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
Q10119 UniProt NPD GO	EF1A2_SCHPO	Elongation factor 1-alpha-B/C (EF-1-alpha-B/C)	0.05	-	cyt	0	Cytoplasm				460
P78590 UniProt NPD GO	EF1B_CANAL	Elongation factor 1-beta (EF-1-beta)	0.05	-	cyt	0					213
P30151 UniProt NPD GO	EF1B_XENLA	Elongation factor 1-beta (EF-1-beta) (p30)	0.05	-	cyt	0					226
P17245 UniProt NPD GO	EFTU_CYAPA	Elongation factor Tu (EF-Tu)	0.05	-	mit	0	Plastid; cyanelle				409
Q9TJQ8 UniProt NPD GO	EFTU_PROWI	Elongation factor Tu (EF-Tu)	0.05	-	mit	0	Plastid				409
P50377 UniProt NPD GO	EFTU_GRALE	Elongation factor Tu (EF-Tu) (Fragment)	0.05	-	cyt	0	Plastid; chloroplast				235
Q9Y700 UniProt NPD GO	EFTU_SCHPO	Elongation factor Tu, mitochondrial precursor	0.05	-	mit	0	Mitochondrion (By similarity)				439
P39540 UniProt NPD GO	ELO1_YEAST	Elongation of fatty acids protein 1	0.05	-	end	5	Membrane; multi-pass membrane protein (Potential)				310
Q9GZR5 UniProt NPD GO	ELOV4_HUMAN	Elongation of very long chain fatty acids protein 4	0.05	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)		605512		314
Q95K73 UniProt NPD GO	ELOV4_MACFA	Elongation of very long chain fatty acids protein 4	0.05	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				314
Q3S8M4 UniProt NPD GO	ELOV4_MACMU	Elongation of very long chain fatty acids protein 4	0.05	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				314
P48793 UniProt NPD GO	XYN_TRIHA	Endo-1,4-beta-xylanase (EC 3.2.1.8) (Xylanase) (1,4-beta-D-xylan xylanohydrolase)	0.05	-	cyt	0				1XND	190
P23666 UniProt NPD GO	GUN2_PERAE	Endoglucanase 2 (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Abscission cellulase 2) (Fragment)	0.05	-	nuc	0					130
Q96RQ1 UniProt NPD GO	ERGI2_HUMAN	Endoplasmic reticulum-Golgi intermediate compartment protein 2	0.05	-	mit	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				377
Q803I2 UniProt NPD GO	ERGI3_BRARE	Endoplasmic reticulum-Golgi intermediate compartment protein 3	0.05	-	end	2 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				383
Q5KCZ0 UniProt NPD GO	YSH1_CRYNE	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1)	0.05	-	mit	0	Nucleus (By similarity)				773
Q5KSU9 UniProt NPD GO	EDNRA_CANFA	Endothelin-1 receptor precursor (Endothelin A receptor) (ET-A)	0.05	-	end	7	Membrane; multi-pass membrane protein				426
Q29010 UniProt NPD GO	EDNRA_PIG	Endothelin-1 receptor precursor (Endothelin A receptor) (ET-A)	0.05	-	end	7	Membrane; multi-pass membrane protein				427
P26684 UniProt NPD GO	EDNRA_RAT	Endothelin-1 receptor precursor (Endothelin A receptor) (ET-A)	0.05	-	end	8 *	Membrane; multi-pass membrane protein	membrane [IDA]			426
P11838 UniProt NPD GO	CARP_CRYPA	Endothiapepsin precursor (EC 3.4.23.22) (Aspartate protease)	0.05	-	exc	0				5ER2	419
Q12560 UniProt NPD GO	ENO_ASPOR	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.05	-	nuc	0	Cytoplasm (By similarity)				438
Q27527 UniProt NPD GO	ENO_CAEEL	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.05	-	nuc	0	Cytoplasm (By similarity)				433
Q6RG04 UniProt NPD GO	ENO_CRYPA	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.05	-	cyt	0	Cytoplasm (By similarity)				438
Q9U615 UniProt NPD GO	ENO_MASBA	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.05	-	cyt	0	Cytoplasm (By similarity)				439
Q7RV85 UniProt NPD GO	ENO_NEUCR	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.05	-	cyt	0	Cytoplasm (By similarity)				438
P40370 UniProt NPD GO	ENO11_SCHPO	Enolase 1-1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 1-1) (2-phospho-D-glycerate hydro-lyase 1- ...	0.05	-	cyt	0	Cytoplasm (By similarity)				439
P32188 UniProt NPD GO	EPD_ESOLU	Ependymin precursor (EPD)	0.05	-	cyt	0	Secreted protein				221
