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
P01393 UniProt NPD GO	NXL1_DENJA	Long neurotoxin 1 (Toxin V-III-N1)	0.09	-	nuc	0	Secreted protein				72
Q9YGH9 UniProt NPD GO	NXLH2_BUNMU	Long neurotoxin homolog NTL2 precursor	0.09	-	nuc	1 *	Secreted protein				89
O88561 UniProt NPD GO	S27A3_MOUSE	Long-chain fatty acid transport protein 3 (EC 6.2.1.-) (Fatty acid transport protein 3) (FATP-3) (So ...	0.09	-	end	0	Membrane; multi-pass membrane protein (Potential). Mitochondrion. Mitochondrial in MA-10 Leydig cell ...	mitochondrion [IDA]			667
Q9ZUL8 UniProt NPD GO	LCR72_ARATH	Low-molecular-weight cysteine-rich protein LCR72 precursor	0.09	-	exc	1 *	Secreted protein (Potential)				73
P82784 UniProt NPD GO	LCR75_ARATH	Low-molecular-weight cysteine-rich protein LCR75 precursor	0.09	-	exc	0	Secreted protein (By similarity)				75
Q03681 UniProt NPD GO	BIP1_TOBAC	Luminal-binding protein 1 (BiP 1) (78 kDa glucose-regulated protein homolog 1) (GRP 78-1) (Fragment) ...	0.09	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				290
Q6EV78 UniProt NPD GO	LSHB_MACFA	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.09	-	mit	0	Secreted protein				141
Q95J85 UniProt NPD GO	LSHB_MONDO	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.09	-	nuc	0	Secreted protein				141
P01230 UniProt NPD GO	LSHB_RAT	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.09	-	mit	0	Secreted protein				141
Q9WUC3 UniProt NPD GO	LY6H_MOUSE	Lymphocyte antigen Ly-6H precursor	0.09	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				139
P10253 UniProt NPD GO	LYAG_HUMAN	Lysosomal alpha-glucosidase precursor (EC 3.2.1.20) (Acid maltase) (Aglucosidase alfa) [Contains: 76 ...	0.09	-	exc	1 *	Lysosome	lysosome [TAS]	606800		952
Q7LZT2 UniProt NPD GO	LYSC_TRATE	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.09	-	nuc	0					129
Q9DD65 UniProt NPD GO	LYSC_PAROL	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.09	-	exc	0					143
P79239 UniProt NPD GO	LYSC_PONPY	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.09	-	vac	0					148
P48816 UniProt NPD GO	LYS_BOMMO	Lysozyme precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.09	-	exc	0				1GD6	137
P31205 UniProt NPD GO	CHLI_EUGGR	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.09	-	cyt	0	Plastid; chloroplast				348
P49451 UniProt NPD GO	CENPB_SHEEP	Major centromere autoantigen B (Centromere protein B) (CENP-B) (Fragment)	0.09	-	cyt	0	Nucleus				239
P82242 UniProt NPD GO	PLAL1_PLALA	Major pollen allergen Pla l 1	0.09	-	nuc	0	Secreted protein				131
Q9ZP06 UniProt NPD GO	MDHM1_ARATH	Malate dehydrogenase 1, mitochondrial precursor (EC 1.1.1.37) (mNAD-MDH 1)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix				341
O48905 UniProt NPD GO	MDHC_MEDSA	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37)	0.09	-	cyt	0	Cytoplasm (By similarity)				332
P57106 UniProt NPD GO	MDHC2_ARATH	Malate dehydrogenase, cytoplasmic 2 (EC 1.1.1.37)	0.09	-	cyt	0	Cytoplasm (By similarity)				332
P17783 UniProt NPD GO	MDHM_CITLA	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix				347
Q95313 UniProt NPD GO	MEA1_PIG	Male-enhanced antigen 1 (Mea-1) (Fragment)	0.09	-	nuc	0					113
O00187 UniProt NPD GO	MASP2_HUMAN	Mannan-binding lectin serine protease 2 precursor (EC 3.4.21.104) (Mannose-binding protein-associate ...	0.09	-	exc	0	Secreted protein		605102	1ZJK	686
P45701 UniProt NPD GO	MA1A1_RABIT	Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA (EC 3.2.1.113) (Processing alpha-1,2-mannosidase I ...	0.09	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				469
Q8MJJ1 UniProt NPD GO	SPG21_BOVIN	Maspardin (Spastic paraplegia 21 autosomal recessive Mast syndrome protein homolog)	0.09	-	mit	0	Cytoplasm (By similarity)	cytosol [ISS] trans-Golgi network transport vesicle [ISS]			308
P04567 UniProt NPD GO	MCDP_MEGPE	Mast cell degranulating peptide (MCDP) (MCD peptide)	0.09	-	nuc	0	Secreted protein				28
