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
Q711G1 UniProt NPD GO	G6PI_AGABI	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.03	-	cyt	0	Cytoplasm (By similarity)				551
P42863 UniProt NPD GO	G6PIB_ORYSA	Glucose-6-phosphate isomerase, cytosolic B (EC 5.3.1.9) (GPI-B) (Phosphoglucose isomerase B) (PGI-B) ...	0.03	-	cyt	0	Cytoplasm	cytosol [IDA]			567
P13377 UniProt NPD GO	G6PI_TRYBB	Glucose-6-phosphate isomerase, glycosomal (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosp ...	0.03	-	nuc	0	Glycosome				607
O43826 UniProt NPD GO	G6PT1_HUMAN	Glucose-6-phosphate translocase (Glucose-5-phosphate transporter) (Solute carrier family 37 member 4 ...	0.03	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [TAS] integral to membrane [NAS]	602671		429
Q12613 UniProt NPD GO	GLNA_COLGL	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.03	-	cyt	0	Cytoplasm (By similarity)				360
Q9UUN6 UniProt NPD GO	GLNA_FUSSH	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.03	-	cyt	0	Cytoplasm (By similarity)				356
Q9C2U9 UniProt NPD GO	GLNA_GIBFU	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.03	-	cyt	0	Cytoplasm (By similarity)				353
Q874T6 UniProt NPD GO	GLNA_KLULA	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.03	-	cyt	0	Cytoplasm (By similarity)				372
Q86ZU6 UniProt NPD GO	GLNA_TUBBO	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.03	-	cyt	0	Cytoplasm (By similarity)				358
Q6C3E0 UniProt NPD GO	GLNA_YARLI	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.03	-	cyt	0	Cytoplasm				364
P38561 UniProt NPD GO	GLNA3_MAIZE	Glutamine synthetase root isozyme 3 (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS112)	0.03	-	cyt	0	Cytoplasm				356
P38562 UniProt NPD GO	GLNA4_MAIZE	Glutamine synthetase root isozyme 4 (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS107)	0.03	-	cyt	0	Cytoplasm				355
P07694 UniProt NPD GO	GLNA3_PEA	Glutamine synthetase root isozyme A (EC 6.3.1.2) (Glutamate--ammonia ligase) (Cytosolic GS3 A)	0.03	-	cyt	0	Cytoplasm				357
Q43066 UniProt NPD GO	GLNA4_PEA	Glutamine synthetase root isozyme B (EC 6.3.1.2) (Glutamate--ammonia ligase) (Cytosolic GS3 B)	0.03	-	cyt	0	Cytoplasm				357
P55143 UniProt NPD GO	GLRX_RICCO	Glutaredoxin	0.03	-	cyt	0	Cytoplasm (By similarity)				102
O18598 UniProt NPD GO	GST1_BLAGE	Glutathione S-transferase (EC 2.5.1.18) (GST class-sigma) (Major allergen Bla g 5)	0.03	-	cyt	0					203
P46434 UniProt NPD GO	GST1_ONCVO	Glutathione S-transferase 1 (EC 2.5.1.18) (Fragment)	0.03	-	cyt	0					235
P46421 UniProt NPD GO	GSTXA_ARATH	Glutathione S-transferase 103-1A (EC 2.5.1.18)	0.03	-	cyt	0					224
P46429 UniProt NPD GO	GST2_MANSE	Glutathione S-transferase 2 (EC 2.5.1.18) (GST class-sigma)	0.03	-	cyt	0					203
P31670 UniProt NPD GO	GST27_FASHE	Glutathione S-transferase 26 kDa 47 (EC 2.5.1.18) (GST47) (FH47) (GST class-mu)	0.03	-	cyt	0	Cytoplasm			1FHE	217
Q9VG95 UniProt NPD GO	GSTT5_DROME	Glutathione S-transferase D5 (EC 2.5.1.18) (DmGST24)	0.03	-	cyt	0					216
P04907 UniProt NPD GO	GSTF3_MAIZE	Glutathione S-transferase III (EC 2.5.1.18) (GST-III) (GST class-phi)	0.03	-	cyt	0					221
P46420 UniProt NPD GO	GSTF4_MAIZE	Glutathione S-transferase IV (EC 2.5.1.18) (GST-IV) (GST-27) (GST class-phi)	0.03	-	cyt	0					222
P10299 UniProt NPD GO	GSTP1_CAEEL	Glutathione S-transferase P (EC 2.5.1.18) (GST class-pi)	0.03	-	cyt	0					208
Q60550 UniProt NPD GO	GSTP1_MESAU	Glutathione S-transferase P (EC 2.5.1.18) (GST class-pi)	0.03	-	cyt	0					209
P11909 UniProt NPD GO	GPX1_RABIT	Glutathione peroxidase 1 (EC 1.11.1.9) (GSHPx-1) (GPx-1) (Cellular glutathione peroxidase)	0.03	-	cyt	0	Cytoplasm				200
Q5RFG3 UniProt NPD GO	GPX3_PONPY	Glutathione peroxidase 3 precursor (EC 1.11.1.9) (GSHPx-3) (GPx-3) (Plasma glutathione peroxidase) ( ...	0.03	-	end	0	Secreted protein	extracellular space [ISS]			226
