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
Q659U1 UniProt NPD GO	LYSC_PHOVI	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.03	-	exc	0					148
Q27996 UniProt NPD GO	LYSCT_BOVIN	Lysozyme C, tracheal isozyme precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.03	-	end	0					147
P12067 UniProt NPD GO	LYSC1_PIG	Lysozyme C-1 (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.03	-	cyt	0					128
Q17005 UniProt NPD GO	LYS_ANOGA	Lysozyme precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.03	-	exc	0					140
Q6UWQ5 UniProt NPD GO	LYZL1_HUMAN	Lysozyme-like protein 1 precursor (EC 3.2.1.17)	0.03	-	vac	0	Secreted protein (Probable)				148
Q7Z4W2 UniProt NPD GO	LYZL2_HUMAN	Lysozyme-like protein 2 precursor (EC 3.2.1.17) (Lysozyme-2)	0.03	-	vac	0	Secreted protein (Probable)				148
Q6Q5K6 UniProt NPD GO	HUG1_YEAST	MEC1-mediated checkpoint protein HUG1	0.03	-	nuc	0	Cytoplasm. Nucleus (Probable)	cytoplasm [IDA]			68
Q9DCI3 UniProt NPD GO	MENTO_MOUSE	MLN64 N-terminal domain homolog (STARD3 N-terminal-like protein)	0.03	-	end	4	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity)				235
P80177 UniProt NPD GO	MIF_BOVIN	Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1) (p12A)	0.03	-	cyt	0	Cytoplasm				114
P56166 UniProt NPD GO	MPA53_PHAAQ	Major pollen allergen Pha a 5.3 precursor (Pha a 5) (Clone 29)	0.03	-	mit	1 *					294
P27177 UniProt NPD GO	PRIO_CHICK	Major prion protein homolog precursor (PR-LP) (Acetylcholine receptor-inducing activity) (ARIA) (65- ...	0.03	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor			1U3M	273
P35496 UniProt NPD GO	PSP2_PIG	Major seminal plasma glycoprotein PSP-II precursor	0.03	-	exc	0	Secreted protein			1SPP	137
O48902 UniProt NPD GO	MDHP_MEDSA	Malate dehydrogenase [NADP], chloroplast precursor (EC 1.1.1.82) (NADP-MDH)	0.03	-	mit	0	Plastid; chloroplast				437
Q9SN86 UniProt NPD GO	MDHP_ARATH	Malate dehydrogenase, chloroplast precursor (EC 1.1.1.37) (pNAD-MDH)	0.03	-	mit	0	Plastid; chloroplast; chloroplast stroma	mitochondrion [IDA]			403
P19446 UniProt NPD GO	MDHG_CITLA	Malate dehydrogenase, glyoxysomal precursor (EC 1.1.1.37)	0.03	-	nuc	0	Glyoxysome			1SMK	356
P46488 UniProt NPD GO	MDHG_CUCSA	Malate dehydrogenase, glyoxysomal precursor (EC 1.1.1.37)	0.03	-	nuc	0	Glyoxysome				356
Q42972 UniProt NPD GO	MDHG_ORYSA	Malate dehydrogenase, glyoxysomal precursor (EC 1.1.1.37)	0.03	-	mit	0	Glyoxysome				356
P40926 UniProt NPD GO	MDHM_HUMAN	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]	154100	2DFD	338
P08249 UniProt NPD GO	MDHM_MOUSE	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			338
P32419 UniProt NPD GO	MDHP_YEAST	Malate dehydrogenase, peroxisomal (EC 1.1.1.37)	0.03	-	pox	0	Peroxisome	peroxisome [IDA]			342
P08175 UniProt NPD GO	MS87F_DROME	Male-specific sperm protein Mst87F	0.03	-	nuc	0					56
O75556 UniProt NPD GO	SG2A1_HUMAN	Mammaglobin-B precursor (Mammaglobin-2) (Lipophilin-C) (Lacryglobin) (Secretoglobin family 2A member ...	0.03	-	exc	0			604398		95
P55298 UniProt NPD GO	MANC_PIRSP	Mannan endo-1,4-beta-mannosidase C precursor (EC 3.2.1.78) (Beta-mannanase C) (1,4-beta-D-mannan man ...	0.03	-	vac	0					569
O74484 UniProt NPD GO	MPG1_SCHPO	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.03	-	cyt	0	Cytoplasm	cell tip [IDA] cytoplasm [IDA]			363
Q66S60 UniProt NPD GO	MBL2_GORGO	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.03	-	exc	0					248
P11226 UniProt NPD GO	MBL2_HUMAN	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.03	-	exc	0		extracellular space [TAS]	154545	1HUP	248
