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
Q812E8 UniProt NPD GO	NADE1_RAT	Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) (NAD(+) synthase [glutamine-hydrolyzing]) (NAD(+) ...	0.37	-	mit	0					725
P34291 UniProt NPD GO	PQN8_CAEEL	Glutamine/asparagine-rich protein pqn-8	0.37	-	exc	0					401
Q09151 UniProt NPD GO	GLUA3_ORYSA	Glutelin type-A 3 precursor [Contains: Glutelin type-A 3 acidic chain; Glutelin type-A 3 basic chain ...	0.37	-	exc	0					496
O93430 UniProt NPD GO	GLRA1_BRARE	Glycine receptor alphaZ1 chain precursor	0.37	-	end	4	Membrane; multi-pass membrane protein				444
P17625 UniProt NPD GO	GYS2_RAT	Glycogen [starch] synthase, liver (EC 2.4.1.11)	0.37	-	end	0		cell cortex [IDA] cortical actin cytoskeleton [IDA] cytoplasm [IDA] cytoskeleton [IDA] cytosol [IDA] ectoplasm [IDA] insoluble fraction [IDA] soluble fraction [IDA]			703
Q9R087 UniProt NPD GO	GPC6_MOUSE	Glypican-6 precursor	0.37	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				555
Q9H2G9 UniProt NPD GO	GO45_HUMAN	Golgin 45 (Basic leucine zipper nuclear factor 1) (JEM-1) (p45 basic leucine-zipper nuclear factor)	0.37	-	nuc	0	Golgi apparatus; Golgi lumen. Isoform 1: Nucleus. Isoform 2: Cytoplasm	cytoplasm [NAS] nucleus [NAS]	608692		400
Q6T5B8 UniProt NPD GO	GDF8_CAPHI	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.37	+	mit	0	Secreted protein (By similarity)				375
Q5USV8 UniProt NPD GO	GDF8_HEMJE	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.37	+	mit	0	Secreted protein (By similarity)				375
Q95J86 UniProt NPD GO	GDF8_MACFA	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.37	+	cyt	0	Secreted protein (By similarity)				375
O18828 UniProt NPD GO	GDF8_PAPHA	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.37	+	mit	0	Secreted protein (By similarity)				375
O18830 UniProt NPD GO	GDF8_SHEEP	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.37	+	mit	0	Secreted protein (By similarity)				375
P01899 UniProt NPD GO	HA11_MOUSE	H-2 class I histocompatibility antigen, D-B alpha chain precursor (H-2D(B))	0.37	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]		2F74	362
Q8N8A4 UniProt NPD GO	GAH6_HUMAN	HERV-H_22q11.2 provirus ancestral Gag polyprotein (Gag polyprotein)	0.37	-	nuc	0	Cell membrane (Potential)				273
Q9UKH7 UniProt NPD GO	ENK9_HUMAN	HERV-K_5q13.3 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (HERV-K104 envelop ...	0.37	-	nuc	1					277
P30464 UniProt NPD GO	1B15_HUMAN	HLA class I histocompatibility antigen, B-15 alpha chain precursor (MHC class I antigen B*15)	0.37	-	end	1	Membrane; single-pass type I membrane protein		142830	1XR9	362
P30479 UniProt NPD GO	1B41_HUMAN	HLA class I histocompatibility antigen, B-41 alpha chain precursor (MHC class I antigen B*41) (Bw-41 ...	0.37	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
P30501 UniProt NPD GO	1C02_HUMAN	HLA class I histocompatibility antigen, Cw-2 alpha chain precursor (MHC class I antigen Cw*2)	0.37	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142840		366
Q7YQC6 UniProt NPD GO	HSP71_CANFA	Heat shock 70 kDa protein 1	0.37	-	cyt	0					641
P08107 UniProt NPD GO	HSP71_HUMAN	Heat shock 70 kDa protein 1 (HSP70.1) (HSP70-1/HSP70-2)	0.37	-	cyt	0		cytoplasm [TAS] endoplasmic reticulum [TAS] mitochondrion [TAS] nucleus [TAS]	140550	1XQS	641
Q6S4N2 UniProt NPD GO	HS70B_PIG	Heat shock 70 kDa protein 1B (HSP70.2)	0.37	-	cyt	0					641
P17066 UniProt NPD GO	HSP76_HUMAN	Heat shock 70 kDa protein 6 (Heat shock 70 kDa protein B')	0.37	-	cyt	0			140555		643
P53421 UniProt NPD GO	HSP71_PICAN	Heat-shock protein 70 1 (HSP72)	0.37	-	cyt	0	Cytoplasm				644