P50339 UniProt NPD GO	MCPT3_RAT	Mast cell protease 3 precursor (EC 3.4.21.-) (Mast cell protease III) (rMCP-III) (rMCP-3) (Chymase 1 ...	0.09	-	exc	0	Secretory granules				247
O35701 UniProt NPD GO	MATN3_MOUSE	Matrilin-3 precursor	0.09	-	mit	0	Secreted protein	extracellular matrix (sensu Metazoa) [IDA]			481
P83081 UniProt NPD GO	M2H1_BOMMX	Maximins 2/H1 precursor [Contains: Maximin-2; Maximin-H1 (Maximin-6)]	0.09	-	end	0	Secreted protein				144
P83083 UniProt NPD GO	M4H31_BOMMX	Maximins 4/H3 type 1 precursor [Contains: Maximin-4; Maximin-H3]	0.09	-	end	0	Secreted protein				144
Q58T62 UniProt NPD GO	M4H36_BOMMX	Maximins 4/H3 type 6 precursor [Contains: Maximin-4; Maximin-H3]	0.09	-	end	0	Secreted protein				139
Q58T74 UniProt NPD GO	M7H1_BOMMX	Maximins 7/H1 precursor [Contains: Maximin-7; Maximin-H1 (Maximin-6)]	0.09	-	end	0	Secreted protein				144
Q58T58 UniProt NPD GO	M7H13_BOMMX	Maximins 7/H13 precursor [Contains: Maximin-7; Maximin-H13]	0.09	-	exc	0	Secreted protein				144
Q58T95 UniProt NPD GO	MYH11_BOMMX	Maximins y/H11 precursor [Contains: Maximin-y; Maximin-H11]	0.09	-	cyt	0	Secreted protein				142
Q5IJ49 UniProt NPD GO	MCHR1_PANTR	Melanin-concentrating hormone receptor 1 (MCH receptor 1) (MCHR-1) (MCH-R1) (MCH1R) (MCH-1R) (MCHR) ...	0.09	-	end	7	Membrane; multi-pass membrane protein				422
Q99705 UniProt NPD GO	MCHR1_HUMAN	Melanin-concentrating hormone receptor 1 (MCH receptor 1) (MCHR-1) (MCH-R1) (MCH1R) (MCH-1R) (MCHR) ...	0.09	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601751		422
Q8JZL2 UniProt NPD GO	MCHR1_MOUSE	Melanin-concentrating hormone receptor 1 (MCH receptor 1) (MCHR-1) (MCH-R1) (MCH1R) (MCH-1R) (MCHR) ...	0.09	-	end	7	Membrane; multi-pass membrane protein	plasma membrane [IDA]			423
Q864K5 UniProt NPD GO	MSHR_ALLNI	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.09	-	end	4 *	Membrane; multi-pass membrane protein				317
P56445 UniProt NPD GO	MSHR_CEREL	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.09	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864J0 UniProt NPD GO	MSHR_COLGU	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.09	-	end	6 *	Membrane; multi-pass membrane protein				317
Q864K8 UniProt NPD GO	MSHR_HYLLA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.09	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864K7 UniProt NPD GO	MSHR_HYLME	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.09	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864F8 UniProt NPD GO	MSHR_VARVR	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.09	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864F7 UniProt NPD GO	MSHR_VARVV	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.09	-	end	7 *	Membrane; multi-pass membrane protein				317
O88495 UniProt NPD GO	MTR1L_MOUSE	Melatonin-related receptor (G protein-coupled receptor 50) (H9)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				583
O08590 UniProt NPD GO	AOC3_RAT	Membrane copper amine oxidase (EC 1.4.3.6) (Semicarbazide-sensitive amine oxidase) (SSAO) (Vascular ...	0.09	-	exc	1 *	Membrane; single-pass type II membrane protein	cell surface [ISS] integral to membrane [ISS] plasma membrane [ISS]			762
Q80ZE4 UniProt NPD GO	MPRA_MOUSE	Membrane progestin receptor alpha (mPR alpha) (Progestin and adipoQ receptor family member VII) (PPA ...	0.09	-	end	6	Membrane; multi-pass membrane protein (By similarity)				345
P70580 UniProt NPD GO	PGRC1_RAT	Membrane-associated progesterone receptor component 1 (Acidic 25 kDa protein) (25-DX)	0.09	-	nuc	1 *	Microsome; microsomal membrane; single-pass membrane protein (By similarity)				194
O54862 UniProt NPD GO	MBPT2_CRIGR	Membrane-bound transcription factor site 2 protease (EC 3.4.24.85) (S2P endopeptidase) (Site-2 prote ...	0.09	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				510

You are viewing entries 66451 to 66500 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.