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
P28844 UniProt NPD GO	G3P_CURLU	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				337
Q01597 UniProt NPD GO	G3P_DROHY	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				332
P20445 UniProt NPD GO	G3P_EMENI	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				336
Q9N2D5 UniProt NPD GO	G3P_FELCA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				332
P00357 UniProt NPD GO	G3P_HOMAM	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm			4GPD	333
P04406 UniProt NPD GO	G3P_HUMAN	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm	cytoplasm [NAS]	138400	3GPD	334
Q9UR38 UniProt NPD GO	G3P_LENED	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				337
Q92243 UniProt NPD GO	G3P_LYOSH	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				337
Q9N655 UniProt NPD GO	G3P_MASBA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	mit	0	Cytoplasm (By similarity)				339
P53430 UniProt NPD GO	G3P_MONAN	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				337
P16858 UniProt NPD GO	G3P_MOUSE	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			332
Q8TFJ2 UniProt NPD GO	G3P_OMPOL	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				337
O42259 UniProt NPD GO	G3P_ONCMY	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				335
P56649 UniProt NPD GO	G3P_PALVE	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm			1SZJ	333
Q9P8C0 UniProt NPD GO	G3P_PHANO	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				337
O13507 UniProt NPD GO	G3P_PHARH	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				338
O59841 UniProt NPD GO	G3P_PICAN	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				335
Q9UVC0 UniProt NPD GO	G3P_PICCI	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				334
Q92263 UniProt NPD GO	G3P_PICPA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	mit	0	Cytoplasm				333
P00355 UniProt NPD GO	G3P_PIG	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				332
Q5RAB4 UniProt NPD GO	G3P_PONPY	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				334
P46406 UniProt NPD GO	G3P_RABIT	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm			1J0X	332
Q8NK47 UniProt NPD GO	G3P_RHIMI	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	mit	0	Cytoplasm (By similarity)				336
P32638 UniProt NPD GO	G3P_SCHCO	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				337
Q96US8 UniProt NPD GO	G3P_SCLSC	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				338
P87197 UniProt NPD GO	G3P_TRIAT	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				338
Q5R2J2 UniProt NPD GO	G3P_TRISI	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				333
P09317 UniProt NPD GO	G3P_USTMA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				337
P51469 UniProt NPD GO	G3P_XENLA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				332
Q6CCU7 UniProt NPD GO	G3P_YARLI	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm (By similarity)				338
P08439 UniProt NPD GO	G3P_ZYGRO	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)	0.00	-	mit	0	Cytoplasm				333
P04797 UniProt NPD GO	G3P_RAT	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (38 kDa BFA-dependent ADP-ribosylatio ...	0.00	-	cyt	0	Cytoplasm				332
Q00301 UniProt NPD GO	G3P_BOLED	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Fragment)	0.00	-	cyt	0	Cytoplasm				291
P55070 UniProt NPD GO	G3P_LACDT	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Fragment)	0.00	-	cyt	0	Cytoplasm				290
O57672 UniProt NPD GO	G3P_MELGA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Fragment)	0.00	-	cyt	0	Cytoplasm				234
P51640 UniProt NPD GO	G3P_MESAU	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Fragment)	0.00	-	mit	0	Cytoplasm				312
Q28554 UniProt NPD GO	G3P_SHEEP	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Fragment)	0.00	-	mit	0	Cytoplasm				322
P19089 UniProt NPD GO	G3P_CRYPA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (GPD-1)	0.00	-	cyt	0	Cytoplasm				337
P20287 UniProt NPD GO	G3P_SCHMA	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Major larval surface antigen) (P-37) ...	0.00	-	cyt	0					338
P32635 UniProt NPD GO	G3P1_AGABI	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH 1)	0.00	-	cyt	0	Cytoplasm				337
P17819 UniProt NPD GO	G3P1_KLULA	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH 1)	0.00	-	mit	0	Cytoplasm				329
Q9C136 UniProt NPD GO	G3P1_RHIRA	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH 1)	0.00	-	cyt	0	Cytoplasm (By similarity)				337
P00360 UniProt NPD GO	G3P1_YEAST	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH 1)	0.00	-	mit	0	Cytoplasm	cell wall (sensu Fungi) [IDA] cytoplasm [IDA] lipid particle [IDA]			331
P04970 UniProt NPD GO	G3P1_CAEEL	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH-1)	0.00	-	cyt	0	Cytoplasm				341
O16027 UniProt NPD GO	G3P1_GLORO	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (GAPDH-1) (Fragment)	0.00	-	cyt	0	Cytoplasm (By similarity)				324
P07486 UniProt NPD GO	G3P1_DROME	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) (Glyceraldehyde-3-phosphate dehydrogenase I ...	0.00	-	cyt	0	Cytoplasm				332
P32636 UniProt NPD GO	G3P2_AGABI	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH 2)	0.00	-	cyt	0	Cytoplasm				338
Q6FSM4 UniProt NPD GO	G3P2_CANGA	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH 2)	0.00	-	mit	0	Cytoplasm (By similarity)				332
Q6CX23 UniProt NPD GO	G3P2_KLULA	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH 2)	0.00	-	mit	0	Cytoplasm (By similarity)				331
Q01077 UniProt NPD GO	G3P2_KLUMA	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH 2)	0.00	-	mit	0	Cytoplasm				331

You are viewing entries 94801 to 94850 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.