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
P69237 UniProt NPD GO	NU3M_BRALA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					117
P24895 UniProt NPD GO	NU3M_CAEEL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					111
Q9ZZ60 UniProt NPD GO	NU3M_CANFA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
P48909 UniProt NPD GO	NU3M_CANPA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					131
P48910 UniProt NPD GO	NU3M_CHOCR	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					121
Q37312 UniProt NPD GO	NU3M_DICDI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					120
O21549 UniProt NPD GO	NU3M_ELITY	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
P15956 UniProt NPD GO	NU3M_EMENI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					136
Q34522 UniProt NPD GO	NU3M_FASHE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					118
Q35100 UniProt NPD GO	NU3M_METSE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					118
Q9G2X1 UniProt NPD GO	NU3M_MYXGL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
O21595 UniProt NPD GO	NU3M_ONYLE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
Q36456 UniProt NPD GO	NU3M_ORNAN	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
O21604 UniProt NPD GO	NU3M_PERER	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
Q95881 UniProt NPD GO	NU3M_PERGO	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
Q95897 UniProt NPD GO	NU3M_PERME	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
O21607 UniProt NPD GO	NU3M_PERMX	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
O21546 UniProt NPD GO	NU3M_PHYDA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
P24997 UniProt NPD GO	NU3M_PISOC	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					116
P15580 UniProt NPD GO	NU3M_PODAN	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					137
Q37625 UniProt NPD GO	NU3M_PROWI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					117
O79434 UniProt NPD GO	NU3M_RABIT	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
O21590 UniProt NPD GO	NU3M_REIME	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
O99823 UniProt NPD GO	NU3M_RHISA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					114
P20113 UniProt NPD GO	NU4M_CHLRE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.00	-	end	15 *					443
Q00231 UniProt NPD GO	NU4M_MYTED	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.00	-	end	12 *					435
P03914 UniProt NPD GO	NU4M_EMENI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.00	-	end	6 *					221
Q37379 UniProt NPD GO	NU4LM_ACACA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					103
P19049 UniProt NPD GO	NU4LM_ARTSA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					86
Q37751 UniProt NPD GO	NU4LM_ARTSF	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					85
Q5YF91 UniProt NPD GO	NU4LM_ASPNG	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					89
Q5S589 UniProt NPD GO	NU4LM_ASPTU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					89
Q9B8T9 UniProt NPD GO	NU4LM_AVALA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
P41301 UniProt NPD GO	NU4LM_BALMU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
P48929 UniProt NPD GO	NU4LM_CANPA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					84
O21333 UniProt NPD GO	NU4LM_DASNO	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q69B76 UniProt NPD GO	NU4LM_DELLE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
P41307 UniProt NPD GO	NU4LM_DIDMA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
O79554 UniProt NPD GO	NU4LM_DINSE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					96
Q8W9M8 UniProt NPD GO	NU4LM_DUGDU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q2I3G6 UniProt NPD GO	NU4LM_ELEMA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
P92483 UniProt NPD GO	NU4LM_EQUAS	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q8HC89 UniProt NPD GO	NU4LM_HAPAU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q8HC87 UniProt NPD GO	NU4LM_HAPSI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q9ZZY3 UniProt NPD GO	NU4LM_HIPAM	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
P48658 UniProt NPD GO	NU4LM_HORSE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
P03901 UniProt NPD GO	NU4LM_HUMAN	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *		respiratory chain complex I (sensu Eukaryota) [NAS]	535000		98
Q679B8 UniProt NPD GO	NU4LM_HYDLE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q95709 UniProt NPD GO	NU4LM_HYLLA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q94Y87 UniProt NPD GO	NU4LM_LEMCA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98

You are viewing entries 95851 to 95900 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.