P12958 UniProt NPD GO	EPD2_CARAU	Ependymin-2 precursor (Ependymin II) (EPD-II)	0.05	-	vac	0	Secreted protein				215
Q39688 UniProt NPD GO	EP1G_DAUCA	Epidermis-specific secreted glycoprotein EP1 precursor (52/54 kDa medium protein)	0.05	-	mit	0	Secreted protein	extracellular region [IDA]			389
P30710 UniProt NPD GO	GPX5_RAT	Epididymal secretory glutathione peroxidase precursor (EC 1.11.1.9) (Epididymis-specific glutathione ...	0.05	-	mit	0	Secreted protein				221
P21765 UniProt NPD GO	GPX5_MOUSE	Epididymal secretory glutathione peroxidase precursor (EC 1.11.1.9) (Epididymis-specific glutathione ...	0.05	-	mit	0	Secreted protein				221
O97763 UniProt NPD GO	NPC2_PIG	Epididymal secretory protein E1 precursor (Niemann Pick type C2 protein homolog) (16 kDa secretory p ...	0.05	-	exc	0	Secreted protein				149
Q6Q2C2 UniProt NPD GO	HYES_PIG	Epoxide hydrolase 2 (EC 3.3.2.3) (Soluble epoxide hydrolase) (SEH) (Epoxide hydratase) (Cytosolic ep ...	0.05	-	pox	0	Cytoplasm (By similarity). Peroxisome (By similarity)				555
Q99808 UniProt NPD GO	S29A1_HUMAN	Equilibrative nucleoside transporter 1 (Equilibrative nitrobenzylmercaptopurine riboside-sensitive n ...	0.05	-	end	11 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	602193		455
O60584 UniProt NPD GO	EDDF1_HUMAN	Erythroid differentiation and denucleation factor 1	0.05	-	mit	0					74
Q28513 UniProt NPD GO	EPO_MACMU	Erythropoietin precursor	0.05	-	mit	0	Secreted protein				192
Q9GKA2 UniProt NPD GO	EPO_RABIT	Erythropoietin precursor	0.05	-	exc	1 *	Secreted protein				195
Q6GME2 UniProt NPD GO	CK054_XENLA	Ester hydrolase C11orf54 homolog (EC 3.1.-.-)	0.05	-	cyt	0	Nucleus (By similarity)				316
Q28GJ2 UniProt NPD GO	CK054_XENTR	Ester hydrolase C11orf54 homolog (EC 3.1.-.-)	0.05	-	cyt	0	Nucleus (By similarity)				313
Q9R0P3 UniProt NPD GO	ESTD_MOUSE	Esterase D (EC 3.1.1.1) (Esterase 10) (Sid 478)	0.05	-	cyt	0	Cytoplasmic vesicle (By similarity)				282
O16168 UniProt NPD GO	EST5A_DROMI	Esterase-5A precursor (EC 3.1.1.1) (Est-5A) (Carboxylic-ester hydrolase 5A) (Carboxylesterase-5A)	0.05	-	mit	0	Secreted protein				555
P14061 UniProt NPD GO	DHB1_HUMAN	Estradiol 17-beta-dehydrogenase 1 (EC 1.1.1.62) (17-beta-HSD 1) (Placental 17-beta-hydroxysteroid de ...	0.05	-	nuc	0	Cytoplasm	cytoplasm [TAS]	109684	3DHE	327
P51658 UniProt NPD GO	DHB2_MOUSE	Estradiol 17-beta-dehydrogenase 2 (EC 1.1.1.62) (17-beta-HSD 2) (17-beta-hydroxysteroid dehydrogenas ...	0.05	-	end	2 *	Membrane; single-pass type II membrane protein (Potential)				381
O00303 UniProt NPD GO	IF35_HUMAN	Eukaryotic translation initiation factor 3 subunit 5 (eIF-3 epsilon) (eIF3 p47 subunit) (eIF3f)	0.05	-	mit	0		eukaryotic translation initiation factor 3 ... [TAS]	603914		357
Q9DCH4 UniProt NPD GO	IF35_MOUSE	Eukaryotic translation initiation factor 3 subunit 5 (eIF-3 epsilon) (eIF3 p47 subunit) (eIF3f)	0.05	-	mit	0					361
Q03389 UniProt NPD GO	IF4E2_WHEAT	Eukaryotic translation initiation factor 4E-2 (eIF4E-2) (eIF-4E-2) (mRNA cap-binding protein) (eIF-( ...	0.05	-	cyt	0					209
Q21693 UniProt NPD GO	IF4E2_CAEEL	Eukaryotic translation initiation factor 4E-2 (eIF4E-2) (eIF-4E-2) (mRNA cap-binding protein) (eIF-4 ...	0.05	-	cyt	0					228
Q9GU68 UniProt NPD GO	IF5A_DROME	Eukaryotic translation initiation factor 5A (eIF-5A)	0.05	-	nuc	0		cytosol [NAS]			159
P26349 UniProt NPD GO	EXE4_HELSU	Exendin-4 precursor	0.05	-	exc	1 *	Secreted protein			1JRJ	87
P11740 UniProt NPD GO	GLB1_PHESE	Extracellular globin-1 (Globin I) (Erythrocruorin)	0.05	-	cyt	0	Secreted protein				141

You are viewing entries 74351 to 74400 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.