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
Q9QZH3 UniProt NPD GO	PPIE_MOUSE	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8) (PPIase E) (Rotamase E) (Cyclophilin E) (Cyclophi ...	0.06	-	cyt	0	Nucleus (By similarity)				301
Q5KA96 UniProt NPD GO	PPIH_CRYNE	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H)	0.06	-	cyt	0	Nucleus (By similarity)				179
P0C1I4 UniProt NPD GO	PPIL1_RHIOR	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.06	-	cyt	0					165
Q03294 UniProt NPD GO	PER_DROIM	Period circadian protein (Fragment)	0.06	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				63
Q03295 UniProt NPD GO	PER_DROMO	Period circadian protein (Fragment)	0.06	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				65
Q26289 UniProt NPD GO	PER_DROOR	Period circadian protein (Fragment)	0.06	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				114
Q03296 UniProt NPD GO	PER_DRORO	Period circadian protein (Fragment)	0.06	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				86
Q06497 UniProt NPD GO	ANT1_YEAST	Peroxisomal adenine nucleotide transporter 1	0.06	-	cyt	1	Peroxisome; peroxisomal membrane; multi-pass membrane protein	cytoplasm [IDA] integral to peroxisomal membrane [IDA]			328
Q8W1L6 UniProt NPD GO	MFP_ORYSA	Peroxisomal fatty acid beta-oxidation multifunctional protein (MFP) [Includes: Enoyl-CoA hydratase ( ...	0.06	-	cyt	0	Peroxisome (Probable)	peroxisome [NAS]			726
Q06438 UniProt NPD GO	PEX2_CRIGR	Peroxisome assembly factor 1 (PAF-1) (Peroxin-2) (Peroxisomal membrane protein 3)	0.06	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				304
P39718 UniProt NPD GO	PEX22_YEAST	Peroxisome assembly protein 22 (Peroxin-22)	0.06	-	mit	1 *	Peroxisome; peroxisomal membrane; single-pass membrane protein (By similarity)				180
Q6PXP0 UniProt NPD GO	PHLIP_ANUPH	Phaiodactylipin precursor [Contains: Phaiodactylipin large subunit (EC 3.1.1.4); Phaiodactylipin sma ...	0.06	-	mit	0	Secreted protein	extracellular region [IDA]			157
P35512 UniProt NPD GO	PALY_MALDO	Phenylalanine ammonia-lyase (EC 4.3.1.5) (Fragment)	0.06	-	mit	0	Cytoplasm (Probable)				235
P53809 UniProt NPD GO	PPCT_RAT	Phosphatidylcholine transfer protein (PC-TP) (StAR-related lipid transfer protein 2) (StARD2) (START ...	0.06	-	cyt	0	Cytoplasm	cytosol [TAS]			214
P16301 UniProt NPD GO	LCAT_MOUSE	Phosphatidylcholine-sterol acyltransferase precursor (EC 2.3.1.43) (Lecithin-cholesterol acyltransfe ...	0.06	-	exc	0					438
Q7T3T4 UniProt NPD GO	SMS1_CHICK	Phosphatidylcholine:ceramide cholinephosphotransferase 1 (EC 2.7.-.-) (Sphingomyelin synthase 1) (MO ...	0.06	-	end	6	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)	integral to Golgi membrane [ISS]			417
Q86VZ5 UniProt NPD GO	SMS1_HUMAN	Phosphatidylcholine:ceramide cholinephosphotransferase 1 (EC 2.7.-.-) (Transmembrane protein 23) (Sp ...	0.06	-	end	6	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi trans cisterna [IDA] integral to Golgi membrane [IDA]			419
Q7TSX5 UniProt NPD GO	SMS1_RAT	Phosphatidylcholine:ceramide cholinephosphotransferase 1 (EC 2.7.-.-) (Transmembrane protein 23) (Sp ...	0.06	-	end	6	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)	integral to Golgi membrane [ISS]			419
Q5R946 UniProt NPD GO	PIGP_PONPY	Phosphatidylinositol N-acetylglucosaminyltransferase subunit P (EC 2.4.1.198) (Phosphatidylinositol- ...	0.06	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				134
Q18268 UniProt NPD GO	PDL1_CAEEL	Phosphodiesterase delta-like protein	0.06	-	nuc	0					159
Q8HYZ4 UniProt NPD GO	PPCKC_BOVIN	Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) ( ...	0.06	-	cyt	0	Cytoplasm (By similarity)				622
P05153 UniProt NPD GO	PPCKC_CHICK	Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) ( ...	0.06	-	cyt	0	Cytoplasm				622
P56839 UniProt NPD GO	PEPM_MYTED	Phosphoenolpyruvate phosphomutase (EC 5.4.2.9) (Phosphoenolpyruvate mutase) (PEP mutase) (PEP phosph ...	0.06	-	cyt	0				1S2W	294
Q4WY53 UniProt NPD GO	PGM_ASPFU	Phosphoglucomutase (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.06	-	cyt	0	Cytoplasm (By similarity)				555
