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
P17745 UniProt NPD GO	EFTU_ARATH	Elongation factor Tu, chloroplast precursor (EF-Tu)	0.07	-	mit	0	Plastid; chloroplast; chloroplast stroma				476
Q9ZT91 UniProt NPD GO	EFTM_ARATH	Elongation factor Tu, mitochondrial precursor	0.07	-	mit	0	Mitochondrion				454
P36218 UniProt NPD GO	XYN1_TRIRE	Endo-1,4-beta-xylanase 1 precursor (EC 3.2.1.8) (Xylanase 1) (1,4-beta-D-xylan xylanohydrolase 1)	0.07	-	exc	0				1XYN	229
P36217 UniProt NPD GO	XYN2_TRIRE	Endo-1,4-beta-xylanase 2 precursor (EC 3.2.1.8) (Xylanase 2) (1,4-beta-D-xylan xylanohydrolase 2)	0.07	-	exc	0				1XYP	222
Q8J0I9 UniProt NPD GO	GUN16_TRIHA	Endo-1,6-beta-D-glucanase BGN16.3 precursor (EC 3.2.1.75) (Beta-1,6-glucanase BGN16.3) (Glucan endo- ...	0.07	-	mit	0	Secreted protein; extracellular space	extracellular region [IDA]			490
Q12708 UniProt NPD GO	PGLR1_SCLSC	Endo-polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.07	-	mit	0					380
P36362 UniProt NPD GO	CHIT_MANSE	Endochitinase precursor (EC 3.2.1.14)	0.07	-	exc	0	Secreted protein				554
P21799 UniProt NPD GO	CUD4_LOCMI	Endocuticle structural glycoprotein ABD-4	0.07	-	nuc	0					116
Q7M4E8 UniProt NPD GO	CUD6_SCHGR	Endocuticle structural protein SgAbd-6	0.07	-	cyt	0					82
Q12679 UniProt NPD GO	GUNA_ASPKA	Endoglucanase A precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase A) (Cellulase A) (Carboxymethylcellu ...	0.07	-	exc	0					239
Q7X9I4 UniProt NPD GO	ERO2_ARATH	Endoplasmic oxidoreductin-2 precursor (EC 1.8.4.-)	0.07	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side				472
Q5A302 UniProt NPD GO	ERV25_CANAL	Endoplasmic reticulum vesicle protein 25 precursor	0.07	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				215
Q5B5L5 UniProt NPD GO	ERV25_EMENI	Endoplasmic reticulum vesicle protein 25 precursor	0.07	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				216
O13946 UniProt NPD GO	ERV25_SCHPO	Endoplasmic reticulum vesicle protein 25 precursor	0.07	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				216
Q6NVS2 UniProt NPD GO	ERGI3_XENTR	Endoplasmic reticulum-Golgi intermediate compartment protein 3	0.07	-	end	2 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				384
Q95L55 UniProt NPD GO	EDNRA_SHEEP	Endothelin-1 receptor precursor (Endothelin A receptor) (ET-A)	0.07	-	end	7	Membrane; multi-pass membrane protein				427
P25101 UniProt NPD GO	EDNRA_HUMAN	Endothelin-1 receptor precursor (Endothelin A receptor) (ET-A) (hET-AR) (ETA-R)	0.07	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane [NAS]	131243		427
Q756H2 UniProt NPD GO	ENO_ASHGO	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.07	-	cyt	0	Cytoplasm (By similarity)				437
Q70CP7 UniProt NPD GO	ENO_KLULA	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.07	-	nuc	0	Cytoplasm (By similarity)				437
P42040 UniProt NPD GO	ENO_CLAHE	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Allergen ...	0.07	-	nuc	0	Cytoplasm (By similarity)				440
Q870B9 UniProt NPD GO	ENO_RHORB	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Allergen ...	0.07	-	cyt	0	Cytoplasm (By similarity)				439
P31683 UniProt NPD GO	ENO_CHLRE	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Fragment ...	0.07	-	mit	0	Cytoplasm				372
P30575 UniProt NPD GO	ENO1_CANAL	Enolase 1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.07	-	cyt	0	Cytoplasm (By similarity)				440
P00925 UniProt NPD GO	ENO2_YEAST	Enolase 2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 2) (2-phospho-D-glycerate hydro-lyase 2)	0.07	-	cyt	0	Cytoplasm	phosphopyruvate hydratase complex [IDA] soluble fraction [IDA]			436
Q58DM8 UniProt NPD GO	ECHM_BOVIN	Enoyl-CoA hydratase, mitochondrial precursor (EC 4.2.1.17) (Short chain enoyl-CoA hydratase) (SCEH) ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				290
P30084 UniProt NPD GO	ECHM_HUMAN	Enoyl-CoA hydratase, mitochondrial precursor (EC 4.2.1.17) (Short chain enoyl-CoA hydratase) (SCEH) ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	602292		290
Q91130 UniProt NPD GO	EPD_NOTCH	Ependymin precursor (EPD)	0.07	-	exc	0	Secreted protein				214
