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
Q28597 UniProt NPD GO	PLP2_SHEEP	Proteolipid protein 2 (Intestinal membrane A4 protein) (Differentiation-dependent protein A4) (Fragm ...	0.01	-	mit	2 *	Membrane; multi-pass membrane protein (By similarity)				76
Q04941 UniProt NPD GO	PLP2_HUMAN	Proteolipid protein 2 (Intestinal membrane A4 protein) (Differentiation-dependent protein A4) (Prote ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] endoplasmic reticulum membrane [TAS] membrane fraction [TAS] plasma membrane [IDA]	300112		152
Q04736 UniProt NPD GO	YES_MOUSE	Proto-oncogene tyrosine-protein kinase Yes (EC 2.7.10.2) (p61-Yes) (c-Yes)	0.01	-	cyt	0	Cytoplasm; cytosol (By similarity)				540
Q01782 UniProt NPD GO	PTR1_LEIMA	Pteridine reductase 1 (EC 1.5.1.33) (H region methotrexate resistance protein)	0.01	-	cyt	0				1W0C	288
P58249 UniProt NPD GO	PHS_DROVI	Pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropterin dehyd ...	0.01	-	cyt	0					101
P17064 UniProt NPD GO	FCY2_YEAST	Purine-cytosine permease FCY2 (PCP FCY2) (Cytosine/purine transport protein FCY2) (Fluorocytosine re ...	0.01	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [IDA]			533
P83380 UniProt NPD GO	PPH1_LYCES	Purple acid phosphatase isozyme LeSAP1 (EC 3.1.3.2) (Fragment)	0.01	-		0	Secreted protein				9
P83379 UniProt NPD GO	PPH2_LYCES	Purple acid phosphatase isozyme LeSAP2 (EC 3.1.3.2) (Fragment)	0.01	-		0	Secreted protein				7
O14075 UniProt NPD GO	YEAA_SCHPO	Putative 2-hydroxyacid dehydrogenase UNK4.10 (EC 1.-.-.-)	0.01	-	cyt	0					334
O04059 UniProt NPD GO	DHBK_LYCES	Putative 3,4-dihydroxy-2-butanone kinase (EC 2.7.1.-)	0.01	-	cyt	0					594
Q3E8B4 UniProt NPD GO	DGP15_ARATH	Putative Do-like 15 protein	0.01	-	cyt	0					198
P83854 UniProt NPD GO	GPCR_MOUSE	Putative G-protein coupled receptor (Fragment)	0.01	-		0	Membrane; multi-pass membrane protein (By similarity)				10
P84732 UniProt NPD GO	PS16_PINST	Putative LRR disease resistance protein/transmembrane receptor kinase PS16 (Fragment)	0.01	-		0					8
P84735 UniProt NPD GO	PS19_PINST	Putative LRR disease resistance protein/transmembrane receptor kinase PS19 (Fragment)	0.01	-		0					8
P84720 UniProt NPD GO	PS4_PINST	Putative LRR-disease resistance protein/transmembrane receptor kinase PS4 (Fragment)	0.01	-		0					8
Q21697 UniProt NPD GO	ASPG_CAEEL	Putative N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase precursor (EC 3.5.1.26) (Glycosylasparagina ...	0.01	-	gol	0	Lysosome (By similarity)				363
P84725 UniProt NPD GO	PS9_PINST	Putative NADH dehydrogenase subunit PS9 (Fragments)	0.01	-	cyt	0					21
P84517 UniProt NPD GO	NU4ML_BOMMO	Putative NADH-ubiquinone oxidoreductase chain 4-like protein (Fragment)	0.01	-		0					10
Q9LUV2 UniProt NPD GO	POP3_ARATH	Putative Pop3 protein	0.01	-	cyt	0				1Q53	109
Q09438 UniProt NPD GO	MTAP_CAEEL	Putative S-methyl-5-thioadenosine phosphorylase (EC 2.4.2.28) (5'-methylthioadenosine phosphorylase) ...	0.01	-	cyt	0					288
Q7XUR3 UniProt NPD GO	FUCO1_ORYSA	Putative alpha-L-fucosidase 1 precursor (EC 3.2.1.51) (Alpha-L-fucoside fucohydrolase)	0.01	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				517
Q9FL80 UniProt NPD GO	EXP22_ARATH	Putative alpha-expansin 22 precursor (AtEXPA22) (At-EXP22) (AtEx22) (Ath-ExpAlpha-1.15)	0.01	-	cyt	0	Cell wall; peripheral membrane protein				273
Q9FL77 UniProt NPD GO	EXP25_ARATH	Putative alpha-expansin 25 precursor (AtEXPA25) (At-EXP25) (AtEx25) (Ath-ExpAlpha-1.18)	0.01	-	mit	1 *	Cell wall; peripheral membrane protein				276
Q9FL78 UniProt NPD GO	EXP26_ARATH	Putative alpha-expansin 26 precursor (AtEXPA26) (At-EXP26) (AtEx26) (Ath-ExpAlpha-1.16)	0.01	-	cyt	1 *	Cell wall; peripheral membrane protein				279
Q8BVM4 UniProt NPD GO	ADC_MOUSE	Putative arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC)	0.01	-	cyt	0					459