Q9ZSQ4 UniProt NPD GO	PGMC_POPTN	Phosphoglucomutase, cytoplasmic (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.06	-	cyt	0	Cytoplasm (By similarity)				582
Q06478 UniProt NPD GO	PA11_DOLMA	Phospholipase A1 1 precursor (EC 3.1.1.32) (EC 3.1.1.4) (Allergen Dol m 1.01) (Dol m I) (Fragment)	0.06	-	cyt	0					317
P31854 UniProt NPD GO	PA2_VIPBB	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	nuc	0	Secreted protein				122
Q10756 UniProt NPD GO	PA2_NAJSP	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Muscarinic inhibitor) (Fragment ...	0.06	-		0	Secreted protein				16
Q9PSF9 UniProt NPD GO	PA2_AGKBI	Phospholipase A2 2 (EC 3.1.1.4) (Phospholipase A2 II) (Phosphatidylcholine 2-acylhydrolase) (PLA2-II ...	0.06	-	nuc	0	Secreted protein				39
Q91133 UniProt NPD GO	PA22_NAJAT	Phospholipase A2 2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	mit	0					146
Q9PVF2 UniProt NPD GO	PA2E_AGKRH	Phospholipase A2 H1E6 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	cyt	0	Secreted protein				139
Q8UUI4 UniProt NPD GO	PA22_LATLA	Phospholipase A2 PC10 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	exc	1 *	Secreted protein (By similarity)				145
Q02471 UniProt NPD GO	PA24_DABRU	Phospholipase A2 RV-4 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	mit	0	Secreted protein			1OQS	138
P59071 UniProt NPD GO	PA28_DABRP	Phospholipase A2 VRV-PL-VIIIa (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (DPLA2)	0.06	-	nuc	0	Secreted protein			2GNS	121
Q9PVF4 UniProt NPD GO	PA2D_AGKRH	Phospholipase A2 W6D49 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	nuc	1 *	Secreted protein				137
Q9I847 UniProt NPD GO	PA2A_LATSE	Phospholipase A2 cL037 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	exc	1 *	Secreted protein (By similarity)				145
Q9I843 UniProt NPD GO	PA2E_LATSE	Phospholipase A2 cPm05 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	exc	1 *	Secreted protein (By similarity)				145
P04361 UniProt NPD GO	PA2H_AGKPI	Phospholipase A2 homolog (APP-K-49)	0.06	-	nuc	0	Secreted protein			1PPA	121
P82144 UniProt NPD GO	PLIGA_AGKBL	Phospholipase A2 inhibitor subunit gamma A precursor (PLI-gamma A) (Phospholipase A2 inhibitor gamma ...	0.06	-	exc	0	Secreted protein				200
P04057 UniProt NPD GO	PA2D_PSEAU	Phospholipase A2 isozyme PA-13 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	nuc	0	Secreted protein				118
Q9PUG7 UniProt NPD GO	PA217_AUSSU	Phospholipase A2 isozyme S17-58 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA1 ...	0.06	-	exc	1 *	Secreted protein (By similarity)				152
P00593 UniProt NPD GO	PA21B_BOVIN	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IB phospholipas ...	0.06	-	nuc	0	Secreted protein			4BP2	145
Q9DF33 UniProt NPD GO	PA22_OPHHA	Phospholipase A2, acidic 2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (APLA2-2)	0.06	-	exc	0	Secreted protein (By similarity)			1M8T	146
P23028 UniProt NPD GO	PA2D_PSETE	Phospholipase A2, textilotoxin D chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.06	-	exc	0	Secreted protein				133
Q9JIZ9 UniProt NPD GO	PLS3_MOUSE	Phospholipid scramblase 3 (PL scramblase 3) (Ca(2+)-dependent phospholipid scramblase 3)	0.06	-	cyt	0	Membrane; single-pass type II membrane protein (By similarity)				296
P55065 UniProt NPD GO	PLTP_MOUSE	Phospholipid transfer protein precursor (Lipid transfer protein II)	0.06	-	exc	0	Secreted protein				493
Q01930 UniProt NPD GO	PUR6_PICME	Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) (AIR carboxylase) (AIRC)	0.06	-	cyt	0					543
Q9TLQ5 UniProt NPD GO	PSAA_CYACA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.06	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				752
P19430 UniProt NPD GO	PSAA_EUGGR	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.06	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				751
Q9XQV3 UniProt NPD GO	PSAA_HETTR	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.06	-	end	11	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				732

You are viewing entries 72751 to 72800 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.