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
P25079 UniProt NPD GO	RBL_SOLTU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				477
P27066 UniProt NPD GO	RBL_SOYBN	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P00875 UniProt NPD GO	RBL_SPIOL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast			8RUC	475
P25838 UniProt NPD GO	RBL_STEHA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				482
P00876 UniProt NPD GO	RBL_TOBAC	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast			4RUB	477
P26964 UniProt NPD GO	RBL_TSUHE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P28459 UniProt NPD GO	RBL_VIBAC	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
O62964 UniProt NPD GO	RBL_VIGUN	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				473
P56648 UniProt NPD GO	RBL_VITVI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
Q31655 UniProt NPD GO	RBL_AJUCH	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				473
Q31809 UniProt NPD GO	RBL_ASPLA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				453
P31180 UniProt NPD GO	RBL_BUXSE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				57
P31181 UniProt NPD GO	RBL_CAMSI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				57
P31183 UniProt NPD GO	RBL_CORLA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				459
P48700 UniProt NPD GO	RBL_DIACA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				469
P31185 UniProt NPD GO	RBL_EUOBU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				58
P31186 UniProt NPD GO	RBL_EUOMA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				58
P69567 UniProt NPD GO	RBL_EUPCH	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				58
P69568 UniProt NPD GO	RBL_EUPDU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				58
P69569 UniProt NPD GO	RBL_EUPES	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				58
Q32255 UniProt NPD GO	RBL_GALAL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				453
Q32256 UniProt NPD GO	RBL_GALAP	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				453
Q32303 UniProt NPD GO	RBL_GALLU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				453
P31188 UniProt NPD GO	RBL_GEUBO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				54
P31190 UniProt NPD GO	RBL_ICAMA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				54
P31191 UniProt NPD GO	RBL_ILEAQ	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				54
P31192 UniProt NPD GO	RBL_ILECI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				54
Q07049 UniProt NPD GO	RBL_ILEPE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				54
P31195 UniProt NPD GO	RBL_MERAN	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				54
P31197 UniProt NPD GO	RBL_PHECO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				457
P31198 UniProt NPD GO	RBL_RHACA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				54
P31199 UniProt NPD GO	RBL_RIBAM	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				54
P31200 UniProt NPD GO	RBL_ROSDA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				58
Q33050 UniProt NPD GO	RBL_RUBTI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				453
P31201 UniProt NPD GO	RBL_SALPE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				452
P31202 UniProt NPD GO	RBL_SALPL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				449
P48715 UniProt NPD GO	RBL_SINAL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				473
P05699 UniProt NPD GO	RBL_VICFA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				26
P31203 UniProt NPD GO	RBL_WEISI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				58
P00870 UniProt NPD GO	RBS1_SPIOL	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.00	-	cyt	0	Plastid; chloroplast			8RUC	123
P23652 UniProt NPD GO	RBS_PYLLI	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.00	-	cyt	0	Plastid; chloroplast				139
P80657 UniProt NPD GO	RBS_PHYPA	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit) (Fragment)	0.00	-		0	Plastid; chloroplast				15
P08706 UniProt NPD GO	RBS1_LYCES	Ribulose bisphosphate carboxylase small chain 1, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.00	-	mit	0	Plastid; chloroplast				181
O24634 UniProt NPD GO	RBS1_FRIAG	Ribulose bisphosphate carboxylase small chain 1/4, chloroplast precursor (EC 4.1.1.39) (RuBisCO smal ...	0.00	-	exc	0	Plastid; chloroplast				179
O22572 UniProt NPD GO	RBS2_FRIAG	Ribulose bisphosphate carboxylase small chain 2, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.00	-	vac	0	Plastid; chloroplast				179
O22573 UniProt NPD GO	RBS3_FRIAG	Ribulose bisphosphate carboxylase small chain 3, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.00	-	end	0	Plastid; chloroplast				179
P32764 UniProt NPD GO	RBS3_SOLTU	Ribulose bisphosphate carboxylase small chain 3, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.00	-	mit	0	Plastid; chloroplast				181
O22645 UniProt NPD GO	RBS5_FRIAG	Ribulose bisphosphate carboxylase small chain 5, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.00	-	end	0	Plastid; chloroplast				179
P10647 UniProt NPD GO	RBS0_SOLTU	Ribulose bisphosphate carboxylase small chain C, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.00	-	mit	0	Plastid; chloroplast				181
P27985 UniProt NPD GO	RBS2_BRANA	Ribulose bisphosphate carboxylase small chain F1, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.00	-	mit	0	Plastid; chloroplast				181

You are viewing entries 97901 to 97950 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.