P62503 UniProt NPD GO	LCN6_MACMU	Epididymal-specific lipocalin-6 precursor	0.07	-	end	0	Secreted protein				180
P54851 UniProt NPD GO	EMP2_HUMAN	Epithelial membrane protein 2 (EMP-2) (Protein XMP)	0.07	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	602334		167
P04068 UniProt NPD GO	HYEP_RABIT	Epoxide hydrolase 1 (EC 3.3.2.3) (Microsomal epoxide hydrolase) (Epoxide hydratase)	0.07	-	nuc	0	Microsome; microsomal membrane; single-pass membrane protein				455
P01588 UniProt NPD GO	EPO_HUMAN	Erythropoietin precursor (Epoetin)	0.07	-	mit	1 *	Secreted protein	extracellular space [TAS]	133170	1EER	193
Q07085 UniProt NPD GO	EST2_CAEEL	Esterase CM06B1 (EC 3.1.1.1)	0.07	-	cyt	0	Cytoplasm. Cell membrane; lipid-anchor; cytoplasmic side				556
O16172 UniProt NPD GO	EST5B_DROPE	Esterase-5B precursor (EC 3.1.1.1) (Est-5B) (Carboxylic-ester hydrolase 5B) (Carboxylesterase-5B)	0.07	-	exc	0	Secreted protein				545
O16169 UniProt NPD GO	EST5C_DROMI	Esterase-5C precursor (EC 3.1.1.1) (Est-5C) (Carboxylic-ester hydrolase 5C) (Carboxylesterase-5C)	0.07	-	end	0	Secreted protein				545
P37059 UniProt NPD GO	DHB2_HUMAN	Estradiol 17-beta-dehydrogenase 2 (EC 1.1.1.62) (17-beta-HSD 2) (Microsomal 17-beta-hydroxysteroid d ...	0.07	-	end	2 *	Membrane; single-pass type II membrane protein (Potential)	endoplasmic reticulum membrane [TAS]	109685		387
P49888 UniProt NPD GO	ST1E1_HUMAN	Estrogen sulfotransferase (EC 2.8.2.4) (Sulfotransferase, estrogen-preferring) (EST-1)	0.07	-	cyt	0	Cytoplasm		600043	1HY3	294
P52845 UniProt NPD GO	ST1E2_RAT	Estrogen sulfotransferase, isoform 2 (EC 2.8.2.4) (EST-2) (Sulfotransferase, estrogen-preferring) (E ...	0.07	-	cyt	0	Cytoplasm (By similarity)				295
P33412 UniProt NPD GO	ECT1_YEAST	Ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14) (Phosphorylethanolamine transferase) (CTP: ...	0.07	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			323
O48929 UniProt NPD GO	ETR1_TOBAC	Ethylene receptor (EC 2.7.13.3) (NT-ETR1)	0.07	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				738
Q5CD96 UniProt NPD GO	ERF1_DILMA	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.07	-	cyt	0	Cytoplasm (By similarity)				436
O59948 UniProt NPD GO	ERF1_PODAN	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.07	-	cyt	0	Cytoplasm (By similarity)				435
P35615 UniProt NPD GO	ERF1_XENLA	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1) (Omnipotent s ...	0.07	-	cyt	0	Cytoplasm				437
O43324 UniProt NPD GO	MCA3_HUMAN	Eukaryotic translation elongation factor 1 epsilon-1 (Multisynthetase complex auxiliary component p1 ...	0.07	-	cyt	0	Cytoplasm. Nucleus. Cytoplasmic under growth arrest conditions. Translocated into the nucleus when g ...	aminoacyl-tRNA synthetase multienzyme complex [ISS] cytoplasm [ISS] nucleus [ISS]	609206		174
P48597 UniProt NPD GO	IF4E_XENLA	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.07	-	cyt	0	Cytoplasm. When interacting with Maskin				213
P48599 UniProt NPD GO	IF4E1_ORYSA	Eukaryotic translation initiation factor 4E-1 (eIF4E-1) (eIF-4E-1) (mRNA cap-binding protein) (eIF-4 ...	0.07	-	cyt	0					227
P29557 UniProt NPD GO	IF4E1_WHEAT	Eukaryotic translation initiation factor 4E-1 (eIF4E-1) (eIF-4E-1) (mRNA cap-binding protein) (eIF-4 ...	0.07	-	cyt	0					215
P51906 UniProt NPD GO	EAA3_MOUSE	Excitatory amino acid transporter 3 (Sodium-dependent glutamate/aspartate transporter 3) (Excitatory ...	0.07	-	end	9 *	Membrane; multi-pass membrane protein				523
P51907 UniProt NPD GO	EAA3_RAT	Excitatory amino acid transporter 3 (Sodium-dependent glutamate/aspartate transporter 3) (Excitatory ...	0.07	-	end	9 *	Membrane; multi-pass membrane protein				523
Q9ES89 UniProt NPD GO	EXTL2_MOUSE	Exostosin-like 2 (EC 2.4.1.223) (Glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltran ...	0.07	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...			1ON8	330
Q9I9P7 UniProt NPD GO	EXFAB_COTJA	Extracellular fatty acid-binding protein precursor (Ex-FABP) (Lipocalin Q83)	0.07	-	exc	0	Secreted protein (By similarity)			1JZU	178

You are viewing entries 69951 to 70000 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.