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
P38547 UniProt NPD GO	RAN2_LYCES	GTP-binding nuclear protein Ran2	0.19	-	cyt	0	Nucleus (By similarity)				221
Q8BGX0 UniProt NPD GO	ARD1_MOUSE	GTP-binding protein ARD-1 (ADP-ribosylation factor domain protein 1) (Tripartite motif-containing pr ...	0.19	-	cyt	0	Intracytoplasmic membrane (By similarity). Golgi apparatus; Golgi membrane (By similarity). Lysosome ...	cytoplasm [IDA] Golgi membrane [ISS] lysosomal membrane [ISS] nucleus [IDA]			574
P36407 UniProt NPD GO	ARD1_RAT	GTP-binding protein ARD-1 (ADP-ribosylation factor domain protein 1) (Tripartite motif-containing pr ...	0.19	-	cyt	0	Intracytoplasmic membrane (By similarity). Golgi apparatus; Golgi membrane (By similarity). Lysosome ...	Golgi membrane [ISS] lysosomal membrane [ISS]			554
P83519 UniProt NPD GO	LECG_BOTJR	Galactose-specific lectin (BJcuL)	0.19	-	cyt	0	Secreted protein				135
Q9M5Q1 UniProt NPD GO	FUT1_PEA	Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) (Xyloglucan alpha-(1,2)-fucosyltransferase) ( ...	0.19	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				565
Q9WU47 UniProt NPD GO	B3GA3_CRIGR	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.19	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				335
P58158 UniProt NPD GO	B3GA3_MOUSE	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.19	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				335
O08726 UniProt NPD GO	GALR2_RAT	Galanin receptor type 2 (GAL2-R) (GALR2)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				372
P10063 UniProt NPD GO	GBRA2_BOVIN	Gamma-aminobutyric-acid receptor alpha-2 subunit precursor (GABA(A) receptor)	0.19	-	mit	4	Membrane; multi-pass membrane protein				451
P23576 UniProt NPD GO	GBRA2_RAT	Gamma-aminobutyric-acid receptor alpha-2 subunit precursor (GABA(A) receptor)	0.19	-	mit	4	Membrane; multi-pass membrane protein				451
P55917 UniProt NPD GO	CXA8_SHEEP	Gap junction alpha-8 protein (Connexin-49) (Cx49) (Lens fiber protein MP70) (MP64) (MP38)	0.19	-	end	4 *	Membrane; multi-pass membrane protein				439
P36380 UniProt NPD GO	CXB4_RAT	Gap junction beta-4 protein (Connexin-30.3) (Cx30.3)	0.19	-	end	4 *	Membrane; multi-pass membrane protein				265
P48756 UniProt NPD GO	GIP_MOUSE	Gastric inhibitory polypeptide precursor (GIP) (Glucose-dependent insulinotropic polypeptide)	0.19	-	vac	0	Secreted protein				144
P01351 UniProt NPD GO	GAST_PIG	Gastrin precursor [Contains: Big gastrin (Gastrin 34) (G34); Gastrin]	0.19	-	exc	0	Secreted protein				104
O02686 UniProt NPD GO	GAST_SHEEP	Gastrin precursor [Contains: Big gastrin (Gastrin 34) (G34); Gastrin]	0.19	-	exc	0	Secreted protein				104
P30550 UniProt NPD GO	GRPR_HUMAN	Gastrin-releasing peptide receptor (GRP-R) (GRP-preferring bombesin receptor)	0.19	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	305670		384
Q9WTN0 UniProt NPD GO	GGPPS_MOUSE	Geranylgeranyl pyrophosphate synthetase (GGPP synthetase) (GGPPSase) (Geranylgeranyl diphosphate syn ...	0.19	-	cyt	0	Cytoplasm (Potential)	soluble fraction [ISS]			300
O04706 UniProt NPD GO	GAO1B_WHEAT	Gibberellin 20 oxidase 1-B (EC 1.14.11.-) (Gibberellin C-20 oxidase 1-B) (GA 20-oxidase 1-B) (Ta20ox ...	0.19	-	cyt	0					365
O04705 UniProt NPD GO	GAO1D_WHEAT	Gibberellin 20 oxidase 1-D (EC 1.14.11.-) (Gibberellin C-20 oxidase 1-D) (GA 20-oxidase 1-D) (Ta20ox ...	0.19	-	cyt	0					361
P54130 UniProt NPD GO	FGF9_MOUSE	Glia-activating factor precursor (GAF) (Fibroblast growth factor 9) (FGF-9) (HBGF-9)	0.19	-	cyt	0	Secreted protein				208
P09682 UniProt NPD GO	GLUC_HYDCO	Glucagon	0.19	-	nuc	0	Secreted protein				36
P23176 UniProt NPD GO	AMYG_ASPKA	Glucoamylase I precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrol ...	0.19	-	exc	0					639
Q9UKD1 UniProt NPD GO	GMEB2_HUMAN	Glucocorticoid modulatory element-binding protein 2 (GMEB-2) (Parvovirus initiation factor p79) (PIF ...	0.19	-	cyt	0	Nucleus. Cytoplasm. May be also cytoplasmic	nucleus [TAS]	607451		530
P30524 UniProt NPD GO	GLGL1_HORVU	Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplast precursor (EC 2.7.7.27) (ADP-gl ...	0.19	-	cyt	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				523
