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
Q9BYR6 UniProt NPD GO	KRA33_HUMAN	Keratin-associated protein 3-3 (Keratin-associated protein 3.3) (High sulfur keratin-associated prot ...	0.16	-	nuc	0					98
Q701N2 UniProt NPD GO	KRA55_HUMAN	Keratin-associated protein 5-5 (Keratin-associated protein 5.5) (Ultrahigh sulfur keratin-associated ...	0.16	-	nuc	0					221
P83056 UniProt NPD GO	KNL1_BOMVA	Kininogen-1 precursor (BVK-1) [Contains: [Ala3,Thr6]-bradykinin; Kininogen-1-associated peptide]	0.16	-	gol	0	Secreted protein	extracellular region [IDA]			97
Q00624 UniProt NPD GO	ASO_BRANA	L-ascorbate oxidase homolog precursor (EC 1.10.3.3) (Ascorbase)	0.16	-	exc	0					555
Q6NQI8 UniProt NPD GO	LAG13_ARATH	LAG1 longevity assurance homolog 3 (LAG1 homolog 3)	0.16	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				308
P07921 UniProt NPD GO	LACP_KLULA	Lactose permease	0.16	-	end	11	Membrane; multi-pass membrane protein				587
Q9CPU0 UniProt NPD GO	LGUL_MOUSE	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.16	-	cyt	0		cytoplasm [ISS]			183
Q90ZL2 UniProt NPD GO	LANC1_BRARE	LanC-like protein 1	0.16	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				405
Q01650 UniProt NPD GO	LAT1_HUMAN	Large neutral amino acids transporter small subunit 1 (L-type amino acid transporter 1) (4F2 light c ...	0.16	-	end	11	Membrane; multi-pass membrane protein (Probable)	plasma membrane [NAS]	600182		507
P83442 UniProt NPD GO	LEAD3_DAUCA	Late embryogenesis abundant protein Dc3	0.16	-	nuc	0					163
P16886 UniProt NPD GO	H2AL_STRPU	Late histone H2A.L3	0.16	-	mit	0	Nucleus				125
Q86YQ2 UniProt NPD GO	LATH_HUMAN	Latherin precursor (Breast cancer and salivary gland expressed protein)	0.16	-	vac	0	Secreted protein		607627		179
P38084 UniProt NPD GO	BAP2_YEAST	Leu/Val/Ile amino-acid permease (Branched-chain amino-acid permease 2)	0.16	-	end	12	Membrane; multi-pass membrane protein (Probable)				609
Q9BXB1 UniProt NPD GO	LGR4_HUMAN	Leucine-rich repeat-containing G-protein coupled receptor 4 precursor (G-protein coupled receptor 48 ...	0.16	-	end	7	Membrane; multi-pass membrane protein		606666		951
Q9HBX8 UniProt NPD GO	LGR6_HUMAN	Leucine-rich repeat-containing G-protein coupled receptor 6 (VTS20631)	0.16	-	end	7	Membrane; multi-pass membrane protein		606653		828
P15181 UniProt NPD GO	SYLM_NEUCR	Leucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix				994
P01540 UniProt NPD GO	THNA_PHOLI	Ligatoxin A	0.16	-	mit	0	Secreted protein				46
Q9P8W2 UniProt NPD GO	LIP3_CANAL	Lipase 3 precursor (EC 3.1.1.3)	0.16	-	end	0	Secreted protein				471
Q9P4E8 UniProt NPD GO	LIP6_CANAL	Lipase 6 precursor (EC 3.1.1.3)	0.16	-	end	0	Secreted protein				463
Q63313 UniProt NPD GO	LBP_RAT	Lipopolysaccharide-binding protein precursor (LBP)	0.16	-	exc	0	Secreted protein				481
P11602 UniProt NPD GO	LIPL_CHICK	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.16	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				490
P29114 UniProt NPD GO	LOX1_HORVU	Lipoxygenase 1 (EC 1.13.11.12)	0.16	-	cyt	0					862
Q9Y6C7 UniProt NPD GO	NAG7_HUMAN	Loss of heterozygosity 3 chromosomal region 2 gene A protein (NAG-7 protein)	0.16	-	mit	1 *					94
Q8SPW2 UniProt NPD GO	FCGR3_MACFA	Low affinity immunoglobulin gamma Fc region receptor III precursor (IgG Fc receptor III) (Fc-gamma R ...	0.16	-	end	1	Membrane; single-pass type I membrane protein (Potential)				254
P82787 UniProt NPD GO	LCR78_ARATH	Low-molecular-weight cysteine-rich protein LCR78 precursor (Putative defensin AMP1 protein)	0.16	-	exc	1 *	Secreted protein (By similarity)				78
Q90674 UniProt NPD GO	LSHR_CHICK	Lutropin-choriogonadotropic hormone receptor (LH/CG-R) (LSH-R) (Luteinizing hormone receptor) (Fragm ...	0.16	+	end	7 *	Membrane; multi-pass membrane protein				366
Q38933 UniProt NPD GO	LCYB_ARATH	Lycopene beta cyclase, chloroplast precursor (EC 1.14.-.-)	0.16	-	cyt	0	Plastid; chloroplast				501
