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
Q9TAB1 UniProt NPD GO	CYB_MANME	Cytochrome b	0.01	-	end	9 *					380
Q9TH45 UniProt NPD GO	CYB_MARBB	Cytochrome b	0.01	-	end	9 *					379
Q9XMC1 UniProt NPD GO	CYB_MARFL	Cytochrome b	0.01	-	end	9 *					379
Q35075 UniProt NPD GO	CYB_MARLE	Cytochrome b	0.01	-	end	9 *					382
Q9XP34 UniProt NPD GO	CYB_MARMR	Cytochrome b	0.01	-	end	9 *					379
Q9TH56 UniProt NPD GO	CYB_MARVA	Cytochrome b	0.01	-	end	9 *					379
Q8W9F9 UniProt NPD GO	CYB_MASMZ	Cytochrome b	0.01	-	end	9 *					379
P41289 UniProt NPD GO	CYB_MEGNO	Cytochrome b	0.01	-	end	9 *					379
P50663 UniProt NPD GO	CYB_MELGA	Cytochrome b	0.01	-	end	9 *					380
Q85IN4 UniProt NPD GO	CYB_MELMS	Cytochrome b	0.01	-	end	9 *					379
Q35066 UniProt NPD GO	CYB_MESPE	Cytochrome b	0.01	-	end	9 *					379
Q9GAW6 UniProt NPD GO	CYB_MICMC	Cytochrome b	0.01	-	end	9 *					379
Q9TFX5 UniProt NPD GO	CYB_MICMS	Cytochrome b	0.01	-	end	9 *					380
Q9G0S9 UniProt NPD GO	CYB_MICMU	Cytochrome b	0.01	-	end	9 *					379
Q35083 UniProt NPD GO	CYB_MICRS	Cytochrome b	0.01	-	end	9 *					380
Q34957 UniProt NPD GO	CYB_MONAD	Cytochrome b	0.01	-	end	9 *					382
P00158 UniProt NPD GO	CYB_MOUSE	Cytochrome b	0.01	-	end	9 *					381
Q94SZ7 UniProt NPD GO	CYB_MUGCE	Cytochrome b	0.01	-	end	8 *					379
Q85RV3 UniProt NPD GO	CYB_MUNCR	Cytochrome b	0.01	-	end	9 *					379
Q71E89 UniProt NPD GO	CYB_MUNMN	Cytochrome b	0.01	-	end	9 *					379
Q9TDQ7 UniProt NPD GO	CYB_MUNMU	Cytochrome b	0.01	-	end	9 *					379
Q35020 UniProt NPD GO	CYB_MURLO	Cytochrome b	0.01	-	end	9 *					381
Q7JE02 UniProt NPD GO	CYB_MUSEV	Cytochrome b	0.01	-	end	9 *					379
Q8WA47 UniProt NPD GO	CYB_MUSMA	Cytochrome b	0.01	-	end	9 *					381
Q35065 UniProt NPD GO	CYB_MUSPU	Cytochrome b	0.01	-	end	9 *					379
Q9MJ99 UniProt NPD GO	CYB_MUSSB	Cytochrome b	0.01	-	end	9 *					379
Q9B1Z4 UniProt NPD GO	CYB_MUSST	Cytochrome b	0.01	-	end	9 *					380
Q957B9 UniProt NPD GO	CYB_MYOBE	Cytochrome b	0.01	-	end	9 *					379
Q957B5 UniProt NPD GO	CYB_MYODA	Cytochrome b	0.01	-	end	9 *					379
Q957B3 UniProt NPD GO	CYB_MYOEM	Cytochrome b	0.01	-	end	9 *					379
Q7Y8L5 UniProt NPD GO	CYB_MYOFO	Cytochrome b	0.01	-	end	9 *					379
Q9ZZT6 UniProt NPD GO	CYB_MYOGL	Cytochrome b	0.01	-	end	9 *					379
Q35038 UniProt NPD GO	CYB_MYOME	Cytochrome b	0.01	-	end	9 *					381
Q8HQE7 UniProt NPD GO	CYB_MYOPR	Cytochrome b	0.01	-	end	9 *					379
Q956Y9 UniProt NPD GO	CYB_MYOWE	Cytochrome b	0.01	-	end	9 *					379
Q9T7N5 UniProt NPD GO	CYB_MYSAL	Cytochrome b	0.01	-	end	9 *					380
O21366 UniProt NPD GO	CYB_NEOFO	Cytochrome b	0.01	-	end	9 *					379
Q35157 UniProt NPD GO	CYB_NEOLO	Cytochrome b	0.01	-	end	9 *					381
O79426 UniProt NPD GO	CYB_NEOMO	Cytochrome b	0.01	-	end	9 *					379
Q85C06 UniProt NPD GO	CYB_NEUGI	Cytochrome b	0.01	-	end	9 *					379
O47890 UniProt NPD GO	CYB_NOMGA	Cytochrome b	0.01	-	end	9 *					380
O79209 UniProt NPD GO	CYB_OCEOC	Cytochrome b	0.01	-	end	9 *					380
Q9GBZ0 UniProt NPD GO	CYB_OCHKO	Cytochrome b	0.01	-	end	9 *					379
O21807 UniProt NPD GO	CYB_OCTDE	Cytochrome b	0.01	-	end	9 *					379
Q9XM10 UniProt NPD GO	CYB_ONCKE	Cytochrome b	0.01	-	end	9 *					380
P48173 UniProt NPD GO	CYB_ONCMY	Cytochrome b	0.01	-	end	9 *					380
Q36461 UniProt NPD GO	CYB_ORNAN	Cytochrome b	0.01	-	end	9 *					379
Q9G9J4 UniProt NPD GO	CYB_OTOGA	Cytochrome b	0.01	-	end	9 *					379
Q35273 UniProt NPD GO	CYB_OVIMO	Cytochrome b	0.01	-	end	9 *					379
O79215 UniProt NPD GO	CYB_PACSA	Cytochrome b	0.01	-	end	9 *					380

You are viewing entries 87451 to 87500 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.