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
Q36082 UniProt NPD GO	CYB_URSMA	Cytochrome b	0.00	-	end	9 *					379
Q9MFN3 UniProt NPD GO	CYB_URSSP	Cytochrome b	0.00	-	end	9 *					379
Q35111 UniProt NPD GO	CYB_URSUR	Cytochrome b	0.00	-	end	9 *					379
Q6YDK5 UniProt NPD GO	CYB_VAMBI	Cytochrome b	0.00	-	end	9 *					379
Q6YDK7 UniProt NPD GO	CYB_VAMBR	Cytochrome b	0.00	-	end	9 *					379
Q6YDL6 UniProt NPD GO	CYB_VAMCA	Cytochrome b	0.00	-	end	9 *					379
O99795 UniProt NPD GO	CYB_VARVV	Cytochrome b	0.00	-	end	9 *					379
O48334 UniProt NPD GO	CYB_VENIN	Cytochrome b	0.00	-	end	9 *					393
Q9MJV1 UniProt NPD GO	CYB_VERRU	Cytochrome b	0.00	-	end	9 *					380
Q957C8 UniProt NPD GO	CYB_VESMU	Cytochrome b	0.00	-	end	9 *					379
Q8HQE6 UniProt NPD GO	CYB_VESSU	Cytochrome b	0.00	-	end	9 *					379
O79785 UniProt NPD GO	CYB_VIRFL	Cytochrome b	0.00	-	end	9 *					380
Q951T4 UniProt NPD GO	CYB_VIRLA	Cytochrome b	0.00	-	end	9 *					380
Q36222 UniProt NPD GO	CYB_VIROL	Cytochrome b	0.00	-	end	9 *					380
Q6XBW7 UniProt NPD GO	CYB_VIVIN	Cytochrome b	0.00	-	end	9 *					379
Q71FI9 UniProt NPD GO	CYB_VIVME	Cytochrome b	0.00	-	end	9 *					379
Q71FJ0 UniProt NPD GO	CYB_VIVTA	Cytochrome b	0.00	-	end	9 *					379
Q71FI8 UniProt NPD GO	CYB_VIVZI	Cytochrome b	0.00	-	end	9 *					379
Q3ZED1 UniProt NPD GO	CYB_VULVU	Cytochrome b	0.00	-	end	9 *					379
P07747 UniProt NPD GO	CYB_WHEAT	Cytochrome b	0.00	-	end	9 *					398
Q8M4D6 UniProt NPD GO	CYB_WILCA	Cytochrome b	0.00	-	end	9 *					380
P00160 UniProt NPD GO	CYB_XENLA	Cytochrome b	0.00	-	end	9 *					380
Q36266 UniProt NPD GO	CYB_ZALCA	Cytochrome b	0.00	-	end	9 *					379
Q9XNN1 UniProt NPD GO	CYB_ZAPTR	Cytochrome b	0.00	-	end	9 *					379
Q36262 UniProt NPD GO	CYB_ZIPCA	Cytochrome b	0.00	-	end	9 *					379
P29632 UniProt NPD GO	CYB_AMBMA	Cytochrome b (Fragment)	0.00	-	end	8 *					308
P34860 UniProt NPD GO	CYB_AMBTI	Cytochrome b (Fragment)	0.00	-	exc	3 *					102
P29633 UniProt NPD GO	CYB_AMPST	Cytochrome b (Fragment)	0.00	-	end	8 *					308
P56629 UniProt NPD GO	CYB_ASPFL	Cytochrome b (Fragment)	0.00	-	end	2 *					145
P56630 UniProt NPD GO	CYB_ASPFU	Cytochrome b (Fragment)	0.00	-	end	2 *					145
P56631 UniProt NPD GO	CYB_ASPTE	Cytochrome b (Fragment)	0.00	-	end	2 *					140
P29635 UniProt NPD GO	CYB_COLRU	Cytochrome b (Fragment)	0.00	-	end	7 *					308
P92600 UniProt NPD GO	CYB_CORCX	Cytochrome b (Fragment)	0.00	-	end	8 *					308
P16359 UniProt NPD GO	CYB_DIPCA	Cytochrome b (Fragment)	0.00	-	mit	1 *					79
P16358 UniProt NPD GO	CYB_DIPHE	Cytochrome b (Fragment)	0.00	-	mit	2 *					79
P16357 UniProt NPD GO	CYB_DIPPA	Cytochrome b (Fragment)	0.00	-	mit	2 *					79
P51941 UniProt NPD GO	CYB_DROSU	Cytochrome b (Fragment)	0.00	-	end	4 *					166
P29665 UniProt NPD GO	CYB_GEOSD	Cytochrome b (Fragment)	0.00	-	nuc	3 *					96
Q7YD73 UniProt NPD GO	CYB_HYPSA	Cytochrome b (Fragment)	0.00	-	end	9 *					367
Q36590 UniProt NPD GO	CYB_NYCLA	Cytochrome b (Fragment)	0.00	-	end	4 *					176
P29638 UniProt NPD GO	CYB_PARIN	Cytochrome b (Fragment)	0.00	-	end	8 *					308
P34862 UniProt NPD GO	CYB_PLEYO	Cytochrome b (Fragment)	0.00	-	end	3 *					102
P16363 UniProt NPD GO	CYB_POMIS	Cytochrome b (Fragment)	0.00	-	end	8 *					308
P29630 UniProt NPD GO	CYB_POMRU	Cytochrome b (Fragment)	0.00	-	end	8 *					308
P29631 UniProt NPD GO	CYB_POMTE	Cytochrome b (Fragment)	0.00	-	end	8 *					308
Q8SG72 UniProt NPD GO	CYB_RAPCU	Cytochrome b (Fragment)	0.00	-	end	5 *					267
P34864 UniProt NPD GO	CYB_SARCH	Cytochrome b (Fragment)	0.00	-	end	5 *					199
O79446 UniProt NPD GO	CYB_SORAC	Cytochrome b (Fragment)	0.00	-	end	8 *					336
O79447 UniProt NPD GO	CYB_SORAL	Cytochrome b (Fragment)	0.00	-	end	8 *					336
O79980 UniProt NPD GO	CYB_SORAS	Cytochrome b (Fragment)	0.00	-	end	8 *					336

You are viewing entries 93801 to 93850 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.