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
P00630 UniProt NPD GO	PA2_APIME	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Allergen Api m 1) (Ap ...	0.11	-	exc	0	Secreted protein			1POC	167
Q45Z27 UniProt NPD GO	PA24_TROCA	Phospholipase A2, acidic 4 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase 4) (PLA-4)	0.11	-	exc	1 *	Secreted protein				151
P04416 UniProt NPD GO	PA22_PIG	Phospholipase A2, minor isoenzyme (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.11	-	nuc	0	Secreted protein				124
Q92085 UniProt NPD GO	PA2B_NAJSP	Phospholipase A2, neutral B precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (NAJPLA-2B) ...	0.11	-	exc	0	Secreted protein (By similarity)				146
Q14558 UniProt NPD GO	KPRA_HUMAN	Phosphoribosyl pyrophosphate synthetase-associated protein 1 (PRPP synthetase-associated protein 1) ...	0.11	-	cyt	0			601249	2C4K	356
Q9D0M1 UniProt NPD GO	KPRA_MOUSE	Phosphoribosyl pyrophosphate synthetase-associated protein 1 (PRPP synthetase-associated protein 1) ...	0.11	-	cyt	0					356
Q63468 UniProt NPD GO	KPRA_RAT	Phosphoribosyl pyrophosphate synthetase-associated protein 1 (PRPP synthetase-associated protein 1) ...	0.11	-	cyt	0					356
O20030 UniProt NPD GO	YCF4_CHLRE	Photosystem I assembly protein ycf4	0.11	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				197
P49483 UniProt NPD GO	PSAF_ODOSI	Photosystem I reaction center subunit III (PSI-F)	0.11	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid lumen				185
Q9SUI5 UniProt NPD GO	PSAK_ARATH	Photosystem I reaction center subunit psaK, chloroplast precursor (Photosystem I subunit X) (PSI-K)	0.11	-	nuc	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				130
Q29627 UniProt NPD GO	PACR_BOVIN	Pituitary adenylate cyclase-activating polypeptide type I receptor precursor (PACAP type I receptor) ...	0.11	-	end	8 *	Membrane; multi-pass membrane protein				513
Q4V7E2 UniProt NPD GO	PLAC1_RAT	Placenta-specific protein 1 precursor	0.11	-	mit	0					173
Q9DAY2 UniProt NPD GO	PRLC1_MOUSE	Placental prolactin-like protein C1 precursor (PRL-like protein C1) (PLP-C1) (Prolactin-like protein ...	0.11	-	cyt	0	Secreted protein (By similarity)				240
P13909 UniProt NPD GO	PAI1_BOVIN	Plasminogen activator inhibitor 1 precursor (PAI-1) (Endothelial plasminogen activator inhibitor) (P ...	0.11	-	exc	0	Secreted protein				402
P50449 UniProt NPD GO	PAI1_MUSVI	Plasminogen activator inhibitor 1 precursor (PAI-1) (Endothelial plasminogen activator inhibitor) (P ...	0.11	-	end	0	Secreted protein				400
P20961 UniProt NPD GO	PAI1_RAT	Plasminogen activator inhibitor 1 precursor (PAI-1) (Endothelial plasminogen activator inhibitor) (P ...	0.11	-	mit	0	Secreted protein				402
Q99487 UniProt NPD GO	PAFA2_HUMAN	Platelet-activating factor acetylhydrolase 2, cytoplasmic (EC 3.1.1.47) (Serine-dependent phospholip ...	0.11	-	cyt	0	Cytoplasm		602344		392
Q13093 UniProt NPD GO	PAFA_HUMAN	Platelet-activating factor acetylhydrolase precursor (EC 3.1.1.47) (PAF acetylhydrolase) (PAF 2-acyl ...	0.11	-	mit	0	Secreted protein; extracellular space	extracellular region [TAS]	601690		441
Q9BPZ3 UniProt NPD GO	PAIP2_HUMAN	Polyadenylate-binding protein-interacting protein 2 (Poly(A)-binding protein-interacting protein 2) ...	0.11	-	cyt	0	Cytoplasm	cytoplasm [IDA]	605604	1JGN	127
O74213 UniProt NPD GO	PGLR1_ASPAC	Polygalacturonase 1 precursor (EC 3.2.1.15) (PG-1) (Pectinase 1)	0.11	-	exc	0				1IB4	378
Q9UKA9 UniProt NPD GO	PTBP2_HUMAN	Polypyrimidine tract-binding protein 2 (Neurally-enriched homolog of PTB) (Neural polypyrimidine tra ...	0.11	-	cyt	0	Nucleus (By similarity)		608449	2CQ1	531
P54660 UniProt NPD GO	PONA_DICDI	Ponticulin precursor	0.11	-	exc	2 *	Cell membrane; multi-pass membrane protein. Cell membrane; lipid-anchor; GPI-anchor. Preferentially ...				143
O22397 UniProt NPD GO	POT1_ARATH	Potassium transporter 1 (AtPOT1) (AtKUP1) (AtKT1)	0.11	+	end	13 *	Cell membrane; multi-pass membrane protein (Potential)				712
Q6VVA6 UniProt NPD GO	HAK1_ORYSA	Potassium transporter 1 (OsHAK1)	0.11	-	end	12	Cell membrane; multi-pass membrane protein (Potential)				801
