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
P16335 UniProt NPD GO	GWIN3_POPSP	Wound-responsive protein GWIN3 precursor	0.00	-	exc	0					200
Q5GH70 UniProt NPD GO	XKR9_HUMAN	XK-related protein 9	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				373
Q49LR9 UniProt NPD GO	XKR9_PANTR	XK-related protein 9	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				373
P33679 UniProt NPD GO	ZEAM_MAIZE	Zeamatin precursor	0.00	-	cyt	1 *				1DU5	227
Q9SLG3 UniProt NPD GO	ZIP3_ARATH	Zinc transporter 3 precursor (ZRT/IRT-like protein 3)	0.00	-	end	9 *	Cell membrane; multi-pass membrane protein (Potential)				339
O64738 UniProt NPD GO	ZIP6_ARATH	Zinc transporter 6, chloroplast precursor (ZRT/IRT-like protein 6)	0.00	-	end	8 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Potential)				341
Q6QQT1 UniProt NPD GO	S39A1_FUGRU	Zinc transporter ZIP1 (Solute carrier family 39 member 1)	0.00	-	end	7 *	Cell membrane; multi-pass membrane protein (By similarity)				302
Q9NP94 UniProt NPD GO	S39A2_HUMAN	Zinc transporter ZIP2 (Eti-1) (6A1) (hZIP2) (Solute carrier family 39 member 2)	0.00	-	end	8 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]			309
P59889 UniProt NPD GO	S39A1_BRARE	Zinc transporter Zip1 (DrZip1) (Solute carrier family 39 member 1)	0.00	-	end	7 *	Cell membrane; multi-pass membrane protein	plasma membrane [IDA]			302
Q8N4Q0 UniProt NPD GO	ZADH2_HUMAN	Zinc-binding alcohol dehydrogenase domain-containing protein 2 (EC 1.-.-.-)	0.00	-	pox	0				2C0C	377
Q8BGC4 UniProt NPD GO	ZADH2_MOUSE	Zinc-binding alcohol dehydrogenase domain-containing protein 2 (EC 1.-.-.-)	0.00	-	pox	0					377
P81020 UniProt NPD GO	ZHP_BOVIN	Zinc-heme protein (Fragments)	0.00	-	cyt	0					57
P19853 UniProt NPD GO	MOSF_CLYJA	[Phe6]-mosact	0.00	-		0					9
Q05394 UniProt NPD GO	FPR1_RABIT	fMet-Leu-Phe receptor (fMLP receptor) (N-formyl peptide receptor) (FPR) (N-formylpeptide chemoattrac ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein				352
P79189 UniProt NPD GO	FPR1_MACMU	fMet-Leu-Phe receptor (fMLP receptor) (N-formyl peptide receptor) (FPR) (N-formylpeptide chemoattrac ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein				346
Q04734 UniProt NPD GO	PALI_YEAST	pH-response regulator protein palI/RIM9 (Regulator of IME2 protein 9)	0.00	-	end	4 *	Cell membrane; multi-pass membrane protein (Potential)				239

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.