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
Q5KEJ9 UniProt NPD GO	TSC10_CRYNE	3-ketodihydrosphingosine reductase TSC10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduct ...	0.02	-	end	2 *	Endoplasmic reticulum (By similarity)				335
Q06136 UniProt NPD GO	FVT1_HUMAN	3-ketodihydrosphingosine reductase precursor (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS re ...	0.02	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	extracellular space [TAS]	136440		332
O00085 UniProt NPD GO	PHYA_ASPTE	3-phytase A precursor (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase A) (3 phytase A) ( ...	0.02	-	exc	0	Secreted protein				466
P80756 UniProt NPD GO	CWP06_DAUCA	30 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				14
P80775 UniProt NPD GO	CWP16_PHAVU	36 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				20
O13837 UniProt NPD GO	GATA_SCHPO	4-aminobutyrate aminotransferase (EC 2.6.1.19) (Gamma-amino-N-butyrate transaminase) (GABA transamin ...	0.02	-	cyt	0					474
P14912 UniProt NPD GO	4CL1_PETCR	4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1)	0.02	-	nuc	0					544
P31684 UniProt NPD GO	4CL1_SOLTU	4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1)	0.02	-	nuc	0					545
P14913 UniProt NPD GO	4CL2_PETCR	4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1)	0.02	-	nuc	0					544
Q42982 UniProt NPD GO	4CL2_ORYSA	4-coumarate--CoA ligase 2 (EC 6.2.1.12) (4CL 2) (4-coumaroyl-CoA synthase 2)	0.02	-	end	0					569
P31685 UniProt NPD GO	4CL2_SOLTU	4-coumarate--CoA ligase 2 (EC 6.2.1.12) (4CL 2) (4-coumaroyl-CoA synthase 2)	0.02	-	nuc	0					545
Q9JLJ3 UniProt NPD GO	AL9A1_RAT	4-trimethylaminobutyraldehyde dehydrogenase (EC 1.2.1.47) (TMABADH) (Aldehyde dehydrogenase 9A1) (EC ...	0.02	-	cyt	0	Cytoplasm	cytosol [NAS]			494
Q6DGG0 UniProt NPD GO	PPID_RAT	40 kDa peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-40) (CYP-40 ...	0.02	-	cyt	0	Cytoplasm (By similarity)				369
P26882 UniProt NPD GO	PPID_BOVIN	40 kDa peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-40) (CYP-40 ...	0.02	-	cyt	0	Cytoplasm			1IIP	369
P42847 UniProt NPD GO	RT18_YEAST	40S ribosomal protein MRP18, mitochondrial precursor (YmS18)	0.02	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IPI]			217
P32905 UniProt NPD GO	RS0A_YEAST	40S ribosomal protein S0-A (Nucleic acid-binding protein NAB1A)	0.02	-	mit	0	Cytoplasm	cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	251
P84175 UniProt NPD GO	RS12_CHICK	40S ribosomal protein S12	0.02	-	cyt	0	Cytoplasm				131
Q9XHS0 UniProt NPD GO	RS12_HORVU	40S ribosomal protein S12	0.02	-	cyt	0					143
P25398 UniProt NPD GO	RS12_HUMAN	40S ribosomal protein S12	0.02	-	cyt	0	Cytoplasm	cytosolic small ribosomal subunit (sensu Eu... [IDA]	603660		131
P63323 UniProt NPD GO	RS12_MOUSE	40S ribosomal protein S12	0.02	-	cyt	0	Cytoplasm				131
P46405 UniProt NPD GO	RS12_PIG	40S ribosomal protein S12	0.02	-	cyt	0	Cytoplasm				131
P63324 UniProt NPD GO	RS12_RAT	40S ribosomal protein S12	0.02	-	cyt	0	Cytoplasm				131
P47840 UniProt NPD GO	RS12_XENLA	40S ribosomal protein S12	0.02	-	cyt	0	Cytoplasm				131
Q9S9P1 UniProt NPD GO	RS12A_ARATH	40S ribosomal protein S12-1	0.02	-	cyt	0					144
