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
Q9T9A6 UniProt NPD GO	CYB_OREOR	Cytochrome b	0.00	-	end	9 *					379
O79440 UniProt NPD GO	CYB_ORYDA	Cytochrome b	0.00	-	end	9 *					379
Q955G6 UniProt NPD GO	CYB_ORYGA	Cytochrome b	0.00	-	end	9 *					379
Q9T9A8 UniProt NPD GO	CYB_ORYLE	Cytochrome b	0.00	-	end	9 *					379
P14833 UniProt NPD GO	CYB_ORYSA	Cytochrome b	0.00	-	end	9 *					397
Q678S2 UniProt NPD GO	CYB_OTABY	Cytochrome b	0.00	-	end	9 *					379
Q9G3T7 UniProt NPD GO	CYB_OUROU	Cytochrome b	0.00	-	end	9 *					379
O78778 UniProt NPD GO	CYB_OVIAD	Cytochrome b	0.00	-	end	9 *					379
O78779 UniProt NPD GO	CYB_OVIDA	Cytochrome b	0.00	-	end	9 *					379
O78780 UniProt NPD GO	CYB_OVIVI	Cytochrome b	0.00	-	end	9 *					379
O78775 UniProt NPD GO	CYB_PANHO	Cytochrome b	0.00	-	end	9 *					379
Q35506 UniProt NPD GO	CYB_PANLE	Cytochrome b	0.00	-	end	9 *					379
P68090 UniProt NPD GO	CYB_PANTI	Cytochrome b	0.00	-	end	9 *					379
P68091 UniProt NPD GO	CYB_PANTS	Cytochrome b	0.00	-	end	9 *					379
Q9MED6 UniProt NPD GO	CYB_PARAM	Cytochrome b	0.00	-	end	9 *					380
Q9MDF2 UniProt NPD GO	CYB_PARGU	Cytochrome b	0.00	-	end	9 *					380
P12778 UniProt NPD GO	CYB_PARLI	Cytochrome b	0.00	-	end	9 *					380
Q35516 UniProt NPD GO	CYB_PARMI	Cytochrome b	0.00	-	end	9 *					380
Q37078 UniProt NPD GO	CYB_PARRA	Cytochrome b	0.00	-	end	9 *					380
Q35621 UniProt NPD GO	CYB_PARRB	Cytochrome b	0.00	-	end	9 *					380
Q35618 UniProt NPD GO	CYB_PARRU	Cytochrome b	0.00	-	end	9 *					380
P15585 UniProt NPD GO	CYB_PARTE	Cytochrome b	0.00	-	end	9 *					391
Q94PA3 UniProt NPD GO	CYB_PASCY	Cytochrome b	0.00	-	end	9 *					380
Q950C2 UniProt NPD GO	CYB_PASMO	Cytochrome b	0.00	-	end	9 *					380
Q9XKK2 UniProt NPD GO	CYB_PASSE	Cytochrome b	0.00	-	end	9 *					380
Q9B1X4 UniProt NPD GO	CYB_PENFU	Cytochrome b	0.00	-	end	9 *					379
Q6V9D6 UniProt NPD GO	CYB_PENMA	Cytochrome b	0.00	-	end	9 *					386
P92717 UniProt NPD GO	CYB_PERNA	Cytochrome b	0.00	-	end	9 *					381
Q8M708 UniProt NPD GO	CYB_PHAAE	Cytochrome b	0.00	-	end	9 *					379
Q8M706 UniProt NPD GO	CYB_PHAAF	Cytochrome b	0.00	-	end	9 *					379
Q35457 UniProt NPD GO	CYB_PHOGR	Cytochrome b	0.00	-	end	9 *					379
Q9GAM6 UniProt NPD GO	CYB_PHYAH	Cytochrome b	0.00	-	end	9 *					379
Q35522 UniProt NPD GO	CYB_PHYME	Cytochrome b	0.00	-	end	10 *					383
P24964 UniProt NPD GO	CYB_PIG	Cytochrome b	0.00	-	end	9 *					379
Q7YD75 UniProt NPD GO	CYB_PIPAB	Cytochrome b	0.00	-	end	9 *					379
O21217 UniProt NPD GO	CYB_PIPKU	Cytochrome b	0.00	-	end	9 *					379
O21220 UniProt NPD GO	CYB_PIPNA	Cytochrome b	0.00	-	end	9 *					379
O21223 UniProt NPD GO	CYB_PIPPI	Cytochrome b	0.00	-	end	9 *					379
Q36654 UniProt NPD GO	CYB_PIPSU	Cytochrome b	0.00	-	end	9 *					379
P81376 UniProt NPD GO	CYB_PLAGA	Cytochrome b	0.00	-	end	6 *					300
Q02655 UniProt NPD GO	CYB_PODAN	Cytochrome b	0.00	-	end	8 *					387
Q8M3J6 UniProt NPD GO	CYB_POEOC	Cytochrome b	0.00	-	end	9 *					379
Q71FI6 UniProt NPD GO	CYB_POIRI	Cytochrome b	0.00	-	end	9 *					379
Q71E87 UniProt NPD GO	CYB_PRIPR	Cytochrome b	0.00	-	end	9 *					379
Q6ELU7 UniProt NPD GO	CYB_PRORA	Cytochrome b	0.00	-	end	9 *					379
Q6ELU9 UniProt NPD GO	CYB_PRORU	Cytochrome b	0.00	-	end	9 *					379
Q6ELU8 UniProt NPD GO	CYB_PROSA	Cytochrome b	0.00	-	end	8 *					379
Q9XP68 UniProt NPD GO	CYB_PSENG	Cytochrome b	0.00	-	end	9 *					379
O78933 UniProt NPD GO	CYB_PTEBR	Cytochrome b	0.00	-	end	9 *					379
Q9G6M3 UniProt NPD GO	CYB_PTEDA	Cytochrome b	0.00	-	end	9 *					379

You are viewing entries 93651 to 93700 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.