytoplasm (By similarity)				568
P54240 UniProt NPD GO	G6PI1_CLAXA	Glucose-6-phosphate isomerase, cytosolic 1 (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phos ...	0.01	-	cyt	0	Cytoplasm (By similarity)				568
P34796 UniProt NPD GO	G6PI1_CLALE	Glucose-6-phosphate isomerase, cytosolic 1A (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Pho ...	0.01	-	cyt	0	Cytoplasm				569
P42862 UniProt NPD GO	G6PIA_ORYSA	Glucose-6-phosphate isomerase, cytosolic A (EC 5.3.1.9) (GPI-A) (Phosphoglucose isomerase A) (PGI-A) ...	0.01	-	cyt	0	Cytoplasm	cytosol [IDA]			567
P22151 UniProt NPD GO	GRG1_NEUCR	Glucose-repressible gene protein	0.01	-	nuc	0					71
P17439 UniProt NPD GO	GLCM_MOUSE	Glucosylceramidase precursor (EC 3.2.1.45) (Beta-glucocerebrosidase) (Acid beta-glucosidase) (D-gluc ...	0.01	-	exc	0	Lysosome; peripheral membrane protein				515
Q43260 UniProt NPD GO	DHE3_MAIZE	Glutamate dehydrogenase (EC 1.4.1.3) (GDH)	0.01	-	nuc	0					411
P28270 UniProt NPD GO	DHE3_ELEEL	Glutamate dehydrogenase (EC 1.4.1.3) (GDH) (Fragments)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				51
P93541 UniProt NPD GO	DHE3_LYCES	Glutamate dehydrogenase (EC 1.4.1.3) (GDH) (Legdh1)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				412
Q9LEC8 UniProt NPD GO	DHEB_NICPL	Glutamate dehydrogenase B (EC 1.4.1.3) (GDH B)	0.01	-	mit	0					411
P23712 UniProt NPD GO	GLNA_LACSA	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS(1))	0.01	-	cyt	0	Cytoplasm				358
Q96UG9 UniProt NPD GO	GLNA_CRYNE	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.01	-	cyt	0	Cytoplasm (By similarity)				358
Q42688 UniProt NPD GO	GLNA1_CHLRE	Glutamine synthetase cytosolic isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS1)	0.01	-	cyt	0	Cytoplasm				382
Q4W8D0 UniProt NPD GO	GLN13_ORYSA	Glutamine synthetase cytosolic isozyme 1-3 (EC 6.3.1.2) (OsGLN1;3) (OsGS1;3) (Glutamate--ammonia lig ...	0.01	-	nuc	0	Cytoplasm				370
P38560 UniProt NPD GO	GLNA2_MAIZE	Glutamine synthetase root isozyme 2 (EC 6.3.1.2) (Glutamate--ammonia ligase)	0.01	-	cyt	0	Cytoplasm				368
Q9ZR41 UniProt NPD GO	GLRX_LYCES	Glutaredoxin	0.01	-	cyt	0	Cytoplasm (By similarity)				108
O81187 UniProt NPD GO	GLRX_VERFO	Glutaredoxin	0.01	-	cyt	0	Cytoplasm (By similarity)				104
P25373 UniProt NPD GO	GLRX1_YEAST	Glutaredoxin-1 (Glutathione-dependent oxidoreductase 1)	0.01	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]			110
P17695 UniProt NPD GO	GLRX2_YEAST	Glutaredoxin-2, mitochondrial precursor (Thioltransferase) (Glutathione-dependent oxidoreductase 2)	0.01	-	mit	1 *	Cytoplasm. Mitochondrion. Two forms, a long and a short one are found in the mitochondrion, but only ...	cytosol [IDA] mitochondrion [IDA]			143
Q04522 UniProt NPD GO	GSTF_SILCU	Glutathione S-transferase (EC 2.5.1.18) (GST class-phi)	0.01	-	cyt	0	Cytoplasm				216
P46423 UniProt NPD GO	GSTF_HYOMU	Glutathione S-transferase (EC 2.5.1.18) (GST class-phi) (25 kDa auxin-binding protein)	0.01	-	cyt	0					212
P46437 UniProt NPD GO	GST_MUSDO	Glutathione S-transferase (EC 2.5.1.18) (GST class-sigma)	0.01	-	cyt	0					241

You are viewing entries 88451 to 88500 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.