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
Q1XIP1 UniProt NPD GO	CYB_ANOSQ	Cytochrome b	0.00	-	end	9 *					379
P24992 UniProt NPD GO	CYB_ANTAM	Cytochrome b	0.00	-	end	9 *					379
O78927 UniProt NPD GO	CYB_AONCA	Cytochrome b	0.00	-	end	9 *					379
Q8W8W1 UniProt NPD GO	CYB_APHAU	Cytochrome b	0.00	-	end	9 *					380
P92493 UniProt NPD GO	CYB_APHCE	Cytochrome b	0.00	-	end	9 *					380
P42792 UniProt NPD GO	CYB_ARATH	Cytochrome b	0.00	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				393
Q33697 UniProt NPD GO	CYB_ARCFO	Cytochrome b	0.00	-	end	9 *					379
Q95719 UniProt NPD GO	CYB_ARTAD	Cytochrome b	0.00	-	end	9 *					379
Q6DUL2 UniProt NPD GO	CYB_ARTAM	Cytochrome b	0.00	-	end	9 *					379
Q95718 UniProt NPD GO	CYB_ARTAZ	Cytochrome b	0.00	-	end	9 *					379
Q95726 UniProt NPD GO	CYB_ARTCI	Cytochrome b	0.00	-	end	9 *					379
Q95723 UniProt NPD GO	CYB_ARTCO	Cytochrome b	0.00	-	end	9 *					379
Q95728 UniProt NPD GO	CYB_ARTFI	Cytochrome b	0.00	-	end	9 *					379
Q95727 UniProt NPD GO	CYB_ARTFR	Cytochrome b	0.00	-	end	9 *					379
Q95731 UniProt NPD GO	CYB_ARTGA	Cytochrome b	0.00	-	end	9 *					379
Q95729 UniProt NPD GO	CYB_ARTGG	Cytochrome b	0.00	-	end	9 *					379
Q95730 UniProt NPD GO	CYB_ARTGW	Cytochrome b	0.00	-	end	9 *					379
Q95734 UniProt NPD GO	CYB_ARTHA	Cytochrome b	0.00	-	end	9 *					379
Q95735 UniProt NPD GO	CYB_ARTHI	Cytochrome b	0.00	-	end	9 *					379
Q95737 UniProt NPD GO	CYB_ARTIO	Cytochrome b	0.00	-	end	9 *					379
Q95736 UniProt NPD GO	CYB_ARTIT	Cytochrome b	0.00	-	end	9 *					379
Q95738 UniProt NPD GO	CYB_ARTJA	Cytochrome b	0.00	-	end	9 *					379
Q95739 UniProt NPD GO	CYB_ARTLI	Cytochrome b	0.00	-	end	9 *					379
Q95741 UniProt NPD GO	CYB_ARTOB	Cytochrome b	0.00	-	end	9 *					379
Q95744 UniProt NPD GO	CYB_ARTPH	Cytochrome b	0.00	-	end	9 *					379
Q95745 UniProt NPD GO	CYB_ARTPL	Cytochrome b	0.00	-	end	9 *					379
Q37713 UniProt NPD GO	CYB_ARTSF	Cytochrome b	0.00	-	end	9 *					381
Q95750 UniProt NPD GO	CYB_ARTTL	Cytochrome b	0.00	-	end	9 *					379
Q33798 UniProt NPD GO	CYB_ASPNG	Cytochrome b	0.00	-	end	9 *					385
Q3LTW2 UniProt NPD GO	CYB_ASPTU	Cytochrome b	0.00	-	end	9 *					385
Q5VJ60 UniProt NPD GO	CYB_AVALA	Cytochrome b	0.00	-	end	9 *					379
Q5UVI4 UniProt NPD GO	CYB_AXIAX	Cytochrome b	0.00	-	end	9 *					379
Q36324 UniProt NPD GO	CYB_BABBA	Cytochrome b	0.00	-	end	9 *					379
P41285 UniProt NPD GO	CYB_BALMU	Cytochrome b	0.00	-	end	9 *					379
Q85IN3 UniProt NPD GO	CYB_BASAS	Cytochrome b	0.00	-	end	9 *					379
Q951T6 UniProt NPD GO	CYB_BASCU	Cytochrome b	0.00	-	end	9 *					380
O47420 UniProt NPD GO	CYB_BEAHU	Cytochrome b	0.00	-	end	9 *					379
Q9T9C1 UniProt NPD GO	CYB_BISBI	Cytochrome b	0.00	-	end	9 *					379
O20998 UniProt NPD GO	CYB_BISBO	Cytochrome b	0.00	-	end	9 *					379
Q8WCK9 UniProt NPD GO	CYB_BLABR	Cytochrome b	0.00	-	end	9 *					379
Q8WCL1 UniProt NPD GO	CYB_BLACA	Cytochrome b	0.00	-	end	9 *					379
Q5UVI6 UniProt NPD GO	CYB_BLADC	Cytochrome b	0.00	-	end	9 *					379
Q8W822 UniProt NPD GO	CYB_BLAHY	Cytochrome b	0.00	-	end	9 *					379
P92583 UniProt NPD GO	CYB_BOSJA	Cytochrome b	0.00	-	end	9 *					379
P00157 UniProt NPD GO	CYB_BOVIN	Cytochrome b	0.00	-	end	9 *				2A06	379
Q9T3S9 UniProt NPD GO	CYB_BRABT	Cytochrome b	0.00	-	end	9 *					380
Q6ELW3 UniProt NPD GO	CYB_BRAID	Cytochrome b	0.00	-	end	9 *					379
Q33950 UniProt NPD GO	CYB_BUBBU	Cytochrome b	0.00	-	end	9 *					379
P92870 UniProt NPD GO	CYB_BUBDE	Cytochrome b	0.00	-	end	9 *					379
P92584 UniProt NPD GO	CYB_BUBMI	Cytochrome b	0.00	-	end	9 *					379

You are viewing entries 93351 to 93400 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.