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
Q61603 UniProt NPD GO	GLRA4_MOUSE	Glycine receptor alpha-4 chain precursor	0.33	+	end	4 *	Membrane; multi-pass membrane protein				456
P06738 UniProt NPD GO	PHSG_YEAST	Glycogen phosphorylase (EC 2.4.1.1)	0.33	-	cyt	0		cytoplasm [IC]		1YGP	901
Q6CTT3 UniProt NPD GO	GPI11_KLULA	Glycosylphosphatidylinositol anchor biosynthesis protein 11	0.33	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				217
Q66PG1 UniProt NPD GO	LARG2_BRARE	Glycosyltransferase-like protein LARGE2 (EC 2.4.-.-) (Glycosyltransferase-like 1B)	0.33	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				750
P51654 UniProt NPD GO	GPC3_HUMAN	Glypican-3 precursor (Intestinal protein OCI-5) (GTR2-2) (MXR7)	0.33	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	integral to plasma membrane [TAS]	312870		580
Q01776 UniProt NPD GO	GNRHR_MOUSE	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R)	0.33	-	nuc	7 *	Membrane; multi-pass membrane protein				327
P22749 UniProt NPD GO	GNLY_HUMAN	Granulysin precursor (Protein NKG5) (Lymphokine LAG-2) (T-cell activation protein 519)	0.33	-	nuc	0	Secreted protein. Located in the cytotoxic granules of T-cells, which are released upon antigen stim ...	extracellular space [TAS]	188855	1L9L	145
Q07370 UniProt NPD GO	SOM2_MACMU	Growth hormone variant precursor (GH-V) (Placenta-specific growth hormone) (Growth hormone 2)	0.33	-	exc	0	Secreted protein (By similarity)				217
O43903 UniProt NPD GO	GAS2_HUMAN	Growth-arrest-specific protein 2 (GAS-2)	0.33	-	nuc	0	Component of the microfilament system. Colocalizes with actin fibers at the cell border and along th ...	actin filament [TAS]	602835		313
P87383 UniProt NPD GO	GNAI1_ORYLA	Guanine nucleotide-binding protein G(i) subunit alpha-1 (Adenylate cyclase-inhibiting G alpha protei ...	0.33	-	gol	0					353
P53359 UniProt NPD GO	GNAO_MANSE	Guanine nucleotide-binding protein G(o) subunit alpha	0.33	-	cyt	0					354
Q9HAV0 UniProt NPD GO	GBB4_HUMAN	Guanine nucleotide-binding protein subunit beta 4 (Transducin beta chain 4)	0.33	-	cyt	0					339
Q7RWT0 UniProt NPD GO	GBG_NEUCR	Guanine nucleotide-binding protein subunit gamma	0.33	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				86
P01895 UniProt NPD GO	HA1Y_MOUSE	H-2 class I histocompatibility antigen, alpha chain (Clone PAG64) (Fragment)	0.33	-	cyt	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			298
Q6FNL3 UniProt NPD GO	NOP10_CANGA	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3) (snoRNP protein NOP1 ...	0.33	-	nuc	0	Nucleus; nucleolus (By similarity)				57
P30481 UniProt NPD GO	1B44_HUMAN	HLA class I histocompatibility antigen, B-44 alpha chain precursor (MHC class I antigen B*44) (Bw-44 ...	0.33	-	end	1 *	Membrane; single-pass type I membrane protein		142830	1SYV	362
Q31612 UniProt NPD GO	1B73_HUMAN	HLA class I histocompatibility antigen, B-73 alpha chain precursor (MHC class I antigen B*73)	0.33	-	end	1	Membrane; single-pass type I membrane protein		142830		363
P41753 UniProt NPD GO	HSP70_ACHKL	Heat shock 70 kDa protein	0.33	-	cyt	0					652
Q00043 UniProt NPD GO	HSP70_AJECA	Heat shock 70 kDa protein	0.33	-	nuc	1					705
P16394 UniProt NPD GO	HSP70_BRELC	Heat shock 70 kDa protein	0.33	-	cyt	0					676
P40918 UniProt NPD GO	HSP70_CLAHE	Heat shock 70 kDa protein (Allergen Cla h 4) (Cla h IV)	0.33	-	cyt	0					643
P16627 UniProt NPD GO	HS70L_MOUSE	Heat shock 70 kDa protein 1L (Heat shock 70 kDa protein 1-like) (Heat shock 70 kDa-like protein 1) ( ...	0.33	-	cyt	0					641
Q06248 UniProt NPD GO	HSP74_PARLI	Heat shock 70 kDa protein IV (HSP70 IV)	0.33	-	cyt	0					639
P06762 UniProt NPD GO	HMOX1_RAT	Heme oxygenase 1 (EC 1.14.99.3) (HO-1) (HSP32)	0.33	-	cyt	1	Microsome	caveolar membrane [IDA] cytosol [IDA] nucleolus [IDA] nucleus [IDA] plasma membrane [TAS]		1VGI	289
