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
O94772 UniProt NPD GO	LY6H_HUMAN	Lymphocyte antigen Ly-6H precursor	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)		603625		140
Q862Z7 UniProt NPD GO	TNFC_PANTR	Lymphotoxin-beta (LT-beta) (Tumor necrosis factor C) (TNF-C) (Tumor necrosis factor ligand superfami ...	0.07	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				244
Q64194 UniProt NPD GO	LICH_RAT	Lysosomal acid lipase/cholesteryl ester hydrolase precursor (EC 3.1.1.13) (LAL) (Acid cholesteryl es ...	0.07	-	end	0	Lysosome				397
Q6PCJ9 UniProt NPD GO	PPT2A_XENLA	Lysosomal thioesterase PPT2-A precursor (EC 3.1.2.-) (PPT-2-A)	0.07	-	mit	0	Lysosome (By similarity)				296
Q08694 UniProt NPD GO	LYSB_DROME	Lysozyme B precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase B)	0.07	-	exc	0					140
Q7LZQ2 UniProt NPD GO	LYSC_AIXSP	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.07	-	nuc	0					129
P84492 UniProt NPD GO	LYSC_CHEMY	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.07	-	nuc	0					130
P49663 UniProt NPD GO	LYSC_PHAVE	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.07	-	nuc	0					130
P79687 UniProt NPD GO	LYSC_ALLNI	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.07	-	vac	0					148
P79179 UniProt NPD GO	LYSC_GORGO	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.07	-	mit	0					148
P61626 UniProt NPD GO	LYSC_HUMAN	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.07	-	vac	0			105200	3LHM	148
P00703 UniProt NPD GO	LYSC_MELGA	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.07	-	end	1 *				3LZ2	147
P61627 UniProt NPD GO	LYSC_PANPA	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.07	-	vac	0					148
P61628 UniProt NPD GO	LYSC_PANTR	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.07	-	vac	0					148
P51782 UniProt NPD GO	LYSC_TRIVU	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.07	-	exc	0					147
Q9CPX3 UniProt NPD GO	LYZL1_MOUSE	Lysozyme-like protein 1 precursor (EC 3.2.1.17)	0.07	-	nuc	0	Secreted protein (Probable)				148
O75951 UniProt NPD GO	LYZL6_HUMAN	Lysozyme-like protein 6 precursor (EC 3.2.1.17)	0.07	-	exc	0	Secreted protein (Probable)				148
Q9SXB6 UniProt NPD GO	MLO2_ARATH	MLO-like protein 2 (AtMlo2)	0.07	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				573
Q8C5T4 UniProt NPD GO	MORN3_MOUSE	MORN repeat-containing protein 3	0.07	-	nuc	0					241
Q9TL08 UniProt NPD GO	CHLI_NEPOL	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.07	-	cyt	0	Plastid; chloroplast				355
P51394 UniProt NPD GO	CHLI_PORPU	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.07	-	cyt	0	Plastid; chloroplast				356
Q7Z1K3 UniProt NPD GO	ANIS1_ANISI	Major allergen Ani s 1 precursor (Excretory gland allergen Ans1) (21 kDa allergen)	0.07	-	exc	0	Secreted protein				194
Q17282 UniProt NPD GO	ALL12_BLOTA	Major allergen Blo t 12 precursor	0.07	-	nuc	1 *					144
Q39967 UniProt NPD GO	ALL5_HEVBR	Major latex allergen Hev b 5	0.07	-	nuc	0					150
P11588 UniProt NPD GO	MUP1_MOUSE	Major urinary protein 1 precursor (MUP 1)	0.07	-	exc	0	Secreted protein			1YP7	180
P02762 UniProt NPD GO	MUP6_MOUSE	Major urinary protein 6 precursor (MUP 6) (Alpha-2U-globulin) (Group 1, BS6) (Allergen Mus m 1)	0.07	-	exc	0	Secreted protein			1MUP	180
