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
P25166 UniProt NPD GO	EF1A_STYLE	Elongation factor 1-alpha (EF-1-alpha)	0.10	-	cyt	0	Cytoplasm				446
P29545 UniProt NPD GO	EF1B_ORYSA	Elongation factor 1-beta (EF-1-beta) (Elongation factor 1B-alpha 2) (eEF-1B alpha) (Elongation facto ...	0.10	-	cyt	0					223
P48006 UniProt NPD GO	EF1D1_ARATH	Elongation factor 1-delta 1 (EF-1-delta 1) (Elongation factor 1B-beta 1) (eEF-1B beta 1)	0.10	-	cyt	0					231
Q9SI20 UniProt NPD GO	EF1D2_ARATH	Elongation factor 1-delta 2 (EF-1-delta 2) (Elongation factor 1B-beta 2) (eEF-1B beta 2)	0.10	-	cyt	0					231
P40921 UniProt NPD GO	EF1G_SCHPO	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.10	-	mit	0					409
Q6BJ25 UniProt NPD GO	EF2_DEBHA	Elongation factor 2 (EF-2)	0.10	-	cyt	0	Cytoplasm (By similarity)				842
P56292 UniProt NPD GO	EFTU_CHLVU	Elongation factor Tu (EF-Tu)	0.10	-	mit	0	Plastid; chloroplast				409
Q03071 UniProt NPD GO	ELOC_YEAST	Elongin-C	0.10	-	nuc	0	Cytoplasm. Nucleus	nucleotide-excision repair factor 4 complex [IDA]		1HV2	99
Q7M4F1 UniProt NPD GO	CUD4_SCHGR	Endocuticle structural glycoprotein SgAbd-4	0.10	-	nuc	0					116
P38534 UniProt NPD GO	GUNX_PRUPE	Endoglucanase CX (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (CX-cellulase) (Fragment)	0.10	-	cyt	0					251
P22699 UniProt NPD GO	GUN6_DICDI	Endoglucanase precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Spore germination protein 270-6) (Ce ...	0.10	-	exc	0					705
P43317 UniProt NPD GO	GUN5_TRIRE	Endoglucanase-5 precursor (EC 3.2.1.4) (Endoglucanase V) (Endo-1,4-beta-glucanase V) (Cellulase V) ( ...	0.10	-	exc	0					242
Q4P958 UniProt NPD GO	ERV25_USTMA	Endoplasmic reticulum vesicle protein 25 precursor	0.10	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				224
Q5EAE0 UniProt NPD GO	ERGI3_BOVIN	Endoplasmic reticulum-Golgi intermediate compartment protein 3	0.10	-	end	2 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				383
Q06224 UniProt NPD GO	YSH1_YEAST	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1) (Yeast 73 kDa homolog 1)	0.10	-	cyt	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI]			779
P35463 UniProt NPD GO	EDNRB_PIG	Endothelin B receptor precursor (ET-B) (Endothelin receptor Non-selective type)	0.10	-	end	8 *	Membrane; multi-pass membrane protein				443
P21451 UniProt NPD GO	EDNRB_RAT	Endothelin B receptor precursor (ET-B) (Endothelin receptor Non-selective type)	0.10	-	end	8 *	Membrane; multi-pass membrane protein	membrane fraction [IDA]			442
P19998 UniProt NPD GO	EDN3_RABIT	Endothelin-3 precursor (ET-3) (Preproendothelin-3) (PPET3) (Fragment)	0.10	-	nuc	0	Secreted protein				114
Q945F0 UniProt NPD GO	EDS5_ARATH	Enhanced disease susceptibility 5 (Eds5) (Salicylic acid induction deficient 1) (Sid1)	0.10	-	end	10	Membrane; multi-pass membrane protein (Potential)				543
P29321 UniProt NPD GO	EPHA8_RAT	Ephrin type-A receptor 8 (EC 2.7.10.1) (Tyrosine-protein kinase receptor EEK) (EPH- and ELK-related ...	0.10	-	cyt	0	Membrane; single-pass type I membrane protein				372
O14944 UniProt NPD GO	EREG_HUMAN	Epiregulin precursor	0.10	-	end	2 *	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...	extracellular space [IDA] integral to plasma membrane [TAS]	602061	1K37	169
Q9D379 UniProt NPD GO	HYEP_MOUSE	Epoxide hydrolase 1 (EC 3.3.2.3) (Microsomal epoxide hydrolase) (Epoxide hydratase)	0.10	-	mit	0	Microsome; microsomal membrane; single-pass membrane protein				455
P60775 UniProt NPD GO	NXSA_LATSE	Erabutoxin a precursor (Short neurotoxin 1a)	0.10	-	nuc	1 *	Secreted protein			5EBX	83
Q90VW1 UniProt NPD GO	NXSB_LATSE	Erabutoxin b precursor (Short neurotoxin 1b)	0.10	-	nuc	1 *	Secreted protein			6EBX	83
Q7T2I5 UniProt NPD GO	NXSC_LATSE	Erabutoxin c precursor (Short neurotoxin 1c)	0.10	-	nuc	1 *	Secreted protein				83
