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
P42554 UniProt NPD GO	S1FA_MAIZE	DNA-binding protein S1FA (Fragment)	0.20	-	nuc	1 *	Nucleus (Probable)				63
Q49CA2 UniProt NPD GO	RPOA_CUSJA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.20	-	mit	0	Plastid				332
Q9FHD4 UniProt NPD GO	UDU2_ARATH	DUF26 domain-containing protein 2 precursor	0.20	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			287
P28311 UniProt NPD GO	DEF4_MOUSE	Defensin-related cryptdin 4 precursor	0.20	-	exc	0	Secreted protein			1TV0	92
P12951 UniProt NPD GO	DHN1_HORVU	Dehydrin DHN1 (B8)	0.20	-	nuc	0					139
Q8LAR7 UniProt NPD GO	DDPS8_ARATH	Dehydrodolichyl diphosphate synthase 8 (EC 2.5.1.-) (Dedol-PP synthase 8)	0.20	-	nuc	0					272
P52824 UniProt NPD GO	DGKQ_HUMAN	Diacylglycerol kinase theta (EC 2.7.1.107) (Diglyceride kinase theta) (DGK-theta) (DAG kinase theta) ...	0.20	-	cyt	0			601207		942
Q28007 UniProt NPD GO	DPYD_BOVIN	Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2) (DPD) (DHPDHase) (Dihydrouracil dehydrogenase) ...	0.20	-	nuc	0					1025
Q7YS44 UniProt NPD GO	FMO3_PANTR	Dimethylaniline monooxygenase [N-oxide-forming] 3 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.20	-	end	1	Microsome				531
P31513 UniProt NPD GO	FMO3_HUMAN	Dimethylaniline monooxygenase [N-oxide-forming] 3 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.20	-	end	1	Microsome	microsome [TAS]	602079		531
P28843 UniProt NPD GO	DPP4_MOUSE	Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen C ...	0.20	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists i ...	intercellular canaliculus [IDA]			760
P40487 UniProt NPD GO	DPH1_YEAST	Diphthamide biosynthesis protein 1	0.20	-	cyt	0	Cytoplasm	cytoplasm [IDA]			425
Q6CS90 UniProt NPD GO	DPH2_KLULA	Diphthamide biosynthesis protein 2	0.20	-	mit	0	Cytoplasm (By similarity)				587
P23323 UniProt NPD GO	DISC_TRIFL	Disintegrin CTF-II (Cytotoxic factor 2) [Contains: Disintegrin CTF-I (Cytotoxic factor 1)]	0.20	-	nuc	0	Secreted protein				75
P31990 UniProt NPD GO	DISI_LACMU	Disintegrin lachesin (Platelet aggregation activation inhibitor)	0.20	-	nuc	0	Secreted protein				73
Q17433 UniProt NPD GO	DNJ2_CAEEL	DnaJ homolog dnj-2 precursor (DnaJ domain protein 2)	0.20	-	end	1					337
O60884 UniProt NPD GO	DNJA2_HUMAN	DnaJ homolog subfamily A member 2 (HIRA-interacting protein 4) (Cell cycle progression restoration g ...	0.20	-	cyt	0	Or: Membrane; lipid-anchor (Potential). Or: Nucleus				412
Q29455 UniProt NPD GO	DNJC5_BOVIN	DnaJ homolog subfamily C member 5 (Cysteine string protein) (CSP)	0.20	-	nuc	1	Membrane; lipid-anchor (By similarity)				198
O94335 UniProt NPD GO	STT3_SCHPO	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3 (EC 2.4.1.119) (Oligosac ...	0.20	-	end	11 *	Membrane; multi-pass membrane protein	oligosaccharyl transferase complex [IGI]			752
O42933 UniProt NPD GO	PMT4_SCHPO	Dolichyl-phosphate-mannose--protein mannosyltransferase 4 (EC 2.4.1.109)	0.20	-	end	11	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	dolichyl-phosphate-mannose-protein mannosyl... [IDA] endomembrane system [IDA]			778
Q99LT0 UniProt NPD GO	DPY30_MOUSE	Dpy-30-like protein	0.20	-	nuc	0	Nucleus (By similarity)				99
Q6AZ60 UniProt NPD GO	EGFL7_RAT	EGF-like domain-containing protein 7 precursor (Multiple EGF-like domain protein 7) (Multiple epider ...	0.20	-	nuc	0	Secreted protein (By similarity)	extracellular region [ISS]			279
Q99944 UniProt NPD GO	EGFL8_HUMAN	EGF-like domain-containing protein 8 precursor (Epidermal growth factor-like protein 8) (Multiple EG ...	0.20	-	end	0	Secreted protein (Potential)	integral to membrane [NAS]	609897		293
Q96A84 UniProt NPD GO	EMID1_HUMAN	EMI domain-containing protein 1 precursor (Protein Emu1) (Emilin and multimerin domain-containing pr ...	0.20	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix		608926		441
Q75CC8 UniProt NPD GO	HRD1_ASHGO	ERAD-associated E3 ubiquitin-protein ligase HDR1 (EC 6.3.2.-)	0.20	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				575
P61564 UniProt NPD GO	ENW1_PONPY	ERV-W1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (ERVWE1 envelope protein) ...	0.20	-	end	1	TM: Cell membrane; single-pass type I membrane protein. SU: Cell membrane; peripheral membrane prote ...				538
