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
Q7Z144 UniProt NPD GO	MMAC_CAEEL	MMACHC-like protein	0.06	-	cyt	0					272
P39900 UniProt NPD GO	MMP12_HUMAN	Macrophage metalloelastase precursor (EC 3.4.24.65) (HME) (Matrix metalloproteinase-12) (MMP-12) (Ma ...	0.06	-	vac	0			601046	1Z3J	470
Q7M425 UniProt NPD GO	TXC3_BUNCI	Major neurotoxin BcIII	0.06	-	nuc	0	Secreted protein. Found in nematocyst				48
P19400 UniProt NPD GO	API3_ASCSU	Major pepsin inhibitor 3 precursor (PI-3)	0.06	-	vac	0	Secreted protein			1F34	169
P56165 UniProt NPD GO	MPA52_PHAAQ	Major pollen allergen Pha a 5.2 precursor (Pha a 5) (Clone 14)	0.06	-	mit	1 *					305
P11589 UniProt NPD GO	MUP2_MOUSE	Major urinary protein 2 precursor (MUP 2)	0.06	-	exc	0	Secreted protein			1ZNL	180
P22133 UniProt NPD GO	MDHC_YEAST	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37)	0.06	-	cyt	0	Cytoplasm	cytoplasm [IDA] cytosol [TAS]			376
Q01643 UniProt NPD GO	MS84B_DROME	Male-specific sperm protein Mst84Db	0.06	-	nuc	0					74
Q9JJS8 UniProt NPD GO	MASP2_RAT	Mannan-binding lectin serine protease 2 precursor (EC 3.4.21.104) (Mannose-binding protein-associate ...	0.06	-	exc	0	Secreted protein			1NT0	685
Q66S50 UniProt NPD GO	MBL2_MACFA	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.06	-	exc	0					248
Q66S65 UniProt NPD GO	MBL2_PAPPA	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.06	-	exc	0					248
Q66S41 UniProt NPD GO	MBL2_PREOB	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.06	-	exc	0					248
Q66S62 UniProt NPD GO	MBL2_SAGOE	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.06	-	exc	0					248
Q7TN41 UniProt NPD GO	MRGRD_RAT	Mas-related G-protein coupled receptor member D (Beta-alanine receptor) (G-protein coupled receptor ...	0.06	-	end	6 *	Membrane; multi-pass membrane protein				319
Q5U9D9 UniProt NPD GO	MRGX2_MACFA	Mas-related G-protein coupled receptor member X2	0.06	-	end	7 *	Membrane; multi-pass membrane protein				330
Q4QXU5 UniProt NPD GO	MRGX2_MACMU	Mas-related G-protein coupled receptor member X2	0.06	-	end	7 *	Membrane; multi-pass membrane protein				329
P21845 UniProt NPD GO	MCPT6_MOUSE	Mast cell protease 6 precursor (EC 3.4.21.59) (MMCP-6) (Tryptase)	0.06	-	exc	0		extracellular region [TAS]			276
P34166 UniProt NPD GO	MFA2_YEAST	Mating hormone A-factor 2 precursor	0.06	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	extracellular region [IDA]			38
O15825 UniProt NPD GO	MER2_EUPOC	Mating pheromone 2 precursor	0.06	-	nuc	0	Secreted protein				154
P10774 UniProt NPD GO	MER1_EUPRA	Mating pheromone Er-1/Er-3 precursor (Euplomone R1/R3)	0.06	-	mit	1 *	Isoform 1: Secreted protein. Isoform 2: Membrane			2ERL	75
Q9GLJ8 UniProt NPD GO	MC4R_BOVIN	Melanocortin receptor 4 (MC4-R)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				332
P32245 UniProt NPD GO	MC4R_HUMAN	Melanocortin receptor 4 (MC4-R)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	601665		332
Q8HXX3 UniProt NPD GO	MC4R_MACFA	Melanocortin receptor 4 (MC4-R)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				332
Q864G7 UniProt NPD GO	MSHR_ATEPA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.06	-	end	4 *	Membrane; multi-pass membrane protein				317
Q865E9 UniProt NPD GO	MSHR_FELCA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864I2 UniProt NPD GO	MSHR_LEOCH	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein				318
