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
Q16658 UniProt NPD GO	FSCN1_HUMAN	Fascin (Singed-like protein) (55 kDa actin-bundling protein) (p55)	0.24	-	cyt	0		actin cytoskeleton [TAS]	602689	1DFC	492
Q9NQT6 UniProt NPD GO	FSCN3_HUMAN	Fascin-3 (Testis fascin)	0.24	-	cyt	0		cytoskeleton [TAS]			498
P04117 UniProt NPD GO	FABPA_MOUSE	Fatty acid-binding protein, adipocyte (AFABP) (Adipocyte lipid-binding protein) (ALBP) (A-FABP) (P2 ...	0.24	-	cyt	0	Cytoplasm (Potential)			2ANS	131
P42044 UniProt NPD GO	HEMH_CUCSA	Ferrochelatase-2, chloroplast precursor (EC 4.99.1.1) (Ferrochelatase II) (Protoheme ferro-lyase 2) ...	0.24	-	nuc	1	Plastid; chloroplast				514
Q9NSA1 UniProt NPD GO	FGF21_HUMAN	Fibroblast growth factor 21 precursor (FGF-21)	0.24	-	nuc	0	Secreted protein (Potential)	extracellular region [TAS] soluble fraction [TAS]	609436		209
P28891 UniProt NPD GO	FIBR_AGKCO	Fibrolase (EC 3.4.24.72) (Fibrinolytic proteinase) (Alfimeprase)	0.24	-	mit	0					203
P15216 UniProt NPD GO	FBP2_STRPU	Fibropellin-2 precursor (Fibropellin II) (Epidermal growth factor-related protein 2)	0.24	-	nuc	1 *					325
Q90844 UniProt NPD GO	FST_CHICK	Follistatin precursor (FS) (Activin-binding protein)	0.24	-	nuc	0	Secreted protein	extracellular region [ISS]			343
Q8N475 UniProt NPD GO	FSTL5_HUMAN	Follistatin-related protein 5 precursor (Follistatin-like 5)	0.24	-	exc	0	Secreted protein (Probable)				847
P37236 UniProt NPD GO	FREQ_DROME	Frequenin-1 (d-FRQ)	0.24	-	cyt	0	Membrane; lipid-anchor (By similarity)				186
Q8BKG4 UniProt NPD GO	FZD10_MOUSE	Frizzled-10 precursor (Fz-10)	0.24	-	end	7	Membrane; multi-pass membrane protein (By similarity)				582
Q8K4Z6 UniProt NPD GO	GPC6A_MOUSE	G-protein coupled receptor family C group 6 member A precursor	0.24	-	end	7	Cell membrane; multi-pass membrane protein	cell surface [IDA]			928
Q12849 UniProt NPD GO	GRSF1_HUMAN	G-rich sequence factor 1 (GRSF-1)	0.24	-	mit	0	Cytoplasm	cytoplasm [TAS]	604851		447
Q2KI22 UniProt NPD GO	CCND1_BOVIN	G1/S-specific cyclin-D1	0.24	-	cyt	0					295
P07818 UniProt NPD GO	CCNB_ARBPU	G2/mitotic-specific cyclin-B	0.24	-	cyt	0					409
Q17045 UniProt NPD GO	AGP1_ASCSU	GTP-binding protein AGP-1	0.24	-	mit	0					591
O82626 UniProt NPD GO	ERG_ANTMA	GTP-binding protein ERG	0.24	-	mit	0					423
O08573 UniProt NPD GO	LEG9_MOUSE	Galectin-9	0.24	-	cyt	0	Cytoplasm. Secreted protein. May also be secreted by a non-classical secretory pathway				353
P97840 UniProt NPD GO	LEG9_RAT	Galectin-9 (36 kDa beta-galactoside-binding lectin) (Urate transporter/channel) (UAT)	0.24	-	cyt	0	Cytoplasm (By similarity). Secreted protein (By similarity). May also be secreted by a non-classical ...				354
P10064 UniProt NPD GO	GBRA3_BOVIN	Gamma-aminobutyric-acid receptor alpha-3 subunit precursor (GABA(A) receptor)	0.24	-	end	4 *	Membrane; multi-pass membrane protein				492
P26049 UniProt NPD GO	GBRA3_MOUSE	Gamma-aminobutyric-acid receptor alpha-3 subunit precursor (GABA(A) receptor)	0.24	-	end	4 *	Membrane; multi-pass membrane protein				492
Q16445 UniProt NPD GO	GBRA6_HUMAN	Gamma-aminobutyric-acid receptor alpha-6 subunit precursor (GABA(A) receptor)	0.24	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137143		453
Q08832 UniProt NPD GO	GBRB3_DROME	Gamma-aminobutyric-acid receptor subunit beta-like precursor (GABA(A) receptor)	0.24	+	end	5 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			496
O14764 UniProt NPD GO	GBRD_HUMAN	Gamma-aminobutyric-acid receptor subunit delta precursor (GABA(A) receptor)	0.24	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137163		452
P28234 UniProt NPD GO	CXA5_RAT	Gap junction alpha-5 protein (Connexin-40) (Cx40)	0.24	-	end	3 *	Membrane; multi-pass membrane protein	connexon complex [IDA]			355
P52500 UniProt NPD GO	GRPR_RAT	Gastrin-releasing peptide receptor (GRP-R) (GRP-preferring bombesin receptor)	0.24	-	end	7 *	Membrane; multi-pass membrane protein				384
