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
Q9WVB6 UniProt NPD GO	LENEP_MOUSE	Lens epithelial cell protein LEP503	0.05	-	mit	0					61
Q7LZ31 UniProt NPD GO	LETH_HELHO	Lethal toxin (Fragment)	0.05	-	cyt	0	Secreted protein				33
O04274 UniProt NPD GO	LDOX_PERFR	Leucoanthocyanidin dioxygenase (EC 1.14.11.19) (LDOX) (Leucocyanidin oxygenase) (Leucoanthocyanidin ...	0.05	-	cyt	0					362
P11049 UniProt NPD GO	CD37_HUMAN	Leukocyte antigen CD37 (Tetraspanin-26) (Tspan-26)	0.05	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	151523		281
Q9GKE8 UniProt NPD GO	CD47_PIG	Leukocyte surface antigen CD47 precursor (Integrin-associated protein) (IAP)	0.05	-	end	5 *	Cell membrane; multi-pass membrane protein				303
Q16873 UniProt NPD GO	LTC4S_HUMAN	Leukotriene C4 synthase (EC 4.4.1.20) (Leukotriene-C(4) synthase) (LTC4 synthase)	0.05	-	end	3 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] membrane fraction [TAS] microsome [TAS]	246530		150
Q00469 UniProt NPD GO	CHLL_CHLRE	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.05	-	nuc	0	Plastid; chloroplast				293
P37849 UniProt NPD GO	CHLB_METGY	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.05	-	mit	0	Plastid; chloroplast				103
P37856 UniProt NPD GO	CHLB_SELMO	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.05	-	mit	0	Plastid; chloroplast				103
P31837 UniProt NPD GO	LIGA_PHACH	Ligninase A precursor (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase)	0.05	-	exc	0					372
Q62813 UniProt NPD GO	LSAMP_RAT	Limbic system-associated membrane protein precursor (LSAMP)	0.05	-	end	1	Cell membrane; lipid-anchor; GPI-anchor				338
Q7M4U7 UniProt NPD GO	LIP_RHIJA	Lipase (EC 3.1.1.3) (Triacylglycerol lipase) (Fragments)	0.05	-	cyt	0	Secreted protein; extracellular space				179
P17573 UniProt NPD GO	LIP1_GEOCN	Lipase 1 precursor (EC 3.1.1.3) (Lipase I) (GCL I)	0.05	-	exc	0	Secreted protein				563
Q9P8W0 UniProt NPD GO	LIP5_CANAL	Lipase 5 precursor (EC 3.1.1.3)	0.05	-	end	0	Secreted protein				463
Q61805 UniProt NPD GO	LBP_MOUSE	Lipopolysaccharide-binding protein precursor (LBP)	0.05	-	exc	0	Secreted protein				481
Q6GMG8 UniProt NPD GO	LITAF_BRARE	Lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog (LPS-induced TNF-alpha factor ...	0.05	-	nuc	1	Cytoplasm (By similarity)				163
P0C0T0 UniProt NPD GO	LITAF_RAT	Lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog (LPS-induced TNF-alpha factor ...	0.05	-	nuc	0	Lysosome; lysosomal membrane; peripheral membrane protein; cytoplasmic side (By similarity). Associa ...				161
Q8QGW7 UniProt NPD GO	LITAF_CHICK	Lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog (LPS-induced TNF-alpha factor ...	0.05	-	nuc	1	Cytoplasm (By similarity)				148
Q7T394 UniProt NPD GO	LIS1A_BRARE	Lissencephaly-1 homolog A	0.05	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Localizes to the plus end of microtubules and ...				409
O46421 UniProt NPD GO	EST1_MACFA	Liver carboxylesterase 1 precursor (EC 3.1.1.1)	0.05	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				566
Q64176 UniProt NPD GO	EST22_MOUSE	Liver carboxylesterase 22 precursor (EC 3.1.1.1) (Egasyn) (Esterase-22) (Es-22)	0.05	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...				562
Q63108 UniProt NPD GO	EST3_RAT	Liver carboxylesterase 3 precursor (EC 3.1.1.1) (Carboxyesterase ES-3) (pI 5.5 esterase) (ES-HTEL)	0.05	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...				561
Q7LZE3 UniProt NPD GO	IVBEH_DENAN	Long epsilon-dendrotoxin His55 [Contains: Short epsilon-dendrotoxin His55]	0.05	-	nuc	0	Secreted protein				59
P01396 UniProt NPD GO	NXL1_DENPO	Long neurotoxin 1 (Neurotoxin gamma) (Toxin VN1)	0.05	-	nuc	0	Secreted protein				72
O12963 UniProt NPD GO	NXLH6_BUNMU	Long neurotoxin homolog TA-bm16 precursor (Delta-protein)	0.05	-	nuc	0	Secreted protein				89
