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
P46521 UniProt NPD GO	LEA5A_GOSHI	Late embryogenesis abundant protein Lea5-A	0.06	-	nuc	0					105
O75845 UniProt NPD GO	SC5D_HUMAN	Lathosterol oxidase (EC 1.14.21.6) (Lathosterol 5-desaturase) (Delta-7-sterol 5-desaturase) (C-5 ste ...	0.06	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)		607330		299
P49291 UniProt NPD GO	LAZA_SCHAM	Lazarillo protein precursor	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				214
P09617 UniProt NPD GO	THN5_HORVU	Leaf-specific thionin precursor [Contains: Leaf-specific thionin; Acidic protein]	0.06	-	nuc	0	Secreted protein (Potential)				137
P42088 UniProt NPD GO	LEC_BOWMI	Lectin (Agglutinin) (BMA) [Contains: Lectin beta chain; Lectin alpha chain]	0.06	-	nuc	0					240
P83956 UniProt NPD GO	LG31_VIGUS	Lectin 31 kDa subunit (Hemagglutinin 31 kDa subunit) (Fragment)	0.06	-		0					15
P56625 UniProt NPD GO	LEC_VICVI	Lectin B4 (VVLB4) (Fragments)	0.06	-	cyt	0				1N47	185
P81637 UniProt NPD GO	LECA_DIOGU	Lectin alpha chain [Contains: Lectin beta chain; Lectin gamma-1 chain; Lectin gamma-2 chain]	0.06	-	nuc	0				1H9W	237
P16030 UniProt NPD GO	LEC_BAUPU	Lectin precursor	0.06	-	cyt	0					290
P84282 UniProt NPD GO	LECA_PHYAM	Lectin-A (PL-A) (Fragments)	0.06	-	nuc	0					64
O88803 UniProt NPD GO	LECT2_MOUSE	Leukocyte cell-derived chemotaxin 2 precursor (Chondromodulin II) (ChM-II)	0.06	-	exc	0	Secreted protein				151
P37854 UniProt NPD GO	CHLB_PLESC	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.06	-	cyt	0	Plastid; chloroplast				100
P37857 UniProt NPD GO	CHLB_ZAMFI	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.06	-	mit	0	Plastid; chloroplast				103
P20261 UniProt NPD GO	LIP1_CANRU	Lipase 1 precursor (EC 3.1.1.3)	0.06	-	mit	0				1TRH	549
Q04396 UniProt NPD GO	LPP1_YEAST	Lipid phosphate phosphatase 1 (EC 3.1.3.-) (Phosphatidate phosphatase) (EC 3.1.3.4)	0.06	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	membrane [IDA]			274
Q99732 UniProt NPD GO	LITAF_HUMAN	Lipopolysaccharide-induced tumor necrosis factor-alpha factor (LPS-induced TNF-alpha factor) (p53-in ...	0.06	-	nuc	0	Lysosome; lysosomal membrane; peripheral membrane protein; cytoplasmic side. Associated with membran ...		603795		161
P27481 UniProt NPD GO	LOXB_PHAVU	Lipoxygenase (EC 1.13.11.12) (Fragment)	0.06	-	cyt	0	Cytoplasm				741
Q7LZS8 UniProt NPD GO	IVBER_DENAN	Long epsilon-dendrotoxin Arg55 [Contains: Short epsilon-dendrotoxin Arg55]	0.06	-	nuc	0	Secreted protein				59
P01385 UniProt NPD GO	NXL1_ACAAN	Long neurotoxin 1	0.06	-	nuc	0	Secreted protein				73
P01389 UniProt NPD GO	NXL1_NAJHC	Long neurotoxin 1 (Toxin III)	0.06	-	nuc	0	Secreted protein				72
P23490 UniProt NPD GO	LORI_HUMAN	Loricrin	0.06	-	nuc	0	Cytoplasm. Nucleus; nucleoplasm	cornified envelope [IDA] insoluble fraction [TAS]	604117		316
P09337 UniProt NPD GO	LP4_BOMMO	Low molecular 30 kDa lipoprotein PBMHPC-21 precursor	0.06	-	exc	0	Secreted protein; extracellular space				251
P82890 UniProt NPD GO	PPA1_DROME	Low molecular weight phosphotyrosine protein phosphatase 1 (EC 3.1.3.48) (Low molecular weight cytos ...	0.06	-	cyt	0	Cytoplasm				155
P32467 UniProt NPD GO	HXT4_YEAST	Low-affinity glucose transporter HXT4 (Low-affinity glucose transporter LGT1)	0.06	-	end	11	Membrane; multi-pass membrane protein				576
Q91YK8 UniProt NPD GO	LYPD3_MOUSE	Ly6/PLAUR domain-containing protein 3 precursor (GPI-anchored metastasis-associated protein C4.4A ho ...	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				363
