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
P60522 UniProt NPD GO	GBRL2_RAT	Gamma-aminobutyric acid receptor-associated protein-like 2 (GABA(A) receptor-associated protein-like ...	0.21	-	cyt	0	Golgi apparatus (By similarity)				117
P60519 UniProt NPD GO	GBRL2_BOVIN	Gamma-aminobutyric acid receptor-associated protein-like 2 (GABA(A) receptor-associated protein-like ...	0.21	-	cyt	0	Golgi apparatus			1EO6	117
P60520 UniProt NPD GO	GBRL2_HUMAN	Gamma-aminobutyric acid receptor-associated protein-like 2 (GABA(A) receptor-associated protein-like ...	0.21	-	cyt	0	Golgi apparatus (By similarity)	cytoskeleton [TAS] plasma membrane [ISS]	607452		117
Q8BQU6 UniProt NPD GO	CXA12_MOUSE	Gap junction alpha-12 protein (Connexin-47) (Cx47)	0.21	-	end	4 *	Membrane; multi-pass membrane protein				440
P48165 UniProt NPD GO	CXA8_HUMAN	Gap junction alpha-8 protein (Connexin-50) (Cx50) (Lens fiber protein MP70)	0.21	-	end	4 *	Membrane; multi-pass membrane protein	connexon complex [TAS] integral to plasma membrane [TAS]	600897		432
Q8MHW5 UniProt NPD GO	CXB2_GORGO	Gap junction beta-2 protein (Connexin-26) (Cx26)	0.21	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				226
P29033 UniProt NPD GO	CXB2_HUMAN	Gap junction beta-2 protein (Connexin-26) (Cx26)	0.21	-	end	4 *	Membrane; multi-pass membrane protein	connexon complex [TAS] plasma membrane [TAS]	601544		226
Q7JGL3 UniProt NPD GO	CXB2_HYLLA	Gap junction beta-2 protein (Connexin-26) (Cx26)	0.21	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				226
Q8MIT8 UniProt NPD GO	CXB2_MACMU	Gap junction beta-2 protein (Connexin-26) (Cx26)	0.21	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				226
Q8MIT9 UniProt NPD GO	CXB2_PONPY	Gap junction beta-2 protein (Connexin-26) (Cx26)	0.21	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				226
P46691 UniProt NPD GO	CXB2_SHEEP	Gap junction beta-2 protein (Connexin-26) (Cx26)	0.21	-	end	4 *	Membrane; multi-pass membrane protein				226
P70689 UniProt NPD GO	CXB6_MOUSE	Gap junction beta-6 protein (Connexin-30) (Cx30)	0.21	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [IDA]			261
P01352 UniProt NPD GO	GAST_BOVIN	Gastrin precursor [Contains: Big gastrin (Gastrin 34) (G34); Gastrin]	0.21	-	exc	0	Secreted protein				104
P24393 UniProt NPD GO	GRP_RAT	Gastrin-releasing peptide precursor (GRP) [Contains: Neuromedin C (GRP-10)]	0.21	-	exc	0	Secreted protein				147
P13466 UniProt NPD GO	GELA_DICDI	Gelation factor (Actin-binding protein 120) (ABP-120)	0.21	-	nuc	0				1WLH	857
P17063 UniProt NPD GO	GIA1_GIALA	Giardin alpha-1 subunit	0.21	+	cyt	0	Most likely in the edges of the ventral disk microribbons				295
Q8LEA2 UniProt NPD GO	G2OX1_ARATH	Gibberellin 2-beta-dioxygenase 1 (EC 1.14.11.13) (Gibberellin 2-beta-hydroxylase 1) (Gibberellin 2-o ...	0.21	-	nuc	0					329
P93771 UniProt NPD GO	GAOX1_ORYSA	Gibberellin 20 oxidase 1 (EC 1.14.11.-) (Gibberellin C-20 oxidase 1) (GA 20-oxidase 1) (Os20ox)	0.21	-	cyt	0					372
Q80WL1 UniProt NPD GO	GLDN_RAT	Gliomedin	0.21	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Localizes to the nodes of Ranvier				549
P15161 UniProt NPD GO	GLB1_PARCH	Globin-1 (Globin I)	0.21	-	cyt	0					157
Q09169 UniProt NPD GO	PACA_RANRI	Glucagon family neuropeptides precursor [Contains: Growth hormone-releasing factor (GRF) (Growth hor ...	0.21	-	mit	0	Secreted protein				171
P33528 UniProt NPD GO	GLUC_AMICA	Glucagon precursor [Contains: Glucagon; Glucagon-like peptide] (Fragments)	0.21	-	cyt	0	Secreted protein				75
P55228 UniProt NPD GO	GLGS_ARATH	Glucose-1-phosphate adenylyltransferase small subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.21	-	cyt	0	Plastid; chloroplast (By similarity)				520
Q04792 UniProt NPD GO	DCE_YEAST	Glutamate decarboxylase (EC 4.1.1.15) (GAD)	0.21	-	cyt	0		cytoplasm [IDA]			585
P42262 UniProt NPD GO	GRIA2_HUMAN	Glutamate receptor 2 precursor (GluR-2) (GluR-B) (GluR-K2) (Glutamate receptor ionotropic, AMPA 2) ( ...	0.21	-	end	4 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]	138247		883
P23819 UniProt NPD GO	GRIA2_MOUSE	Glutamate receptor 2 precursor (GluR-2) (GluR-B) (GluR-K2) (Glutamate receptor ionotropic, AMPA 2) ( ...	0.21	-	end	4 *	Membrane; multi-pass membrane protein	membrane fraction [IDA]			883
