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
P07902 UniProt NPD GO	GALT_HUMAN	Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-glucose-- ...	0.48	-	nuc	0			606999		379
Q5CAZ6 UniProt NPD GO	B3GA2_CANFA	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.48	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				329
Q925E1 UniProt NPD GO	SNTG1_MOUSE	Gamma-1-syntrophin (G1SYN) (Syntrophin 4) (SYN4)	0.48	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Mainly cytoplasmic and weakly nuclear (By simila ...				517
P26714 UniProt NPD GO	GBRB_LYMST	Gamma-aminobutyric-acid receptor subunit beta precursor (GABA(A) receptor)	0.48	+	end	4	Membrane; multi-pass membrane protein				499
P18860 UniProt NPD GO	CXA5_CHICK	Gap junction alpha-5 protein (Connexin-42) (Cx42)	0.48	-	end	4 *	Membrane; multi-pass membrane protein				368
P48540 UniProt NPD GO	GDNF_MOUSE	Glial cell line-derived neurotrophic factor precursor	0.48	-	nuc	0	Secreted protein				211
Q07731 UniProt NPD GO	GDNF_RAT	Glial cell line-derived neurotrophic factor precursor	0.48	-	nuc	0	Secreted protein	extracellular space [IDA]		1AGQ	211
Q9FY99 UniProt NPD GO	G6PD2_ARATH	Glucose-6-phosphate 1-dehydrogenase 2, chloroplast precursor (EC 1.1.1.49) (G6PD2) (G6PDH2)	0.48	-	cyt	0	Plastid; chloroplast				596
Q28034 UniProt NPD GO	GLU2B_BOVIN	Glucosidase 2 subunit beta precursor (Glucosidase II subunit beta) (Protein kinase C substrate, 60.1 ...	0.48	-	end	0	Endoplasmic reticulum (By similarity)				533
O15399 UniProt NPD GO	NMDE4_HUMAN	Glutamate [NMDA] receptor subunit epsilon 4 precursor (N-methyl D-aspartate receptor subtype 2D) (NR ...	0.48	-	end	4	Membrane; multi-pass membrane protein		602717		1336
O09172 UniProt NPD GO	GSH0_MOUSE	Glutamate--cysteine ligase regulatory subunit (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamm ...	0.48	-	nuc	0					274
P10385 UniProt NPD GO	GLTA_WHEAT	Glutenin, low molecular weight subunit precursor	0.48	-	nuc	0					356
P36148 UniProt NPD GO	GPT2_YEAST	Glycerol-3-phosphate O-acyltransferase 2 (EC 2.3.1.15) (G-3-P acyltransferase 2) (Dihydroxyacetone p ...	0.48	-	end	4 *	Membrane; multi-pass membrane protein (Probable)	cytoplasm [IDA] endoplasmic reticulum [IDA]			743
P23416 UniProt NPD GO	GLRA2_HUMAN	Glycine receptor alpha-2 chain precursor	0.48	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	305990		452
P13807 UniProt NPD GO	GYS1_HUMAN	Glycogen [starch] synthase, muscle (EC 2.4.1.11)	0.48	-	cyt	0			138570		737
Q8R2X8 UniProt NPD GO	GO45_MOUSE	Golgin 45 (Basic leucine zipper nuclear factor 1)	0.48	-	nuc	0	Golgi apparatus; Golgi lumen (By similarity). Nucleus (By similarity). Cytoplasm (By similarity). Al ...	Golgi apparatus [IDA]			403
Q99062 UniProt NPD GO	CSF3R_HUMAN	Granulocyte colony-stimulating factor receptor precursor (G-CSF-R) (CD114 antigen)	0.48	-	nuc	1	Cell membrane; single-pass type I membrane protein. Isoform GCSFR2: Secreted protein (Probable). Iso ...	integral to plasma membrane [TAS]	138971	2D9Q	836
Q02092 UniProt NPD GO	GHR_CHICK	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.48	-	end	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				608
Q9Z1W4 UniProt NPD GO	GDF11_MOUSE	Growth/differentiation factor 11 precursor (GDF-11) (Bone morphogenetic protein 11)	0.48	-	exc	0	Secreted protein (Probable)	extracellular space [IDA]			405
O42222 UniProt NPD GO	GDF8_BRARE	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.48	-	nuc	0	Secreted protein (By similarity)	extracellular region [NAS]			374
Q619V5 UniProt NPD GO	GPA5_CAEBR	Guanine nucleotide-binding protein alpha-5 subunit	0.48	-	nuc	0					385
