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
O03042 UniProt NPD GO	RBL_ARATH	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				479
Q8RU60 UniProt NPD GO	RBL_ATRBE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				477
P20455 UniProt NPD GO	RBL_ATRRS	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P28381 UniProt NPD GO	RBL_BARCA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				476
P48685 UniProt NPD GO	RBL_BAZTR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
Q31886 UniProt NPD GO	RBL_BOUGL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P48686 UniProt NPD GO	RBL_BRAOL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				479
O63094 UniProt NPD GO	RBL_CAJCA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				473
Q7YJW4 UniProt NPD GO	RBL_CALFE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P48689 UniProt NPD GO	RBL_CARTI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				477
P26959 UniProt NPD GO	RBL_CEDDE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P08211 UniProt NPD GO	RBL_CHLMO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P00877 UniProt NPD GO	RBL_CHLRE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast			1UZH	475
P48694 UniProt NPD GO	RBL_COFAR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				481
P28399 UniProt NPD GO	RBL_DIGPU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				477
P48702 UniProt NPD GO	RBL_EQUAR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P26960 UniProt NPD GO	RBL_KETDA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P69570 UniProt NPD GO	RBL_LAROX	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
Q33584 UniProt NPD GO	RBL_LATCL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid				477
P27065 UniProt NPD GO	RBL_LYCES	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				477
P30732 UniProt NPD GO	RBL_MAGAC	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P30829 UniProt NPD GO	RBL_MAGMA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P61293 UniProt NPD GO	RBL_MAGTR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
Q9MUT6 UniProt NPD GO	RBL_MESVI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P25832 UniProt NPD GO	RBL_MOLVE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				480
P19164 UniProt NPD GO	RBL_NEUTE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				478
P11421 UniProt NPD GO	RBL_NICAC	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				477
P48709 UniProt NPD GO	RBL_NICDE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				477
P11422 UniProt NPD GO	RBL_NICOT	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				477
Q6EW71 UniProt NPD GO	RBL_NYMAL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
Q68RZ8 UniProt NPD GO	RBL_PANGI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				478
P04717 UniProt NPD GO	RBL_PEA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P48711 UniProt NPD GO	RBL_PICAB	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P24674 UniProt NPD GO	RBL_PICPU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P26961 UniProt NPD GO	RBL_PICSI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P26962 UniProt NPD GO	RBL_PINBA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P24675 UniProt NPD GO	RBL_PINED	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
Q7GUD0 UniProt NPD GO	RBL_PINKO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P26963 UniProt NPD GO	RBL_PINKR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P24677 UniProt NPD GO	RBL_PINLO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P24678 UniProt NPD GO	RBL_PINPI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P24679 UniProt NPD GO	RBL_PINRA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P41621 UniProt NPD GO	RBL_PINTH	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P24676 UniProt NPD GO	RBL_PINWA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
Q43036 UniProt NPD GO	RBL_PLUAU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P24680 UniProt NPD GO	RBL_PODGR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P24681 UniProt NPD GO	RBL_PSEKA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P69571 UniProt NPD GO	RBL_PSEMZ	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P48714 UniProt NPD GO	RBL_PSINU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
Q01874 UniProt NPD GO	RBL_QUERU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475

You are viewing entries 97851 to 97900 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.