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
P13939 UniProt NPD GO	LEAD7_GOSHI	Late embryogenesis abundant protein D-7 (LEA D-7)	0.23	-	nuc	0					136
P70202 UniProt NPD GO	LXN_MOUSE	Latexin (Endogenous carboxypeptidase inhibitor) (ECI) (Tissue carboxypeptidase inhibitor) (TCI)	0.23	-	cyt	0	Cytoplasm (Probable)			1WNH	222
Q41635 UniProt NPD GO	FATB_UMBCA	Lauroyl-acyl carrier protein thioesterase, chloroplast precursor (EC 3.1.2.-) (12:0-acyl-carrier pro ...	0.23	-	cyt	0	Plastid; chloroplast				382
P82149 UniProt NPD GO	NT53_DROME	Lethal(2)neighbour of tid protein 2 (NOT53)	0.23	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				484
Q9BTN0 UniProt NPD GO	LRFN3_HUMAN	Leucine-rich repeat and fibronectin type-III domain-containing protein 3 precursor	0.23	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				628
Q2T9T5 UniProt NPD GO	LRC61_BOVIN	Leucine-rich repeat-containing protein 61	0.23	-	mit	0					261
P28175 UniProt NPD GO	LFC_TACTR	Limulus clotting factor C precursor (EC 3.4.21.84) (FC) [Contains: Limulus clotting factor C heavy c ...	0.23	-	exc	0	Secreted protein. Secreted in hemolymph				1019
O43561 UniProt NPD GO	LAT_HUMAN	Linker for activation of T-cells family member 1 (36 kDa phospho-tyrosine adapter protein) (pp36) (p ...	0.23	-	nuc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts	immunological synapse [IDA] integral to membrane [TAS] lipid raft [TAS]	602354		262
Q99M04 UniProt NPD GO	LIAS_MOUSE	Lipoic acid synthetase, mitochondrial precursor (Lip-syn) (Lipoate synthase) (mLIP1)	0.23	-	mit	0	Mitochondrion	mitochondrion [IDA]			373
Q8GSM2 UniProt NPD GO	LOX23_HORVU	Lipoxygenase 2.3, chloroplast precursor (EC 1.13.11.12) (LOX2:Hv:3)	0.23	-	mit	0	Plastid; chloroplast				896
Q8VCM4 UniProt NPD GO	LIPB_MOUSE	Lipoyltransferase 1, mitochondrial precursor (EC 6.-.-.-) (Lipoate-protein ligase) (Lipoate biosynth ...	0.23	-	cyt	0	Mitochondrion (By similarity)				373
P25672 UniProt NPD GO	NXL4_NAJNA	Long neurotoxin 4 (Toxin D)	0.23	-	nuc	0	Secreted protein				71
P25673 UniProt NPD GO	NXL5_NAJNA	Long neurotoxin 5 (Toxin E)	0.23	-	nuc	0	Secreted protein				71
P31994 UniProt NPD GO	FCG2B_HUMAN	Low affinity immunoglobulin gamma Fc region receptor II-b precursor (Fc-gamma RII-b) (FcRII-b) (IgG ...	0.23	-	exc	1	Membrane; single-pass type I membrane protein	plasma membrane [NAS]	604590	2FCB	310
Q04980 UniProt NPD GO	LTI65_ARATH	Low-temperature-induced 65 kDa protein (Desiccation-responsive protein 29B)	0.23	-	nuc	0					619
P51884 UniProt NPD GO	LUM_HUMAN	Lumican precursor (Keratan sulfate proteoglycan lumican) (KSPG lumican)	0.23	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [TAS] extracellular region [NAS] fibrillar collagen [IDA]	600616		338
O46641 UniProt NPD GO	LSHB_EQUBU	Lutropin/choriogonadotropin beta chain precursor (LSH-B/CG-B) (Luteinizing hormone subunit beta)	0.23	-	exc	0	Secreted protein				169
P08751 UniProt NPD GO	LSHB_HORSE	Lutropin/choriogonadotropin beta chain precursor (LSH-B/CG-B) (Luteinizing hormone subunit beta)	0.23	-	exc	0	Secreted protein				169
O65837 UniProt NPD GO	LCYE_LYCES	Lycopene epsilon cyclase, chloroplast precursor (EC 1.14.-.-)	0.23	-	end	1	Plastid; chloroplast				526
Q06600 UniProt NPD GO	TNFB_BOVIN	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.23	-	exc	1 *	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				204
P41155 UniProt NPD GO	TNFC_MOUSE	Lymphotoxin-beta (LT-beta) (Tumor necrosis factor C) (TNF-C) (Tumor necrosis factor ligand superfami ...	0.23	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)	plasma membrane [TAS]			306
Q9TLR8 UniProt NPD GO	ACSF_CYACA	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (EC 1.14.13.81) (Mg-protoporphyrin ...	0.23	-	nuc	1	Plastid; chloroplast				354
Q9AR22 UniProt NPD GO	CTH1_CHLRE	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase 2, chloroplast precursor (EC 1.14.1 ...	0.23	-	mit	0	Plastid; chloroplast (By similarity)				407
P40246 UniProt NPD GO	PRIO_ATEGE	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.23	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				232
Q9EQK5 UniProt NPD GO	MVP_MOUSE	Major vault protein (MVP)	0.23	-	cyt	0	Cytoplasm (By similarity)				860
Q62667 UniProt NPD GO	MVP_RAT	Major vault protein (MVP)	0.23	-	cyt	0	Cytoplasm				860
