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
Q9M462 UniProt NPD GO	GLGS_BRANA	Glucose-1-phosphate adenylyltransferase small subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.40	-	mit	0	Plastid; chloroplast (By similarity)				520
Q42882 UniProt NPD GO	GLGS_LYCES	Glucose-1-phosphate adenylyltransferase small subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.40	-	nuc	0	Plastid; chloroplast (By similarity)				521
P23509 UniProt NPD GO	GLGS_SOLTU	Glucose-1-phosphate adenylyltransferase small subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.40	-	nuc	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...			1YP4	521
Q8L743 UniProt NPD GO	G6PD3_ARATH	Glucose-6-phosphate 1-dehydrogenase 3, chloroplast precursor (EC 1.1.1.49) (G6PD3) (G6PDH3)	0.40	-	mit	0	Plastid; chloroplast (By similarity)				599
O09131 UniProt NPD GO	GSTO1_MOUSE	Glutathione transferase omega-1 (EC 2.5.1.18) (GSTO 1-1) (p28)	0.40	-	nuc	0	Cytoplasm (By similarity)				240
P07730 UniProt NPD GO	GLUA2_ORYSA	Glutelin type-A 2 precursor (Glutelin type II) [Contains: Glutelin type-A 2 acidic chain; Glutelin t ...	0.40	-	exc	0					499
Q42713 UniProt NPD GO	PLSB_CARTI	Glycerol-3-phosphate acyltransferase, chloroplast precursor (EC 2.3.1.15) (GPAT)	0.40	-	mit	0	Plastid; chloroplast; chloroplast stroma				463
Q06625 UniProt NPD GO	GDE_YEAST	Glycogen debranching enzyme (Glycogen debrancher) [Includes: 4-alpha-glucanotransferase (EC 2.4.1.25 ...	0.40	-	nuc	0	Mitochondrion. Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			1536
Q9XTL9 UniProt NPD GO	PYG_DROME	Glycogen phosphorylase (EC 2.4.1.1)	0.40	-	nuc	0					844
P11217 UniProt NPD GO	PYGM_HUMAN	Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase)	0.40	-	cyt	0			232600	1Z8D	841
Q9CZD3 UniProt NPD GO	SYG_MOUSE	Glycyl-tRNA synthetase (EC 6.1.1.14) (Glycine--tRNA ligase) (GlyRS)	0.40	-	mit	0		secretory granule [IDA]			729
Q8K1Q0 UniProt NPD GO	NMT1_RAT	Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) (Peptide N-myristoyltransferase 1) (Myristo ...	0.40	+	cyt	0	Cytoplasm (By similarity)				496
Q9JI97 UniProt NPD GO	GHR_CAVPO	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.40	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				628
P16882 UniProt NPD GO	GHR_MOUSE	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.40	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...	extrinsic to membrane [IDA]			650
P01242 UniProt NPD GO	SOM2_HUMAN	Growth hormone variant precursor (GH-V) (Placenta-specific growth hormone) (Growth hormone 2)	0.40	-	exc	0	Secreted protein		139240		217
Q01721 UniProt NPD GO	GAS1_MOUSE	Growth-arrest-specific protein 1 precursor (GAS-1)	0.40	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	anchored to plasma membrane [ISS] membrane [IDA]			343
O08689 UniProt NPD GO	GDF8_MOUSE	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.40	+	cyt	0	Secreted protein (By similarity)				376
P27045 UniProt NPD GO	GNAI3_XENLA	Guanine nucleotide-binding protein G(k) subunit alpha (G(i) alpha-3) (Fragment)	0.40	-	mit	0					345
Q4VT38 UniProt NPD GO	GPA14_CAEBR	Guanine nucleotide-binding protein alpha-14 subunit	0.40	-	cyt	0					369
Q9V5P6 UniProt NPD GO	NOLA3_DROME	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3) (snoRNP protein dNop ...	0.40	-	nuc	0	Nucleus; nucleolus (By similarity)				64
P30484 UniProt NPD GO	1B46_HUMAN	HLA class I histocompatibility antigen, B-46 alpha chain precursor (MHC class I antigen B*46) (Bw-46 ...	0.40	-	end	1	Membrane; single-pass type I membrane protein		142830		362
Q07000 UniProt NPD GO	1C15_HUMAN	HLA class I histocompatibility antigen, Cw-15 alpha chain precursor (MHC class I antigen Cw*15)	0.40	-	end	1	Membrane; single-pass type I membrane protein		142840		366
P30505 UniProt NPD GO	1C08_HUMAN	HLA class I histocompatibility antigen, Cw-8 alpha chain precursor (MHC class I antigen Cw*8)	0.40	-	end	1	Membrane; single-pass type I membrane protein		142840		366
