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
P20012 UniProt NPD GO	LIGB_TRAVE	Ligninase B (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase) (Fragment)	0.00	-		0					13
Q96VC9 UniProt NPD GO	LIP3_YARLI	Lipase 3 precursor (EC 3.1.1.3)	0.00	-	cyt	0					498
O59952 UniProt NPD GO	LIP_THELA	Lipase precursor (EC 3.1.1.3) (Triacylglycerol lipase)	0.00	-	exc	0				1TIB	291
Q9XI60 UniProt NPD GO	LPP2_ARATH	Lipid phosphate phosphatase 2 (EC 3.1.3.-) (AtLPP2) (Phosphatidic acid phosphatase 2) (AtPAP2) (Pren ...	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				290
O08564 UniProt NPD GO	LPP1_RAT	Lipid phosphate phosphohydrolase 1 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2a) (Phosphatidate ph ...	0.00	-	end	5 *	Cell membrane; multi-pass membrane protein (By similarity)	membrane fraction [ISS]			282
Q8K593 UniProt NPD GO	LPP2_RAT	Lipid phosphate phosphohydrolase 2 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2c) (Phosphatidate ph ...	0.00	-	end	6 *	Membrane; multi-pass membrane protein				276
P84809 UniProt NPD GO	LVP1B_BUTOC	Lipolysis-activating peptide 1-beta chain precursor (LVP1-beta)	0.00	-	cyt	1 *	Secreted protein	extracellular region [IDA]			95
Q86WI0 UniProt NPD GO	LHPL1_HUMAN	Lipoma HMGIC fusion partner-like 1 protein precursor	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		300566		220
Q80SV1 UniProt NPD GO	LHPL1_MOUSE	Lipoma HMGIC fusion partner-like 1 protein precursor	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				220
Q80WE5 UniProt NPD GO	LHPL1_RAT	Lipoma HMGIC fusion partner-like 1 protein precursor	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				220
Q6ZUX7 UniProt NPD GO	LHPL2_HUMAN	Lipoma HMGIC fusion partner-like 2 protein	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		609718		228
Q6P0C6 UniProt NPD GO	LHPL2_BRARE	Lipoma HMGIC fusion partner-like 2 protein homolog	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				225
O95968 UniProt NPD GO	SG1D1_HUMAN	Lipophilin-A precursor (Secretoglobin family 1D member 1)	0.00	-	end	0	Secreted protein (Potential)	extracellular space [TAS]			90
P31799 UniProt NPD GO	LMIP_LOCMI	Locustamyoinhibiting peptide (LOM-MIP)	0.00	-		0					9
P01380 UniProt NPD GO	NXL1_ASTST	Long neurotoxin 1 (Toxin B)	0.00	-	nuc	0	Secreted protein				70
P25670 UniProt NPD GO	NXL1_ASPSC	Long neurotoxin 1 (Toxin S4C6)	0.00	-	nuc	0	Secreted protein				68
P01381 UniProt NPD GO	NXL2_ASTST	Long neurotoxin 2 (Toxin C)	0.00	-	nuc	0	Secreted protein				72
P82662 UniProt NPD GO	NXL6_OPHHA	Long neurotoxin OH-6A/OH-6B (Alpha-neurotoxin)	0.00	-	nuc	0	Secreted protein				70
P15818 UniProt NPD GO	NXLH_BUNMU	Long neurotoxin homolog precursor (BM10-1)	0.00	-	mit	0	Secreted protein				87
P14897 UniProt NPD GO	ELI9_HORVU	Low molecular mass early light-inducible protein HV90, chloroplast precursor (ELIP)	0.00	-	mit	0	Plastid; chloroplast. Associated with both photosystems I and II				172
P40347 UniProt NPD GO	PPAL_YEAST	Low molecular weight phosphotyrosine protein phosphatase (EC 3.1.3.48) (Low molecular weight cytosol ...	0.00	-	mit	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]		1D2A	161
P41893 UniProt NPD GO	PPAL_SCHPO	Low molecular weight phosphotyrosine protein phosphatase (EC 3.1.3.48) (Low molecular weight cytosol ...	0.00	-	cyt	0	Cytoplasm				156
