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
P79385 UniProt NPD GO	MFGM_PIG	Lactadherin (Milk fat globule-EGF factor 8) (MFG-E8) (MFGM) (Sperm surface protein SP47) (PP47)	0.11	-	cyt	0	Membrane; peripheral membrane protein. Located in the acrosomal region of zona-pellucida bound sperm ...				409
Q8K1F9 UniProt NPD GO	LCTL_MOUSE	Lactase-like protein precursor (Klotho/lactase-phlorizin hydrolase-related protein)	0.11	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Probable)	endoplasmic reticulum [IDA]			566
Q9UNP4 UniProt NPD GO	SIAT9_HUMAN	Lactosylceramide alpha-2,3-sialyltransferase (EC 2.4.99.9) (CMP-NeuAc:lactosylceramide alpha-2,3-sia ...	0.11	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	Golgi membrane [NAS] integral to plasma membrane [TAS]	609056		362
O77698 UniProt NPD GO	TRFL_BUBBU	Lactotransferrin precursor (EC 3.4.21.-) (Lactoferrin)	0.11	-	exc	0	Secreted protein			1CE2	708
Q09751 UniProt NPD GO	LGUL_SCHPO	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.11	-	cyt	0					302
Q948T6 UniProt NPD GO	LGUL_ORYSA	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.11	+	cyt	0					291
O75387 UniProt NPD GO	LAT3_HUMAN	Large neutral amino acids transporter small subunit 3 (L-type amino acid transporter 3) (Solute carr ...	0.11	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	603733		559
P11997 UniProt NPD GO	LSP1G_DROME	Larval serum protein 1 gamma chain precursor (Hexamerin 1 gamma)	0.11	-	exc	0	Secreted protein; extracellular space	larval serum protein complex [IDA]			772
P46522 UniProt NPD GO	LEA5D_GOSHI	Late embryogenesis abundant protein Lea5-D	0.11	-	nuc	0					105
P04735 UniProt NPD GO	H2A1_PSAMI	Late histone H2A.1	0.11	-	mit	0	Nucleus				124
P41159 UniProt NPD GO	LEP_HUMAN	Leptin precursor (Obesity factor) (Obese protein)	0.11	-	mit	0	Secreted protein	extracellular space [TAS]	164160	1AX8	167
Q9NT99 UniProt NPD GO	LRC4B_HUMAN	Leucine-rich repeat-containing protein 4B precursor	0.11	-	nuc	1	Membrane; single-pass membrane protein (Potential)				713
Q8N7C0 UniProt NPD GO	LRC52_HUMAN	Leucine-rich repeat-containing protein 52 precursor	0.11	-	end	1	Membrane; single-pass membrane protein (Potential)				313
P08246 UniProt NPD GO	ELNE_HUMAN	Leukocyte elastase precursor (EC 3.4.21.37) (Elastase-2) (Neutrophil elastase) (PMN elastase) (Bone ...	0.11	-	vac	1 *		cell surface [IDA] extracellular region [NAS]	130130	1PPG	267
P06181 UniProt NPD GO	LIG8_PHACH	Ligninase H8 precursor (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase)	0.11	-	vac	0				1B85	372
P21764 UniProt NPD GO	LIG3_PHACH	Ligninase LG3 precursor (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase)	0.11	-	exc	0					372
Q98919 UniProt NPD GO	LSAMP_CHICK	Limbic system-associated membrane protein precursor (E19S) (CHLAMP, G19-isoform)	0.11	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				338
Q8BLK3 UniProt NPD GO	LSAMP_MOUSE	Limbic system-associated membrane protein precursor (LSAMP)	0.11	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				341
P32948 UniProt NPD GO	LIP4_CANRU	Lipase 4 precursor (EC 3.1.1.3)	0.11	-	exc	0					549
Q6P828 UniProt NPD GO	LITAF_XENTR	Lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog (LPS-induced TNF-alpha factor ...	0.11	-	nuc	1	Cytoplasm (By similarity)				148
P11153 UniProt NPD GO	LIPL_CAVPO	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.11	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				465
P55031 UniProt NPD GO	LIPL_FELCA	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.11	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				478
P06858 UniProt NPD GO	LIPL_HUMAN	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.11	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor	extracellular region [TAS]	609708		475
O46647 UniProt NPD GO	LIPL_MUSVI	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.11	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				475
P38415 UniProt NPD GO	LOXA_LYCES	Lipoxygenase A (EC 1.13.11.12)	0.11	-	cyt	0	Cytoplasm				860
