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
P16127 UniProt NPD GO	CHLI_ARATH	Magnesium-chelatase subunit chlI, chloroplast precursor (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase ...	0.10	-	mit	0	Plastid; chloroplast; chloroplast stroma				424
Q9D967 UniProt NPD GO	MGDP1_MOUSE	Magnesium-dependent phosphatase 1 (EC 3.1.3.-) (EC 3.1.3.48) (MDP-1)	0.10	-	cyt	0				1U7P	164
Q84ZX5 UniProt NPD GO	ALL1_ARTVU	Major pollen allergen Art v 1 precursor	0.10	-	exc	1 *					132
P04938 UniProt NPD GO	MUP8_MOUSE	Major urinary proteins 11 and 8 (MUP11 and MUP8) (Fragment)	0.10	-	cyt	0	Secreted protein				151
P93819 UniProt NPD GO	MDHC1_ARATH	Malate dehydrogenase, cytoplasmic 1 (EC 1.1.1.37)	0.10	-	cyt	0	Cytoplasm (By similarity)				332
Q43744 UniProt NPD GO	MDHM_BRANA	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix				341
O24493 UniProt NPD GO	MC1_PINRA	Male-cone protein 1 precursor (PRMC1)	0.10	-	exc	0					92
P23488 UniProt NPD GO	OPAP_DROME	Male-specific opa-containing protein precursor (Protein dromsopa)	0.10	-	exc	0					83
P78715 UniProt NPD GO	MAOH_NEOFR	Malic enzyme, hydrogenosomal precursor (EC 1.1.1.40) (ME)	0.10	-	cyt	0	Hydrogenosome				592
O16099 UniProt NPD GO	MAL2_DROVI	Maltase 2 precursor (EC 3.2.1.20)	0.10	-	exc	0					524
Q9YGG9 UniProt NPD GO	MMHA_AGKHA	Mamushigin alpha chain precursor	0.10	-	exc	0	Secreted protein				157
P81035 UniProt NPD GO	MOIH2_CANPG	Mandibular organ-inhibiting hormone 2 (MOIH-2)	0.10	-	mit	0	Secreted protein				78
Q3SZI0 UniProt NPD GO	MANA_BOVIN	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.10	-	mit	0	Cytoplasm (Probable)				422
Q8HXX2 UniProt NPD GO	MANA_MACFA	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.10	-	nuc	0	Cytoplasm (By similarity)				422
O02659 UniProt NPD GO	MBL2_BOVIN	Mannose-binding protein C precursor (MBP-C) (Mannan-binding protein)	0.10	-	exc	0					249
P45700 UniProt NPD GO	MA1A1_MOUSE	Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA (EC 3.2.1.113) (Processing alpha-1,2-mannosidase I ...	0.10	-	mit	2 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi membrane [IDA]		1NXC	655
Q75W54 UniProt NPD GO	EBM_ARATH	Mannosylglycoprotein endo-beta-mannosidase (EC 3.2.1.152) (Endo-beta-mannosidase) (AtEBM) [Contains: ...	0.10	-	nuc	0					943
Q5FVD6 UniProt NPD GO	SPG21_XENLA	Maspardin (Spastic paraplegia 21 autosomal recessive Mast syndrome protein homolog)	0.10	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS] trans-Golgi network transport vesicle [ISS]			310
Q00356 UniProt NPD GO	MCPTX_MOUSE	Mast cell protease-like protein precursor (EC 3.4.21.-)	0.10	-	exc	0					246
Q61450 UniProt NPD GO	GP49A_MOUSE	Mast cell surface glycoprotein Gp49A precursor	0.10	-	end	1	Membrane; single-pass type I membrane protein				303
P01149 UniProt NPD GO	MFAL1_YEAST	Mating factor alpha-1 precursor (Alpha-1 mating pheromone) [Contains: Alpha-1 mating pheromone; Mati ...	0.10	-	exc	0		extracellular region [TAS]			165
P78744 UniProt NPD GO	BB13_SCHCO	Mating-type pheromone BBP1(3) precursor	0.10	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				73
Q58T79 UniProt NPD GO	M4H32_BOMMX	Maximins 4/H3 type 2 precursor [Contains: Maximin-4; Maximin-H3]	0.10	-	end	0	Secreted protein				144
Q58T52 UniProt NPD GO	M4H33_BOMMX	Maximins 4/H3 type 3 precursor [Contains: Maximin-4; Maximin-H3]	0.10	-	end	0	Secreted protein				144
Q58T77 UniProt NPD GO	M4H37_BOMMX	Maximins 4/H3 type 7 precursor [Contains: Maximin-4; Maximin-H3]	0.10	-	end	0	Secreted protein				139
