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
Q5DWG5 UniProt NPD GO	CYB_EURMC	Cytochrome b	0.00	-	end	9 *					379
Q9MQY3 UniProt NPD GO	CYB_EURMI	Cytochrome b	0.00	-	end	9 *					379
Q9TF32 UniProt NPD GO	CYB_EUTDO	Cytochrome b	0.00	-	end	9 *					379
P48886 UniProt NPD GO	CYB_FELCA	Cytochrome b	0.00	-	end	9 *					379
Q85PN6 UniProt NPD GO	CYB_FELSI	Cytochrome b	0.00	-	end	9 *					379
Q9B203 UniProt NPD GO	CYB_FICPA	Cytochrome b	0.00	-	end	9 *					380
Q85PP0 UniProt NPD GO	CYB_GALEE	Cytochrome b	0.00	-	end	9 *					379
Q5VJ46 UniProt NPD GO	CYB_GALGB	Cytochrome b	0.00	-	end	9 *					379
Q85IN7 UniProt NPD GO	CYB_GALVI	Cytochrome b	0.00	-	end	9 *					379
O48336 UniProt NPD GO	CYB_GAZGA	Cytochrome b	0.00	-	end	9 *					379
O78774 UniProt NPD GO	CYB_GAZGR	Cytochrome b	0.00	-	end	9 *					379
Q9T9B2 UniProt NPD GO	CYB_GAZSU	Cytochrome b	0.00	-	end	9 *					379
Q6XBV1 UniProt NPD GO	CYB_GENGE	Cytochrome b	0.00	-	end	9 *					379
Q6XBV6 UniProt NPD GO	CYB_GENMA	Cytochrome b	0.00	-	end	9 *					379
Q6XBW1 UniProt NPD GO	CYB_GENPA	Cytochrome b	0.00	-	end	9 *					379
Q6XBW8 UniProt NPD GO	CYB_GENTG	Cytochrome b	0.00	-	end	9 *					379
Q950B9 UniProt NPD GO	CYB_GEOAE	Cytochrome b	0.00	-	end	9 *					380
Q9TEZ5 UniProt NPD GO	CYB_GEOPI	Cytochrome b	0.00	-	end	9 *					379
Q8M4E6 UniProt NPD GO	CYB_GEOTR	Cytochrome b	0.00	-	end	9 *					380
P24957 UniProt NPD GO	CYB_GIRCA	Cytochrome b	0.00	-	end	9 *					379
Q9TF34 UniProt NPD GO	CYB_GLAVO	Cytochrome b	0.00	-	end	9 *					379
Q8WGG5 UniProt NPD GO	CYB_GLOLE	Cytochrome b	0.00	-	end	9 *					379
Q8WGG8 UniProt NPD GO	CYB_GLOLO	Cytochrome b	0.00	-	end	9 *					379
Q8W8Y1 UniProt NPD GO	CYB_GLOMN	Cytochrome b	0.00	-	end	9 *					379
Q33487 UniProt NPD GO	CYB_GLOSR	Cytochrome b	0.00	-	end	9 *					379
P56697 UniProt NPD GO	CYB_GULGU	Cytochrome b	0.00	-	end	9 *					379
O78783 UniProt NPD GO	CYB_HEMJE	Cytochrome b	0.00	-	end	9 *					379
Q85PN4 UniProt NPD GO	CYB_HERED	Cytochrome b	0.00	-	end	9 *					379
Q5I191 UniProt NPD GO	CYB_HERJA	Cytochrome b	0.00	-	end	9 *					379
O03363 UniProt NPD GO	CYB_HEXLI	Cytochrome b	0.00	-	end	9 *					379
Q9T9I2 UniProt NPD GO	CYB_HIMCH	Cytochrome b	0.00	-	end	8 *					380
Q9XKK0 UniProt NPD GO	CYB_HIMGE	Cytochrome b	0.00	-	end	9 *					380
Q33500 UniProt NPD GO	CYB_HIPAM	Cytochrome b	0.00	-	end	9 *					379
O47930 UniProt NPD GO	CYB_HYDIN	Cytochrome b	0.00	-	end	9 *					379
Q71E95 UniProt NPD GO	CYB_ICHAL	Cytochrome b	0.00	-	end	9 *					379
Q85IN6 UniProt NPD GO	CYB_ICTST	Cytochrome b	0.00	-	end	9 *					379
Q8M4C6 UniProt NPD GO	CYB_ICTVI	Cytochrome b	0.00	-	end	9 *					380
Q9B2F7 UniProt NPD GO	CYB_ISOMA	Cytochrome b	0.00	-	end	9 *					381
O99342 UniProt NPD GO	CYB_KOBEL	Cytochrome b	0.00	-	end	9 *					379
O78858 UniProt NPD GO	CYB_KOBKO	Cytochrome b	0.00	-	end	9 *					379
Q34891 UniProt NPD GO	CYB_LAMGL	Cytochrome b	0.00	-	end	9 *					379
Q94T68 UniProt NPD GO	CYB_LAMGT	Cytochrome b	0.00	-	end	9 *					380
Q34890 UniProt NPD GO	CYB_LAMGU	Cytochrome b	0.00	-	end	9 *					379
O03176 UniProt NPD GO	CYB_LATCH	Cytochrome b	0.00	-	end	9 *					380
Q8HG55 UniProt NPD GO	CYB_LECMU	Cytochrome b	0.00	-	end	9 *					385
P14548 UniProt NPD GO	CYB_LEITA	Cytochrome b	0.00	-	end	10 *					371
O47554 UniProt NPD GO	CYB_LEPAM	Cytochrome b	0.00	-	end	9 *					379
Q959V6 UniProt NPD GO	CYB_LEPBR	Cytochrome b	0.00	-	end	9 *					379
Q6ELV2 UniProt NPD GO	CYB_LEPCA	Cytochrome b	0.00	-	end	9 *					379
O47560 UniProt NPD GO	CYB_LEPCL	Cytochrome b	0.00	-	end	9 *					379

You are viewing entries 93501 to 93550 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.