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
Q05315 UniProt NPD GO	LPPL_HUMAN	Eosinophil lysophospholipase (EC 3.1.1.5) (Charcot-Leyden crystal protein) (Lysolecithin acylhydrola ...	0.09	-	cyt	0	Localized in granules from where it may be secreted or transported to other locations in the cell		153310	1QKQ	141
O08545 UniProt NPD GO	EFNA3_MOUSE	Ephrin-A3 precursor (EPH-related receptor tyrosine kinase ligand 3) (LERK-3) (EHK1 ligand) (EHK1-L) ...	0.09	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				187
P52798 UniProt NPD GO	EFNA4_HUMAN	Ephrin-A4 precursor (EPH-related receptor tyrosine kinase ligand 4) (LERK-4)	0.09	-	exc	0	Isoform 1: Cell membrane; lipid-anchor; GPI-anchor. Isoform 2: Secreted protein (Probable)	integral to plasma membrane [TAS]	601380		201
P52803 UniProt NPD GO	EFNA5_HUMAN	Ephrin-A5 precursor (EPH-related receptor tyrosine kinase ligand 7) (LERK-7) (AL-1)	0.09	-	end	0	Cell membrane; lipid-anchor; GPI-anchor. Compartmentalized in discrete caveolae-like membrane microd ...	anchored to plasma membrane [TAS] extracellular space [TAS]	601535		228
Q6JVE6 UniProt NPD GO	LCN10_HUMAN	Epididymal-specific lipocalin-10 precursor	0.09	-	end	1 *	Secreted protein (Potential)				187
Q9Y1U9 UniProt NPD GO	ACTP4_ACTEQ	Equinatoxin-4 precursor (Equinatoxin IV) (EqTIV) (EqT-IV)	0.09	-	cyt	0	Secreted protein. Found in nematocyst				214
P84525 UniProt NPD GO	ERYGN_PLEER	Eryngin (Fragment)	0.09	-	cyt	0					25
Q02026 UniProt NPD GO	ESCA_PHOPA	Escargot/snail protein homolog (Fragment)	0.09	-	nuc	0	Nucleus (Probable)				46
P18167 UniProt NPD GO	ESTP_DROME	Esterase P precursor (EC 3.1.1.1) (Est-P) (Carboxylic-ester hydrolase P) (Carboxylesterase-P)	0.09	-	exc	0	Secreted protein				544
Q05487 UniProt NPD GO	ESTS_DROVI	Esterase S precursor (EC 3.1.1.1) (Est-S) (Carboxylic-ester hydrolase S) (Carboxylesterase-S)	0.09	-	vac	0	Secreted protein				542
O16171 UniProt NPD GO	EST5C_DROPE	Esterase-5C precursor (EC 3.1.1.1) (Est-5C) (Carboxylic-ester hydrolase 5C) (Carboxylesterase-5C)	0.09	-	end	0	Secreted protein				545
Q94HF1 UniProt NPD GO	IF3C_ORYSA	Eukaryotic translation initiation factor 3 subunit 12 (eIF-3 p25) (eIF3k)	0.09	-	cyt	0					226
O77210 UniProt NPD GO	IF4E_APLCA	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.09	-	cyt	0					215
P78954 UniProt NPD GO	IF4E1_SCHPO	Eukaryotic translation initiation factor 4E-1 (eIF4E-1) (eIF-4E-1) (mRNA cap-binding protein 1) (eIF ...	0.09	-	cyt	0		eukaryotic translation initiation factor 4F... [TAS]			218
O04663 UniProt NPD GO	IF4E2_ARATH	Eukaryotic translation initiation factor 4E-2 (eIF4E-2) (eIF-4E-2) (mRNA cap-binding protein) (eIF-( ...	0.09	-	cyt	0					198
P04204 UniProt NPD GO	EXE2_HELSU	Exendin-2 (Helodermin)	0.09	-	nuc	0	Secreted protein				35
P46075 UniProt NPD GO	ELM_ASPFU	Extracellular elastinolytic metalloproteinase precursor (EC 3.4.24.-)	0.09	-	exc	0					634
P34685 UniProt NPD GO	CAPZA_CAEEL	F-actin capping protein subunit alpha	0.09	-	cyt	0					282
Q8N461 UniProt NPD GO	FXL16_HUMAN	F-box/LRR-repeat protein 16 (F-box and leucine-rich repeat protein 16)	0.09	-	cyt	0			609082		479
Q9UKT8 UniProt NPD GO	FBXW2_HUMAN	F-box/WD repeat protein 2 (F-box and WD-40 domain protein 2) (MD6 protein)	0.09	-	nuc	0			609071		454
Q4W9R2 UniProt NPD GO	FKB1B_ASPFU	FK506-binding protein 1B (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyc ...	0.09	-	cyt	0					120
O60046 UniProt NPD GO	FKBP2_NEUCR	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.09	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				217
Q38935 UniProt NPD GO	FKB21_ARATH	FK506-binding protein 2-1 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rot ...	0.09	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				153
Q9TRY0 UniProt NPD GO	FKBP4_BOVIN	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (p59 ...	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				458
Q9VL78 UniProt NPD GO	FKB59_DROME	FK506-binding protein 59 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (dFK ...	0.09	-	cyt	0		inaD signaling complex [IPI]			439
