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
P39925 UniProt NPD GO	AFG3_YEAST	Mitochondrial respiratory chain complexes assembly protein AFG3 (EC 3.4.24.-) (TAT-binding homolog 1 ...	0.37	-	mit	1	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	m-AAA complex [IDA]			761
Q9LQQ9 UniProt NPD GO	MPK13_ARATH	Mitogen-activated protein kinase 13 (EC 2.7.11.24) (MAP kinase 13) (AtMPK13)	0.37	-	cyt	0					363
Q9SKX0 UniProt NPD GO	MRP11_ARATH	Multidrug resistance-associated protein 11 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPas ...	0.37	-	end	9	Membrane; multi-pass membrane protein (Potential)				1194
Q9LYS2 UniProt NPD GO	MRP14_ARATH	Multidrug resistance-associated protein 14 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPas ...	0.37	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				1389
Q7GB25 UniProt NPD GO	MRP5_ARATH	Multidrug resistance-associated protein 5 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPase ...	0.37	+	end	14 *	Membrane; multi-pass membrane protein (Potential)				1514
O88269 UniProt NPD GO	MRP6_RAT	Multidrug resistance-associated protein 6 (ATP-binding cassette sub-family C member 6) (MRP-like pro ...	0.37	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)	lateral plasma membrane [IDA] membrane fraction [IDA]			1502
Q9UNW1 UniProt NPD GO	MINP1_HUMAN	Multiple inositol polyphosphate phosphatase 1 precursor (EC 3.1.3.62) (Inositol (1,3,4,5)-tetrakisph ...	0.37	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)		605391		487
P08485 UniProt NPD GO	ACM4_RAT	Muscarinic acetylcholine receptor M4	0.37	-	end	7 *	Membrane; multi-pass membrane protein				478
P32211 UniProt NPD GO	ACM4_MOUSE	Muscarinic acetylcholine receptor M4 (Mm4 mAChR)	0.37	-	end	7 *	Membrane; multi-pass membrane protein				479
Q9JKP5 UniProt NPD GO	MBNL_MOUSE	Muscleblind-like protein (Triplet-expansion RNA-binding protein)	0.37	-	nuc	0	Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			341
Q53NK6 UniProt NPD GO	MYBA1_ORYSA	Myb-related protein MYBAS1	0.37	-	nuc	0	Nucleus (By similarity)				237
P90648 UniProt NPD GO	KMHB_DICDI	Myosin heavy chain kinase B (EC 2.7.11.7) (MHCK B)	0.37	-	nuc	0					732
Q9H1R3 UniProt NPD GO	MYLK2_HUMAN	Myosin light chain kinase 2, skeletal/cardiac muscle (EC 2.7.11.18) (MLCK2)	0.37	-	nuc	0	Cytoplasm. Colocalizes with phosphorylated myosin light chain (RLCP) at filaments of the myofibrils		606566		595
Q8R4H7 UniProt NPD GO	NAGS_MOUSE	N-acetylglutamate synthase, mitochondrial precursor (EC 2.3.1.1) (Amino-acid acetyltransferase) [Con ...	0.37	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]			527
P55806 UniProt NPD GO	NRT1_CHICK	NAD(P)(+)--arginine ADP-ribosyltransferase 1 precursor (EC 2.4.2.31) (Mono(ADP-ribosyl)transferase 1 ...	0.37	-	exc	0	Secreted protein; extracellular space. The mature enzyme is probably secreted from granulocytes into ...				312
Q8HVV4 UniProt NPD GO	NUIC_BAHAB	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.37	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				166
Q8WHX5 UniProt NPD GO	NUIC_PSINU	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.37	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				165
Q8HVK7 UniProt NPD GO	NUIC_STERE	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.37	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				166
Q8HVJ8 UniProt NPD GO	NUIC_VARMX	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.37	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				166
Q8K2C6 UniProt NPD GO	SIRT5_MOUSE	NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-) (SIR2-like protein 5)	0.37	-	nuc	0					310
P21976 UniProt NPD GO	NDUA8_NEUCR	NADH-ubiquinone oxidoreductase 20.8 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3)	0.37	-	nuc	0	Mitochondrion; mitochondrial inner membrane				183
Q8W9M7 UniProt NPD GO	NU4M_DUGDU	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.37	-	end	13 *					459
