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
Q5VJ44 UniProt NPD GO	CYB_EUOEL	Cytochrome b	0.01	-	end	9 *					379
Q85PP1 UniProt NPD GO	CYB_FOSFO	Cytochrome b	0.01	-	end	9 *					379
O79201 UniProt NPD GO	CYB_FREGA	Cytochrome b	0.01	-	end	9 *					380
O79200 UniProt NPD GO	CYB_FRETR	Cytochrome b	0.01	-	end	9 *					380
O79202 UniProt NPD GO	CYB_FULGL	Cytochrome b	0.01	-	end	9 *					380
Q85PN8 UniProt NPD GO	CYB_GALFA	Cytochrome b	0.01	-	end	9 *					379
Q5VJ45 UniProt NPD GO	CYB_GALGR	Cytochrome b	0.01	-	end	9 *					379
Q9G9J7 UniProt NPD GO	CYB_GALMA	Cytochrome b	0.01	-	end	9 *					379
Q5VJ42 UniProt NPD GO	CYB_GALSE	Cytochrome b	0.01	-	end	9 *					379
O79203 UniProt NPD GO	CYB_GARNE	Cytochrome b	0.01	-	end	9 *					380
O48372 UniProt NPD GO	CYB_GLASA	Cytochrome b	0.01	-	end	9 *					379
Q34677 UniProt NPD GO	CYB_GLIVE	Cytochrome b	0.01	-	end	9 *					382
Q34534 UniProt NPD GO	CYB_GRUAN	Cytochrome b	0.01	-	end	8 *					380
Q33954 UniProt NPD GO	CYB_GRUCA	Cytochrome b	0.01	-	end	8 *					380
Q34607 UniProt NPD GO	CYB_GRUNI	Cytochrome b	0.01	-	end	9 *					380
Q34653 UniProt NPD GO	CYB_GRURU	Cytochrome b	0.01	-	end	8 *					380
Q9T7Q5 UniProt NPD GO	CYB_GYMRO	Cytochrome b	0.01	-	end	9 *					380
P29637 UniProt NPD GO	CYB_GYMTI	Cytochrome b	0.01	-	end	9 *					380
O79204 UniProt NPD GO	CYB_HALCA	Cytochrome b	0.01	-	end	9 *					380
P38593 UniProt NPD GO	CYB_HALGR	Cytochrome b	0.01	-	end	9 *					379
Q4VKI6 UniProt NPD GO	CYB_HEMHY	Cytochrome b	0.01	-	end	9 *					379
Q4VKI7 UniProt NPD GO	CYB_HEMJA	Cytochrome b	0.01	-	end	9 *					379
O21175 UniProt NPD GO	CYB_HERCA	Cytochrome b	0.01	-	end	9 *					380
Q8W9L2 UniProt NPD GO	CYB_HETGU	Cytochrome b	0.01	-	end	8 *					379
Q34717 UniProt NPD GO	CYB_HIPEQ	Cytochrome b	0.01	-	end	9 *					379
Q34760 UniProt NPD GO	CYB_HIPNI	Cytochrome b	0.01	-	end	9 *					379
P48665 UniProt NPD GO	CYB_HORSE	Cytochrome b	0.01	-	end	9 *					379
Q34732 UniProt NPD GO	CYB_HYDLE	Cytochrome b	0.01	-	end	9 *					379
Q8WA39 UniProt NPD GO	CYB_HYLAL	Cytochrome b	0.01	-	end	9 *					380
Q95711 UniProt NPD GO	CYB_HYLLA	Cytochrome b	0.01	-	end	9 *					380
O47892 UniProt NPD GO	CYB_HYLLE	Cytochrome b	0.01	-	end	9 *					380
O47893 UniProt NPD GO	CYB_HYLME	Cytochrome b	0.01	-	end	9 *					380
Q8LZ94 UniProt NPD GO	CYB_HYPTE	Cytochrome b	0.01	-	end	9 *					378
Q5VJ58 UniProt NPD GO	CYB_INDIN	Cytochrome b	0.01	-	end	9 *					379
P34870 UniProt NPD GO	CYB_ISUOX	Cytochrome b	0.01	-	end	9 *					381
P81381 UniProt NPD GO	CYB_KLULA	Cytochrome b	0.01	-	end	9 *					386
O79360 UniProt NPD GO	CYB_KOBME	Cytochrome b	0.01	-	end	9 *					379
O03810 UniProt NPD GO	CYB_KOGBR	Cytochrome b	0.01	-	end	9 *					379
Q9B7W3 UniProt NPD GO	CYB_KOGSI	Cytochrome b	0.01	-	end	9 *					379
O48089 UniProt NPD GO	CYB_LACVV	Cytochrome b	0.01	-	end	9 *					380
Q9TDJ6 UniProt NPD GO	CYB_LAGHO	Cytochrome b	0.01	-	end	9 *					379
Q34916 UniProt NPD GO	CYB_LAMPA	Cytochrome b	0.01	-	end	9 *					379
Q36227 UniProt NPD GO	CYB_LAMVI	Cytochrome b	0.01	-	end	9 *					379
Q34902 UniProt NPD GO	CYB_LANLU	Cytochrome b	0.01	-	end	9 *					380
P38594 UniProt NPD GO	CYB_LEPWE	Cytochrome b	0.01	-	end	9 *					379
Q34893 UniProt NPD GO	CYB_LESIN	Cytochrome b	0.01	-	end	9 *					381
O48094 UniProt NPD GO	CYB_LIAMS	Cytochrome b	0.01	-	end	10 *					371
O79207 UniProt NPD GO	CYB_MACGA	Cytochrome b	0.01	-	end	9 *					380
O79208 UniProt NPD GO	CYB_MACHA	Cytochrome b	0.01	-	end	9 *					380
P92671 UniProt NPD GO	CYB_MACRO	Cytochrome b	0.01	-	end	9 *					381

You are viewing entries 87401 to 87450 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.