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
Q92236 UniProt NPD GO	GGPPS_GIBFU	Geranylgeranyl pyrophosphate synthetase (GGPP synthetase) (GGPPSase) (Geranylgeranyl diphosphate syn ...	0.34	-	nuc	0	Cytoplasm				418
Q9XHM5 UniProt NPD GO	G2OX2_PEA	Gibberellin 2-beta-dioxygenase 2 (EC 1.14.11.13) (Gibberellin 2-beta-hydroxylase 2) (Gibberellin 2-o ...	0.34	-	nuc	0					345
O59709 UniProt NPD GO	GIT7_SCHPO	Glucose insensitive transcription protein 7	0.34	-	nuc	0					379
O60391 UniProt NPD GO	NMD3B_HUMAN	Glutamate [NMDA] receptor subunit 3B precursor (N-methyl-D-aspartate receptor subtype NR3B) (NR3B) ( ...	0.34	+	end	4	Cell membrane; multi-pass membrane protein (By similarity). Requires the presence of GRIN1 to be tar ...		606651		1043
P42261 UniProt NPD GO	GRIA1_HUMAN	Glutamate receptor 1 precursor (GluR-1) (GluR-A) (GluR-K1) (Glutamate receptor ionotropic, AMPA 1) ( ...	0.34	-	end	3	Membrane; multi-pass membrane protein	plasma membrane [TAS]	138248		906
Q4R5Y2 UniProt NPD GO	NADE1_MACFA	Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) (NAD(+) synthase [glutamine-hydrolyzing]) (NAD(+) ...	0.34	-	cyt	0					706
Q43307 UniProt NPD GO	PLSB_ARATH	Glycerol-3-phosphate acyltransferase, chloroplast precursor (EC 2.3.1.15) (GPAT)	0.34	-	mit	0	Plastid; chloroplast; chloroplast stroma				459
P23337 UniProt NPD GO	GYS1_YEAST	Glycogen [starch] synthase isoform 1 (EC 2.4.1.11)	0.34	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			707
Q3B7M9 UniProt NPD GO	PYGB_BOVIN	Glycogen phosphorylase, brain form (EC 2.4.1.1)	0.34	-	nuc	0					842
P51136 UniProt NPD GO	GSK3H_DICDI	Glycogen synthase kinase-3 homolog (EC 2.7.11.26) (GSK-3)	0.34	-	nuc	0					467
Q06885 UniProt NPD GO	GP10_DICDI	Glycoprotein gp100 precursor (P29F8)	0.34	-	exc	1	Membrane; single-pass type I membrane protein				544
Q9DGD4 UniProt NPD GO	GNIH_COTJA	Gonadotropin inhibitory hormone precursor [Contains: Gonadotropin inhibitory hormone (GnIH); Gonadot ...	0.34	-	nuc	0	Secreted protein				173
Q90375 UniProt NPD GO	GHR_COLLI	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.34	-	end	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				611
Q5USV7 UniProt NPD GO	GDF8_AEPME	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.34	+	cyt	0	Secreted protein (By similarity)				375
O35312 UniProt NPD GO	GDF8_RAT	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.34	+	cyt	0	Secreted protein (By similarity)				376
P30676 UniProt NPD GO	GNAI_ASTPE	Guanine nucleotide-binding protein G(i) subunit alpha (Adenylate cyclase-inhibiting G alpha protein) ...	0.34	-	gol	0					353
P38402 UniProt NPD GO	GNAI2_CAVPO	Guanine nucleotide-binding protein G(i), alpha-2 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.34	-	gol	0					354
Q9DC51 UniProt NPD GO	GNAI3_MOUSE	Guanine nucleotide-binding protein G(k) subunit alpha (G(i) alpha-3)	0.34	-	cyt	0		cytoplasm [IDA] Golgi apparatus [IDA] heterotrimeric G-protein complex [TAS]			353
P28051 UniProt NPD GO	GPA1_CAEEL	Guanine nucleotide-binding protein alpha-1 subunit	0.34	-	cyt	0					357
Q60XS3 UniProt NPD GO	GPA16_CAEBR	Guanine nucleotide-binding protein alpha-16 subunit	0.34	-	cyt	0					353
P01900 UniProt NPD GO	HA12_MOUSE	H-2 class I histocompatibility antigen, D-D alpha chain precursor (H-2D(D))	0.34	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]		1QO3	365
P60507 UniProt NPD GO	EFC1_HUMAN	HERV-F(c)1_Xq21.33 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Fc1env) (HER ...	0.34	-	end	1 *					584
P61567 UniProt NPD GO	ENK12_HUMAN	HERV-K_1q22 provirus ancestral Env polyprotein (Envelope polyprotein) (HERV-K102 envelope protein) ( ...	0.34	-	end	2					588
