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
Q3SZM7 UniProt NPD GO	DPEP1_BOVIN	Dipeptidase 1 precursor (EC 3.4.13.19) (Microsomal dipeptidase)	0.12	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Brush border membrane (By similarity)				410
Q9Y8E3 UniProt NPD GO	DPP5_ASPOR	Dipeptidyl-peptidase 5 precursor (EC 3.4.14.-) (Dipeptidyl-peptidase V) (DPP V) (DppV) (Alanyl dipep ...	0.12	-	exc	0	Secreted protein				725
Q9UUG3 UniProt NPD GO	DPH4_SCHPO	Diphthamide biosynthesis protein 4	0.12	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				139
P22827 UniProt NPD GO	DISI_SISBA	Disintegrin barbourin (Platelet aggregation activation inhibitor)	0.12	-	nuc	0	Secreted protein				73
Q9Y672 UniProt NPD GO	ALG6_HUMAN	Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl-P-Glc:Man9Gl ...	0.12	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)		604566		507
P38179 UniProt NPD GO	ALG3_YEAST	Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase (EC 2.4.1.-) (Dol-P-Man-dependent alp ...	0.12	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [IMP]			458
Q9Y673 UniProt NPD GO	ALG5_HUMAN	Dolichyl-phosphate beta-glucosyltransferase (EC 2.4.1.117) (DolP-glucosyltransferase)	0.12	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...		604565		324
Q9BVJ7 UniProt NPD GO	DUS23_HUMAN	Dual specificity protein phosphatase 23 (EC 3.1.3.48) (EC 3.1.3.16) (Low molecular mass dual specifi ...	0.12	-	cyt	0	Cytoplasm; cytosol. Mainly. Nucleus. Also nuclear				150
Q29243 UniProt NPD GO	DAG1_PIG	Dystroglycan (Dystrophin-associated glycoprotein 1) (Fragment)	0.12	-	mit	0	Alpha-dystroglycan: Secreted protein; extracellular space. Beta-dystroglycan: Cell membrane; single- ...				128
P11530 UniProt NPD GO	DMD_RAT	Dystrophin (Fragment)	0.12	-	nuc	0					29
Q14576 UniProt NPD GO	ELAV3_HUMAN	ELAV-like protein 3 (Hu-antigen C) (HuC) (Paraneoplastic cerebellar degeneration-associated antigen) ...	0.12	-	cyt	0			603458		367
P53337 UniProt NPD GO	ERV29_YEAST	ER-derived vesicles protein ERV29	0.12	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	ER to Golgi transport vesicle [IDA]			310
P39727 UniProt NPD GO	ERV46_YEAST	ER-derived vesicles protein ERV46	0.12	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	ER to Golgi transport vesicle [IDA] integral to endoplasmic reticulum membrane [IDA] integral to Golgi membrane [IDA]			415
P61560 UniProt NPD GO	ENH2_PANTR	ERV-H2 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (ERV-H/env60) [Includes: ...	0.12	-	nuc	1 *					94
P70352 UniProt NPD GO	NAR5_MOUSE	Ecto-ADP-ribosyltransferase 5 precursor (EC 2.4.2.31) (NAD(P)(+)--arginine ADP-ribosyltransferase 5) ...	0.12	-	mit	0	Secreted protein. Membrane-associated	extracellular region [IDA]			309
P41801 UniProt NPD GO	ELI_PHYPR	Elicitin precursor	0.12	-	exc	0	Secreted protein				118
Q25820 UniProt NPD GO	EFTU_PLAFA	Elongation factor Tu (EF-Tu)	0.12	-	nuc	0	Plastid; apicoplast				410
P02992 UniProt NPD GO	EFTU_YEAST	Elongation factor Tu, mitochondrial precursor (tufM)	0.12	-	mit	0	Mitochondrion				437
Q9NXB9 UniProt NPD GO	ELOV2_HUMAN	Elongation of very long chain fatty acids protein 2	0.12	-	nuc	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				296
O35949 UniProt NPD GO	ELOV3_MOUSE	Elongation of very long chain fatty acids protein 3 (Cold-inducible glycoprotein of 30 kDa) (CIN-2)	0.12	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				271
P21995 UniProt NPD GO	EMB_MOUSE	Embigin precursor (Teratocarcinoma glycoprotein Gp-70)	0.12	-	end	1	Membrane; single-pass type I membrane protein				330
P55333 UniProt NPD GO	XYNB_EMENI	Endo-1,4-beta-xylanase B precursor (EC 3.2.1.8) (Xylanase B) (1,4-beta-D-xylan xylanohydrolase B) (2 ...	0.12	-	vac	0					221
O60206 UniProt NPD GO	XLNA_AGABI	Endo-1,4-beta-xylanase precursor (EC 3.2.1.8) (Xylanase)	0.12	-	vac	0	Secreted protein				333
Q00446 UniProt NPD GO	PGLR1_COLLN	Endopolygalacturonase 1 precursor (EC 3.2.1.15) (Pectinase) (Clpg1)	0.12	-	exc	0	Secreted protein				363
Q6CUI5 UniProt NPD GO	YSH1_KLULA	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1)	0.12	-	cyt	0	Nucleus (By similarity)				764
