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
P91698 UniProt NPD GO	PER_DROPV	Period circadian protein (Fragment)	0.22	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				396
P30782 UniProt NPD GO	GRO1_RABIT	Permeability factor 2 (RPF2) (Fragment)	0.22	-	nuc	0	Secreted protein				71
P32800 UniProt NPD GO	PEX2_YEAST	Peroxisomal biogenesis factor 2 (Peroxin-2) (Peroxisomal protein PAS5) (Protein CRT1)	0.22	-	cyt	0		peroxisomal membrane [TAS]			271
Q9DC50 UniProt NPD GO	OCTC_MOUSE	Peroxisomal carnitine O-octanoyltransferase (EC 2.3.1.137) (COT)	0.22	-	cyt	0	Peroxisome (Potential)	peroxisome [IDA]		1XMD	612
O70300 UniProt NPD GO	PSPN_MOUSE	Persephin precursor (PSP)	0.22	-	exc	0	Secreted protein	extracellular space [IDA]			156
P14166 UniProt NPD GO	PAL1_IPOBA	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.22	-	nuc	0	Cytoplasm (Probable)				707
P25872 UniProt NPD GO	PAL1_TOBAC	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.22	-	nuc	0	Cytoplasm (Probable)				715
P45728 UniProt NPD GO	PAL2_PETCR	Phenylalanine ammonia-lyase 2 (EC 4.3.1.5)	0.22	-	nuc	0	Cytoplasm (Probable)				716
Q8BVF2 UniProt NPD GO	PDCL3_MOUSE	Phosducin-like protein 3 (Viral IAP-associated factor 1) (VIAF-1)	0.22	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			240
Q95ZE3 UniProt NPD GO	CDS1_ENCCU	Phosphatidate cytidylyltransferase (EC 2.7.7.41) (CDP-diglyceride synthetase) (CDP-diglyceride pyrop ...	0.22	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				393
P00613 UniProt NPD GO	PA24_LATSE	Phospholipase A2 isozyme 4 (EC 3.1.1.4) (Phospholipase A2 isozyme IV) (Phosphatidylcholine 2-acylhyd ...	0.22	-	nuc	0	Secreted protein				118
Q9PUH5 UniProt NPD GO	PA29_AUSSU	Phospholipase A2 isozyme S11-61 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA9 ...	0.22	-	exc	0	Secreted protein (By similarity)				145
P93844 UniProt NPD GO	PLDA2_ORYSA	Phospholipase D alpha 2 (EC 3.1.4.4) (PLD alpha 2) (Choline phosphatase 2) (Phosphatidylcholine-hydr ...	0.22	-	cyt	0					817
P58196 UniProt NPD GO	PLS4_MOUSE	Phospholipid scramblase 4 (PL scramblase 4) (Ca(2+)-dependent phospholipid scramblase 4)	0.22	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				326
P25697 UniProt NPD GO	KPPR_ARATH	Phosphoribulokinase, chloroplast precursor (EC 2.7.1.19) (Phosphopentokinase) (PRKase) (PRK)	0.22	-	mit	0	Plastid; chloroplast				395
P56530 UniProt NPD GO	VIT_ANAPL	Phosvitin (PV) (Fragment)	0.22	-	nuc	0					46
Q6B8S3 UniProt NPD GO	YCF3_GRATL	Photosystem I assembly protein ycf3	0.22	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				170
Q9BBT4 UniProt NPD GO	YCF3_LOTJA	Photosystem I assembly protein ycf3	0.22	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
Q6EW47 UniProt NPD GO	YCF3_NYMAL	Photosystem I assembly protein ycf3	0.22	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
Q68S05 UniProt NPD GO	YCF3_PANGI	Photosystem I assembly protein ycf3	0.22	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
P48115 UniProt NPD GO	PSAF_CYAPA	Photosystem I reaction center subunit III precursor (PSI-F)	0.22	-	end	0	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein. The soluble domain is a ...				186
P42496 UniProt NPD GO	PHY_ADICA	Phytochrome 1	0.22	-	mit	0					1118
Q7XPY2 UniProt NPD GO	PMA1_ORYSA	Plasma membrane ATPase (EC 3.6.3.6) (Proton pump)	0.22	-	end	9	Cell membrane; multi-pass membrane protein				951
Q16720 UniProt NPD GO	AT2B3_HUMAN	Plasma membrane calcium-transporting ATPase 3 (EC 3.6.3.8) (PMCA3) (Plasma membrane calcium pump iso ...	0.22	-	end	6	Cell membrane; multi-pass membrane protein	plasma membrane [TAS]	300014		1220
P79335 UniProt NPD GO	PAI1_PIG	Plasminogen activator inhibitor 1 precursor (PAI-1) (Endothelial plasminogen activator inhibitor) (P ...	0.22	-	end	0	Secreted protein				402
Q95242 UniProt NPD GO	PECA1_PIG	Platelet endothelial cell adhesion molecule precursor (PECAM-1) (CD31 antigen)	0.22	-	end	1	Membrane; single-pass type I membrane protein				740
P16284 UniProt NPD GO	PECA1_HUMAN	Platelet endothelial cell adhesion molecule precursor (PECAM-1) (EndoCAM) (GPIIA') (CD31 antigen)	0.22	-	exc	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	173445		738
