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
P46820 UniProt NPD GO	RBL_STEME	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P25839 UniProt NPD GO	RBL_TRIPO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	mit	0	Plastid; chloroplast				480
P48718 UniProt NPD GO	RBL_VISAL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				475
P11383 UniProt NPD GO	RBL_WHEAT	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	cyt	0	Plastid; chloroplast				477
P19160 UniProt NPD GO	RBL_ATRPA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				469
Q31738 UniProt NPD GO	RBL_BREMA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				469
P31182 UniProt NPD GO	RBL_COLAR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				54
Q31946 UniProt NPD GO	RBL_CRUAN	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				453
Q31992 UniProt NPD GO	RBL_CRUGL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				453
P31184 UniProt NPD GO	RBL_DICCR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				448
Q32271 UniProt NPD GO	RBL_GALCO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				453
Q32283 UniProt NPD GO	RBL_GALEL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				453
Q32345 UniProt NPD GO	RBL_GALPA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				453
Q32344 UniProt NPD GO	RBL_GALPR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				453
Q32360 UniProt NPD GO	RBL_GALSC	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				453
P05698 UniProt NPD GO	RBL_HORVU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				426
Q33600 UniProt NPD GO	RBL_LAVLA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				473
P31193 UniProt NPD GO	RBL_MAGLI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	nuc	0	Plastid; chloroplast				54
P31194 UniProt NPD GO	RBL_MALDO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				53
Q33619 UniProt NPD GO	RBL_MONDI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				473
P31196 UniProt NPD GO	RBL_NEMMU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				143
P28262 UniProt NPD GO	RBL_PHORE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				467
Q32908 UniProt NPD GO	RBL_PHOST	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				453
Q33274 UniProt NPD GO	RBL_VALMU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.01	-	cyt	0	Plastid; chloroplast				453
P16032 UniProt NPD GO	RBS1_MESCR	Ribulose bisphosphate carboxylase small chain 1, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.01	-	cyt	0	Plastid; chloroplast				182
Q08184 UniProt NPD GO	RBS4_MESCR	Ribulose bisphosphate carboxylase small chain 4, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.01	-	mit	0	Plastid; chloroplast				183
Q08185 UniProt NPD GO	RBS5_MESCR	Ribulose bisphosphate carboxylase small chain 5, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.01	-	mit	0	Plastid; chloroplast				182
P00872 UniProt NPD GO	RBS1_LEMGI	Ribulose bisphosphate carboxylase small chain SSU1, chloroplast precursor (EC 4.1.1.39) (RuBisCO sma ...	0.01	-	mit	0	Plastid; chloroplast				173
P19308 UniProt NPD GO	RBS2_LEMGI	Ribulose bisphosphate carboxylase small chain SSU26, chloroplast precursor (EC 4.1.1.39) (RuBisCO sm ...	0.01	-	vac	0	Plastid; chloroplast				177
P19309 UniProt NPD GO	RBS3_LEMGI	Ribulose bisphosphate carboxylase small chain SSU40A, chloroplast precursor (EC 4.1.1.39) (RuBisCO s ...	0.01	-	mit	0	Plastid; chloroplast				177
P19311 UniProt NPD GO	RBS5_LEMGI	Ribulose bisphosphate carboxylase small chain SSU5A, chloroplast precursor (EC 4.1.1.39) (RuBisCO sm ...	0.01	-	vac	0	Plastid; chloroplast				177
P19312 UniProt NPD GO	RBS6_LEMGI	Ribulose bisphosphate carboxylase small chain SSU5B, chloroplast precursor (EC 4.1.1.39) (RuBisCO sm ...	0.01	-	mit	0	Plastid; chloroplast				177
O24045 UniProt NPD GO	RBS_MUSAC	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.01	-	mit	0	Plastid; chloroplast				180
P05347 UniProt NPD GO	RBS1_ORYSA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.01	-	mit	0	Plastid; chloroplast			1WDD	175
P84562 UniProt NPD GO	RCA_POPEU	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast (RuBisCO activase) (RA) (Fragments ...	0.01	-	cyt	0	Plastid; chloroplast; chloroplast stroma				32
O98997 UniProt NPD GO	RCA_PHAAU	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.01	-	nuc	0	Plastid; chloroplast; chloroplast stroma				439
O64981 UniProt NPD GO	RCA_PHAVU	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast stroma				441
P52205 UniProt NPD GO	ROM1_BOVIN	Rod outer segment membrane protein 1 (ROSP1)	0.01	-	end	3 *	Membrane; multi-pass membrane protein				351
P28346 UniProt NPD GO	RODL_EMENI	Rodlet protein precursor	0.01	-	cyt	0	Secreted protein				157
P82073 UniProt NPD GO	RBE32_LITRU	Rubellidin-3.2	0.01	-		0	Secreted protein				5
P82074 UniProt NPD GO	RBE41_LITRU	Rubellidin-4.1	0.01	-		0	Secreted protein				11
P08616 UniProt NPD GO	TKN2_UPERU	Rugosauperolein-2 (Rugosauperolein II) ([Lys5,Thr6]-physalaemin)	0.01	-		0	Secreted protein				11
P80955 UniProt NPD GO	RUGB_RANRU	Rugosin-B	0.01	-	nuc	0	Secreted protein				33
Q06099 UniProt NPD GO	FADH_CANMA	S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284) (Glutathione-dependent formaldehyde dehydr ...	0.01	-	cyt	0					381
O74685 UniProt NPD GO	FADH_PICPA	S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284) (Glutathione-dependent formaldehyde dehydr ...	0.01	-	cyt	0					379
Q8R197 UniProt NPD GO	SAST_MOUSE	S-acyl fatty acid synthase thioesterase, medium chain (EC 3.1.2.14) (Oleoyl-ACP hydrolase) (Thioeste ...	0.01	-	mit	0					265
P50244 UniProt NPD GO	DCAM_TRYBB	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.01	-	mit	0					370
P49611 UniProt NPD GO	METK_BRAJU	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.01	-	cyt	0					393
O22338 UniProt NPD GO	METK_MUSAC	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.01	-	cyt	0					393
P48466 UniProt NPD GO	METK_NEUCR	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.01	-	cyt	0					395

You are viewing entries 91351 to 91400 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.