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
Q3I411 UniProt NPD GO	G3O21_WHEAT	Gibberellin 3-beta-dioxygenase 2-1 (EC 1.14.11.15) (Gibberellin 3 beta-hydroxylase 2-1) (Gibberellin ...	0.02	-	nuc	0					370
Q3I410 UniProt NPD GO	G3O22_WHEAT	Gibberellin 3-beta-dioxygenase 2-2 (EC 1.14.11.15) (Gibberellin 3 beta-hydroxylase 2-2) (Gibberellin ...	0.02	-	nuc	0					370
Q3I409 UniProt NPD GO	G3O23_WHEAT	Gibberellin 3-beta-dioxygenase 2-3 (EC 1.14.11.15) (Gibberellin 3 beta-hydroxylase 2-3) (Gibberellin ...	0.02	-	cyt	0					369
P00752 UniProt NPD GO	KLK_PIG	Glandular kallikrein precursor (EC 3.4.21.35) (Tissue kallikrein)	0.02	-	cyt	0				2PKA	246
P02214 UniProt NPD GO	GLB_BUSCA	Globin (Myoglobin)	0.02	-	cyt	0	Cytoplasm				147
P02224 UniProt NPD GO	GLB6_CHITH	Globin CTT-VI precursor	0.02	-	exc	0					162
P30627 UniProt NPD GO	GLBH_CAEEL	Globin-like protein	0.02	-	cyt	0	Cytoplasm (Potential)				159
P81048 UniProt NPD GO	GLOV_HYACE	Gloverin	0.02	-	cyt	0	Secreted protein				130
P09567 UniProt NPD GO	GLUC_TORMA	Glucagon	0.02	-	nuc	0	Secreted protein				29
P63294 UniProt NPD GO	GLUCL_ANGAN	Glucagon-like peptide (GLP)	0.02	-	cyt	0	Secreted protein				30
P63295 UniProt NPD GO	GLUCL_ANGRO	Glucagon-like peptide (GLP)	0.02	-	cyt	0	Secreted protein				30
Q96V64 UniProt NPD GO	EXG_BLUGR	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.02	-	exc	0	Secreted protein (Potential)				426
Q02126 UniProt NPD GO	E13C_HORVU	Glucan endo-1,3-beta-glucosidase GIII precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase GIII ...	0.02	-	mit	1 *					330
Q02438 UniProt NPD GO	E13E_HORVU	Glucan endo-1,3-beta-glucosidase GV (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase GV) ((1->3)-beta ...	0.02	-	cyt	0	Cytoplasm (Probable)				316
P43577 UniProt NPD GO	GNA1_YEAST	Glucosamine 6-phosphate N-acetyltransferase (EC 2.3.1.4) (Phosphoglucosamine transacetylase) (Phosph ...	0.02	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		1I21	159
Q06221 UniProt NPD GO	TH11_TRYBB	Glucose transporter 1B/1C/1D/1F/2B	0.02	-	end	12 *	Membrane; multi-pass membrane protein				527
Q09037 UniProt NPD GO	TH12_TRYBB	Glucose transporter 1E	0.02	-	end	12 *	Membrane; multi-pass membrane protein				528
Q00081 UniProt NPD GO	GLGL1_SOLTU	Glucose-1-phosphate adenylyltransferase large subunit 1 (EC 2.7.7.27) (ADP-glucose synthase) (ADP-gl ...	0.02	-	cyt	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				470
P54996 UniProt NPD GO	G6PD_FUGRU	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.02	-	cyt	0					530
P80619 UniProt NPD GO	G6PD_MAIZE	Glucose-6-phosphate 1-dehydrogenase, cytoplasmic isoform (EC 1.1.1.49) (G6PD) (2D-page of etiolated ...	0.02	-		0	Cytoplasm (By similarity)				15
Q9N1E2 UniProt NPD GO	G6PI_RABIT	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.02	-	cyt	0	Cytoplasm			1XTB	557
P49105 UniProt NPD GO	G6PI_MAIZE	Glucose-6-phosphate isomerase, cytosolic (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosph ...	0.02	-	nuc	0	Cytoplasm				567
P34797 UniProt NPD GO	G6PI3_CLALE	Glucose-6-phosphate isomerase, cytosolic 2B (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Pho ...	0.02	-	cyt	0	Cytoplasm				317
Q43314 UniProt NPD GO	DHE1_ARATH	Glutamate dehydrogenase 1 (EC 1.4.1.3) (GDH 1)	0.02	-	cyt	0					411
Q39566 UniProt NPD GO	GSA_CHLRE	Glutamate-1-semialdehyde 2,1-aminomutase, chloroplast precursor (EC 5.4.3.8) (GSA) (Glutamate-1-semi ...	0.02	-	mit	0	Plastid; chloroplast				463
