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
Q9SZY1 UniProt NPD GO	NACA4_ARATH	Nascent polypeptide-associated complex subunit alpha-like protein 4 (NAC-alpha-like protein 4) (Alph ...	0.15	-	cyt	0					212
P17157 UniProt NPD GO	PHO85_YEAST	Negative regulator of the PHO system (EC 2.7.11.22) (Serine/threonine-protein kinase PHO85)	0.15	-	cyt	0		nucleus [IDA]			305
Q9JI33 UniProt NPD GO	NET4_MOUSE	Netrin-4 precursor (Beta-netrin)	0.15	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basement membrane [IDA]			628
P13592 UniProt NPD GO	NCA12_HUMAN	Neural cell adhesion molecule 1, 120 kDa isoform precursor (N-CAM 120) (NCAM-120) (CD56 antigen)	0.15	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	integral to membrane [TAS] plasma membrane [TAS]	116930		761
P36335 UniProt NPD GO	NCA12_XENLA	Neural cell adhesion molecule 1-B precursor	0.15	-	nuc	1 *	Membrane; single-pass type I membrane protein				1092
P36609 UniProt NPD GO	NCS2_CAEEL	Neuronal calcium sensor 2 (NCS-2)	0.15	+	cyt	0					189
P83996 UniProt NPD GO	TX27_PHONI	Neurotoxin PNTx27C4	0.15	-	nuc	0	Secreted protein				36
P34130 UniProt NPD GO	NT5_HUMAN	Neurotrophin-5 precursor (NT-5) (Neutrophic factor 5) (Neurotrophin-4) (NT-4) (Neutrophic factor 4)	0.15	-	end	0	Secreted protein		162662	1HCF	210
Q5G862 UniProt NPD GO	DEF4_PANTR	Neutrophil defensin 4 precursor (Defensin, alpha 4)	0.15	-	exc	0	Secreted protein				97
P12838 UniProt NPD GO	DEF4_HUMAN	Neutrophil defensin 4 precursor (HNP-4) (HP-4) (Defensin, alpha 4)	0.15	-	exc	0	Secreted protein		601157		97
O35604 UniProt NPD GO	NPC1_MOUSE	Niemann-Pick C1 protein precursor	0.15	-	end	12	Endosome; late endosome; late endosomal membrane; single-pass membrane protein. Lysosome; lysosomal ...	endoplasmic reticulum [ISS] integral to plasma membrane [ISS] lysosome [ISS] nuclear envelope [ISS] perinuclear region [ISS]			1278
Q8SPY6 UniProt NPD GO	RNAS2_CERAE	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.15	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule (By similarity)				160
P11654 UniProt NPD GO	PO210_RAT	Nuclear pore membrane glycoprotein 210 precursor (POM210) (Nuclear pore protein gp210)	0.15	-	end	1	Nucleus; nuclear envelope; nuclear pore complex; single-pass type I membrane protein. Endoplasmic re ...	nuclear pore [TAS]			1886
Q9P926 UniProt NPD GO	NTF2_CANAL	Nuclear transport factor 2 (NTF-2)	0.15	-	cyt	0	Cytoplasm (By similarity)				124
Q96UP2 UniProt NPD GO	NEP1_CANGA	Nucleolar essential protein 1 (Essential for mitotic growth 1)	0.15	-	nuc	0	Nucleus; nucleolus (By similarity)				229
P59235 UniProt NPD GO	NUP43_MOUSE	Nucleoporin Nup43	0.15	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity)				380
Q8NFH3 UniProt NPD GO	NUP43_HUMAN	Nucleoporin Nup43 (p42)	0.15	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex		608141		380
Q9Y5B8 UniProt NPD GO	NDK7_HUMAN	Nucleoside diphosphate kinase 7 (EC 2.7.4.6) (NDK 7) (NDP kinase 7) (nm23-H7)	0.15	-	cyt	0					376
Q8WV74 UniProt NPD GO	NUDT8_HUMAN	Nucleoside diphosphate-linked moiety X motif 8, mitochondrial precursor (EC 3.6.1.-) (Nudix motif 8) ...	0.15	-	cyt	0	Mitochondrion (By similarity)				236
Q8L831 UniProt NPD GO	NUDT3_ARATH	Nudix hydrolase 3 (EC 3.6.1.-) (AtNUDT3)	0.15	-	cyt	0					772
O46077 UniProt NPD GO	OR2A_DROME	Odorant receptor 2a	0.15	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			397
Q8NGS6 UniProt NPD GO	O13C3_HUMAN	Olfactory receptor 13C3	0.15	-	end	7 *	Membrane; multi-pass membrane protein				317
Q9TUA1 UniProt NPD GO	OR1E5_PANTR	Olfactory receptor 1E5	0.15	-	end	6 *	Membrane; multi-pass membrane protein				314
