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
Q24214 UniProt NPD GO	CANB2_DROME	Calcineurin subunit B isoform 2 (Protein phosphatase 2B regulatory subunit)	0.06	-	cyt	0		synaptic vesicle [NAS]			170
Q03975 UniProt NPD GO	LPS1B_LYTPI	Calcium-binding protein LPS1-beta (Fragment)	0.06	-	mit	0					243
P51433 UniProt NPD GO	PA2G5_RAT	Calcium-dependent phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (PLA ...	0.06	-	exc	0	Secreted protein				137
P35316 UniProt NPD GO	ATC_ARTSF	Calcium-transporting ATPase sarcoplasmic/endoplasmic reticulum type (EC 3.6.3.8) (Calcium pump)	0.06	-	end	8	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; multi-pass membrane protein				1003
Q8AY75 UniProt NPD GO	CALGL_BOTIN	Calglandulin	0.06	-	cyt	0	Cytoplasm (Probable). Not found in venom				156
P27161 UniProt NPD GO	CALM_LYCES	Calmodulin (CaM)	0.06	-	cyt	0					148
P07463 UniProt NPD GO	CALM_PARTE	Calmodulin (CaM)	0.06	-	cyt	0				1OSA	148
Q8STF0 UniProt NPD GO	CALM_STRIE	Calmodulin (CaM)	0.06	-	cyt	0					155
P69097 UniProt NPD GO	CALM_TRYBB	Calmodulin (CaM)	0.06	-	cyt	0					148
P69098 UniProt NPD GO	CALM_TRYBG	Calmodulin (CaM)	0.06	-	cyt	0					148
P18061 UniProt NPD GO	CALM_TRYCR	Calmodulin (CaM)	0.06	-	cyt	0					148
P13868 UniProt NPD GO	CALM1_SOLTU	Calmodulin-1 (CaM-1)	0.06	-	cyt	0					148
P20728 UniProt NPD GO	CAL1_CALGI	Calotropin-DI (EC 3.4.22.-) (Fragment)	0.06	-		0					14
Q9VXH6 UniProt NPD GO	CANC_DROME	Calpain C (Calcium-activated neutral proteinase homolog C) (CANP C)	0.06	-	cyt	0	Cytoplasm	cytoplasm [IDA]			681
P31231 UniProt NPD GO	CASQ1_RANES	Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform)	0.06	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...				420
O35887 UniProt NPD GO	CALU_MOUSE	Calumenin precursor (Crocalbin)	0.06	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				315
O43852 UniProt NPD GO	CALU_HUMAN	Calumenin precursor (Crocalbin) (IEF SSP 9302)	0.06	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Secreted protein	endoplasmic reticulum [TAS] Golgi apparatus [TAS]	603420		315
Q71SP5 UniProt NPD GO	CNR1_MACMU	Cannabinoid receptor 1 (CB1) (CB-R)	0.06	-	end	7	Membrane; multi-pass membrane protein (By similarity)				472
Q5IS73 UniProt NPD GO	CNR1_PANTR	Cannabinoid receptor 1 (CB1) (CB-R)	0.06	-	end	7	Membrane; multi-pass membrane protein (By similarity)				472
P21554 UniProt NPD GO	CNR1_HUMAN	Cannabinoid receptor 1 (CB1) (CB-R) (CANN6)	0.06	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	114610	1LVR	472
Q9QZN9 UniProt NPD GO	CNR2_RAT	Cannabinoid receptor 2 (CB2) (CB-2)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			410
O42207 UniProt NPD GO	VSP2_AGKCA	Capillary permeability-increasing enzyme 2 precursor (EC 3.4.21.-) (CPI-enzyme 2)	0.06	-	exc	0	Secreted protein				258
Q92051 UniProt NPD GO	CAHZ_BRARE	Carbonic anhydrase (EC 4.2.1.1) (Carbonate dehydratase)	0.06	-	cyt	0					260
Q8HY33 UniProt NPD GO	CAH1_MONDO	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I)	0.06	-	nuc	0	Cytoplasm (By similarity)				262
Q7M317 UniProt NPD GO	CAH1_PANTR	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I)	0.06	-	nuc	0	Cytoplasm (By similarity)				260
P20507 UniProt NPD GO	CAH1_CHLRE	Carbonic anhydrase 1 precursor (EC 4.2.1.1) (Carbonate dehydratase 1) (CA1) [Contains: Carbonic anhy ...	0.06	-	cyt	0	Periplasm				377
