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
P83246 UniProt NPD GO	GST_ASADI	Glutathione S-transferase (EC 2.5.1.18) (GST class-sigma) (adGST) (Fragment)	0.01	-		0					15
P42760 UniProt NPD GO	GSTF1_ARATH	Glutathione S-transferase 1 (EC 2.5.1.18) (GST class-phi)	0.01	-	cyt	0	Cytoplasm (Probable)				208
P30110 UniProt NPD GO	GSTF1_WHEAT	Glutathione S-transferase 1 (EC 2.5.1.18) (GST class-phi)	0.01	-	end	0					229
Q9SRY5 UniProt NPD GO	GST11_ARATH	Glutathione S-transferase 11 (EC 2.5.1.18) (GST class-phi)	0.01	-	cyt	0	Cytoplasm (Probable)				209
P48429 UniProt NPD GO	GST2_ASCSU	Glutathione S-transferase 2 (EC 2.5.1.18) (GST class-sigma) (Fragment)	0.01	-		0					20
Q21355 UniProt NPD GO	GST4_CAEEL	Glutathione S-transferase 4 (EC 2.5.1.18) (GST class-sigma) (CeGST1)	0.01	-	cyt	0					207
P46440 UniProt NPD GO	GSTF2_TOBAC	Glutathione S-transferase APIC (EC 2.5.1.18) (GST class-phi)	0.01	-	cyt	0					213
P42761 UniProt NPD GO	GSTF3_ARATH	Glutathione S-transferase ERD13 (EC 2.5.1.18) (GST class-phi)	0.01	-	mit	0	Cytoplasm (Probable)				214
P12653 UniProt NPD GO	GSTF1_MAIZE	Glutathione S-transferase I (EC 2.5.1.18) (GST-I) (GST-29) (GST class-phi)	0.01	-	cyt	0				1BYE	213
O59827 UniProt NPD GO	GST2_SCHPO	Glutathione S-transferase II (EC 2.5.1.18) (GST-II)	0.01	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			230
P41043 UniProt NPD GO	GST1_DROME	Glutathione S-transferase S1 (EC 2.5.1.18) (GST class-sigma 1) (Glutathione S-transferase 2)	0.01	-	cyt	0				1M0U	249
P46418 UniProt NPD GO	GSTA5_RAT	Glutathione S-transferase alpha-5 (EC 2.5.1.18) (Glutathione S-transferase Yc-2) (GST Yc2) (GST A5-5 ...	0.01	-	cyt	0	Cytoplasm				220
Q00277 UniProt NPD GO	GPX1_SCHMA	Glutathione peroxidase (EC 1.11.1.9) (GPX)	0.01	-	cyt	0					169
O23970 UniProt NPD GO	GPX1_HELAN	Glutathione peroxidase 1 (EC 1.11.1.9)	0.01	-	cyt	0					167
P81087 UniProt NPD GO	GPX4_PINPS	Glutathione peroxidase homolog (EC 1.11.1.9) (Water stress-responsive protein 8/9) (Fragment)	0.01	-		0					17
P83564 UniProt NPD GO	GPX1_CHLRE	Glutathione peroxidase, mitochondrial precursor (EC 1.11.1.9) (CrGPx)	0.01	-	mit	0	Mitochondrion (Probable)	mitochondrion [NAS]			201
Q12552 UniProt NPD GO	G3P_ASPNG	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm				336
Q9HGY7 UniProt NPD GO	G3P_ASPOR	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm (By similarity)				338
Q8J1H3 UniProt NPD GO	G3P_COCIM	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm (By similarity)				337
Q6BMK0 UniProt NPD GO	G3P_DEBHA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm (By similarity)				335
Q00640 UniProt NPD GO	G3P_ERYGR	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm				338
Q8X1X3 UniProt NPD GO	G3P_PARBR	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm (By similarity)				338
Q01982 UniProt NPD GO	G3P_PHACH	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm				337
P26988 UniProt NPD GO	G3P_PHYIN	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm				332
Q9UW96 UniProt NPD GO	G3P_PLESA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm (By similarity)				335
P32637 UniProt NPD GO	G3P_PODAN	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm				337
