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
Q03045 UniProt NPD GO	AMYG_HORRE	Glucoamylase P precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrol ...	0.06	-	exc	0	Secreted protein				616
Q9FXM5 UniProt NPD GO	G6PI_ARAGE	Glucose-6-phosphate isomerase, cytosolic (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosph ...	0.06	-	cyt	0	Cytoplasm				560
Q9FXM4 UniProt NPD GO	G6PI_ARALP	Glucose-6-phosphate isomerase, cytosolic (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosph ...	0.06	-	cyt	0	Cytoplasm				560
P34795 UniProt NPD GO	G6PI_ARATH	Glucose-6-phosphate isomerase, cytosolic (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosph ...	0.06	-	cyt	0	Cytoplasm				560
Q42522 UniProt NPD GO	GSA2_ARATH	Glutamate-1-semialdehyde 2,1-aminomutase 2, chloroplast precursor (EC 5.4.3.8) (GSA 2) (Glutamate-1- ...	0.06	-	mit	0	Plastid; chloroplast				472
Q40147 UniProt NPD GO	GSA_LYCES	Glutamate-1-semialdehyde 2,1-aminomutase, chloroplast precursor (EC 5.4.3.8) (GSA) (Glutamate-1-semi ...	0.06	-	mit	0	Plastid; chloroplast				481
O00088 UniProt NPD GO	GLNA_AGABI	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.06	-	cyt	0	Cytoplasm				354
Q6B4U7 UniProt NPD GO	GLNA_DEBHA	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.06	-	cyt	0	Cytoplasm				370
Q96V52 UniProt NPD GO	GLNA_EMENI	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.06	-	cyt	0	Cytoplasm (By similarity)				345
Q09179 UniProt NPD GO	GLNA_SCHPO	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.06	-	cyt	0	Cytoplasm (By similarity)				359
Q8J1R3 UniProt NPD GO	GLNA_SUIBO	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.06	-	cyt	0	Cytoplasm (By similarity)				354
P24099 UniProt NPD GO	GLNA1_SOYBN	Glutamine synthetase cytosolic isozyme 1 (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS1-1)	0.06	-	cyt	0	Cytoplasm				355
P14656 UniProt NPD GO	GLN11_ORYSA	Glutamine synthetase cytosolic isozyme 1-1 (EC 6.3.1.2) (OsGLN1;1) (OsGS1;1) (Glutamate--ammonia lig ...	0.06	-	cyt	0	Cytoplasm				356
P38563 UniProt NPD GO	GLNA5_MAIZE	Glutamine synthetase root isozyme 5 (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS117)	0.06	-	cyt	0	Cytoplasm				357
P25462 UniProt NPD GO	GLNAC_MAIZE	Glutamine synthetase, chloroplast precursor (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS2)	0.06	-	mit	0	Plastid; chloroplast				423
P14655 UniProt NPD GO	GLNA2_ORYSA	Glutamine synthetase, chloroplast precursor (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS2) (OsGS2)	0.06	-	mit	0	Plastid; chloroplast				428
Q86SX6 UniProt NPD GO	GLRX5_HUMAN	Glutaredoxin-related protein 5	0.06	-	cyt	0		mitochondrion [ISS]	609588		157
Q08393 UniProt NPD GO	GSTA2_CHICK	Glutathione S-transferase (EC 2.5.1.18) (Class-alpha)	0.06	-	cyt	0	Cytoplasm (By similarity)				222
O04437 UniProt NPD GO	GSTZ_WHEAT	Glutathione S-transferase (EC 2.5.1.18) (GST class-zeta)	0.06	-	cyt	0	Cytoplasm (By similarity)				213
P28342 UniProt NPD GO	GSTZ1_DIACA	Glutathione S-transferase 1 (EC 2.5.1.18) (SR8) (GST class-zeta)	0.06	-	mit	0					221
Q93113 UniProt NPD GO	GSTT6_ANOGA	Glutathione S-transferase 1-6 (EC 2.5.1.18) (GST class-theta)	0.06	-	cyt	0				1PN9	209
P15964 UniProt NPD GO	GST26_SCHMA	Glutathione S-transferase 26 kDa (EC 2.5.1.18) (GST 26) (SM26/1 antigen) (GST class-mu)	0.06	-	cyt	0					218
Q12390 UniProt NPD GO	GST2_YEAST	Glutathione S-transferase II (EC 2.5.1.18) (GST-II)	0.06	-	mit	0		mitochondrion [IDA]			233
P47954 UniProt NPD GO	GSTP1_CRIMI	Glutathione S-transferase P (EC 2.5.1.18) (GST class-pi)	0.06	-	cyt	0					209
