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
Q6CF78 UniProt NPD GO	BRE1_YARLI	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-)	0.59	-	nuc	0	Nucleus (By similarity)				700
Q9UMW8 UniProt NPD GO	UBP18_HUMAN	Ubl carboxyl-terminal hydrolase 18 (EC 3.1.2.-) (Ubl thioesterase 18) (ISG15-specific-processing pro ...	0.59	-	nuc	0		nucleus [TAS]	607057		372
Q96MK2 UniProt NPD GO	CT175_HUMAN	Uncharacterized protein C20orf175	0.59	-	mit	0					593
Q6NS82 UniProt NPD GO	CB017_MOUSE	Uncharacterized protein C2orf17 homolog	0.59	-	end	1	Membrane; multi-pass membrane protein (Potential)				541
P35723 UniProt NPD GO	YKG5_YEAST	Uncharacterized protein YKL065C	0.59	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			206
Q3E747 UniProt NPD GO	YL363_YEAST	Uncharacterized protein YLR363W-A	0.59	+	nuc	0	Nucleus	nucleus [IDA]			85
P12868 UniProt NPD GO	PEP5_YEAST	Vacuolar membrane protein PEP5 (Vacuolar biogenesis protein END1) (Vacuolar protein sorting 11)	0.59	-	vac	0	Vacuole; vacuolar membrane; peripheral membrane protein; cytoplasmic side	HOPS complex [IPI] vacuolar membrane (sensu Fungi) [IDA]			1029
Q91W86 UniProt NPD GO	VPS11_MOUSE	Vacuolar protein sorting 11	0.59	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...	actin filament [IDA] early endosome [IDA]			941
Q4X0Z5 UniProt NPD GO	BRO1_ASPFU	Vacuolar protein-sorting protein bro1 (BRO domain-containing protein 1)	0.59	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				976
P15691 UniProt NPD GO	VEGFA_BOVIN	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.59	-	nuc	0	Secreted protein (By similarity). Secreted but remains associated to cells or to the extracellular m ...				190
Q99PS1 UniProt NPD GO	VEGFA_MESAU	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.59	-	exc	0	Secreted protein (By similarity). Secreted but remains associated to cells or to the extracellular m ...				190
P35918 UniProt NPD GO	VGFR2_MOUSE	Vascular endothelial growth factor receptor 2 precursor (EC 2.7.10.1) (VEGFR-2) (Protein-tyrosine ki ...	0.59	-	end	0	Membrane; single-pass type I membrane protein				1367
Q3HXY7 UniProt NPD GO	NGFV1_NOTSC	Venom nerve growth factor 1 precursor (vNGF-1)	0.59	-	exc	0	Secreted protein				244
Q6FKA1 UniProt NPD GO	BOS1_CANGA	Vesicular transport protein BOS1	0.59	-	cyt	1	Secretory vesicle; secretory vesicle membrane; peripheral membrane protein (By similarity). Secretor ...				240
Q9QYC7 UniProt NPD GO	VKGC_MOUSE	Vitamin K-dependent gamma-carboxylase (EC 6.4.-.-) (Gamma-glutamyl carboxylase) (Vitamin K gamma glu ...	0.59	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				757
Q9UBN1 UniProt NPD GO	CCG4_HUMAN	Voltage-dependent calcium channel gamma-4 subunit (Neuronal voltage-gated calcium channel gamma-4 su ...	0.59	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	606404		327
Q8VHW9 UniProt NPD GO	CCG4_RAT	Voltage-dependent calcium channel gamma-4 subunit (Neuronal voltage-gated calcium channel gamma-4 su ...	0.59	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				327
Q9UNX4 UniProt NPD GO	WDR3_HUMAN	WD repeat protein 3	0.59	+	nuc	0	Nucleus; nucleolus	nucleus [TAS]	604737		943
O81788 UniProt NPD GO	WOX13_ARATH	WUSCHEL-related homeobox 13	0.59	+	nuc	0	Nucleus (By similarity)				268
Q810J8 UniProt NPD GO	ZFYV1_MOUSE	Zinc finger FYVE domain-containing protein 1	0.59	-	nuc	0	Golgi apparatus; Golgi stack (By similarity). Resides predominantly in the cisternal stacks of the G ...	endoplasmic reticulum [ISS] Golgi stack [ISS] perinuclear region [ISS]			777
O95789 UniProt NPD GO	ZMYM6_HUMAN	Zinc finger MYM-type protein 6 (Zinc finger protein 258)	0.59	-	nuc	0	Nucleus (Potential)				723
P08048 UniProt NPD GO	ZFY_HUMAN	Zinc finger Y-chromosomal protein	0.59	+	nuc	0	Nucleus		490000	7ZNF	801
Q05516 UniProt NPD GO	ZBT16_HUMAN	Zinc finger and BTB domain-containing protein 16 (Zinc finger protein PLZF) (Promyelocytic leukemia ...	0.59	-	nuc	0	Nucleus	nuclear speck [IDA] nucleus [IDA] transcriptional repressor complex [IDA]	176797	1CS3	673
