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
Q14332 UniProt NPD GO	FZD2_HUMAN	Frizzled-2 precursor (Fz-2) (hFz2) (FzE2)	0.08	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600667		565
Q08464 UniProt NPD GO	FZD2_RAT	Frizzled-2 precursor (Fz-2) (rFz2)	0.08	-	end	6	Membrane; multi-pass membrane protein	integral to membrane [TAS]			570
Q9IA05 UniProt NPD GO	FZD4_CHICK	Frizzled-4 precursor (Fz-4) (cFz-4)	0.08	-	end	6	Membrane; multi-pass membrane protein				525
Q9ULV1 UniProt NPD GO	FZD4_HUMAN	Frizzled-4 precursor (Fz-4) (hFz4) (FzE4)	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	604579		537
Q61088 UniProt NPD GO	FZD4_MOUSE	Frizzled-4 precursor (Fz-4) (mFz4)	0.08	-	end	7	Membrane; multi-pass membrane protein				537
Q9QZH0 UniProt NPD GO	FZD4_RAT	Frizzled-4 precursor (Fz-4) (rFz4)	0.08	-	end	7	Membrane; multi-pass membrane protein				538
Q7KQL9 UniProt NPD GO	ALF_PLAF7	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.08	-	cyt	0					369
P14223 UniProt NPD GO	ALF_PLAFA	Fructose-bisphosphate aldolase (EC 4.1.2.13) (41 kDa antigen)	0.08	-	cyt	0				1A5C	369
P49577 UniProt NPD GO	ALF2_PLABA	Fructose-bisphosphate aldolase 2 (EC 4.1.2.13) (ALDO-2)	0.08	-	cyt	0					358
P53448 UniProt NPD GO	ALDOC_CARAU	Fructose-bisphosphate aldolase C (EC 4.1.2.13) (Brain-type aldolase)	0.08	-	cyt	0					362
P16096 UniProt NPD GO	ALFC_SPIOL	Fructose-bisphosphate aldolase, chloroplast precursor (EC 4.1.2.13)	0.08	-	cyt	0	Plastid; chloroplast				394
P51810 UniProt NPD GO	GP143_HUMAN	G-protein coupled receptor 143 (Ocular albinism type 1 protein)	0.08	-	end	6	Melanosome; melanosomal membrane; multi-pass membrane protein. Targeted to intracellular organelles, ...	cytoplasm [TAS] integral to membrane [TAS] membrane [TAS] membrane fraction [TAS]	300500		404
Q923Z0 UniProt NPD GO	GPC5B_MOUSE	G-protein coupled receptor family C group 5 member B precursor (Retinoic acid-induced gene 2 protein ...	0.08	-	end	7	Membrane; multi-pass membrane protein				410
P40801 UniProt NPD GO	GAL10_PACTA	GAL10 bifunctional protein [Includes: UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase); Aldos ...	0.08	-	cyt	0					689
Q6FJ81 UniProt NPD GO	MCD4_CANGA	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.08	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				921
Q6C0Z3 UniProt NPD GO	MCD4_YARLI	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.08	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				932
P39012 UniProt NPD GO	GAA1_YEAST	GPI transamidase component GAA1	0.08	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	GPI-anchor transamidase complex [IPI]			614
P41733 UniProt NPD GO	CDC91_YEAST	GPI transamidase component GAB1 (Cell division control protein 91)	0.08	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	GPI-anchor transamidase complex [IMP]			394
Q04080 UniProt NPD GO	GPI17_YEAST	GPI transamidase component GPI17	0.08	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	GPI-anchor transamidase complex [IMP]			534
Q9UTL4 UniProt NPD GO	GWT1_SCHPO	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.08	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				459
Q9VUN3 UniProt NPD GO	RANL_DROME	GTP-binding nuclear protein Ran-like	0.08	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			217
Q8MQT8 UniProt NPD GO	SAR1_GIALA	GTP-binding protein Sar1	0.08	-	cyt	0					191
P36586 UniProt NPD GO	YPT5_SCHPO	GTP-binding protein ypt5	0.08	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				211
Q9WTP7 UniProt NPD GO	KAD3_MOUSE	GTP:AMP phosphotransferase mitochondrial (EC 2.7.4.10) (Adenylate kinase 3) (AK3) (Adenylate kinase ...	0.08	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			226
P09608 UniProt NPD GO	GAL1_KLULA	Galactokinase (EC 2.7.1.6) (Galactose kinase)	0.08	-	mit	0					503
