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
P80759 UniProt NPD GO	CWP09_DAUCA	30 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				7
P80777 UniProt NPD GO	CWP18_PHAVU	30 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				15
P25619 UniProt NPD GO	HSP30_YEAST	30 kDa heat shock protein	0.01	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			332
P80780 UniProt NPD GO	CWP03_TOBAC	34 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				10
P82446 UniProt NPD GO	CWP38_TOBAC	34 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				15
P42055 UniProt NPD GO	VDAC1_SOLTU	34 kDa outer mitochondrial membrane protein porin (Voltage-dependent anion-selective channel protein ...	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane				275
P82444 UniProt NPD GO	CWP36_TOBAC	36 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				16
P42056 UniProt NPD GO	VDAC2_SOLTU	36 kDa outer mitochondrial membrane protein porin (Voltage-dependent anion-selective channel protein ...	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane				275
P80824 UniProt NPD GO	CWP28_LYCES	38 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				15
P80807 UniProt NPD GO	CWP10_LYCES	39 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				11
Q7XA48 UniProt NPD GO	DODA_PORGR	4,5-DOPA dioxygenase extradiol (EC 1.13.-.-)	0.01	-	cyt	0	Cytoplasm (Probable)				271
O24540 UniProt NPD GO	4CL_VANPL	4-coumarate--CoA ligase (EC 6.2.1.12) (4CL) (4-coumaroyl-CoA synthase)	0.01	-	cyt	0					553
P31686 UniProt NPD GO	4CL1_SOYBN	4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1) (Clone 4CL14) (Fragment ...	0.01	-	cyt	0					293
O24146 UniProt NPD GO	4CL2_TOBAC	4-coumarate--CoA ligase 2 (EC 6.2.1.12) (4CL 2) (4-coumaroyl-CoA synthase 2)	0.01	-	nuc	0					542
Q01213 UniProt NPD GO	DTDH_MUCMU	4-dihydromethyl-trisporate dehydrogenase (EC 1.1.1.-) (4-dihydromethyl-TA dehydrogenase)	0.01	-	cyt	0					321
Q2KJH9 UniProt NPD GO	AL9A1_BOVIN	4-trimethylaminobutyraldehyde dehydrogenase (EC 1.2.1.47) (TMABADH) (Aldehyde dehydrogenase 9A1) (EC ...	0.01	-	cyt	0	Cytoplasm (By similarity)				494
Q9JLJ2 UniProt NPD GO	AL9A1_MOUSE	4-trimethylaminobutyraldehyde dehydrogenase (EC 1.2.1.47) (TMABADH) (Aldehyde dehydrogenase 9A1) (EC ...	0.01	-	cyt	0	Cytoplasm (By similarity)	cytosol [IDA]			494
Q5R8A4 UniProt NPD GO	AL9A1_PONPY	4-trimethylaminobutyraldehyde dehydrogenase (EC 1.2.1.47) (TMABADH) (Aldehyde dehydrogenase 9A1) (EC ...	0.01	-	cyt	0	Cytoplasm (By similarity)				494
P49189 UniProt NPD GO	AL9A1_HUMAN	4-trimethylaminobutyraldehyde dehydrogenase (EC 1.2.1.47) (TMABADH) (Aldehyde dehydrogenase 9A1) (EC ...	0.01	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]	602733		494
P80818 UniProt NPD GO	CWP22_LYCES	40 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				15
P25608 UniProt NPD GO	YCZ2_YEAST	40.1 kDa protein in GIT1-PAU3 intergenic region	0.01	+	cyt	0					368
Q01291 UniProt NPD GO	RS0_NEUCR	40S ribosomal protein S0 (Ribosome-associated protein 1)	0.01	-	cyt	0					290
P49196 UniProt NPD GO	RS12_CAEEL	40S ribosomal protein S12	0.01	-	cyt	0					140
O59936 UniProt NPD GO	RS12_ERYGR	40S ribosomal protein S12	0.01	-	cyt	0					132
