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
Q9XNV4 UniProt NPD GO	CYB_AULMI	Cytochrome b	0.02	-	end	9 *					381
Q33987 UniProt NPD GO	CYB_BALPA	Cytochrome b	0.02	-	end	9 *					380
Q7GEV4 UniProt NPD GO	CYB_CANPA	Cytochrome b	0.02	-	end	9 *					384
P34866 UniProt NPD GO	CYB_CARPL	Cytochrome b	0.02	-	end	9 *					381
P34867 UniProt NPD GO	CYB_CARPO	Cytochrome b	0.02	-	end	9 *					381
O03520 UniProt NPD GO	CYB_CASBE	Cytochrome b	0.02	-	end	9 *					379
Q8SGA0 UniProt NPD GO	CYB_CHAAI	Cytochrome b	0.02	-	end	9 *					398
Q94TE4 UniProt NPD GO	CYB_CHLAG	Cytochrome b	0.02	-	end	9 *					379
Q9MR49 UniProt NPD GO	CYB_CICCI	Cytochrome b	0.02	-	end	9 *					380
Q9TEX8 UniProt NPD GO	CYB_CLEGL	Cytochrome b	0.02	-	end	9 *					380
O79925 UniProt NPD GO	CYB_COLLE	Cytochrome b	0.02	-	end	9 *					380
O79927 UniProt NPD GO	CYB_COLST	Cytochrome b	0.02	-	end	7 *					380
Q8SEP4 UniProt NPD GO	CYB_CROSH	Cytochrome b	0.02	-	end	9 *					379
Q94WX5 UniProt NPD GO	CYB_CTEME	Cytochrome b	0.02	-	end	9 *					379
Q9ZY14 UniProt NPD GO	CYB_CTEPE	Cytochrome b	0.02	-	end	9 *					379
Q94P21 UniProt NPD GO	CYB_CTETU	Cytochrome b	0.02	-	end	9 *					379
Q9MLI3 UniProt NPD GO	CYB_CYAFO	Cytochrome b	0.02	-	end	9 *					379
Q34300 UniProt NPD GO	CYB_DASBY	Cytochrome b	0.02	-	end	8 *					381
Q34302 UniProt NPD GO	CYB_DASCR	Cytochrome b	0.02	-	end	9 *					381
O03522 UniProt NPD GO	CYB_DASMA	Cytochrome b	0.02	-	end	9 *					381
O03812 UniProt NPD GO	CYB_DELLE	Cytochrome b	0.02	-	end	9 *					379
Q9XNV7 UniProt NPD GO	CYB_DELSU	Cytochrome b	0.02	-	end	9 *					380
Q9TDK2 UniProt NPD GO	CYB_DELTR	Cytochrome b	0.02	-	end	9 *					379
Q9GAW0 UniProt NPD GO	CYB_DIPNE	Cytochrome b	0.02	-	end	9 *					379
Q9GAW3 UniProt NPD GO	CYB_DIPOR	Cytochrome b	0.02	-	end	9 *					379
O03523 UniProt NPD GO	CYB_DRONO	Cytochrome b	0.02	-	end	9 *					379
O03713 UniProt NPD GO	CYB_DRYNI	Cytochrome b	0.02	-	end	9 *					379
O48076 UniProt NPD GO	CYB_ERYJA	Cytochrome b	0.02	-	end	8 *					371
O79198 UniProt NPD GO	CYB_EUDCH	Cytochrome b	0.02	-	end	9 *					380
O79199 UniProt NPD GO	CYB_EUDCY	Cytochrome b	0.02	-	end	9 *					380
O99799 UniProt NPD GO	CYB_EULMO	Cytochrome b	0.02	-	end	9 *					379
O48065 UniProt NPD GO	CYB_EUNNO	Cytochrome b	0.02	-	end	10 *					370
O21167 UniProt NPD GO	CYB_FALSP	Cytochrome b	0.02	-	end	9 *					380
O20644 UniProt NPD GO	CYB_FRAFR	Cytochrome b	0.02	-	end	9 *					380
Q5VJ41 UniProt NPD GO	CYB_GALDE	Cytochrome b	0.02	-	end	9 *					379
Q9G9J6 UniProt NPD GO	CYB_GALMO	Cytochrome b	0.02	-	end	9 *					379
Q5VJ67 UniProt NPD GO	CYB_HAPAU	Cytochrome b	0.02	-	end	9 *					379
P34869 UniProt NPD GO	CYB_HETFR	Cytochrome b	0.02	-	end	9 *					381
Q71FH2 UniProt NPD GO	CYB_HYAHY	Cytochrome b	0.02	-	end	9 *					379
Q9B9Z1 UniProt NPD GO	CYB_HYPCM	Cytochrome b	0.02	-	end	9 *					398
Q956S6 UniProt NPD GO	CYB_IGUIG	Cytochrome b	0.02	-	end	9 *					379
Q8HL93 UniProt NPD GO	CYB_INDPA	Cytochrome b	0.02	-	end	9 *					378
P34871 UniProt NPD GO	CYB_ISUPA	Cytochrome b	0.02	-	end	9 *					381
Q9TDL0 UniProt NPD GO	CYB_LAGAC	Cytochrome b	0.02	-	end	9 *					379
Q9TDL1 UniProt NPD GO	CYB_LAGAL	Cytochrome b	0.02	-	end	9 *					379
Q9TDL8 UniProt NPD GO	CYB_LAGOL	Cytochrome b	0.02	-	end	9 *					379
P29667 UniProt NPD GO	CYB_LEPOC	Cytochrome b	0.02	-	end	9 *					380
O48090 UniProt NPD GO	CYB_LIAAL	Cytochrome b	0.02	-	end	10 *					371
O48096 UniProt NPD GO	CYB_LIAOV	Cytochrome b	0.02	-	end	10 *					371
Q9MI64 UniProt NPD GO	CYB_LIPVE	Cytochrome b	0.02	-	end	9 *					379

You are viewing entries 82951 to 83000 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.