O42422 UniProt NPD GO	EPHA7_CHICK	Ephrin type-A receptor 7 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor CEPHA7) (Tyrosine ...	0.12	-	nuc	1	Membrane; single-pass type I membrane protein				993
P52801 UniProt NPD GO	EFNA2_MOUSE	Ephrin-A2 precursor (EPH-related receptor tyrosine kinase ligand 6) (LERK-6) (ELF-1) (CEK7-ligand) ( ...	0.12	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				209
P61917 UniProt NPD GO	NPC2_PANTR	Epididymal secretory protein E1 precursor (Niemann Pick type C2 protein homolog) (EPI-1)	0.12	-	exc	0	Secreted protein (Potential)				151
P61918 UniProt NPD GO	NPC2_MACFA	Epididymal secretory protein E1 precursor (Niemann Pick type C2 protein homolog) (Epididymal secreto ...	0.12	-	exc	0	Secreted protein (Potential)				151
P61916 UniProt NPD GO	NPC2_HUMAN	Epididymal secretory protein E1 precursor (Niemann-Pick disease type C2 protein) (hE1)	0.12	-	exc	0	Secreted protein (Potential)		607625		151
P19235 UniProt NPD GO	EPOR_HUMAN	Erythropoietin receptor precursor (EPO-R)	0.12	-	nuc	1	Cell membrane; single-pass type I membrane protein. Isoform EPOR-S: Secreted protein. Isoform EPOR-S ...	integral to plasma membrane [TAS]	133100	1ERN	508
Q01797 UniProt NPD GO	ESCA_CALVI	Escargot/snail protein homolog (Fragment)	0.12	-	nuc	0	Nucleus (Probable)				82
Q01798 UniProt NPD GO	ESCA_ORYLA	Escargot/snail protein homolog (Fragment)	0.12	-	nuc	0	Nucleus (Probable)				46
P52844 UniProt NPD GO	ST1E1_RAT	Estrogen sulfotransferase, isoform 1 (EC 2.8.2.4) (EST-1) (Sulfotransferase, estrogen-preferring) (E ...	0.12	-	cyt	0	Cytoplasm (By similarity)				295
Q9ZWL6 UniProt NPD GO	ETR1_PASED	Ethylene receptor (EC 2.7.13.3) (PE-ETR1)	0.12	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				738
Q40477 UniProt NPD GO	ERF4_TOBAC	Ethylene-responsive transcription factor 4 (Ethylene-responsive element-binding factor 4 homolog) (E ...	0.12	-	nuc	0	Nucleus				225
Q9BMX3 UniProt NPD GO	ERF1_OXYTR	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.12	-	cyt	0	Cytoplasm				445
Q9BMM1 UniProt NPD GO	ERF1_STYMT	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.12	-	cyt	0	Cytoplasm				445
Q7TQK4 UniProt NPD GO	EXOS3_MOUSE	Exosome complex exonuclease RRP40 (EC 3.1.13.-) (Ribosomal RNA-processing protein 40) (Exosome compo ...	0.12	-	cyt	0	Cytoplasm. Nucleus; nucleolus				273
P38836 UniProt NPD GO	ECM14_YEAST	Extracellular matrix protein 14 precursor (EC 3.4.17.-)	0.12	-	exc	1 *	Vacuole	vacuole (sensu Fungi) [IDA]			430
O82631 UniProt NPD GO	CAPZA_ARATH	F-actin capping protein subunit alpha (CapZ-alpha)	0.12	-	cyt	0					308
Q9BZK7 UniProt NPD GO	TBL1R_HUMAN	F-box-like/WD repeat protein TBL1XR1 (Transducin beta-like 1X-related protein 1) (Nuclear receptor c ...	0.12	-	cyt	0	Nucleus (Probable)		608628		514
Q60584 UniProt NPD GO	FBXW2_MOUSE	F-box/WD repeat protein 2 (F-box and WD-40 domain protein 2) (MD6 protein)	0.12	-	nuc	0		cytoplasm [IDA]			422
P08836 UniProt NPD GO	FPPS_CHICK	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.12	-	mit	0	Cytoplasm			1UBY	367
P10674 UniProt NPD GO	FAS1_DROME	Fasciclin-1 precursor (Fasciclin I) (FAS I) (FCN)	0.12	-	end	0	Cell membrane; lipid-anchor; GPI-anchor	plasma membrane [IDA]		1O70	652
P22648 UniProt NPD GO	FAS2_SCHAM	Fasciclin-2 precursor (Fasciclin II) (FAS II)	0.12	-	end	2 *	Membrane; single-pass type I membrane protein				898
O22126 UniProt NPD GO	FLA8_ARATH	Fasciclin-like arabinogalactan protein 8 precursor (AtAGP8)	0.12	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			420
P07149 UniProt NPD GO	FAS1_YEAST	Fatty acid synthase subunit beta (EC 2.3.1.86) [Includes: 3-hydroxypalmitoyl-[acyl-carrier-protein] ...	0.12	-	end	0		fatty acid synthase complex [IDA] mitochondrion [IDA]			2051
O02323 UniProt NPD GO	FABP7_CAEEL	Fatty acid-binding protein homolog 7	0.12	-	cyt	0					137
P27787 UniProt NPD GO	FER1_MAIZE	Ferredoxin-1, chloroplast precursor (Ferredoxin I) (Fd I)	0.12	-	mit	0	Plastid; chloroplast			1GAQ	150

You are viewing entries 61101 to 61150 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.