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
Q8VDR7 UniProt NPD GO	TGDS_MOUSE	dTDP-D-glucose 4,6-dehydratase (EC 4.2.1.46)	0.05	-	cyt	0					355
Q9JK95 UniProt NPD GO	PERP_MOUSE	p53 apoptosis effector related to PMP-22 (Keratinocytes-associated protein 1) (KCP-1)	0.05	-	end	4 *	Cell membrane; cell-cell junction; desmosome; multi-pass membrane protein. Associated with desmosome ...	Golgi apparatus [IDA] integral to plasma membrane [IDA] mitochondrion [IDA]			193
Q6CXZ7 UniProt NPD GO	PALI1_KLULA	pH-response regulator palI/RIM9 homolog 1	0.05	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity)				220
Q8R3W5 UniProt NPD GO	SEN15_MOUSE	tRNA-splicing endonuclease subunit Sen15 (tRNA-intron endonuclease Sen15)	0.05	-	cyt	0	Nucleus (Probable). Nucleus; nucleolus (Probable). May be transiently localized in the nucleolus (Pr ...				168
O24243 UniProt NPD GO	MDL1_PRUDU	(R)-mandelonitrile lyase 1 precursor (EC 4.1.2.10) (Hydroxynitrile lyase 1) ((R)-oxynitrilase 1)	0.04	-	cyt	0					559
P52706 UniProt NPD GO	MDL1_PRUSE	(R)-mandelonitrile lyase 1 precursor (EC 4.1.2.10) (Hydroxynitrile lyase 1) ((R)-oxynitrilase 1)	0.04	-	cyt	0	Protein body. Primarily found within protein bodies of the cotyledonary parenchyma cells, with lesse ...				563
Q757Q6 UniProt NPD GO	GLGB_ASHGO	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.04	-	cyt	0					703
Q6FPN5 UniProt NPD GO	HIS4_CANGA	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase ( ...	0.04	-	cyt	0	Cytoplasm (By similarity)				261
Q5E9R2 UniProt NPD GO	PLCD_BOVIN	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (EC 2.3.1.51) (1-AGP acyltransferase 4) (1-AGPA ...	0.04	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				378
O75891 UniProt NPD GO	FTHFD_HUMAN	10-formyltetrahydrofolate dehydrogenase (EC 1.5.1.6) (10-FTHFDH) (Aldehyde dehydrogenase 1 family me ...	0.04	-	cyt	0	Cytoplasm		600249	2CQ8	902
Q8R0Y6 UniProt NPD GO	FTHFD_MOUSE	10-formyltetrahydrofolate dehydrogenase (EC 1.5.1.6) (10-FTHFDH) (Aldehyde dehydrogenase 1 family me ...	0.04	-	cyt	0	Cytoplasm				902
Q6X4M2 UniProt NPD GO	SEP15_ONCMY	15 kDa selenoprotein precursor	0.04	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum lumen [ISS]			157
P12810 UniProt NPD GO	HSP11_WHEAT	16.9 kDa class I heat shock protein (Low molecular weight heat shock protein) (Heat shock protein 17 ...	0.04	-	cyt	0	Cytoplasm				151
P02519 UniProt NPD GO	HSP11_SOYBN	17.3 kDa class I heat shock protein (HSP 17.3)	0.04	-	cyt	0	Cytoplasm				153
P31673 UniProt NPD GO	HSP21_ORYSA	17.4 kDa class I heat shock protein 1	0.04	-	cyt	0	Cytoplasm				154
P04794 UniProt NPD GO	HSP14_SOYBN	17.5 kDa class I heat shock protein (HSP 17.5-E)	0.04	-	cyt	0	Cytoplasm				154
P80839 UniProt NPD GO	CWP18_ARATH	18 kDa cell wall protein (Fragment)	0.04	-		0	Cell wall				5
P27397 UniProt NPD GO	HSP12_DAUCA	18.0 kDa class I heat shock protein (Clone DCHSP17.9)	0.04	-	cyt	0	Cytoplasm				159
Q05832 UniProt NPD GO	HSP11_CHERU	18.3 kDa class I heat shock protein (HSP 18.3)	0.04	-	cyt	0	Cytoplasm				161
P05478 UniProt NPD GO	HSP16_SOYBN	18.5 kDa class I heat shock protein (HSP 18.5)	0.04	-	cyt	0	Cytoplasm				161
P35494 UniProt NPD GO	PMGI_TOBAC	2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (BPG ...	0.04	-	nuc	0	Cytoplasm				559
O24246 UniProt NPD GO	PMGI_PRUDU	2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (BPG ...	0.04	-	cyt	0	Cytoplasm				488
Q16698 UniProt NPD GO	DECR_HUMAN	2,4-dienoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.34) (2,4-dienoyl-CoA reductase [NADPH]) ...	0.04	-	mit	0	Mitochondrion	mitochondrion [TAS]	222745	1W8D	335
P81895 UniProt NPD GO	ODO1_SOLTU	2-oxoglutarate dehydrogenase E1 component (EC 1.2.4.2) (Alpha-ketoglutarate dehydrogenase) (OGDC-E1) ...	0.04	-		0	Mitochondrion; mitochondrial membrane				19
P21839 UniProt NPD GO	ODBB_BOVIN	2-oxoisovalerate dehydrogenase subunit beta, mitochondrial precursor (EC 1.2.4.4) (Branched-chain al ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				392
