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
Q9XP89 UniProt NPD GO	CYB_SMIAI	Cytochrome b	0.01	-	end	9 *					381
O79451 UniProt NPD GO	CYB_SORCI	Cytochrome b	0.01	-	end	9 *					379
Q94QQ7 UniProt NPD GO	CYB_SORFM	Cytochrome b	0.01	-	end	9 *					379
O79993 UniProt NPD GO	CYB_SORFU	Cytochrome b	0.01	-	end	9 *					379
O79452 UniProt NPD GO	CYB_SORHA	Cytochrome b	0.01	-	end	9 *					379
O79453 UniProt NPD GO	CYB_SORHY	Cytochrome b	0.01	-	end	9 *					379
O80005 UniProt NPD GO	CYB_SORIS	Cytochrome b	0.01	-	end	9 *					379
Q8SE00 UniProt NPD GO	CYB_SORJA	Cytochrome b	0.01	-	end	9 *					379
O79454 UniProt NPD GO	CYB_SORMI	Cytochrome b	0.01	-	end	9 *					379
O79455 UniProt NPD GO	CYB_SORMN	Cytochrome b	0.01	-	end	9 *					379
O79969 UniProt NPD GO	CYB_SORMO	Cytochrome b	0.01	-	end	9 *					379
O21416 UniProt NPD GO	CYB_SORMR	Cytochrome b	0.01	-	end	9 *					379
O79460 UniProt NPD GO	CYB_SORPA	Cytochrome b	0.01	-	end	9 *					379
Q8SE72 UniProt NPD GO	CYB_SORPE	Cytochrome b	0.01	-	end	9 *					379
O79967 UniProt NPD GO	CYB_SORSM	Cytochrome b	0.01	-	end	9 *					379
O79465 UniProt NPD GO	CYB_SORTR	Cytochrome b	0.01	-	end	9 *					379
O80019 UniProt NPD GO	CYB_SORVA	Cytochrome b	0.01	-	end	9 *					379
Q9TF74 UniProt NPD GO	CYB_SPEER	Cytochrome b	0.01	-	end	9 *					379
Q9TF49 UniProt NPD GO	CYB_SPEMA	Cytochrome b	0.01	-	end	9 *					379
Q9T3Y2 UniProt NPD GO	CYB_SPEMU	Cytochrome b	0.01	-	end	9 *					379
Q9TF10 UniProt NPD GO	CYB_SPEPE	Cytochrome b	0.01	-	end	9 *					379
Q9TF73 UniProt NPD GO	CYB_SPERE	Cytochrome b	0.01	-	end	9 *					379
Q9TF93 UniProt NPD GO	CYB_SPESP	Cytochrome b	0.01	-	end	9 *					379
Q9TF17 UniProt NPD GO	CYB_SPETE	Cytochrome b	0.01	-	end	9 *					379
P34874 UniProt NPD GO	CYB_SPHLE	Cytochrome b	0.01	-	end	9 *					381
P68092 UniProt NPD GO	CYB_STEAT	Cytochrome b	0.01	-	end	9 *					379
P68093 UniProt NPD GO	CYB_STECL	Cytochrome b	0.01	-	end	9 *					379
P68094 UniProt NPD GO	CYB_STECO	Cytochrome b	0.01	-	end	9 *					379
P68095 UniProt NPD GO	CYB_STEFR	Cytochrome b	0.01	-	end	9 *					379
Q1XIQ4 UniProt NPD GO	CYB_SUNST	Cytochrome b	0.01	-	end	9 *					379
Q8M703 UniProt NPD GO	CYB_SUSBA	Cytochrome b	0.01	-	end	9 *					379
Q9T9B9 UniProt NPD GO	CYB_SYNCA	Cytochrome b	0.01	-	end	9 *					379
O63699 UniProt NPD GO	CYB_TAPTE	Cytochrome b	0.01	-	end	9 *					379
O47488 UniProt NPD GO	CYB_TARBA	Cytochrome b	0.01	-	end	9 *					379
O78937 UniProt NPD GO	CYB_TAXTA	Cytochrome b	0.01	-	end	9 *					379
O79230 UniProt NPD GO	CYB_THAAN	Cytochrome b	0.01	-	end	9 *					380
O47976 UniProt NPD GO	CYB_THOBO	Cytochrome b	0.01	-	end	9 *					380
Q9XNX1 UniProt NPD GO	CYB_THODA	Cytochrome b	0.01	-	end	9 *					381
P24965 UniProt NPD GO	CYB_TRANA	Cytochrome b	0.01	-	end	9 *					379
Q8SEJ1 UniProt NPD GO	CYB_TRICS	Cytochrome b	0.01	-	end	9 *					381
Q9T9J2 UniProt NPD GO	CYB_TROMR	Cytochrome b	0.01	-	end	9 *					380
Q33568 UniProt NPD GO	CYB_TRYBO	Cytochrome b	0.01	-	end	10 *					372
Q9TDJ9 UniProt NPD GO	CYB_TURTR	Cytochrome b	0.01	-	end	9 *					379
O20546 UniProt NPD GO	CYB_TYMBA	Cytochrome b	0.01	-	end	9 *					379
Q8LWM4 UniProt NPD GO	CYB_URIAL	Cytochrome b	0.01	-	end	9 *					380
Q8LWM2 UniProt NPD GO	CYB_URILO	Cytochrome b	0.01	-	end	9 *					380
Q85DE4 UniProt NPD GO	CYB_UROPI	Cytochrome b	0.01	-	end	9 *					379
Q9TDT5 UniProt NPD GO	CYB_UROTA	Cytochrome b	0.01	-	end	9 *					379
Q36209 UniProt NPD GO	CYB_URSTH	Cytochrome b	0.01	-	end	9 *					379
Q36229 UniProt NPD GO	CYB_VARVR	Cytochrome b	0.01	-	end	9 *					379

You are viewing entries 87551 to 87600 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.