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
P61872 UniProt NPD GO	LIP_RHIOR	Lipase precursor (EC 3.1.1.3) (Triacylglycerol lipase) (ROL) (RDL)	0.12	-	exc	0	Secreted protein; extracellular space			1TIC	392
P53715 UniProt NPD GO	LCN1_PIG	Lipocalin-1 precursor (Von Ebner gland protein) (VEG protein) (Tear prealbumin) (TP) (Tear lipocalin ...	0.12	-	exc	0	Secreted protein				176
P49060 UniProt NPD GO	LIPL_PAPAN	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.12	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				475
P27480 UniProt NPD GO	LOXA_PHAVU	Lipoxygenase 1 (EC 1.13.11.12)	0.12	-	cyt	0	Cytoplasm				862
P41489 UniProt NPD GO	LMT3_LOCMI	Locustamyotropin-3 (Lom-MT-3)	0.12	-		0	Secreted protein				9
Q60714 UniProt NPD GO	S27A1_MOUSE	Long-chain fatty acid transport protein 1 (EC 6.2.1.-) (Fatty acid transport protein 1) (FATP-1) (So ...	0.12	-	end	1 *	Cell membrane; peripheral membrane protein. Intracellular membrane; peripheral membrane protein. Pla ...	cytoplasmic vesicle [TAS] plasma membrane [TAS]			646
Q60513 UniProt NPD GO	FCGR2_CAVPO	Low affinity immunoglobulin gamma Fc region receptor II precursor (Fc-gamma RII) (FcRII) (IgG Fc rec ...	0.12	-	end	1	Membrane; single-pass type I membrane protein				341
P31579 UniProt NPD GO	LCE_ORYLA	Low choriolytic enzyme precursor (EC 3.4.24.66) (Hatching enzyme zinc-protease LCE subunit) (Choriol ...	0.12	-	exc	0	Stored as proenzymes in the zymogen granules				271
P82716 UniProt NPD GO	LCR1_ARATH	Low-molecular-weight cysteine-rich protein LCR1 precursor	0.12	-	vac	1 *					89
Q6IY74 UniProt NPD GO	LSHB_RABIT	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.12	-	nuc	0	Secreted protein				141
Q43415 UniProt NPD GO	LCYB_CAPAN	Lycopene beta cyclase, chloroplast precursor (EC 1.14.-.-)	0.12	-	nuc	0	Plastid; chloroplast. Plastid; chromoplast				498
Q5WR07 UniProt NPD GO	TNFB_CANFA	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.12	-	mit	0	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				204
Q9JM09 UniProt NPD GO	TNFB_MARMO	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.12	-	cyt	0	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				205
Q06332 UniProt NPD GO	TNFB_RAT	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.12	-	vac	1 *	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				202
P46628 UniProt NPD GO	EDG2_SHEEP	Lysophosphatidic acid receptor Edg-2 (LPA receptor 1) (LPA-1)	0.12	-	end	7	Membrane; multi-pass membrane protein				393
Q28031 UniProt NPD GO	EDG2_BOVIN	Lysophosphatidic acid receptor Edg-2 (LPA receptor 1) (LPA-1) (Rec1.3)	0.12	-	end	7	Membrane; multi-pass membrane protein				364
Q60961 UniProt NPD GO	MTRP_MOUSE	Lysosomal-associated transmembrane protein 4A (Golgi 4-transmembrane spanning transporter) (Mouse tr ...	0.12	-	end	4 *	Intracytoplasmic membrane; multi-pass membrane protein (Potential). May reside in an intracellular m ...				233
Q7LZQ3 UniProt NPD GO	LYSC_CRAFA	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.12	-	nuc	0					129
P81708 UniProt NPD GO	LYSC1_CANFA	Lysozyme C, milk isozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.12	-	nuc	0				2CWI	129
P00718 UniProt NPD GO	LYG_ANSAN	Lysozyme G (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase) (Goose-type lysozyme)	0.12	-	cyt	0	Secreted protein			154L	185
P79017 UniProt NPD GO	ALL2_ASPFU	Major allergen Asp f 2 precursor (Asp f II)	0.12	-	exc	0	Secreted protein. Cell-associated				310
P05634 UniProt NPD GO	MSP10_CAEEL	Major sperm protein 10/36/56/76 (MSP)	0.12	-	cyt	0					126
Q18461 UniProt NPD GO	MSP49_CAEEL	Major sperm protein 49 (MSP)	0.12	-	cyt	0					126
