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
Q32890 UniProt NPD GO	RBL_PELRO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
O04435 UniProt NPD GO	RBL_PERSE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	nuc	0	Plastid; chloroplast	ribulose bisphosphate carboxylase complex (... [NAS]			469
P48712 UniProt NPD GO	RBL_POLMU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				440
Q05992 UniProt NPD GO	RBL_POLRE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
Q9GHP8 UniProt NPD GO	RBL_POLSI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28447 UniProt NPD GO	RBL_RHOHI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
P28449 UniProt NPD GO	RBL_RUTFR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P28450 UniProt NPD GO	RBL_SANCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				436
P36486 UniProt NPD GO	RBL_SAUCE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
Q05994 UniProt NPD GO	RBL_VILCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				443
Q05995 UniProt NPD GO	RBL_VIOSO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				441
P28460 UniProt NPD GO	RBL_VITAE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
P93936 UniProt NPD GO	RBL_WATAN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				444
O98681 UniProt NPD GO	RBL_ZAMZA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				449
P36476 UniProt NPD GO	RBL_ADICA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
Q06021 UniProt NPD GO	RBL_ALNIN	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P48682 UniProt NPD GO	RBL_AMATR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P48683 UniProt NPD GO	RBL_ANACO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				479
P28258 UniProt NPD GO	RBL_ANGLY	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P25827 UniProt NPD GO	RBL_AREDR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				476
P48684 UniProt NPD GO	RBL_AVESA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				477
P25828 UniProt NPD GO	RBL_BASAL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				480
Q06022 UniProt NPD GO	RBL_BETPA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P26958 UniProt NPD GO	RBL_BRYMA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
Q06023 UniProt NPD GO	RBL_CARCO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P48688 UniProt NPD GO	RBL_CARPA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P48690 UniProt NPD GO	RBL_CASSA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P25830 UniProt NPD GO	RBL_CERGL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P48693 UniProt NPD GO	RBL_CICIN	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				477
P28392 UniProt NPD GO	RBL_CLAXA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P48695 UniProt NPD GO	RBL_COLOB	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
Q06024 UniProt NPD GO	RBL_CORCO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P27064 UniProt NPD GO	RBL_CUCSA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				476
P51101 UniProt NPD GO	RBL_GERJA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				477
Q5SCV9 UniProt NPD GO	RBL_HUPLU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
Q9BA49 UniProt NPD GO	RBL_HYOLA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				477
P48706 UniProt NPD GO	RBL_LACSA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				477
Q01873 UniProt NPD GO	RBL_LIQST	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
Q9BBU1 UniProt NPD GO	RBL_LOTJA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P06292 UniProt NPD GO	RBL_MARPO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P04991 UniProt NPD GO	RBL_MEDSA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				474
P19163 UniProt NPD GO	RBL_NEUMU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				478
Q32701 UniProt NPD GO	RBL_NOTSU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
Q9MTP9 UniProt NPD GO	RBL_OENHO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
Q06025 UniProt NPD GO	RBL_OSTVI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P04992 UniProt NPD GO	RBL_PETHY	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				477
P25833 UniProt NPD GO	RBL_PHYAM	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				482
P48713 UniProt NPD GO	RBL_POPTM	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P25834 UniProt NPD GO	RBL_RIVHU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				480
O62943 UniProt NPD GO	RBL_SESSE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				473

You are viewing entries 91301 to 91350 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.