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
Q36445 UniProt NPD GO	CYB_MYCVI	Cytochrome b	0.00	-	end	9 *					389
Q7Y8M0 UniProt NPD GO	CYB_MYOAD	Cytochrome b	0.00	-	end	9 *					379
Q957C1 UniProt NPD GO	CYB_MYOBO	Cytochrome b	0.00	-	end	9 *					379
Q957B8 UniProt NPD GO	CYB_MYOBR	Cytochrome b	0.00	-	end	9 *					379
Q957B7 UniProt NPD GO	CYB_MYOCA	Cytochrome b	0.00	-	end	8 *					379
Q7Y8L9 UniProt NPD GO	CYB_MYOCH	Cytochrome b	0.00	-	end	9 *					379
Q7Y8L4 UniProt NPD GO	CYB_MYOFR	Cytochrome b	0.00	-	end	9 *					379
Q957B0 UniProt NPD GO	CYB_MYOKE	Cytochrome b	0.00	-	end	9 *					379
Q64J97 UniProt NPD GO	CYB_MYOLS	Cytochrome b	0.00	-	end	9 *					379
Q957A9 UniProt NPD GO	CYB_MYOLV	Cytochrome b	0.00	-	end	9 *					379
Q8HQE8 UniProt NPD GO	CYB_MYOMC	Cytochrome b	0.00	-	end	9 *					379
Q957A1 UniProt NPD GO	CYB_MYOMS	Cytochrome b	0.00	-	end	9 *					379
Q957A2 UniProt NPD GO	CYB_MYOMY	Cytochrome b	0.00	-	end	9 *					379
Q956Z9 UniProt NPD GO	CYB_MYONA	Cytochrome b	0.00	-	end	9 *					379
Q956Z8 UniProt NPD GO	CYB_MYONI	Cytochrome b	0.00	-	end	9 *					379
Q956Z5 UniProt NPD GO	CYB_MYORU	Cytochrome b	0.00	-	end	9 *					379
Q64JA0 UniProt NPD GO	CYB_MYOSE	Cytochrome b	0.00	-	end	9 *					379
Q956Z3 UniProt NPD GO	CYB_MYOTH	Cytochrome b	0.00	-	end	9 *					379
Q956Z1 UniProt NPD GO	CYB_MYOVO	Cytochrome b	0.00	-	end	9 *					379
Q7Y8K8 UniProt NPD GO	CYB_MYOYA	Cytochrome b	0.00	-	end	9 *					379
Q956Y7 UniProt NPD GO	CYB_MYOYU	Cytochrome b	0.00	-	end	9 *					379
Q00228 UniProt NPD GO	CYB_MYTED	Cytochrome b	0.00	-	end	9 *					397
Q35130 UniProt NPD GO	CYB_NAECA	Cytochrome b	0.00	-	end	9 *					379
Q8W9F5 UniProt NPD GO	CYB_NAPIN	Cytochrome b	0.00	-	end	9 *					379
Q9XNU4 UniProt NPD GO	CYB_NEOAL	Cytochrome b	0.00	-	end	9 *					381
P00162 UniProt NPD GO	CYB_NEUCR	Cytochrome b	0.00	-	end	8 *					385
Q8W926 UniProt NPD GO	CYB_NOCAL	Cytochrome b	0.00	-	end	9 *					379
Q8W7G4 UniProt NPD GO	CYB_NOCLE	Cytochrome b	0.00	-	end	9 *					379
Q5VJ36 UniProt NPD GO	CYB_NYCBE	Cytochrome b	0.00	-	end	9 *					379
Q35131 UniProt NPD GO	CYB_NYCCO	Cytochrome b	0.00	-	end	9 *					379
Q5VJ37 UniProt NPD GO	CYB_NYCPY	Cytochrome b	0.00	-	end	9 *					379
Q9GBY1 UniProt NPD GO	CYB_OCHAL	Cytochrome b	0.00	-	end	9 *					379
Q953J5 UniProt NPD GO	CYB_OCHCO	Cytochrome b	0.00	-	end	9 *					379
Q9G1B9 UniProt NPD GO	CYB_OCHCU	Cytochrome b	0.00	-	end	9 *					379
Q9GBY4 UniProt NPD GO	CYB_OCHER	Cytochrome b	0.00	-	end	9 *					379
Q9GBY5 UniProt NPD GO	CYB_OCHFO	Cytochrome b	0.00	-	end	9 *					379
Q9GBY6 UniProt NPD GO	CYB_OCHHI	Cytochrome b	0.00	-	end	9 *					379
Q9G6G2 UniProt NPD GO	CYB_OCHHY	Cytochrome b	0.00	-	end	9 *					379
Q9GBZ1 UniProt NPD GO	CYB_OCHLA	Cytochrome b	0.00	-	end	9 *					379
Q9GBZ2 UniProt NPD GO	CYB_OCHNB	Cytochrome b	0.00	-	end	9 *					379
Q9GBZ4 UniProt NPD GO	CYB_OCHPR	Cytochrome b	0.00	-	end	9 *					379
Q9GBZ5 UniProt NPD GO	CYB_OCHRO	Cytochrome b	0.00	-	end	9 *					379
Q9ZZU1 UniProt NPD GO	CYB_OCHRU	Cytochrome b	0.00	-	end	9 *					379
Q9GBZ6 UniProt NPD GO	CYB_OCHTH	Cytochrome b	0.00	-	end	9 *					379
Q9GBZ7 UniProt NPD GO	CYB_OCHTI	Cytochrome b	0.00	-	end	9 *					379
P24960 UniProt NPD GO	CYB_ODOHE	Cytochrome b	0.00	-	end	9 *					379
Q7HKW1 UniProt NPD GO	CYB_ODORR	Cytochrome b	0.00	-	end	9 *					379
P09843 UniProt NPD GO	CYB_OENBE	Cytochrome b	0.00	-	end	9 *					394
Q6YLN1 UniProt NPD GO	CYB_OKAJO	Cytochrome b	0.00	-	end	9 *					379
Q9MMZ2 UniProt NPD GO	CYB_OREAM	Cytochrome b	0.00	-	end	9 *					379

You are viewing entries 93601 to 93650 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.