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
P80035 UniProt NPD GO	LIPG_CANFA	Gastric triacylglycerol lipase precursor (EC 3.1.1.3) (Gastric lipase) (GL)	0.04	-	mit	0	Secreted protein			1K8Q	398
Q9GMY2 UniProt NPD GO	PEPC_RABIT	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C)	0.04	-	exc	0	Secreted protein				388
P31886 UniProt NPD GO	GRP_ALLMI	Gastrin-releasing peptide (GRP) [Contains: Neuromedin C (GRP-10)]	0.04	-	cyt	0	Secreted protein				28
P80110 UniProt NPD GO	ANTR_TRASC	Gastrin/cholecystokinin-like peptide (Antral peptide)	0.04	-	cyt	0					52
Q39108 UniProt NPD GO	GGR_ARATH	Geranylgeranyl pyrophosphate synthase-related protein, chloroplast precursor	0.04	-	cyt	0	Plastid; chloroplast (Potential)				326
P34802 UniProt NPD GO	GGPP1_ARATH	Geranylgeranyl pyrophosphate synthetase 1, chloroplast precursor (GGPP synthetase 1) (GGPS1) [Includ ...	0.04	-	mit	0	Plastid; chloroplast				371
Q94ID7 UniProt NPD GO	GGPPS_HEVBR	Geranylgeranyl pyrophosphate synthetase, chloroplast precursor (GGPP synthetase) [Includes: Dimethyl ...	0.04	-	mit	0	Plastid; chloroplast (Potential)				370
P92998 UniProt NPD GO	GL11_ARATH	Germin-like protein subfamily 1 member 1 precursor	0.04	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				217
P80592 UniProt NPD GO	GLBB_RIFPA	Giant hemoglobins B chain	0.04	-	cyt	0	Secreted protein; extracellular space			1YHU	144
Q9XG83 UniProt NPD GO	G2OX_PHACN	Gibberellin 2-beta-dioxygenase (EC 1.14.11.13) (Gibberellin 2-beta-hydroxylase) (Gibberellin 2-oxida ...	0.04	-	cyt	0					332
Q6L545 UniProt NPD GO	GID1_ORYSA	Gibberellin receptor GID1 (EC 3.-.-.-) (Gibberellin-insensitive dwarf protein 1) (Protein GIBBERELLI ...	0.04	-	cyt	0	Nucleus	nucleus [IC]			354
P46688 UniProt NPD GO	GASA2_ARATH	Gibberellin-regulated protein 2 precursor	0.04	-	exc	0	Secreted protein				99
Q76CA0 UniProt NPD GO	GIG3_STIGI	Gigantoxin-3 precursor (Gigantoxin III) (Gigt III)	0.04	-	vac	0	Secreted protein. Found in nematocyst				84
P15950 UniProt NPD GO	KLK3_RAT	Glandular kallikrein-3, submandibular (EC 3.4.21.35) (Tissue kallikrein) (S1 kallikrein) (RGK-3) (RS ...	0.04	-	nuc	0					188
P48060 UniProt NPD GO	GLIP1_HUMAN	Glioma pathogenesis-related protein 1 precursor (GliPR 1) (RTVP-1 protein)	0.04	-	cyt	1			602692		266
Q9PRQ9 UniProt NPD GO	GLUC_LAMFL	Glucagon	0.04	-	nuc	0	Secreted protein				29
P30082 UniProt NPD GO	GLR_RAT	Glucagon receptor precursor (GL-R)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				485
P81027 UniProt NPD GO	GLUC2_ORENI	Glucagon-2 (Glucagon II)	0.04	-	nuc	0	Secreted protein				33
P43220 UniProt NPD GO	GLP1R_HUMAN	Glucagon-like peptide 1 receptor precursor (GLP-1 receptor) (GLP-1-R) (GLP-1R)	0.04	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	138032		463
O35659 UniProt NPD GO	GLP1R_MOUSE	Glucagon-like peptide 1 receptor precursor (GLP-1 receptor) (GLP-1-R) (GLP-1R)	0.04	-	end	7	Membrane; multi-pass membrane protein				489
Q12626 UniProt NPD GO	EXG_PICAN	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.04	-	mit	0	Secreted protein (Potential)				435
P15703 UniProt NPD GO	BGL2_YEAST	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase) (GP29) (Soluble cell wa ...	0.04	-	exc	0	Cell wall. Tightly bound to cell wall	cell wall (sensu Fungi) [TAS]			313
O13716 UniProt NPD GO	AGN1_SCHPO	Glucan endo-1,3-alpha-glucosidase agn1 precursor (EC 3.2.1.59) (Endo-1,3-alpha-glucanase agn1)	0.04	-	end	0	Secreted protein. Cell wall. Associates with the cell wall	cell septum edging [IDA] cell surface [IDA] extracellular region [IDA]			424
Q01413 UniProt NPD GO	E13B_LYCES	Glucan endo-1,3-beta-glucosidase B precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase B) ((1- ...	0.04	-	cyt	1 *	Vacuole (Potential)				360
P23547 UniProt NPD GO	E13G_TOBAC	Glucan endo-1,3-beta-glucosidase, acidic isoform GI9 precursor (EC 3.2.1.39) ((1->3)-beta-glucan end ...	0.04	-	vac	1 *	Secreted protein; extracellular space				343
