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
P79294 UniProt NPD GO	LYSC_SAISC	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.05	-	vac	0					148
P83972 UniProt NPD GO	LYSD_DROME	Lysozyme D precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase D)	0.05	-	exc	0					140
P37159 UniProt NPD GO	LYSE_DROME	Lysozyme E precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase E)	0.05	-	exc	0					140
Q90X99 UniProt NPD GO	LYG_EPICO	Lysozyme g (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.05	-	cyt	0					194
P05105 UniProt NPD GO	LYS_HYACE	Lysozyme precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.05	-	vac	0					139
O95772 UniProt NPD GO	MENTO_HUMAN	MLN64 N-terminal domain homolog (STARD3 N-terminal-like protein)	0.05	-	end	4	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein				234
Q9C7I3 UniProt NPD GO	ML168_ARATH	MLP-like protein 168	0.05	-	cyt	0					151
Q621Z7 UniProt NPD GO	MMAC_CAEBR	MMACHC-like protein	0.05	-	cyt	0					268
Q4R549 UniProt NPD GO	MIF_MACFA	Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1)	0.05	-	cyt	0					114
Q6DN04 UniProt NPD GO	MIF_MACMU	Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1)	0.05	-	cyt	0					114
P14174 UniProt NPD GO	MIF_HUMAN	Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1) (Glycosylatio ...	0.05	-	cyt	0		extracellular region [IDA]	153620	1P1G	114
P11006 UniProt NPD GO	MAGA_XENLA	Magainins precursor [Contains: Small acidic peptide; Magainin-1 (Magainin I); Magainin-2 (Magainin I ...	0.05	-	exc	0	Secreted protein			2MAG	303
P49469 UniProt NPD GO	CHLI_ODOSI	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.05	-	cyt	0	Plastid; chloroplast				353
P04939 UniProt NPD GO	MUP3_MOUSE	Major urinary protein 3 precursor (MUP 3) (Non-group 1/group 2 MUP15)	0.05	-	exc	0	Secreted protein				184
P37227 UniProt NPD GO	MDHM_SCHMA	Malate dehydrogenase, mitochondrial (EC 1.1.1.37) (Fragment)	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				142
P55297 UniProt NPD GO	MANB_PIRSP	Mannan endo-1,4-beta-mannosidase B precursor (EC 3.2.1.78) (Beta-mannanase B) (1,4-beta-D-mannan man ...	0.05	-	vac	0					571
Q9CQC8 UniProt NPD GO	SPG21_MOUSE	Maspardin (Spastic paraplegia 21 autosomal recessive Mast syndrome protein homolog) (Acid cluster pr ...	0.05	-	mit	0	Cytoplasm (By similarity)	cytosol [ISS] trans-Golgi network transport vesicle [ISS]			308
Q9NZD8 UniProt NPD GO	SPG21_HUMAN	Maspardin (Spastic paraplegia 21 autosomal recessive Mast syndrome protein) (Acid cluster protein 33 ...	0.05	-	mit	0	Cytoplasm; cytosol. Membrane; peripheral membrane protein. Endosome; endosomal membrane; peripheral ...	cytosol [IDA] trans-Golgi network transport vesicle [IDA]	608181		308
P00770 UniProt NPD GO	MCPT2_RAT	Mast cell protease 2 precursor (EC 3.4.21.-) (Mast cell protease II) (rMCP-II) (rMCP-2) (Group-speci ...	0.05	-	exc	0				3RP2	247
P25501 UniProt NPD GO	MFA1_SACBA	Mating factor alpha precursor (Alpha mating pheromone) [Contains: Alpha-1 mating pheromone; Mating f ...	0.05	-	exc	0					144
P58548 UniProt NPD GO	MER22_EUPRA	Mating pheromone Er-22 (Euplomone R22)	0.05	-	nuc	0	Secreted protein			1HD6	37
Q98917 UniProt NPD GO	PME17_CHICK	Melanocyte protein Pmel 17 precursor (115 kDa melanosomal matrix protein)	0.05	-	end	0	On the fibrous matrix structure of the premelanosome				763
