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
O75072 UniProt NPD GO	FCMD_HUMAN	Fukutin (EC 2.-.-.-) (Fukuyama-type congenital muscular dystrophy protein)	0.13	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	extracellular space [TAS]	607440		461
P55250 UniProt NPD GO	FUMH_RHIOR	Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase)	0.13	-	mit	0	Mitochondrion. Cytoplasm				494
P25093 UniProt NPD GO	FAAA_RAT	Fumarylacetoacetase (EC 3.7.1.2) (Fumarylacetoacetate hydrolase) (Beta-diketonase) (FAA)	0.13	-	cyt	0					419
O97148 UniProt NPD GO	MTH_DROME	G-protein coupled receptor Mth precursor (Protein methuselah)	0.13	-	end	7	Cell membrane; multi-pass membrane protein. Plasma membrane of presynaptic terminals and innervating ...	integral to membrane [TAS]		1FJR	514
P25106 UniProt NPD GO	RDC1_HUMAN	G-protein coupled receptor RDC1 homolog (Chemokine orphan receptor 1) (G-protein coupled receptor 15 ...	0.13	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			362
Q5U9X3 UniProt NPD GO	GPC6A_BRARE	G-protein coupled receptor family C group 6 member A precursor (Odorant receptor ZO6)	0.13	-	end	7	Membrane; multi-pass membrane protein (By similarity)				867
P37882 UniProt NPD GO	CCNB1_MESAU	G2/mitotic-specific cyclin-B1	0.13	-	mit	0					429
Q9DGA4 UniProt NPD GO	CCNB1_ORYCU	G2/mitotic-specific cyclin-B1	0.13	-	mit	0					401
P30277 UniProt NPD GO	CCNB1_RAT	G2/mitotic-specific cyclin-B1	0.13	-	mit	0					423
P59075 UniProt NPD GO	GMPR_PHYIN	GMP reductase (EC 1.7.1.7) (Guanosine 5'-monophosphate oxidoreductase) (Guanosine monophosphate redu ...	0.13	-	mit	0					362
Q5AMR5 UniProt NPD GO	GPI14_CANAL	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.13	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				398
Q4I073 UniProt NPD GO	GPI14_GIBZE	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.13	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				422
Q6BH65 UniProt NPD GO	GPI10_DEBHA	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.13	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				517
Q4IQ08 UniProt NPD GO	GWT1_GIBZE	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.13	+	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				501
Q6FR65 UniProt NPD GO	GSP1_CANGA	GTP-binding nuclear protein GSP1/Ran	0.13	+	cyt	0	Nucleus (By similarity)				214
P53290 UniProt NPD GO	GTR2_YEAST	GTP-binding protein GTR2	0.13	-	cyt	0		cytoplasm [IDA] nucleus [IDA] vacuolar membrane [IDA]			341
Q9PSM4 UniProt NPD GO	LECG_LACST	Galactose-specific lectin (Mutina)	0.13	-	cyt	0	Secreted protein	extracellular region [NAS]			135
Q90845 UniProt NPD GO	GBRA6_CHICK	Gamma-aminobutyric-acid receptor alpha-6 subunit precursor (GABA(A) receptor)	0.13	-	end	4	Membrane; multi-pass membrane protein				465
P30191 UniProt NPD GO	GBRA6_RAT	Gamma-aminobutyric-acid receptor alpha-6 subunit precursor (GABA(A) receptor)	0.13	-	end	4	Membrane; multi-pass membrane protein				453
Q924Y0 UniProt NPD GO	BODG_MOUSE	Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine,2-oxoglutarate dioxygenase) (Gam ...	0.13	-	cyt	0	Cytoplasm (By similarity)				387
P81127 UniProt NPD GO	SNAG_BOVIN	Gamma-soluble NSF attachment protein (SNAP-gamma) (N-ethylmaleimide-sensitive factor attachment prot ...	0.13	-	nuc	0	Membrane; peripheral membrane protein				312
Q7T047 UniProt NPD GO	CX32_BRARE	Gap junction Cx32.2 protein (Connexin-32.2)	0.13	-	end	3 *	Membrane; multi-pass membrane protein				276
P16864 UniProt NPD GO	CXA2_XENLA	Gap junction alpha-2 protein (Connexin-38) (Cx38)	0.13	-	end	4 *	Membrane; multi-pass membrane protein				334
O18968 UniProt NPD GO	CXB1_BOVIN	Gap junction beta-1 protein (Connexin-32) (Cx32)	0.13	-	end	4 *	Membrane; multi-pass membrane protein				284
Q6WGK6 UniProt NPD GO	CXB1_HORSE	Gap junction beta-1 protein (Connexin-32) (Cx32)	0.13	-	end	4 *	Membrane; multi-pass membrane protein				283
Q60HF7 UniProt NPD GO	CXB1_MACFA	Gap junction beta-1 protein (Connexin-32) (Cx32)	0.13	-	end	4 *	Membrane; multi-pass membrane protein				283