Q9SHD1 UniProt NPD GO	EXPB4_ARATH	Putative beta-expansin 4 precursor (AtEXPB4) (At-EXPB4) (Ath-ExpBeta-1.1)	0.01	-	exc	0	Cell wall; peripheral membrane protein				259
Q98855 UniProt NPD GO	KCMB1_COTJA	Putative calcium-activated potassium channel subunit beta	0.01	-	end	2 *	Membrane; multi-pass membrane protein				200
P47925 UniProt NPD GO	CWPX_ARATH	Putative cell wall protein precursor	0.01	-	exc	0					140
O77256 UniProt NPD GO	CXY1_CONIM	Putative conus peptide precursor	0.01	-	vac	1 *	Secreted protein (Potential)				59
P43623 UniProt NPD GO	METC_YEAST	Putative cystathionine beta-lyase (EC 4.4.1.8) (CBL) (Beta-cystathionase) (Cysteine lyase)	0.01	-	nuc	0					340
P92527 UniProt NPD GO	CCMC_ARATH	Putative cytochrome c biosynthesis ccmC-like mitochondrial protein	0.01	-	end	6 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				232
Q9M883 UniProt NPD GO	SC5D2_ARATH	Putative delta-7-sterol-C5(6)-desaturase 2 (EC 1.3.3.-) (Delta-7-C-5 sterol desaturase 2) (Delta7-st ...	0.01	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				279
Q9Y315 UniProt NPD GO	DEOC_HUMAN	Putative deoxyribose-phosphate aldolase (EC 4.1.2.4) (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) ...	0.01	-	cyt	0					318
Q00222 UniProt NPD GO	XP1_XENLA	Putative gastrointestinal growth factor xP1 precursor	0.01	-	nuc	1 *	Secreted protein				78
Q9FLT3 UniProt NPD GO	GL34_ARATH	Putative germin-like protein subfamily 3 member 4 precursor	0.01	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				210
Q9S772 UniProt NPD GO	GLT3_ARATH	Putative germin-like protein subfamily T member 3 precursor	0.01	-	end	1 *	Secreted protein; extracellular space; apoplast (By similarity)				227
Q9M088 UniProt NPD GO	E135_ARATH	Putative glucan endo-1,3-beta-glucosidase 5 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolas ...	0.01	-	end	1 *	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			484
Q93Z08 UniProt NPD GO	E136_ARATH	Putative glucan endo-1,3-beta-glucosidase 6 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolas ...	0.01	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				477
Q02439 UniProt NPD GO	E13F_HORVU	Putative glucan endo-1,3-beta-glucosidase GVI precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrol ...	0.01	-	cyt	0					321
P35895 UniProt NPD GO	GU03_RAT	Putative gustatory receptor clone PTE03 (Fragment)	0.01	-	end	3 *	Membrane; multi-pass membrane protein				168
P84577 UniProt NPD GO	HSP90_POPEU	Putative heat shock protein HSP90 (Fragments)	0.01	-	cyt	0	Cytoplasm (By similarity)				47
Q5KGE6 UniProt NPD GO	CCPR2_CRYNE	Putative heme-binding peroxidase (EC 1.11.1.-)	0.01	-	pox	0					315
Q9C8L4 UniProt NPD GO	GLO2O_ARATH	Putative hydroxyacylglutathione hydrolase 3, mitochondrial precursor (EC 3.1.2.6) (Glyoxalase II) (G ...	0.01	-	nuc	0	Mitochondrion (Potential)			2GCU	256
Q9P6J9 UniProt NPD GO	YHD1_SCHPO	Putative inorganic phosphate transporter C1683.01	0.01	-	end	11	Membrane; multi-pass membrane protein (Probable)				573
P84719 UniProt NPD GO	LGUL_PINST	Putative lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (G ...	0.01	-	nuc	0					22
Q08448 UniProt NPD GO	YO059_YEAST	Putative lipase YOR059C (EC 3.1.-.-)	0.01	-	gol	1	Lipid particle; lipid particle membrane; single-pass membrane protein (Potential)	lipid particle [IDA]			450
P82732 UniProt NPD GO	LCR18_ARATH	Putative low-molecular-weight cysteine-rich protein LCR18 precursor	0.01	-	end	1 *					76
Q9M0F3 UniProt NPD GO	LCR22_ARATH	Putative low-molecular-weight cysteine-rich protein LCR22 precursor	0.01	-	exc	1 *					77
P82754 UniProt NPD GO	LCR39_ARATH	Putative low-molecular-weight cysteine-rich protein LCR39 precursor	0.01	-	vac	0					77
P82756 UniProt NPD GO	LCR41_ARATH	Putative low-molecular-weight cysteine-rich protein LCR41 precursor	0.01	-	exc	0					81

You are viewing entries 91001 to 91050 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.