P68179 UniProt NPD GO	LT01_HORVU	Low temperature-induced protein lt101.1 (Blt101) (Blt101.1)	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				54
Q9ARD5 UniProt NPD GO	LT02_HORVU	Low temperature-induced protein lt101.2	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				54
Q9FI23 UniProt NPD GO	LCR77_ARATH	Low-molecular cysteine-rich antifungal protein LCR77 precursor	0.00	-	exc	1 *	Secreted protein (By similarity)				80
Q9DD23 UniProt NPD GO	LYPD2_MOUSE	Ly6/PLAUR domain-containing protein 2 precursor	0.00	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				127
Q6UWN0 UniProt NPD GO	LYPD4_HUMAN	Ly6/PLAUR domain-containing protein 4 precursor	0.00	-	vac	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				246
P61508 UniProt NPD GO	LYT2_HOGCA	Lycotoxin-2 (Lycotoxin II)	0.00	-	cyt	0	Secreted protein				27
Q90986 UniProt NPD GO	LY6E_CHICK	Lymphocyte antigen Ly-6E precursor (Stem cell antigen 2) (SCA-2)	0.00	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				126
P35461 UniProt NPD GO	LY6G_MOUSE	Lymphocyte antigen Ly-6G.1 precursor (Fragment)	0.00	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	external side of plasma membrane [IDA]			111
Q03168 UniProt NPD GO	ASPP_AEDAE	Lysosomal aspartic protease precursor (EC 3.4.23.-)	0.00	-	vac	0	Lysosome				387
P37155 UniProt NPD GO	LYSC_FELCA	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C) (Fragment)	0.00	-		0					20
P04421 UniProt NPD GO	LYSC_BOVIN	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.00	-	vac	0					147
Q06285 UniProt NPD GO	LYSC1_BOVIN	Lysozyme C-1 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.00	-	vac	0					147
Q06283 UniProt NPD GO	LYSC2_BOVIN	Lysozyme C-2 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.00	-	vac	0					147
Q06284 UniProt NPD GO	LYSC3_BOVIN	Lysozyme C-3 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.00	-	vac	0					147
Q9TUN1 UniProt NPD GO	LYSC3_SHEEP	Lysozyme C-3 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.00	-	end	0					147
Q9D925 UniProt NPD GO	LYZL4_MOUSE	Lysozyme-like protein 4 precursor	0.00	-	exc	1 *	Secreted protein (Probable)				145
Q40189 UniProt NPD GO	M6_LILHE	M6 protein (LHM6) (Fragment)	0.00	-	cyt	0					78
P81785 UniProt NPD GO	MLOL_LINUS	MLO-like protein (Fragment)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (By similarity)				217
Q9SSK7 UniProt NPD GO	MLP34_ARATH	MLP-like protein 34	0.00	-	cyt	0					316
Q93VR4 UniProt NPD GO	ML423_ARATH	MLP-like protein 423	0.00	-	cyt	0					155
Q502X0 UniProt NPD GO	MORN2_HUMAN	MORN repeat-containing protein 2 (MORN motif protein in testis)	0.00	-	cyt	0					79
P81532 UniProt NPD GO	MP1_MICOC	MP1 protein (Fragments)	0.00	-		0					13
P81533 UniProt NPD GO	MP2_MICOC	MP2 protein (Fragment)	0.00	-		0					10
O44786 UniProt NPD GO	MIFH_WUCBA	Macrophage migration inhibitory factor homolog	0.00	-	nuc	0	Secreted protein (Potential)				114
P91850 UniProt NPD GO	MIFH_BRUMA	Macrophage migration inhibitory factor homolog (BmMIF) (Bm-MIF-1)	0.00	-	cyt	0	Secreted protein				114
P82066 UniProt NPD GO	MCU11_LITGE	Maculatin-1.1 [Contains: Maculatin-1.1.1]	0.00	-	cyt	0	Secreted protein				21
P82067 UniProt NPD GO	MCU12_LITGE	Maculatin-1.2	0.00	-	cyt	0	Secreted protein				23
P82068 UniProt NPD GO	MCU21_LITGE	Maculatin-2.1	0.00	-		0	Secreted protein				18

You are viewing entries 95501 to 95550 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.