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
P47884 UniProt NPD GO	OR1D4_HUMAN	Olfactory receptor 1D4 (Olfactory receptor 17-30) (OR17-30)	0.04	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			311
Q9TU90 UniProt NPD GO	OR1D5_GORGO	Olfactory receptor 1D5	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312
Q9TU95 UniProt NPD GO	OR1D5_PANPA	Olfactory receptor 1D5	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312
Q9TUA6 UniProt NPD GO	OR1D5_PANTR	Olfactory receptor 1D5	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312
O60431 UniProt NPD GO	OR1I1_HUMAN	Olfactory receptor 1I1 (Olfactory receptor 19-20) (OR19-20)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				355
Q8NGS1 UniProt NPD GO	OR1J4_HUMAN	Olfactory receptor 1J4 (HTPCRX01) (Olfactory receptor OR9-21)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				313
Q8NGA1 UniProt NPD GO	OR1M1_HUMAN	Olfactory receptor 1M1 (Olfactory receptor 19-6) (OR19-6)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				313
O95371 UniProt NPD GO	OR2C1_HUMAN	Olfactory receptor 2C1 (OLFmf3)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312
O43869 UniProt NPD GO	OR2T1_HUMAN	Olfactory receptor 2T1 (Olfactory receptor 1-25) (OR1-25) (Olfactory receptor OR1-61)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				311
Q9Y3N9 UniProt NPD GO	OR2W1_HUMAN	Olfactory receptor 2W1 (Hs6M1-15)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				320
Q8VG04 UniProt NPD GO	OL478_MOUSE	Olfactory receptor 478 (Olfactory receptor 204-13)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8VFD2 UniProt NPD GO	OL490_MOUSE	Olfactory receptor 490 (Olfactory receptor 204-17)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NGD0 UniProt NPD GO	OR4M1_HUMAN	Olfactory receptor 4M1	0.04	-	end	7 *	Membrane; multi-pass membrane protein				313
Q8NH49 UniProt NPD GO	OR4X1_HUMAN	Olfactory receptor 4X1	0.04	-	end	6 *	Membrane; multi-pass membrane protein				305
Q8NGF0 UniProt NPD GO	O52B6_HUMAN	Olfactory receptor 52B6	0.04	-	end	7 *	Membrane; multi-pass membrane protein				314
Q9NZP5 UniProt NPD GO	O5AC2_HUMAN	Olfactory receptor 5AC2 (HSA1)	0.04	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			309
Q8NH90 UniProt NPD GO	O5AK2_HUMAN	Olfactory receptor 5AK2	0.04	-	end	7 *	Membrane; multi-pass membrane protein				309
Q8NHC5 UniProt NPD GO	O5AT1_HUMAN	Olfactory receptor 5AT1	0.04	-	end	6 *	Membrane; multi-pass membrane protein				309
Q6IFH4 UniProt NPD GO	OR6B2_HUMAN	Olfactory receptor 6B2 (Olfactory receptor OR2-1)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NGW1 UniProt NPD GO	OR6B3_HUMAN	Olfactory receptor 6B3 (Olfactory receptor OR2-2)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				331
Q8NGM8 UniProt NPD GO	OR6M1_HUMAN	Olfactory receptor 6M1 (Olfactory receptor OR11-271)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				313
Q96RA2 UniProt NPD GO	OR7D2_HUMAN	Olfactory receptor 7D2 (Olfactory receptor 19-4) (OR19-4) (HTPCRH03)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NGQ5 UniProt NPD GO	OR9Q1_HUMAN	Olfactory receptor 9Q1	0.04	-	end	7 *	Membrane; multi-pass membrane protein				310
P37072 UniProt NPD GO	OLF6_CHICK	Olfactory receptor-like protein COR6	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312
P48619 UniProt NPD GO	FAD3C_RICCO	Omega-3 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-)	0.04	-	cyt	1	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Probable)				460
P48620 UniProt NPD GO	FAD3C_SESIN	Omega-3 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-)	0.04	-	mit	2	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Probable)				447
P81745 UniProt NPD GO	TOG3C_AGEAP	Omega-agatoxin-3C (Omega-agatoxin IIIC) (Omega-Aga-IIIC) (Fragment)	0.04	-	nuc	0	Secreted protein				43
P81746 UniProt NPD GO	TOG3D_AGEAP	Omega-agatoxin-3D (Omega-agatoxin IIID) (Omega-Aga-IIID) (Fragment)	0.04	-	nuc	0	Secreted protein				37
P83287 UniProt NPD GO	ONC1_ONCMY	Oncorhyncin-1 (Oncorhyncin I) (Fragment)	0.04	-		0	Secreted protein	extracellular region [NAS]			15
O01668 UniProt NPD GO	OPS6_DROME	Opsin Rh6 (Rhodopsin Rh6, long-wavelength)	0.04	-	end	6 *	Membrane; multi-pass membrane protein	rhabdomere [IDA]			369
O61303 UniProt NPD GO	OPSUV_APIME	Opsin, ultraviolet-sensitive (AMUVOP) (BUVOPS)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				371
O97661 UniProt NPD GO	OX1R_PIG	Orexin receptor type 1 (Ox1r) (Hypocretin receptor type 1) (Fragment)	0.04	-	cyt	0	Membrane; multi-pass membrane protein				86
Q4XWV5 UniProt NPD GO	OAT_PLACH	Ornithine aminotransferase (EC 2.6.1.13) (Ornithine--oxo-acid aminotransferase)	0.04	-	cyt	0	Cytoplasm (Probable)				414
P50134 UniProt NPD GO	DCOR_DATST	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.04	-	cyt	0					431
P00860 UniProt NPD GO	DCOR_MOUSE	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.04	-	cyt	0				7ODC	461
Q6FJC4 UniProt NPD GO	OAZ_CANGA	Ornithine decarboxylase antizyme	0.04	-	cyt	0					255
P18132 UniProt NPD GO	PYRE_CRYNE	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.04	-	mit	0					225
O13416 UniProt NPD GO	PYRF_ASPOR	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	mit	0					277
Q01378 UniProt NPD GO	PYRF_CANBO	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	cyt	0					270
Q9HFN9 UniProt NPD GO	PYRF_CANRU	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	cyt	0					265
O42771 UniProt NPD GO	PYRF_CANTR	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	cyt	0					268
P14017 UniProt NPD GO	PYRF_CEPAC	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	nuc	0					376
Q4VWW3 UniProt NPD GO	PYRF_COCPO	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	cyt	0					274
P10652 UniProt NPD GO	PYRF_EMENI	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	mit	0					274
Q12604 UniProt NPD GO	PYRF_ENDMA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	mit	0					284
P49434 UniProt NPD GO	PYRF_PICST	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	cyt	0					267
Q9Y726 UniProt NPD GO	PYRF_SACEX	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	cyt	0					268
P14965 UniProt NPD GO	PYRF_SCHPO	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	cyt	0					264
P48844 UniProt NPD GO	PYRF_YAMOH	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.04	-	mit	0					261
Q9XS59 UniProt NPD GO	S6A15_BOVIN	Orphan sodium- and chloride-dependent neurotransmitter transporter NTT73 (Orphan transporter v7-3) ( ...	0.04	-	end	12	Membrane; multi-pass membrane protein				729

You are viewing entries 77751 to 77800 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.