P52402 UniProt NPD GO	E133_SOLTU	Glucan endo-1,3-beta-glucosidase, basic isoform 3 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohy ...	0.04	-	cyt	0	Vacuole (By similarity)				328
P23546 UniProt NPD GO	E13E_TOBAC	Glucan endo-1,3-beta-glucosidase, basic vacuolar isoform GGIB50 precursor (EC 3.2.1.39) ((1->3)-beta ...	0.04	-	exc	1 *	Vacuole				370
P27666 UniProt NPD GO	E13F_TOBAC	Glucan endo-1,3-beta-glucosidase, basic vacuolar isoform GLB precursor (EC 3.2.1.39) ((1->3)-beta-gl ...	0.04	-	vac	1 *	Vacuole				370
P15797 UniProt NPD GO	E13B_TOBAC	Glucan endo-1,3-beta-glucosidase, basic vacuolar isoform precursor (EC 3.2.1.39) ((1->3)-beta-glucan ...	0.04	-	exc	1 *	Vacuole				371
Q9QUZ8 UniProt NPD GO	GMEB1_RAT	Glucocorticoid modulatory element-binding protein 1 (GMEB-1) (Fragments)	0.04	-	cyt	0	Nucleus. Cytoplasm. May be also cytoplasmic				38
P35576 UniProt NPD GO	G6PT_MOUSE	Glucose-6-phosphatase (EC 3.1.3.9) (G6Pase) (G-6-Pase)	0.04	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				357
P06745 UniProt NPD GO	G6PI_MOUSE	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.04	-	cyt	0	Cytoplasm			1U0G	557
Q9M5A9 UniProt NPD GO	GPT1_ARATH	Glucose-6-phosphate/phosphate translocator 1, chloroplast precursor	0.04	-	end	8	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				388
P32264 UniProt NPD GO	PROB_YEAST	Glutamate 5-kinase (EC 2.7.2.11) (Gamma-glutamyl kinase) (GK)	0.04	-	cyt	0	Cytoplasm	cytoplasm [IDA]			428
P12424 UniProt NPD GO	GLNA_NICPL	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase)	0.04	-	cyt	0	Cytoplasm				356
Q8X169 UniProt NPD GO	GLNA_AMAMU	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.04	-	cyt	0	Cytoplasm (By similarity)				354
O22504 UniProt NPD GO	GLNA1_DAUCA	Glutamine synthetase cytosolic isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS1)	0.04	-	cyt	0	Cytoplasm (By similarity)				352
Q42899 UniProt NPD GO	GLNA1_LOTJA	Glutamine synthetase cytosolic isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS1)	0.04	-	cyt	0	Cytoplasm				356
P52783 UniProt NPD GO	GLNA_PINSY	Glutamine synthetase cytosolic isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS1)	0.04	-	cyt	0	Cytoplasm				357
P51118 UniProt NPD GO	GLNA1_VITVI	Glutamine synthetase cytosolic isozyme 1 (EC 6.3.1.2) (Glutamate--ammonia ligase)	0.04	-	cyt	0	Cytoplasm				356
P14654 UniProt NPD GO	GLN12_ORYSA	Glutamine synthetase cytosolic isozyme 1-2 (EC 6.3.1.2) (OsGLN1;2) (OsGS1;2) (Glutamate--ammonia lig ...	0.04	-	cyt	0	Cytoplasm				357
Q9LVI8 UniProt NPD GO	GLN13_ARATH	Glutamine synthetase cytosolic isozyme 1-3 (EC 6.3.1.2) (GLN1;3) (Glutamate--ammonia ligase GLN1;3) ...	0.04	-	cyt	0	Cytoplasm				354
Q8GXW5 UniProt NPD GO	GLN15_ARATH	Glutamine synthetase cytosolic isozyme 1-5 (EC 6.3.1.2) (GLN1;5) (Glutamate--ammonia ligase GLN1;5)	0.04	-	cyt	0	Cytoplasm				353
P51119 UniProt NPD GO	GLNA2_VITVI	Glutamine synthetase cytosolic isozyme 2 (EC 6.3.1.2) (Glutamate--ammonia ligase)	0.04	-	cyt	0	Cytoplasm				356
P13564 UniProt NPD GO	GLNA2_HORVU	Glutamine synthetase leaf isozyme, chloroplast precursor (EC 6.3.1.2) (Glutamate--ammonia ligase) (C ...	0.04	-	mit	0	Plastid; chloroplast				434
Q43785 UniProt NPD GO	GLNA3_MEDSA	Glutamine synthetase nodule isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase)	0.04	-	cyt	0	Cytoplasm				356
P08282 UniProt NPD GO	GLNA1_PEA	Glutamine synthetase nodule isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase) (Cytosolic GS1)	0.04	-	cyt	0	Cytoplasm				355
Q08392 UniProt NPD GO	GSTA1_CHICK	Glutathione S-transferase (EC 2.5.1.18) (GST class-alpha)	0.04	-	cyt	0					221
P30112 UniProt NPD GO	GST26_FASHE	Glutathione S-transferase 26 kDa 51 (EC 2.5.1.18) (GST51) (FH51) (GST class-mu)	0.04	-	cyt	0	Cytoplasm				217
O16116 UniProt NPD GO	GST3_CAEEL	Glutathione S-transferase 3 (EC 2.5.1.18) (GST class-sigma) (CeGST3)	0.04	-	cyt	0					207

You are viewing entries 77101 to 77150 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.