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
Q8WGF6 UniProt NPD GO	CYB_LEPCU	Cytochrome b	0.00	-	end	9 *					379
O47561 UniProt NPD GO	CYB_LEPEU	Cytochrome b	0.00	-	end	9 *					379
Q9T6J0 UniProt NPD GO	CYB_LEPMN	Cytochrome b	0.00	-	end	9 *					379
Q9T6I4 UniProt NPD GO	CYB_LEPSI	Cytochrome b	0.00	-	end	9 *					379
Q6ELV4 UniProt NPD GO	CYB_LEPSX	Cytochrome b	0.00	-	end	9 *					379
O47557 UniProt NPD GO	CYB_LEPTI	Cytochrome b	0.00	-	end	9 *					379
Q692W3 UniProt NPD GO	CYB_LEPTL	Cytochrome b	0.00	-	end	9 *					379
Q6ELV5 UniProt NPD GO	CYB_LEPTO	Cytochrome b	0.00	-	end	9 *					379
O48092 UniProt NPD GO	CYB_LIACH	Cytochrome b	0.00	-	end	10 *					371
Q7Y5X9 UniProt NPD GO	CYB_LIOSP	Cytochrome b	0.00	-	end	9 *					379
Q36427 UniProt NPD GO	CYB_LOCMI	Cytochrome b	0.00	-	end	9 *					379
O47477 UniProt NPD GO	CYB_LOLBL	Cytochrome b	0.00	-	end	9 *					379
O78929 UniProt NPD GO	CYB_LONCN	Cytochrome b	0.00	-	end	9 *					379
O78930 UniProt NPD GO	CYB_LONFE	Cytochrome b	0.00	-	end	9 *					379
O78931 UniProt NPD GO	CYB_LONLO	Cytochrome b	0.00	-	end	9 *					379
O78932 UniProt NPD GO	CYB_LUTMA	Cytochrome b	0.00	-	end	9 *					379
Q3ZEC9 UniProt NPD GO	CYB_LYNCA	Cytochrome b	0.00	-	end	9 *					379
Q9T7Q0 UniProt NPD GO	CYB_MACBA	Cytochrome b	0.00	-	end	9 *					380
O47721 UniProt NPD GO	CYB_MADGU	Cytochrome b	0.00	-	end	9 *					379
O99345 UniProt NPD GO	CYB_MADKI	Cytochrome b	0.00	-	end	9 *					379
P04165 UniProt NPD GO	CYB_MAIZE	Cytochrome b	0.00	-	end	9 *					388
O78935 UniProt NPD GO	CYB_MARAM	Cytochrome b	0.00	-	end	9 *					379
Q9TH43 UniProt NPD GO	CYB_MARBA	Cytochrome b	0.00	-	end	9 *					379
Q9T3H9 UniProt NPD GO	CYB_MARME	Cytochrome b	0.00	-	end	9 *					379
O78936 UniProt NPD GO	CYB_MARPE	Cytochrome b	0.00	-	end	9 *					379
P26852 UniProt NPD GO	CYB_MARPO	Cytochrome b	0.00	-	end	10 *					404
Q9TEB5 UniProt NPD GO	CYB_MARZI	Cytochrome b	0.00	-	end	9 *					379
Q6YDL2 UniProt NPD GO	CYB_MESMC	Cytochrome b	0.00	-	end	9 *					379
O47499 UniProt NPD GO	CYB_METSE	Cytochrome b	0.00	-	end	9 *					393
Q34973 UniProt NPD GO	CYB_MICDE	Cytochrome b	0.00	-	end	9 *					382
Q8HQE9 UniProt NPD GO	CYB_MINFU	Cytochrome b	0.00	-	end	9 *					379
Q9MQX8 UniProt NPD GO	CYB_MOGIM	Cytochrome b	0.00	-	end	9 *					379
Q9MQY1 UniProt NPD GO	CYB_MOGIN	Cytochrome b	0.00	-	end	9 *					379
Q9MQY0 UniProt NPD GO	CYB_MOGTO	Cytochrome b	0.00	-	end	9 *					379
Q9MQX1 UniProt NPD GO	CYB_MOGWO	Cytochrome b	0.00	-	end	9 *					379
Q04911 UniProt NPD GO	CYB_MONDO	Cytochrome b	0.00	-	end	9 *					382
Q8WGF8 UniProt NPD GO	CYB_MONPL	Cytochrome b	0.00	-	end	9 *					379
Q9B167 UniProt NPD GO	CYB_MORBL	Cytochrome b	0.00	-	end	9 *					379
Q9B161 UniProt NPD GO	CYB_MORME	Cytochrome b	0.00	-	end	9 *					379
O48309 UniProt NPD GO	CYB_MOSFU	Cytochrome b	0.00	-	end	9 *					379
O47584 UniProt NPD GO	CYB_MOSLE	Cytochrome b	0.00	-	end	9 *					379
O47583 UniProt NPD GO	CYB_MOSMO	Cytochrome b	0.00	-	end	9 *					379
Q8M0K9 UniProt NPD GO	CYB_MUNRE	Cytochrome b	0.00	-	end	9 *					379
Q8HQF1 UniProt NPD GO	CYB_MURLE	Cytochrome b	0.00	-	end	9 *					379
Q9GBG9 UniProt NPD GO	CYB_MUSAL	Cytochrome b	0.00	-	end	9 *					379
O78934 UniProt NPD GO	CYB_MUSER	Cytochrome b	0.00	-	end	9 *					379
Q85IN9 UniProt NPD GO	CYB_MUSFR	Cytochrome b	0.00	-	end	9 *					379
Q9MIZ2 UniProt NPD GO	CYB_MUSNI	Cytochrome b	0.00	-	end	9 *					379
Q35113 UniProt NPD GO	CYB_MUSVI	Cytochrome b	0.00	-	end	9 *					379
Q6X9S4 UniProt NPD GO	CYB_MYCGR	Cytochrome b	0.00	-	end	9 *					388

You are viewing entries 93551 to 93600 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.