P13224 UniProt NPD GO	GP1BB_HUMAN	Platelet glycoprotein Ib beta chain precursor (GP-Ib beta) (GPIbB) (GPIb-beta) (Antigen CD42b-beta) ...	0.22	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	231200		206
Q90678 UniProt NPD GO	PAFA_CHICK	Platelet-activating factor acetylhydrolase precursor (EC 3.1.1.47) (PAF acetylhydrolase) (PAF 2-acyl ...	0.22	-	mit	0	Secreted protein; extracellular space				422
Q9N5L4 UniProt NPD GO	PME4_CAEEL	Poly(ADP-ribose) glycohydrolase pme-4 (EC 3.2.1.143) (Poly ADP-ribose metabolism enzyme 4)	0.22	-	cyt	0					485
P93217 UniProt NPD GO	GP2_LYCES	Polygalacturonase non-catalytic subunit AroGP2 precursor	0.22	-	exc	1 *	Secreted protein; extracellular space; apoplast (By similarity). Cell wall (By similarity). Associat ...				629
P93218 UniProt NPD GO	GP3_LYCES	Polygalacturonase non-catalytic subunit AroGP3 precursor	0.22	-	exc	1 *	Secreted protein; extracellular space; apoplast (By similarity). Cell wall (By similarity). Associat ...				632
Q10473 UniProt NPD GO	GALT1_RAT	Polypeptide N-acetylgalactosaminyltransferase 1 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.22	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				559
Q9ERS0 UniProt NPD GO	KCNKD_RAT	Potassium channel subfamily K member 13 (Tandem pore domain halothane-inhibited potassium channel 1) ...	0.22	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				405
O95069 UniProt NPD GO	KCNK2_HUMAN	Potassium channel subfamily K member 2 (Outward rectifying potassium channel protein TREK-1) (TREK-1 ...	0.22	-	end	6	Membrane; multi-pass membrane protein (Potential)	membrane [NAS]	603219		426
P0C166 UniProt NPD GO	KAX6C_ANUPH	Potassium channel toxin alpha-KTx 6.12 (Anuroctoxin)	0.22	-	nuc	0	Secreted protein				35
P58498 UniProt NPD GO	KAX64_PANIM	Potassium channel toxin alpha-KTx 6.4 (Potassium channel-blocking toxin 4) (Pi4) (Pi-4)	0.22	-	nuc	0	Secreted protein			1N8M	38
Q9Y6J6 UniProt NPD GO	KCNE2_HUMAN	Potassium voltage-gated channel subfamily E member 2 (Minimum potassium ion channel-related peptide ...	0.22	-	nuc	1 *	Membrane; single-pass type I membrane protein	voltage-gated potassium channel complex [TAS]	603796		123
Q9D808 UniProt NPD GO	KCNE2_MOUSE	Potassium voltage-gated channel subfamily E member 2 (Minimum potassium ion channel-related peptide ...	0.22	-	nuc	1 *	Membrane; single-pass type I membrane protein				123
Q92126 UniProt NPD GO	ATP4A_XENLA	Potassium-transporting ATPase alpha chain 1 (EC 3.6.3.10) (Proton pump) (Gastric H+/K+ ATPase subuni ...	0.22	-	end	8	Membrane; multi-pass membrane protein				1030
P54707 UniProt NPD GO	AT12A_HUMAN	Potassium-transporting ATPase alpha chain 2 (EC 3.6.3.10) (Proton pump) (Non-gastric H(+)/K(+) ATPas ...	0.22	-	end	8	Membrane; multi-pass membrane protein	hydrogen:potassium-exchanging ATPase complex [TAS]	182360		1042
P54704 UniProt NPD GO	PSPB_DICDI	Prespore protein B precursor	0.22	-	exc	0					379
Q9WTX4 UniProt NPD GO	NRG4_MOUSE	Pro-neuregulin-4, membrane-bound isoform (Pro-NRG4) [Contains: Neuregulin-4 (NRG-4)]	0.22	-	nuc	1	Pro-neuregulin-4, membrane-bound isoform: Cell membrane; single-pass type I membrane protein (By sim ...				115
Q9LU46 UniProt NPD GO	RH35_ARATH	Probable DEAD-box ATP-dependent RNA helicase 35 (EC 3.6.1.-)	0.22	-	cyt	0					591
P34476 UniProt NPD GO	RPO1D_CAEEL	Probable DNA-directed RNA polymerase I subunit D (EC 2.7.7.6)	0.22	-	nuc	0	Nucleus (By similarity)				144
Q15760 UniProt NPD GO	GPR19_HUMAN	Probable G-protein coupled receptor 19 (GPR-NGA)	0.22	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602927		415
Q19952 UniProt NPD GO	LSM4_CAEEL	Probable U6 snRNA-associated Sm-like protein LSm4	0.22	-	cyt	0	Nucleus (Potential)				123
P22580 UniProt NPD GO	AMDY_YEAST	Probable amidase (EC 3.5.1.4)	0.22	-	nuc	0					549
P91408 UniProt NPD GO	YO1J_CAEEL	Probable aminotransferase T01B11.2 (EC 2.6.1.-)	0.22	-	mit	0					467
O94281 UniProt NPD GO	CSK2C_SCHPO	Probable casein kinase II subunit beta-2 (CK II beta-2)	0.22	-	mit	0					254

You are viewing entries 48751 to 48800 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.