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
P52495 UniProt NPD GO	UBA1_CANAL	Ubiquitin-activating enzyme E1 1 (Fragment)	0.01	-	cyt	0	Cytoplasm. Nucleus				205
Q803Y4 UniProt NPD GO	UFM1_BRARE	Ubiquitin-fold modifier 1 precursor	0.01	-	mit	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity). Also expressed diffusely in the c ...				90
Q6FIX7 UniProt NPD GO	HUB1_CANGA	Ubiquitin-like modifier HUB1	0.01	-	cyt	0					73
Q6Q546 UniProt NPD GO	HUB1_YEAST	Ubiquitin-like modifier HUB1	0.01	-	cyt	0		mating projection [IPI]		1M94	73
O94650 UniProt NPD GO	HUB1_SCHPO	Ubiquitin-like modifier hub1	0.01	-	cyt	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			73
Q9FGZ9 UniProt NPD GO	UBL5_ARATH	Ubiquitin-like protein 5	0.01	-	cyt	0	Cytoplasm (By similarity)				73
Q60435 UniProt NPD GO	UBIM_CRIGR	Ubiquitin-like protein FUBI (Arsenite-resistance protein)	0.01	-	cyt	0					74
P40554 UniProt NPD GO	URM1_YEAST	Ubiquitin-related modifier 1	0.01	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]		2AX5	99
O80517 UniProt NPD GO	BCB2_ARATH	Uclacyanin-2 precursor (Uclacyanin-II) (Blue copper-binding protein II) (BCB II) (Phytocyanin 2)	0.01	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			202
O57605 UniProt NPD GO	OPSUV_MELUD	Ultraviolet-sensitive opsin (Ultraviolet cone photoreceptor pigment)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				347
P42942 UniProt NPD GO	YG4I_YEAST	Uncharacterized GTP-binding protein YGR210C	0.01	-	cyt	0		cytoplasm [IDA]			411
Q9P7L4 UniProt NPD GO	YOS9_SCHPO	Uncharacterized hydrolase C21C3.09c (EC 3.-.-.-)	0.01	-	mit	0	Cytoplasm				221
Q9NX78 UniProt NPD GO	CN101_HUMAN	Uncharacterized protein C14orf101	0.01	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				707
Q13653 UniProt NPD GO	CO031_HUMAN	Uncharacterized protein C15orf31 (Pre-T/NK cell-associated protein 6H9A)	0.01	-	mit	0					57
P62248 UniProt NPD GO	CS010_BOVIN	Uncharacterized protein C19orf10 homolog precursor	0.01	-	exc	0	Secreted protein (By similarity)				174
Q969H8 UniProt NPD GO	CS010_HUMAN	Uncharacterized protein C19orf10 precursor (Stromal cell-derived growth factor SF20) (Interleukin-25 ...	0.01	-	exc	0	Secreted protein (By similarity)		606746		173
Q96KR6 UniProt NPD GO	CT108_HUMAN	Uncharacterized protein C20orf108	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				192
Q8N6M3 UniProt NPD GO	CT142_HUMAN	Uncharacterized protein C20orf142 precursor	0.01	-	end	5	Membrane; multi-pass membrane protein (Potential)				262
Q9GZN8 UniProt NPD GO	CT027_HUMAN	Uncharacterized protein C20orf27	0.01	-	mit	0					173
Q96A57 UniProt NPD GO	CT030_HUMAN	Uncharacterized protein C20orf30	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				120
Q5E975 UniProt NPD GO	CT030_BOVIN	Uncharacterized protein C20orf30 homolog	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				120
P60602 UniProt NPD GO	CT052_HUMAN	Uncharacterized protein C20orf52	0.01	-	nuc	1 *					79
P60603 UniProt NPD GO	CT052_MOUSE	Uncharacterized protein C20orf52 homolog	0.01	-	nuc	1 *		mitochondrion [IDA]			79
Q9JMG4 UniProt NPD GO	CT058_MOUSE	Uncharacterized protein C20orf58 homolog	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				208
Q8C138 UniProt NPD GO	CF105_MOUSE	Uncharacterized protein C6orf105 homolog	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				230
P38172 UniProt NPD GO	YBJ5_YEAST	Uncharacterized protein YBL095W	0.01	-	mit	0		mitochondrion [IDA]			270
P38235 UniProt NPD GO	YBQ3_YEAST	Uncharacterized protein YBR053C	0.01	-	cyt	0					358
Q07738 UniProt NPD GO	YD241_YEAST	Uncharacterized protein YDL241W	0.01	-	nuc	0					123
Q3E844 UniProt NPD GO	YE039_YEAST	Uncharacterized protein YER039C-A	0.01	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				72
P40043 UniProt NPD GO	YEP7_YEAST	Uncharacterized protein YER067W	0.01	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			161
P40081 UniProt NPD GO	YEW4_YEAST	Uncharacterized protein YER134C	0.01	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			178
Q2V2P6 UniProt NPD GO	YG194_YEAST	Uncharacterized protein YGL194C-A	0.01	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				80
Q3E740 UniProt NPD GO	YG258_YEAST	Uncharacterized protein YGL258W-A	0.01	-	cyt	0					77
Q3E816 UniProt NPD GO	YG121_YEAST	Uncharacterized protein YGR121W-A	0.01	-	cyt	0					71
Q8TGT7 UniProt NPD GO	YG204_YEAST	Uncharacterized protein YGR204C-A	0.01	-	mit	0					37
Q3E7Z6 UniProt NPD GO	YH015_YEAST	Uncharacterized protein YHL015W-A	0.01	-	mit	0					27
Q3E758 UniProt NPD GO	YH048_YEAST	Uncharacterized protein YHL048C-A	0.01	-	cyt	0					44
Q8TGT6 UniProt NPD GO	YH022_YEAST	Uncharacterized protein YHR022C-A	0.01	-	cyt	0					29
P38868 UniProt NPD GO	YHY0_YEAST	Uncharacterized protein YHR180W	0.01	-	mit	0					163
Q45U18 UniProt NPD GO	YI134_YEAST	Uncharacterized protein YIL134C-A	0.01	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				67
P40893 UniProt NPD GO	YJV7_YEAST	Uncharacterized protein YJL217W	0.01	-	cyt	0		cytoplasm [IDA]			198
Q05905 UniProt NPD GO	YL301_YEAST	Uncharacterized protein YLR301W	0.01	-	cyt	0	Cytoplasm. Nucleus	endoplasmic reticulum membrane [IPI]			244
P54007 UniProt NPD GO	YL460_YEAST	Uncharacterized protein YLR460C	0.01	+	cyt	0					376
Q8TGT0 UniProt NPD GO	YM100_YEAST	Uncharacterized protein YML100W-A	0.01	-	mit	0					57
Q3E782 UniProt NPD GO	YM247_YEAST	Uncharacterized protein YMR247W-A precursor	0.01	-	nuc	0					47
Q08734 UniProt NPD GO	YO268_YEAST	Uncharacterized protein YOR268C	0.01	-	mit	1	Membrane; single-pass membrane protein (Potential)				132
P83728 UniProt NPD GO	NF40_NAEFO	Unknown protein NF040 from 2D-PAGE (Fragment)	0.01	-		0					20
P80609 UniProt NPD GO	UC03_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 146) (Fragments)	0.01	-		0					18
P80611 UniProt NPD GO	UC05_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 154) (Fragments)	0.01	-	cyt	0					28
P80618 UniProt NPD GO	UC12_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 237) (Fragments)	0.01	-	cyt	0					40

You are viewing entries 91951 to 92000 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.