O95571 UniProt NPD GO	ETHE1_HUMAN	ETHE1 protein, mitochondrial precursor (EC 3.-.-.-) (Ethylmalonic encephalopathy protein 1) (Hepatom ...	0.20	-	mit	0	Cytoplasm (Ref.1). Nucleus (Ref.1). Mitochondrion; mitochondrial matrix (Ref.2)		608451		254
Q40339 UniProt NPD GO	NO12B_MEDSA	Early nodulin 12B precursor (N-12B)	0.20	-	nuc	1 *	Cell wall (By similarity)				113
Q9DBT4 UniProt NPD GO	ENP4_MOUSE	Ectonucleoside triphosphate diphosphohydrolase 4 (EC 3.6.1.6) (NTPDase4) (Uridine-diphosphatase) (UD ...	0.20	-	end	2 *	Membrane; multi-pass membrane protein (Potential). Localizes in the Golgi and autophagic vacuoles/ly ...				613
Q9GZT9 UniProt NPD GO	EGLN1_HUMAN	Egl nine homolog 1 (EC 1.14.11.-) (Hypoxia-inducible factor prolyl hydroxylase 2) (HIF-prolyl hydrox ...	0.20	-	nuc	0		cytosol [TAS]	606425		426
P53787 UniProt NPD GO	EF1D_RABIT	Elongation factor 1-delta (EF-1-delta)	0.20	-	cyt	0					280
P29693 UniProt NPD GO	EF1D_XENLA	Elongation factor 1-delta (EF-1-delta) (P36)	0.20	-	nuc	0					265
P36008 UniProt NPD GO	EF1G2_YEAST	Elongation factor 1-gamma 2 (EF-1-gamma 2) (Translation elongation factor 1B gamma 2) (Eukaryotic el ...	0.20	-	cyt	0	Cytoplasm	mitochondrion [IDA] ribosome [TAS]			412
Q06193 UniProt NPD GO	EF2_ENTHI	Elongation factor 2 (EF-2)	0.20	-	cyt	0	Cytoplasm				840
Q874B9 UniProt NPD GO	EF2_PICPA	Elongation factor 2 (EF-2)	0.20	-	cyt	0	Cytoplasm (By similarity)				842
Q07803 UniProt NPD GO	EFG1_RAT	Elongation factor G 1, mitochondrial precursor (mEF-G 1) (Elongation factor G1)	0.20	-	nuc	0	Mitochondrion				752
Q04868 UniProt NPD GO	ELP6_YEAST	Elongator complex protein 5 (Gamma-toxin target 6) (HAT-associated protein 3)	0.20	-	nuc	0	Cytoplasm. Nucleus	transcription elongation factor complex [IDA]			273
Q9TTE1 UniProt NPD GO	ENDP1_BOVIN	Endopin-1 precursor (Muscle endopin-1a) (mEndopin 1)	0.20	-	end	0	In longissimus muscle myocytes highest levels are found between the plasma membrane and the myofibri ...	cytoplasm [IDA] extracellular space [IDA]			411
Q4WRC2 UniProt NPD GO	YSH1_ASPFU	Endoribonuclease ysh1 (EC 3.1.27.-) (mRNA 3'-end-processing protein ysh1)	0.20	-	mit	0	Nucleus (By similarity)				872
Q64695 UniProt NPD GO	EPCR_MOUSE	Endothelial protein C receptor precursor (Endothelial cell protein C receptor) (Activated protein C ...	0.20	-	end	1	Membrane; single-pass type I membrane protein	centrosome [IDA]			242
Q00868 UniProt NPD GO	ESYN_GIBPU	Enniatin synthetase [Includes: N-methylcyclopeptide synthetase (EC 6.3.2.-); S-adenosyl-L-methionine ...	0.20	-	cyt	0					983
O13284 UniProt NPD GO	CPSKS_PHASA	Ent-kaurene synthase (EC 4.2.3.19) (EC 5.5.1.13) (Ent-copalyl diphosphate synthase) (CPS/KS) (FCPS/K ...	0.20	-	cyt	0					946
Q39548 UniProt NPD GO	KSB_CUCMA	Ent-kaurene synthase B, chloroplast precursor (EC 4.2.3.19) (KSB)	0.20	-	nuc	0	Plastid; chloroplast				789
O35292 UniProt NPD GO	ECP5_MOUSE	Eosinophil cationic-type ribonuclease 5 precursor (MR-5)	0.20	-	exc	0					155
P13727 UniProt NPD GO	EMBP_HUMAN	Eosinophil granule major basic protein precursor (MBP) (EMBP) (Pregnancy-associated major basic prot ...	0.20	-	vac	0	The proform is secreted. The mature protein is found in the matrix of the eosinophil's large specifi ...	extracellular region [TAS]	605601	2BRS	222
O08680 UniProt NPD GO	EPHA3_RAT	Ephrin type-A receptor 3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor REK4) (TYRO-4)	0.20	-	end	1	Membrane; single-pass type I membrane protein				984
P52793 UniProt NPD GO	EFNA1_MOUSE	Ephrin-A1 precursor (EPH-related receptor tyrosine kinase ligand 1) (LERK-1) (Immediate early respon ...	0.20	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				205
O70258 UniProt NPD GO	SGCE_MOUSE	Epsilon-sarcoglycan precursor (Epsilon-SG)	0.20	-	end	1	Sarcolemma; sarcolemmal membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]			413
P33709 UniProt NPD GO	EPO_SHEEP	Erythropoietin precursor	0.20	-	exc	1 *	Secreted protein				194
P79063 UniProt NPD GO	ERF1_SCHPO	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.20	-	cyt	0	Cytoplasm				433

You are viewing entries 50551 to 50600 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.