Q8WZN0 UniProt NPD GO	G3P_SORMA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.01	-	cyt	0	Cytoplasm (By similarity)				338
P70685 UniProt NPD GO	G3P_CAVPO	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Fragment)	0.01	-	cyt	0	Cytoplasm				123
Q94469 UniProt NPD GO	G3P_DICDI	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Fragment)	0.01	-	cyt	0	Cytoplasm (By similarity)				299
P78958 UniProt NPD GO	G3P1_SCHPO	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH 1)	0.01	-	cyt	0	Cytoplasm (By similarity)				336
P53429 UniProt NPD GO	G3P1_GIALA	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH)	0.01	-	mit	0	Cytoplasm (By similarity)				337
P17729 UniProt NPD GO	G3P1_TRIKO	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH1)	0.01	-	cyt	0	Cytoplasm				335
O43026 UniProt NPD GO	G3P2_SCHPO	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH 2)	0.01	-	cyt	0	Cytoplasm (By similarity)				335
P32810 UniProt NPD GO	G3P3_CAEBR	Glyceraldehyde-3-phosphate dehydrogenase 3 (EC 1.2.1.12) (GAPDH-3)	0.01	-	cyt	0	Cytoplasm				341
P12859 UniProt NPD GO	G3PB_PEA	Glyceraldehyde-3-phosphate dehydrogenase B, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.01	-	mit	0	Plastid; chloroplast				451
P34919 UniProt NPD GO	G3PA_CHOCR	Glyceraldehyde-3-phosphate dehydrogenase, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glycer ...	0.01	-	mit	0	Plastid; chloroplast				414
P49644 UniProt NPD GO	G3PC_CHLRE	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.01	-	cyt	0	Cytoplasm				341
Q42671 UniProt NPD GO	G3PC_CRAPL	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.01	-	cyt	0	Cytoplasm				337
P26518 UniProt NPD GO	G3PC_MAGLI	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.01	-	cyt	0	Cytoplasm				341
P17878 UniProt NPD GO	G3PC_MESCR	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.01	-	cyt	0	Cytoplasm				337
P34922 UniProt NPD GO	G3PC_PEA	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.01	-	cyt	0	Cytoplasm				338
P26519 UniProt NPD GO	G3PC_PETCR	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.01	-	cyt	0	Cytoplasm				336
P34923 UniProt NPD GO	G3PC_PHYPA	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.01	-	cyt	0	Cytoplasm				342
P26521 UniProt NPD GO	G3PC_RANAC	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.01	-	cyt	0	Cytoplasm				338
P26517 UniProt NPD GO	G3PX_HORVU	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.01	-	cyt	0	Cytoplasm				337
P10097 UniProt NPD GO	G3PC_TRYBB	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) (GAPDH)	0.01	-	mit	0	Cytoplasm				330
Q42977 UniProt NPD GO	G3PC_ORYSA	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) (PP38)	0.01	-	cyt	0	Cytoplasm				336
Q43247 UniProt NPD GO	G3PE_MAIZE	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 3 (EC 1.2.1.12)	0.01	-	cyt	0					337
P80447 UniProt NPD GO	G3P2_JACOR	Glyceraldehyde-3-phosphate dehydrogenase, liver (EC 1.2.1.12) (GAPDH) (Fragment)	0.01	-	cyt	0	Cytoplasm				34
O14556 UniProt NPD GO	G3PT_HUMAN	Glyceraldehyde-3-phosphate dehydrogenase, testis-specific (EC 1.2.1.12) (Spermatogenic cell-specific ...	0.01	-	mit	0	Cytoplasm (By similarity)		609169		408

You are viewing entries 88501 to 88550 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.