P18718 UniProt NPD GO	ZG3_XENLA	Gastrula zinc finger protein XLCGF3.1 (Fragment)	0.24	-	nuc	0	Nucleus (Potential)				196
Q9H840 UniProt NPD GO	GEMI7_HUMAN	Gem-associated protein 7 (Gemin-7) (SIP3)	0.24	-	cyt	0	Nucleus. Found both in the nucleoplasm and in nuclear bodies called gems (Gemini of Cajal bodies) th ...	cytoplasm [IDA] nuclear body [IDA] nucleoplasm [IDA]	607419	1Y96	131
P07092 UniProt NPD GO	GDN_RAT	Glia-derived nexin precursor (GDN) (Protease nexin I) (PN-1)	0.24	-	exc	0	Secreted protein; extracellular space				397
Q9PUR0 UniProt NPD GO	GLUC2_PETMA	Glucagon-2 precursor [Contains: Glucagon-2 (Glucagon II) (Glu II); Glucagon-like peptide 2-II (GLP-2 ...	0.24	-	exc	1 *	Secreted protein				120
P42042 UniProt NPD GO	AMYG_ARXAD	Glucoamylase precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrolas ...	0.24	-	vac	0					624
Q43793 UniProt NPD GO	G6PDC_TOBAC	Glucose-6-phosphate 1-dehydrogenase, chloroplast precursor (EC 1.1.1.49) (G6PD)	0.24	-	mit	0	Plastid; chloroplast				593
P34299 UniProt NPD GO	GLR1_CAEEL	Glutamate receptor 1 precursor	0.24	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	cell soma [IDA] neuron projection [IDA] postsynaptic membrane [IDA]			962
Q9ZNX6 UniProt NPD GO	GSH1_MEDTR	Glutamate--cysteine ligase, chloroplast precursor (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) ( ...	0.24	-	mit	0	Plastid; chloroplast (By similarity)				508
Q28120 UniProt NPD GO	QPCT_BOVIN	Glutaminyl-peptide cyclotransferase precursor (EC 2.3.2.5) (QC) (Glutaminyl-tRNA cyclotransferase) ( ...	0.24	-	end	0					361
Q3MHH4 UniProt NPD GO	SYQ_BOVIN	Glutaminyl-tRNA synthetase (EC 6.1.1.18) (Glutamine--tRNA ligase) (GlnRS)	0.24	-	cyt	0	Cytoplasm (By similarity)				775
Q96563 UniProt NPD GO	HEM12_HORVU	Glutamyl-tRNA reductase 2 (EC 1.2.1.70) (GluTR) (Fragment)	0.24	-	cyt	0	Plastid; chloroplast				465
Q5RC53 UniProt NPD GO	GLRX2_PONPY	Glutaredoxin-2, mitochondrial precursor	0.24	-	mit	0	Mitochondrion (By similarity)				161
P28161 UniProt NPD GO	GSTM2_HUMAN	Glutathione S-transferase Mu 2 (EC 2.5.1.18) (GSTM2-2) (GST class-mu 2)	0.24	-	cyt	0	Cytoplasm		138380	3GTU	217
O35660 UniProt NPD GO	GSTM6_MOUSE	Glutathione S-transferase Mu 6 (EC 2.5.1.18) (GST class-mu 6) (Glutathione-S-transferase class M5)	0.24	-	cyt	0	Cytoplasm (By similarity)				218
Q10075 UniProt NPD GO	PCS_SCHPO	Glutathione gamma-glutamylcysteinyltransferase (EC 2.3.2.15) (Phytochelatin synthase)	0.24	-	mit	0					414
P78965 UniProt NPD GO	GSHR_SCHPO	Glutathione reductase (EC 1.8.1.7) (GR) (GRase)	0.24	-	nuc	0	Cytoplasm (By similarity)				464
Q43822 UniProt NPD GO	PLSB_PHAVU	Glycerol-3-phosphate acyltransferase, chloroplast precursor (EC 2.3.1.15) (GPAT)	0.24	-	mit	0	Plastid; chloroplast; chloroplast stroma				461
P49362 UniProt NPD GO	GCSPB_FLAPR	Glycine dehydrogenase [decarboxylating] B, mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxyla ...	0.24	-	mit	0	Mitochondrion				1034
Q8CI94 UniProt NPD GO	PYGB_MOUSE	Glycogen phosphorylase, brain form (EC 2.4.1.1)	0.24	-	nuc	0					842
P06737 UniProt NPD GO	PYGL_HUMAN	Glycogen phosphorylase, liver form (EC 2.4.1.1)	0.24	-	nuc	0			232700	1XOI	846
Q9NHB0 UniProt NPD GO	BGBP1_DROME	Gram-negative bacteria-binding protein 1 precursor	0.24	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted and attached to the membrane by a GPI-anchor	extracellular region [IDA]			494
P35834 UniProt NPD GO	CSF3_CANFA	Granulocyte colony-stimulating factor (G-CSF)	0.24	-	cyt	0	Secreted protein			1BGE	175
P35833 UniProt NPD GO	CSF3_BOVIN	Granulocyte colony-stimulating factor precursor (G-CSF)	0.24	-	exc	0	Secreted protein			1BGC	195
P04141 UniProt NPD GO	CSF2_HUMAN	Granulocyte-macrophage colony-stimulating factor precursor (GM-CSF) (Colony-stimulating factor) (CSF ...	0.24	-	exc	0	Secreted protein		138960	2GMF	144

You are viewing entries 46301 to 46350 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.