Q866C5 UniProt NPD GO	FUT1_CALBN	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.08	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
Q9TUD4 UniProt NPD GO	FUT1_GORGO	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.08	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
O09160 UniProt NPD GO	FUT1_MOUSE	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.08	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				376
Q10980 UniProt NPD GO	FUT1_RAT	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.08	-	vac	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				376
Q866F0 UniProt NPD GO	FUT1_SAIBB	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.08	-	vac	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
Q866F1 UniProt NPD GO	FUT1_SAISC	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.08	-	vac	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
Q9NY99 UniProt NPD GO	SNTG2_HUMAN	Gamma-2-syntrophin (G2SYN) (Syntrophin 5) (SYN5)	0.08	-	cyt	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side. In skeletal muscle, ...	syntrophin complex [TAS]	608715		539
Q9QWE9 UniProt NPD GO	GGT5_RAT	Gamma-glutamyltransferase 5 precursor (EC 2.3.2.2) (Gamma-glutamyltransferase-like activity 1) (Gamm ...	0.08	-	end	1 *	Membrane; single-pass type II membrane protein (By similarity)				572
P36268 UniProt NPD GO	GGTL2_HUMAN	Gamma-glutamyltransferase-like protein 2	0.08	-	cyt	0			137181		215
Q9US04 UniProt NPD GO	GGT1_SCHPO	Gamma-glutamyltranspeptidase 1 precursor (EC 2.3.2.2) (Gamma-glutamyltransferase 1) [Contains: Gamma ...	0.08	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				630
Q90358 UniProt NPD GO	PA2I_CRODU	Gamma-phospholipase A2 inhibitor CNF precursor (Crotalus neutralizing factor) (Crotoxin inhibitor)	0.08	-	nuc	0	Secreted protein				200
Q8BVF7 UniProt NPD GO	APH1A_MOUSE	Gamma-secretase subunit APH-1A (APH-1a) (Aph-1alpha)	0.08	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to plasma membrane [ISS]			265
P51915 UniProt NPD GO	CX32_MICUN	Gap junction Cx32.2 protein (Connexin-32.2)	0.08	-	end	3 *	Membrane; multi-pass membrane protein				284
P28231 UniProt NPD GO	CXB3_MOUSE	Gap junction beta-3 protein (Connexin-31) (Cx31)	0.08	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [IDA]			270
Q02739 UniProt NPD GO	CXB5_MOUSE	Gap junction beta-5 protein (Connexin-31.1) (Cx31.1)	0.08	-	end	4 *	Membrane; multi-pass membrane protein				271
Q9N2D3 UniProt NPD GO	PEPC_CALJA	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C)	0.08	-	nuc	0	Secreted protein				388
Q28372 UniProt NPD GO	GELS_HORSE	Gelsolin (Actin-depolymerizing factor) (ADF) (Brevin)	0.08	-	cyt	0	Cytoplasm			2FGH	730
P06396 UniProt NPD GO	GELS_HUMAN	Gelsolin precursor (Actin-depolymerizing factor) (ADF) (Brevin) (AGEL)	0.08	-	exc	0	Isoform 2: Cytoplasm. Isoform 1: Secreted protein	actin cytoskeleton [TAS] cytosol [IDA] extracellular region [IDA]	105120	2FF6	782
P80042 UniProt NPD GO	GGPPS_CAPAN	Geranylgeranyl pyrophosphate synthetase, chloroplast precursor (GGPP synthetase) (GGPS) [Includes: D ...	0.08	-	cyt	0	Plastid; chloroplast	plastid [IDA]			369
P83171 UniProt NPD GO	GKBL_GINBI	Ginkbilobin (GNL) (Fragment)	0.08	-	nuc	0					40
P60984 UniProt NPD GO	GMFB_BOVIN	Glia maturation factor beta (GMF-beta)	0.08	+	cyt	0					141
P60983 UniProt NPD GO	GMFB_HUMAN	Glia maturation factor beta (GMF-beta)	0.08	+	cyt	0			601713		141
Q5R6P6 UniProt NPD GO	GMFB_PONPY	Glia maturation factor beta (GMF-beta)	0.08	+	cyt	0					141
Q63228 UniProt NPD GO	GMFB_RAT	Glia maturation factor beta (GMF-beta)	0.08	+	cyt	0					141
P52334 UniProt NPD GO	GLB2_CHLEU	Globin LI410	0.08	-	mit	0	Plastid; chloroplast. Particularly in the pyrenoid and the thylakoid region				171

You are viewing entries 68051 to 68100 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.