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
P19040 UniProt NPD GO	NU1M_ARTSA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.01	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				130
P24877 UniProt NPD GO	NU2M_ASCSU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.01	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				300
O47434 UniProt NPD GO	NU2M_BRAFL	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.01	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
O21001 UniProt NPD GO	NU2M_BRALA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.01	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
Q00229 UniProt NPD GO	NU2M_MYTED	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.01	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				314
P48904 UniProt NPD GO	NU2M_CYACA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2) (Fragment)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				99
Q37399 UniProt NPD GO	NU3M_ALLMA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					114
O47874 UniProt NPD GO	NU3M_ALLMI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P33509 UniProt NPD GO	NU3M_ANOQU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					117
P92533 UniProt NPD GO	NU3M_ARATH	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				119
Q37709 UniProt NPD GO	NU3M_ARTSF	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					111
O21584 UniProt NPD GO	NU3M_BAITA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P68307 UniProt NPD GO	NU3M_BALMU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P68308 UniProt NPD GO	NU3M_BALPH	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P03898 UniProt NPD GO	NU3M_BOVIN	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P68160 UniProt NPD GO	NU3M_BRANA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				119
Q9MIY3 UniProt NPD GO	NU3M_BRARE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					116
P34192 UniProt NPD GO	NU3M_CROLA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					116
P48911 UniProt NPD GO	NU3M_CYACA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					120
Q8W9M9 UniProt NPD GO	NU3M_DUGDU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
O21610 UniProt NPD GO	NU3M_HABLO	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P38600 UniProt NPD GO	NU3M_HALGR	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P60159 UniProt NPD GO	NU3M_HELAN	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					118
Q9ZZY4 UniProt NPD GO	NU3M_HIPAM	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
O21598 UniProt NPD GO	NU3M_ISTPI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
Q8HQB1 UniProt NPD GO	NU3M_LEMCA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P16265 UniProt NPD GO	NU3M_MAIZE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					118
P26847 UniProt NPD GO	NU3M_MARPO	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					118
O21519 UniProt NPD GO	NU3M_MICPE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
Q00568 UniProt NPD GO	NU3M_MYTED	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					116
O21578 UniProt NPD GO	NU3M_NEOFL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
O21543 UniProt NPD GO	NU3M_NOTED	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P18630 UniProt NPD GO	NU3M_OENBE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					118
O21601 UniProt NPD GO	NU3M_OSGBA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P12774 UniProt NPD GO	NU3M_PARLI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					117
P15579 UniProt NPD GO	NU3M_PARTE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					120
O21613 UniProt NPD GO	NU3M_PERBO	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
Q95891 UniProt NPD GO	NU3M_PERMA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
Q95921 UniProt NPD GO	NU3M_PERPL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
Q36664 UniProt NPD GO	NU3M_PINSY	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					118
Q36518 UniProt NPD GO	NU3M_PLASU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					117
P68159 UniProt NPD GO	NU3M_RAPSA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				119
O21273 UniProt NPD GO	NU3M_RECAM	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					122
Q94P36 UniProt NPD GO	NU3M_RHIPI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
O63850 UniProt NPD GO	NU3M_SARGL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					117
O21566 UniProt NPD GO	NU3M_SIGHI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
O21563 UniProt NPD GO	NU3M_SIGOC	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					115
P60160 UniProt NPD GO	NU3M_WHEAT	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					118
Q9B6C7 UniProt NPD GO	NU3M_YARLI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.01	-	end	3 *					128
Q35141 UniProt NPD GO	NU3M_NEUCR	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3) (Fragment)	0.01	-	mit	1 *					52

You are viewing entries 89751 to 89800 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.