O00165 UniProt NPD GO	HAX1_HUMAN	HS1-associating protein X-1 (HAX-1) (HS1-binding protein)	0.40	-	nuc	0	Mitochondrion. Endoplasmic reticulum. Nuclear membrane. Predominantly mitochondrial, but also to a l ...	actin cytoskeleton [NAS] endoplasmic reticulum [TAS] mitochondrion [TAS] nuclear envelope [TAS] soluble fraction [TAS]	605998		279
Q91233 UniProt NPD GO	HSP70_ONCTS	Heat shock 70 kDa protein (HSP70)	0.40	-	cyt	0					644
Q96MM6 UniProt NPD GO	HS12B_HUMAN	Heat shock 70 kDa protein 12B	0.40	-	cyt	0					686
P42931 UniProt NPD GO	HSP30_ONCTS	Heat shock protein 30 (HSP 30)	0.40	-	nuc	0					214
Q673U1 UniProt NPD GO	OST2_MOUSE	Heparan sulfate glucosamine 3-O-sulfotransferase 2 (EC 2.8.2.29) (Heparan sulfate D-glucosaminyl 3-O ...	0.40	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				367
Q80W66 UniProt NPD GO	OST2_RAT	Heparan sulfate glucosamine 3-O-sulfotransferase 2 (EC 2.8.2.29) (Heparan sulfate D-glucosaminyl 3-O ...	0.40	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				367
O77768 UniProt NPD GO	HNRPC_RABIT	Heterogeneous nuclear ribonucleoprotein C (hnRNP C)	0.40	-	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				306
Q9Z204 UniProt NPD GO	HNRPC_MOUSE	Heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNP C1 / hnRNP C2)	0.40	-	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)	pronucleus [IDA]			313
P12314 UniProt NPD GO	FCGR1_HUMAN	High affinity immunoglobulin gamma Fc receptor I precursor (Fc-gamma RI) (FcRI) (IgG Fc receptor I) ...	0.40	-	end	1	Membrane; single-pass type I membrane protein		146760		374
P16453 UniProt NPD GO	DCHS_RAT	Histidine decarboxylase (EC 4.1.1.22) (HDC)	0.40	-	mit	0					656
P10156 UniProt NPD GO	H1_TETTH	Histone H1	0.40	-	nuc	0	Nucleus. Macronuclei				163
P02252 UniProt NPD GO	H14_RABIT	Histone H1.4 (Fragment)	0.40	-	nuc	0	Nucleus				73
P04255 UniProt NPD GO	H2B1_CAEEL	Histone H2B 1	0.40	-	nuc	0	Nucleus				121
Q27894 UniProt NPD GO	H2B2_CAEEL	Histone H2B 2	0.40	-	nuc	0	Nucleus				122
Q5MYA4 UniProt NPD GO	H3_CICIN	Histone H3	0.40	-	mit	0	Nucleus (By similarity)				135
P23751 UniProt NPD GO	H42_EMENI	Histone H4.2	0.40	-	cyt	0	Nucleus (By similarity)				102
O55128 UniProt NPD GO	SAP18_MOUSE	Histone deacetylase complex subunit SAP18 (Sin3-associated polypeptide, 18 kDa) (Sin3-associated pol ...	0.40	-	nuc	0					153
Q945S8 UniProt NPD GO	ASHH3_ARATH	Histone-lysine N-methyltransferase ASHH3 (EC 2.1.1.43) (ASH1-homolog protein 3) (Protein SET DOMAIN ...	0.40	-	nuc	0	Nucleus (By similarity). Associates with centromeric constitutive heterochromatin (By similarity)				363
Q02814 UniProt NPD GO	HMD2_CHICK	Homeobox protein CHOX-CAD2 (Fragment)	0.40	+	nuc	0	Nucleus (Probable)				60
P87393 UniProt NPD GO	DLX2_ELECQ	Homeobox protein DLX-2 (Fragment)	0.40	-	nuc	0	Nucleus (Potential)				103
Q9GZZ0 UniProt NPD GO	HXD1_HUMAN	Homeobox protein Hox-D1	0.40	+	nuc	0	Nucleus		142987		328
Q63630 UniProt NPD GO	RHOX5_RAT	Homeobox protein Rhox5 (Reproductive homeobox on chromosome X 5) (Homeobox protein Pem) (Placenta an ...	0.40	+	nuc	0	Nucleus (Potential)				211
P38733 UniProt NPD GO	YHD7_YEAST	Hypothetical 18.4 kDa protein in CBP2-MUP3 intergenic region	0.40	-	mit	0					159
P31918 UniProt NPD GO	YCX1_EUGGR	Hypothetical 33.0 kDa protein in psbD intron 8 (ORF281A)	0.40	-	nuc	1 *	Plastid; chloroplast				281
P38478 UniProt NPD GO	YMF40_MARPO	Hypothetical 57.7 kDa protein in 18S rRNA intron 1 (ORF 502)	0.40	-	cyt	0					502
O78439 UniProt NPD GO	YCF46_GUITH	Hypothetical 57.8 kDa protein ycf46	0.40	-	cyt	0	Plastid; chloroplast				506
P31921 UniProt NPD GO	YCX2_EUGGR	Hypothetical 59.8 kDa protein in psbD intron 8 (ORF506)	0.40	+	cyt	3	Plastid; chloroplast				506

You are viewing entries 31851 to 31900 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.