Q58T72 UniProt NPD GO	M7H6_BOMMX	Maximins 7/H6 precursor [Contains: Maximin-7; Maximin-H6]	0.10	-	exc	0	Secreted protein				144
Q58T92 UniProt NPD GO	MYHW_BOMMX	Maximins y/Hw precursor [Contains: Maximin-y; Maximin-Hw]	0.10	-	end	0	Secreted protein				142
Q96449 UniProt NPD GO	DMC1_SOYBN	Meiotic recombination protein DMC1 homolog	0.10	-	cyt	0	Nucleus (Potential)				345
Q864K0 UniProt NPD GO	MSHR_CERDI	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.10	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864K4 UniProt NPD GO	MSHR_MIOTA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.10	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864L0 UniProt NPD GO	MSHR_PONPY	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.10	-	end	4 *	Membrane; multi-pass membrane protein				317
P56448 UniProt NPD GO	MSHR_RANTA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.10	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864I8 UniProt NPD GO	MSHR_SEMEN	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.10	-	end	7 *	Membrane; multi-pass membrane protein				317
P47798 UniProt NPD GO	MSHR_BOVIN	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.10	-	end	7 *	Membrane; multi-pass membrane protein				317
P43356 UniProt NPD GO	MAGA2_HUMAN	Melanoma-associated antigen 2 (MAGE-2 antigen)	0.10	-	end	0			300549		314
P43358 UniProt NPD GO	MAGA4_HUMAN	Melanoma-associated antigen 4 (MAGE-4 antigen) (MAGE-X2) (MAGE-41)	0.10	-	mit	0			300175	1I4F	317
P43359 UniProt NPD GO	MAGA5_HUMAN	Melanoma-associated antigen 5 (MAGE-5 antigen)	0.10	-	nuc	0			300340		124
P51046 UniProt NPD GO	MR1A1_BRARE	Melatonin receptor type 1A Z1.7 (MEL-1A-R) (Fragment)	0.10	-	end	3 *	Membrane; multi-pass membrane protein				153
O70423 UniProt NPD GO	AOC3_MOUSE	Membrane copper amine oxidase (EC 1.4.3.6) (Semicarbazide-sensitive amine oxidase) (SSAO) (Vascular ...	0.10	-	exc	1 *	Membrane; single-pass type II membrane protein (By similarity)	cell surface [ISS] integral to membrane [ISS] plasma membrane [ISS]			764
P58355 UniProt NPD GO	S45A2_MOUSE	Membrane-associated transporter protein (AIM-1 protein) (Melanoma antigen AIM1) (Solute carrier fami ...	0.10	-	end	11	Melanosome; melanosomal membrane; multi-pass membrane protein (By similarity)				530
Q9H2W1 UniProt NPD GO	M4A6A_HUMAN	Membrane-spanning 4-domains subfamily A member 6A (Four-span transmembrane protein 3) (CD20 antigen- ...	0.10	-	end	4 *	Membrane; multi-pass membrane protein		606548		248
P29136 UniProt NPD GO	MEP1_SOYBN	Metalloendoproteinase 1 precursor (EC 3.4.24.-) (SMEP1)	0.10	-	exc	0					305
Q91ZG2 UniProt NPD GO	MPPD1_MOUSE	Metallophosphoesterase domain-containing protein 1	0.10	-	mit	0					326
O15442 UniProt NPD GO	MPPD1_HUMAN	Metallophosphoesterase domain-containing protein 1 (Adult brain protein 239) (239AB)	0.10	-	mit	0			602112		326
Q9WUC6 UniProt NPD GO	TIMP2_CAVPO	Metalloproteinase inhibitor 2 precursor (TIMP-2) (Tissue inhibitor of metalloproteinases 2)	0.10	-	exc	0	Secreted protein				220
Q94550 UniProt NPD GO	MT_DREPO	Metallothionein (MT)	0.10	-	nuc	0					73
Q8UVY1 UniProt NPD GO	MT_LITMO	Metallothionein (MT)	0.10	-	nuc	0					60
P52726 UniProt NPD GO	MT_OREMO	Metallothionein (MT)	0.10	-	nuc	0					60
Q9U568 UniProt NPD GO	MT_PERVI	Metallothionein (MT)	0.10	-	nuc	0					73
O93593 UniProt NPD GO	MTA_CHAAC	Metallothionein A (MT-A)	0.10	-	nuc	0					60

You are viewing entries 64651 to 64700 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.