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
Q13485 UniProt NPD GO	SMAD4_HUMAN	Mothers against decapentaplegic homolog 4 (SMAD 4) (Mothers against DPP homolog 4) (Deletion target ...	0.39	-	nuc	0	Cytoplasm. In the cytoplasm in the absence of ligand. Nucleus. Migration to the nucleus when complex ...	nucleus [TAS]	174900	1YGS	552
Q13477 UniProt NPD GO	MADCA_HUMAN	Mucosal addressin cell adhesion molecule 1 precursor (MAdCAM-1) (hMAdCAM-1)	0.39	-	nuc	0	Membrane; single-pass type I membrane protein	membrane fraction [TAS]	102670	1GSM	406
P08173 UniProt NPD GO	ACM4_HUMAN	Muscarinic acetylcholine receptor M4	0.39	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	118495		479
P15720 UniProt NPD GO	MBP_CHICK	Myelin basic protein (MBP)	0.39	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				173
Q91325 UniProt NPD GO	MBP_RAJER	Myelin basic protein (MBP)	0.39	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				154
P25274 UniProt NPD GO	MBP_RABIT	Myelin basic protein (MBP) (Myelin A1 protein) (Myelin P1 protein)	0.39	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				168
Q00872 UniProt NPD GO	MYPC1_HUMAN	Myosin-binding protein C, slow-type (Slow MyBP-C) (C-protein, skeletal muscle slow-isoform)	0.39	-	cyt	0			160794	2DAV	1141
Q8IA42 UniProt NPD GO	GALT4_DROME	N-acetylgalactosaminyltransferase 4 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransferase 4) (UD ...	0.39	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [NAS]			659
Q8N159 UniProt NPD GO	NAGS_HUMAN	N-acetylglutamate synthase, mitochondrial precursor (EC 2.3.1.1) (Amino-acid acetyltransferase) [Con ...	0.39	-	mit	0	Mitochondrion; mitochondrial matrix		608300		534
Q6C668 UniProt NPD GO	ECO1_YARLI	N-acetyltransferase ECO1 (EC 2.3.1.-) (Establishment of cohesion protein 1)	0.39	-	nuc	0	Nucleus (By similarity)				271
P31175 UniProt NPD GO	NUKC_SOYBN	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.39	-	nuc	0	Plastid; chloroplast				212
Q70XW0 UniProt NPD GO	NUIC_AMBTC	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.39	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				180
Q8VDQ8 UniProt NPD GO	SIRT2_MOUSE	NAD-dependent deacetylase sirtuin-2 (EC 3.5.1.-) (SIR2-like protein 2) (mSIR2L2)	0.39	-	nuc	0	Cytoplasm. Colocalizes with microtubules	cytoplasm [ISS] microtubule [ISS]			389
Q6DQX6 UniProt NPD GO	NDUBB_CRIGR	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial precursor (EC 1.6.5.3) ( ...	0.39	-	nuc	1	Mitochondrion; mitochondrial inner membrane (Potential)				151
O95168 UniProt NPD GO	NDUB4_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.39	-	nuc	1	Mitochondrion; mitochondrial inner membrane; matrix side		603840		128
P25711 UniProt NPD GO	NUYM_NEUCR	NADH-ubiquinone oxidoreductase 21 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.39	-	mit	0	Mitochondrion; mitochondrial inner membrane				218
P15688 UniProt NPD GO	NU2M_BETVU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.39	-	end	6	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				515
O70215 UniProt NPD GO	NKG2D_RAT	NKG2-D type II integral membrane protein (NKG2-D-activating NK receptor) (NK cell receptor D) (Kille ...	0.39	-	nuc	1	Membrane; single-pass type II membrane protein (By similarity)				215
P17333 UniProt NPD GO	2SS4_BRANA	Napin precursor (1.7S seed storage protein) [Contains: Napin small chain; Napin large chain]	0.39	-	nuc	1 *					180
Q63374 UniProt NPD GO	NRX2A_RAT	Neurexin-2-alpha precursor (Neurexin II-alpha)	0.39	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1715
Q9Z2N5 UniProt NPD GO	NXPH3_RAT	Neurexophilin-3 precursor	0.39	-	mit	0	Secreted protein (Potential)				252
P16519 UniProt NPD GO	NEC2_HUMAN	Neuroendocrine convertase 2 precursor (EC 3.4.21.94) (NEC 2) (PC2) (Prohormone convertase 2) (Propro ...	0.39	-	cyt	0	Secretory vesicle. Localized in the secretion granules	extracellular space [TAS] Golgi apparatus [TAS]	162151		638
Q9NZ94 UniProt NPD GO	NLGN3_HUMAN	Neuroligin-3 precursor (Gliotactin homolog)	0.39	-	end	1	Membrane; single-pass type I membrane protein (Potential)		300494		848
Q8K4P1 UniProt NPD GO	NPB_MOUSE	Neuropeptide B precursor (Preproprotein L7) (mPPL7) [Contains: Neuropeptide B-29 (NPB29) (L7C)]	0.39	-	mit	0	Secreted protein				119