P31508 UniProt NPD GO	ESCA_APIME	Escargot/snail protein homolog (Fragment)	0.10	-	nuc	0	Nucleus (Probable)				81
O16170 UniProt NPD GO	EST5B_DROMI	Esterase-5B precursor (EC 3.1.1.1) (Est-5B) (Carboxylic-ester hydrolase 5B) (Carboxylesterase-5B)	0.10	-	vac	0	Secreted protein				545
Q9TTE5 UniProt NPD GO	ESR2_MACMU	Estrogen receptor beta (ER-beta) (Fragment)	0.10	-	mit	0	Nucleus				279
P70102 UniProt NPD GO	MCA3_CRIGR	Eukaryotic translation elongation factor 1 epsilon-1 (Multisynthetase complex auxiliary component p1 ...	0.10	-	cyt	0		aminoacyl-tRNA synthetase multienzyme complex [ISS] cytoplasm [ISS] nucleus [ISS]			174
Q9SZA3 UniProt NPD GO	IF3C_ARATH	Eukaryotic translation initiation factor 3 subunit 12 (eIF-3 p25) (eIF3k)	0.10	-	cyt	0					226
P34563 UniProt NPD GO	IF5A1_CAEEL	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (Initiation factor five protein 1)	0.10	-	cyt	0					161
P13860 UniProt NPD GO	GUX1_PHACH	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase I) (1,4-beta-cellobioh ...	0.10	-	mit	0	Secreted protein				516
Q00293 UniProt NPD GO	PGLRX_ASPTU	Exopolygalacturonase precursor (EC 3.2.1.67) (ExoPG) (Galacturan 1,4-alpha-galacturonidase) (Poly(1, ...	0.10	-	exc	0	Secreted protein				435
Q00359 UniProt NPD GO	PGLRX_COCCA	Exopolygalacturonase precursor (EC 3.2.1.67) (ExoPG) (Galacturan 1,4-alpha-galacturonidase) (Poly(1, ...	0.10	-	mit	0	Secreted protein				446
P38728 UniProt NPD GO	ECM34_YEAST	Extracellular matrix protein 34	0.10	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				170
Q08356 UniProt NPD GO	EZY3_CHLRE	Ezy-1 protein (Fragment)	0.10	-	cyt	0					297
P59024 UniProt NPD GO	FKB14_MOUSE	FK506-binding protein 14 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rota ...	0.10	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				211
Q2UPT7 UniProt NPD GO	FKBP2_ASPOR	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.10	-	end	0	Endoplasmic reticulum (By similarity)				134
Q5KGT9 UniProt NPD GO	FKBP2_CRYNE	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.10	-	vac	0	Endoplasmic reticulum (By similarity)				141
P27124 UniProt NPD GO	FKBP4_RABIT	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (p59 ...	0.10	-	cyt	0	Cytoplasm. Nucleus			1ROU	457
P79191 UniProt NPD GO	FPRL2_MACMU	FMLP-related receptor II (FMLP-R-II) (Formylpeptide receptor-like 2) (Fragment)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				349
P83321 UniProt NPD GO	FAR6_PENMO	FMRFamide-like neuropeptide FLP6 (DGRTPALRLRF-amide)	0.10	-		0	Secreted protein				11
P38224 UniProt NPD GO	FIG1_YEAST	Factor-induced gene 1	0.10	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	cell wall (sensu Fungi) [IDA] mating projection tip [IDA]			298
P48035 UniProt NPD GO	FABPA_BOVIN	Fatty acid-binding protein, adipocyte (AFABP) (Adipocyte lipid-binding protein) (ALBP)	0.10	-	cyt	0	Cytoplasm (Potential)				131
Q93142 UniProt NPD GO	FAR1_BRUMA	Fatty-acid and retinol-binding protein 1 precursor (Bm-FAR-1) (Bm20)	0.10	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			178
Q8WT55 UniProt NPD GO	FAR1_BRUPA	Fatty-acid and retinol-binding protein 1 precursor (Bp-FAR-1)	0.10	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			178
Q8WT56 UniProt NPD GO	FAR1_LITSI	Fatty-acid and retinol-binding protein 1 precursor (Ls-FAR-1)	0.10	-	gol	0	Secreted protein	extracellular region [IDA]			178
P20308 UniProt NPD GO	KRFA_CHICK	Feather keratin IV (Keratin gene A protein) (F-ker)	0.10	-	nuc	0					97
Q43155 UniProt NPD GO	GLTB_SPIOL	Ferredoxin-dependent glutamate synthase, chloroplast (EC 1.4.7.1) (Fd-GOGAT)	0.10	-	cyt	0	Plastid; chloroplast; chloroplast stroma				1517
O65100 UniProt NPD GO	FRI3_VIGUN	Ferritin-3, chloroplast precursor (EC 1.16.3.1)	0.10	-	nuc	0	Plastid; chloroplast (By similarity)				256

You are viewing entries 64301 to 64350 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.