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
P92592 UniProt NPD GO	CYB_BUBQU	Cytochrome b	0.00	-	end	9 *					379
Q6ELW6 UniProt NPD GO	CYB_BUNMO	Cytochrome b	0.00	-	end	9 *					379
Q8HEC2 UniProt NPD GO	CYB_CAEBR	Cytochrome b	0.00	-	end	9 *					370
P24890 UniProt NPD GO	CYB_CAEEL	Cytochrome b	0.00	-	end	10 *					370
P92605 UniProt NPD GO	CYB_CALFO	Cytochrome b	0.00	-	end	9 *					380
P24952 UniProt NPD GO	CYB_CAMDR	Cytochrome b	0.00	-	end	9 *					379
Q6JWX5 UniProt NPD GO	CYB_CANAU	Cytochrome b	0.00	-	end	9 *					379
Q34101 UniProt NPD GO	CYB_CANFA	Cytochrome b	0.00	-	end	9 *					379
Q6Y8J2 UniProt NPD GO	CYB_CANLU	Cytochrome b	0.00	-	end	9 *					379
O78789 UniProt NPD GO	CYB_CAPAE	Cytochrome b	0.00	-	end	9 *					379
Q34045 UniProt NPD GO	CYB_CAPCR	Cytochrome b	0.00	-	end	9 *					379
O78788 UniProt NPD GO	CYB_CAPCU	Cytochrome b	0.00	-	end	9 *					379
O78787 UniProt NPD GO	CYB_CAPCY	Cytochrome b	0.00	-	end	9 *					379
O78786 UniProt NPD GO	CYB_CAPFA	Cytochrome b	0.00	-	end	9 *					379
P24953 UniProt NPD GO	CYB_CAPHI	Cytochrome b	0.00	-	end	9 *					379
P41287 UniProt NPD GO	CYB_CAPMR	Cytochrome b	0.00	-	end	9 *					379
O78790 UniProt NPD GO	CYB_CAPNU	Cytochrome b	0.00	-	end	9 *					379
O47926 UniProt NPD GO	CYB_CAPPY	Cytochrome b	0.00	-	end	9 *					379
O78784 UniProt NPD GO	CYB_CAPSI	Cytochrome b	0.00	-	end	9 *					380
Q5C9H5 UniProt NPD GO	CYB_CAPSU	Cytochrome b	0.00	-	end	9 *					379
Q9GAP0 UniProt NPD GO	CYB_CARBR	Cytochrome b	0.00	-	end	9 *					379
Q9GAN2 UniProt NPD GO	CYB_CARPS	Cytochrome b	0.00	-	end	9 *					379
Q9GAN4 UniProt NPD GO	CYB_CARSU	Cytochrome b	0.00	-	end	9 *					379
Q9B5R8 UniProt NPD GO	CYB_CEPCA	Cytochrome b	0.00	-	end	9 *					379
O79327 UniProt NPD GO	CYB_CEPLE	Cytochrome b	0.00	-	end	9 *					379
Q9B5R2 UniProt NPD GO	CYB_CEPMA	Cytochrome b	0.00	-	end	9 *					379
Q9B5R3 UniProt NPD GO	CYB_CEPMO	Cytochrome b	0.00	-	end	9 *					379
Q34179 UniProt NPD GO	CYB_CEPNE	Cytochrome b	0.00	-	end	10 *					380
Q9B5R0 UniProt NPD GO	CYB_CEPNG	Cytochrome b	0.00	-	end	9 *					379
Q9B5R1 UniProt NPD GO	CYB_CEPNI	Cytochrome b	0.00	-	end	9 *					379
Q9B5Q6 UniProt NPD GO	CYB_CEPRU	Cytochrome b	0.00	-	end	9 *					379
Q5UVI3 UniProt NPD GO	CYB_CERDU	Cytochrome b	0.00	-	end	9 *					379
O47924 UniProt NPD GO	CYB_CEREL	Cytochrome b	0.00	-	end	9 *					379
Q34172 UniProt NPD GO	CYB_CERNI	Cytochrome b	0.00	-	end	9 *					379
Q75R30 UniProt NPD GO	CYB_CERNY	Cytochrome b	0.00	-	end	9 *					379
Q5UVI8 UniProt NPD GO	CYB_CERSC	Cytochrome b	0.00	-	end	9 *					379
O03207 UniProt NPD GO	CYB_CERSI	Cytochrome b	0.00	-	end	9 *					379
Q6Y8J6 UniProt NPD GO	CYB_CHIDO	Cytochrome b	0.00	-	end	9 *					379
P23662 UniProt NPD GO	CYB_CHLRE	Cytochrome b	0.00	-	end	9 *					381
P23663 UniProt NPD GO	CYB_CHLSM	Cytochrome b	0.00	-	end	9 *					381
P48875 UniProt NPD GO	CYB_CHOCR	Cytochrome b	0.00	-	end	10 *					381
Q7Y8I2 UniProt NPD GO	CYB_CHRAS	Cytochrome b	0.00	-	end	9 *					379
Q9MLL0 UniProt NPD GO	CYB_COLCO	Cytochrome b	0.00	-	end	10 *					371
Q9MFN9 UniProt NPD GO	CYB_COLHO	Cytochrome b	0.00	-	end	9 *					378
O99258 UniProt NPD GO	CYB_CONGN	Cytochrome b	0.00	-	end	9 *					379
O47421 UniProt NPD GO	CYB_CONTA	Cytochrome b	0.00	-	end	9 *					379
Q8WBP9 UniProt NPD GO	CYB_CONVI	Cytochrome b	0.00	-	end	9 *					380
Q950C7 UniProt NPD GO	CYB_CORBR	Cytochrome b	0.00	-	end	9 *					380
Q9TAD3 UniProt NPD GO	CYB_CORCD	Cytochrome b	0.00	-	end	9 *					380
Q8WDV0 UniProt NPD GO	CYB_CRACA	Cytochrome b	0.00	-	end	9 *					379

You are viewing entries 93401 to 93450 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.