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
P61050 UniProt NPD GO	LYNX1_MACMU	Ly-6/neurotoxin-like protein 1 precursor	0.02	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				118
Q5IS42 UniProt NPD GO	LYNX1_PANTR	Ly-6/neurotoxin-like protein 1 precursor	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				116
Q5IS87 UniProt NPD GO	LYNX1_SAIBB	Ly-6/neurotoxin-like protein 1 precursor	0.02	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				116
Q6UXB3 UniProt NPD GO	LYPD2_HUMAN	Ly6/PLAUR domain-containing protein 2 precursor	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				125
Q16553 UniProt NPD GO	LY6E_HUMAN	Lymphocyte antigen Ly-6E precursor (Retinoic acid-induced gene E protein) (RIG-E) (Thymic shared ant ...	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	integral to plasma membrane [TAS]	601384		131
Q9XT47 UniProt NPD GO	TNFC_MACEU	Lymphotoxin-beta (LT-beta) (Tumor necrosis factor C) (TNF-C) (Tumor necrosis factor ligand superfami ...	0.02	-	cyt	1 *	Membrane; single-pass type II membrane protein (Potential)				250
Q9Z0M5 UniProt NPD GO	LICH_MOUSE	Lysosomal acid lipase/cholesteryl ester hydrolase precursor (EC 3.1.1.13) (LAL) (Acid cholesteryl es ...	0.02	-	mit	0	Lysosome				397
O35448 UniProt NPD GO	PPT2_MOUSE	Lysosomal thioesterase PPT2 precursor (EC 3.1.2.-) (PPT-2)	0.02	-	exc	0	Lysosome				302
Q9UMR5 UniProt NPD GO	PPT2_HUMAN	Lysosomal thioesterase PPT2 precursor (EC 3.1.2.-) (PPT-2) (S-thioesterase G14)	0.02	-	exc	1 *	Lysosome	lysosome [NAS]	603298	1PJA	302
Q14108 UniProt NPD GO	SCRB2_HUMAN	Lysosome membrane protein 2 (Lysosome membrane protein II) (LIMP II) (Scavenger receptor class B mem ...	0.02	-	end	2 *	Lysosome; lysosomal membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	602257		477
P27615 UniProt NPD GO	SCRB2_RAT	Lysosome membrane protein 2 (Lysosome membrane protein II) (LIMP II) (Scavenger receptor class B mem ...	0.02	-	end	2 *	Lysosome; lysosomal membrane; multi-pass membrane protein	lysosomal membrane [TAS]			477
Q7LZQ1 UniProt NPD GO	LYSC_TRISI	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.02	-	cyt	0					131
Q91159 UniProt NPD GO	LYSC_OPIHO	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.02	-	exc	0					145
Q6B410 UniProt NPD GO	LYSI_BOVIN	Lysozyme C, intestinal isozyme precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.02	-	end	0					147
P12066 UniProt NPD GO	LYSC_AXIAX	Lysozyme C-1/C-2 (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.02	-	cyt	0					129
Q8JFR1 UniProt NPD GO	LYG_CYPCA	Lysozyme g (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.02	-	cyt	0					185
Q96KX0 UniProt NPD GO	LYZL4_HUMAN	Lysozyme-like protein 4 precursor	0.02	-	mit	0	Secreted protein (Probable)				146
P34068 UniProt NPD GO	MFM1_SCHPO	M-factor precursor 1	0.02	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				42
P34069 UniProt NPD GO	MFM2_SCHPO	M-factor precursor 2	0.02	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				44
P40849 UniProt NPD GO	MFM3_SCHPO	M-factor precursor 3	0.02	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				41
Q13021 UniProt NPD GO	MALL_HUMAN	MAL-like protein (Protein BENE)	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	clathrin-coated vesicle [IDA] cytoplasmic membrane-bound vesicle [IDA] Golgi membrane [IDA] integral to membrane [NAS] lipid raft [IDA] plasma membrane [IDA]	602022		153
Q91X49 UniProt NPD GO	MALL_MOUSE	MAL-like protein (Protein BENE)	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	clathrin-coated vesicle [ISS] cytoplasmic membrane-bound vesicle [ISS] Golgi membrane [ISS] integral to membrane [ISS] lipid raft [ISS] plasma membrane [ISS]			154
