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
Q9B1N0 UniProt NPD GO	CYB_PTEDV	Cytochrome b	0.00	-	end	9 *					379
Q9B0S2 UniProt NPD GO	CYB_PTEGY	Cytochrome b	0.00	-	end	9 *					379
Q8SJZ4 UniProt NPD GO	CYB_PTEHP	Cytochrome b	0.00	-	end	9 *					379
Q94YL4 UniProt NPD GO	CYB_PTEJA	Cytochrome b	0.00	-	end	9 *					379
Q9B106 UniProt NPD GO	CYB_PTEMA	Cytochrome b	0.00	-	end	9 *					379
Q8WDK6 UniProt NPD GO	CYB_PTEPA	Cytochrome b	0.00	-	end	9 *					379
Q9B365 UniProt NPD GO	CYB_PTEPR	Cytochrome b	0.00	-	end	9 *					379
Q9B0Y1 UniProt NPD GO	CYB_PTEQU	Cytochrome b	0.00	-	end	9 *					379
Q9G3S4 UniProt NPD GO	CYB_PTESA	Cytochrome b	0.00	-	end	9 *					379
Q8SJZ1 UniProt NPD GO	CYB_PTEVA	Cytochrome b	0.00	-	end	9 *					379
Q3L701 UniProt NPD GO	CYB_PUMCO	Cytochrome b	0.00	-	end	9 *					379
P34863 UniProt NPD GO	CYB_RABIT	Cytochrome b	0.00	-	end	9 *					379
P16674 UniProt NPD GO	CYB_RANCA	Cytochrome b	0.00	-	end	9 *					380
Q9T6R5 UniProt NPD GO	CYB_RANDY	Cytochrome b	0.00	-	end	9 *					380
Q9T6R9 UniProt NPD GO	CYB_RANNI	Cytochrome b	0.00	-	end	8 *					380
O47718 UniProt NPD GO	CYB_RAPCA	Cytochrome b	0.00	-	end	9 *					379
O99338 UniProt NPD GO	CYB_RAPSH	Cytochrome b	0.00	-	end	9 *					379
Q9XLE1 UniProt NPD GO	CYB_REDFU	Cytochrome b	0.00	-	end	9 *					379
Q9G1F7 UniProt NPD GO	CYB_RHIAL	Cytochrome b	0.00	-	end	9 *					379
O21298 UniProt NPD GO	CYB_RHIFE	Cytochrome b	0.00	-	end	9 *					379
Q9GAM7 UniProt NPD GO	CYB_RHIFI	Cytochrome b	0.00	-	end	9 *					379
Q94VK4 UniProt NPD GO	CYB_RHIMO	Cytochrome b	0.00	-	end	9 *					379
Q3T4F1 UniProt NPD GO	CYB_RHIOR	Cytochrome b	0.00	-	end	9 *					386
Q94YE5 UniProt NPD GO	CYB_RHIPI	Cytochrome b	0.00	-	end	9 *					379
Q9GAM9 UniProt NPD GO	CYB_RHIPM	Cytochrome b	0.00	-	end	9 *					379
Q96071 UniProt NPD GO	CYB_RHIUN	Cytochrome b	0.00	-	end	9 *					379
Q9G6G3 UniProt NPD GO	CYB_ROMDI	Cytochrome b	0.00	-	end	9 *					379
Q94NF7 UniProt NPD GO	CYB_ROUAM	Cytochrome b	0.00	-	end	9 *					379
O78777 UniProt NPD GO	CYB_RUPPY	Cytochrome b	0.00	-	end	9 *					380
O78776 UniProt NPD GO	CYB_RUPRU	Cytochrome b	0.00	-	end	9 *					380
Q9T5N4 UniProt NPD GO	CYB_SAITA	Cytochrome b	0.00	-	end	9 *					380
O63848 UniProt NPD GO	CYB_SARGL	Cytochrome b	0.00	-	end	8 *					386
Q85PM6 UniProt NPD GO	CYB_SCAAQ	Cytochrome b	0.00	-	end	9 *					379
Q5DX17 UniProt NPD GO	CYB_SCAFU	Cytochrome b	0.00	-	end	9 *					379
Q94ZJ2 UniProt NPD GO	CYB_SCHCO	Cytochrome b	0.00	-	end	9 *					383
Q8HMZ7 UniProt NPD GO	CYB_SCHJP	Cytochrome b	0.00	-	end	9 *					389
Q8HQ92 UniProt NPD GO	CYB_SCHOT	Cytochrome b	0.00	-	end	9 *					387
P05501 UniProt NPD GO	CYB_SCHPO	Cytochrome b	0.00	-	end	9 *		mitochondrial inner membrane [TAS] ubiquinol-cytochrome-c reductase complex [TAS]			387
Q37064 UniProt NPD GO	CYB_SCIAB	Cytochrome b	0.00	-	end	9 *					378
Q35895 UniProt NPD GO	CYB_SCINI	Cytochrome b	0.00	-	end	9 *					379
Q35877 UniProt NPD GO	CYB_SELME	Cytochrome b	0.00	-	end	9 *					380
Q9TGL9 UniProt NPD GO	CYB_SELTH	Cytochrome b	0.00	-	end	9 *					379
Q8M4E2 UniProt NPD GO	CYB_SETRU	Cytochrome b	0.00	-	end	9 *					380
P24959 UniProt NPD GO	CYB_SHEEP	Cytochrome b	0.00	-	end	9 *					379
Q9XNU6 UniProt NPD GO	CYB_SIGHI	Cytochrome b	0.00	-	end	9 *					381
O47419 UniProt NPD GO	CYB_SIGLI	Cytochrome b	0.00	-	end	9 *					379
Q3T4C8 UniProt NPD GO	CYB_SMICU	Cytochrome b	0.00	-	end	10 *					396
P29757 UniProt NPD GO	CYB_SOLTU	Cytochrome b	0.00	-	end	9 *					392
Q9TF14 UniProt NPD GO	CYB_SPEAI	Cytochrome b	0.00	-	end	9 *					379
Q9TF51 UniProt NPD GO	CYB_SPEAR	Cytochrome b	0.00	-	end	9 *					379

You are viewing entries 93701 to 93750 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.