P48589 UniProt NPD GO	RS12_YEAST	40S ribosomal protein S12	0.01	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			143
Q90YS3 UniProt NPD GO	RS2_ICTPU	40S ribosomal protein S2	0.01	-	nuc	0					277
P46791 UniProt NPD GO	RS2_CRIGR	40S ribosomal protein S2 (Fragment)	0.01	-	nuc	0					202
P35686 UniProt NPD GO	RS20_ORYSA	40S ribosomal protein S20	0.01	-	cyt	0					128
Q9DFR4 UniProt NPD GO	RS23_GILMI	40S ribosomal protein S23	0.01	-	nuc	0					143
P79103 UniProt NPD GO	RS4_BOVIN	40S ribosomal protein S4 (Fragment)	0.01	-	cyt	0					194
P55832 UniProt NPD GO	RS4_HORSE	40S ribosomal protein S4 (Fragment)	0.01	-	cyt	0					194
P80754 UniProt NPD GO	CWP04_DAUCA	43 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				14
P80769 UniProt NPD GO	CWP10_PHAVU	44 kDa cell wall protein (Fragment)	0.01	-	nuc	0	Cell wall				25
P80835 UniProt NPD GO	CWP13_ARATH	44 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				10
P80825 UniProt NPD GO	CWP29_LYCES	44 kDa cell wall protein 2 (Fragment)	0.01	-		0	Cell wall				20
P80768 UniProt NPD GO	CWP09_PHAVU	45 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				15
P80797 UniProt NPD GO	CWP20_TOBAC	46 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				7
P80387 UniProt NPD GO	AAKB1_PIG	5'-AMP-activated protein kinase subunit beta-1 (AMPK beta-1 chain) (AMPKb) (5'-AMP-activated protein ...	0.01	-	cyt	0					122
Q05927 UniProt NPD GO	5NTD_BOVIN	5'-nucleotidase precursor (EC 3.1.3.5) (Ecto-5'-nucleotidase) (5'-NT) (CD73 antigen)	0.01	-	cyt	1	Cell membrane; lipid-anchor; GPI-anchor				574
P21589 UniProt NPD GO	5NTD_HUMAN	5'-nucleotidase precursor (EC 3.1.3.5) (Ecto-5'-nucleotidase) (5'-NT) (CD73 antigen)	0.01	-	end	2 *	Cell membrane; lipid-anchor; GPI-anchor	membrane fraction [TAS]	129190		574
P29240 UniProt NPD GO	5NTD_DISOM	5'-nucleotidase precursor (EC 3.1.3.5) (Ecto-nucleotidase)	0.01	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				577
Q6CJ61 UniProt NPD GO	RIB7_KLULA	5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) (HTP reductase)	0.01	-	cyt	0					252
P82610 UniProt NPD GO	METE_CANAL	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) (Methionine synt ...	0.01	-	cyt	0					25
P84542 UniProt NPD GO	METE_POPEU	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) (Vitamin-B12-ind ...	0.01	-	cyt	0	Cytoplasm (Potential)				21
P80805 UniProt NPD GO	CWP08_LYCES	50 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				11
P80766 UniProt NPD GO	CWP07_PHAVU	53 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				14
P80758 UniProt NPD GO	CWP08_DAUCA	56 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				7
Q9UVT8 UniProt NPD GO	RIB4_MAGGR	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9) (DMRL synthase) (Lumazine synthase) (Riboflavin ...	0.01	-	cyt	0				1C41	200
Q9UUB1 UniProt NPD GO	RIB4_SCHPO	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.9) (DMRL synthase) (Lumazine synthase) (Riboflavin ...	0.01	-	mit	0				2A59	159
Q27543 UniProt NPD GO	K6PF_CALFI	6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase) (Fragment)	0.01	-	cyt	0					184

You are viewing entries 86351 to 86400 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.