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
Q8IVV8 UniProt NPD GO	CT058_HUMAN	Uncharacterized protein C20orf58	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				208
O94348 UniProt NPD GO	YCB4_SCHPO	Uncharacterized protein C61.04c	0.00	-	end	5	Membrane; multi-pass membrane protein (Potential)				227
Q8WWP8 UniProt NPD GO	CH005_HUMAN	Uncharacterized protein C8orf5	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				96
P39721 UniProt NPD GO	YAE9_YEAST	Uncharacterized protein YAL049C	0.00	-	cyt	0		cytoplasm [IDA]			246
P38234 UniProt NPD GO	YBQ2_YEAST	Uncharacterized protein YBR052C	0.00	-	cyt	0		cytoplasm [IDA]			210
P25613 UniProt NPD GO	YCQ0_YEAST	Uncharacterized protein YCR010C	0.00	-	end	5	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			283
Q3E7B0 UniProt NPD GO	YE053_YEAST	Uncharacterized protein YER053C-A	0.00	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			37
Q3E750 UniProt NPD GO	YG041_YEAST	Uncharacterized protein YGL041C-B	0.00	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				60
Q3E786 UniProt NPD GO	YG240_YEAST	Uncharacterized protein YGR240C-A	0.00	-	cyt	0					66
P38804 UniProt NPD GO	YHO7_YEAST	Uncharacterized protein YHR087W	0.00	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1NYN	111
P38841 UniProt NPD GO	YHT8_YEAST	Uncharacterized protein YHR138C precursor	0.00	-	exc	1 *					114
Q8TGT4 UniProt NPD GO	YH213_YEAST	Uncharacterized protein YHR213W-A	0.00	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				77
Q12177 UniProt NPD GO	YL056_YEAST	Uncharacterized protein YLL056C	0.00	-	cyt	0					298
Q06252 UniProt NPD GO	YL179_YEAST	Uncharacterized protein YLR179C	0.00	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			201
Q3E810 UniProt NPD GO	YL342_YEAST	Uncharacterized protein YLR342W-A	0.00	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)				57
Q03629 UniProt NPD GO	YMH9_YEAST	Uncharacterized protein YML079W	0.00	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1XE8	201
Q03759 UniProt NPD GO	YMK8_YEAST	Uncharacterized protein YML108W	0.00	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1N6Z	105
Q8TGS5 UniProt NPD GO	YM272_YEAST	Uncharacterized protein YMR272W-B precursor	0.00	-	vac	0					35
Q3E7Y8 UniProt NPD GO	YO155_YEAST	Uncharacterized protein YOL155W-A	0.00	-	mit	0					44
Q08910 UniProt NPD GO	YO387_YEAST	Uncharacterized protein YOR387C precursor	0.00	-	exc	0	Cytoplasm; cytosol. Soluble fraction	soluble fraction [IDA]			206
Q08913 UniProt NPD GO	YO390_YEAST	Uncharacterized protein YOR390W	0.00	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				375
Q3E751 UniProt NPD GO	YP119_YEAST	Uncharacterized protein YPL119C-A	0.00	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				87
Q8TGQ7 UniProt NPD GO	YP159_YEAST	Uncharacterized protein YPR159C-A	0.00	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				33
Q9SX77 UniProt NPD GO	UMP6_ARATH	Unknown protein At1g47420, mitochondrial precursor	0.00	-	mit	0	Mitochondrion				257
P83723 UniProt NPD GO	NF04_NAEFO	Unknown protein NF004 from 2D-PAGE (Fragment)	0.00	-	nuc	0					24
P83737 UniProt NPD GO	NF07_NAEFO	Unknown protein NF007 from 2D-PAGE (Fragment)	0.00	-		0					20
P83725 UniProt NPD GO	NF28_NAEFO	Unknown protein NF028 from 2D-PAGE (Fragment)	0.00	-		0					20
P83727 UniProt NPD GO	NF37_NAEFO	Unknown protein NF037 from 2D-PAGE (Fragment)	0.00	-		0					19
P83730 UniProt NPD GO	NF42_NAEFO	Unknown protein NF042 from 2D-PAGE (Fragment)	0.00	-		0					20
P83600 UniProt NPD GO	NF45_NAEFO	Unknown protein NF045 from 2D-PAGE (Fragment)	0.00	-		0					20
P99012 UniProt NPD GO	UXB1_YEAST	Unknown protein from 2D-PAGE (Spot 2D-000JYC) (Fragment)	0.00	-		0					10
P31940 UniProt NPD GO	UKA1_HUMAN	Unknown protein from 2D-PAGE of epidermal keratinocytes (Spot 1118) (Fragments)	0.00	-		0					19
P80613 UniProt NPD GO	UC07_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 168) (Fragments)	0.00	-	mit	0					22
P80615 UniProt NPD GO	UC09_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 206) (Fragments)	0.00	-	cyt	0					32
P80617 UniProt NPD GO	UC11_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 207) (Fragments)	0.00	-	cyt	0					40
P80640 UniProt NPD GO	UC34_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 360) (Fragments)	0.00	-		0					14
P80641 UniProt NPD GO	UC35_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 365) (Fragments)	0.00	-	cyt	0					30
P80626 UniProt NPD GO	UC20_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 445) (Fragment)	0.00	-		0					15
P80628 UniProt NPD GO	UC22_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 474) (Fragment)	0.00	-		0					5
P80636 UniProt NPD GO	UC30_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 662) (Fragment)	0.00	-		0					15
P80638 UniProt NPD GO	UC32_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 75) (Fragments)	0.00	-	cyt	0					49
P80631 UniProt NPD GO	UC25_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 77) (Fragment)	0.00	-		0					15
P80634 UniProt NPD GO	UC28_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 984) (Fragment)	0.00	-		0					15
P38640 UniProt NPD GO	UF02_MOUSE	Unknown protein from 2D-PAGE of fibroblasts (P32) (Fragment)	0.00	-		0					9
P38641 UniProt NPD GO	UF03_MOUSE	Unknown protein from 2D-PAGE of fibroblasts (P36) (Fragment)	0.00	-		0					7
P38643 UniProt NPD GO	UF05_MOUSE	Unknown protein from 2D-PAGE of fibroblasts (P48) (Fragment)	0.00	-		0					11
P49289 UniProt NPD GO	UHA4_HUMAN	Unknown protein from 2D-PAGE of heart (Fragments)	0.00	-	cyt	0					23
P40928 UniProt NPD GO	UHA1_HUMAN	Unknown protein from 2D-PAGE of heart (Spot 4304) (Fragment)	0.00	-		0					13
P40929 UniProt NPD GO	UHA2_HUMAN	Unknown protein from 2D-PAGE of heart (Spot 5603) (Fragment)	0.00	-		0					9
P99506 UniProt NPD GO	UHA2_CANFA	Unknown protein from 2D-PAGE of heart tissue (Spot 6109) (Fragment)	0.00	-		0					14

You are viewing entries 98551 to 98600 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.