Q5R4M0 UniProt NPD GO	GRIA2_PONPY	Glutamate receptor 2 precursor (GluR-2) (GluR-B) (GluR-K2) (Glutamate receptor ionotropic, AMPA 2) ( ...	0.21	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				883
P19491 UniProt NPD GO	GRIA2_RAT	Glutamate receptor 2 precursor (GluR-2) (GluR-B) (GluR-K2) (Glutamate receptor ionotropic, AMPA 2) ( ...	0.21	-	end	4 *	Membrane; multi-pass membrane protein	cell soma [IDA] dendritic shaft [IDA] dendritic spine [IDA] growth cone [IDA] ionotropic glutamate receptor complex [TAS] presynaptic membrane [IDA] protein complex [IPI] synaptic vesicle membrane [IDA]		2CMO	883
P46410 UniProt NPD GO	GLNA_PIG	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.21	-	cyt	0	Cytoplasm (By similarity)				372
P42804 UniProt NPD GO	HEM11_ARATH	Glutamyl-tRNA reductase 1, chloroplast precursor (EC 1.2.1.70) (GluTR)	0.21	-	mit	0	Plastid; chloroplast				543
P20136 UniProt NPD GO	GSTM2_CHICK	Glutathione S-transferase 2 (EC 2.5.1.18) (GST-CL2) (GST class-mu) (GSTM1-1)	0.21	-	cyt	0	Cytoplasm			1GSU	219
P09210 UniProt NPD GO	GSTA2_HUMAN	Glutathione S-transferase A2 (EC 2.5.1.18) (GTH2) (HA subunit 2) (GST-gamma) (GSTA2-2) (GST class-al ...	0.21	-	cyt	0	Cytoplasm		138360	1AGS	221
P21266 UniProt NPD GO	GSTM3_HUMAN	Glutathione S-transferase Mu 3 (EC 2.5.1.18) (GSTM3-3) (GST class-mu 3) (hGSTM3-3)	0.21	-	cyt	0	Cytoplasm		138390	3GTU	224
P08009 UniProt NPD GO	GSTM4_RAT	Glutathione S-transferase Yb-3 (EC 2.5.1.18) (Chain 4) (GST Yb3) (GST class-mu 3)	0.21	-	cyt	0	Cytoplasm				217
P83645 UniProt NPD GO	GPX2_RAT	Glutathione peroxidase 2 (EC 1.11.1.9) (GSHPx-2) (GPx-2) (Glutathione peroxidase-gastrointestinal) ( ...	0.21	-	cyt	0	Cytoplasm (By similarity)				190
P46413 UniProt NPD GO	GSHB_RAT	Glutathione synthetase (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) (GSH-S)	0.21	-	cyt	0					474
P53154 UniProt NPD GO	GUP1_YEAST	Glycerol uptake protein 1	0.21	-	end	10 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] plasma membrane [IDA]			560
Q64521 UniProt NPD GO	GPDM_MOUSE	Glycerol-3-phosphate dehydrogenase, mitochondrial precursor (EC 1.1.99.5) (GPD-M) (GPDH-M)	0.21	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane	glycerol-3-phosphate dehydrogenase complex [TAS] mitochondrial inner membrane [IDA] mitochondrion [IDA]			727
P35571 UniProt NPD GO	GPDM_RAT	Glycerol-3-phosphate dehydrogenase, mitochondrial precursor (EC 1.1.99.5) (GPD-M) (GPDH-M)	0.21	-	mit	1 *	Mitochondrion				727
Q5RFB9 UniProt NPD GO	GATM_PONPY	Glycine amidinotransferase, mitochondrial precursor (EC 2.1.4.1) (L-arginine:glycine amidinotransfer ...	0.21	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				423
P46976 UniProt NPD GO	GLYG_HUMAN	Glycogenin-1 (EC 2.4.1.186)	0.21	-	cyt	0			603942		349
Q03655 UniProt NPD GO	GAS3_YEAST	Glycolipid-anchored surface protein 3 precursor	0.21	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			524
O23627 UniProt NPD GO	SYGM1_ARATH	Glycyl-tRNA synthetase 1, mitochondrial precursor (EC 6.1.1.14) (Glycine--tRNA ligase 1) (GlyRS 1)	0.21	-	mit	0	Mitochondrion. Cytoplasm				729
P30418 UniProt NPD GO	NMT_CANAL	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.21	-	nuc	0	Cytoplasm			1NMT	451
O35254 UniProt NPD GO	GR65_RAT	Golgi reassembly-stacking protein 1 (Golgi reassembly-stacking protein of 65 kDa) (GRASP65) (Golgi p ...	0.21	-	nuc	0	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; peripherical membrane protein; cytop ...				450
Q9BQQ3 UniProt NPD GO	GR65_HUMAN	Golgi reassembly-stacking protein 1 (Golgi reassembly-stacking protein of 65 kDa) (GRASP65) (Golgi p ...	0.21	-	nuc	0	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; peripherical membrane protein; cytop ...		606867		439
Q91W53 UniProt NPD GO	GOGA7_MOUSE	Golgin subfamily A member 7	0.21	-	cyt	0	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				137
P11033 UniProt NPD GO	GRAD_MOUSE	Granzyme D precursor (EC 3.4.21.-)	0.21	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes				248
P08883 UniProt NPD GO	GRAF_MOUSE	Granzyme F precursor (EC 3.4.21.-) (Cytotoxic cell protease 4) (CCP4) (CTL serine protease 3) (C134) ...	0.21	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes				248
P09340 UniProt NPD GO	GROA_CRIGR	Growth-regulated alpha protein precursor (CXCL1)	0.21	-	exc	0	Secreted protein				101

You are viewing entries 49501 to 49550 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.