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
Q00357 UniProt NPD GO	TOXA_COCCA	Putative HC-toxin efflux carrier TOXA	0.03	-	end	14 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			548
Q9Y519 UniProt NPD GO	CV005_HUMAN	Putative MAP kinase-activating protein C22orf5 (Putative MAPK-activating protein FM08)	0.03	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				407
Q3SZL3 UniProt NPD GO	OACT5_BOVIN	Putative O-acyltransferase OACT5 (EC 2.3.1.-) (O-acyltransferase domain-containing protein 5)	0.03	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				485
Q9M2B0 UniProt NPD GO	RBX1B_ARATH	Putative RING-box protein 1b (RBX1b-At) (At-Rbx1;2) (RBX1-1)	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				115
Q09293 UniProt NPD GO	YQO1_CAEEL	Putative RNA-binding protein EEED8.1	0.03	-	cyt	0					367
O74540 UniProt NPD GO	FADH2_SCHPO	Putative S-(hydroxymethyl)glutathione dehydrogenase 2 (EC 1.1.1.284) (Glutathione-dependent formalde ...	0.03	-	nuc	0					380
P93738 UniProt NPD GO	ACT9_ARATH	Putative actin-9	0.03	-	cyt	0	Cytoplasm				366
Q5I7T1 UniProt NPD GO	AG10B_HUMAN	Putative alpha-1,2-glucosyltransferase ALG10-B (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10-B) (A ...	0.03	-	end	11 *	Cell membrane; multi-pass membrane protein (By similarity)		603313		473
Q9VTJ4 UniProt NPD GO	FUCO_DROME	Putative alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucoside fucohydrolase)	0.03	-	mit	0		cytoplasm [IC]			494
Q9P5N2 UniProt NPD GO	YH83_SCHPO	Putative amino-acid permease C359.03c	0.03	-	end	11	Membrane; multi-pass membrane protein (Potential)				579
P82886 UniProt NPD GO	PBCB_SCHGR	Putative beta-carotene-binding protein	0.03	-	cyt	0					250
Q27519 UniProt NPD GO	C13A7_CAEEL	Putative cytochrome P450 CYP13A7 (EC 1.14.-.-)	0.03	-	mit	2 *					518
Q33884 UniProt NPD GO	CCF2_ARATH	Putative cytochrome c biogenesis ccmF C-terminal-like mitochondrial protein 3 (Fragment)	0.03	-	end	4 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				203
P46239 UniProt NPD GO	GUNF_FUSOX	Putative endoglucanase type F precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase)	0.03	-	end	0					385
P84722 UniProt NPD GO	ALFC_PINST	Putative fructose-bisphosphate aldolase, chloroplast (EC 4.1.2.13) (PS6) (Fragments)	0.03	-	cyt	0	Plastid; chloroplast				71
Q9LHS7 UniProt NPD GO	GPAT7_ARATH	Putative glycerol-3-phosphate acyltransferase 7 (EC 2.3.1.15) (AtGPAT7)	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				500
P58960 UniProt NPD GO	GR39B_DROME	Putative gustatory receptor 39b	0.03	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			369
Q9W1N6 UniProt NPD GO	GR59E_DROME	Putative gustatory receptor 59e	0.03	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			399
P35898 UniProt NPD GO	GU45_RAT	Putative gustatory receptor clone PTE45 (Fragment)	0.03	-	end	5 *	Membrane; multi-pass membrane protein				234
Q6PBT8 UniProt NPD GO	FGF1_BRARE	Putative heparin-binding growth factor 1 (HBGF-1) (Fibroblast growth factor 1) (FGF-1) (Acidic fibro ...	0.03	-	cyt	0					147
O42878 UniProt NPD GO	INVX_SCHPO	Putative invertase (EC 3.2.1.26) (Beta-fructofuranosidase) (Saccharase)	0.03	-	cyt	0					448
Q8LFD1 UniProt NPD GO	LPP3_ARATH	Putative lipid phosphate phosphatase 3, chloroplast precursor (EC 3.1.3.-) (AtLPP3) (Phosphatidic ac ...	0.03	-	end	4	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Probable)				364
P82750 UniProt NPD GO	LCR35_ARATH	Putative low-molecular-weight cysteine-rich protein LCR35 precursor	0.03	-	exc	1 *					78
P82752 UniProt NPD GO	LCR37_ARATH	Putative low-molecular-weight cysteine-rich protein LCR37 precursor	0.03	-	nuc	0					69
