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
O22967 UniProt NPD GO	DOF23_ARATH	Dof zinc finger protein DOF2.3 (AtDOF2.3)	0.32	-	nuc	0	Nucleus (Probable)				170
Q06644 UniProt NPD GO	PMT7_YEAST	Dolichyl-phosphate-mannose--protein mannosyltransferase 7 (EC 2.4.1.109)	0.32	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [IDA]			662
Q9D9R7 UniProt NPD GO	DMRTC_MOUSE	Doublesex- and mab-3-related transcription factor C1 (Doublesex- and mab-3-related transcription fac ...	0.32	-	nuc	0					182
Q05922 UniProt NPD GO	DUS2_MOUSE	Dual specificity protein phosphatase 2 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity protein phospha ...	0.32	-	mit	0	Nucleus				318
Q16828 UniProt NPD GO	DUS6_HUMAN	Dual specificity protein phosphatase 6 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinase ...	0.32	-	nuc	0	Cytoplasm	cytoplasm [IDA] soluble fraction [TAS]	602748	1MKP	381
Q8BPB5 UniProt NPD GO	FBLN3_MOUSE	EGF-containing fibulin-like extracellular matrix protein 1 precursor (Fibulin-3) (FIBL-3)	0.32	-	exc	0	Secreted protein				493
O35568 UniProt NPD GO	FBLN3_RAT	EGF-containing fibulin-like extracellular matrix protein 1 precursor (Fibulin-3) (FIBL-3) (T16 prote ...	0.32	-	exc	0	Secreted protein				493
Q8MIB6 UniProt NPD GO	EFC1_PANTR	ERV-F(c)1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (CpzERV-Fc1env envelop ...	0.32	-	end	1					584
Q9JHC9 UniProt NPD GO	ELF2_MOUSE	ETS-related transcription factor Elf-2 (E74-like factor 2) (New ETS-related factor)	0.32	+	nuc	0	Nucleus	nucleus [ISS]			593
O45487 UniProt NPD GO	EMAL_CAEEL	Echinoderm microtubule-associated protein-like elp-1	0.32	-	nuc	0					891
Q13822 UniProt NPD GO	ENPP2_HUMAN	Ectonucleotide pyrophosphatase/phosphodiesterase 2 (E-NPP 2) (Phosphodiesterase I/nucleotide pyropho ...	0.32	-	mit	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601060		863
Q91YE2 UniProt NPD GO	EGLN2_MOUSE	Egl nine homolog 2 (EC 1.14.11.-) (Hypoxia-inducible factor prolyl hydroxylase 1) (HIF-prolyl hydrox ...	0.32	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)	nucleus [ISS]			419
P12261 UniProt NPD GO	EF1G_ARTSA	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.32	-	cyt	0					429
P26642 UniProt NPD GO	EF1GA_XENLA	Elongation factor 1-gamma-A (EF-1-gamma-A) (eEF-1B gamma-A) (p47)	0.32	+	cyt	0					436
Q41596 UniProt NPD GO	CHI1_THECC	Endochitinase 1 precursor (EC 3.2.1.14)	0.32	-	exc	0	Vacuole (By similarity). Vacuolar and protoplast (By similarity)				321
P52404 UniProt NPD GO	CHI2_SOLTU	Endochitinase 2 precursor (EC 3.2.1.14) (Fragment)	0.32	-	mit	0	Vacuole (By similarity). Vacuolar and protoplast (By similarity)				316
P36183 UniProt NPD GO	ENPL_HORVU	Endoplasmin homolog precursor (GRP94 homolog)	0.32	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				809
P51559 UniProt NPD GO	BLI4_CAEEL	Endoprotease bli-4 precursor (EC 3.4.21.-) (Blisterase) (Blistered cuticle protein 4)	0.32	-	exc	1		integral to membrane [NAS] nucleus [IDA]			943
Q9C5Y2 UniProt NPD GO	KAO2_ARATH	Ent-kaurenoic acid oxidase 2 (EC 1.14.13.79) (AtKAO2) (Cytochrome P450 88A4)	0.32	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				489
P47780 UniProt NPD GO	ECP_PANTR	Eosinophil cationic protein precursor (EC 3.1.27.-) (ECP) (Ribonuclease 3) (RNase 3)	0.32	-	exc	0	Matrix of eosinophil's large specific granule				160
P33707 UniProt NPD GO	EPO_CANFA	Erythropoietin precursor	0.32	-	nuc	1 *	Secreted protein				206
O74718 UniProt NPD GO	ERF2_SCHPO	Eukaryotic peptide chain release factor GTP-binding subunit (ERF2) (Translation release factor 3) (P ...	0.32	-	nuc	0	Cytoplasm (Probable)			1R5O	662
P38698 UniProt NPD GO	PPX1_YEAST	Exopolyphosphatase (EC 3.6.1.11) (ExopolyPase) (Metaphosphatase)	0.32	-	nuc	0		cytoplasm [IDA] cytosol [TAS] mitochondrial matrix [TAS] plasma membrane [TAS]			397
P46948 UniProt NPD GO	RRP41_YEAST	Exosome complex exonuclease RRP41 (EC 3.1.13.-) (Ribosomal RNA-processing protein 41) (SKI6 protein) ...	0.32	-	nuc	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]			246
Q9GV77 UniProt NPD GO	FREM2_LYTVA	Extracellular matrix protein 3 precursor (FREM2 homolog)	0.32	+	end	1	Cell membrane; single-pass type I membrane protein; extracellular side				3103
