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
Q66IV3 UniProt NPD GO	LHPL3_XENLA	Lipoma HMGIC fusion partner-like 3 protein homolog	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				218
Q2TBI0 UniProt NPD GO	LBP_BOVIN	Lipopolysaccharide-binding protein precursor (LBP)	0.04	-	exc	0	Secreted protein (By similarity)				481
Q90ZL4 UniProt NPD GO	LIS1B_XENLA	Lissencephaly-1 homolog B	0.04	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Localizes to the plus end of microtubules and ...				409
P05451 UniProt NPD GO	REG1A_HUMAN	Lithostathine 1 alpha precursor (Pancreatic stone protein) (PSP) (Pancreatic thread protein) (PTP) ( ...	0.04	-	exc	0			167770	1QDD	166
P12337 UniProt NPD GO	EST1_RABIT	Liver carboxylesterase 1 precursor (EC 3.1.1.1) (Acyl coenzyme A:cholesterol acyltransferase)	0.04	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...			1K4Y	565
P23141 UniProt NPD GO	EST1_HUMAN	Liver carboxylesterase 1 precursor (EC 3.1.1.1) (Acyl coenzyme A:cholesterol acyltransferase) (ACAT) ...	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen		114835	1YAJ	567
Q64573 UniProt NPD GO	EST4_RAT	Liver carboxylesterase 4 precursor (EC 3.1.1.1) (Carboxyesterase ES-4) (Microsomal palmitoyl-CoA hyd ...	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...				561
P22396 UniProt NPD GO	LMT2_LOCMI	Locustamyotropin-2 (Lom-MT-2)	0.04	-		0	Secreted protein				8
P16223 UniProt NPD GO	TKL1_LOCMI	Locustatachykinin-1 (Locustatachykinin I) (TK-I)	0.04	-		0	Secreted protein				9
P01394 UniProt NPD GO	NXL1_DENVI	Long neurotoxin 1 (Neurotoxin 4.7.3/4.9.3)	0.04	-	nuc	0	Secreted protein				72
P07526 UniProt NPD GO	NXL3_OPHHA	Long neurotoxin 3 (Neurotoxin CM-9)	0.04	-	nuc	0	Secreted protein				73
Q80ZU7 UniProt NPD GO	LPLC3_MOUSE	Long palate, lung and nasal epithelium carcinoma-associated protein 3 precursor (Ligand-binding prot ...	0.04	-	end	0	Secreted protein (By similarity)	cytoplasm [ISS]			473
Q05701 UniProt NPD GO	LPLC3_RAT	Long palate, lung and nasal epithelium carcinoma-associated protein 3 precursor (Ligand-binding prot ...	0.04	-	end	0	Secreted protein (By similarity)	cytoplasm [ISS]			473
Q9NY91 UniProt NPD GO	SC5A4_HUMAN	Low affinity sodium-glucose cotransporter (Sodium/glucose cotransporter 3) (Na(+)/glucose cotranspor ...	0.04	-	end	14 *	Membrane; multi-pass membrane protein				659
P09335 UniProt NPD GO	LP2_BOMMO	Low molecular 30 kDa lipoprotein PBMHP-12 precursor	0.04	-	exc	0	Secreted protein; extracellular space				264
P09334 UniProt NPD GO	LP1_BOMMO	Low molecular 30 kDa lipoprotein PBMHP-6 precursor	0.04	-	mit	0	Secreted protein; extracellular space				256
Q39182 UniProt NPD GO	LCR69_ARATH	Low-molecular-weight cysteine-rich protein LCR69 precursor	0.04	-	mit	1 *	Secreted protein (Potential)				77
Q26304 UniProt NPD GO	LUCI_LUCMI	Luciferin 4-monooxygenase (EC 1.13.12.7) (Luciferase)	0.04	-	nuc	0	Peroxisome (By similarity)	peroxisome [ISS]			548
P04651 UniProt NPD GO	LSHB_BOVIN	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.04	-	nuc	0	Secreted protein				141
P01231 UniProt NPD GO	LSHB_SHEEP	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B) (Intersti ...	0.04	-	nuc	0	Secreted protein				141
P58755 UniProt NPD GO	LY96_CRIGR	Lymphocyte antigen 96 precursor (MD-2 protein)	0.04	-	exc	0	Secreted protein; extracellular space				160
Q64253 UniProt NPD GO	LY6E_MOUSE	Lymphocyte antigen Ly-6E precursor (Thymic shared antigen 1) (TSA-1) (Stem cell antigen 2)	0.04	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				130