P05533 UniProt NPD GO	LY6A_MOUSE	Lymphocyte antigen Ly-6A.2/Ly-6E.1 precursor (T-cell-activating protein) (TAP)	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	external side of plasma membrane [IDA]			134
P51672 UniProt NPD GO	XCL1_RAT	Lymphotactin precursor (XCL1) (Cytokine SCM-1) (Small inducible cytokine C1)	0.06	-	vac	0	Secreted protein (By similarity)				114
P09225 UniProt NPD GO	TNFB_MOUSE	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.06	-	exc	1 *	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				202
Q84MC2 UniProt NPD GO	Y5195_ARATH	Lysine decarboxylase-like protein At5g11950	0.06	-	cyt	0				1YDH	216
P32487 UniProt NPD GO	LYP1_YEAST	Lysine-specific permease	0.06	-	end	11	Membrane; multi-pass membrane protein	mitochondrion [IDA]			611
P43059 UniProt NPD GO	CAN1_CANAL	Lysine/arginine permease (Basic amino acids permease)	0.06	-	end	12	Membrane; multi-pass membrane protein				571
Q5R8C2 UniProt NPD GO	LYPL1_PONPY	Lysophospholipase-like protein 1 (EC 3.1.2.-)	0.06	-	cyt	0	Cytoplasm (By similarity)				236
Q5RBU7 UniProt NPD GO	PCP_PONPY	Lysosomal Pro-X carboxypeptidase precursor (EC 3.4.16.2) (Prolylcarboxypeptidase) (PRCP) (Proline ca ...	0.06	-	mit	1 *	Lysosome (By similarity)				496
P42785 UniProt NPD GO	PCP_HUMAN	Lysosomal Pro-X carboxypeptidase precursor (EC 3.4.16.2) (Prolylcarboxypeptidase) (PRCP) (Proline ca ...	0.06	-	mit	1 *	Lysosome		176785		496
Q9VKH6 UniProt NPD GO	PPT2_DROME	Lysosomal thioesterase PPT2 homolog precursor (EC 3.1.2.-) (PPT-2)	0.06	-	end	1 *	Lysosome (By similarity)				288
Q61168 UniProt NPD GO	LAPM5_MOUSE	Lysosomal-associated multitransmembrane protein (Retinoic acid-inducible E3 protein)	0.06	-	end	4 *	Lysosome; lysosomal membrane; multi-pass membrane protein				261
P17047 UniProt NPD GO	LAMP2_MOUSE	Lysosome-associated membrane glycoprotein 2 precursor (LAMP-2) (Lysosomal membrane glycoprotein type ...	0.06	-	end	1 *	Cell membrane; single-pass type I membrane protein. Endosome; endosomal membrane; single-pass type I ...	late endosome [IDA] lysosome [IDA]			415
Q27650 UniProt NPD GO	LYS4_ENTHI	Lysozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.06	-	mit	0	Cytoplasmic granule				198
P00700 UniProt NPD GO	LYSC_COLVI	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.06	-	nuc	0				1DKK	129
P00702 UniProt NPD GO	LYSC_PHACO	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.06	-	end	0				1JHL	147
P79268 UniProt NPD GO	LYSC_SAGOE	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.06	-	vac	0					148
Q9PU28 UniProt NPD GO	LYSC_SCOMX	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.06	-	end	0					143
P00698 UniProt NPD GO	LYSC_CHICK	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C) (Allergen Gal d 4) (Gal d IV)	0.06	-	end	1 *				8LYZ	147
P81709 UniProt NPD GO	LYSC2_CANFA	Lysozyme C, spleen isozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.06	-	nuc	0					130
P81710 UniProt NPD GO	LYSC2_HORSE	Lysozyme C, spleen isozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C) (Fragment)	0.06	-	cyt	0					33
Q9D7Q0 UniProt NPD GO	LYG1_MOUSE	Lysozyme g-like protein 1 precursor	0.06	-	exc	0	Secreted protein (Probable)				197
P50717 UniProt NPD GO	LYS_HYPCU	Lysozyme precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.06	-	nuc	0					142
Q40190 UniProt NPD GO	M7_LILHE	M7 protein precursor (LHM7)	0.06	-	exc	0					89
Q9C7I7 UniProt NPD GO	ML165_ARATH	MLP-like protein 165	0.06	-	cyt	0					152
Q9ZVF2 UniProt NPD GO	ML329_ARATH	MLP-like protein 329	0.06	-	cyt	0					151

You are viewing entries 72401 to 72450 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.