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
P43224 UniProt NPD GO	RBL_ANTRE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				414
P36479 UniProt NPD GO	RBL_ASACA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P36480 UniProt NPD GO	RBL_ASCEX	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
O99001 UniProt NPD GO	RBL_BEAGR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28383 UniProt NPD GO	RBL_BEGMS	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
P28384 UniProt NPD GO	RBL_BETNI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
O19872 UniProt NPD GO	RBL_BIXOR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
Q05985 UniProt NPD GO	RBL_BOROF	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				443
Q05796 UniProt NPD GO	RBL_BRASC	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				394
P93988 UniProt NPD GO	RBL_BROCO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				455
P28387 UniProt NPD GO	RBL_BYRCR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
Q05797 UniProt NPD GO	RBL_CABCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				394
P93880 UniProt NPD GO	RBL_CASDI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				455
O20304 UniProt NPD GO	RBL_CASFS	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
P28389 UniProt NPD GO	RBL_CASLI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
P43227 UniProt NPD GO	RBL_CHEBI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				416
Q07210 UniProt NPD GO	RBL_COLPU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				469
Q05988 UniProt NPD GO	RBL_CONTR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				447
Q32041 UniProt NPD GO	RBL_COROL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
Q05579 UniProt NPD GO	RBL_CORSA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
O98883 UniProt NPD GO	RBL_COUGU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	nuc	0	Plastid; chloroplast				468
P28395 UniProt NPD GO	RBL_CRAMA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				450
P48697 UniProt NPD GO	RBL_CUCPE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28397 UniProt NPD GO	RBL_DAPSP	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
P28398 UniProt NPD GO	RBL_DARCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
P48699 UniProt NPD GO	RBL_DENCL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				474
P28403 UniProt NPD GO	RBL_DROBI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28407 UniProt NPD GO	RBL_DROFI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28408 UniProt NPD GO	RBL_DROLU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28409 UniProt NPD GO	RBL_DROPA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28410 UniProt NPD GO	RBL_DROPT	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
P28412 UniProt NPD GO	RBL_EPASP	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
P28414 UniProt NPD GO	RBL_EUCLU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				448
Q05989 UniProt NPD GO	RBL_EXAAF	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				446
Q05990 UniProt NPD GO	RBL_FOUSP	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
P48705 UniProt NPD GO	RBL_GLEJA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				410
O62970 UniProt NPD GO	RBL_GLYEC	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
P28419 UniProt NPD GO	RBL_HAMMO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
P28422 UniProt NPD GO	RBL_HELNU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
Q9XPR5 UniProt NPD GO	RBL_IDEPO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
Q05991 UniProt NPD GO	RBL_LIGVU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				447
P93913 UniProt NPD GO	RBL_LIRPL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				449
P92401 UniProt NPD GO	RBL_LUPDE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				455
P92406 UniProt NPD GO	RBL_LUPMI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				455
P48708 UniProt NPD GO	RBL_MOROL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28261 UniProt NPD GO	RBL_NYPFR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				459
P28435 UniProt NPD GO	RBL_NYSOG	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				459
P28436 UniProt NPD GO	RBL_OXADI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28437 UniProt NPD GO	RBL_PARFI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				459
P28438 UniProt NPD GO	RBL_PASGU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465

You are viewing entries 91251 to 91300 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.