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
P42222 UniProt NPD GO	ERR3_YEAST	Enolase-related protein 3 (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydr ...	0.03	-	cyt	0		cytoplasm [IDA]			437
P28771 UniProt NPD GO	EPD2_ONCMY	Ependymin-2 precursor (Ependymin II) (EPD-II)	0.03	-	mit	0	Secreted protein				221
P28772 UniProt NPD GO	EPD2_SALSA	Ependymin-2 precursor (Ependymin II) (EPD-II)	0.03	-	mit	0	Secreted protein				221
P52802 UniProt NPD GO	EFNA2_CHICK	Ephrin-A2 precursor (EPH-related receptor tyrosine kinase ligand 6) (LERK-6) (ELF-1)	0.03	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				200
P55245 UniProt NPD GO	EGFR_MACMU	Epidermal growth factor receptor (EC 2.7.10.1) (Fragment)	0.03	-	cyt	0	Membrane; single-pass type I membrane protein				85
Q8K1H9 UniProt NPD GO	LCN13_MOUSE	Epididymal-specific lipocalin-13 precursor	0.03	-	exc	0	Secreted protein (By similarity)				176
Q924P3 UniProt NPD GO	LCN8_MOUSE	Epididymal-specific lipocalin-8 precursor (Epididymal 17 kDa lipocalin) (EP17) (mEP17)	0.03	-	mit	0	Secreted protein (By similarity)				175
Q6UW88 UniProt NPD GO	EPGN_HUMAN	Epigen precursor (Epithelial mitogen) (EPG)	0.03	-	nuc	1	Membrane; single-pass type I membrane protein (Probable)				133
Q58DR6 UniProt NPD GO	EMP3_BOVIN	Epithelial membrane protein 3 (EMP-3)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				163
P83654 UniProt NPD GO	ERVC_TABDI	Ervatamin-C (EC 3.4.22.-) (ERV-C)	0.03	-	cyt	0	Secreted protein			1O0E	208
P68311 UniProt NPD GO	ERTS_BOVIN	Erythrodihydroneopterin triphosphate synthetase (EC 6.-.-.-)	0.03	-	cyt	0					68
P68312 UniProt NPD GO	ERTS_CAVPO	Erythrodihydroneopterin triphosphate synthetase (EC 6.-.-.-)	0.03	-	cyt	0					68
P68313 UniProt NPD GO	ERTS_RAT	Erythrodihydroneopterin triphosphate synthetase (EC 6.-.-.-)	0.03	-	cyt	0					68
P40844 UniProt NPD GO	ES1B_RANES	Esculentin-1B precursor	0.03	-	exc	0	Secreted protein				84
Q6NWE0 UniProt NPD GO	CK054_BRARE	Ester hydrolase C11orf54 homolog (EC 3.1.-.-)	0.03	-	cyt	0	Nucleus (By similarity)				319
Q7Y1X1 UniProt NPD GO	EST_HEVBR	Esterase precursor (EC 3.1.1.-) (Early nodule-specific protein homolog) (Latex allergen Hev b 13)	0.03	-	cyt	0					391
P25727 UniProt NPD GO	EST5A_DROPS	Esterase-5A precursor (EC 3.1.1.1) (Est-5A) (Carboxylic-ester hydrolase 5A) (Carboxylesterase-5A)	0.03	-	mit	0	Secreted protein				547
Q62730 UniProt NPD GO	DHB2_RAT	Estradiol 17-beta-dehydrogenase 2 (EC 1.1.1.62) (17-beta-HSD 2) (17-beta-hydroxysteroid dehydrogenas ...	0.03	-	end	2 *	Membrane; single-pass type II membrane protein (Potential)				381
Q92506 UniProt NPD GO	DHB8_HUMAN	Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) (17-beta-HSD 8) (17-beta-hydroxysteroid dehydrogenas ...	0.03	-	exc	0			601417		261
P12385 UniProt NPD GO	ERF1_YEAST	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1) (Omnipotent s ...	0.03	-	nuc	0	Cytoplasm	cytosol [IPI] translation release factor complex [IDA]			437
Q9Z0N2 UniProt NPD GO	IF2H_MOUSE	Eukaryotic translation initiation factor 2 subunit 3, Y-linked (Eukaryotic translation initiation fa ...	0.03	-	cyt	0					471
P40217 UniProt NPD GO	IF32_YEAST	Eukaryotic translation initiation factor 3 39 kDa subunit (eIF3 p39) (Translation initiation factor ...	0.03	-	cyt	0		eukaryotic translation initiation factor 3 ... [IDA] multi-eIF complex [IDA]			347
Q38884 UniProt NPD GO	IF32_ARATH	Eukaryotic translation initiation factor 3 subunit 2 (eIF-3 beta) (eIF3 p36) (eIF3i) (TGF-beta recep ...	0.03	-	mit	0					328
Q9P974 UniProt NPD GO	IF4E_CANGA	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.03	-	cyt	0					209
