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
P05065 UniProt NPD GO	ALDOA_RAT	Fructose-bisphosphate aldolase A (EC 4.1.2.13) (Muscle-type aldolase)	0.09	-	cyt	0					363
P52210 UniProt NPD GO	ALDOB_SHEEP	Fructose-bisphosphate aldolase B (EC 4.1.2.13) (Liver-type aldolase)	0.09	-	cyt	0					363
P18891 UniProt NPD GO	LECF_ALEAU	Fucose-specific lectin (Aleuria aurantia lectin) (AAL)	0.09	-	cyt	0				1OFZ	312
Q08585 UniProt NPD GO	FCPB_PHATR	Fucoxanthin-chlorophyll a-c binding protein B, chloroplast precursor	0.09	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				198
Q9H9S5 UniProt NPD GO	FKRP_HUMAN	Fukutin-related protein (EC 2.-.-.-)	0.09	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		607155		495
P93033 UniProt NPD GO	FUM1_ARATH	Fumarate hydratase 1, mitochondrial precursor (EC 4.2.1.2) (Fumarase 1)	0.09	-	mit	0	Mitochondrion				492
Q9GT50 UniProt NPD GO	MTH_DROYA	G-protein coupled receptor Mth precursor (Protein methuselah)	0.09	-	end	7	Membrane; multi-pass membrane protein (Potential)				517
Q9NZD1 UniProt NPD GO	GPC5D_HUMAN	G-protein coupled receptor family C group 5 member D	0.09	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [NAS]	607437		345
Q9PW88 UniProt NPD GO	GPC6A_CARAU	G-protein coupled receptor family C group 6 member A precursor (Odorant receptor 5.24)	0.09	-	end	7	Membrane; multi-pass membrane protein (By similarity)				877
Q8R050 UniProt NPD GO	GSPT1_MOUSE	G1 to S phase transition protein 1 homolog	0.09	-	cyt	0		intracellular [ISS]			499
P15170 UniProt NPD GO	GSPT1_HUMAN	G1 to S phase transition protein 1 homolog (GTP-binding protein GST1-HS)	0.09	-	cyt	0		intracellular [NAS]	139259		499
Q8K3X2 UniProt NPD GO	FCL_CRIGR	GDP-L-fucose synthetase (EC 1.1.1.271) (Protein FX) (Red cell NADP(H)-binding protein) (GDP-4-keto-6 ...	0.09	-	cyt	0					321
Q13630 UniProt NPD GO	FCL_HUMAN	GDP-L-fucose synthetase (EC 1.1.1.271) (Protein FX) (Red cell NADP(H)-binding protein) (GDP-4-keto-6 ...	0.09	-	cyt	0		cytoplasm [IC]	137020		321
Q5RBE5 UniProt NPD GO	FCL_PONPY	GDP-L-fucose synthetase (EC 1.1.1.271) (Protein FX) (Red cell NADP(H)-binding protein) (GDP-4-keto-6 ...	0.09	-	cyt	0					321
Q9H488 UniProt NPD GO	OFUT1_HUMAN	GDP-fucose protein O-fucosyltransferase 1 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.09	-	exc	0	Endoplasmic reticulum (By similarity)	cytoplasm [ISS] integral to Golgi membrane [NAS]	607491		388
Q6EV69 UniProt NPD GO	OFUT1_PANTR	GDP-fucose protein O-fucosyltransferase 1 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.09	-	exc	0	Endoplasmic reticulum (By similarity)				388
Q9SNY3 UniProt NPD GO	GMD1_ARATH	GDP-mannose 4,6 dehydratase 1 (EC 4.2.1.47) (GDP-D-mannose dehydratase 1) (GMD 1)	0.09	-	cyt	0					361
Q6CW36 UniProt NPD GO	MCD4_KLULA	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.09	-	end	15 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				919
Q9P6R5 UniProt NPD GO	GPI14_SCHPO	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.09	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				371
Q7T310 UniProt NPD GO	PIGM_BRARE	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.09	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				392
Q6BRZ9 UniProt NPD GO	GPI18_DEBHA	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.09	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				428
Q6FTY5 UniProt NPD GO	GPI10_CANGA	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.09	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				612
Q9USN0 UniProt NPD GO	GPI10_SCHPO	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.09	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				506
Q5A0L9 UniProt NPD GO	SMP3_CANAL	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV) (CaSMP3)	0.09	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				498
Q754I2 UniProt NPD GO	GWT1_ASHGO	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.09	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				480
O61573 UniProt NPD GO	GCH1_OSTOS	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I)	0.09	-	cyt	0					213
Q19705 UniProt NPD GO	ARFM_CAEEL	GTP-binding ADP-ribosylation factor homolog protein evl-20	0.09	-	nuc	0					184