P17432 UniProt NPD GO	MASY_GOSHI	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.23	-	pox	0	Glyoxysome				567
P56688 UniProt NPD GO	MOIH_LIBEM	Mandibular organ-inhibiting hormone precursor (MOIH) [Contains: MOIH precursor-related peptide; Mand ...	0.23	-	exc	1 *	Secreted protein				137
P33908 UniProt NPD GO	MA1A1_HUMAN	Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA (EC 3.2.1.113) (Processing alpha-1,2-mannosidase I ...	0.23	-	mit	2 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	endoplasmic reticulum [TAS] ER-Golgi intermediate compartment [IDA] membrane fraction [TAS]	604344		653
P35410 UniProt NPD GO	MAS1L_HUMAN	Mas-related G-protein coupled receptor MRG (MAS-R) (MAS1-like)	0.23	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [NAS]	607235		378
Q6L786 UniProt NPD GO	MRGRD_MACFA	Mas-related G-protein coupled receptor member D (Beta-alanine receptor) (G-protein coupled receptor ...	0.23	-	end	7 *	Membrane; multi-pass membrane protein				320
Q6PC62 UniProt NPD GO	SPG21_BRARE	Maspardin (Spastic paraplegia 21 autosomal recessive Mast syndrome protein homolog)	0.23	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS] trans-Golgi network transport vesicle [ISS]			311
P80931 UniProt NPD GO	MCT1A_SHEEP	Mast cell protease 1A precursor (EC 3.4.21.-) (SMCP-1A)	0.23	-	exc	0	Secretory granules				245
P21812 UniProt NPD GO	MCPT4_MOUSE	Mast cell protease 4 precursor (EC 3.4.21.-) (MMCP-4) (Serosal mast cell protease) (MSMCP) (Myonase) ...	0.23	-	end	0					246
P79287 UniProt NPD GO	MMP20_PIG	Matrix metalloproteinase-20 precursor (EC 3.4.24.-) (MMP-20) (Enamel metalloproteinase) (Enamelysin) ...	0.23	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				483
P41246 UniProt NPD GO	MMP9_RABIT	Matrix metalloproteinase-9 precursor (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gel ...	0.23	-	exc	0		extracellular space [ISS]			707
P11310 UniProt NPD GO	ACADM_HUMAN	Medium-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.3) (MCAD)	0.23	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IEP] mitochondrion [TAS]	201450	2A1T	421
Q14565 UniProt NPD GO	DMC1_HUMAN	Meiotic recombination protein DMC1/LIM15 homolog	0.23	-	cyt	0	Nucleus (Potential)	condensed nuclear chromosome [TAS]	602721	1V5W	340
Q9D159 UniProt NPD GO	MRAP_MOUSE	Melanocortin 2 receptor accessory protein (Fat cell-specific low molecular weight protein) (Fat tiss ...	0.23	-	nuc	1 *	Cell membrane (By similarity). Endoplasmic reticulum (By similarity). Cytoplasm; perinuclear region. ...				127
Q06154 UniProt NPD GO	PME17_BOVIN	Melanocyte protein Pmel 17 (Retinal pigment epithelial-specific protein) (Fragment)	0.23	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				491
P49287 UniProt NPD GO	MTR1B_RAT	Melatonin receptor type 1B (Mel-1B-R) (Mel1b melatonin receptor) (Fragment)	0.23	-	end	2 *	Membrane; multi-pass membrane protein				120
Q03994 UniProt NPD GO	MSA2_PLAF9	Merozoite surface antigen 2 precursor (MSA-2)	0.23	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				302
Q03644 UniProt NPD GO	MSA2_PLAFI	Merozoite surface antigen 2 precursor (MSA-2)	0.23	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				300
Q9ZT63 UniProt NPD GO	MTP1_ARATH	Metal tolerance protein 1 (AtMTP1) (Zinc transporter ZAT-1) (ZAT1p) [Contains: Metal tolerance prote ...	0.23	-	end	6	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				398
P50122 UniProt NPD GO	TIMP1_SHEEP	Metalloproteinase inhibitor 1 precursor (TIMP-1)	0.23	-	exc	0	Secreted protein				207
P79376 UniProt NPD GO	MT1C_PIG	Metallothionein-1C (MT-1C) (Metallothionein-IC) (MT-IC)	0.23	-	nuc	0					61
Q6AXU8 UniProt NPD GO	METL6_RAT	Methyltransferase-like protein 6 (EC 2.1.1.-)	0.23	-	cyt	0					287
P82669 UniProt NPD GO	RT25_BOVIN	Mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25)	0.23	-	cyt	0	Mitochondrion				173
Q9Y6G3 UniProt NPD GO	RT32_HUMAN	Mitochondrial 28S ribosomal protein S32 (S32mt) (MRP-S32)	0.23	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			142
Q9W021 UniProt NPD GO	RM23_DROME	Mitochondrial 39S ribosomal protein L23 (L23mt) (MRP-L23)	0.23	-	mit	0	Mitochondrion (By similarity)	mitochondrial large ribosomal subunit [ISS]			150

You are viewing entries 47551 to 47600 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.