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
P48264 UniProt NPD GO	PSBW_CYAPA	Photosystem II reaction center W protein	0.05	-	cyt	0	Plastid; cyanelle				112
O78418 UniProt NPD GO	PSBW_GUITH	Photosystem II reaction center W protein	0.05	-	cyt	0	Plastid; chloroplast				116
Q7LZ52 UniProt NPD GO	BRKP_PHYRO	Phyllokinin (Bradykinyl-isoleucyl-tyrosine O-sulfate)	0.05	-		0	Secreted protein				11
P84697 UniProt NPD GO	KNL2_PHYSA	Phyllokinin [Contains: Bradykinin]	0.05	-		0	Secreted protein				11
Q23755 UniProt NPD GO	PDH1_CALSI	Pigment-dispersing hormone 1 precursor [Contains: PDH precursor-related peptide 1; Pigment-dispersin ...	0.05	-	exc	1 *	Secreted protein				78
P81499 UniProt NPD GO	PIGU_HIRNI	Piguamerin	0.05	-	nuc	0	Secreted protein				48
P51475 UniProt NPD GO	OPSP_CHICK	Pinopsin (Pineal opsin) (P-opsin) (Pineal gland-specific opsin)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				351
P48407 UniProt NPD GO	DPS1_PINST	Pinosylvin synthase 1 (EC 2.3.1.-) (Stilbene synthase 1) (STS 1)	0.05	-	cyt	0	Cytoplasm				396
P05120 UniProt NPD GO	PAI2_HUMAN	Plasminogen activator inhibitor 2 precursor (PAI-2) (Placental plasminogen activator inhibitor) (Mon ...	0.05	-	mit	0	Or: Cytoplasm. Or: Extracellular space		173390	1JRR	415
O88818 UniProt NPD GO	PLST_CRIGR	Plastin-3 (T-plastin)	0.05	-	cyt	0	Cytoplasm				627
P30034 UniProt NPD GO	PLF4_PIG	Platelet factor 4 (PF-4) (CXCL4)	0.05	-	nuc	0	Secreted protein	extracellular region [ISS]			90
P83470 UniProt NPD GO	PLF4_RABIT	Platelet factor 4 (PF-4) (CXCL4) (Fragment)	0.05	-	nuc	0	Secreted protein				30
P02776 UniProt NPD GO	PLF4_HUMAN	Platelet factor 4 precursor (PF-4) (CXCL4) (Oncostatin A) (Iroplact)	0.05	-	exc	1 *	Secreted protein	extracellular region [NAS]	173460	1RHP	101
P70110 UniProt NPD GO	CD36_MESAU	Platelet glycoprotein 4 (Platelet glycoprotein IV) (GPIV) (GPIIIB) (CD36 antigen) (PAS IV) (PAS-4 pr ...	0.05	-	end	2 *	Membrane; multi-pass membrane protein				471
P36986 UniProt NPD GO	TXP12_PLETR	Plectoxin-12 (Plectoxin XII) (PLT-XII) (PLTXII) (Fragment)	0.05	-	nuc	0	Secreted protein				45
P00304 UniProt NPD GO	MPAA3_AMBEL	Pollen allergen Amb a 3 (Amb a III) (Allergen Ra3)	0.05	-	cyt	0					101
Q8H6L7 UniProt NPD GO	PHLB_PHLPR	Pollen allergen Phl p 11	0.05	-	cyt	0	Secreted protein				143
P41749 UniProt NPD GO	PGLRA_ASPFL	Polygalacturonase A precursor (EC 3.2.1.15) (Pectinase) (PGL) (P2C)	0.05	-	cyt	0					363
P26215 UniProt NPD GO	PGLR_COCCA	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.05	-	mit	0					364
Q39786 UniProt NPD GO	PGLR_GOSHI	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.05	-	exc	0					407
Q5K2P9 UniProt NPD GO	POLS2_RAT	Polyserase-2 precursor (EC 3.4.21.-) (Polyserine protease 2)	0.05	-	end	0	Secreted protein; extracellular space; extracellular matrix. Not attached to membranes (By similarit ...				875
Q6C097 UniProt NPD GO	HEM3_YARLI	Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri ...	0.05	-	cyt	0					338
P01154 UniProt NPD GO	POPI_BOVIN	Posterior pituitary peptide	0.05	-	nuc	0					48
P40755 UniProt NPD GO	KAX22_CENMA	Potassium channel toxin alpha-KTx 2.2 (Margatoxin) (MgTX)	0.05	-	nuc	0	Secreted protein			1MTX	39
P0C183 UniProt NPD GO	KA201_TITTR	Potassium channel toxin alpha-KTx 20.1 (Toxin Tt28)	0.05	-	nuc	0	Secreted protein				29
P24662 UniProt NPD GO	KAX31_ANDMA	Potassium channel toxin alpha-KTx 3.1 (Kaliotoxin-1) (KTX-1)	0.05	-	nuc	0	Secreted protein			2KTX	38
P16341 UniProt NPD GO	KAX51_LEIQH	Potassium channel toxin alpha-KTx 5.1 (Leiurotoxin-1) (Leiurotoxin I) (LeTx I) (Scyllatoxin) (ScyTx) ...	0.05	-	nuc	0	Secreted protein			1SCY	31
P31719 UniProt NPD GO	KAX52_ANDMA	Potassium channel toxin alpha-KTx 5.2 (Leiurotoxin I-like toxin P05) (AmP05)	0.05	-	mit	0	Secreted protein			1PNH	31