O88813 UniProt NPD GO	ACSL5_RAT	Long-chain-fatty-acid--CoA ligase 5 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 5) (LACS 5)	0.05	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...				683
P79107 UniProt NPD GO	FCGR3_BOVIN	Low affinity immunoglobulin gamma Fc region receptor III precursor (IgG Fc receptor III) (Fc-gamma R ...	0.05	-	cyt	0	Membrane; single-pass type I membrane protein (Potential)				250
O75015 UniProt NPD GO	FCG3B_HUMAN	Low affinity immunoglobulin gamma Fc region receptor III-B precursor (IgG Fc receptor III-1) (Fc-gam ...	0.05	-	end	1	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein. Secreted after cleavage			1T89	233
P09338 UniProt NPD GO	LP5_BOMMO	Low molecular 30 kDa lipoprotein PBMHPC-23 precursor	0.05	-	cyt	0	Secreted protein; extracellular space				264
P37303 UniProt NPD GO	GLY1_YEAST	Low specificity L-threonine aldolase (EC 4.1.2.5) (Low specificity L-TA) (TA)	0.05	-	cyt	0		cytosol [IDA]			387
P18581 UniProt NPD GO	CTR2_MOUSE	Low-affinity cationic amino acid transporter 2 (CAT-2) (CAT2) (TEA protein) (T-cell early activation ...	0.05	-	end	14 *	Membrane; multi-pass membrane protein				657
P20721 UniProt NPD GO	CYSPL_LYCES	Low-temperature-induced cysteine proteinase precursor (EC 3.4.22.-) (Fragment)	0.05	-	nuc	0					346
Q03686 UniProt NPD GO	BIP8_TOBAC	Luminal-binding protein 8 (BiP 8) (78 kDa glucose-regulated protein homolog 8) (GRP 78-8) (Fragment) ...	0.05	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				293
P45657 UniProt NPD GO	LSHB_COTJA	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.05	-	end	0	Secreted protein				166
Q2Q1P1 UniProt NPD GO	LSHB_GORGO	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.05	-	mit	0	Secreted protein				141
O09108 UniProt NPD GO	LSHB_MOUSE	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.05	-	mit	0	Secreted protein				141
P01232 UniProt NPD GO	LSHB_PIG	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.05	-	nuc	0	Secreted protein				141
P18842 UniProt NPD GO	LSHB_CANFA	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B) (Fragment ...	0.05	-	exc	0	Secreted protein				138
Q9QYA9 UniProt NPD GO	LSHB_PHOSU	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B) (Fragment ...	0.05	-	mit	0	Secreted protein				128
Q9Z1Q4 UniProt NPD GO	LYG6C_MOUSE	Lymphocyte antigen 6 complex locus protein G6c precursor	0.05	-	exc	0	Secreted protein (Potential)				126
P58754 UniProt NPD GO	LY96_BOVIN	Lymphocyte antigen 96 precursor (MD-2 protein)	0.05	-	vac	0	Secreted protein; extracellular space (By similarity)				160
P47993 UniProt NPD GO	XCL1_MOUSE	Lymphotactin precursor (XCL1) (Cytokine SCM-1) (Lymphotaxin) (Small inducible cytokine C1)	0.05	-	exc	0	Secreted protein				114
Q06643 UniProt NPD GO	TNFC_HUMAN	Lymphotoxin-beta (LT-beta) (Tumor necrosis factor C) (TNF-C) (Tumor necrosis factor ligand superfami ...	0.05	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)		600978		244
P56643 UniProt NPD GO	LPH3_HUMAN	Lysophospholipase HL-60 peak 3 (EC 3.1.1.5) (Fragment)	0.05	-		0					20
Q5VWZ2 UniProt NPD GO	LYPL1_HUMAN	Lysophospholipase-like protein 1 (EC 3.1.2.-)	0.05	-	cyt	0	Cytoplasm (By similarity)				236
P38571 UniProt NPD GO	LICH_HUMAN	Lysosomal acid lipase/cholesteryl ester hydrolase precursor (EC 3.1.1.13) (LAL) (Acid cholesteryl es ...	0.05	-	cyt	0	Lysosome	lysosome [TAS]	278000		399
Q4R4S5 UniProt NPD GO	LICH_MACFA	Lysosomal acid lipase/cholesteryl ester hydrolase precursor (EC 3.1.1.13) (LAL) (Acid cholesteryl es ...	0.05	-	mit	0	Lysosome (By similarity)				399
P83971 UniProt NPD GO	LYSA_DROME	Lysozyme A/C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase A/C)	0.05	-	exc	0					140
P00708 UniProt NPD GO	LYSC_COLLI	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.05	-	nuc	0					127
P00699 UniProt NPD GO	LYSC_LOPCA	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.05	-	nuc	0					129

You are viewing entries 74801 to 74850 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.