Q63880 UniProt NPD GO	EST31_MOUSE	Liver carboxylesterase 31 precursor (EC 3.1.1.1) (ES-Male) (Esterase-31)	0.11	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...				554
Q3ZKN0 UniProt NPD GO	S27A1_BOVIN	Long-chain fatty acid transport protein 1 (EC 6.2.1.-) (Fatty acid transport protein 1) (FATP-1) (So ...	0.11	-	end	1 *	Cell membrane; peripheral membrane protein. Intracellular membrane; peripheral membrane protein. Pla ...				646
Q6P1M0 UniProt NPD GO	S27A4_HUMAN	Long-chain fatty acid transport protein 4 (EC 6.2.1.-) (Fatty acid transport protein 4) (FATP-4) (So ...	0.11	-	nuc	2 *	Membrane; multi-pass membrane protein (Probable)		604194		643
P28330 UniProt NPD GO	ACADL_HUMAN	Long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.13) (LCAD)	0.11	-	mit	0	Mitochondrion; mitochondrial matrix		609576		430
P24067 UniProt NPD GO	BIP2_MAIZE	Luminal-binding protein 2 precursor (BiP2) (Heat shock protein 70 homolog 2) (B70) (B-70)	0.11	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				663
O24581 UniProt NPD GO	BIP3_MAIZE	Luminal-binding protein 3 precursor (BiP3)	0.11	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				663
Q03684 UniProt NPD GO	BIP4_TOBAC	Luminal-binding protein 4 precursor (BiP 4) (78 kDa glucose-regulated protein homolog 4) (GRP 78-4)	0.11	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				667
Q42434 UniProt NPD GO	BIP_SPIOL	Luminal-binding protein precursor (BiP) (78 kDa glucose-regulated protein homolog) (GRP 78)	0.11	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				668
O77805 UniProt NPD GO	LSHB_FELCA	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.11	-	nuc	0	Secreted protein				143
Q2Q1P2 UniProt NPD GO	LSHB_PANTR	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.11	-	mit	0	Secreted protein				141
O46482 UniProt NPD GO	LSHB_TRIVU	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.11	-	nuc	0	Secreted protein				141
Q28585 UniProt NPD GO	LSHR_SHEEP	Lutropin-choriogonadotropic hormone receptor (LH/CG-R) (LSH-R) (Luteinizing hormone receptor) (Fragm ...	0.11	-	end	6	Membrane; multi-pass membrane protein				538
O55162 UniProt NPD GO	LYPD3_RAT	Ly6/PLAUR domain-containing protein 3 precursor (GPI-anchored metastasis-associated protein C4.4A)	0.11	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor	membrane [IDA]			352
P01374 UniProt NPD GO	TNFB_HUMAN	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.11	-	exc	1 *	Homotrimer: Secreted protein. Heterotrimer: Membrane		153440	1TNR	205
Q92633 UniProt NPD GO	EDG2_HUMAN	Lysophosphatidic acid receptor Edg-2 (LPA receptor 1) (LPA-1)	0.11	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	602282		364
P61794 UniProt NPD GO	EDG2_RAT	Lysophosphatidic acid receptor Edg-2 (LPA receptor 1) (LPA-1)	0.11	-	end	7	Membrane; multi-pass membrane protein				364
P61793 UniProt NPD GO	EDG2_MOUSE	Lysophosphatidic acid receptor Edg-2 (LPA receptor 1) (LPA-1) (Rec1.3) (VZG-1)	0.11	-	end	7	Membrane; multi-pass membrane protein				364
Q9PU17 UniProt NPD GO	LPA11_XENLA	Lysophosphatidic acid receptor LPA1 homolog 1 (xLPA1-1)	0.11	-	end	7	Membrane; multi-pass membrane protein				366
Q6U820 UniProt NPD GO	PLB1_ASPFU	Lysophospholipase 1 precursor (EC 3.1.1.5) (Phospholipase B 1)	0.11	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				633
Q6U819 UniProt NPD GO	PLB3_ASPFU	Lysophospholipase 3 precursor (EC 3.1.1.5) (Phospholipase B 3)	0.11	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				630
Q7LZI3 UniProt NPD GO	LYSC_TRASA	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.11	-	nuc	0					129
P19849 UniProt NPD GO	LYSC_PAVCR	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.11	-	nuc	0					129
P24533 UniProt NPD GO	LYSC_SYRRE	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.11	-	nuc	0					129
P00706 UniProt NPD GO	LYSC3_ANAPL	Lysozyme C-3 (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.11	-	nuc	0					129
Q9PRZ1 UniProt NPD GO	BRK_ONCMY	Lysyl-bradykinin-like	0.11	-		0	Secreted protein				10

You are viewing entries 62951 to 63000 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.