Q66S58 UniProt NPD GO	MBL2_HYLCO	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.03	-	exc	0					248
Q66S64 UniProt NPD GO	MBL2_PONPY	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.03	-	exc	0					248
P49329 UniProt NPD GO	LEC_ALOAR	Mannose-specific lectin precursor (Agglutinin) [Contains: Mannose-specific lectin heavy chain; Manno ...	0.03	-	cyt	0	Secreted protein				109
Q91ZC6 UniProt NPD GO	MRGA6_MOUSE	Mas-related G-protein coupled receptor member A6	0.03	-	end	7 *	Membrane; multi-pass membrane protein				301
Q4QXU0 UniProt NPD GO	MRGX2_GORGO	Mas-related G-protein coupled receptor member X2	0.03	-	end	7 *	Membrane; multi-pass membrane protein				329
Q96LB1 UniProt NPD GO	MRGX2_HUMAN	Mas-related G-protein coupled receptor member X2	0.03	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	607228		330
Q4QXX9 UniProt NPD GO	MRGX2_PANTR	Mas-related G-protein coupled receptor member X2	0.03	-	end	7 *	Membrane; multi-pass membrane protein				329
Q4QXU3 UniProt NPD GO	MRGX2_PONPY	Mas-related G-protein coupled receptor member X2	0.03	-	end	7 *	Membrane; multi-pass membrane protein				330
Q4QXU2 UniProt NPD GO	MRGX2_PYGBI	Mas-related G-protein coupled receptor member X2	0.03	-	end	7 *	Membrane; multi-pass membrane protein				330
Q5RES2 UniProt NPD GO	SPG21_PONPY	Maspardin (Spastic paraplegia 21 autosomal recessive Mast syndrome protein homolog)	0.03	-	mit	0	Cytoplasm (By similarity)	cytosol [ISS] trans-Golgi network transport vesicle [ISS]			308
Q5XIC4 UniProt NPD GO	SPG21_RAT	Maspardin (Spastic paraplegia 21 autosomal recessive Mast syndrome protein homolog)	0.03	-	mit	0	Cytoplasm (By similarity)	cytosol [ISS] trans-Golgi network transport vesicle [ISS]			261
P09650 UniProt NPD GO	MCPT1_RAT	Mast cell protease 1 precursor (EC 3.4.21.39) (Mast cell protease I) (RMCP-I) (RMCP-1) (Chymase) (Ch ...	0.03	-	exc	0					260
P50343 UniProt NPD GO	MCPT6_RAT	Mast cell protease 6 precursor (EC 3.4.21.59) (rMCP-6) (Tryptase)	0.03	-	exc	0					274
P50342 UniProt NPD GO	TRYT_MERUN	Mast cell tryptase precursor (EC 3.4.21.59)	0.03	-	exc	0					270
P19236 UniProt NPD GO	TRYM_CANFA	Mastin precursor (EC 3.4.21.-) (Mast cell protease 3) (MCP-3) (dMCP-3) (DMP) (Mastocytoma protease)	0.03	-	end	0	Cytoplasm				280
P06648 UniProt NPD GO	MFAP_SACKL	Mating factor alpha precursor (Alpha mating pheromone) [Contains: Alpha-mating pheromone; Mating fac ...	0.03	-	exc	0					125
P83441 UniProt NPD GO	MEN1_EUPNO	Mating pheromone En-1	0.03	-	nuc	0	Secreted protein				52
P26888 UniProt NPD GO	MER20_EUPRA	Mating pheromone Er-20 (Euplomone R20) (Fragment)	0.03	-	nuc	0	Secreted protein				37
O13740 UniProt NPD GO	MDE1_SCHPO	Mei4-dependent protein 1 precursor	0.03	-	exc	1 *	Secreted protein (Potential)				209
O13980 UniProt NPD GO	MEU29_SCHPO	Meiotic expression up-regulated protein 29 precursor	0.03	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				217
O97504 UniProt NPD GO	MC4R_PIG	Melanocortin receptor 4 (MC4-R)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				332
P56451 UniProt NPD GO	MC5R_BOVIN	Melanocortin receptor 5 (MC5-R)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				325
Q864H8 UniProt NPD GO	MSHR_CALGE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein				344
Q864H7 UniProt NPD GO	MSHR_CALJA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein				344

You are viewing entries 80501 to 80550 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.