P46422 UniProt NPD GO	GSTF4_ARATH	Glutathione S-transferase PM24 (EC 2.5.1.18) (24 kDa auxin-binding protein) (GST class-phi)	0.06	-	cyt	0	Microsomes and plasma membrane vesicles			1GNW	211
Q08863 UniProt NPD GO	GSTA1_RABIT	Glutathione S-transferase alpha I (EC 2.5.1.18) (GSTA1-1) (GST class-alpha)	0.06	-	mit	0	Cytoplasm				223
Q865R2 UniProt NPD GO	GPX1_MACFU	Glutathione peroxidase 1 (EC 1.11.1.9) (GSHPx-1) (GPx-1) (Cellular glutathione peroxidase)	0.06	-	mit	0	Cytoplasm (By similarity)				201
P04041 UniProt NPD GO	GPX1_RAT	Glutathione peroxidase 1 (EC 1.11.1.9) (GSHPx-1) (GPx-1) (Cellular glutathione peroxidase)	0.06	-	mit	0	Cytoplasm	cytosol [TAS]			201
P23764 UniProt NPD GO	GPX3_RAT	Glutathione peroxidase 3 precursor (EC 1.11.1.9) (GSHPx-3) (GPx-3) (Plasma glutathione peroxidase) ( ...	0.06	-	exc	0	Secreted protein	extracellular space [ISS]			226
Q64625 UniProt NPD GO	GPX6_RAT	Glutathione peroxidase 6 precursor (EC 1.11.1.9) (Odorant-metabolizing protein RY2D1)	0.06	-	end	0	Secreted protein				221
O09452 UniProt NPD GO	G3PA_GUITH	Glyceraldehyde-3-phosphate dehydrogenase, chloroplast precursor (EC 1.2.1.59) (NAD(P)-dependent glyc ...	0.06	-	mit	0	Plastid; chloroplast				386
Q7ZA43 UniProt NPD GO	GPD_PICAN	Glycerol-3-phosphate dehydrogenase [NAD+] (EC 1.1.1.8)	0.06	-	cyt	0					381
Q6FWJ7 UniProt NPD GO	GPD2_CANGA	Glycerol-3-phosphate dehydrogenase [NAD+] 2 (EC 1.1.1.8)	0.06	-	mit	0					422
P13255 UniProt NPD GO	GNMT_RAT	Glycine N-methyltransferase (EC 2.1.1.20) (Folate-binding protein)	0.06	-	cyt	0	Cytoplasm	cytosol [IDA] nucleus [IDA]		1XVA	292
Q29513 UniProt NPD GO	GNMT_RABIT	Glycine N-methyltransferase (EC 2.1.1.20) (Fragment)	0.06	-	cyt	0	Cytoplasm				292
P23137 UniProt NPD GO	GRP1_TOBAC	Glycine-rich protein precursor	0.06	+	exc	1 *	Cell wall				109
Q28913 UniProt NPD GO	GLPA_PANTR	Glycophorin A precursor (CD235a antigen)	0.06	-	end	2 *	Membrane; single-pass type I membrane protein				149
P37204 UniProt NPD GO	GLHA_THUOB	Glycoprotein hormones alpha chain (Gonadotropin alpha chain) (GTH-alpha)	0.06	-	nuc	0	Secreted protein				94
Q8WN20 UniProt NPD GO	GLHA_AILME	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.06	-	exc	1 *	Secreted protein				120
Q9ERG4 UniProt NPD GO	GLHA_MASCO	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.06	-	exc	1 *	Secreted protein				120
Q9ERG3 UniProt NPD GO	GLHA_MICMO	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.06	-	exc	1 *	Secreted protein				120
Q8JIE9 UniProt NPD GO	GLHA_NIPNI	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.06	-	exc	1 *	Secreted protein				120
P01219 UniProt NPD GO	GLHA_PIG	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.06	-	exc	1 *	Secreted protein				120
P11962 UniProt NPD GO	GLHA_RAT	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.06	-	exc	1 *	Secreted protein				120
P22762 UniProt NPD GO	GLHA_MACMU	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.06	-	exc	1 *	Secreted protein				120
Q9UBQ7 UniProt NPD GO	GRHPR_HUMAN	Glyoxylate reductase/hydroxypyruvate reductase (EC 1.1.1.79)	0.06	-	mit	0			260000	2H1S	328
P48250 UniProt NPD GO	GTHB1_CORAU	Gonadotropin beta-1 subunit precursor (Gonadotropin beta-I chain) (GTH-I-beta)	0.06	-	mit	0	Secreted protein				137
Q95MH6 UniProt NPD GO	GNRR2_CERAE	Gonadotropin-releasing hormone II receptor (Type II GnRH receptor) (GnRH-II-R)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				379
Q9TTI8 UniProt NPD GO	GNRHR_TRIVU	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				328
P81015 UniProt NPD GO	GRN3_CYPCA	Granulin-3	0.06	-	nuc	0	Secreted protein				57

You are viewing entries 72151 to 72200 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.