Q9JJV7 UniProt NPD GO	KCNE3_RAT	Potassium voltage-gated channel subfamily E member 3 (Minimum potassium ion channel-related peptide ...	0.11	-	nuc	1	Membrane; single-pass type I membrane protein				107
P33704 UniProt NPD GO	ATP4B_CANFA	Potassium-transporting ATPase subunit beta (Proton pump beta chain) (Gastric H(+)/K(+) ATPase beta s ...	0.11	-	cyt	1 *	Membrane; single-pass type II membrane protein				290
Q9VRV7 UniProt NPD GO	PM14_DROME	Pre-mRNA branch site p14-like protein	0.11	-	mit	0	Nucleus (Potential)				121
Q29078 UniProt NPD GO	PAG1_PIG	Pregnancy-associated glycoprotein 1 precursor (EC 3.4.23.-) (PAG 1)	0.11	-	exc	0	Secreted protein; extracellular space				389
P51268 UniProt NPD GO	PREA_PORPU	Prenyl transferase (EC 2.5.1.-)	0.11	-	cyt	0	Plastid; chloroplast				323
Q99ML5 UniProt NPD GO	PCYOX_RAT	Prenylcysteine oxidase precursor (EC 1.8.3.5) (Chloride ion pump-associated 55 kDa protein)	0.11	-	end	0	Lysosome (By similarity)	plasma membrane [IDA]			504
O78328 UniProt NPD GO	DXS_CAPAN	Probable 1-deoxy-D-xylulose-5-phosphate synthase, chloroplast precursor (EC 2.2.1.7) (1-deoxyxylulos ...	0.11	-	cyt	0	Plastid; chloroplast (Probable)				719
Q09672 UniProt NPD GO	PANB_SCHPO	Probable 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) (Ketopantoate hydroxymethylt ...	0.11	-	cyt	0					267
Q8BG93 UniProt NPD GO	NUD15_MOUSE	Probable 7,8-dihydro-8-oxoguanine triphosphatase NUDT15 (EC 3.1.6.-) (8-oxo-dGTPase NUDT15) (Nucleos ...	0.11	-	cyt	0					170
Q8SQI5 UniProt NPD GO	ABC1_ENCCU	Probable ABC transporter ECU01_0200/ECU01_1410	0.11	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)				596
Q00830 UniProt NPD GO	ABCX_ODOSI	Probable ATP-dependent transporter ycf16	0.11	-	cyt	0	Plastid; chloroplast				251
Q8K087 UniProt NPD GO	GPR1_MOUSE	Probable G-protein coupled receptor 1	0.11	-	end	7 *	Membrane; multi-pass membrane protein				353
Q3U3F9 UniProt NPD GO	GP160_MOUSE	Probable G-protein coupled receptor 160	0.11	-	end	7 *	Membrane; multi-pass membrane protein				336
Q9Y2T6 UniProt NPD GO	GPR55_HUMAN	Probable G-protein coupled receptor 55	0.11	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604107		319
Q9EPB7 UniProt NPD GO	GPR88_MOUSE	Probable G-protein coupled receptor 88 (Striatum-specific G-protein coupled receptor)	0.11	-	end	6 *	Membrane; multi-pass membrane protein				384
Q9ESP4 UniProt NPD GO	GPR88_RAT	Probable G-protein coupled receptor 88 (Striatum-specific G-protein coupled receptor)	0.11	-	end	6 *	Membrane; multi-pass membrane protein				384
P0C0L1 UniProt NPD GO	APX6_ORYSA	Probable L-ascorbate peroxidase 6, chloroplast precursor (EC 1.11.1.11)	0.11	-	mit	0	Plastid; chloroplast; chloroplast stroma (Probable)				309
Q941Z0 UniProt NPD GO	NQR1_ORYSA	Probable NADPH:quinone oxidoreductase 1 (EC 1.6.5.2)	0.11	-	cyt	0					197
P56175 UniProt NPD GO	RCL1_DROME	Probable RNA 3'-terminal phosphate cyclase-like protein	0.11	-	cyt	0	Nucleus; nucleolus (By similarity)				384
Q96301 UniProt NPD GO	SPY_ARATH	Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY (EC 2.4.1.-)	0.11	-	cyt	0	Cytoplasm. Nucleus	nucleus [TAS]			914
Q8H0B6 UniProt NPD GO	ARAE2_ORYSA	Probable UDP-arabinose 4-epimerase 2 (EC 5.1.3.5) (UDP-D-xylose 4-epimerase 2) (UDP-galactose 4-epim ...	0.11	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Potential) ...				391
Q5R7G6 UniProt NPD GO	PEPL1_PONPY	Probable aminopeptidase NPEPL1 (EC 3.4.11.-) (Aminopeptidase-like 1)	0.11	+	cyt	0					523
Q9M8W5 UniProt NPD GO	SIP11_ARATH	Probable aquaporin SIP1.1 (Small basic intrinsic protein 1.1)	0.11	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				240
Q9FL25 UniProt NPD GO	KCO2_ARATH	Probable calcium-activated outward-rectifying potassium channel 2 (AtKCO2)	0.11	+	end	5	Membrane; multi-pass membrane protein				443
Q19529 UniProt NPD GO	CMC3_CAEEL	Probable calcium-binding mitochondrial carrier F17E5.2	0.11	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				531
Q09236 UniProt NPD GO	COPD_CAEEL	Probable coatomer subunit delta (Delta-coat protein) (Delta-COP)	0.11	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				515

You are viewing entries 63251 to 63300 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.