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
Q8JZV9 UniProt NPD GO	DHRS6_MOUSE	Dehydrogenase/reductase SDR family member 6 precursor (EC 1.1.-.-)	0.15	-	cyt	0	Secreted protein (Potential)	cytoplasm [ISS]			245
Q9Y394 UniProt NPD GO	DHRS7_HUMAN	Dehydrogenase/reductase SDR family member 7 precursor (EC 1.1.-.-) (Retinal short-chain dehydrogenas ...	0.15	-	end	1 *					339
Q9EQ06 UniProt NPD GO	DHRS8_MOUSE	Dehydrogenase/reductase SDR family member 8 precursor (EC 1.1.1.-) (17-beta-hydroxysteroid dehydroge ...	0.15	-	mit	0	Secreted protein (Potential). Ref.5: Cytoplasm. However the relevance of such result remains unclear ...				298
Q9YGW7 UniProt NPD GO	DAZL_BRARE	Deleted in azoospermia-like (DAZ-like protein) (zDazl)	0.15	-	mit	0	Cytoplasm	cytoplasm [IDA]			229
O13597 UniProt NPD GO	ERG24_SEPLY	Delta(14)-sterol reductase (EC 1.3.1.70) (C-14 sterol reductase) (Sterol C14-reductase)	0.15	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				512
Q42682 UniProt NPD GO	HEM2_CHLRE	Delta-aminolevulinic acid dehydratase, chloroplast precursor (EC 4.2.1.24) (Porphobilinogen synthase ...	0.15	-	mit	0	Plastid; chloroplast				390
Q43058 UniProt NPD GO	HEM2_PHYPA	Delta-aminolevulinic acid dehydratase, chloroplast precursor (EC 4.2.1.24) (Porphobilinogen synthase ...	0.15	-	cyt	0	Plastid; chloroplast				430
P83608 UniProt NPD GO	TDM1A_MISBR	Delta-missulenatoxin-Mb1a (Delta-MSTX-Mb1a)	0.15	-	nuc	0	Secreted protein				42
Q9PS08 UniProt NPD GO	TXDA_DENAN	Dendrotoxin A (DTX-A) (Fragment)	0.15	-	nuc	0	Secreted protein				30
P81488 UniProt NPD GO	DRG3_PHYBI	Dermaseptin DRG3 precursor (Dermaseptin-3)	0.15	-	exc	0	Secreted protein				77
P28294 UniProt NPD GO	PYRD_AGRAE	Dihydroorotate dehydrogenase (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (DHODase) (DHOD)	0.15	-	cyt	0	Cytoplasm (Probable)				328
Q8K4B7 UniProt NPD GO	FMO4_RAT	Dimethylaniline monooxygenase [N-oxide-forming] 4 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.15	-	end	0	Microsome (By similarity)				559
Q9NY33 UniProt NPD GO	DPP3_HUMAN	Dipeptidyl-peptidase 3 (EC 3.4.14.4) (Dipeptidyl-peptidase III) (DPP III) (Dipeptidyl aminopeptidase ...	0.15	-	nuc	0	Cytoplasm		606818		737
Q99KK7 UniProt NPD GO	DPP3_MOUSE	Dipeptidyl-peptidase 3 (EC 3.4.14.4) (Dipeptidyl-peptidase III) (DPP III) (Dipeptidyl aminopeptidase ...	0.15	-	nuc	0	Cytoplasm (By similarity)				738
Q4I9U7 UniProt NPD GO	DPH3_GIBZE	Diphthamide biosynthesis protein 3	0.15	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				108
Q16832 UniProt NPD GO	DDR2_HUMAN	Discoidin domain-containing receptor 2 precursor (EC 2.7.10.1) (Discoidin domain receptor 2) (Recept ...	0.15	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	191311		855
P31382 UniProt NPD GO	PMT2_YEAST	Dolichyl-phosphate-mannose--protein mannosyltransferase 2 (EC 2.4.1.109)	0.15	-	end	10	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [TAS]			759
P52867 UniProt NPD GO	PMT5_YEAST	Dolichyl-phosphate-mannose--protein mannosyltransferase 5 (EC 2.4.1.109)	0.15	-	end	11	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [TAS]			743
Q5XHB2 UniProt NPD GO	DUS22_XENTR	Dual specificity protein phosphatase 22 (EC 3.1.3.48) (EC 3.1.3.16)	0.15	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				209
P15305 UniProt NPD GO	DYHC_ONCMY	Dynein heavy chain (DYHC) (Fragment)	0.15	-	mit	0					515
Q8K1E3 UniProt NPD GO	EGFL9_MOUSE	EGF-like domain-containing protein 9 precursor (Multiple EGF-like domain protein 9) (Endothelial cel ...	0.15	-	end	1	Membrane; single-pass type I membrane protein (Potential)				382
O00423 UniProt NPD GO	EMAL1_HUMAN	Echinoderm microtubule-associated protein-like 1 (EMAP-1) (HuEMAP-1)	0.15	-	cyt	0		microtubule associated complex [TAS]	602033		717
Q01380 UniProt NPD GO	ELYS_HALCR	Egg-lysin precursor (Sperm-lysin)	0.15	-	mit	0					156
O23755 UniProt NPD GO	EF2_BETVU	Elongation factor 2 (EF-2)	0.15	-	cyt	0	Cytoplasm				843
Q9TK50 UniProt NPD GO	EFTS_PHATR	Elongation factor Ts (EF-Ts)	0.15	-	nuc	0	Plastid; chloroplast				202
Q9JLJ4 UniProt NPD GO	ELOV2_MOUSE	Elongation of very long chain fatty acids protein 2	0.15	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	microsome [IDA]			292