Q8BID8 UniProt NPD GO	FXL14_MOUSE	F-box/LRR-repeat protein 14 (F-box and leucine-rich repeat protein 14)	0.32	-	cyt	0					400
Q8C4V4 UniProt NPD GO	FBXL3_MOUSE	F-box/LRR-repeat protein 3 (F-box/LRR-repeat protein 3A) (F-box and leucine-rich repeat protein 3A)	0.32	-	mit	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity)				428
Q6BS60 UniProt NPD GO	POB3_DEBHA	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.32	-	nuc	0	Nucleus (By similarity)				540
Q4WGK6 UniProt NPD GO	POB3_ASPFU	FACT complex subunit pob3 (Facilitates chromatin transcription complex subunit pob3)	0.32	-	cyt	0	Nucleus (By similarity)				568
Q91XW8 UniProt NPD GO	FKBP6_MOUSE	FK506-binding protein 6 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (36 k ...	0.32	-	nuc	0		cytosol [TAS] membrane fraction [TAS]			327
Q5H8C1 UniProt NPD GO	FREM1_HUMAN	FRAS1-related extracellular matrix protein 1 precursor (Protein QBRICK)	0.32	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix; basement membrane (By similarity). Loca ...		608944		2179
Q95LB4 UniProt NPD GO	FATE1_PIG	Fetal and adult testis-expressed transcript protein homolog	0.32	-	nuc	1					171
Q9ESS2 UniProt NPD GO	FGF22_MOUSE	Fibroblast growth factor 22 precursor (FGF-22)	0.32	-	end	0	Secreted protein (Potential)	cell surface [IDA] Golgi apparatus [IDA] nucleolus [IDA]			162
Q9EPC2 UniProt NPD GO	FGF23_MOUSE	Fibroblast growth factor 23 precursor (FGF-23)	0.32	-	exc	0	Secreted protein (Potential)				251
Q9WVH8 UniProt NPD GO	FBLN5_RAT	Fibulin-5 precursor (FIBL-5) (Developmental arteries and neural crest EGF-like protein) (Dance) (Emb ...	0.32	-	exc	0	Secreted protein				448
Q8WUP2 UniProt NPD GO	FBLI1_HUMAN	Filamin-binding LIM protein 1 (Filamin-binding LIM protein 1) (FBLP-1) (Mitogen-inducible 2-interact ...	0.32	-	nuc	0	Cytoplasm; cell cortex. Associated with actin stress fiber at cell-ECM focal adhesion sites. Isoform ...		607747		373
O75955 UniProt NPD GO	FLOT1_HUMAN	Flotillin-1	0.32	-	cyt	0	Cell membrane; caveola; peripheral membrane protein. Membrane-associated protein of caveolae	caveola [TAS] integral to membrane [TAS]	606998		427
O08917 UniProt NPD GO	FLOT1_MOUSE	Flotillin-1	0.32	-	cyt	0	Cell membrane; caveola; peripheral membrane protein. Membrane-associated protein of caveolae	flotillin complex [IDA] lipid raft [IDA]			428
Q7YR41 UniProt NPD GO	FLOT1_PANTR	Flotillin-1	0.32	-	cyt	0	Cell membrane; caveola; peripheral membrane protein (By similarity). Membrane-associated protein of ...				427
Q9Z1E1 UniProt NPD GO	FLOT1_RAT	Flotillin-1 (Reggie-2) (REG-2)	0.32	-	cyt	0	Cell membrane; caveola; peripheral membrane protein. Membrane-associated protein of caveolae	caveola [IDA] flotillin complex [IDA]			428
P70213 UniProt NPD GO	FV1_MOUSE	Friend virus susceptibility protein 1	0.32	-	cyt	0		Golgi apparatus [IDA]			459
Q13067 UniProt NPD GO	GAGE3_HUMAN	G antigen 3 (GAGE-3)	0.32	-	nuc	0			604245		118
Q8C5Q4 UniProt NPD GO	GRSF1_MOUSE	G-rich sequence factor 1 (GRSF-1)	0.32	-	mit	0	Cytoplasm (By similarity)				479
P30286 UniProt NPD GO	CCNB1_MEDSA	G2/mitotic-specific cyclin-1 (B-like cyclin) (CycMs1) (Fragment)	0.32	-	nuc	0					213
O95067 UniProt NPD GO	CCNB2_HUMAN	G2/mitotic-specific cyclin-B2	0.32	-	mit	0			602755		398
Q60935 UniProt NPD GO	NAR1_MOUSE	GPI-linked NAD(P)(+)--arginine ADP-ribosyltransferase 1 precursor (EC 2.4.2.31) (Mono(ADP-ribosyl)tr ...	0.32	-	nuc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; lipid-anchor; GPI-anchor				325
Q9YH38 UniProt NPD GO	RASK_CYPCA	GTPase KRas (Ki-Ras) (K-ras)	0.32	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				188
P32806 UniProt NPD GO	GYP6_YEAST	GTPase-activating protein GYP6 (GAP for YPT6)	0.32	-	mit	0	Cytoplasm (Probable)	endosome [IDA]			458
P46672 UniProt NPD GO	G4P1_YEAST	GU4 nucleic-binding protein 1 (G4p1 protein) (P42) (Protein ARC1)	0.32	+	nuc	0		cytoplasm [IDA] methionyl glutamyl tRNA synthetase complex [IMP]			376
P28022 UniProt NPD GO	CRGM3_CYPCA	Gamma crystallin M3 (Gamma-M3)	0.32	-	nuc	0					173

You are viewing entries 38451 to 38500 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.