Q9Y680 UniProt NPD GO	FKBP7_HUMAN	FK506-binding protein 7 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.09	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)		607062		259
O54998 UniProt NPD GO	FKBP7_MOUSE	FK506-binding protein 7 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.09	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				218
Q66H94 UniProt NPD GO	FKBP9_RAT	FK506-binding protein 9 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.09	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				570
P83320 UniProt NPD GO	FAR5_PENMO	FMRFamide-like neuropeptide FLP5 (SMPSLRLRF-amide)	0.09	-		0	Secreted protein				9
Q09152 UniProt NPD GO	FPPS1_ARATH	Farnesyl pyrophosphate synthetase 1, mitochondrial precursor (FPP synthetase 1) (FPS 1) (Farnesyl di ...	0.09	-	mit	0	Mitochondrion. Cytoplasm				384
P12104 UniProt NPD GO	FABPI_HUMAN	Fatty acid-binding protein, intestinal (I-FABP) (FABPI)	0.09	-	cyt	0	Cytoplasm		134640	3IFB	131
P82289 UniProt NPD GO	FABPL_LEPPA	Fatty acid-binding protein, liver (L-FABP)	0.09	-	cyt	0	Cytoplasm (By similarity)				125
O00519 UniProt NPD GO	FAAH_HUMAN	Fatty-acid amide hydrolase (EC 3.1.-.-) (Oleamide hydrolase) (Anandamide amidohydrolase)	0.09	-	nuc	1 *	Intracytoplasmic membrane; single-pass membrane protein. Cytoskeleton. Seems to be attached to intra ...	insoluble fraction [TAS] membrane fraction [TAS]	602935		579
P00241 UniProt NPD GO	FER3_CYACA	Ferredoxin	0.09	-	nuc	0	Plastid; chloroplast				98
O23877 UniProt NPD GO	FENR3_ORYSA	Ferredoxin--NADP reductase, embryo isozyme, chloroplast precursor (EC 1.18.1.2) (FNR)	0.09	-	nuc	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				378
Q9LYN2 UniProt NPD GO	FRI3_ARATH	Ferritin-3, chloroplast precursor (EC 1.16.3.1)	0.09	-	nuc	0	Plastid; chloroplast (By similarity)				259
Q24957 UniProt NPD GO	FBRL_GIALA	Fibrillarin	0.09	-	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)				327
P83298 UniProt NPD GO	FIBC_LUMRU	Fibrinolytic enzyme, isozyme C (EC 3.4.21.-) (F-II)	0.09	-	nuc	0					242
P57756 UniProt NPD GO	FCN2_RAT	Ficolin-2 precursor (Collagen/fibrinogen domain-containing protein 2) (Ficolin-B) (Ficolin B) (Serum ...	0.09	-	mit	0	Secreted protein (By similarity)				319
P93107 UniProt NPD GO	PF20_CHLRE	Flagellar WD repeat protein PF20	0.09	-	nuc	0					606
Q96418 UniProt NPD GO	C75A5_EUSGR	Flavonoid 3',5'-hydroxylase (EC 1.14.13.88) (F3'5'H) (Cytochrome P450 75A5)	0.09	-	cyt	0					510
P52836 UniProt NPD GO	F3ST_FLACH	Flavonol 3-sulfotransferase (EC 2.8.2.-) (F3-ST)	0.09	-	cyt	0	Cytoplasm				312
Q99PW7 UniProt NPD GO	FSTL3_RAT	Follistatin-related protein 3 precursor (Follistatin-like 3) (Follistatin-related gene protein)	0.09	-	end	0	Secreted protein (Probable)	secretory granule [IMP]			256
Q8HY84 UniProt NPD GO	FSHB_CERNI	Follitropin beta chain precursor (Follicle-stimulating hormone subunit beta) (FSH-beta) (FSH-B)	0.09	-	exc	0	Secreted protein (By similarity)				129
Q76JU8 UniProt NPD GO	FFAR1_MESAU	Free fatty acid receptor 1 (G-protein coupled receptor 40)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				300
Q9JIP6 UniProt NPD GO	FZD2_MOUSE	Frizzled-2 precursor (Fz-2) (mFz2) (mFz10)	0.09	-	end	6	Membrane; multi-pass membrane protein				570
P25851 UniProt NPD GO	F16P1_ARATH	Fructose-1,6-bisphosphatase, chloroplast precursor (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phos ...	0.09	-	mit	0	Plastid; chloroplast				417
O64422 UniProt NPD GO	F16P1_ORYSA	Fructose-1,6-bisphosphatase, chloroplast precursor (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phos ...	0.09	-	end	0	Plastid; chloroplast; chloroplast stroma				406
P22418 UniProt NPD GO	F16P1_SPIOL	Fructose-1,6-bisphosphatase, chloroplast precursor (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phos ...	0.09	-	mit	0	Plastid; chloroplast			1SPI	415
P00883 UniProt NPD GO	ALDOA_RABIT	Fructose-bisphosphate aldolase A (EC 4.1.2.13) (Muscle-type aldolase)	0.09	-	cyt	0				6ALD	363

You are viewing entries 66101 to 66150 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.