Q05145 UniProt NPD GO	MDHP_MESCR	Malate dehydrogenase [NADP], chloroplast precursor (EC 1.1.1.82) (NADP-MDH)	0.07	-	mit	0	Plastid; chloroplast				441
Q08062 UniProt NPD GO	MDHC_MAIZE	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37)	0.07	-	cyt	0	Cytoplasm (By similarity)				332
O24047 UniProt NPD GO	MDHC_MESCR	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37)	0.07	-	cyt	0	Cytoplasm				332
P37228 UniProt NPD GO	MDHG_SOYBN	Malate dehydrogenase, glyoxysomal precursor (EC 1.1.1.37)	0.07	-	mit	1 *	Glyoxysome				353
Q01644 UniProt NPD GO	MS84C_DROME	Male-specific sperm protein Mst84Dc	0.07	-	nuc	0					55
Q9LF50 UniProt NPD GO	MEX1_ARATH	Maltose excess protein 1, chloroplast precursor (Root cap protein 1)	0.07	-	end	9	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein				415
Q91WP0 UniProt NPD GO	MASP2_MOUSE	Mannan-binding lectin serine protease 2 precursor (EC 3.4.21.104) (Mannose-binding protein-associate ...	0.07	-	exc	0	Secreted protein				685
Q75AB5 UniProt NPD GO	MANA_ASHGO	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.07	-	cyt	0	Cytoplasm (By similarity)				429
Q924M7 UniProt NPD GO	MANA_MOUSE	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.07	-	mit	0	Cytoplasm				423
Q68FX1 UniProt NPD GO	MANA_RAT	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.07	-	nuc	0	Cytoplasm (By similarity)				423
Q66S37 UniProt NPD GO	MBL2_CERAE	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.07	-	exc	0					248
P83304 UniProt NPD GO	LEC_PARPC	Mannose/glucose-specific lectin (Fragment)	0.07	-	cyt	0				1ZGS	447
Q91ZC4 UniProt NPD GO	MRGA8_MOUSE	Mas-related G-protein coupled receptor member A8	0.07	-	end	7 *	Membrane; multi-pass membrane protein				305
Q96LB0 UniProt NPD GO	MRGX3_HUMAN	Mas-related G-protein coupled receptor member X3 (Sensory neuron-specific G-protein coupled receptor ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein		607229		322
P79204 UniProt NPD GO	MCPT2_SHEEP	Mast cell protease 2 precursor (EC 3.4.21.-) (SMCP-2)	0.07	-	end	0	Secretory granules				246
P21844 UniProt NPD GO	MCPT5_MOUSE	Mast cell protease 5 precursor (EC 3.4.21.-) (MMCP-5) (Mast cell chymase 1)	0.07	-	exc	0	Secretory granules				247
Q9Y8D1 UniProt NPD GO	MAT1_COCCY	Mating-type protein MAT-1	0.07	-	cyt	0	Nucleus (Potential)				354
Q9P055 UniProt NPD GO	CN100_HUMAN	Medulloblastoma antigen MU-MB-50.4	0.07	-	end	7	Membrane; multi-pass membrane protein (Potential)				326
Q8BI36 UniProt NPD GO	CN100_MOUSE	Medulloblastoma antigen MU-MB-50.4 homolog	0.07	-	end	7					311
Q96WS1 UniProt NPD GO	MEU24_SCHPO	Meiotic expression up-regulated protein 24	0.07	-	end	4	Membrane; multi-pass membrane protein (Potential)				264
Q9Y826 UniProt NPD GO	MEU31_SCHPO	Meiotic expression up-regulated protein 31	0.07	-	end	4 *					185
Q864G3 UniProt NPD GO	MSHR_ALOCA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864G2 UniProt NPD GO	MSHR_ALOPA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864G1 UniProt NPD GO	MSHR_ALOPI	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				317

You are viewing entries 70351 to 70400 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.