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
O79216 UniProt NPD GO	CYB_PACTU	Cytochrome b	0.01	-	end	9 *					380
Q35377 UniProt NPD GO	CYB_PARAP	Cytochrome b	0.01	-	end	9 *					381
Q85DF8 UniProt NPD GO	CYB_PARBE	Cytochrome b	0.01	-	end	9 *					379
Q9T9C8 UniProt NPD GO	CYB_PAROL	Cytochrome b	0.01	-	end	9 *					380
Q9ZZT8 UniProt NPD GO	CYB_PEA	Cytochrome b	0.01	-	end	9 *					392
O47714 UniProt NPD GO	CYB_PELCP	Cytochrome b	0.01	-	end	9 *					379
O79218 UniProt NPD GO	CYB_PELGA	Cytochrome b	0.01	-	end	9 *					380
O79217 UniProt NPD GO	CYB_PELMA	Cytochrome b	0.01	-	end	9 *					380
Q9XNU5 UniProt NPD GO	CYB_PERTU	Cytochrome b	0.01	-	end	9 *					381
Q9T7P1 UniProt NPD GO	CYB_PETCO	Cytochrome b	0.01	-	end	9 *					379
O79936 UniProt NPD GO	CYB_PHAAA	Cytochrome b	0.01	-	end	9 *					380
Q9TEU7 UniProt NPD GO	CYB_PHACI	Cytochrome b	0.01	-	end	9 *					381
Q35425 UniProt NPD GO	CYB_PHADO	Cytochrome b	0.01	-	end	9 *					381
Q5VJ57 UniProt NPD GO	CYB_PHAFU	Cytochrome b	0.01	-	end	9 *					379
Q9XNN3 UniProt NPD GO	CYB_PHEIN	Cytochrome b	0.01	-	end	9 *					380
Q35438 UniProt NPD GO	CYB_PHOFA	Cytochrome b	0.01	-	end	9 *					379
Q35468 UniProt NPD GO	CYB_PHOHI	Cytochrome b	0.01	-	end	9 *					379
Q35505 UniProt NPD GO	CYB_PHOLR	Cytochrome b	0.01	-	end	9 *					379
Q00530 UniProt NPD GO	CYB_PHOVI	Cytochrome b	0.01	-	end	9 *					379
Q9ZZF6 UniProt NPD GO	CYB_PHYXA	Cytochrome b	0.01	-	end	9 *					381
Q8LW83 UniProt NPD GO	CYB_PINIM	Cytochrome b	0.01	-	end	9 *					380
Q94S78 UniProt NPD GO	CYB_PLABI	Cytochrome b	0.01	-	end	9 *					380
O79657 UniProt NPD GO	CYB_POLBI	Cytochrome b	0.01	-	end	9 *					380
Q9G2S5 UniProt NPD GO	CYB_POLSP	Cytochrome b	0.01	-	end	9 *					380
Q6ELU6 UniProt NPD GO	CYB_PROCS	Cytochrome b	0.01	-	end	9 *					379
Q9G2U7 UniProt NPD GO	CYB_PROCY	Cytochrome b	0.01	-	end	9 *					379
Q5VJ61 UniProt NPD GO	CYB_PRODD	Cytochrome b	0.01	-	end	9 *					379
O79222 UniProt NPD GO	CYB_PROPA	Cytochrome b	0.01	-	end	9 *					380
Q35677 UniProt NPD GO	CYB_PROTA	Cytochrome b	0.01	-	end	9 *					379
O79223 UniProt NPD GO	CYB_PROWE	Cytochrome b	0.01	-	end	9 *					380
O78782 UniProt NPD GO	CYB_PSENA	Cytochrome b	0.01	-	end	9 *					379
O79224 UniProt NPD GO	CYB_PTEHY	Cytochrome b	0.01	-	end	9 *					380
O79225 UniProt NPD GO	CYB_PUFNA	Cytochrome b	0.01	-	end	9 *					380
O79226 UniProt NPD GO	CYB_PUFOP	Cytochrome b	0.01	-	end	9 *					380
Q35653 UniProt NPD GO	CYB_PUFTE	Cytochrome b	0.01	-	end	9 *					380
O79227 UniProt NPD GO	CYB_PYGAN	Cytochrome b	0.01	-	end	8 *					380
Q9T6R3 UniProt NPD GO	CYB_RANRU	Cytochrome b	0.01	-	end	8 *					380
P00159 UniProt NPD GO	CYB_RAT	Cytochrome b	0.01	-	end	9 *					380
Q9XLE0 UniProt NPD GO	CYB_REDRE	Cytochrome b	0.01	-	end	9 *					379
O99828 UniProt NPD GO	CYB_RHISA	Cytochrome b	0.01	-	end	8 *					358
Q8M354 UniProt NPD GO	CYB_SACCA	Cytochrome b	0.01	-	end	9 *					390
Q35819 UniProt NPD GO	CYB_SACDO	Cytochrome b	0.01	-	end	9 *					385
Q7YEV2 UniProt NPD GO	CYB_SACSE	Cytochrome b	0.01	-	end	9 *					385
Q85PK7 UniProt NPD GO	CYB_SALCN	Cytochrome b	0.01	-	end	9 *					379
Q35925 UniProt NPD GO	CYB_SALSA	Cytochrome b	0.01	-	end	9 *					380
P29671 UniProt NPD GO	CYB_SALTR	Cytochrome b	0.01	-	end	9 *					380
Q35861 UniProt NPD GO	CYB_SARHA	Cytochrome b	0.01	-	end	9 *					381
Q85C43 UniProt NPD GO	CYB_SCAOR	Cytochrome b	0.01	-	end	9 *					379
Q85DF2 UniProt NPD GO	CYB_SCATO	Cytochrome b	0.01	-	end	9 *					379
O79413 UniProt NPD GO	CYB_SCYCA	Cytochrome b	0.01	-	end	9 *					381

You are viewing entries 87501 to 87550 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.