Q61MC6 UniProt NPD GO	GPA8_CAEBR	Guanine nucleotide-binding protein alpha-8 subunit	0.48	-	cyt	0					364
P34046 UniProt NPD GO	GPA8_DICDI	Guanine nucleotide-binding protein alpha-8 subunit (G alpha-8)	0.48	-	nuc	0					403
O74227 UniProt NPD GO	GPA1_COCHE	Guanine nucleotide-binding protein subunit alpha	0.48	-	cyt	0					352
O74259 UniProt NPD GO	GPA1_SPOSC	Guanine nucleotide-binding protein subunit alpha	0.48	-	cyt	0					352
P13746 UniProt NPD GO	1A11_HUMAN	HLA class I histocompatibility antigen, A-11 alpha chain precursor (MHC class I antigen A*11)	0.48	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142800	1X7Q	365
P36182 UniProt NPD GO	HSP82_TOBAC	Heat shock protein 82 (Fragment)	0.48	+	cyt	0	Cytoplasm (Potential)				499
Q7PT10 UniProt NPD GO	HSP83_ANOGA	Heat shock protein 83	0.48	-	cyt	0	Cytoplasm (By similarity)				689
P14530 UniProt NPD GO	HR2A_TRIFL	Hemorrhagic metalloproteinase HR2a precursor (EC 3.4.24.53) (Trimerelysin II) [Contains: Disintegrin ...	0.48	-	nuc	0	Secreted protein				478
Q9QZS6 UniProt NPD GO	OST3B_MOUSE	Heparan sulfate glucosamine 3-O-sulfotransferase 3B1 (EC 2.8.2.30) (Heparan sulfate D-glucosaminyl 3 ...	0.48	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to plasma membrane [IDA]			390
Q8WWQ2 UniProt NPD GO	HPSE2_HUMAN	Heparanase-2 (EC 3.2.-.-) (Hpa2)	0.48	-	nuc	0	Membrane; peripheral membrane protein				592
Q3SZ79 UniProt NPD GO	LIPH_BOVIN	Hepatic triacylglycerol lipase precursor (EC 3.1.1.3) (Hepatic lipase) (HL)	0.48	-	nuc	0	Secreted protein (By similarity)				500
P14210 UniProt NPD GO	HGF_HUMAN	Hepatocyte growth factor precursor (Scatter factor) (SF) (Hepatopoeitin A) [Contains: Hepatocyte gro ...	0.48	+	exc	1 *			142409	2HGF	728
Q2QLA9 UniProt NPD GO	MET_HORSE	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.48	-	end	1	Membrane; single-pass type I membrane protein				1381
Q2QL89 UniProt NPD GO	MET_MICMU	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.48	-	end	1	Membrane; single-pass type I membrane protein				1382
Q29RT0 UniProt NPD GO	HNRPG_BOVIN	Heterogeneous nuclear ribonucleoprotein G (hnRNP G) (RNA-binding motif protein, X chromosome)	0.48	-	nuc	0	Nucleus. Component of ribonucleosomes (By similarity)				396
P51348 UniProt NPD GO	SYH_PORPU	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.48	-	nuc	0	Plastid; chloroplast				430
P43274 UniProt NPD GO	H14_MOUSE	Histone H1.4 (H1 VAR.2) (H1e)	0.48	+	nuc	0	Nucleus				218
P06894 UniProt NPD GO	H1A_PLADU	Histone H1A, sperm	0.48	-	nuc	0	Nucleus				121
P06895 UniProt NPD GO	H1B_PLADU	Histone H1B, sperm	0.48	-	nuc	0	Nucleus				119
Q2HH38 UniProt NPD GO	H2B_CHAGB	Histone H2B	0.48	-	nuc	0	Nucleus				136
Q00715 UniProt NPD GO	H2B1_RAT	Histone H2B type 1	0.48	-	nuc	0	Nucleus				124
Q6CMV8 UniProt NPD GO	H2B2_KLULA	Histone H2B.2	0.48	-	nuc	0	Nucleus (By similarity)				131
P90543 UniProt NPD GO	H3_EUPCR	Histone H3	0.48	-	nuc	0	Nucleus (By similarity)				135
Q10453 UniProt NPD GO	H33_CAEEL	Histone H3.3	0.48	-	nuc	0	Nucleus (By similarity)				135
Q8WSF1 UniProt NPD GO	H33_TRIPS	Histone H3.3	0.48	-	nuc	0	Nucleus (By similarity)				135
O14929 UniProt NPD GO	HAT1_HUMAN	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.48	-	cyt	0	Nucleus. Cytoplasm. Nuclear in S-phase cells and cytoplasmic	nucleus [TAS]	603053		419
Q07424 UniProt NPD GO	CDX4_MOUSE	Homeobox protein CDX-4 (Caudal-type homeobox protein 4)	0.48	+	nuc	0	Nucleus				282
P50219 UniProt NPD GO	HLXB9_HUMAN	Homeobox protein HB9	0.48	+	nuc	0	Nucleus	nucleus [NAS]	176450		403
Q7SI91 UniProt NPD GO	HD9_ENCCU	Homeobox protein HD-9 (EcHD-9)	0.48	-	nuc	0	Nucleus				97

You are viewing entries 26251 to 26300 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.