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
Q85FN8 UniProt NPD GO	CHLB_ADICA	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.08	-	cyt	0	Plastid; chloroplast				518
Q9MUR9 UniProt NPD GO	CHLB_MESVI	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.08	-	cyt	0	Plastid; chloroplast				509
P51278 UniProt NPD GO	CHLB_PORPU	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.08	-	cyt	0	Plastid; chloroplast				507
P50622 UniProt NPD GO	LIG6_PHACH	Ligninase LG6 precursor (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase)	0.08	-	vac	0					372
P20010 UniProt NPD GO	LIG_PHLRA	Ligninase-3 precursor (EC 1.11.1.14) (Ligninase III) (Diarylpropane peroxidase) (Lignin peroxidase)	0.08	-	exc	0					361
Q9P8W1 UniProt NPD GO	LIP4_CANAL	Lipase 4 precursor (EC 3.1.1.3)	0.08	-	exc	0	Secreted protein				459
Q9P4E7 UniProt NPD GO	LIP7_CANAL	Lipase 7 precursor (EC 3.1.1.3)	0.08	-	vac	0	Secreted protein				426
O95969 UniProt NPD GO	SG1D2_HUMAN	Lipophilin-B precursor (Secretoglobin family 1D member 2)	0.08	-	exc	0	Secreted protein (Potential)	extracellular space [TAS]			90
P38417 UniProt NPD GO	LOX4_SOYBN	Lipoxygenase-4 (EC 1.13.11.12) (L-4) (VSP94)	0.08	-	cyt	0	Cytoplasm				853
P14943 UniProt NPD GO	EST2_RABIT	Liver carboxylesterase 2 (EC 3.1.1.1)	0.08	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...				532
O15991 UniProt NPD GO	KLOM_EISFO	Lombricine kinase (EC 2.7.3.5) (LK)	0.08	-	cyt	0					371
Q9ULC5 UniProt NPD GO	ACSL5_HUMAN	Long-chain-fatty-acid--CoA ligase 5 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 5) (LACS 5)	0.08	-	mit	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...		605677		683
P78970 UniProt NPD GO	LAG1_SCHPO	Longevity-assurance protein 1 (Longevity assurance factor 1)	0.08	-	end	7	Membrane; multi-pass membrane protein (Potential)				390
Q28942 UniProt NPD GO	FCGR3_PIG	Low affinity immunoglobulin gamma Fc region receptor III precursor (IgG Fc receptor III) (Fc-gamma R ...	0.08	-	end	1	Membrane; single-pass type I membrane protein (Potential)				257
Q9ET37 UniProt NPD GO	SC5A4_MOUSE	Low affinity sodium-glucose cotransporter (Sodium/glucose cotransporter 3) (Na(+)/glucose cotranspor ...	0.08	-	end	14 *	Membrane; multi-pass membrane protein				656
Q03682 UniProt NPD GO	BIP2_TOBAC	Luminal-binding protein 2 (BiP 2) (78 kDa glucose-regulated protein homolog 2) (GRP 78-2) (Fragment) ...	0.08	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				292
O77835 UniProt NPD GO	LSHB_CERSI	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.08	-	exc	0	Secreted protein				141
O95867 UniProt NPD GO	LYG6C_HUMAN	Lymphocyte antigen 6 complex locus protein G6c precursor	0.08	-	exc	0	Secreted protein (Potential)				125
Q9JM10 UniProt NPD GO	TNFC_MARMO	Lymphotoxin-beta (LT-beta) (Tumor necrosis factor C) (TNF-C) (Tumor necrosis factor ligand superfami ...	0.08	-	cyt	1 *	Membrane; single-pass type II membrane protein (Potential)				310
Q9JL06 UniProt NPD GO	EDG4_MOUSE	Lysophosphatidic acid receptor Edg-4 (LPA receptor 2) (LPA-2)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				348
Q3UFF7 UniProt NPD GO	LYPL1_MOUSE	Lysophospholipase-like protein 1 (EC 3.1.2.-)	0.08	-	mit	0	Cytoplasm (By similarity)				238
Q7TMR0 UniProt NPD GO	PCP_MOUSE	Lysosomal Pro-X carboxypeptidase precursor (EC 3.4.16.2) (Prolylcarboxypeptidase) (PRCP) (Proline ca ...	0.08	-	vac	0	Lysosome (By similarity)				491
Q15012 UniProt NPD GO	MTRP_HUMAN	Lysosomal-associated transmembrane protein 4A (Golgi 4-transmembrane spanning transporter MTP)	0.08	-	end	4 *	Intracytoplasmic membrane; multi-pass membrane protein (Potential). May reside in an intracellular m ...	Golgi apparatus [IDA]			233
Q7LZQ0 UniProt NPD GO	LYSC_CATWA	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.08	-	nuc	0					129
