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
P49462 UniProt NPD GO	EFTU_ODOSI	Elongation factor Tu (EF-Tu)	0.02	-	cyt	0	Plastid; chloroplast				409
P50374 UniProt NPD GO	EFTU_BRYPL	Elongation factor Tu (EF-Tu) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				235
P50376 UniProt NPD GO	EFTU_COSCS	Elongation factor Tu (EF-Tu) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				235
P50375 UniProt NPD GO	EFTU_DERMA	Elongation factor Tu (EF-Tu) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				235
Q8BFR5 UniProt NPD GO	EFTU_MOUSE	Elongation factor Tu, mitochondrial precursor	0.02	-	mit	0	Mitochondrion (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			452
P49411 UniProt NPD GO	EFTU_HUMAN	Elongation factor Tu, mitochondrial precursor (EF-Tu) (P43)	0.02	-	mit	0	Mitochondrion	mitochondrion [TAS]	602389		452
Q9BW60 UniProt NPD GO	ELOV1_HUMAN	Elongation of very long chain fatty acids protein 1	0.02	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				279
Q9JLJ5 UniProt NPD GO	ELOV1_MOUSE	Elongation of very long chain fatty acids protein 1	0.02	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				279
P33559 UniProt NPD GO	XYNA_ASPKA	Endo-1,4-beta-xylanase A precursor (EC 3.2.1.8) (Xylanase A) (1,4-beta-D-xylan xylanohydrolase A)	0.02	-	exc	0	Secreted protein				327
Q06012 UniProt NPD GO	CHIA_ARAHY	Endochitinase 1A (EC 3.2.1.14) (CHIT 1A) (Fragment)	0.02	-	cyt	0					46
Q06013 UniProt NPD GO	CHIB_ARAHY	Endochitinase 1B (EC 3.2.1.14) (CHIT 1B) (Fragment)	0.02	-	cyt	0					46
Q04469 UniProt NPD GO	GUN1_CRYFL	Endoglucanase 1 precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase 1) (Carboxymethyl-cellulase 1) (CMCa ...	0.02	-	end	0					341
P38447 UniProt NPD GO	NUCG_BOVIN	Endonuclease G, mitochondrial precursor (EC 3.1.30.-) (Endo G)	0.02	-	mit	0	Mitochondrion				299
Q4WQL0 UniProt NPD GO	ERV25_ASPFU	Endoplasmic reticulum vesicle protein 25 precursor	0.02	-	exc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				266
Q969X5 UniProt NPD GO	ERGI1_HUMAN	Endoplasmic reticulum-Golgi intermediate compartment protein 1 (ER-Golgi intermediate compartment 32 ...	0.02	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Endoplasmic reti ...	ER-Golgi intermediate compartment [IDA]			290
Q9DC16 UniProt NPD GO	ERGI1_MOUSE	Endoplasmic reticulum-Golgi intermediate compartment protein 1 (ER-Golgi intermediate compartment 32 ...	0.02	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Endoplasmic reti ...				290
P32803 UniProt NPD GO	EMP24_YEAST	Endosomal protein P24B precursor (24 kDa endomembrane protein) (Basic 24 kDa late endocytic intermed ...	0.02	-	exc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein. Golgi ap ...	endoplasmic reticulum [IDA] ER to Golgi transport vesicle [IDA]			203
O42478 UniProt NPD GO	TLE2_XENLA	Enhancer of split groucho-like protein 2 (Fragment)	0.02	-	cyt	0	Nucleus (Probable)				198
Q967Y8 UniProt NPD GO	ENO_EIMTE	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.02	-	mit	0	Cytoplasm (By similarity)				445
P42894 UniProt NPD GO	ENO_NEOFR	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.02	-	nuc	0	Cytoplasm (By similarity)			2GE6	436
P33676 UniProt NPD GO	ENO_SCHJA	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.02	-	nuc	0	Cytoplasm				434
Q27877 UniProt NPD GO	ENO_SCHMA	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.02	-	cyt	0	Cytoplasm				434
P42897 UniProt NPD GO	ENO_ALLMI	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Fragment ...	0.02	-	cyt	0	Cytoplasm				395
P84541 UniProt NPD GO	ENO_POPEU	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Fragment ...	0.02	-	cyt	0	Cytoplasm (By similarity)				26
Q6FTW6 UniProt NPD GO	ENO1_CANGA	Enolase 1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 1) (2-phospho-D-glycerate hydro-lyase 1)	0.02	-	cyt	0	Cytoplasm (By similarity)				438
P26301 UniProt NPD GO	ENO1_MAIZE	Enolase 1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 1) (2-phospho-D-glycerate hydro-lyase 1)	0.02	-	nuc	0	Cytoplasm				446