Q99075 UniProt NPD GO	HBEGF_HUMAN	Heparin-binding EGF-like growth factor precursor (HB-EGF) (HBEGF) (Diphtheria toxin receptor) (DT-R) ...	0.33	-	end	1 *	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...	cell surface [NAS] extracellular space [TAS] integral to plasma membrane [TAS]	126150	1XDT	208
P26928 UniProt NPD GO	HGFL_MOUSE	Hepatocyte growth factor-like protein precursor (Macrophage stimulatory protein) (MSP) [Contains: He ...	0.33	-	exc	0					716
P51858 UniProt NPD GO	HDGF_HUMAN	Hepatoma-derived growth factor (HDGF) (High-mobility group protein 1-like 2) (HMG-1L2)	0.33	-	nuc	0	Cytoplasm	cytoplasm [TAS] extracellular space [TAS]	300043	1RI0	240
Q9GKZ0 UniProt NPD GO	HFE_CERSI	Hereditary hemochromatosis protein homolog precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein				348
Q9GL43 UniProt NPD GO	HFE_DICBI	Hereditary hemochromatosis protein homolog precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein				348
P17710 UniProt NPD GO	HXK1_MOUSE	Hexokinase-1 (EC 2.7.1.1) (Hexokinase type I) (HK I) (Hexokinase, tumor isozyme)	0.33	-	cyt	0	Isoform HK1: Mitochondrion; mitochondrial outer membrane; peripheral membrane protein. Its hydrophob ...	cytosol [IDA] mitochondrion [IDA]			974
P16402 UniProt NPD GO	H13_HUMAN	Histone H1.3 (Histone H1c)	0.33	+	nuc	0	Nucleus	nucleosome [NAS]	142210		220
P40269 UniProt NPD GO	H1C6_TRYCR	Histone H1.C6/H1.C9	0.33	+	nuc	0					87
P15867 UniProt NPD GO	H1C2_XENLA	Histone H1C (Clone XLHW8)	0.33	+	nuc	0	Nucleus				220
P25470 UniProt NPD GO	H2A1_PEA	Histone H2A.1	0.33	+	nuc	0	Nucleus				150
Q9XG56 UniProt NPD GO	H2A1_LILLO	Histone H2A.1 (GcH2A)	0.33	-	nuc	0	Nucleus (By similarity)				110
P09322 UniProt NPD GO	H4_SCHPO	Histone H4	0.33	-	cyt	0	Nucleus (By similarity)				102
P08436 UniProt NPD GO	H4_VOLCA	Histone H4	0.33	-	cyt	0	Nucleus (By similarity)				102
Q6CC99 UniProt NPD GO	HAT1_YARLI	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				451
O00422 UniProt NPD GO	SAP18_HUMAN	Histone deacetylase complex subunit SAP18 (Sin3-associated polypeptide, 18 kDa) (Sin3-associated pol ...	0.33	-	nuc	0		histone deacetylase complex [TAS]	602949		153
Q9SRV2 UniProt NPD GO	SUVR3_ARATH	Histone-lysine N-methyltransferase SUVR3 (EC 2.1.1.43) (Suppressor of variegation 3-9-related protei ...	0.33	-	nuc	0	Nucleus (By similarity). Associates with euchromatic regions (By similarity)				338
Q9C5P1 UniProt NPD GO	SUVH7_ARATH	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH7 (EC 2.1.1.43) (Histone H3-K9 methyltr ...	0.33	-	cyt	0	Nucleus (By similarity). Associates with centromeric constitutive heterochromatin (By similarity)				693
P70354 UniProt NPD GO	MSX3_MOUSE	Homeobox protein MSX-3	0.33	+	nuc	0	Nucleus				204
P35733 UniProt NPD GO	YKF3_YEAST	Hypothetical 14.7 kDa protein in NUP120-CSE4 intergenic region	0.33	-	end	3 *					124
Q04655 UniProt NPD GO	YMA6_VICFA	Hypothetical 17.9 kDa protein in ATP6 5'region (ORF154)	0.33	-	nuc	0					154
P36042 UniProt NPD GO	YKU2_YEAST	Hypothetical 21.2 kDa protein in TOR2-MNN4 intergenic region	0.33	-	nuc	0					193
P39978 UniProt NPD GO	YEH7_YEAST	Hypothetical 21.7 kDa protein in HXT8-CAN1 intergenic region	0.33	-	cyt	0					195
P48238 UniProt NPD GO	YG3O_YEAST	Hypothetical 25.2 kDa protein in RSR1-CYS4 intergenic region	0.33	-	nuc	0					217
P53275 UniProt NPD GO	YG37_YEAST	Hypothetical 35.7 kDa protein in ASN2-PHB1 intergenic region	0.33	-	nuc	0					312
Q03687 UniProt NPD GO	YMP0_YEAST	Hypothetical 46.9 kDa protein in PLB1-HXT2 intergenic region	0.33	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			405
P32035 UniProt NPD GO	YCX1_CUSRE	Hypothetical 6.8 kDa protein in trnL 3'region (ORF 55)	0.33	-	cyt	0	Plastid				55

You are viewing entries 37601 to 37650 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.