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
P69031 UniProt NPD GO	AUR52_LITAU	Aurein-5.2	0.00	-	cyt	0	Secreted protein				25
P69030 UniProt NPD GO	AUR52_LITRA	Aurein-5.2	0.00	-	cyt	0	Secreted protein				25
P33487 UniProt NPD GO	ABP1_ARATH	Auxin-binding protein 1 precursor (ABP)	0.00	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				198
Q9ZRA4 UniProt NPD GO	AB19A_PRUPE	Auxin-binding protein ABP19a precursor	0.00	-	mit	0	Cell wall				209
O04012 UniProt NPD GO	AB19B_PRUPE	Auxin-binding protein ABP19b precursor	0.00	-	mit	0	Cell wall				209
P33083 UniProt NPD GO	AX6B_SOYBN	Auxin-induced protein 6B	0.00	-	cyt	0					90
Q86Y28 UniProt NPD GO	BAGE4_HUMAN	B melanoma antigen 4 precursor	0.00	-	vac	0					39
Q27018 UniProt NPD GO	B2_TENMO	B2 protein precursor (Fragment)	0.00	-	cyt	0	Secreted protein (Potential)				128
P59891 UniProt NPD GO	BCTX1_BABCE	Babycurus-toxin 1 (BcTx1) (Fragment)	0.00	-	nuc	0	Secreted protein				30
P14665 UniProt NPD GO	CEC5_MANSE	Bactericidin B-5P precursor (Cecropin-like peptide B-5)	0.00	-	end	2 *	Secreted protein				61
O24313 UniProt NPD GO	LEC1_PSOTE	Basic agglutinin (WBA I)	0.00	-	cyt	0				2D3S	242
P00303 UniProt NPD GO	BABL_CUCSA	Basic blue protein (Cusacyanin) (Plantacyanin) (CBP)	0.00	-	cyt	0				2CBP	96
P84035 UniProt NPD GO	BASPA_BOTAS	Basparin-A (EC 3.4.24.-) (Fragments)	0.00	-	cyt	0	Secreted protein				63
Q07440 UniProt NPD GO	B2LA1_MOUSE	Bcl-2-related protein A1 (Protein BFL-1) (Hemopoietic-specific early response protein) (A1-A)	0.00	-	cyt	0	Cytoplasm				172
P0C1B6 UniProt NPD GO	BEST_PARTR	Bestoxin	0.00	-	cyt	0	Secreted protein				58
P80225 UniProt NPD GO	B4GT1_RAT	Beta-1,4-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,4-GalTase 1) (Beta4Gal-T1) (b4Gal-T1) (UDP-gal ...	0.00	-	cyt	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				32
Q01339 UniProt NPD GO	APOH_MOUSE	Beta-2-glycoprotein 1 precursor (Beta-2-glycoprotein I) (Apolipoprotein H) (Apo-H) (B2GPI) (Beta(2)G ...	0.00	-	nuc	0	Secreted protein				345
P30442 UniProt NPD GO	B2MG_MESAU	Beta-2-microglobulin (Fragment)	0.00	-	cyt	0	Secreted protein				54
Q03423 UniProt NPD GO	B2MG_ORENI	Beta-2-microglobulin (Fragment)	0.00	-	cyt	0	Secreted protein				37
O77523 UniProt NPD GO	B2MG_ALOSE	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77537 UniProt NPD GO	B2MG_AOTAZ	Beta-2-microglobulin precursor	0.00	-	end	0	Secreted protein				119
P63063 UniProt NPD GO	B2MG_AOTLE	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
P63064 UniProt NPD GO	B2MG_AOTNA	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77536 UniProt NPD GO	B2MG_ATEPA	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77524 UniProt NPD GO	B2MG_BRAAR	Beta-2-microglobulin precursor	0.00	-	end	0	Secreted protein				119
O77533 UniProt NPD GO	B2MG_CACME	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
P63060 UniProt NPD GO	B2MG_CALAU	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77521 UniProt NPD GO	B2MG_CALEM	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77520 UniProt NPD GO	B2MG_CALGO	Beta-2-microglobulin precursor	0.00	-	end	0	Secreted protein				119
O77529 UniProt NPD GO	B2MG_CALHO	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
Q71UN4 UniProt NPD GO	B2MG_CALHU	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
P63061 UniProt NPD GO	B2MG_CALJA	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
P63062 UniProt NPD GO	B2MG_CALKU	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
Q71UN3 UniProt NPD GO	B2MG_CALMO	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
Q71UN5 UniProt NPD GO	B2MG_CALPI	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77528 UniProt NPD GO	B2MG_CALPN	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77526 UniProt NPD GO	B2MG_CALPP	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77530 UniProt NPD GO	B2MG_CALTO	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
P63065 UniProt NPD GO	B2MG_CEBAL	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
P63066 UniProt NPD GO	B2MG_CEBAP	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
P63067 UniProt NPD GO	B2MG_CEBOL	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77535 UniProt NPD GO	B2MG_CEBPY	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
Q6PZD3 UniProt NPD GO	B2MG_CERAE	Beta-2-microglobulin precursor	0.00	-	end	0	Secreted protein				119
O77532 UniProt NPD GO	B2MG_CHISA	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
Q861S3 UniProt NPD GO	B2MG_EQUAS	Beta-2-microglobulin precursor	0.00	-	end	0	Secreted protein				118
Q863B1 UniProt NPD GO	B2MG_EQUBA	Beta-2-microglobulin precursor	0.00	-	end	0	Secreted protein				118
O77525 UniProt NPD GO	B2MG_LAGLA	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77519 UniProt NPD GO	B2MG_LEOCH	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
Q6V7J5 UniProt NPD GO	B2MG_MACMU	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
Q6T672 UniProt NPD GO	B2MG_PAPAN	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119

You are viewing entries 92801 to 92850 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.