P16188 UniProt NPD GO	1A30_HUMAN	HLA class I histocompatibility antigen, A-30 alpha chain precursor (MHC class I antigen A*30)	0.34	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142800		365
P30480 UniProt NPD GO	1B42_HUMAN	HLA class I histocompatibility antigen, B-42 alpha chain precursor (MHC class I antigen B*42)	0.34	-	end	1	Membrane; single-pass type I membrane protein		142830		362
P30495 UniProt NPD GO	1B56_HUMAN	HLA class I histocompatibility antigen, B-56 alpha chain precursor (MHC class I antigen B*56) (Bw-56 ...	0.34	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
Q29836 UniProt NPD GO	1B67_HUMAN	HLA class I histocompatibility antigen, B-67 alpha chain precursor (MHC class I antigen B*67)	0.34	-	end	1	Membrane; single-pass type I membrane protein		142830		362
P30460 UniProt NPD GO	1B08_HUMAN	HLA class I histocompatibility antigen, B-8 alpha chain precursor (MHC class I antigen B*8)	0.34	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142830	1MI5	362
P04222 UniProt NPD GO	1C03_HUMAN	HLA class I histocompatibility antigen, Cw-3 alpha chain precursor (MHC class I antigen Cw*3)	0.34	-	end	1	Membrane; single-pass type I membrane protein		142840	1EFX	366
P34934 UniProt NPD GO	HSP7X_PIG	Heat shock 70 kDa protein (Fragment)	0.34	-	mit	0					379
P16019 UniProt NPD GO	HSP70_THEAN	Heat shock 70 kDa protein (HSP 70.1) (70 kDa heat shock protein)	0.34	+	cyt	0					646
Q27031 UniProt NPD GO	HSP70_THEPA	Heat shock 70 kDa protein (HSP 70.1) (70 kDa heat shock protein)	0.34	+	cyt	0					647
P41825 UniProt NPD GO	HSP71_ANOAL	Heat shock protein 70 A1	0.34	-	cyt	0					640
P41826 UniProt NPD GO	HSP72_ANOAL	Heat shock protein 70 A2	0.34	-	cyt	0					640
P09841 UniProt NPD GO	HGLB_SCHMA	Hemoglobinase precursor (EC 3.4.22.34) (Antigen SM32)	0.34	-	nuc	0					429
Q76KB1 UniProt NPD GO	HS2ST_CHICK	Heparan sulfate 2-O-sulfotransferase 1 (EC 2.8.2.-) (cHS2ST)	0.34	+	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				356
Q06175 UniProt NPD GO	HBEGF_RAT	Heparin-binding EGF-like growth factor precursor (HB-EGF) (HBEGF)	0.34	-	end	1 *	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...				208
P60018 UniProt NPD GO	HFE_PANTR	Hereditary hemochromatosis protein homolog precursor (HLA-H)	0.34	-	end	1	Membrane; single-pass type I membrane protein				348
Q30201 UniProt NPD GO	HFE_HUMAN	Hereditary hemochromatosis protein precursor (HLA-H)	0.34	-	end	1	Membrane; single-pass type I membrane protein	cytoplasm [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	176200	1DE4	348
Q8BLY7 UniProt NPD GO	HPS6_MOUSE	Hermansky-Pudlak syndrome 6 protein homolog (Ruby-eye protein) (Ru)	0.34	-	mit	0					805
O74712 UniProt NPD GO	HIS2_CANAL	Histidine biosynthesis trifunctional protein [Includes: Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4. ...	0.34	-	cyt	0					838
P15868 UniProt NPD GO	H1_PSAMI	Histone H1 (Fragment)	0.34	+	nuc	0	Nucleus				159
P15869 UniProt NPD GO	H1B_STRPU	Histone H1-beta, late embryonic	0.34	+	nuc	0	Nucleus				211
P15870 UniProt NPD GO	H1D_STRPU	Histone H1-delta	0.34	+	nuc	0	Nucleus				185
P43277 UniProt NPD GO	H13_MOUSE	Histone H1.3 (H1 VAR.4) (H1d)	0.34	+	nuc	0	Nucleus				220
P81199 UniProt NPD GO	H35_STYLE	Histone H3-5 (Fragment)	0.34	-	nuc	0	Nucleus (By similarity)				114
P81200 UniProt NPD GO	H36_STYLE	Histone H3-6 (Fragment)	0.34	-	nuc	0	Nucleus (By similarity)				114
P17319 UniProt NPD GO	H32_TETBO	Histone H3.2 (Fragment)	0.34	-	nuc	0	Nucleus (By similarity)				40
P62793 UniProt NPD GO	H4_AGABI	Histone H4	0.34	-	cyt	0	Nucleus (By similarity)				102
Q7LKT3 UniProt NPD GO	H4_ASPFU	Histone H4	0.34	-	cyt	0	Nucleus (By similarity)				102

You are viewing entries 36701 to 36750 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.