P52739 UniProt NPD GO	ZN131_HUMAN	Zinc finger protein 131	0.59	-	cyt	0	Nucleus (Potential)	nucleus [NAS]	604073		623
O95201 UniProt NPD GO	ZN205_HUMAN	Zinc finger protein 205 (Zinc finger protein 210)	0.59	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	603436		504
Q13398 UniProt NPD GO	ZN211_HUMAN	Zinc finger protein 211 (Zinc finger protein C2H2-25)	0.59	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	601856		367
Q9UJU3 UniProt NPD GO	ZN228_HUMAN	Zinc finger protein 228	0.59	-	nuc	0	Nucleus (Probable)				913
Q9UDV7 UniProt NPD GO	ZN282_HUMAN	Zinc finger protein 282 (HTLV-I U5RE-binding protein 1) (HUB-1)	0.59	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	603397		671
Q96LW9 UniProt NPD GO	ZN323_HUMAN	Zinc finger protein 323	0.59	-	nuc	0	Nucleus (Probable)				406
Q9Y3S2 UniProt NPD GO	ZN330_HUMAN	Zinc finger protein 330 (Nucleolar cysteine-rich protein) (Nucleolar autoantigen 36)	0.59	-	nuc	0	Nucleus. Nucleus; nucleolus. Predominantly expressed in the nucleolus. In mitosis associated with ce ...	chromosome, pericentric region [IDA] midbody [IDA] nucleolus [IDA]	609550		320
Q8IZ26 UniProt NPD GO	ZNF34_HUMAN	Zinc finger protein 34 (Zinc finger protein KOX32)	0.59	-	nuc	0	Nucleus (Probable)		194526		549
Q9Z1D9 UniProt NPD GO	ZN394_MOUSE	Zinc finger protein 394 (Zinc finger protein 94) (Zfp-94)	0.59	-	nuc	0	Nucleus (Potential)				521
Q6J6I6 UniProt NPD GO	ZN566_PANTR	Zinc finger protein 566	0.59	-	nuc	0	Nucleus (Probable)				418
Q9UII5 UniProt NPD GO	ZN588_HUMAN	Zinc finger protein 588 (Zinc finger protein ZFD25)	0.59	-	nuc	0	Nucleus (Potential)				783
Q8IZ20 UniProt NPD GO	ZN683_HUMAN	Zinc finger protein 683	0.59	-	nuc	0	Nucleus (Probable)				509
Q03923 UniProt NPD GO	ZNF85_HUMAN	Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)	0.59	-	nuc	0	Nucleus	nucleus [TAS]	603899		595
Q09436 UniProt NPD GO	MEX6_CAEEL	Zinc finger protein mex-6	0.59	-	exc	0	Nucleus (Potential)				467
Q4KLI1 UniProt NPD GO	ZKSC1_RAT	Zinc finger with KRAB and SCAN domain-containing protein 1	0.59	-	nuc	0	Nucleus (Potential)				562
P48834 UniProt NPD GO	ZP4_FELCA	Zona pellucida sperm-binding protein 4 precursor (Zona pellucida sperm-binding protein B)	0.59	-	exc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				570
P54682 UniProt NPD GO	D7_DICDI	cAMP-inducible prespore protein D7 precursor	0.59	-	nuc	0					850
Q9DCB4 UniProt NPD GO	ARP21_MOUSE	cAMP-regulated phosphoprotein 21 (ARPP-21)	0.59	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [TAS]			88
Q4WKD9 UniProt NPD GO	YTH1_ASPFU	mRNA 3'-end-processing protein yth1	0.59	-	nuc	0	Nucleus (By similarity)				254
Q6C1E4 UniProt NPD GO	PALC_YARLI	pH-response regulator protein palC	0.59	-	nuc	0					441
Q6FVR8 UniProt NPD GO	PALF_CANGA	pH-response regulator protein palF/RIM8	0.59	-	nuc	0					649
Q91XA5 UniProt NPD GO	SNPC2_MOUSE	snRNA-activating protein complex subunit 2 (SNAPc subunit 2) (snRNA-activating protein complex 45 kD ...	0.59	+	nuc	0	Nucleus (By similarity)				359
Q6FV05 UniProt NPD GO	PUS1_CANGA	tRNA pseudouridine synthase 1 (EC 5.4.99.-) (tRNA-uridine isomerase 1) (tRNA pseudouridylate synthas ...	0.59	-	nuc	0	Nucleus (By similarity)				549
Q63617 UniProt NPD GO	OXRP_RAT	150 kDa oxygen-regulated protein precursor (Orp150) (Hypoxia up-regulated 1)	0.58	-	gol	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				999
P49260 UniProt NPD GO	PLA2R_RABIT	180 kDa secretory phospholipase A2 receptor precursor (PLA2-R)	0.58	-	end	1	Membrane; single-pass type I membrane protein				1458
Q623T0 UniProt NPD GO	ODO1_CAEBR	2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2) (Alpha-ketoglutarate ...	0.58	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				1027
Q5FVR4 UniProt NPD GO	THEX1_RAT	3' histone mRNA exonuclease 1 (EC 3.1.-.-) (3'-5' exonuclease ERI1)	0.58	-	nuc	0					345

You are viewing entries 19951 to 20000 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.