P43166 UniProt NPD GO	CAH7_HUMAN	Carbonic anhydrase 7 (EC 4.2.1.1) (Carbonic anhydrase VII) (Carbonate dehydratase VII) (CA-VII)	0.06	-	cyt	0	Cytoplasm (Probable)		114770		264
P52719 UniProt NPD GO	PEPS_ASPSA	Carboxypeptidase cpdS precursor (EC 3.4.16.-)	0.06	-	mit	0					523
P79688 UniProt NPD GO	CXH_BUNMU	Cardiotoxin homolog TA-ctx-like precursor	0.06	-	exc	0	Secreted protein				86
P05099 UniProt NPD GO	MATN1_CHICK	Cartilage matrix protein precursor (Matrilin-1)	0.06	-	nuc	0				1AQ5	493
P58780 UniProt NPD GO	CECR1_PIG	Cat eye syndrome critical region protein 1 homolog precursor	0.06	-	mit	0					510
O88587 UniProt NPD GO	COMT_MOUSE	Catechol O-methyltransferase (EC 2.1.1.6)	0.06	-	end	1 *	Isoform S-COMT: Cytoplasm. Isoform MB-COMT: Cell membrane; single-pass type II membrane protein; ext ...				265
P22734 UniProt NPD GO	COMT_RAT	Catechol O-methyltransferase (EC 2.1.1.6)	0.06	-	end	1 *	Isoform S-COMT: Cytoplasm. Isoform MB-COMT: Cell membrane; single-pass type II membrane protein; ext ...			1VID	264
Q9DEX3 UniProt NPD GO	CATD_CLUHA	Cathepsin D precursor (EC 3.4.23.5)	0.06	-	end	0	Lysosome				396
P17977 UniProt NPD GO	CATG_RAT	Cathepsin G (EC 3.4.21.20) (Fragment)	0.06	-	nuc	0					26
O35186 UniProt NPD GO	CATK_RAT	Cathepsin K precursor (EC 3.4.22.38)	0.06	-	mit	0	Lysosome (By similarity)				329
P25975 UniProt NPD GO	CATL_BOVIN	Cathepsin L precursor (EC 3.4.22.15) [Contains: Cathepsin L heavy chain; Cathepsin L light chain]	0.06	-	exc	0	Lysosome				334
O97397 UniProt NPD GO	CATLL_PHACE	Cathepsin L-like proteinase precursor (EC 3.4.22.-)	0.06	-	exc	0					324
P80342 UniProt NPD GO	CATL2_FASHE	Cathepsin L2 (EC 3.4.22.15) (Fragment)	0.06	-		0	Lysosome				14
Q5E998 UniProt NPD GO	CATL2_BOVIN	Cathepsin L2 precursor (EC 3.4.22.43)	0.06	-	exc	0	Lysosome (Potential)				334
Q9JIA9 UniProt NPD GO	CATR_MOUSE	Cathepsin R precursor (EC 3.4.22.-)	0.06	-	end	0	Lysosome (Potential)				334
O43246 UniProt NPD GO	CTR4_HUMAN	Cationic amino acid transporter 4 (CAT-4) (CAT4)	0.06	-	end	14 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS]	603752		635
P84516 UniProt NPD GO	PER1_SORBI	Cationic peroxidase SPC4 precursor (EC 1.11.1.7) (Fragment)	0.06	-	exc	0	Secreted protein				213
Q27032 UniProt NPD GO	CDC2H_THEPA	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23)	0.06	-	cyt	0	Cytoplasm (By similarity)				298
P34556 UniProt NPD GO	CDC2_CAEEL	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase)	0.06	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			332
P11440 UniProt NPD GO	CDC2_MOUSE	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.06	-	cyt	0	Nucleus (By similarity)				297
P39951 UniProt NPD GO	CDC2_RAT	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.06	-	cyt	0	Nucleus				297
P93101 UniProt NPD GO	CDC2_CHERU	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34cdc2)	0.06	-	cyt	0					294
P29619 UniProt NPD GO	CDC22_ORYSA	Cell division control protein 2 homolog 2 (EC 2.7.11.22)	0.06	-	cyt	0					292
P19073 UniProt NPD GO	CDC42_YEAST	Cell division control protein 42 (Suppressor of RHO3 protein 2)	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	bud neck [IDA] bud tip [IDA] mating projection tip [IDA] plasma membrane [IDA] soluble fraction [IDA]			191

You are viewing entries 71701 to 71750 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.