P37229 UniProt NPD GO	MDHP2_SORBI	Malate dehydrogenase [NADP] 2, chloroplast precursor (EC 1.1.1.82) (NADP-MDH-2)	0.12	-	mit	0	Plastid; chloroplast				432
P21826 UniProt NPD GO	MASZ_YEAST	Malate synthase 2, glyoxysomal (EC 2.3.3.9)	0.12	-	pox	0	Glyoxysome				554
P81034 UniProt NPD GO	MOIH1_CANPG	Mandibular organ-inhibiting hormone 1 (MOIH-1)	0.12	-	mit	0	Secreted protein				78
Q20157 UniProt NPD GO	MPU1_CAEEL	Mannose-P-dolichol utilization defect 1 protein homolog	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				238
P83721 UniProt NPD GO	LEC1_CRAMO	Mannose/glucose-specific lectin Cramoll (Iso1) [Contains: Cramoll alpha chain; Cramoll beta chain] ( ...	0.12	-	nuc	0				1MVQ	234
P12350 UniProt NPD GO	MER10_EUPRA	Mating pheromone Er-10 precursor (Euplomone R10)	0.12	-	nuc	1 *	Secreted protein			1ERP	75
P50282 UniProt NPD GO	MMP9_RAT	Matrix metalloproteinase-9 precursor (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gel ...	0.12	-	exc	0		extracellular space [ISS]			708
Q58T42 UniProt NPD GO	M4H34_BOMMX	Maximins 4/H3 type 4 precursor [Contains: Maximin-4; Maximin-H3]	0.12	-	end	0	Secreted protein				139
Q58T91 UniProt NPD GO	MYHV1_BOMMX	Maximins y/Hv type 1 precursor [Contains: Maximin-y; Maximin-Hv]	0.12	-	end	0	Secreted protein				142
P37384 UniProt NPD GO	DMC1_LILLO	Meiotic recombination protein DMC1 homolog	0.12	-	cyt	0	Nucleus (Potential)				349
Q8MJ89 UniProt NPD GO	MCHR1_MACMU	Melanin-concentrating hormone receptor 1 (MCH receptor 1) (MCHR-1) (MCH-R1) (MCH1R) (MCH-1R) (MCHR) ...	0.12	-	end	7	Membrane; multi-pass membrane protein				388
P97639 UniProt NPD GO	MCHR1_RAT	Melanin-concentrating hormone receptor 1 (MCH receptor 1) (MCHR-1) (MCH-R1) (MCH1R) (MCH-1R) (MCHR) ...	0.12	-	end	7 *	Membrane; multi-pass membrane protein				360
Q6A155 UniProt NPD GO	MSHR_ALOLA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	7 *	Membrane; multi-pass membrane protein				317
P56444 UniProt NPD GO	MSHR_CAPHI	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864J4 UniProt NPD GO	MSHR_MACMU	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	6 *	Membrane; multi-pass membrane protein				317
Q864J8 UniProt NPD GO	MSHR_MACNE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	6 *	Membrane; multi-pass membrane protein				317
Q864J7 UniProt NPD GO	MSHR_MACSL	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	6 *	Membrane; multi-pass membrane protein				317
Q864J6 UniProt NPD GO	MSHR_MACSY	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	4 *	Membrane; multi-pass membrane protein				317
P56447 UniProt NPD GO	MSHR_OVIMO	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864I7 UniProt NPD GO	MSHR_TRAAU	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	8 *	Membrane; multi-pass membrane protein				317
Q864I6 UniProt NPD GO	MSHR_TRACR	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	8 *	Membrane; multi-pass membrane protein				317
Q864I4 UniProt NPD GO	MSHR_TRAFR	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	8 *	Membrane; multi-pass membrane protein				317
Q864I5 UniProt NPD GO	MSHR_TRAOB	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.12	-	end	8 *	Membrane; multi-pass membrane protein				317
P43361 UniProt NPD GO	MAGA8_HUMAN	Melanoma-associated antigen 8 (MAGE-8 antigen)	0.12	-	nuc	0			300341		234
P01202 UniProt NPD GO	MLB_HORSE	Melanotropin beta (Beta-MSH)	0.12	-		0	Secreted protein				18
P49286 UniProt NPD GO	MTR1B_HUMAN	Melatonin receptor type 1B (Mel-1B-R) (Mel1b melatonin receptor)	0.12	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600804		362
P01504 UniProt NPD GO	MEL_APIFL	Melittin	0.12	-	mit	0	Secreted protein				26

You are viewing entries 61401 to 61450 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.