Q9ZZY2 UniProt NPD GO	NU4M_HIPAM	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.37	-	end	12 *					459
P92698 UniProt NPD GO	NU4M_PONPA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.37	-	end	12 *					459
P27740 UniProt NPD GO	2SSB_BRANA	Napin-B precursor (1.7S seed storage protein) [Contains: Napin-B small chain; Napin-B large chain]	0.37	-	nuc	1 *					178
Q99608 UniProt NPD GO	NECD_HUMAN	Necdin	0.37	-	nuc	0	Cytoplasm; perikarya. Nucleus. Neural perikarya, translocates to the nucleus of postmitotic neurons ...		602117		321
P47937 UniProt NPD GO	NK3R_MOUSE	Neuromedin K receptor (NKR) (Neurokinin B receptor) (NK-3 receptor) (NK-3R) (Tachykinin receptor 3)	0.37	-	end	7	Membrane; multi-pass membrane protein				452
P28673 UniProt NPD GO	NEUY_CHICK	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.37	-	exc	1 *	Secreted protein				97
Q95WC9 UniProt NPD GO	SCX9_CENSC	Neurotoxin 9 precursor (CsE9)	0.37	-	exc	1 *	Secreted protein				84
P79403 UniProt NPD GO	GANAB_PIG	Neutral alpha-glucosidase AB precursor (EC 3.2.1.84) (Glucosidase II subunit alpha)	0.37	-	end	1 *	Endoplasmic reticulum. Golgi apparatus				944
Q15080 UniProt NPD GO	NCF4_HUMAN	Neutrophil cytosol factor 4 (NCF-4) (Neutrophil NADPH oxidase factor 4) (p40-phox) (p40phox)	0.37	-	nuc	0	Cytoplasm	cytosol [IDA] membrane [IDA] NADPH oxidase complex [IDA]	601488	1Z9Q	339
P82320 UniProt NPD GO	DEF6_MACMU	Neutrophil defensin 6 precursor (RMAD-6) [Contains: Neutrophil defensin 7 (RMAD-7)]	0.37	-	exc	0	Secreted protein				94
P43101 UniProt NPD GO	NIA_CICIN	Nitrate reductase [NADH] (EC 1.7.1.1) (NR)	0.37	-	nuc	0					920
Q66GP9 UniProt NPD GO	NOS1_ARATH	Nitric-oxide synthase 1 (EC 1.14.13.39) (AtNOS1)	0.37	-	mit	0					561
P22944 UniProt NPD GO	NIR_EMENI	Nitrite reductase [NAD(P)H] (EC 1.7.1.4)	0.37	-	mit	0					1104
Q9YHT8 UniProt NPD GO	NOGG_FUGRU	Noggin precursor	0.37	-	exc	1 *	Secreted protein				223
P16274 UniProt NPD GO	IFEA_HELPO	Non-neuronal cytoplasmic intermediate filament protein A (IFA) (Fragments)	0.37	-	cyt	0	Cytoplasm				551
P47784 UniProt NPD GO	RNAS2_PONPY	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.37	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule				161
Q9LNH6 UniProt NPD GO	NPS12_ARATH	Novel plant SNARE 12 (AtNPSN12)	0.37	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				265
Q9D2F7 UniProt NPD GO	P210L_MOUSE	Nuclear pore membrane glycoprotein 210-like precursor (Nucleoporin 210 kDa-like)	0.37	-	end	2 *	Membrane; single-pass membrane protein (Potential)				1881
P70503 UniProt NPD GO	DAX1_RAT	Nuclear receptor 0B1 (Nuclear receptor DAX-1)	0.37	-	pox	0	Nucleus (By similarity)				472
Q8BJW5 UniProt NPD GO	NOL11_MOUSE	Nucleolar protein 11	0.37	-	nuc	0	Nucleus; nucleolus (By similarity)				723
P09405 UniProt NPD GO	NUCL_MOUSE	Nucleolin (Protein C23)	0.37	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			706
Q9BVL2 UniProt NPD GO	NUPL1_HUMAN	Nucleoporin p58/p45 (Nucleoporin-like 1)	0.37	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...		607615		599
Q9QXL7 UniProt NPD GO	NDK7_RAT	Nucleoside diphosphate kinase 7 (EC 2.7.4.6) (NDK 7) (NDP kinase 7) (nm23-R7)	0.37	-	cyt	0					395
Q5R4D4 UniProt NPD GO	NP1L1_PONPY	Nucleosome assembly protein 1-like 1	0.37	+	cyt	0	Nucleus (By similarity)				391
P55209 UniProt NPD GO	NP1L1_HUMAN	Nucleosome assembly protein 1-like 1 (NAP-1-related protein) (hNRP)	0.37	+	cyt	0	Nucleus	chromatin assembly complex [TAS]	164060		391
Q8GYB1 UniProt NPD GO	NUD15_ARATH	Nudix hydrolase 15, mitochondrial precursor (EC 3.6.1.-) (AtNUDT15)	0.37	-	mit	0	Mitochondrion (Potential)				285
P48629 UniProt NPD GO	FAD6C_SPIOL	Omega-6 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-)	0.37	-	end	4	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Probable)				447
P28880 UniProt NPD GO	CXO6A_CONST	Omega-conotoxin SVIA precursor (SNX-157)	0.37	-	exc	0	Secreted protein				72

You are viewing entries 34351 to 34400 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.