Q9SKZ3 UniProt NPD GO	RS12C_ARATH	40S ribosomal protein S12-3	0.02	-	cyt	0					144
O14062 UniProt NPD GO	RS12A_SCHPO	40S ribosomal protein S12-A	0.02	-	cyt	0					145
O74322 UniProt NPD GO	RS12B_SCHPO	40S ribosomal protein S12-B	0.02	-	cyt	0					148
P61155 UniProt NPD GO	RS19_PAGMA	40S ribosomal protein S19	0.02	-	cyt	0					146
Q08068 UniProt NPD GO	RS20_MAIZE	40S ribosomal protein S20 (S22) (Fragment)	0.02	-	nuc	0					60
Q8I7N7 UniProt NPD GO	RS21_CERCA	40S ribosomal protein S21	0.02	-	nuc	0					83
Q9SMI2 UniProt NPD GO	RS21_CYAPA	40S ribosomal protein S21	0.02	-	cyt	0					82
Q8T3U2 UniProt NPD GO	RS23_DROME	40S ribosomal protein S23	0.02	-	nuc	0					143
Q6EV23 UniProt NPD GO	RS23_PAPDA	40S ribosomal protein S23	0.02	-	nuc	0					143
Q962Q7 UniProt NPD GO	RS23_SPOFR	40S ribosomal protein S23	0.02	-	nuc	0					143
Q9SF35 UniProt NPD GO	RS23A_ARATH	40S ribosomal protein S23-1 (S12)	0.02	-	mit	0					142
P19955 UniProt NPD GO	RT31_YEAST	40S ribosomal protein YMR-31, mitochondrial precursor	0.02	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [TAS]			123
P80806 UniProt NPD GO	CWP09_LYCES	44 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				14
P80789 UniProt NPD GO	CWP12_TOBAC	45 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				13
Q61503 UniProt NPD GO	5NTD_MOUSE	5'-nucleotidase precursor (EC 3.1.3.5) (Ecto-5'-nucleotidase) (5'-NT) (CD73 antigen)	0.02	-	end	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				576
P21588 UniProt NPD GO	5NTD_RAT	5'-nucleotidase precursor (EC 3.1.3.5) (Ecto-5'-nucleotidase) (5'-NT) (CD73 antigen)	0.02	-	end	1	Cell membrane; lipid-anchor; GPI-anchor	integral to membrane [TAS]			576
Q6BII9 UniProt NPD GO	RIB7_DEBHA	5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) (HTP reductase)	0.02	-	mit	0					247
Q6CCW0 UniProt NPD GO	HEM1_YARLI	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				563
Q29005 UniProt NPD GO	5HT2B_PIG	5-hydroxytryptamine 2B receptor (5-HT-2B) (Serotonin receptor 2B) (5-HT2B) (Fragment)	0.02	-	mit	1 *	Membrane; multi-pass membrane protein				60
P32305 UniProt NPD GO	5HT7R_RAT	5-hydroxytryptamine 7 receptor (5-HT-7) (Serotonin receptor 7) (5-HT-X) (5HT7) (GPRFO)	0.02	-	end	7	Membrane; multi-pass membrane protein				448
P81420 UniProt NPD GO	ODP3_SOLTU	55 kDa dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC ...	0.02	-		0	Mitochondrion; mitochondrial matrix				15
O80575 UniProt NPD GO	RISB_ARATH	6,7-dimethyl-8-ribityllumazine synthase, chloroplast precursor (EC 2.5.1.9) (DMRL synthase) (Lumazin ...	0.02	-	mit	0	Plastid; chloroplast				227
Q9XH32 UniProt NPD GO	RISB_SPIOL	6,7-dimethyl-8-ribityllumazine synthase, chloroplast precursor (EC 2.5.1.9) (DMRL synthase) (Lumazin ...	0.02	-	mit	0	Plastid; chloroplast			1C2Y	222
Q17761 UniProt NPD GO	6PGD_CAEEL	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.02	-	cyt	0					484
P41570 UniProt NPD GO	6PGD_CERCA	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.02	-	cyt	0					481
P41572 UniProt NPD GO	6PGD_DROME	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.02	-	cyt	0					481

You are viewing entries 82151 to 82200 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.