Q9VZ23 UniProt NPD GO	RAN_DROME	GTP-binding nuclear protein Ran	0.09	+	cyt	0	Nucleus. Cytoplasm. Localizes around the microtubule spindle during mitosis	cytoplasm [IDA] nuclear microtubule [IDA]			216
Q8K586 UniProt NPD GO	RANT_RAT	GTP-binding nuclear protein Ran, testis-specific isoform	0.09	+	cyt	0	Nucleus				216
Q05737 UniProt NPD GO	YPTM2_MAIZE	GTP-binding protein YPTM2	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
Q95ME4 UniProt NPD GO	RASN_MONDO	GTPase NRas precursor (Transforming protein N-Ras)	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				189
Q9TUD6 UniProt NPD GO	FUT1_PANTR	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.09	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
P19526 UniProt NPD GO	FUT1_HUMAN	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.09	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	Golgi apparatus [TAS] integral to plasma membrane [TAS] membrane fraction [TAS]	211100		365
Q96DT0 UniProt NPD GO	LEG12_HUMAN	Galectin-12 (Galectin-related inhibitor of proliferation)	0.09	-	mit	0	Nucleus		606096		336
P16110 UniProt NPD GO	LEG3_MOUSE	Galectin-3 (Galactose-specific lectin 3) (Mac-2 antigen) (IgE-binding protein) (35 kDa lectin) (Carb ...	0.09	-	nuc	0	Nucleus. Cytoplasmic in adenomas and carcinomas (By similarity). May be secreted by a non-classical ...	cytoplasm [IDA] extracellular matrix (sensu Metazoa) [IDA] nucleus [IDA]			263
Q925E0 UniProt NPD GO	SNTG2_MOUSE	Gamma-2-syntrophin (G2SYN) (Syntrophin 5) (SYN5)	0.09	-	cyt	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side. In skeletal muscle, ...				539
Q9YGJ0 UniProt NPD GO	NXLHI_BUNMU	Gamma-bungarotoxin precursor 1 (Long neurotoxin homolog NTL2I)	0.09	-	nuc	0	Secreted protein				89
Q9W796 UniProt NPD GO	NXLH5_BUNMU	Gamma-bungarotoxin precursor 2 (Long neurotoxin homolog)	0.09	-	nuc	0	Secreted protein			1MR6	89
Q62867 UniProt NPD GO	GGH_RAT	Gamma-glutamyl hydrolase precursor (EC 3.4.19.9) (Gamma-Glu-X carboxypeptidase) (Conjugase) (GH)	0.09	-	exc	0	Secreted protein; extracellular space. Lysosome. While its intracellular location is primarily the l ...	extracellular space [TAS] lysosome [TAS]			317
Q9Z0L8 UniProt NPD GO	GGH_MOUSE	Gamma-glutamyl hydrolase precursor (EC 3.4.19.9) (Gamma-Glu-x carboxypeptidase) (Conjugase) (GH) (Fo ...	0.09	-	exc	0	Secreted protein; extracellular space (By similarity). Lysosome (By similarity). While its intracell ...	lysosome [TAS]			317
P36269 UniProt NPD GO	GGT5_HUMAN	Gamma-glutamyltransferase 5 precursor (EC 2.3.2.2) (Gamma-glutamyltranspeptidase 5) (Gamma-glutamylt ...	0.09	-	end	1 *	Membrane; single-pass type II membrane protein (By similarity)	integral to membrane [TAS]	137168		586
P51916 UniProt NPD GO	CX33_MICUN	Gap junction Cx32.7 protein (Connexin-32.7)	0.09	-	end	4 *	Membrane; multi-pass membrane protein				281
P08050 UniProt NPD GO	CXA1_RAT	Gap junction alpha-1 protein (Connexin-43) (Cx43) (Gap junction 43 kDa heart protein)	0.09	-	end	4 *	Membrane; multi-pass membrane protein	connexon complex [TAS] integral to plasma membrane [TAS]		1R5S	381
P28235 UniProt NPD GO	CXA4_MOUSE	Gap junction alpha-4 protein (Connexin-37) (Cx37)	0.09	-	end	4 *	Membrane; multi-pass membrane protein				332
P25305 UniProt NPD GO	CXB3_RAT	Gap junction beta-3 protein (Connexin-31) (Cx31)	0.09	-	end	4 *	Membrane; multi-pass membrane protein				270
O95377 UniProt NPD GO	CXB5_HUMAN	Gap junction beta-5 protein (Connexin-31.1) (Cx31.1)	0.09	-	end	4 *	Membrane; multi-pass membrane protein		604493		273
P87508 UniProt NPD GO	OBP1_ANTPE	General odorant-binding protein 1 precursor (GOBP 1)	0.09	-	mit	0					167
O22043 UniProt NPD GO	GGPP6_ARATH	Geranylgeranyl pyrophosphate synthetase 6, mitochondrial precursor (GGPP synthetase 6) (GGPS6) [Incl ...	0.09	-	mit	0	Mitochondrion				336
Q76IQ4 UniProt NPD GO	GHRL_ONCMY	Ghrelin precursor [Contains: Ghrelin-23; Ghrelin-24]	0.09	-	exc	0	Secreted protein	extracellular space [ISS]			111
P27613 UniProt NPD GO	GLBH_TRICO	Globin-like host-protective antigen precursor	0.09	-	exc	0	Secreted protein; extracellular space				173

You are viewing entries 66151 to 66200 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.