P12299 UniProt NPD GO	GLGL2_WHEAT	Glucose-1-phosphate adenylyltransferase large subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.19	-	cyt	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				522
Q27464 UniProt NPD GO	G6PD_CAEEL	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.19	-	cyt	0					522
P05370 UniProt NPD GO	G6PD_RAT	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.19	-	cyt	0					514
P41571 UniProt NPD GO	G6PD_CERCA	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD) (Zwischenferment)	0.19	-	cyt	0					526
Q9FH75 UniProt NPD GO	GLR13_ARATH	Glutamate receptor 1.3 precursor (Ligand-gated ion channel 1.3)	0.19	-	end	3 *	Membrane; multi-pass membrane protein				860
P19493 UniProt NPD GO	GRIA4_RAT	Glutamate receptor 4 precursor (GluR-4) (GluR4) (GluR-D) (Glutamate receptor ionotropic, AMPA 4) (AM ...	0.19	-	end	4 *	Membrane; multi-pass membrane protein	cell soma [IDA] dendrite [IMP] ionotropic glutamate receptor complex [TAS] plasma membrane [IMP] postsynaptic density [IDA] synapse [IMP]			902
P13264 UniProt NPD GO	GLSK_RAT	Glutaminase kidney isoform, mitochondrial precursor (EC 3.5.1.2) (GLS) (L-glutamine amidohydrolase) ...	0.19	-	nuc	0	Mitochondrion	mitochondrion [IPI]			674
Q9QY94 UniProt NPD GO	GLNA_ACOCA	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.19	-	cyt	0	Cytoplasm (By similarity)				372
Q42843 UniProt NPD GO	HEM11_HORVU	Glutamyl-tRNA reductase 1, chloroplast precursor (EC 1.2.1.70) (GluTR)	0.19	-	mit	0	Plastid; chloroplast			1B61	527
P46655 UniProt NPD GO	SYEC_YEAST	Glutamyl-tRNA synthetase, cytoplasmic (EC 6.1.1.17) (Glutamate--tRNA ligase) (GluRS) (P85)	0.19	-	cyt	0	Cytoplasm	cytoplasm [IDA] methionyl glutamyl tRNA synthetase complex [IDA]			724
P46430 UniProt NPD GO	GSTT1_MANSE	Glutathione S-transferase 1 (EC 2.5.1.18) (GST class-theta)	0.19	-	cyt	0					217
P46427 UniProt NPD GO	GSTP_ONCVO	Glutathione S-transferase 2 (EC 2.5.1.18) (GST class-pi)	0.19	-	cyt	0				1TU8	208
Q9Y7Q2 UniProt NPD GO	GST1_SCHPO	Glutathione S-transferase I (EC 2.5.1.18) (GST-I)	0.19	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			229
Q8JFZ2 UniProt NPD GO	GSTP1_XENLA	Glutathione S-transferase P 1 (EC 2.5.1.18) (XlGSTP1-1) (GST class-pi)	0.19	-	cyt	0					212
Q6AYQ1 UniProt NPD GO	GOGA7_RAT	Golgin subfamily A member 7	0.19	-	cyt	0	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				137
P51748 UniProt NPD GO	CSF2_CEREL	Granulocyte-macrophage colony-stimulating factor precursor (GM-CSF) (Colony-stimulating factor) (CSF ...	0.19	-	nuc	0	Secreted protein				144
Q14393 UniProt NPD GO	GAS6_HUMAN	Growth-arrest-specific protein 6 precursor (GAS-6)	0.19	-	nuc	0	Secreted protein		600441	2C5D	721
Q6CRQ1 UniProt NPD GO	GRPE_KLULA	GrpE protein homolog, mitochondrial precursor	0.19	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				243
P17806 UniProt NPD GO	GNAO2_CRILO	Guanine nucleotide-binding protein G(o) subunit alpha 2	0.19	-	cyt	0					353
P29777 UniProt NPD GO	GNAO2_HUMAN	Guanine nucleotide-binding protein G(o) subunit alpha 2	0.19	-	cyt	0			139311		353
P11488 UniProt NPD GO	GNAT1_HUMAN	Guanine nucleotide-binding protein G(t), alpha-1 subunit (Transducin alpha-1 chain)	0.19	-	gol	0			163500		349
Q86D96 UniProt NPD GO	GPA1_TRIVA	Guanine nucleotide-binding protein subunit alpha-1 (G alpha-1) (GTP-binding protein subunit alpha 1) ...	0.19	-	cyt	0	Cytoplasm. Cytoplasm; perinuclear region; peripheral membrane protein. Predominantly perinuclear				402
Q9BYB4 UniProt NPD GO	GNB1L_HUMAN	Guanine nucleotide-binding protein subunit beta-like protein 1 (G protein subunit beta-like protein ...	0.19	-	mit	0		internal side of plasma membrane [NAS]			327
O09051 UniProt NPD GO	GUC2B_MOUSE	Guanylate cyclase activator 2B precursor [Contains: Uroguanylin (UGN)]	0.19	-	exc	0	Secreted protein				106
Q16774 UniProt NPD GO	KGUA_HUMAN	Guanylate kinase (EC 2.7.4.8) (GMP kinase)	0.19	-	mit	0			139270		196
P06344 UniProt NPD GO	HB2U_MOUSE	H-2 class II histocompatibility antigen, A-U beta chain precursor	0.19	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)			1U3H	263

You are viewing entries 51851 to 51900 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.