P22910 UniProt NPD GO	LYSC_CHRAM	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.08	-	nuc	0					129
Q7LZP9 UniProt NPD GO	LYSC_LOPIM	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.08	-	nuc	0					129
P00704 UniProt NPD GO	LYSC_NUMME	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.08	-	nuc	0				1HHL	129
P24364 UniProt NPD GO	LYSC_LOPLE	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.08	-	nuc	0					129
P37156 UniProt NPD GO	LYSC1_TACAC	Lysozyme C I (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.08	-	nuc	0				1JUG	125
P61944 UniProt NPD GO	LYSC_FUGRU	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.08	-	exc	0					143
P80189 UniProt NPD GO	LYSCN_BOVIN	Lysozyme C, non-stomach isozyme precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.08	-	exc	0					148
Q86SG7 UniProt NPD GO	LYG2_HUMAN	Lysozyme g-like protein 2 precursor	0.08	-	end	0	Secreted protein (Probable)				212
P30348 UniProt NPD GO	MIP2_RAT	Macrophage inflammatory protein 2 precursor (MIP2) (CINC-3)	0.08	-	exc	0	Secreted protein				100
P79227 UniProt NPD GO	MMP12_RABIT	Macrophage metalloelastase precursor (EC 3.4.24.65) (MME) (Matrix metalloproteinase-12) (MMP-12)	0.08	-	exc	0					464
P93162 UniProt NPD GO	CHLI_SOYBN	Magnesium-chelatase subunit chlI, chloroplast precursor (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase ...	0.08	-	mit	0	Plastid; chloroplast; chloroplast stroma				421
O22436 UniProt NPD GO	CHLI_TOBAC	Magnesium-chelatase subunit chlI, chloroplast precursor (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase ...	0.08	-	mit	0	Plastid; chloroplast; chloroplast stroma				426
Q9LKA3 UniProt NPD GO	MDHM2_ARATH	Malate dehydrogenase 2, mitochondrial precursor (EC 1.1.1.37) (mNAD-MDH 2)	0.08	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			341
Q7XDC8 UniProt NPD GO	MDHC_ORYSA	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (PP37)	0.08	-	cyt	1 *	Cytoplasm (By similarity)				331
P46487 UniProt NPD GO	MDHM_EUCGU	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.08	-	mit	0	Mitochondrion; mitochondrial matrix				347
P83373 UniProt NPD GO	MDHM_FRAAN	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.08	-	mit	0	Mitochondrion; mitochondrial matrix				339
P11424 UniProt NPD GO	IMAP_DROFU	Male accessory gland serine protease inhibitor (Paragonial peptide D) (Acrosin inhibitor)	0.08	-	nuc	0					63
Q08891 UniProt NPD GO	MS2_ARATH	Male sterility protein 2	0.08	-	mit	0					616
Q8WPJ2 UniProt NPD GO	MANA_MYTED	Mannan endo-1,4-beta-mannosidase precursor (EC 3.2.1.78) (Beta-mannanase) (Endo-beta-1,4-mannanase) ...	0.08	-	exc	0				2C0H	367
P34948 UniProt NPD GO	MANA_CANAL	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.08	-	cyt	0	Cytoplasm (Probable)			1PMI	440
Q9HFU4 UniProt NPD GO	MANA_CRYNE	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.08	-	mit	0	Cytoplasm (By similarity)				434
P35206 UniProt NPD GO	CSG2_YEAST	Mannosyl phosphorylinositol ceramide synthase regulatory protein CSG2 precursor	0.08	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]			410
Q96LB2 UniProt NPD GO	MRGX1_HUMAN	Mas-related G-protein coupled receptor member X1 (Sensory neuron-specific G-protein coupled receptor ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein		607227		322
Q96LA9 UniProt NPD GO	MRGX4_HUMAN	Mas-related G-protein coupled receptor member X4 (Sensory neuron-specific G-protein coupled receptor ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein		607230		322
P01499 UniProt NPD GO	MCDP_APIME	Mast cell degranulating peptide precursor (MCDP) (MCD peptide) (Peptide 401)	0.08	-	mit	1 *	Secreted protein				50
P50341 UniProt NPD GO	MCPT2_MERUN	Mast cell protease 2 precursor (EC 3.4.21.-)	0.08	-	exc	0					247

You are viewing entries 68351 to 68400 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.)

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