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
P24289 UniProt NPD GO	NUP1_PENCI	Nuclease P1 (EC 3.1.30.1) (Endonuclease P1) (Deoxyribonuclease P1)	0.05	-	cyt	0	Secreted protein			1AK0	270
P24504 UniProt NPD GO	NUP3_PENSQ	Nuclease PA3 (EC 3.1.3.6) (Endonuclease PA3) (Deoxyribonuclease PA3)	0.05	-	cyt	0	Secreted protein				270
P52914 UniProt NPD GO	NTPA_PEA	Nucleoside-triphosphatase (EC 3.6.1.15) (Nucleoside triphosphate phosphohydrolase) (NTPase) (Apyrase ...	0.05	-	exc	0	Nucleus				455
Q9LQU5 UniProt NPD GO	NUD18_ARATH	Nudix hydrolase 18, mitochondrial precursor (EC 3.6.1.-) (AtNUDT18)	0.05	-	mit	0	Mitochondrion (Potential)				176
Q94B74 UniProt NPD GO	NUDT2_ARATH	Nudix hydrolase 2 (EC 3.6.1.-) (AtNUDT2) (ADP-ribose pyrophosphatase) (EC 3.6.1.13) (NADH pyrophosph ...	0.05	-	cyt	0					278
P47917 UniProt NPD GO	ZRP4_MAIZE	O-methyltransferase ZRP4 (EC 2.1.1.-) (OMT)	0.05	-	cyt	0					364
P81647 UniProt NPD GO	OBP1_HYSCR	Odorant-binding protein 1 (Odorant-binding protein I) (OBP I) (Olfactory mucosa pyrazine-binding pro ...	0.05	-	nuc	0	Secreted protein; extracellular space				28
P13436 UniProt NPD GO	OLEO1_MAIZE	Oleosin Zm-I (Oleosin 16 kDa) (Lipid body-associated major protein) (Lipid body-associated protein L ...	0.05	-	end	2 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				156
P23268 UniProt NPD GO	O1082_RAT	Olfactory receptor 1082 (Olfactory receptor-like protein F12)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				317
Q8NGE5 UniProt NPD GO	O10A7_HUMAN	Olfactory receptor 10A7	0.05	-	end	7 *	Membrane; multi-pass membrane protein				316
Q5JRS4 UniProt NPD GO	O10J3_HUMAN	Olfactory receptor 10J3	0.05	-	end	6 *	Membrane; multi-pass membrane protein				329
Q6IF99 UniProt NPD GO	O10K2_HUMAN	Olfactory receptor 10K2 (Olfactory receptor OR1-4)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				312
P34984 UniProt NPD GO	OLF13_MOUSE	Olfactory receptor 13 (Olfactory receptor 261-6) (Odorant receptor K7)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				310
P34983 UniProt NPD GO	OL144_MOUSE	Olfactory receptor 144 (Olfactory receptor 7B) (Odorant receptor K4)	0.05	-	end	8 *	Membrane; multi-pass membrane protein				314
Q60887 UniProt NPD GO	OL148_MOUSE	Olfactory receptor 148 (Olfactory receptor 7F) (Olfactory receptor 224-4) (Odorant receptor M30)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				310
P23271 UniProt NPD GO	O1493_RAT	Olfactory receptor 1493 (Olfactory receptor-like protein I8)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				312
P23275 UniProt NPD GO	OLF15_MOUSE	Olfactory receptor 15 (Odorant receptor OR3)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NGR6 UniProt NPD GO	OR1B1_HUMAN	Olfactory receptor 1B1 (Olfactory receptor 9-B) (OR9-B) (Olfactory receptor OR9-26)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				317
Q15619 UniProt NPD GO	OR1C1_HUMAN	Olfactory receptor 1C1 (Olfactory receptor TPCR27) (Olfactory receptor OR1-42)	0.05	-	end	8 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			314
Q8NGR5 UniProt NPD GO	OR1L4_HUMAN	Olfactory receptor 1L4 (Olfactory receptor 9-E) (OR9-E) (OST046)	0.05	-	end	6 *	Membrane; multi-pass membrane protein				311
Q6IF00 UniProt NPD GO	OR2T2_HUMAN	Olfactory receptor 2T2 (Olfactory receptor OR1-43)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				324
Q8NGX2 UniProt NPD GO	O2T35_HUMAN	Olfactory receptor 2T35 (Olfactory receptor OR1-66)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				323
Q8NGB2 UniProt NPD GO	OR4C5_HUMAN	Olfactory receptor 4C5 (Olfactory receptor OR11-99)	0.05	-	end	6 *	Membrane; multi-pass membrane protein				326
