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
P81490 UniProt NPD GO	DMS6_PHYBI	Dermaseptin-B6 precursor (Dermaseptin BVI)	0.06	-	exc	0	Secreted protein				72
P83553 UniProt NPD GO	DERM_BIOGL	Dermatopontin (Tyrosine-rich acidic matrix protein) (TRAMP)	0.06	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				148
Q91610 UniProt NPD GO	DHH1_XENLA	Desert hedgehog protein 1 precursor (DHH-1) (Cephalic hedgehog protein) (X-CHH) [Contains: Desert he ...	0.06	-	mit	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				396
Q01458 UniProt NPD GO	DIAC_BOVIN	Di-N-acetylchitobiase precursor (EC 3.2.1.-) (Fragment)	0.06	-	mit	0	Lysosome				175
P53388 UniProt NPD GO	DIP5_YEAST	Dicarboxylic amino acid permease	0.06	-	end	11	Membrane; multi-pass membrane protein				608
P52898 UniProt NPD GO	DDBX_BOVIN	Dihydrodiol dehydrogenase 3 (EC 1.-.-.-) (Prostaglandin F synthase)	0.06	-	cyt	0	Cytoplasm (Potential)				323
P00375 UniProt NPD GO	DYR_MOUSE	Dihydrofolate reductase (EC 1.5.1.3)	0.06	-	mit	0				1U70	186
P16184 UniProt NPD GO	DYR_PNECA	Dihydrofolate reductase (EC 1.5.1.3)	0.06	-	mit	0				4CD2	206
P32746 UniProt NPD GO	PYRD_ARATH	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane				460
Q14194 UniProt NPD GO	DPYL1_HUMAN	Dihydropyrimidinase-related protein 1 (DRP-1) (Collapsin response mediator protein 1) (CRMP-1)	0.06	-	cyt	0	Cytoplasm (Potential)		602462		572
O14531 UniProt NPD GO	DPYL4_HUMAN	Dihydropyrimidinase-related protein 4 (DRP-4) (Collapsin response mediator protein 3) (CRMP-3) (UNC3 ...	0.06	-	cyt	0	Cytoplasm (Potential)		608407		572
Q95LA1 UniProt NPD GO	FMO3_CANFA	Dimethylaniline monooxygenase [N-oxide-forming] 3 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.06	-	nuc	1	Microsome (By similarity)				531
P49109 UniProt NPD GO	FMO5_CAVPO	Dimethylaniline monooxygenase [N-oxide-forming] 5 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.06	-	end	1	Microsome				532
P31430 UniProt NPD GO	DPEP1_RAT	Dipeptidase 1 precursor (EC 3.4.13.19) (Microsomal dipeptidase) (Renal dipeptidase)	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Brush border membrane				410
Q8J1L4 UniProt NPD GO	DPP5_TRISH	Dipeptidyl-peptidase 5 precursor (EC 3.4.14.-) (Dipeptidyl-peptidase V) (DPP V) (DppV) (Allergen Tri ...	0.06	-	exc	0	Secreted protein (By similarity)				726
Q59SJ9 UniProt NPD GO	DPH2_CANAL	Diphthamide biosynthesis protein 2	0.06	-	cyt	0	Cytoplasm (By similarity)				529
Q6FPD9 UniProt NPD GO	DPH2_CANGA	Diphthamide biosynthesis protein 2	0.06	-	cyt	0	Cytoplasm (By similarity)				551
Q4WPU8 UniProt NPD GO	DPH3_ASPFU	Diphthamide biosynthesis protein 3	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				106
Q6FXS6 UniProt NPD GO	DPH3_CANGA	Diphthamide biosynthesis protein 3	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				82
Q754E7 UniProt NPD GO	DPH5_ASHGO	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.06	-	cyt	0	Cytoplasm (By similarity)				298
Q4HZI0 UniProt NPD GO	DPH5_GIBZE	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.06	-	cyt	0	Cytoplasm (By similarity)				287
P24492 UniProt NPD GO	DIP_DROME	Diptericin precursor	0.06	-	vac	0	Secreted protein				106
P02887 UniProt NPD GO	DIS1C_DICDI	Discoidin I, C chain and B chain	0.06	-	cyt	0	Cytoplasm				253
P83044 UniProt NPD GO	DIS8B_CERCE	Disintegrin CC8B	0.06	-	nuc	0	Secreted protein				65
P16338 UniProt NPD GO	DISI_AGKPI	Disintegrin applagin (Platelet aggregation activation inhibitor)	0.06	-	nuc	0	Secreted protein				71