P45621 UniProt NPD GO	GSA_SOYBN	Glutamate-1-semialdehyde 2,1-aminomutase, chloroplast precursor (EC 5.4.3.8) (GSA) (Glutamate-1-semi ...	0.02	-	end	0	Plastid; chloroplast				466
Q06378 UniProt NPD GO	GLNA3_HORVU	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (Cytoplasmic GS3)	0.02	-	cyt	0	Cytoplasm				356
O04867 UniProt NPD GO	GLNA1_ALNGL	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS(1))	0.02	-	cyt	0	Cytoplasm				356
Q96UV5 UniProt NPD GO	GLNA_HEBCY	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.02	-	cyt	0	Cytoplasm (By similarity)				354
P04771 UniProt NPD GO	GLNA2_PHAVU	Glutamine synthetase PR-2 (EC 6.3.1.2) (Gln isozyme alpha) (Glutamate--ammonia ligase)	0.02	-	cyt	0	Cytoplasm				356
Q42689 UniProt NPD GO	GLNA2_CHLRE	Glutamine synthetase, chloroplast precursor (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS2)	0.02	-	mit	0	Plastid; chloroplast				380
Q9SLM6 UniProt NPD GO	GST16_ARATH	Glutathione S-transferase 16 (EC 2.5.1.18) (GST class-phi)	0.02	-	cyt	0	Cytoplasm (Probable)				212
P82607 UniProt NPD GO	GST67_DICLA	Glutathione S-transferase 6.7 (EC 2.5.1.18) (GST-6.7) (GST class-theta) (Fragments)	0.02	-	cyt	0	Cytoplasm				54
Q9VG94 UniProt NPD GO	GSTT6_DROME	Glutathione S-transferase D6 (EC 2.5.1.18) (DmGST25)	0.02	-	cyt	0					215
P30109 UniProt NPD GO	GSTF1_TOBAC	Glutathione S-transferase PARB (EC 2.5.1.18) (GST class-phi)	0.02	-	cyt	0					213
P42769 UniProt NPD GO	GSTF5_ARATH	Glutathione S-transferase PM239X14 (EC 2.5.1.18) (GST class-phi)	0.02	-	cyt	0	Cytoplasm (Probable)				218
P30102 UniProt NPD GO	GSTY2_ISSOR	Glutathione S-transferase Y-2 (EC 2.5.1.18)	0.02	-	cyt	0					190
Q74ZK4 UniProt NPD GO	GSHR_ASHGO	Glutathione reductase (EC 1.8.1.7) (GR) (GRase)	0.02	-	cyt	0	Cytoplasm (By similarity)				480
Q6C5H4 UniProt NPD GO	GSHR_YARLI	Glutathione reductase (EC 1.8.1.7) (GR) (GRase)	0.02	-	cyt	0	Cytoplasm (By similarity)				470
P48641 UniProt NPD GO	GSHRC_ARATH	Glutathione reductase, cytosolic (EC 1.8.1.7) (GR) (GRase) (OBP29)	0.02	-	mit	0	Cytoplasm (Potential)				499
Q9HFX1 UniProt NPD GO	G3P_AJECA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.02	-	cyt	0	Cytoplasm (By similarity)				337
P83601 UniProt NPD GO	G3P_NAEFO	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Fragment)	0.02	-		0	Cytoplasm (By similarity)				18
Q6FPW3 UniProt NPD GO	G3P1_CANGA	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH 1)	0.02	-	mit	0	Cytoplasm (By similarity)				332
P25856 UniProt NPD GO	G3PA_ARATH	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.02	-	cyt	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				396
P50362 UniProt NPD GO	G3PA_CHLRE	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.02	-	cyt	0	Plastid; chloroplast			1NLH	374
P09315 UniProt NPD GO	G3PA_MAIZE	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.02	-	cyt	0	Plastid; chloroplast				403
P30724 UniProt NPD GO	G3PA_GRAVE	Glyceraldehyde-3-phosphate dehydrogenase, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glycer ...	0.02	-	mit	0	Plastid; chloroplast				416
P08477 UniProt NPD GO	G3PC_HORVU	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) (Fragment)	0.02	-	cyt	0	Cytoplasm				305
O96423 UniProt NPD GO	G3PG_CRIFA	Glyceraldehyde-3-phosphate dehydrogenase, glycosomal (EC 1.2.1.12) (GAPDH)	0.02	-	pox	0	Glycosome				360
P22512 UniProt NPD GO	G3PG_TRYBB	Glyceraldehyde-3-phosphate dehydrogenase, glycosomal (EC 1.2.1.12) (GAPDH)	0.02	-	pox	0	Glycosome			1GGA	358

You are viewing entries 83601 to 83650 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.