Q40424 UniProt NPD GO	LCYB_NARPS	Lycopene beta cyclase, chloroplast precursor (EC 1.14.-.-)	0.16	-	cyt	0	Plastid; chloroplast. Plastid; chromoplast. Exists as an inactive soluble form and an active membran ...				503
Q5TM20 UniProt NPD GO	TNFB_MACMU	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.16	-	nuc	0	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				205
Q7SID7 UniProt NPD GO	LYS_ANTMY	Lysozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.16	-	nuc	0				1IIZ	120
Q7Z553 UniProt NPD GO	MAMC1_HUMAN	MAM domain-containing protein 1 precursor (MAM domain-containing glycosylphosphatidylinositol anchor ...	0.16	-	end	1	Membrane; single-pass type I membrane protein (Potential)				956
P60755 UniProt NPD GO	MAMC1_MOUSE	MAM domain-containing protein 1 precursor (MAM domain-containing glycosylphosphatidylinositol anchor ...	0.16	-	end	1	Membrane; single-pass type I membrane protein (Potential)				949
P60756 UniProt NPD GO	MAMC1_RAT	MAM domain-containing protein 1 precursor (MAM domain-containing glycosylphosphatidylinositol anchor ...	0.16	-	end	1	Membrane; single-pass type I membrane protein (Potential)				949
O80961 UniProt NPD GO	MLO12_ARATH	MLO-like protein 12 (AtMlo12) (AtMlo18)	0.16	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				576
P15798 UniProt NPD GO	MNCP_OXYFA	Macronuclear solute carrier homolog CR-MSC	0.16	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				371
P19876 UniProt NPD GO	MIP2B_HUMAN	Macrophage inflammatory protein 2-beta precursor (MIP2-beta) (CXCL3) (Growth-regulated protein gamma ...	0.16	-	mit	0	Secreted protein	extracellular space [TAS]	139111		107
P08176 UniProt NPD GO	DERP1_DERPT	Major mite fecal allergen Der p 1 precursor (EC 3.4.22.-) (Der p I)	0.16	-	exc	0	Secreted protein			2AS8	320
P40243 UniProt NPD GO	PRIO2_TRAST	Major prion protein 2 precursor (PrP) (Major scrapie-associated fibril protein 2) (CD230 antigen)	0.16	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor				256
P79141 UniProt NPD GO	PRIO_CAMDR	Major prion protein precursor (PrP) (CD230 antigen)	0.16	-	nuc	3 *	Cell membrane; lipid-anchor; GPI-anchor				255
O18330 UniProt NPD GO	MRJP1_APIME	Major royal jelly protein 1 precursor (MRJP-1) (Bee-milk protein) [Contains: Jellein-1 (Jelleine-I); ...	0.16	-	exc	0	Secreted protein	extracellular region [IDA]			432
Q23519 UniProt NPD GO	MS152_CAEEL	Major sperm protein 152 (MSP)	0.16	-	cyt	0					126
Q21244 UniProt NPD GO	MSP63_CAEEL	Major sperm protein 63 (MSP)	0.16	-	cyt	0					126
P27440 UniProt NPD GO	MSP2_ASCSU	Major sperm protein, isoform beta (Beta-MSP)	0.16	-	nuc	0				2MSP	126
P57748 UniProt NPD GO	MMP20_MOUSE	Matrix metalloproteinase-20 precursor (EC 3.4.24.-) (MMP-20) (Enamel metalloproteinase) (Enamelysin) ...	0.16	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				482
O18733 UniProt NPD GO	MMP9_CANFA	Matrix metalloproteinase-9 precursor (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gel ...	0.16	-	exc	0		extracellular space [ISS]			704
O42634 UniProt NPD GO	DMC1_SCHPO	Meiotic recombination protein dmc1	0.16	-	cyt	0	Nucleus				332
Q969V1 UniProt NPD GO	MCHR2_HUMAN	Melanin-concentrating hormone receptor 2 (MCH receptor 2) (MCHR-2) (MCH-R2) (MCH2R) (MCH-2R) (MCH2) ...	0.16	-	end	7 *	Membrane; multi-pass membrane protein		606111		340
Q801G2 UniProt NPD GO	MPRA_BRARE	Membrane progestin receptor alpha (mPR alpha) (Progestin and adipoQ receptor family member VII)	0.16	-	end	6	Membrane; multi-pass membrane protein (By similarity)				354
O55022 UniProt NPD GO	PGRC1_MOUSE	Membrane-associated progesterone receptor component 1	0.16	-	nuc	1 *	Microsome; microsomal membrane; single-pass membrane protein (By similarity)				194
Q9UMX9 UniProt NPD GO	S45A2_HUMAN	Membrane-associated transporter protein (AIM-1 protein) (Melanoma antigen AIM1) (Solute carrier fami ...	0.16	-	end	12 *	Melanosome; melanosomal membrane; multi-pass membrane protein (By similarity)		606574		530

You are viewing entries 55851 to 55900 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.