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
P51554 UniProt NPD GO	EF1A_HYDAT	Elongation factor 1-alpha (EF-1-alpha)	0.04	-	cyt	0	Cytoplasm				468
Q08046 UniProt NPD GO	EF1A_GIALA	Elongation factor 1-alpha (EF-1-alpha) (14 NM filament-associated protein) (Fragment)	0.04	-	cyt	0	Cytoplasm				396
Q04634 UniProt NPD GO	EF1A_TETPY	Elongation factor 1-alpha (EF-1-alpha) (14-nm filament-associated protein)	0.04	-	cyt	0	Cytoplasm				435
Q07051 UniProt NPD GO	EF1A_EIMBO	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.04	-	cyt	0	Cytoplasm				346
P32192 UniProt NPD GO	EF1D_ARTSA	Elongation factor 1-delta (EF-1-delta)	0.04	-	cyt	0					237
P93447 UniProt NPD GO	EF1D_PIMBR	Elongation factor 1-delta (EF-1-delta) (Elongation factor 1B-beta) (eEF-1B beta)	0.04	-	cyt	0					225
Q40680 UniProt NPD GO	EF1D1_ORYSA	Elongation factor 1-delta 1 (EF-1-delta 1) (Elongation factor 1B-beta 1) (eEF-1B beta 1)	0.04	-	cyt	0					228
Q40682 UniProt NPD GO	EF1D2_ORYSA	Elongation factor 1-delta 2 (EF-1-delta 2) (Elongation factor 1B-beta 2) (eEF-1B beta 2)	0.04	-	cyt	0					225
P14634 UniProt NPD GO	EFTU_ASTLO	Elongation factor Tu (EF-Tu)	0.04	-	cyt	0	Plastid				409
Q85FT7 UniProt NPD GO	EFTU_CYAME	Elongation factor Tu (EF-Tu)	0.04	-	mit	0	Plastid; chloroplast				410
P02991 UniProt NPD GO	EFTU_EUGGR	Elongation factor Tu (EF-Tu)	0.04	-	mit	0	Plastid; chloroplast				409
Q6B8Y0 UniProt NPD GO	EFTU_GRATL	Elongation factor Tu (EF-Tu)	0.04	-	cyt	0	Plastid; chloroplast				409
P51287 UniProt NPD GO	EFTU_PORPU	Elongation factor Tu (EF-Tu)	0.04	-	mit	0	Plastid; chloroplast				409
P49410 UniProt NPD GO	EFTU_BOVIN	Elongation factor Tu, mitochondrial precursor (EF-Tu)	0.04	-	mit	0	Mitochondrion			1XB2	452
P21746 UniProt NPD GO	EA87_VICFA	Embryonic abundant protein USP87 precursor	0.04	-	mit	0					268
P21747 UniProt NPD GO	EA92_VICFA	Embryonic abundant protein USP92 precursor	0.04	-	cyt	0					268
P55332 UniProt NPD GO	XYNA_EMENI	Endo-1,4-beta-xylanase A precursor (EC 3.2.1.8) (Xylanase A) (1,4-beta-D-xylan xylanohydrolase A) (2 ...	0.04	-	exc	0					225
P23360 UniProt NPD GO	XYNA_THEAU	Endo-1,4-beta-xylanase precursor (EC 3.2.1.8) (Xylanase) (1,4-beta-D-xylan xylanohydrolase) (TAXI)	0.04	-	exc	0				2BNJ	329
P43316 UniProt NPD GO	GUN5_HUMIN	Endoglucanase-5 (EC 3.2.1.4) (Endoglucanase V) (Endo-1,4-beta-glucanase V) (Cellulase V) (EG V)	0.04	-	cyt	0				4ENG	213
Q9HEK4 UniProt NPD GO	ERV25_NEUCR	Endoplasmic reticulum vesicle protein 25 precursor	0.04	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				223
Q7T2D4 UniProt NPD GO	ERGI2_BRARE	Endoplasmic reticulum-Golgi intermediate compartment protein 2	0.04	-	mit	1 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				376
Q5EHU7 UniProt NPD GO	ERGI2_GECJA	Endoplasmic reticulum-Golgi intermediate compartment protein 2	0.04	-	mit	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				377
Q4R5C3 UniProt NPD GO	ERGI2_MACFA	Endoplasmic reticulum-Golgi intermediate compartment protein 2	0.04	-	mit	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				377
Q5R8G3 UniProt NPD GO	ERGI3_PONPY	Endoplasmic reticulum-Golgi intermediate compartment protein 3	0.04	-	end	2 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				383
Q9Y282 UniProt NPD GO	ERGI3_HUMAN	Endoplasmic reticulum-Golgi intermediate compartment protein 3 (Serologically defined breast cancer ...	0.04	-	end	2 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				383
Q6C2Z7 UniProt NPD GO	YSH1_YARLI	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1)	0.04	-	mit	1 *	Nucleus (By similarity)				677