P28230 UniProt NPD GO	CXB1_MOUSE	Gap junction beta-1 protein (Connexin-32) (Cx32)	0.13	-	end	4 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			283
P08034 UniProt NPD GO	CXB1_HUMAN	Gap junction beta-1 protein (Connexin-32) (Cx32) (GAP junction 28 kDa liver protein)	0.13	-	end	4 *	Membrane; multi-pass membrane protein	connexon complex [TAS]	302800	1TXH	283
P08033 UniProt NPD GO	CXB1_RAT	Gap junction beta-1 protein (Connexin-32) (Cx32) (GAP junction 28 kDa liver protein)	0.13	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [IDA]			283
Q5E9Z5 UniProt NPD GO	CXB6_BOVIN	Gap junction beta-6 protein	0.13	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				261
P17267 UniProt NPD GO	IF_RAT	Gastric intrinsic factor precursor (Intrinsic factor) (IF) (INF)	0.13	-	nuc	0	Secreted protein				417
P79266 UniProt NPD GO	GASR_BOVIN	Gastrin/cholecystokinin type B receptor (CCK-B receptor) (CCK-BR) (Cholecystokinin-2 receptor) (CCK2 ...	0.13	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS] plasma membrane [ISS]			454
Q27319 UniProt NPD GO	GELS_HOMAM	Gelsolin, cytoplasmic (Actin-depolymerizing factor) (ADF)	0.13	-	cyt	0	Cytoplasm				754
O61270 UniProt NPD GO	GELS_HALRO	Gelsolin, cytoplasmic (Actin-depolymerizing factor) (ADF) (Ascidian gelsolin)	0.13	-	cyt	0	Cytoplasm				715
Q8MKJ4 UniProt NPD GO	OB57B_DROME	General odorant-binding protein 57b precursor	0.13	-	exc	1 *					141
Q9NQX3 UniProt NPD GO	GEPH_HUMAN	Gephyrin	0.13	-	cyt	0			603930	1JLJ	736
Q758K0 UniProt NPD GO	GGPPS_ASHGO	Geranylgeranyl pyrophosphate synthetase (GGPP synthetase) (GGPPSase) (Geranylgeranyl diphosphate syn ...	0.13	-	cyt	0	Cytoplasm (By similarity)				320
P18108 UniProt NPD GO	GLUC_DIDMA	Glucagon	0.13	-	nuc	0	Secreted protein				29
P68260 UniProt NPD GO	GLUC_MELGA	Glucagon	0.13	-	nuc	0	Secreted protein (By similarity)				29
P04093 UniProt NPD GO	GLUC_ICTPU	Glucagon precursor [Contains: Glucagon; Glucagon-like peptide] (Fragment)	0.13	-	cyt	0	Secreted protein				71
P47871 UniProt NPD GO	GLR_HUMAN	Glucagon receptor precursor (GL-R)	0.13	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	138033		477
P15737 UniProt NPD GO	E13B_HORVU	Glucan endo-1,3-beta-glucosidase GII precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase GII) ...	0.13	-	exc	1 *				1GHS	334
P49237 UniProt NPD GO	E13B_MAIZE	Glucan endo-1,3-beta-glucosidase, acidic isoform precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohyd ...	0.13	-	exc	1 *	Secreted protein; extracellular space (Potential)				335
P14804 UniProt NPD GO	AMYG_NEUCR	Glucoamylase precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrolas ...	0.13	-	vac	0					626
P52792 UniProt NPD GO	HXK4_MOUSE	Glucokinase (EC 2.7.1.2) (Hexokinase-4) (Hexokinase type IV) (HK IV) (HK4) (Hexokinase-D)	0.13	-	cyt	0		mitochondrion [IDA] soluble fraction [IDA]			465
P53704 UniProt NPD GO	GFA1_CANAL	Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] (EC 2.6.1.16) (Hexosephosphate amin ...	0.13	-	cyt	0					712
Q04697 UniProt NPD GO	GSF2_YEAST	Glucose signaling factor 2 (Extracellular matrix protein 6)	0.13	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (Potenti ...	cytoplasm [IDA] integral to endoplasmic reticulum membrane [IDA] mitochondrial outer membrane [IDA]			403
P12298 UniProt NPD GO	GLGL1_WHEAT	Glucose-1-phosphate adenylyltransferase large subunit (EC 2.7.7.27) (ADP-glucose synthase) (ADP-gluc ...	0.13	-	mit	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				301
Q25537 UniProt NPD GO	G6PD_SARBU	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD) (Zwischenferment) (Fragment)	0.13	-	cyt	0					153
P54241 UniProt NPD GO	G6PI2_CLACO	Glucose-6-phosphate isomerase, cytosolic 2 (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phos ...	0.13	-	cyt	0	Cytoplasm (By similarity)				569

You are viewing entries 59701 to 59750 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.