Q9TU89 UniProt NPD GO	OR3A1_GORGO	Olfactory receptor 3A1	0.15	-	end	7 *	Membrane; multi-pass membrane protein				315
Q9TUA4 UniProt NPD GO	OR3A1_PANTR	Olfactory receptor 3A1	0.15	-	end	6 *	Membrane; multi-pass membrane protein				315
P47881 UniProt NPD GO	OR3A1_HUMAN	Olfactory receptor 3A1 (Olfactory receptor 17-40) (OR17-40)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				315
P58180 UniProt NPD GO	OR4D2_HUMAN	Olfactory receptor 4D2 (Olfactory receptor OR17-24) (B-lymphocyte membrane protein BC2009)	0.15	-	end	6 *	Membrane; multi-pass membrane protein				307
Q8NGN0 UniProt NPD GO	OR4D5_HUMAN	Olfactory receptor 4D5 (Olfactory receptor OR11-276)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				318
P81596 UniProt NPD GO	TOT1C_HADVE	Omega-atracotoxin-Hv1c (Omega-AcTx-Hv1c)	0.15	+	nuc	0	Secreted protein				37
P58914 UniProt NPD GO	CXO6A_CONRA	Omega-conotoxin RVIA	0.15	-	nuc	0	Secreted protein				27
P11916 UniProt NPD GO	RNASO_RANCA	Oocytes ribonuclease precursor (EC 3.1.27.-) (RC-RNase) (Sialic acid-binding lectin) (SBL-C)	0.15	-	nuc	0	Secreted protein			1M07	133
Q9H6K4 UniProt NPD GO	OPA3_HUMAN	Optic atrophy 3 protein	0.15	-	nuc	0			606580		179
Q9WTW5 UniProt NPD GO	S22A3_MOUSE	Organic cation transporter 3 (Solute carrier family 22 member 3)	0.15	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			551
O88446 UniProt NPD GO	S22A3_RAT	Organic cation transporter 3 (Solute carrier family 22 member 3)	0.15	-	end	12 *	Membrane; multi-pass membrane protein				551
P08432 UniProt NPD GO	DCOR_YEAST	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.15	-	cyt	0		cytoplasm [IDA]			466
P10588 UniProt NPD GO	EAR2_HUMAN	Orphan nuclear receptor EAR-2 (V-erbA-related protein EAR-2)	0.15	-	cyt	0	Nucleus (Potential)		132880		404
P25776 UniProt NPD GO	ORYA_ORYSA	Oryzain alpha chain precursor (EC 3.4.22.-)	0.15	-	exc	1 *					458
P83371 UniProt NPD GO	OTO1_ONCKE	Otolin-1 precursor	0.15	-	mit	0	Secreted protein	extracellular region [IDA]			508
Q9PRS8 UniProt NPD GO	OC17_CHICK	Ovocleidin-17 (OC-17)	0.15	-	cyt	0	Eggshell matrix; mostly in the mammillary bodies			1GZ2	142
P10184 UniProt NPD GO	IOV7_CHICK	Ovoinhibitor precursor	0.15	-	exc	0	Secreted protein				472
Q8TDS5 UniProt NPD GO	OXER1_HUMAN	Oxoeicosanoid receptor 1 (G-protein coupled receptor TG1019) (5-oxo-ETE G-protein coupled receptor) ...	0.15	-	end	6	Membrane; multi-pass membrane protein				423
Q9UW25 UniProt NPD GO	OBPA_CANAL	Oxysterol-binding protein-like protein OBPa	0.15	-	cyt	0					433
Q9UW21 UniProt NPD GO	OBPAL_CANAL	Oxysterol-binding protein-like protein OBPalpha	0.15	-	cyt	0					429
P01178 UniProt NPD GO	NEU1_HUMAN	Oxytocin-neurophysin 1 precursor (OT-NPI) [Contains: Oxytocin (Ocytocin); Neurophysin 1]	0.15	-	exc	0	Secreted protein		167050	1XY2	125
Q04671 UniProt NPD GO	P_HUMAN	P protein (Melanocyte-specific transporter protein) (Pink-eyed dilution protein homolog)	0.15	-	end	12	Melanosome; melanosomal membrane; multi-pass membrane protein	cytoplasm [TAS] integral to membrane [TAS]	203310		838
Q99677 UniProt NPD GO	P2RY9_HUMAN	P2Y purinoceptor 9 (P2Y9) (Purinergic receptor 9) (G-protein coupled receptor 23) (P2Y5-like recepto ...	0.15	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	300086		370
Q6P7E4 UniProt NPD GO	PDLI7_BRARE	PDZ and LIM domain protein 7	0.15	-	nuc	0					419
Q32LE7 UniProt NPD GO	PDZ11_BOVIN	PDZ domain-containing protein 11	0.15	-	cyt	0					140
Q9CZG9 UniProt NPD GO	PDZ11_MOUSE	PDZ domain-containing protein 11	0.15	-	cyt	0				1WI2	140
Q6QA76 UniProt NPD GO	PDZ11_PIG	PDZ domain-containing protein 11	0.15	-	cyt	0					140

You are viewing entries 57301 to 57350 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.