P0C0L6 UniProt NPD GO	NPSR1_RAT	Neuropeptide S receptor (G-protein coupled receptor 154)	0.39	-	end	7	Membrane; multi-pass membrane protein (By similarity)				372
Q9PSN6 UniProt NPD GO	NXS3_NAJSP	Neurotoxin 3 (Toxin 3)	0.39	-	nuc	0	Secreted protein				62
O88766 UniProt NPD GO	MMP8_RAT	Neutrophil collagenase precursor (EC 3.4.24.34) (Matrix metalloproteinase-8) (MMP-8)	0.39	-	exc	0	Stored in intracellular granules	extracellular space [ISS]			466
P14543 UniProt NPD GO	NID1_HUMAN	Nidogen-1 precursor (Entactin)	0.39	-	mit	0	Secreted protein; extracellular space; extracellular matrix; basement membrane		131390	1NDX	1247
Q94733 UniProt NPD GO	NP3_RHOPR	Nitrophorin-3 precursor (NP3)	0.39	-	nuc	0	Secreted protein				202
P04671 UniProt NPD GO	NO51_SOYBN	Nodulin C51 precursor	0.39	-	exc	1 *					224
O88998 UniProt NPD GO	NOE1_MOUSE	Noelin precursor (Neuronal olfactomedin-related ER localized protein) (Olfactomedin-1) (Pancortin)	0.39	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)	extracellular space [IDA]			485
P47782 UniProt NPD GO	RNAS2_GORGO	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.39	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule				161
P10153 UniProt NPD GO	RNAS2_HUMAN	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.39	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule	extracellular region [TAS]	131410	2C05	161
Q8SPY8 UniProt NPD GO	RNAS2_HYLLE	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.39	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule (By similarity)				161
P47785 UniProt NPD GO	RNAS2_PANTR	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.39	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule (By similarity)				161
Q5A7Q6 UniProt NPD GO	NUDF_CANAL	Nuclear distribution protein PAC1 (nudF homolog)	0.39	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules and the mitotic spindle poles (By similarity)				486
O16662 UniProt NPD GO	NH115_CAEEL	Nuclear hormone receptor family member nhr-115	0.39	-	mit	0	Nucleus (Potential)				391
O17748 UniProt NPD GO	NH174_CAEEL	Nuclear hormone receptor family member nhr-174	0.39	-	end	1 *	Nucleus (Potential)				382
P25211 UniProt NPD GO	NFYB_XENLA	Nuclear transcription factor Y subunit beta (Nuclear transcription factor Y subunit B) (NF-YB) (CAAT ...	0.39	-	cyt	0	Nucleus				122
Q01560 UniProt NPD GO	NOP3_YEAST	Nucleolar protein 3 (Mitochondrial targeting suppressor 1 protein) (Nuclear polyadenylated RNA-bindi ...	0.39	-	nuc	0	Nucleus; nucleolus	cytoplasm [IMP] nucleus [IDA]			414
P25293 UniProt NPD GO	NAP1_YEAST	Nucleosome assembly protein	0.39	-	cyt	0	Nucleus	cytoplasm [TAS] nucleus [IPI]		2AYU	417
Q9H173 UniProt NPD GO	SIL1_HUMAN	Nucleotide exchange factor SIL1 precursor (BiP-associated protein) (BAP)	0.39	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [NAS]	608005		461
Q9U539 UniProt NPD GO	OCT1_CAEEL	Organic cation transporter 1 (CeOCT1)	0.39	+	end	12 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]			576
O42148 UniProt NPD GO	OAZ_CHICK	Ornithine decarboxylase antizyme (ODC-Az)	0.39	-	nuc	0					215
Q9USQ5 UniProt NPD GO	OAZ_SCHPO	Ornithine decarboxylase antizyme (ODC-Az)	0.39	-	nuc	0					226
Q9Y466 UniProt NPD GO	NR2E1_HUMAN	Orphan nuclear receptor NR2E1 (Nuclear receptor TLX) (Tailless homolog) (Tll) (hTll)	0.39	-	nuc	0	Nucleus (By similarity)		603849		385
Q64104 UniProt NPD GO	NR2E1_MOUSE	Orphan nuclear receptor NR2E1 (Nuclear receptor TLX) (Tailless homolog) (Tll) (mTll)	0.39	-	nuc	0	Nucleus (By similarity)				385
O35103 UniProt NPD GO	OMD_MOUSE	Osteomodulin precursor (Osteoadherin) (OSAD) (Keratan sulfate proteoglycan osteomodulin) (KSPG osteo ...	0.39	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				423
P08721 UniProt NPD GO	OSTP_RAT	Osteopontin precursor (Bone sialoprotein-1) (Secreted phosphoprotein 1) (SPP-1)	0.39	-	exc	0	Secreted protein	cell projection [IDA] extracellular matrix (sensu Metazoa) [ISS] extracellular region [ISS] extracellular space [TAS]			317
O45027 UniProt NPD GO	PBAN_MAMBR	PBAN-type neuropeptides precursor [Contains: Diapause hormone homolog (DH); Alpha-SG neuropeptide (M ...	0.39	-	nuc	0	Secreted protein				155

You are viewing entries 32801 to 32850 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.