Q864I3 UniProt NPD GO	MSHR_LEORO	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein				318
Q864G0 UniProt NPD GO	MSHR_LORTA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein				317
Q9BZ81 UniProt NPD GO	MAGB5_HUMAN	Melanoma-associated antigen B5 (MAGE-B5 antigen) (Fragment)	0.06	-	cyt	0			300466		111
O02769 UniProt NPD GO	MTR1A_BOVIN	Melatonin receptor type 1A (Mel-1A-R) (Mel1a melatonin receptor) (Fragment)	0.06	-	end	5 *	Membrane; multi-pass membrane protein				257
Q90456 UniProt NPD GO	MR1B2_BRARE	Melatonin receptor type 1B Z6.2 (Fragment)	0.06	-	end	3 *	Membrane; multi-pass membrane protein				157
Q801D8 UniProt NPD GO	MPRA_CYNNE	Membrane progestin receptor alpha (mPR alpha) (Membrane progesterone receptor)	0.06	-	end	6	Cell membrane; multi-pass membrane protein. Localized to the cell membrane of oocytes and sperm				352
Q01440 UniProt NPD GO	GTR1_LEIDO	Membrane transporter D1	0.06	-	end	12 *	Membrane; multi-pass membrane protein				547
Q5XIU9 UniProt NPD GO	PGRC2_RAT	Membrane-associated progesterone receptor component 2	0.06	-	nuc	1 *					217
Q80UU9 UniProt NPD GO	PGRC2_MOUSE	Membrane-associated progesterone receptor component 2 (Fragment)	0.06	-	nuc	1 *					214
O15173 UniProt NPD GO	PGRC2_HUMAN	Membrane-associated progesterone receptor component 2 (Progesterone membrane-binding protein) (Stero ...	0.06	-	nuc	1 *		integral to membrane [TAS]	607735		223
Q96JQ5 UniProt NPD GO	M4A4A_HUMAN	Membrane-spanning 4-domains subfamily A member 4A (Four-span transmembrane protein 1) (CD20 antigen- ...	0.06	-	end	4	Membrane; multi-pass membrane protein		606547		239
P31421 UniProt NPD GO	MGR2_RAT	Metabotropic glutamate receptor 2 precursor (mGluR2)	0.06	-	end	7	Membrane; multi-pass membrane protein	axon [IDA] integral to plasma membrane [TAS] intracellular [IDA] presynaptic membrane [IDA]			872
Q9QYS2 UniProt NPD GO	MGR3_MOUSE	Metabotropic glutamate receptor 3 precursor (mGluR3)	0.06	-	end	6	Membrane; multi-pass membrane protein	axon [IDA] dendritic spine [IDA] plasma membrane [IGI] postsynaptic membrane [IDA] presynaptic active zone [NAS] presynaptic membrane [IDA]			879
Q9SN36 UniProt NPD GO	NRAM5_ARATH	Metal transporter Nramp5 (AtNramp5)	0.06	-	end	10	Membrane; multi-pass membrane protein (Probable)				530
P01075 UniProt NPD GO	MCPI_SOLTU	Metallocarboxypeptidase inhibitor (MCPI) (Carboxypeptidase inhibitor)	0.06	-	nuc	0				4CPA	39
P80247 UniProt NPD GO	MT12_MYTED	Metallothionein 10-II (MT-10-II)	0.06	-	nuc	0					72
P15113 UniProt NPD GO	MT1_CANGA	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.06	-	nuc	0					62
P04733 UniProt NPD GO	MT1F_HUMAN	Metallothionein-1F (MT-1F) (Metallothionein-IF) (MT-IF)	0.06	-	nuc	0		cytoplasm [NAS]	156352		61
P80295 UniProt NPD GO	MT1I_HUMAN	Metallothionein-1I (MT-1I) (Metallothionein-II)	0.06	-	nuc	0			156355		61
Q8N339 UniProt NPD GO	MT1M_HUMAN	Metallothionein-1M (MT-1M) (Metallothionein-IM) (MT-IM)	0.06	-	nuc	0					61
P68304 UniProt NPD GO	MT2_CERAE	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.06	-	nuc	0					61
P68303 UniProt NPD GO	MT2_MACFA	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.06	-	nuc	0					61
P14425 UniProt NPD GO	MT2_STECO	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.06	-	nuc	0					61
P79379 UniProt NPD GO	MT2A_PIG	Metallothionein-2A (MT-2A) (Metallothionein-IIA) (MT-IIA)	0.06	-	nuc	0					61

You are viewing entries 72451 to 72500 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.