P41543 UniProt NPD GO	OST1_YEAST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST1 precursor (EC 2.4.1.119) ...	0.06	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	oligosaccharyl transferase complex [IPI]			476
P46978 UniProt NPD GO	STT3A_MOUSE	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A (EC 2.4.1.119) (Oligosa ...	0.06	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	membrane fraction [IDA] oligosaccharyl transferase complex [ISS]			705
P46977 UniProt NPD GO	STT3A_HUMAN	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A (EC 2.4.1.119) (Oligosa ...	0.06	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	oligosaccharyl transferase complex [IDA]	601134		705
P33767 UniProt NPD GO	OSTB_YEAST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 precursor (EC 2.4.1.119) ...	0.06	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum [IDA] nuclear envelope [IDA] oligosaccharyl transferase complex [IPI]			430
P47190 UniProt NPD GO	PMT3_YEAST	Dolichyl-phosphate-mannose--protein mannosyltransferase 3 (EC 2.4.1.109)	0.06	-	end	10	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [TAS]			753
P59022 UniProt NPD GO	DSC10_HUMAN	Down syndrome critical region protein 10	0.06	-	mit	0					87
P25027 UniProt NPD GO	EFH5_TRYBB	EF-hand protein 5 (EFH5)	0.06	-	cyt	0					192
Q9BV94 UniProt NPD GO	EDEM2_HUMAN	ER degradation-enhancing alpha-mannosidase-like 2 precursor	0.06	-	end	0	Secreted protein (Potential)				578
Q9ZTN2 UniProt NPD GO	ERD2_PETHY	ER lumen protein retaining receptor (HDEL receptor) (PGP169-12)	0.06	-	end	6 *	Membrane; multi-pass membrane protein				215
P11432 UniProt NPD GO	ELI_PEA	Early light-induced protein, chloroplast precursor (ELIP)	0.06	-	nuc	2	Plastid; chloroplast. Associated with both photosystems I and II				196
P49344 UniProt NPD GO	ECAB_ECTTU	Ectatomin subunit B (EA)	0.06	-	nuc	0	Secreted protein			1ECI	34
P49961 UniProt NPD GO	ENP1_HUMAN	Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) (NTPDase1) (Ecto-ATP diphosphohydrolas ...	0.06	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS] plasma membrane [NAS]	601752		510
P19470 UniProt NPD GO	EGG1_SCHJA	Eggshell protein 1 precursor	0.06	+	exc	0					212
P08419 UniProt NPD GO	ELA2A_PIG	Elastase-2A precursor (EC 3.4.21.71) (Elastase-2)	0.06	-	exc	0	Secreted protein			1BRU	269
P15502 UniProt NPD GO	ELN_HUMAN	Elastin precursor (Tropoelastin)	0.06	-	mit	3 *	Secreted protein; extracellular space; extracellular matrix. Extracellular matrix of elastic fibers	extracellular matrix (sensu Metazoa) [NAS]	194050		786
P29521 UniProt NPD GO	EF1A1_DAUCA	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				449
P34824 UniProt NPD GO	EF1A1_HORVU	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				447
P34823 UniProt NPD GO	EF1A2_DAUCA	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				447
Q40034 UniProt NPD GO	EF1A2_HORVU	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				447
P28295 UniProt NPD GO	EF1A_ABSGL	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				458
P41745 UniProt NPD GO	EF1A_ARXAD	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				459
P17786 UniProt NPD GO	EF1A_LYCES	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				448
Q41803 UniProt NPD GO	EF1A_MAIZE	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				447
O49169 UniProt NPD GO	EF1A_MANES	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				449
O64937 UniProt NPD GO	EF1A_ORYSA	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				447

You are viewing entries 71951 to 72000 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.