P0C194 UniProt NPD GO	KAX6B_OPIMA	Potassium channel toxin alpha-KTx 6.11 precursor (Male-specific potassium channel inhibitor IsTX)	0.05	-	nuc	0	Secreted protein			1WMT	63
P59939 UniProt NPD GO	KGX31_CENNO	Potassium channel toxin gamma-KTx 3.1 (Ergtoxin-like protein 2) (ErgTx2) (CnErg2) (CnErgTx2)	0.05	-	nuc	0	Secreted protein				43
Q86QU0 UniProt NPD GO	KGX43_CENEX	Potassium channel toxin gamma-KTx 4.3 (Ergtoxin-like protein 2) (ErgTx2) (CexErg2) (CexErgTx2)	0.05	-	nuc	0	Secreted protein				43
P83655 UniProt NPD GO	KKX13_HETSP	Potassium channel toxin kappa-KTx 1.3	0.05	-	nuc	0	Secreted protein				23
O88759 UniProt NPD GO	KCNS3_RAT	Potassium voltage-gated channel subfamily S member 3 (Voltage-gated potassium channel subunit Kv9.3) ...	0.05	-	end	3	Cell membrane; multi-pass membrane protein (By similarity). Membrane; multi-pass membrane protein (B ...				491
P83126 UniProt NPD GO	PAG67_BOSIN	Pregnancy-associated glycoprotein 67 (EC 3.4.23.-) (boPAG67) (Fragment)	0.05	-	cyt	0					25
P49461 UniProt NPD GO	SECY_ODOSI	Preprotein translocase secY subunit	0.05	-	end	8 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				425
Q9QUG3 UniProt NPD GO	PRND_MOUSE	Prion-like protein doppel precursor (PrPLP) (Doppelganger)	0.05	-	nuc	2 *	Cell membrane; lipid-anchor; GPI-anchor			1Z65	179
P07602 UniProt NPD GO	SAP_HUMAN	Proactivator polypeptide precursor [Contains: Saposin A (Protein A); Saposin B-Val; Saposin B (Sphin ...	0.05	-	end	0	Lysosome	extracellular space [TAS] integral to membrane [TAS]	176801	1SN6	524
Q18803 UniProt NPD GO	ATPL2_CAEEL	Probable ATP synthase subunit g 2, mitochondrial (EC 3.6.3.14)	0.05	-	mit	0					131
Q9P5K9 UniProt NPD GO	CAPZA_NEUCR	Probable F-actin capping protein subunit alpha	0.05	-	nuc	0					269
P35412 UniProt NPD GO	GPR12_MOUSE	Probable G-protein coupled receptor 12 (GPCR01)	0.05	-	end	7	Membrane; multi-pass membrane protein				334
P46093 UniProt NPD GO	GPR4_HUMAN	Probable G-protein coupled receptor 4 (G-protein coupled receptor 19)	0.05	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600551		362
Q8C010 UniProt NPD GO	GPR61_MOUSE	Probable G-protein coupled receptor 61	0.05	-	end	7 *	Membrane; multi-pass membrane protein				449
Q9VHT4 UniProt NPD GO	FUCT1_DROME	Probable GDP-fucose transporter	0.05	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (Potential)				337
Q9VMW9 UniProt NPD GO	GMDS_DROME	Probable GDP-mannose 4,6 dehydratase (EC 4.2.1.47) (GDP-D-mannose dehydratase) (Dm-gmd)	0.05	-	cyt	0		cytoplasm [ISS]			395
Q6TY83 UniProt NPD GO	APX3_ORYSA	Probable L-ascorbate peroxidase 3 (EC 1.11.1.11)	0.05	-	cyt	1	Membrane; single-pass membrane protein (Potential)				291
Q6ZJJ1 UniProt NPD GO	APX4_ORYSA	Probable L-ascorbate peroxidase 4 (EC 1.11.1.11)	0.05	-	cyt	1	Membrane; single-pass membrane protein (Potential)				291
P0C0L0 UniProt NPD GO	APX5_ORYSA	Probable L-ascorbate peroxidase 5, chloroplast precursor (EC 1.11.1.11)	0.05	-	mit	0	Plastid; chloroplast; chloroplast stroma (Probable)				320
Q93Z70 UniProt NPD GO	ARGC_ARATH	Probable N-acetyl-gamma-glutamyl-phosphate reductase, chloroplast precursor (EC 1.2.1.38) (AGPR) (N- ...	0.05	-	cyt	0	Plastid; chloroplast (Potential)			1XYG	401
O45293 UniProt NPD GO	GALT8_CAEEL	Probable N-acetylgalactosaminyltransferase 8 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransfera ...	0.05	-	end	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				421
P35449 UniProt NPD GO	NHX9_CAEEL	Probable Na(+)/H(+) antiporter nhx-9 (Na(+)-H(+) exchanger protein 9)	0.05	-	end	11 *	Cell membrane; multi-pass membrane protein. Excretory cell	integral to membrane [NAS]			667

You are viewing entries 75251 to 75300 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.