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
P21719 UniProt NPD GO	CYB_AKOPU	Cytochrome b	0.01	-	end	9 *					379
P48521 UniProt NPD GO	CYB_AKOSI	Cytochrome b	0.01	-	end	9 *					379
P21720 UniProt NPD GO	CYB_AKOSU	Cytochrome b	0.01	-	end	9 *					379
P21721 UniProt NPD GO	CYB_AKOTO	Cytochrome b	0.01	-	end	9 *					379
P48884 UniProt NPD GO	CYB_ALBCO	Cytochrome b	0.01	-	end	9 *					367
Q8M0A6 UniProt NPD GO	CYB_ALCTO	Cytochrome b	0.01	-	end	9 *					380
P48885 UniProt NPD GO	CYB_ALECH	Cytochrome b	0.01	-	end	9 *					380
Q8M6Z3 UniProt NPD GO	CYB_ALLAL	Cytochrome b	0.01	-	end	9 *					380
Q9ZZD8 UniProt NPD GO	CYB_AMATZ	Cytochrome b	0.01	-	end	9 *					380
O63535 UniProt NPD GO	CYB_ANTBE	Cytochrome b	0.01	-	end	9 *					381
Q33706 UniProt NPD GO	CYB_ANTFL	Cytochrome b	0.01	-	end	9 *					381
O63536 UniProt NPD GO	CYB_ANTGO	Cytochrome b	0.01	-	end	9 *					381
Q33782 UniProt NPD GO	CYB_ANTME	Cytochrome b	0.01	-	end	9 *					381
O47723 UniProt NPD GO	CYB_ANTMR	Cytochrome b	0.01	-	end	9 *					379
P92509 UniProt NPD GO	CYB_ANTST	Cytochrome b	0.01	-	end	9 *					381
Q33865 UniProt NPD GO	CYB_ANTSW	Cytochrome b	0.01	-	end	9 *					381
Q33941 UniProt NPD GO	CYB_ANTVI	Cytochrome b	0.01	-	end	9 *					380
Q9TEY8 UniProt NPD GO	CYB_APOAL	Cytochrome b	0.01	-	end	9 *					381
Q9TEY7 UniProt NPD GO	CYB_APOFL	Cytochrome b	0.01	-	end	9 *					381
Q9T9I7 UniProt NPD GO	CYB_APOSE	Cytochrome b	0.01	-	end	9 *					380
Q9TEY4 UniProt NPD GO	CYB_APOSY	Cytochrome b	0.01	-	end	9 *					381
Q9G0M4 UniProt NPD GO	CYB_ARAGI	Cytochrome b	0.01	-	end	9 *					380
Q5VJ39 UniProt NPD GO	CYB_ARCCA	Cytochrome b	0.01	-	end	9 *					379
Q33688 UniProt NPD GO	CYB_ARCGZ	Cytochrome b	0.01	-	end	9 *					379
Q9B9F9 UniProt NPD GO	CYB_ARCTR	Cytochrome b	0.01	-	end	9 *					379
P24878 UniProt NPD GO	CYB_ASCSU	Cytochrome b	0.01	-	end	9 *					365
P62513 UniProt NPD GO	CYB_ASHGO	Cytochrome b	0.01	-	end	9 *					384
O48017 UniProt NPD GO	CYB_ASPME	Cytochrome b	0.01	-	end	10 *					371
Q9T9J5 UniProt NPD GO	CYB_ASTOC	Cytochrome b	0.01	-	end	9 *					380
P41280 UniProt NPD GO	CYB_BALAC	Cytochrome b	0.01	-	end	9 *					379
P41281 UniProt NPD GO	CYB_BALBN	Cytochrome b	0.01	-	end	9 *					379
P41282 UniProt NPD GO	CYB_BALBO	Cytochrome b	0.01	-	end	9 *					379
Q599A4 UniProt NPD GO	CYB_BALBR	Cytochrome b	0.01	-	end	9 *					379
P41283 UniProt NPD GO	CYB_BALED	Cytochrome b	0.01	-	end	9 *					379
P41284 UniProt NPD GO	CYB_BALGL	Cytochrome b	0.01	-	end	9 *					379
P41286 UniProt NPD GO	CYB_BALMY	Cytochrome b	0.01	-	end	9 *					379
P24950 UniProt NPD GO	CYB_BALPH	Cytochrome b	0.01	-	end	9 *					379
Q33989 UniProt NPD GO	CYB_BALRE	Cytochrome b	0.01	-	end	9 *					380
O79648 UniProt NPD GO	CYB_BAMTH	Cytochrome b	0.01	-	end	9 *					380
P92848 UniProt NPD GO	CYB_BOACO	Cytochrome b	0.01	-	end	10 *					371
P21722 UniProt NPD GO	CYB_BOLAM	Cytochrome b	0.01	-	end	9 *					379
O79311 UniProt NPD GO	CYB_BOSTR	Cytochrome b	0.01	-	end	9 *					379
Q9T7T7 UniProt NPD GO	CYB_BRAAL	Cytochrome b	0.01	-	end	9 *					380
O47431 UniProt NPD GO	CYB_BRAFL	Cytochrome b	0.01	-	end	9 *					380
P92472 UniProt NPD GO	CYB_BRALA	Cytochrome b	0.01	-	end	9 *					380
O48321 UniProt NPD GO	CYB_BUNHO	Cytochrome b	0.01	-	end	9 *					380
Q9ZY46 UniProt NPD GO	CYB_CAEFU	Cytochrome b	0.01	-	end	9 *					381
Q9MLJ7 UniProt NPD GO	CYB_CALJP	Cytochrome b	0.01	-	end	10 *					372
O79196 UniProt NPD GO	CYB_CALLE	Cytochrome b	0.01	-	end	9 *					380
Q34028 UniProt NPD GO	CYB_CAMBA	Cytochrome b	0.01	-	end	9 *					379

You are viewing entries 87301 to 87350 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.