Q8NH42 UniProt NPD GO	OR4KD_HUMAN	Olfactory receptor 4K13 (Olfactory receptor OR14-27)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				304
Q8NGD3 UniProt NPD GO	OR4K5_HUMAN	Olfactory receptor 4K5	0.05	-	end	7 *	Membrane; multi-pass membrane protein				323
Q8VG13 UniProt NPD GO	OL507_MOUSE	Olfactory receptor 507 (Olfactory receptor 204-7)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				316
Q8NH59 UniProt NPD GO	O51Q1_HUMAN	Olfactory receptor 51Q1	0.05	-	end	7 *	Membrane; multi-pass membrane protein				317
Q8NGI3 UniProt NPD GO	O56B1_HUMAN	Olfactory receptor 56B1 (Olfactory receptor OR11-65)	0.05	-	end	5 *	Membrane; multi-pass membrane protein				321
Q8NGZ2 UniProt NPD GO	O5AY1_HUMAN	Olfactory receptor 5AY1	0.05	-	end	6 *	Membrane; multi-pass membrane protein				315
Q8NHC7 UniProt NPD GO	O5BF1_HUMAN	Olfactory receptor 5BF1	0.05	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NGL4 UniProt NPD GO	OR5DD_HUMAN	Olfactory receptor 5D13	0.05	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NGX9 UniProt NPD GO	OR6P1_HUMAN	Olfactory receptor 6P1 (Olfactory receptor OR1-12)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				317
Q15622 UniProt NPD GO	OR7A5_HUMAN	Olfactory receptor 7A5 (Olfactory receptor TPCR92)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			319
Q15617 UniProt NPD GO	OR8G1_HUMAN	Olfactory receptor 8G1 (Olfactory receptor TPCR25) (Olfactory receptor OR11-281)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			311
Q8N0Y5 UniProt NPD GO	OR8I2_HUMAN	Olfactory receptor 8I2	0.05	-	end	7 *	Membrane; multi-pass membrane protein				310
Q8NH87 UniProt NPD GO	OR9G1_HUMAN	Olfactory receptor 9G1	0.05	-	end	7 *	Membrane; multi-pass membrane protein				305
Q8NGQ0 UniProt NPD GO	OR9G5_HUMAN	Olfactory receptor 9G5 (Olfactory receptor OR11-114)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				305
Q8NGE9 UniProt NPD GO	OR9Q2_HUMAN	Olfactory receptor 9Q2	0.05	-	end	7 *	Membrane; multi-pass membrane protein				314
Q16348 UniProt NPD GO	S15A2_HUMAN	Oligopeptide transporter, kidney isoform (Peptide transporter 2) (Kidney H(+)/peptide cotransporter) ...	0.05	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602339		729
Q9XZK3 UniProt NPD GO	CXSO4_CONST	Omega-type conotoxin SO4 precursor	0.05	-	exc	0	Secreted protein (By similarity)				78
O43482 UniProt NPD GO	OIP5_HUMAN	Opa-interacting protein 5	0.05	-	mit	0			606020		229
P28678 UniProt NPD GO	OPS1_DROPS	Opsin Rh1 (Outer R1-R6 photoreceptor cells opsin)	0.05	-	end	7	Membrane; multi-pass membrane protein				422
Q6LFH8 UniProt NPD GO	OAT_PLAF7	Ornithine aminotransferase (EC 2.6.1.13) (Ornithine--oxo-acid aminotransferase)	0.05	-	cyt	0	Cytoplasm (Probable)				414
Q07805 UniProt NPD GO	OAT_PLAFD	Ornithine aminotransferase (EC 2.6.1.13) (Ornithine--oxo-acid aminotransferase)	0.05	-	cyt	0	Cytoplasm (Probable)			1LX9	414
P31893 UniProt NPD GO	OAT_VIGAC	Ornithine aminotransferase (EC 2.6.1.13) (Ornithine--oxo-acid aminotransferase)	0.05	-	cyt	0					426
P41931 UniProt NPD GO	DCOR_CAEEL	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.05	-	cyt	0					422
P14019 UniProt NPD GO	DCOR_CRIGR	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.05	-	cyt	0					455
P49725 UniProt NPD GO	DCOR_PANRE	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.05	-	cyt	0					435
Q8S3N2 UniProt NPD GO	DCOR_CAPAN	Ornithine decarboxylase (EC 4.1.1.17) (ODC) (CaODC1) (CapODC)	0.05	-	cyt	0					435
O22616 UniProt NPD GO	DCOR_LYCES	Ornithine decarboxylase (EC 4.1.1.17) (ODC) (LeODC)	0.05	-	cyt	0					431

You are viewing entries 75051 to 75100 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.