O23252 UniProt NPD GO	IF4E1_ARATH	Eukaryotic translation initiation factor 4E-1 (eIF4E-1) (eIF-4E-1) (mRNA cap-binding protein) (eIF-4 ...	0.03	-	cyt	0					235
P23301 UniProt NPD GO	IF5A2_YEAST	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2) (eIF-4D) (Hypusine-containing protein HP2)	0.03	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA] ribosome [TAS]			156
P56537 UniProt NPD GO	IF6_HUMAN	Eukaryotic translation initiation factor 6 (eIF-6) (B4 integrin interactor) (CAB) (p27(BBP)) (B(2)GC ...	0.03	-	cyt	0	Cytoplasm. Nucleus	nucleus [TAS]	602912		245
Q10901 UniProt NPD GO	EAA1_CAEEL	Excitatory amino acid transporter (Sodium-dependent glutamate/ aspartate transporter)	0.03	-	end	9 *	Membrane; multi-pass membrane protein				503
Q25605 UniProt NPD GO	EAAT_ONCVO	Excitatory amino acid transporter (Sodium-dependent glutamate/ aspartate transporter)	0.03	-	end	8 *	Membrane; multi-pass membrane protein				492
P49062 UniProt NPD GO	PGLR1_ARATH	Exopolygalacturonase clone GBGE184 precursor (EC 3.2.1.67) (ExoPG) (Pectinase) (Galacturan 1,4-alpha ...	0.03	-	end	1 *	Secreted protein				422
P35339 UniProt NPD GO	PGLR3_MAIZE	Exopolygalacturonase precursor (EC 3.2.1.67) (ExoPG) (Pectinase) (Galacturan 1,4-alpha-galacturonida ...	0.03	-	exc	0	Secreted protein				410
Q6H9K0 UniProt NPD GO	PGLR2_PLAAC	Exopolygalacturonase precursor (EC 3.2.1.67) (Pollen allergen Pla a 2) (Fragment)	0.03	-	nuc	0					377
Q05636 UniProt NPD GO	RRP45_YEAST	Exosome complex exonuclease RRP45 (EC 3.1.13.-) (Ribosomal RNA-processing protein 45)	0.03	-	cyt	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]			305
P08924 UniProt NPD GO	GLB1_LUMTE	Extracellular globin-1 (Globin I) (Erythrocruorin) (Globin D)	0.03	-	cyt	0					142
P19363 UniProt NPD GO	GLB1_ARTSX	Extracellular globin-E1 (Fragment)	0.03	-	cyt	0					194
Q9GZZ8 UniProt NPD GO	LACRT_HUMAN	Extracellular glycoprotein lacritin precursor	0.03	-	exc	0	Secreted protein		607360		138
P16026 UniProt NPD GO	SODE_SCHMA	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD)	0.03	-	end	1 *	Secreted protein; extracellular space				184
Q9YHA1 UniProt NPD GO	EYA4_FUGRU	Eyes absent homolog 4 (EC 3.1.3.48) (Fragment)	0.03	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				119
Q6C7M4 UniProt NPD GO	YFAS1_YARLI	FAS1 domain-containing protein YALI0D26906g precursor	0.03	-	exc	0	Vacuole (By similarity)				238
P18203 UniProt NPD GO	FKB1A_BOVIN	FK506-binding protein 1A (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (12 ...	0.03	-	cyt	0	Cytoplasm			1FKL	107
P62942 UniProt NPD GO	FKB1A_HUMAN	FK506-binding protein 1A (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (12 ...	0.03	-	cyt	0	Cytoplasm		186945	4FAP	107
P26883 UniProt NPD GO	FKB1A_MOUSE	FK506-binding protein 1A (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (12 ...	0.03	-	cyt	0	Cytoplasm				107
P62943 UniProt NPD GO	FKB1A_RABIT	FK506-binding protein 1A (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (12 ...	0.03	-	cyt	0	Cytoplasm (By similarity)				107
P69148 UniProt NPD GO	FMRF_HELTI	FMRFamide	0.03	-		0	Secreted protein				4
P69147 UniProt NPD GO	FMRF_HIRME	FMRFamide	0.03	-		0	Secreted protein				4
P69146 UniProt NPD GO	FMRF_NERVI	FMRFamide	0.03	-		0	Secreted protein				4
P69145 UniProt NPD GO	FMRF_MACNI	FMRFamide (Peak C) (Cardioexcitatory neuropeptide)	0.03	-		0	Secreted protein				4
P67879 UniProt NPD GO	FAF2_ASCSU	FMRFamide-like neuropeptide AF2	0.03	-		0	Secreted protein				7
P67880 UniProt NPD GO	FAF2_PANRE	FMRFamide-like neuropeptide AF2	0.03	-		0	Secreted protein				7
P83280 UniProt NPD GO	FAR7_MACRS	FMRFamide-like neuropeptide FLP7 (GYGDRNFLRF-amide)	0.03	-		0	Secreted protein				10

You are viewing entries 79851 to 79900 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.