Q9QYY7 UniProt NPD GO	ESM1_MOUSE	Endothelial cell-specific molecule 1 precursor (ESM-1 secretory protein) (ESM-1)	0.04	-	exc	0	Secreted protein (By similarity)				184
Q99JG2 UniProt NPD GO	ETBR2_MOUSE	Endothelin B receptor-like protein 2 precursor (ETBR-LP-2) (G-protein coupled receptor 37-like 1)	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				481
Q61614 UniProt NPD GO	EDNRA_MOUSE	Endothelin-1 receptor precursor (Endothelin A receptor) (ET-A) (ET-AR)	0.04	-	end	8 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			427
Q43321 UniProt NPD GO	ENO_ALNGL	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.04	-	nuc	0	Cytoplasm				440
P26300 UniProt NPD GO	ENO_LYCES	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.04	-	nuc	0	Cytoplasm				444
Q76KF9 UniProt NPD GO	ENO_PENCH	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.04	-	cyt	0	Cytoplasm (By similarity)				438
Q8IJN7 UniProt NPD GO	ENO_PLAF7	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.04	-	nuc	0	Cytoplasm				446
Q27727 UniProt NPD GO	ENO_PLAFA	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.04	-	nuc	0	Cytoplasm				446
Q9UAL5 UniProt NPD GO	ENO_PLAFG	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.04	-	nuc	0	Cytoplasm (By similarity)				446
Q7RA60 UniProt NPD GO	ENO_PLAYO	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.04	-	cyt	0	Cytoplasm (By similarity)				444
Q96X46 UniProt NPD GO	ENO_PENCI	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Allergen ...	0.04	-	mit	0	Cytoplasm (By similarity)				437
Q42971 UniProt NPD GO	ENO_ORYSA	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (OSE1)	0.04	-	nuc	0	Cytoplasm				446
Q9LEJ0 UniProt NPD GO	ENO1_HEVBR	Enolase 1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 1) (2-phospho-D-glycerate hydro-lyase 1) (Al ...	0.04	-	nuc	0	Cytoplasm				445
P42895 UniProt NPD GO	ENO2_MAIZE	Enolase 2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 2) (2-phospho-D-glycerate hydro-lyase 2)	0.04	-	nuc	0	Cytoplasm				446
Q9BPL7 UniProt NPD GO	ENO2_TOXGO	Enolase 2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 2) (2-phospho-D-glycerate hydro-lyase 2)	0.04	-	cyt	0	Cytoplasm (By similarity)				444
Q9LEI9 UniProt NPD GO	ENO2_HEVBR	Enolase 2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 2) (2-phospho-D-glycerate hydro-lyase 2) (Al ...	0.04	-	nuc	0	Cytoplasm				445
Q90399 UniProt NPD GO	EPD_DANAE	Ependymin precursor (EPD)	0.04	-	vac	0	Secreted protein				218
P28770 UniProt NPD GO	EPD1_ONCMY	Ependymin-1 precursor (Ependymin I) (EPD-I)	0.04	-	end	0	Secreted protein				221
P52794 UniProt NPD GO	EFNA1_XENLA	Ephrin-A1 precursor (EPH-related receptor tyrosine kinase ligand 1) (LERK-1) (xELF-a)	0.04	-	mit	0	Isoform A: Membrane; lipid-anchor; GPI-anchor (By similarity)				216
O46607 UniProt NPD GO	GPX5_CANFA	Epididymal secretory glutathione peroxidase precursor (EC 1.11.1.9) (Epididymis-specific glutathione ...	0.04	-	end	0	Secreted protein				221
Q9DGJ3 UniProt NPD GO	NPC2_BRARE	Epididymal secretory protein E1 precursor (Niemann Pick type C2 protein homolog) (16.5 kDa secretory ...	0.04	-	mit	0	Secreted protein				149
Q9D267 UniProt NPD GO	LCN9_MOUSE	Epididymal-specific lipocalin-9 precursor (MUP-like lipocalin)	0.04	-	exc	0	Secreted protein				178
P79381 UniProt NPD GO	HYEP_PIG	Epoxide hydrolase 1 (EC 3.3.2.3) (Microsomal epoxide hydrolase) (Epoxide hydratase)	0.04	-	mit	0	Microsome; microsomal membrane; single-pass membrane protein (By similarity)				454
Q93109 UniProt NPD GO	ACTP5_ACTEQ	Equinatoxin-5 precursor (Equinatoxin V) (EqTV) (EqT-V)	0.04	-	cyt	2 *	Secreted protein. Found in nematocyst				214

You are viewing entries 76901 to 76950 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.