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
P05589 UniProt NPD GO	IOVO_CALSC	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				56
P05588 UniProt NPD GO	IOVO_CALSP	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				56
P52242 UniProt NPD GO	IOVO_CARME	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P05616 UniProt NPD GO	IOVO_CARRE	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P05591 UniProt NPD GO	IOVO_COLVI	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				56
P52243 UniProt NPD GO	IOVO_CORAL	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P52244 UniProt NPD GO	IOVO_CORMO	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P67890 UniProt NPD GO	IOVO_DENAC	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P67889 UniProt NPD GO	IOVO_DENAR	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P67891 UniProt NPD GO	IOVO_DENAU	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P67892 UniProt NPD GO	IOVO_DENBI	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P05569 UniProt NPD GO	IOVO_DENEY	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P05595 UniProt NPD GO	IOVO_FRACO	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				53
P05597 UniProt NPD GO	IOVO_FRAFR	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				53
P05598 UniProt NPD GO	IOVO_FRAPO	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				56
P52267 UniProt NPD GO	IOVO_GALVA	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				56
P05615 UniProt NPD GO	IOVO_GEOCA	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P68374 UniProt NPD GO	IOVO_GYPCO	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P52268 UniProt NPD GO	IOVO_HALAL	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P05577 UniProt NPD GO	IOVO_HALIN	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P52262 UniProt NPD GO	IOVO_LOPLE	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				56
P68377 UniProt NPD GO	IOVO_NECMO	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P67940 UniProt NPD GO	IOVO_PHAAL	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P05564 UniProt NPD GO	IOVO_PHASU	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P52264 UniProt NPD GO	IOVO_PODST	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P52265 UniProt NPD GO	IOVO_POLPL	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P68375 UniProt NPD GO	IOVO_POLRA	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P67943 UniProt NPD GO	IOVO_PTEPE	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P67941 UniProt NPD GO	IOVO_PYGAD	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P67942 UniProt NPD GO	IOVO_RHEAM	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P05611 UniProt NPD GO	IOVO_TURSY	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				53
P20846 UniProt NPD GO	IOVO_VULGR	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P01005 UniProt NPD GO	IOVO_CHICK	Ovomucoid precursor (Allergen Gal d 1) (Gal d I)	0.01	-	exc	0	Secreted protein				210
P81668 UniProt NPD GO	PSBP_PINPS	Oxygen-evolving enhancer protein 2 (OEE2) (23 kDa subunit of oxygen evolving system of photosystem I ...	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				13
P80662 UniProt NPD GO	PSBP3_PHYPA	Oxygen-evolving enhancer protein 2 (OEE2) (24 kDa subunit of oxygen evolving system of photosystem I ...	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				12
P16059 UniProt NPD GO	PSBP_PEA	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				259
P19589 UniProt NPD GO	PSBQ_PEA	Oxygen-evolving enhancer protein 3 (OEE3) (16 kDa subunit of oxygen-evolving system of photosystem I ...	0.01	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				32
P83248 UniProt NPD GO	TOP2A_OXYKI	Oxyopinin-2a (Oxki2a)	0.01	-	cyt	0	Secreted protein	extracellular region [NAS]			37
P83249 UniProt NPD GO	TOP2B_OXYKI	Oxyopinin-2b (Oxki2b)	0.01	-	cyt	0	Secreted protein	extracellular region [NAS]			37
P83250 UniProt NPD GO	TOP2C_OXYKI	Oxyopinin-2c (Oxki2c)	0.01	-	cyt	0	Secreted protein	extracellular region [NAS]			37
P83251 UniProt NPD GO	TOP2D_OXYKI	Oxyopinin-2d (Oxki2d)	0.01	-	cyt	0	Secreted protein	extracellular region [NAS]			37
P22069 UniProt NPD GO	RNP30_RANPI	P-30 protein (EC 3.1.27.-) (Onconase)	0.01	-	nuc	0				2GMK	104
P30821 UniProt NPD GO	P25_SCHPO	P25 protein (Brefeldin A resistance protein)	0.01	-	cyt	0					202
P56373 UniProt NPD GO	P2RX3_HUMAN	P2X purinoceptor 3 (ATP receptor) (P2X3) (Purinergic receptor)	0.01	-	end	2 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600843		397
Q99PE3 UniProt NPD GO	P2RY2_MERUN	P2Y purinoceptor 2 (P2Y2) (Fragment)	0.01	-	vac	2 *	Membrane; multi-pass membrane protein				82
Q38945 UniProt NPD GO	DPNPH_ARATH	PAP-specific phosphatase HAL2-like (3'(2'),5'-bisphosphate nucleotidase) (EC 3.1.3.7) (3'(2'),5-bisp ...	0.01	-	cyt	0				1Q00	373
Q99MJ6 UniProt NPD GO	PDZD3_MOUSE	PDZ domain-containing protein 3 (PDZ domain-containing protein 2) (Natrium-phosphate cotransporter I ...	0.01	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Cytoplasm (By similarity). In kidney, predomi ...	apical part of cell [IDA]			498
Q9CQH0 UniProt NPD GO	PDZ1I_MOUSE	PDZK1-interacting protein 1 (17 kDa membrane-associated protein)	0.01	-	end	1 *	Membrane; single-pass membrane protein (By similarity)				114
Q923S2 UniProt NPD GO	PDZ1I_RAT	PDZK1-interacting protein 1 (17 kDa membrane-associated protein)	0.01	-	end	1 *	Membrane; single-pass membrane protein (By similarity)				114
Q9UUN5 UniProt NPD GO	PRA1_SCHPO	PRA1-like protein	0.01	-	end	3	Membrane; multi-pass membrane protein (Potential)				171

You are viewing entries 90101 to 90150 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.