Q5TM22 UniProt NPD GO	TNFC_MACMU	Lymphotoxin-beta (LT-beta) (Tumor necrosis factor C) (TNF-C) (Tumor necrosis factor ligand superfami ...	0.04	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				244
P56642 UniProt NPD GO	LPH2_HUMAN	Lysophospholipase HL-60 peak 2 (EC 3.1.1.5) (Fragment)	0.04	-		0					20
P17046 UniProt NPD GO	LAMP2_RAT	Lysosome-associated membrane glycoprotein 2 precursor (LAMP-2) (Lysosomal membrane glycoprotein-type ...	0.04	-	end	1	Cell membrane; single-pass type I membrane protein. Endosome; endosomal membrane; single-pass type I ...				411
P82175 UniProt NPD GO	LYS_ESTAC	Lysozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase) (Fragment)	0.04	-		0					18
P61633 UniProt NPD GO	LYSC_CERAE	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.04	-	vac	0					148
P61630 UniProt NPD GO	LYSC_CERTO	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.04	-	vac	0					148
P61634 UniProt NPD GO	LYSC_ERYPA	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.04	-	vac	0					148
P30201 UniProt NPD GO	LYSC_MACMU	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.04	-	vac	0					148
P61629 UniProt NPD GO	LYSC_PAPAN	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.04	-	vac	0					148
P37160 UniProt NPD GO	LYSS_DROME	Lysozyme S precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase S)	0.04	-	exc	0					140
P61133 UniProt NPD GO	LYG_FUGRU	Lysozyme g (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.04	-	cyt	0					190
O24356 UniProt NPD GO	MEN8_SILLA	MEN-8 protein precursor	0.04	-	nuc	1 *					100
O80580 UniProt NPD GO	MLO15_ARATH	MLO-like protein 15 (AtMlo15)	0.04	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				496
P83443 UniProt NPD GO	MDO1_PSEMR	Macrodontain-1 (EC 3.4.22.-) (Macrodontain I)	0.04	-	cyt	0					213
O55052 UniProt NPD GO	MIF_MERUN	Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1)	0.04	-	nuc	0					114
Q32742 UniProt NPD GO	CHLI_OLILU	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.04	-	cyt	0	Plastid; chloroplast				334
P79085 UniProt NPD GO	ALTA1_ALTAL	Major allergen Alt a 1 precursor	0.04	-	mit	0	Secreted protein				157
O24248 UniProt NPD GO	PRU1_PRUAV	Major allergen Pru av 1 (Pru a 1)	0.04	-	cyt	0				1H2O	160
P19963 UniProt NPD GO	ALL1_OLEEU	Major pollen allergen (Allergen Ole e 1) (Ole e I)	0.04	-	cyt	0	Secreted protein				145
O82015 UniProt NPD GO	LIGV1_LIGVU	Major pollen allergen Lig v 1	0.04	-	cyt	0	Secreted protein				145
P02761 UniProt NPD GO	MUP_RAT	Major urinary protein precursor (MUP) (Alpha-2u-globulin) (Alpha(2)-euglobulin) (Allergen Rat n 1) ( ...	0.04	-	exc	0	15.5 kDa fatty acid-binding protein: Cytoplasm; cytosol. It is probably taken up from the urinary lu ...			2A2U	181
P56569 UniProt NPD GO	MKTX1_MESMA	Makatoxin-1 (Makatoxin I) (MkTx I)	0.04	-	nuc	0	Secreted protein				64
Q86BW9 UniProt NPD GO	MKTX2_MESMA	Makatoxin-2 precursor (Makatoxin II) (MkTx II)	0.04	-	exc	0	Secreted protein				85
P17606 UniProt NPD GO	MDHP1_SORBI	Malate dehydrogenase [NADP] 1, chloroplast precursor (EC 1.1.1.82) (NADP-MDH-1)	0.04	-	mit	0	Plastid; chloroplast			7MDH	429
P15719 UniProt NPD GO	MDHP_MAIZE	Malate dehydrogenase [NADP], chloroplast precursor (EC 1.1.1.82) (NADP-MDH)	0.04	-	mit	0	Plastid; chloroplast				432
P21528 UniProt NPD GO	MDHP_PEA	Malate dehydrogenase [NADP], chloroplast precursor (EC 1.1.1.82) (NADP-MDH)	0.04	-	mit	0	Plastid; chloroplast				441
P00346 UniProt NPD GO	MDHM_PIG	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix			1MLD	338
P04636 UniProt NPD GO	MDHM_RAT	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				338

You are viewing entries 77451 to 77500 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.