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
Q8WDV6 UniProt NPD GO	CYB_CRAFU	Cytochrome b	0.00	-	end	9 *					379
Q34106 UniProt NPD GO	CYB_CRAGG	Cytochrome b	0.00	-	end	9 *					379
Q34108 UniProt NPD GO	CYB_CRAGR	Cytochrome b	0.00	-	end	8 *					379
Q34107 UniProt NPD GO	CYB_CRAGY	Cytochrome b	0.00	-	end	8 *					379
Q34161 UniProt NPD GO	CYB_CRAME	Cytochrome b	0.00	-	end	9 *					379
Q8WDU1 UniProt NPD GO	CYB_CRATY	Cytochrome b	0.00	-	end	9 *					379
Q9T7N2 UniProt NPD GO	CYB_CRIEM	Cytochrome b	0.00	-	end	9 *					380
Q85PN7 UniProt NPD GO	CYB_CROOB	Cytochrome b	0.00	-	end	9 *					379
Q9B9G0 UniProt NPD GO	CYB_CRYFE	Cytochrome b	0.00	-	end	9 *					379
Q1XIJ0 UniProt NPD GO	CYB_CRYMA	Cytochrome b	0.00	-	end	9 *					379
Q8WCJ7 UniProt NPD GO	CYB_CRYPR	Cytochrome b	0.00	-	end	9 *					379
Q94WX2 UniProt NPD GO	CYB_CTETA	Cytochrome b	0.00	-	end	9 *					379
P48876 UniProt NPD GO	CYB_CYACA	Cytochrome b	0.00	-	end	9 *					384
P92599 UniProt NPD GO	CYB_CYACH	Cytochrome b	0.00	-	end	9 *					380
Q950C6 UniProt NPD GO	CYB_CYAST	Cytochrome b	0.00	-	end	9 *					380
Q94YL9 UniProt NPD GO	CYB_CYNBR	Cytochrome b	0.00	-	end	9 *					379
P24955 UniProt NPD GO	CYB_DAMDA	Cytochrome b	0.00	-	end	9 *					379
Q5UVJ0 UniProt NPD GO	CYB_DAMME	Cytochrome b	0.00	-	end	9 *					379
Q9T9A7 UniProt NPD GO	CYB_DAMPY	Cytochrome b	0.00	-	end	9 *					379
Q9XKK5 UniProt NPD GO	CYB_DASLA	Cytochrome b	0.00	-	end	8 *					380
O21337 UniProt NPD GO	CYB_DASNO	Cytochrome b	0.00	-	end	9 *					379
Q94S37 UniProt NPD GO	CYB_DAUCA	Cytochrome b	0.00	-	end	9 *					398
Q8M4C7 UniProt NPD GO	CYB_DENPI	Cytochrome b	0.00	-	end	9 *					380
Q85DD9 UniProt NPD GO	CYB_DESMS	Cytochrome b	0.00	-	end	9 *					379
P24954 UniProt NPD GO	CYB_DICBI	Cytochrome b	0.00	-	end	9 *					379
Q37311 UniProt NPD GO	CYB_DICDI	Cytochrome b	0.00	-	end	9 *					389
Q9MGM4 UniProt NPD GO	CYB_DROMA	Cytochrome b	0.00	-	end	9 *					378
P18935 UniProt NPD GO	CYB_DROME	Cytochrome b	0.00	-	end	9 *					378
Q9MGL5 UniProt NPD GO	CYB_DROSE	Cytochrome b	0.00	-	end	9 *					378
Q9MDZ9 UniProt NPD GO	CYB_DROSI	Cytochrome b	0.00	-	end	9 *					378
P07704 UniProt NPD GO	CYB_DROYA	Cytochrome b	0.00	-	end	9 *					378
Q33401 UniProt NPD GO	CYB_DUGDU	Cytochrome b	0.00	-	end	9 *					379
Q34473 UniProt NPD GO	CYB_ECHKA	Cytochrome b	0.00	-	end	9 *					381
Q6YDL7 UniProt NPD GO	CYB_ECTAL	Cytochrome b	0.00	-	end	9 *					379
Q85IN8 UniProt NPD GO	CYB_EIRBA	Cytochrome b	0.00	-	end	9 *					379
Q9T4R0 UniProt NPD GO	CYB_ELIMA	Cytochrome b	0.00	-	end	9 *					380
Q9T7S2 UniProt NPD GO	CYB_ELIMI	Cytochrome b	0.00	-	end	9 *					380
Q9XNV3 UniProt NPD GO	CYB_ELIMO	Cytochrome b	0.00	-	end	9 *					381
Q9T7Q9 UniProt NPD GO	CYB_ELIMY	Cytochrome b	0.00	-	end	9 *					380
Q9T443 UniProt NPD GO	CYB_ELIWE	Cytochrome b	0.00	-	end	9 *					380
P00161 UniProt NPD GO	CYB_EMENI	Cytochrome b	0.00	-	end	9 *					387
Q94YL5 UniProt NPD GO	CYB_EONSP	Cytochrome b	0.00	-	end	9 *					379
P29636 UniProt NPD GO	CYB_EPIAL	Cytochrome b	0.00	-	end	9 *					380
Q1XIM1 UniProt NPD GO	CYB_EPIMC	Cytochrome b	0.00	-	end	9 *					379
Q957C7 UniProt NPD GO	CYB_EPTFU	Cytochrome b	0.00	-	end	9 *					379
Q957C6 UniProt NPD GO	CYB_EPTNI	Cytochrome b	0.00	-	end	9 *					379
O21159 UniProt NPD GO	CYB_EPTSE	Cytochrome b	0.00	-	end	9 *					379
Q4VUY8 UniProt NPD GO	CYB_EROSE	Cytochrome b	0.00	-	end	9 *					379
Q5VJ65 UniProt NPD GO	CYB_EULCO	Cytochrome b	0.00	-	end	9 *					379
Q34471 UniProt NPD GO	CYB_EUMJU	Cytochrome b	0.00	-	end	9 *					379

You are viewing entries 93451 to 93500 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.