P32439 UniProt NPD GO	MFS18_MAIZE	MFS18 protein precursor	0.02	-	mit	0					128
P90835 UniProt NPD GO	MIF3_CAEEL	MIF-like protein mif-3	0.02	-	cyt	1					146
Q32KU3 UniProt NPD GO	MORN2_BOVIN	MORN repeat-containing protein 2	0.02	-	cyt	0					79
Q9DAT2 UniProt NPD GO	MRGBP_MOUSE	MRG-binding protein	0.02	-	nuc	0	Nucleus (By similarity)				218
P83447 UniProt NPD GO	MDO2_PSEMR	Macrodontain-2 (EC 3.4.22.-) (Macrodontain II) (Fragment)	0.02	-	nuc	0					27
P30904 UniProt NPD GO	MIF_RAT	Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1) (Glutathione- ...	0.02	-	cyt	0				1FIM	114
P34884 UniProt NPD GO	MIF_MOUSE	Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1) (Glycosylatio ...	0.02	-	cyt	0				1MFI	114
P80928 UniProt NPD GO	MIF_PIG	Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1) (Glycosylatio ...	0.02	-	cyt	0					110
P82069 UniProt NPD GO	MCU31_LITGE	Maculatin-3.1	0.02	-	cyt	0	Secreted protein				26
Q9TLX7 UniProt NPD GO	CHLI_CYACA	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.02	-	cyt	0	Plastid; chloroplast				353
P43211 UniProt NPD GO	MAL11_MALDO	Major allergen Mal d 1 (Mal d I)	0.02	-	cyt	0					158
O65200 UniProt NPD GO	PYRC1_PYRCO	Major allergen Pyr c 1	0.02	-	cyt	0					159
Q40237 UniProt NPD GO	MPA5B_LOLPR	Major pollen allergen Lol p 5b precursor (Lol p Vb)	0.02	-	mit	1 *	Starch granule (By similarity)				339
Q40638 UniProt NPD GO	MPAO1_ORYSA	Major pollen allergen Ory s 1 precursor (Ory s I)	0.02	-	vac	0	Secreted protein				267
P56164 UniProt NPD GO	MPA51_PHAAQ	Major pollen allergen Pha a 5.1 precursor (Pha A 5) (Clone 28)	0.02	-	mit	0					320
P35495 UniProt NPD GO	PSP1_PIG	Major seminal plasma glycoprotein PSP-I precursor (SP3)	0.02	-	exc	0	Secreted protein			1SPP	133
P23636 UniProt NPD GO	PP2A2_SCHPO	Major serine/threonine-protein phosphatase PP2A-2 catalytic subunit (EC 3.1.3.16)	0.02	-	cyt	0		cytoplasm [IDA]			322
P84855 UniProt NPD GO	MUP_RATRT	Major urinary protein (MUP) (Alpha-2u-globulin) (Alpha(2)-euglobulin) (Fragments)	0.02	-	nuc	0	Secreted protein (By similarity)				30
P11590 UniProt NPD GO	MUP4_MOUSE	Major urinary protein 4 precursor (MUP 4)	0.02	-	exc	0	Secreted protein				178
P11591 UniProt NPD GO	MUP5_MOUSE	Major urinary protein 5 precursor (MUP 5)	0.02	-	exc	0	Secreted protein				180
Q43743 UniProt NPD GO	MDHG1_BRANA	Malate dehydrogenase 1, glyoxysomal precursor (EC 1.1.1.37)	0.02	-	cyt	0	Glyoxysome				358
Q9XFW3 UniProt NPD GO	MDHG2_BRANA	Malate dehydrogenase 2, glyoxysomal precursor (EC 1.1.1.37)	0.02	-	cyt	0	Glyoxysome				358
P46489 UniProt NPD GO	MDHP_FLABI	Malate dehydrogenase [NADP], chloroplast precursor (EC 1.1.1.82) (NADP-MDH)	0.02	-	cyt	0	Plastid; chloroplast			1CIV	453
Q9SML8 UniProt NPD GO	MDHC_BETVU	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37)	0.02	-	cyt	0	Cytoplasm (By similarity)				332
Q04820 UniProt NPD GO	MDHC_ECHGR	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37)	0.02	-	cyt	0	Cytoplasm				332
P83778 UniProt NPD GO	MDHC_CANAL	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Fragments)	0.02	-	cyt	0	Cytoplasm				51
Q9ZP05 UniProt NPD GO	MDHG1_ARATH	Malate dehydrogenase, glyoxysomal precursor (EC 1.1.1.37) (mbNAD-MDH)	0.02	-	cyt	0	Glyoxysome (Potential)				354
P84575 UniProt NPD GO	MAF_SCHMA	Male attracting factor (Sm-MAF) (Fragment)	0.02	-		0					6

You are viewing entries 84251 to 84300 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.