P82758 UniProt NPD GO	LCR43_ARATH	Putative low-molecular-weight cysteine-rich protein LCR43 precursor	0.03	-	mit	1 *					75
P82767 UniProt NPD GO	LCR53_ARATH	Putative low-molecular-weight cysteine-rich protein LCR53 precursor	0.03	-	nuc	1 *					75
P82768 UniProt NPD GO	LCR54_ARATH	Putative low-molecular-weight cysteine-rich protein LCR54 precursor	0.03	-	cyt	0					76
P82769 UniProt NPD GO	LCR55_ARATH	Putative low-molecular-weight cysteine-rich protein LCR55 precursor	0.03	-	cyt	1 *					76
P82773 UniProt NPD GO	LCR59_ARATH	Putative low-molecular-weight cysteine-rich protein LCR59 precursor	0.03	-	nuc	1 *					129
P82779 UniProt NPD GO	LCR65_ARATH	Putative low-molecular-weight cysteine-rich protein LCR65 precursor	0.03	-	cyt	1 *					87
Q9VZS6 UniProt NPD GO	NSMA_DROME	Putative neutral sphingomyelinase (EC 3.1.4.12)	0.03	-	end	2	Membrane; multi-pass membrane protein (Potential)				442
Q6BKI8 UniProt NPD GO	NNT1_DEBHA	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.03	-	cyt	0	Cytoplasm (By similarity)				254
Q9V8Y7 UniProt NPD GO	OR56A_DROME	Putative odorant receptor 56a	0.03	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			419
P82984 UniProt NPD GO	OR65C_DROME	Putative odorant receptor 65c	0.03	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			410
Q9VHQ6 UniProt NPD GO	OR85C_DROME	Putative odorant receptor 85c	0.03	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			389
O01840 UniProt NPD GO	OPT3_CAEEL	Putative oligopeptide transporter opt-3	0.03	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				701
Q9M7T0 UniProt NPD GO	PDX_ARATH	Putative peroxiredoxin, mitochondrial precursor (EC 1.11.1.15) (Thioredoxin reductase)	0.03	-	mit	0	Mitochondrion				201
O74976 UniProt NPD GO	FAT2_SCHPO	Putative peroxisomal-coenzyme A synthetase (EC 6.-.-.-)	0.03	-	pox	0	Peroxisome (Potential)				512
Q10349 UniProt NPD GO	SERC_SCHPO	Putative phosphoserine aminotransferase (EC 2.6.1.52) (PSAT)	0.03	-	cyt	0					389
Q9LK70 UniProt NPD GO	DGP12_ARATH	Putative protease Do-like 12, mitochondrial precursor (EC 3.4.21.-)	0.03	+	mit	0	Mitochondrion; mitochondrial matrix (Potential)				499
Q18347 UniProt NPD GO	YBWL_CAEEL	Putative protein C31H2.4	0.03	-	cyt	0					364
Q10057 UniProt NPD GO	PDI1_SCHPO	Putative protein disulfide-isomerase C1F5.02 precursor (EC 5.3.4.1)	0.03	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				492
P34315 UniProt NPD GO	NCX6_CAEEL	Putative sodium/calcium exchanger 6 precursor (Na(+)/Ca(2+)-exchange protein 6)	0.03	-	end	11	Membrane; multi-pass membrane protein (Potential)				590
Q17703 UniProt NPD GO	DHBV_CAEEL	Putative steroid dehydrogenase C06B3.4 (EC 1.1.1.-)	0.03	-	nuc	1 *					314
Q9M2Z4 UniProt NPD GO	SBP2_ARATH	Putative steroid-binding protein 2 (AtMP2)	0.03	-	cyt	1 *	Cell membrane (By similarity)	thylakoid membrane (sensu Viridiplantae) [IDA]			233
Q08686 UniProt NPD GO	THTR_YEAST	Putative thiosulfate sulfurtransferase (EC 2.8.1.1)	0.03	-	cyt	0	Mitochondrion. Cytoplasm	cytoplasm [IDA]			304
Q10084 UniProt NPD GO	YAO5_SCHPO	Putative transporter C11D3.05	0.03	-	end	11	Membrane; multi-pass membrane protein (Potential)				546
O22866 UniProt NPD GO	ITI4_ARATH	Putative trypsin inhibitor At2g43520 precursor	0.03	-	mit	0	Secreted protein (Potential)				90
O22867 UniProt NPD GO	ITI5_ARATH	Putative trypsin inhibitor At2g43530 precursor	0.03	-	mit	0	Secreted protein (Potential)				85
P38161 UniProt NPD GO	YBK8_YEAST	Putative uncharacterized protein YBL108W	0.03	-	cyt	0					101

You are viewing entries 81451 to 81500 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.