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
Q9GKW3 UniProt NPD GO	ALDOC_MACFA	Fructose-bisphosphate aldolase C (EC 4.1.2.13) (Brain-type aldolase)	0.06	-	cyt	0					363
P09117 UniProt NPD GO	ALDOC_RAT	Fructose-bisphosphate aldolase C (EC 4.1.2.13) (Brain-type aldolase)	0.06	-	cyt	0					362
Q40298 UniProt NPD GO	FCPD_MACPY	Fucoxanthin-chlorophyll a-c binding protein D, chloroplast precursor (Fragment)	0.06	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				182
P16930 UniProt NPD GO	FAAA_HUMAN	Fumarylacetoacetase (EC 3.7.1.2) (Fumarylacetoacetate hydrolase) (Beta-diketonase) (FAA)	0.06	-	cyt	0			276700		419
P48543 UniProt NPD GO	IRK9_MOUSE	G protein-activated inward rectifier potassium channel 3 (GIRK3) (Potassium channel, inwardly rectif ...	0.06	+	end	3	Membrane; multi-pass membrane protein				393
Q63511 UniProt NPD GO	IRK9_RAT	G protein-activated inward rectifier potassium channel 3 (GIRK3) (Potassium channel, inwardly rectif ...	0.06	+	end	3	Membrane; multi-pass membrane protein				393
P56485 UniProt NPD GO	RDC1_MOUSE	G-protein coupled receptor RDC1 homolog (Chemokine orphan receptor 1)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				362
O89039 UniProt NPD GO	RDC1_RAT	G-protein coupled receptor RDC1 homolog (RDC-1) (Chemokine orphan receptor 1)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				362
P13350 UniProt NPD GO	CCNB1_XENLA	G2/mitotic-specific cyclin-B1	0.06	-	mit	0					397
Q9HDU3 UniProt NPD GO	GAL10_SCHPO	GAL10 bifunctional protein [Includes: UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase); Aldos ...	0.06	-	cyt	0					713
P93031 UniProt NPD GO	GMD2_ARATH	GDP-mannose 4,6 dehydratase 2 (EC 4.2.1.47) (GDP-D-mannose dehydratase 2) (GMD 2)	0.06	-	cyt	0				1N7H	373
Q9NKZ7 UniProt NPD GO	GPI10_TRYBB	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.06	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				558
Q6FMA9 UniProt NPD GO	SMP3_CANGA	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.06	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				496
Q6NVA8 UniProt NPD GO	GFRP_XENTR	GTP cyclohydrolase 1 feedback regulatory protein (GTP cyclohydrolase I feedback regulatory protein) ...	0.06	-	cyt	0					84
P01123 UniProt NPD GO	YPT1_YEAST	GTP-binding protein YPT1 (Rab GTPase YPT1) (Transport GTPase YPT1) (Protein YP2)	0.06	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Golgi apparatus; ...	endoplasmic reticulum membrane [IDA] Golgi membrane [IDA] mitochondrion [IDA]		2BCG	206
P38555 UniProt NPD GO	YPT31_YEAST	GTP-binding protein YPT31/YPT8 (Rab GTPase YPT31)	0.06	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor	endosome [IDA] Golgi apparatus [IDA] mitochondrial outer membrane [IDA]			222
P36019 UniProt NPD GO	YPT53_YEAST	GTP-binding protein YPT53	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	late endosome [IMP]			220
Q9HDY0 UniProt NPD GO	YPT71_SCHPO	GTP-binding protein ypt71	0.06	-	cyt	0	Vacuole (By similarity)				208
Q5RDZ0 UniProt NPD GO	KAD3_PONPY	GTP:AMP phosphotransferase mitochondrial (EC 2.7.4.10) (Adenylate kinase 3) (AK3)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				226
Q866E6 UniProt NPD GO	FUT1_AOTAZ	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.06	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
Q866E7 UniProt NPD GO	FUT1_AOTNA	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.06	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
Q866E8 UniProt NPD GO	FUT1_CEBAP	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.06	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
Q9JL27 UniProt NPD GO	FUT2_MOUSE	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.06	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				347
P47212 UniProt NPD GO	GALA_MOUSE	Galanin precursor [Contains: Galanin; Galanin message-associated peptide (GMAP)]	0.06	-	end	1 *	Secreted protein				124
Q8K419 UniProt NPD GO	LEG4_MOUSE	Galectin-4 (Lactose-binding lectin 4)	0.06	-	cyt	0					326