P21953 UniProt NPD GO	ODBB_HUMAN	2-oxoisovalerate dehydrogenase subunit beta, mitochondrial precursor (EC 1.2.4.4) (Branched-chain al ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix	alpha-ketoglutarate dehydrogenase complex (... [TAS] mitochondrion [TAS]	248600	2BFF	392
P32765 UniProt NPD GO	ASP_THECC	21 kDa seed protein precursor	0.04	-	mit	0					221
Q9XXX1 UniProt NPD GO	P23_THEBU	23 kDa piroplasm membrane protein precursor (p23)	0.04	-	end	2 *	Membrane; single-pass membrane protein (Potential)				223
P80762 UniProt NPD GO	CWP03_PHAVU	230 kDa cell wall protein (Fragment)	0.04	-		0	Cell wall				16
P80757 UniProt NPD GO	CWP07_DAUCA	24 kDa cell wall protein (Fragment)	0.04	-		0	Cell wall				15
Q9Z2X3 UniProt NPD GO	PSD10_RAT	26S proteasome non-ATPase regulatory subunit 10 (26S proteasome regulatory subunit p28) (Gankyrin)	0.04	-	cyt	0					231
P82434 UniProt NPD GO	CWP26_TOBAC	28 kDa cell wall protein (Fragment)	0.04	-		0	Cell wall				10
P14060 UniProt NPD GO	3BHS1_HUMAN	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type I (3Beta-HSD I) (Trophoblast antigen ...	0.04	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...	microsome [IDA] mitochondrial inner membrane [IDA] mitochondrial intermembrane space [IDA] smooth endoplasmic reticulum membrane [ISS]	109715		372
Q64421 UniProt NPD GO	3BHS2_MESAU	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type II (3Beta-HSD II) [Includes: 3-beta-h ...	0.04	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
P00347 UniProt NPD GO	HMDH_CRIGR	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.04	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				887
P14773 UniProt NPD GO	HMDH_DROME	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.04	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	intracellular [TAS]			920
Q29512 UniProt NPD GO	HMDH_RABIT	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.04	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Peroxisome; pero ...				888
P48019 UniProt NPD GO	HMDH1_ORYSA	3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (EC 1.1.1.34) (HMG-CoA reductase 1)	0.04	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				509
P87186 UniProt NPD GO	LEU3_CANAL	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.04	-	cyt	0	Cytoplasm				373
P29696 UniProt NPD GO	LEU3_SOLTU	3-isopropylmalate dehydrogenase, chloroplast precursor (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) ...	0.04	-	mit	0	Plastid; chloroplast				357
Q874K0 UniProt NPD GO	ERG27_CANAL	3-keto-steroid reductase (EC 1.1.1.270)	0.04	-	cyt	1					346
Q6FIV3 UniProt NPD GO	ERG27_CANGA	3-keto-steroid reductase (EC 1.1.1.270)	0.04	-	cyt	1					348
P42765 UniProt NPD GO	THIM_HUMAN	3-ketoacyl-CoA thiolase, mitochondrial (EC 2.3.1.16) (Beta-ketothiolase) (Acetyl-CoA acyltransferase ...	0.04	-	cyt	0	Mitochondrion	mitochondrion [NAS]	604770		397
Q99J99 UniProt NPD GO	THTM_MOUSE	3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) (MST)	0.04	-	cyt	0	Cytoplasm (By similarity). Mostly. Mitochondrion (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			296
P38122 UniProt NPD GO	PANB_YEAST	3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) (Ketopantoate hydroxymethyltransferas ...	0.04	-	mit	0		mitochondrion [IDA]			312
Q9TV64 UniProt NPD GO	AK1D1_RABIT	3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.99.6) (Delta(4)-3-ketosteroid 5-beta-reductase) (Aldo-k ...	0.04	-	cyt	0	Cytoplasm (By similarity)				326
P49243 UniProt NPD GO	FABH_ARATH	3-oxoacyl-[acyl-carrier-protein] synthase III, chloroplast precursor (EC 2.3.1.41) (Beta-ketoacyl-AC ...	0.04	-	nuc	0	Plastid; chloroplast				404
P23981 UniProt NPD GO	AROA1_TOBAC	3-phosphoshikimate 1-carboxyvinyltransferase 1, chloroplast precursor (EC 2.5.1.19) (5-enolpyruvylsh ...	0.04	-	cyt	0	Plastid; chloroplast				518
P05466 UniProt NPD GO	AROA_ARATH	3-phosphoshikimate 1-carboxyvinyltransferase, chloroplast precursor (EC 2.5.1.19) (5-enolpyruvylshik ...	0.04	-	mit	0	Plastid; chloroplast				520
P80926 UniProt NPD GO	CS33_ARAHY	33.0 kDa cold shock protein (AHCSP33) (Fragment)	0.04	-	nuc	0	Secreted protein; extracellular space; apoplast				24

You are viewing entries 76001 to 76050 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.