Q9UT45 UniProt NPD GO	ENG1_SCHPO	Endo-1,3(4)-beta-glucanase 1 precursor (EC 3.2.1.6) (Endo-1,4-beta-glucanase 1) (Endo-1,3-beta-gluca ...	0.15	-	exc	0	Membrane. Localized in a ring-like structure around the septum	cell septum surface [IDA] cell surface [IDA]			1016
P07529 UniProt NPD GO	XYNA_CRYAL	Endo-1,4-beta-xylanase precursor (EC 3.2.1.8) (Xylanase) (1,4-beta-D-xylan xylanohydrolase)	0.15	-	end	0	Secreted protein				332
P29023 UniProt NPD GO	CHIB_MAIZE	Endochitinase B precursor (EC 3.2.1.14) (Seed chitinase B) (Fragment)	0.15	-	exc	0					269
P56680 UniProt NPD GO	GUN1_HUMIN	Endoglucanase 1 (EC 3.2.1.4) (Endoglucanase I) (Endo-1,4-beta-glucanase) (Cellulase)	0.15	-	cyt	0	Secreted protein			2A39	402
Q8WZS6 UniProt NPD GO	YSH1_NEUCR	Endoribonuclease ysh-1 (EC 3.1.27.-) (mRNA 3'-end-processing protein ysh-1)	0.15	-	mit	0	Nucleus (By similarity)				850
Q925F2 UniProt NPD GO	ESAM_MOUSE	Endothelial cell-selective adhesion molecule precursor	0.15	-	mit	1	Cell membrane; cell-cell junction; adherens junction; single-pass type I membrane protein (Potential ...	adherens junction [IDA] plasma membrane [IDA] tight junction [IDA]			394
Q9Y5X9 UniProt NPD GO	LIPE_HUMAN	Endothelial lipase precursor (EC 3.1.1.3) (Endothelial cell-derived lipase) (EDL) (EL)	0.15	-	exc	0	Secreted protein		603684		500
Q9N0W7 UniProt NPD GO	EDNRB_RABIT	Endothelin B receptor precursor (ET-B) (Endothelin receptor Non-selective type)	0.15	-	end	8 *	Membrane; multi-pass membrane protein				441
P32940 UniProt NPD GO	EDNR3_XENLA	Endothelin-3 receptor precursor (ET-C)	0.15	-	end	8 *	Membrane; multi-pass membrane protein				444
P38071 UniProt NPD GO	ETR1_YEAST	Enoyl-[acyl-carrier protein] reductase [NADPH, B-specific] (EC 1.3.1.10) (Trans-2-enoyl-CoA reductas ...	0.15	+	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			371
P54763 UniProt NPD GO	EPHB2_MOUSE	Ephrin type-B receptor 2 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EPH-3) (Neural ki ...	0.15	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] synapse [NAS]		1SHW	994
Q61521 UniProt NPD GO	EREG_MOUSE	Epiregulin precursor	0.15	-	nuc	2 *	Precursor form: Cell membrane; single-pass type I membrane protein (By similarity). Mature form: Sec ...	extracellular space [IDA]			162
Q03146 UniProt NPD GO	DDR1_MOUSE	Epithelial discoidin domain-containing receptor 1 precursor (EC 2.7.10.1) (Epithelial discoidin doma ...	0.15	-	end	1	Membrane; single-pass type I membrane protein				911
O88662 UniProt NPD GO	EMP2_MOUSE	Epithelial membrane protein 2 (EMP-2) (Protein XMP)	0.15	-	end	4 *	Membrane; multi-pass membrane protein				172
P61914 UniProt NPD GO	ACTP2_ACTEQ	Equinatoxin-2 precursor (Equinatoxin II) (EqTII) (EqT-II)	0.15	-	mit	0	Secreted protein. Found in nematocyst			1TZQ	214
P27105 UniProt NPD GO	STOM_HUMAN	Erythrocyte band 7 integral membrane protein (Stomatin) (Protein 7.2b)	0.15	-	nuc	1 *	Cell membrane; single-pass membrane protein; lipid-anchor; cytoplasmic side. Exposed on the cytoplas ...	cytoskeleton [TAS] integral to plasma membrane [TAS]	133090		287
P31509 UniProt NPD GO	ESCA_CRYAP	Escargot/snail protein homolog (Fragment)	0.15	-	nuc	0	Nucleus (Probable)				46
Q02027 UniProt NPD GO	ESCA_PSYCI	Escargot/snail protein homolog (Fragment)	0.15	-	nuc	0	Nucleus (Probable)				46
P51656 UniProt NPD GO	DHB1_MOUSE	Estradiol 17-beta-dehydrogenase 1 (EC 1.1.1.62) (17-beta-HSD 1) (17-beta-hydroxysteroid dehydrogenas ...	0.15	-	nuc	0	Cytoplasm				344
O81122 UniProt NPD GO	ETR1_MALDO	Ethylene receptor (EC 2.7.13.3)	0.15	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				741
Q41342 UniProt NPD GO	ETR1_LYCES	Ethylene receptor 1 (EC 2.7.13.3) (LeETR1)	0.15	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				754
Q5CG95 UniProt NPD GO	ERF1_CRYHO	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.15	-	cyt	0	Cytoplasm (By similarity)				429
O94236 UniProt NPD GO	IF37_SCHPO	Eukaryotic translation initiation factor 3 subunit 7 homolog (Microtubule-destabilizing protein moe1 ...	0.15	-	cyt	0	Nucleus	eukaryotic translation initiation factor 3 ... [TAS]			567
O61955 UniProt NPD GO	IF4E3_CAEEL	Eukaryotic translation initiation factor 4E-3 (eIF4E-3) (eIF-4E-3) (mRNA cap-binding protein) (eIF-4 ...	0.15	-	cyt	0					248

You are viewing entries 56851 to 56900 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.