Q9UAE6 UniProt NPD GO	ENO1_TOXGO	Enolase 1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 1) (2-phospho-D-glycerate hydro-lyase 1)	0.02	-	cyt	0	Cytoplasm (By similarity)				444
P79727 UniProt NPD GO	EFNA2_BRARE	Ephrin-A2 precursor (EPH-related receptor tyrosine kinase ligand 6) (LERK-6) (ELF-1) (ZfEPHL3)	0.02	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				195
P52797 UniProt NPD GO	EFNA3_HUMAN	Ephrin-A3 precursor (EPH-related receptor tyrosine kinase ligand 3) (LERK-3) (EHK1 ligand) (EHK1-L) ...	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS]	601381		238
P36368 UniProt NPD GO	EGFB2_MOUSE	Epidermal growth factor-binding protein type B precursor (EC 3.4.21.35) (EGF-BP B) (Glandular kallik ...	0.02	-	end	0				1AO5	261
P79345 UniProt NPD GO	NPC2_BOVIN	Epididymal secretory protein E1 precursor (Niemann Pick type C2 protein homolog) (EPV20)	0.02	-	exc	0	Secreted protein			1NEP	149
Q9Z0J0 UniProt NPD GO	NPC2_MOUSE	Epididymal secretory protein E1 precursor (Niemann Pick type C2 protein homolog) (mE1)	0.02	-	exc	0	Secreted protein				149
Q8WX39 UniProt NPD GO	LCN9_HUMAN	Epididymal-specific lipocalin-9 precursor (MUP-like lipocalin)	0.02	-	exc	0	Secreted protein				190
Q5RCY3 UniProt NPD GO	EMP1_PONPY	Epithelial membrane protein 1 (EMP-1)	0.02	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				157
P54848 UniProt NPD GO	EMP1_RAT	Epithelial membrane protein 1 (EMP-1) (Tumor-associated membrane protein)	0.02	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [IPI]			160
P54849 UniProt NPD GO	EMP1_HUMAN	Epithelial membrane protein 1 (EMP-1) (Tumor-associated membrane protein) (CL-20) (B4B protein)	0.02	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] membrane fraction [TAS]	602333		157
Q9QYW5 UniProt NPD GO	EMP3_RAT	Epithelial membrane protein 3 (EMP-3)	0.02	-	end	4 *	Membrane; multi-pass membrane protein				163
P54852 UniProt NPD GO	EMP3_HUMAN	Epithelial membrane protein 3 (EMP-3) (YMP protein) (Hematopoietic neural membrane protein) (HNMP-1) ...	0.02	-	end	4 *	Membrane; multi-pass membrane protein		602335		163
O35912 UniProt NPD GO	EMP3_MOUSE	Epithelial membrane protein 3 (EMP-3) (YMP protein) (Hematopoietic neural membrane protein) (HNMP-1) ...	0.02	-	end	4 *	Membrane; multi-pass membrane protein				163
P40030 UniProt NPD GO	ERG28_YEAST	Ergosterol biosynthetic protein 28	0.02	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum membrane [IDA]			148
P32414 UniProt NPD GO	ES1_RANES	Esculentin-1	0.02	-	cyt	0	Secreted protein	extracellular region [IDA]			46
P84840 UniProt NPD GO	ES1_RANSA	Esculentin-1	0.02	-	cyt	0	Secreted protein	extracellular region [IDA]			46
P10768 UniProt NPD GO	ESTD_HUMAN	Esterase D (EC 3.1.1.1)	0.02	-	cyt	0	Cytoplasmic vesicle	cytoplasmic membrane-bound vesicle [NAS]	133280		282
Q43360 UniProt NPD GO	PIR7B_ORYSA	Esterase PIR7B (EC 3.1.-.-)	0.02	-	mit	0					268
P81429 UniProt NPD GO	EST1_SCHGA	Esterase SG1 precursor (EC 3.1.1.1) (Carboxylic-ester hydrolase) (Fragment)	0.02	-	exc	0					198
Q5TJF5 UniProt NPD GO	DHB8_CANFA	Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) (17-beta-HSD 8) (17-beta-hydroxysteroid dehydrogenas ...	0.02	-	mit	0					259
P50171 UniProt NPD GO	DHB8_MOUSE	Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) (17-beta-HSD 8) (17-beta-hydroxysteroid dehydrogenas ...	0.02	-	mit	0		membrane fraction [IDA] mitochondrial envelope [IDA] mitochondrion [IDA] plasma membrane [IDA]			260
P20076 UniProt NPD GO	IER1_LYCES	Ethylene-responsive proteinase inhibitor 1 precursor (Ethylene-responsive proteinase inhibitor I)	0.02	-	exc	0	Secreted protein (Potential)				119
P41091 UniProt NPD GO	IF2G_HUMAN	Eukaryotic translation initiation factor 2 subunit 3 (Eukaryotic translation initiation factor 2 sub ...	0.02	-	cyt	0			300161		471
P81795 UniProt NPD GO	IF2G_RAT	Eukaryotic translation initiation factor 2 subunit 3 (Eukaryotic translation initiation factor 2 sub ...	0.02	-		0					14

You are viewing entries 83401 to 83450 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.