P22352 UniProt NPD GO	GPX3_HUMAN	Glutathione peroxidase 3 precursor (EC 1.11.1.9) (GSHPx-3) (GPx-3) (Plasma glutathione peroxidase) ( ...	0.03	-	end	0	Secreted protein	extracellular space [IDA]	138321		226
Q91WR8 UniProt NPD GO	GPX6_MOUSE	Glutathione peroxidase 6 precursor (EC 1.11.1.9)	0.03	-	end	0	Secreted protein (By similarity)				221
Q43154 UniProt NPD GO	GSHRP_SPIOL	Glutathione reductase, chloroplast precursor (EC 1.8.1.7) (GR) (GRase) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast				489
Q43621 UniProt NPD GO	GSHRC_PEA	Glutathione reductase, cytosolic (EC 1.8.1.7) (GR) (GRase) (GOR2)	0.03	-	nuc	0	Cytoplasm				498
Q27652 UniProt NPD GO	G3P_ECHMU	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.03	-	cyt	0	Cytoplasm (By similarity)				336
P09672 UniProt NPD GO	G3PA_SINAL	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast (EC 1.2.1.13) (NADP-dependent glyceraldehyde ...	0.03	-	cyt	0	Plastid; chloroplast				233
P12858 UniProt NPD GO	G3PA_PEA	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.03	-	cyt	0	Plastid; chloroplast				405
P09044 UniProt NPD GO	G3PB_TOBAC	Glyceraldehyde-3-phosphate dehydrogenase B, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.03	-	cyt	0	Plastid; chloroplast				438
Q4R3T1 UniProt NPD GO	G3PT_MACFA	Glyceraldehyde-3-phosphate dehydrogenase, testis-specific (EC 1.2.1.12) (Spermatogenic cell-specific ...	0.03	-	mit	0	Cytoplasm (By similarity)				409
P32189 UniProt NPD GO	GLPK_HUMAN	Glycerol kinase (EC 2.7.1.30) (ATP:glycerol 3-phosphotransferase) (Glycerokinase) (GK)	0.03	-	cyt	0	Mitochondrion; mitochondrial outer membrane; peripheral membrane protein; cytoplasmic side. Cytoplas ...	cytoplasm [NAS] mitochondrial outer membrane [NAS]	307030		524
Q64516 UniProt NPD GO	GLPK_MOUSE	Glycerol kinase (EC 2.7.1.30) (ATP:glycerol 3-phosphotransferase) (Glycerokinase) (GK)	0.03	-	cyt	0	Or: Mitochondrion; mitochondrial outer membrane; peripheral membrane protein; cytoplasmic side. Or: ...				524
Q63060 UniProt NPD GO	GLPK_RAT	Glycerol kinase (EC 2.7.1.30) (ATP:glycerol 3-phosphotransferase) (Glycerokinase) (GK) (ATP-stimulat ...	0.03	-	cyt	0	Or: Mitochondrion; mitochondrial outer membrane; peripheral membrane protein; cytoplasmic side. Or: ...				524
Q6ZZF4 UniProt NPD GO	GPD1_PICJA	Glycerol-3-phosphate dehydrogenase [NAD+] 1 (EC 1.1.1.8)	0.03	-	mit	0					393
P25855 UniProt NPD GO	GCSH1_ARATH	Glycine cleavage system H protein 1, mitochondrial precursor	0.03	-	mit	0	Mitochondrion				165
Q5I0P2 UniProt NPD GO	GCSH_RAT	Glycine cleavage system H protein, mitochondrial precursor	0.03	-	mit	0	Mitochondrion (By similarity)				170
P39726 UniProt NPD GO	GCSH_YEAST	Glycine cleavage system H protein, mitochondrial precursor (Glycine decarboxylase complex subunit H) ...	0.03	-	mit	0	Mitochondrion	glycine cleavage complex [TAS] mitochondrion [IDA]			170
P09789 UniProt NPD GO	GRP1_PETHY	Glycine-rich cell wall structural protein 1 precursor	0.03	-	exc	1 *	Cell wall (Potential)				384
P10495 UniProt NPD GO	GRP1_PHAVU	Glycine-rich cell wall structural protein 1.0 precursor (GRP 1.0)	0.03	+	vac	1 *	Cell wall (Potential)				252
P27483 UniProt NPD GO	GRP1_ARATH	Glycine-rich cell wall structural protein precursor	0.03	+	nuc	1 *	Cell wall (Potential)				349
P37704 UniProt NPD GO	GRP7_DAUCA	Glycine-rich protein DC7.1 precursor	0.03	-	vac	0					96
P51546 UniProt NPD GO	KGCY_NERDI	Glycocyamine kinase (EC 2.7.3.1) (GK) (Guanidinoacetate kinase)	0.03	-	cyt	0					393
Q9NZD2 UniProt NPD GO	GLTP_HUMAN	Glycolipid transfer protein (GLTP)	0.03	-	cyt	0	Cytoplasm (By similarity)	membrane [IC]	608949	2EVT	208
P53542 UniProt NPD GO	GLHA_CLAGA	Glycoprotein hormones alpha chain precursor (Gonadotropin alpha chain) (GTH-alpha)	0.03	-	nuc	0	Secreted protein				116

You are viewing entries 80051 to 80100 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.