P97590 UniProt NPD GO	LEG7_RAT	Galectin-7 (Gal-7)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity). May be secrete ...				135
P13284 UniProt NPD GO	GILT_HUMAN	Gamma-interferon-inducible lysosomal thiol reductase precursor (Gamma-interferon-inducible protein I ...	0.06	-	end	1 *	Lysosome	extracellular region [TAS] lysosome [TAS]	604664		261
Q9U357 UniProt NPD GO	PEN2_CAEEL	Gamma-secretase subunit pen-2 (Presenilin enhancer protein 2)	0.06	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				101
Q6S5G4 UniProt NPD GO	CXA6_MOUSE	Gap junction alpha-6 protein (Connexin-33) (Cx33)	0.06	-	end	3 *	Membrane; multi-pass membrane protein				283
P20142 UniProt NPD GO	PEPC_HUMAN	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C)	0.06	-	vac	0	Secreted protein	extracellular space [TAS]	169740	1HTR	388
Q9D7R7 UniProt NPD GO	PEPC_MOUSE	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C)	0.06	-	vac	0	Secreted protein				392
Q9CX53 UniProt NPD GO	GEMI6_MOUSE	Gem-associated protein 6 (Gemin-6)	0.06	-	nuc	0	Nucleus (By similarity). Found both in the nucleoplasm and in nuclear bodies called gems (Gemini of ...	nuclear body [ISS]			166
Q8MKK0 UniProt NPD GO	OB57A_DROME	General odorant-binding protein 57a precursor	0.06	-	exc	0					169
Q5FVN1 UniProt NPD GO	GET1_RAT	Genethonin-1	0.06	-	end	1 *	Membrane; single-pass type III membrane protein. Distributed in the transverse tubules and/or near t ...				333
O95210 UniProt NPD GO	GET1_HUMAN	Genethonin-1 (GENX-3414)	0.06	-	cyt	1 *	Membrane; single-pass type III membrane protein (Probable). Distributed in the transverse tubules an ...	integral to plasma membrane [TAS] membrane fraction [TAS]	607406		358
Q9M8X6 UniProt NPD GO	GL16_ARATH	Germin-like protein subfamily 1 member 6 precursor	0.06	-	vac	0	Secreted protein; extracellular space; apoplast (By similarity)				227
P46687 UniProt NPD GO	GASA3_ARATH	Gibberellin-regulated protein 3 precursor	0.06	-	exc	0	Secreted protein				99
P12323 UniProt NPD GO	KLK2_CAVPO	Glandular kallikrein, prostatic (EC 3.4.21.35) (Tissue kallikrein) (Prostate esterase)	0.06	-	cyt	0					239
Q9CQI3 UniProt NPD GO	GMFB_MOUSE	Glia maturation factor beta (GMF-beta)	0.06	+	cyt	0				1V6F	141
P80017 UniProt NPD GO	GLBD_CAUAR	Globin D, coelomic	0.06	-	cyt	0				1HLM	158
P14394 UniProt NPD GO	GLB2_ANATR	Globin-2B (Globin IIB)	0.06	-	cyt	0					146
P13189 UniProt NPD GO	GLUC_CALMI	Glucagon	0.06	-	nuc	0	Secreted protein				29
P31297 UniProt NPD GO	GLUC_CHIBR	Glucagon	0.06	-	nuc	0	Secreted protein				29
O13990 UniProt NPD GO	BGL2_SCHPO	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.06	-	vac	0	Cell wall (By similarity). Tightly bound to cell wall (By similarity)				321
Q12628 UniProt NPD GO	EXG_KLULA	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.06	-	exc	0	Secreted protein (Potential)				429
O94510 UniProt NPD GO	AGN2_SCHPO	Glucan endo-1,3-alpha-glucosidase agn2 (EC 3.2.1.59) (Endo-1,3-alpha-glucanase agn2)	0.06	-	cyt	0	Cytoplasm	cell surface [IDA] spore wall (sensu Fungi) [IDA]			433
Q03773 UniProt NPD GO	E13A_SOYBN	Glucan endo-1,3-beta-glucosidase precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase) ((1->3)- ...	0.06	-	exc	1 *	Vacuole. In intact tissues (By similarity)				347
P52399 UniProt NPD GO	E13L_TOBAC	Glucan endo-1,3-beta-glucosidase, acidic isoform GL153 precursor (EC 3.2.1.39) ((1->3)-beta-glucan e ...	0.06	-	vac	1 *	Secreted protein; extracellular space				356
P52398 UniProt NPD GO	E13K_TOBAC	Glucan endo-1,3-beta-glucosidase, acidic isoform GL161 precursor (EC 3.2.1.39) ((1->3)-beta-glucan e ...	0.06	-	cyt	0	Secreted protein; extracellular space				331
P33157 UniProt NPD GO	E13A_ARATH	Glucan endo-1,3-beta-glucosidase, acidic isoform precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohyd ...	0.06	-	mit	1 *	Secreted protein; extracellular space; apoplast. Accumulates in the apoplast before secretion				339

You are viewing entries 72101 to 72150 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.