Q9BQS6 UniProt NPD GO	HSPB9_HUMAN	Heat-shock protein beta-9 (HspB9)	0.37	-	nuc	0			608344		159
Q8BSL4 UniProt NPD GO	OST5_MOUSE	Heparan sulfate glucosamine 3-O-sulfotransferase 5 (EC 2.8.2.23) (Heparan sulfate D-glucosaminyl 3-O ...	0.37	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to membrane [ISS]			346
Q8IZT8 UniProt NPD GO	OST5_HUMAN	Heparan sulfate glucosamine 3-O-sulfotransferase 5 (EC 2.8.2.23) (Heparan sulfate D-glucosaminyl 3-O ...	0.37	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to membrane [NAS]	609407		346
P27656 UniProt NPD GO	LIPH_MOUSE	Hepatic triacylglycerol lipase precursor (EC 3.1.1.3) (Hepatic lipase) (HL)	0.37	-	exc	0	Secreted protein				510
P26927 UniProt NPD GO	HGFL_HUMAN	Hepatocyte growth factor-like protein precursor (Macrophage stimulatory protein) (MSP) (Macrophage-s ...	0.37	-	exc	0			142408	2ASU	711
Q8VHK7 UniProt NPD GO	HDGF_RAT	Hepatoma-derived growth factor (HDGF)	0.37	-	nuc	0	Cytoplasm (By similarity)			2B8A	237
Q99KG7 UniProt NPD GO	HPS4_MOUSE	Hermansky-Pudlak syndrome 4 protein homolog (Light-ear protein) (Le protein)	0.37	-	nuc	0		cytoplasm [ISS] cytoplasmic membrane-bound vesicle [IDA] lysosome [ISS] melanosome [ISS] membrane fraction [ISS]			671
P40270 UniProt NPD GO	H1C8_TRYCR	Histone H1.C8/H1.M1	0.37	+	nuc	0					74
P09590 UniProt NPD GO	H2A3_STRPU	Histone H2A-beta, sperm (Fragment)	0.37	-	nuc	0	Nucleus				88
P23754 UniProt NPD GO	H2B_EMENI	Histone H2B	0.37	-	nuc	0	Nucleus				139
Q9LQQ4 UniProt NPD GO	H2B1_ARATH	Histone H2B.1 (HTB1)	0.37	+	nuc	0	Nucleus (By similarity)				147
P40287 UniProt NPD GO	H4_ENTHI	Histone H4	0.37	-	cyt	0	Nucleus (By similarity)				118
Q8NIQ8 UniProt NPD GO	H42_PENFN	Histone H4.2	0.37	-	cyt	0	Nucleus (By similarity)				102
Q6BGW1 UniProt NPD GO	GCN5_DEBHA	Histone acetyltransferase GCN5 (EC 2.3.1.48)	0.37	-	cyt	0	Nucleus (By similarity)				455
P87394 UniProt NPD GO	DLX4_ELECQ	Homeobox protein DLX-4 (Fragment)	0.37	-	nuc	0	Nucleus (Potential)				131
P13297 UniProt NPD GO	MSX1_MOUSE	Homeobox protein MSX-1 (Msh homeobox 1-like protein) (Hox-7) (Hox-7.1)	0.37	+	nuc	0	Nucleus			1IG7	293
Q8N196 UniProt NPD GO	SIX5_HUMAN	Homeobox protein SIX5 (DM locus-associated homeodomain protein)	0.37	-	nuc	0	Cytoplasm. Nucleus		600963		739
Q23946 UniProt NPD GO	UBX_DROHY	Homeotic protein ultrabithorax (Fragment)	0.37	+	nuc	0	Nucleus				87
P09932 UniProt NPD GO	HO_YEAST	Homothallic switching endonuclease (Ho endonuclease)	0.37	-	cyt	0		nucleus [TAS]			586
Q68J42 UniProt NPD GO	LIPS_PIG	Hormone-sensitive lipase (EC 3.1.1.79) (HSL)	0.37	-	cyt	0					764
Q9NZL4 UniProt NPD GO	HPBP1_HUMAN	Hsp70-binding protein 1 (HspBP1) (Heat shock protein-binding protein 1) (Hsp70-interacting protein 1 ...	0.37	-	mit	0				1XQS	362
P47009 UniProt NPD GO	YJO4_YEAST	Hypothetical 11.7 kDa protein in IDS2-MPI2 intergenic region	0.37	-	mit	0		cytoplasm [IDA]			104
P47059 UniProt NPD GO	YJD2_YEAST	Hypothetical 12.4 kDa protein in DBP4-BET4 intergenic region	0.37	-	nuc	0					104
Q04438 UniProt NPD GO	YMZ7_YEAST	Hypothetical 13.2 kDa protein in HDF2-ILV2 intergenic region	0.37	-	nuc	0					115
P47152 UniProt NPD GO	YJ85_YEAST	Hypothetical 19.0 kDa protein in NNF1-STE24 intergenic region	0.37	-	mit	0					169
P38477 UniProt NPD GO	YMF39_MARPO	Hypothetical 21.1 kDa protein in COX1 3'region (ORF 183)	0.37	-	end	0					183
Q06463 UniProt NPD GO	YCF21_ANTSP	Hypothetical 21.4 kDa protein ycf21 (ORF 179)	0.37	-	nuc	0	Plastid; chloroplast				179

You are viewing entries 34201 to 34250 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.