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
P41766 UniProt NPD GO	LEU3_KLUMA	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.00	-	cyt	0	Cytoplasm				359
Q9Y897 UniProt NPD GO	LEU3_MYCGR	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.00	-	cyt	0	Cytoplasm				365
P08791 UniProt NPD GO	LEU3_PICJA	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.00	-	cyt	0	Cytoplasm				363
P87257 UniProt NPD GO	LEU3B_ASPNG	3-isopropylmalate dehydrogenase B (EC 1.1.1.85) (Beta-IPM dehydrogenase B) (IMDH B) (3-IPM-DH B)	0.00	-	cyt	0	Cytoplasm				371
Q6GV12 UniProt NPD GO	FVT1_MOUSE	3-ketodihydrosphingosine reductase precursor (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS re ...	0.00	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				332
P24008 UniProt NPD GO	S5A1_RAT	3-oxo-5-alpha-steroid 4-dehydrogenase 1 (EC 1.3.99.5) (Steroid 5-alpha-reductase 1) (SR type 1)	0.00	-	end	3 *	Microsome; microsomal membrane; multi-pass membrane protein	microsome [TAS]			259
Q28892 UniProt NPD GO	S5A2_MACFA	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (EC 1.3.99.5) (Steroid 5-alpha-reductase 2) (SR type 2) (5 a ...	0.00	-	end	6 *	Microsome; microsomal membrane; multi-pass membrane protein				254
Q99N99 UniProt NPD GO	S5A2_MOUSE	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (EC 1.3.99.5) (Steroid 5-alpha-reductase 2) (SR type 2) (5 a ...	0.00	-	nuc	5 *	Microsome; microsomal membrane; multi-pass membrane protein (By similarity)				254
O18765 UniProt NPD GO	S5A2_PIG	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (EC 1.3.99.5) (Steroid 5-alpha-reductase 2) (SR type 2) (5 a ...	0.00	-	end	6 *	Microsome; microsomal membrane; multi-pass membrane protein (By similarity)				254
P31214 UniProt NPD GO	S5A2_RAT	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (EC 1.3.99.5) (Steroid 5-alpha-reductase 2) (SR type 2) (5 a ...	0.00	-	cyt	5 *	Microsome; microsomal membrane; multi-pass membrane protein				254
P31210 UniProt NPD GO	AK1D1_RAT	3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.99.6) (Delta(4)-3-ketosteroid 5-beta-reductase) (Aldo-k ...	0.00	-	cyt	0	Cytoplasm				326
P80832 UniProt NPD GO	CWP08_ARATH	31 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				5
P80755 UniProt NPD GO	CWP05_DAUCA	32 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				15
P82432 UniProt NPD GO	CWP24_TOBAC	32 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				13
P80772 UniProt NPD GO	CWP13_PHAVU	33 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				12
P80776 UniProt NPD GO	CWP17_PHAVU	33 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				15
P80799 UniProt NPD GO	CWP02_LYCES	35 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				10
P80771 UniProt NPD GO	CWP12_PHAVU	35 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				20
P80849 UniProt NPD GO	CWP29_ARATH	36 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				6
P23525 UniProt NPD GO	IN37_SPIOL	37 kDa inner envelope membrane protein, chloroplast precursor (E37)	0.00	-	cyt	1	Plastid; chloroplast; chloroplast inner membrane				344
O42817 UniProt NPD GO	RS0_CANAL	40S ribosomal protein S0	0.00	-	mit	0					253
P46654 UniProt NPD GO	RS0B_YEAST	40S ribosomal protein S0-B (Nucleic acid-binding protein NAB1B)	0.00	-	mit	0	Cytoplasm	cytosolic small ribosomal subunit (sensu Eu... [TAS]			251
O97249 UniProt NPD GO	RS12_PLAF7	40S ribosomal protein S12	0.00	-	cyt	0					141
Q29303 UniProt NPD GO	RS14_PIG	40S ribosomal protein S14 (Fragment)	0.00	+	cyt	0					79
Q3T199 UniProt NPD GO	RS23_BOVIN	40S ribosomal protein S23	0.00	-	nuc	0		ribosome [ISS]			143
P90707 UniProt NPD GO	RS23_BRUMA	40S ribosomal protein S23	0.00	-	cyt	0					143
P62298 UniProt NPD GO	RS23_CHILA	40S ribosomal protein S23	0.00	-	nuc	0		ribosome [ISS]			143
P62266 UniProt NPD GO	RS23_HUMAN	40S ribosomal protein S23	0.00	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [IDA] ribosome [ISS]	603683		142
Q90YQ1 UniProt NPD GO	RS23_ICTPU	40S ribosomal protein S23	0.00	-	nuc	0					143
P62267 UniProt NPD GO	RS23_MOUSE	40S ribosomal protein S23	0.00	-	mit	0		ribosome [ISS]			142
Q6SA96 UniProt NPD GO	RS23_PIG	40S ribosomal protein S23	0.00	-	mit	0					142
P62268 UniProt NPD GO	RS23_RAT	40S ribosomal protein S23	0.00	-	mit	0		ribosome [NAS]			142
P80779 UniProt NPD GO	CWP02_TOBAC	41 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				14
P80830 UniProt NPD GO	CWP06_ARATH	42 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				7
P80820 UniProt NPD GO	CWP24_LYCES	42 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				5
P82440 UniProt NPD GO	CWP32_TOBAC	42 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				9
P80770 UniProt NPD GO	CWP11_PHAVU	43 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				15
P19617 UniProt NPD GO	45KD_TAEOV	45 kDa antigen (45W antigen) (Fragment)	0.00	-	nuc	0					240
P80767 UniProt NPD GO	CWP08_PHAVU	46 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				10
P80788 UniProt NPD GO	CWP11_TOBAC	47 kDa cell wall protein (Fragment)	0.00	-	cyt	0	Cell wall				24
Q9P4B8 UniProt NPD GO	RIB7_KLUMA	5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) (HTP reductase)	0.00	-	cyt	0					249
P30358 UniProt NPD GO	FLAP_SHEEP	5-lipoxygenase-activating protein (FLAP) (MK-886-binding protein) (Fragment)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				153
P80786 UniProt NPD GO	CWP09_TOBAC	50 kDa cell wall protein (Fragment)	0.00	-	cyt	0	Cell wall				22
P82438 UniProt NPD GO	CWP30_TOBAC	50 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				10
P84558 UniProt NPD GO	RK12_POPEU	50S ribosomal protein L12, chloroplast (Fragment)	0.00	-		0	Plastid; chloroplast				14
P80834 UniProt NPD GO	CWP12_ARATH	52 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				10
P80841 UniProt NPD GO	CWP20_ARATH	55 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				9
P80784 UniProt NPD GO	CWP07_TOBAC	57 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				9
P80752 UniProt NPD GO	CWP02_DAUCA	58 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				9
P50861 UniProt NPD GO	RIB4_YEAST	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9) (DMRL synthase) (Lumazine synthase) (Riboflavin ...	0.00	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1EJB	169

You are viewing entries 92201 to 92250 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.