P56442 UniProt NPD GO	MSHR_ALCAA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.05	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864H6 UniProt NPD GO	MSHR_CALGO	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.05	-	end	7 *	Membrane; multi-pass membrane protein				344
Q864F9 UniProt NPD GO	MSHR_GALSE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.05	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864H5 UniProt NPD GO	MSHR_SAGIM	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.05	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864H0 UniProt NPD GO	MSHR_SAIOE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.05	-	end	7 *	Membrane; multi-pass membrane protein				317
P43365 UniProt NPD GO	MAGAC_HUMAN	Melanoma-associated antigen 12 (MAGE-12 antigen) (MAGE12F)	0.05	-	cyt	0			300177		314
Q9R0R1 UniProt NPD GO	TRFM_MOUSE	Melanotransferrin precursor (Membrane-bound transferrin-like protein p97) (MTf) (CD228 antigen)	0.05	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				738
Q61184 UniProt NPD GO	MTR1A_MOUSE	Melatonin receptor type 1A (Mel-1A-R) (Mel1a melatonin receptor)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				353
P48040 UniProt NPD GO	MTR1A_SHEEP	Melatonin receptor type 1A (Mel-1A-R) (Mel1a melatonin receptor)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				366
P49219 UniProt NPD GO	MTR1C_XENLA	Melatonin receptor type 1C (MEL-1C-R)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				420
Q5REB1 UniProt NPD GO	MPPD2_PONPY	Metallophosphoesterase domain-containing protein 2	0.05	-	cyt	0					294
Q15777 UniProt NPD GO	MPPD2_HUMAN	Metallophosphoesterase domain-containing protein 2 (Fetal brain protein 239) (239FB)	0.05	-	cyt	0			600911		294
P55946 UniProt NPD GO	MT_ARIAR	Metallothionein (MT)	0.05	-	nuc	0					66
O02033 UniProt NPD GO	MT_LYTPI	Metallothionein (MT) (LpMT1)	0.05	-	nuc	0					68
O62554 UniProt NPD GO	MT10B_MYTED	Metallothionein 10-Ib (MT-10-Ib)	0.05	-	nuc	0					72
P02797 UniProt NPD GO	MT1_CERAE	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.05	-	nuc	0					61
O97388 UniProt NPD GO	MT1_TETPY	Metallothionein-1 precursor (MT-1) [Contains: Metallothionein-2 (MT-2)]	0.05	-	nuc	0					107
P17512 UniProt NPD GO	MT2_CAEEL	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II) (Metallothionein-like protein) (MT-Ce)	0.05	-	nuc	0					62
Q39458 UniProt NPD GO	MT1_CICAR	Metallothionein-like protein 1 (MT-1)	0.05	-	nuc	0					75
O48951 UniProt NPD GO	MT3_PRUAV	Metallothionein-like protein 1 (MT-1)	0.05	-	nuc	0					64
Q39459 UniProt NPD GO	MT2_CICAR	Metallothionein-like protein 2 (MT-2)	0.05	-	nuc	0					79
P43398 UniProt NPD GO	MTA_TRIRP	Metallothionein-like protein A (MT-A)	0.05	-	nuc	0					77
P43399 UniProt NPD GO	MTB_TRIRP	Metallothionein-like protein B (MT-B)	0.05	-	nuc	0					75
P41902 UniProt NPD GO	CRS5_YEAST	Metallothionein-like protein CRS5	0.05	-	nuc	0					69
Q40396 UniProt NPD GO	MT2_NICGU	Metallothionein-like protein type 2	0.05	-	nuc	0					78
Q41657 UniProt NPD GO	MT2_VICFA	Metallothionein-like protein type 2	0.05	-	nuc	0					77
O80585 UniProt NPD GO	MTHR2_ARATH	Methylenetetrahydrofolate reductase 2 (EC 1.5.1.20) (AtMTHFR2)	0.05	-	cyt	0					594
Q9JLZ3 UniProt NPD GO	AUHM_MOUSE	Methylglutaconyl-CoA hydratase, mitochondrial precursor (EC 4.2.1.18) (AU-specific RNA-binding enoyl ...	0.05	-	mit	0	Mitochondrion	mitochondrion [IDA]			314

You are viewing entries 74851 to 74900 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.