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
Q95234 UniProt NPD GO	LEP_PONPY	Leptin (Obesity factor)	0.20	-	nuc	0	Secreted protein (Probable)				146
Q8K1S1 UniProt NPD GO	LGI4_MOUSE	Leucine-rich repeat LGI family member 4 precursor (Leucine-rich glioma-inactivated protein 4) (LGI1- ...	0.20	-	vac	0	Secreted protein (Potential)				537
Q3KRC6 UniProt NPD GO	LRC8E_RAT	Leucine-rich repeat-containing protein 8E	0.20	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				795
P34074 UniProt NPD GO	NXL1_BOUAN	Long neurotoxin 1 (NXL1)	0.20	-	nuc	0	Secreted protein				71
P01390 UniProt NPD GO	NXL1_NAJNI	Long neurotoxin 1 (Neurotoxin alpha)	0.20	-	nuc	0	Secreted protein				71
P41216 UniProt NPD GO	ACSL1_MOUSE	Long-chain-fatty-acid--CoA ligase 1 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 1) (LACS 1)	0.20	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...	mitochondrion [IDA]			699
P18163 UniProt NPD GO	ACSL1_RAT	Long-chain-fatty-acid--CoA ligase 1 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 1) (LACS 1) (Long-c ...	0.20	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...				699
O35547 UniProt NPD GO	ACSL4_RAT	Long-chain-fatty-acid--CoA ligase 4 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 4) (LACS 4)	0.20	-	cyt	0					670
P25330 UniProt NPD GO	LSHB_PHYCA	Lutropin beta chain (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.20	-	mit	0	Secreted protein				118
P19256 UniProt NPD GO	LFA3_HUMAN	Lymphocyte function-associated antigen 3 precursor (Ag3) (Surface glycoprotein LFA-3) (CD58 antigen) ...	0.20	-	exc	2 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Cell membrane; lipid-ancho ...	integral to plasma membrane [NAS]	153420	1CI5	250
Q9P8P4 UniProt NPD GO	PLB2_ASPFU	Lysophospholipase 2 (EC 3.1.1.5) (Phospholipase B 2)	0.20	-	nuc	0					588
P50718 UniProt NPD GO	LYS_TRINI	Lysozyme precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.20	-	exc	0					141
Q96JB6 UniProt NPD GO	LOXL4_HUMAN	Lysyl oxidase homolog 4 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 4) (Lysyl oxidase-related ...	0.20	-	exc	0	Secreted protein; extracellular space (Potential)		607318		756
P49301 UniProt NPD GO	MMGL_RAT	Macrophage asialoglycoprotein-binding protein (M-ASGP-BP) (Macrophage galactose/N-acetylgalactosamin ...	0.20	-	cyt	1 *	Membrane; single-pass type II membrane protein				306
O18873 UniProt NPD GO	ALL1_CANFA	Major allergen Can f 1 precursor (Allergen Dog 1)	0.20	-	cyt	0	Secreted protein				174
P29111 UniProt NPD GO	OLEO2_BRANA	Major oleosin NAP-II (Fragment)	0.20	-	mit	2	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				175
Q9Z0T3 UniProt NPD GO	PRIO_SIGHI	Major prion protein precursor (PrP) (CD230 antigen)	0.20	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor				254
Q60506 UniProt NPD GO	PRIO_CRIGR	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.20	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor				254
P61766 UniProt NPD GO	PRIO_HYLLA	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.20	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				253
P61767 UniProt NPD GO	PRIO_HYLSY	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.20	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				253
P52114 UniProt NPD GO	PRIO_MUSPF	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.20	-	nuc	2 *	Cell membrane; lipid-anchor; GPI-anchor				257
P61768 UniProt NPD GO	PRIO_PANTR	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.20	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				253
P40256 UniProt NPD GO	PRIO_PONPY	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.20	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor				253
Q95211 UniProt NPD GO	PRIO_RABIT	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.20	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				252
P40248 UniProt NPD GO	PRIO_CALMO	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.20	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				241
P67990 UniProt NPD GO	PRIO_CERAT	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.20	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				238
P61761 UniProt NPD GO	PRIO_CERMO	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.20	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor				246
P61762 UniProt NPD GO	PRIO_CERNE	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.20	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor				246
Q95176 UniProt NPD GO	PRIO_CERTO	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.20	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor				246
Q95174 UniProt NPD GO	PRIO_ERYPA	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.20	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor				246
P67991 UniProt NPD GO	PRIO_MACSY	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.20	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				238
Q95270 UniProt NPD GO	PRIO_THEGE	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.20	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor				238
Q9TVW5 UniProt NPD GO	MSP77_CAEEL	Major sperm protein 77/79 (MSP)	0.20	-	cyt	0					126
P27439 UniProt NPD GO	MSP1_ASCSU	Major sperm protein, isoform alpha (Alpha-MSP)	0.20	-	nuc	0				3MSP	126
Q920F5 UniProt NPD GO	DCMC_RAT	Malonyl-CoA decarboxylase, mitochondrial precursor (EC 4.1.1.9) (MCD)	0.20	-	pox	0	Mitochondrion. Cytoplasm. Peroxisome				492
Q8TDS7 UniProt NPD GO	MRGRD_HUMAN	Mas-related G-protein coupled receptor member D (Beta-alanine receptor) (G-protein coupled receptor ...	0.20	-	end	7 *	Cell membrane; multi-pass membrane protein. Localized at the plasma membrane but internalized into t ...		607231		321
Q8VCJ6 UniProt NPD GO	MRGRF_MOUSE	Mas-related G-protein coupled receptor member F (Mas-related gene F protein)	0.20	-	end	6 *	Membrane; multi-pass membrane protein				343
P21961 UniProt NPD GO	CBPA3_RAT	Mast cell carboxypeptidase A precursor (EC 3.4.17.1) (RMC-CP) (Carboxypeptidase A3) (R-CPA) (Fragmen ...	0.20	-	cyt	0	Secretory granules				412
Q6H2Z4 UniProt NPD GO	MCDP_APICC	Mast cell degranulating peptide precursor	0.20	-	mit	1 *	Secreted protein				50
P43430 UniProt NPD GO	MCPT8_MOUSE	Mast cell protease 8 precursor (EC 3.4.21.-) (MMCP-8)	0.20	-	vac	0	Secretory granules (By similarity)				247
Q8BR76 UniProt NPD GO	MKS3_MOUSE	Meckelin (Meckel syndrome type 3 protein homolog) (Transmembrane protein 67)	0.20	-	end	3 *	Cell membrane; multi-pass membrane protein (Potential)				992
P0C152 UniProt NPD GO	MKS3_RAT	Meckelin (Meckel syndrome type 3 protein homolog) (Transmembrane protein 67)	0.20	-	end	3 *	Cell membrane; multi-pass membrane protein (Potential)				992
P45952 UniProt NPD GO	ACADM_MOUSE	Medium-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.3) (MCAD)	0.20	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [ISS] mitochondrion [ISS]			421
P40967 UniProt NPD GO	PME17_HUMAN	Melanocyte protein Pmel 17 precursor (Melanocyte lineage-specific antigen GP100) (Melanoma-associate ...	0.20	-	end	1	Membrane; single-pass type I membrane protein (Potential). ME20-S: Secreted protein. There is also a ...	plasma membrane [TAS]	155550	1TVH	661
Q96PC5 UniProt NPD GO	MIA2_HUMAN	Melanoma inhibitory activity protein 2 precursor	0.20	-	mit	0	Secreted protein (Potential)		608001		541
Q5R9I0 UniProt NPD GO	AOC3_PONPY	Membrane copper amine oxidase (EC 1.4.3.6) (Semicarbazide-sensitive amine oxidase) (SSAO) (Vascular ...	0.20	-	vac	1 *	Membrane; single-pass type II membrane protein (By similarity)	cell surface [ISS] integral to membrane [ISS] plasma membrane [ISS]			762
P19259 UniProt NPD GO	PF12_PLAFA	Membrane protein PF12 precursor	0.20	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				347
O42146 UniProt NPD GO	TIMP2_CHICK	Metalloproteinase inhibitor 2 precursor (TIMP-2) (Tissue inhibitor of metalloproteinases 2)	0.20	-	nuc	0	Secreted protein				220
P09577 UniProt NPD GO	MT1B_SHEEP	Metallothionein-1B (MT-1B) (Metallothionein-IB) (MT-IB)	0.20	-	nuc	0					61
P47945 UniProt NPD GO	MT4_MOUSE	Metallothionein-4 (MT-4) (Metallothionein-IV) (MT-IV)	0.20	-	nuc	0					62

You are viewing entries 50801 to 50850 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.