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
Q96FX2 UniProt NPD GO	ZCSL2_HUMAN	CSL-type zinc finger-containing protein 2 (DelGEF-interacting protein 1) (DelGIP1)	0.01	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]	608959		82
Q8K0W9 UniProt NPD GO	ZCSL2_MOUSE	CSL-type zinc finger-containing protein 2 (DelGEF-interacting protein 1) (DelGIP1)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]		1WGE	82
Q6VUC1 UniProt NPD GO	ZCSL2_CRIGR	CSL-type zinc finger-containing protein 2 (Diphtheria toxin and Pseudomonas exotoxin A sensitivity r ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			82
P49238 UniProt NPD GO	CX3C1_HUMAN	CX3C chemokine receptor 1 (C-X3-C CKR-1) (CX3CR1) (Fractalkine receptor) (G-protein coupled receptor ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	609423		355
P82077 UniProt NPD GO	CDN5_LITCE	Caeridin-5	0.01	-		0	Secreted protein				15
P56244 UniProt NPD GO	CR43_LITCE	Caerin-4.3	0.01	-	cyt	0	Secreted protein				23
P82087 UniProt NPD GO	CAE21_LITCI	Caerulein-2.1/2.1Y4	0.01	-		0	Secreted protein				11
P82088 UniProt NPD GO	CAE22_LITCI	Caerulein-2.2/2.2Y4	0.01	-		0	Secreted protein				11
P82091 UniProt NPD GO	CAE41_LITCI	Caerulein-4.1/4.1Y4	0.01	-		0	Secreted protein				11
P82092 UniProt NPD GO	CAE42_LITCI	Caerulein-4.2/4.2Y4	0.01	-		0	Secreted protein				11
Q8W013 UniProt NPD GO	COMT1_CATRO	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.01	-	nuc	0					363
P46484 UniProt NPD GO	COMT1_EUCGU	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.01	-	cyt	0					366
Q9XGW0 UniProt NPD GO	COMT1_OCIBA	Caffeic acid 3-O-methyltransferase 1 (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyl ...	0.01	-	nuc	0					361
Q43046 UniProt NPD GO	COMT1_POPKI	Caffeic acid 3-O-methyltransferase 1 (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyl ...	0.01	-	cyt	0					365
Q00763 UniProt NPD GO	COMT1_POPTM	Caffeic acid 3-O-methyltransferase 1 (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyl ...	0.01	-	cyt	0					365
Q9XGV9 UniProt NPD GO	COMT2_OCIBA	Caffeic acid 3-O-methyltransferase 2 (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyl ...	0.01	-	nuc	0					361
Q43047 UniProt NPD GO	COMT3_POPKI	Caffeic acid 3-O-methyltransferase 3 (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyl ...	0.01	-	cyt	0					364
O94528 UniProt NPD GO	CAF5_SCHPO	Caffeine resistance protein 5	0.01	-	end	11	Membrane; multi-pass membrane protein (Potential)				531
P28034 UniProt NPD GO	CAMT_PETCR	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCOAMT) ...	0.01	-	cyt	0					241
Q9ZTT5 UniProt NPD GO	CAMT_PINTA	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.01	-	cyt	0					259
Q8H9B6 UniProt NPD GO	CAMT_SOLTU	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.01	-	cyt	0					242
O24149 UniProt NPD GO	CAMT2_TOBAC	Caffeoyl-CoA O-methyltransferase 2 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 2) (CCoA ...	0.01	-	cyt	0					242
P01259 UniProt NPD GO	CALC_PIG	Calcitonin	0.01	-	nuc	0	Secreted protein				32
P30881 UniProt NPD GO	CALCA_SHEEP	Calcitonin gene-related peptide (CGRP)	0.01	-	mit	0	Secreted protein				37
Q16602 UniProt NPD GO	CALRL_HUMAN	Calcitonin gene-related peptide type 1 receptor precursor (CGRP type 1 receptor) (Calcitonin recepto ...	0.01	-	end	8 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	114190		461
P69165 UniProt NPD GO	CALC2_ONCGO	Calcitonin-2	0.01	-	nuc	0	Secreted protein				32
P69067 UniProt NPD GO	CALC2_ONCKE	Calcitonin-2	0.01	-	nuc	0	Secreted protein				32
P69068 UniProt NPD GO	CALC2_ONCNE	Calcitonin-2	0.01	-	nuc	0	Secreted protein				32
P39877 UniProt NPD GO	PA2G5_HUMAN	Calcium-dependent phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (PLA ...	0.01	-	cyt	0	Secreted protein	extracellular region [TAS]	601192		138
P55091 UniProt NPD GO	CLCR_RAT	Caldecrin precursor (EC 3.4.21.2) (Chymotrypsin C) (Serum calcium-decreasing factor)	0.01	-	exc	0					268
P14531 UniProt NPD GO	TXCL1_CALPA	Calitoxin-1 precursor (CLX-1) (Neurotoxic peptide)	0.01	-	exc	0	Secreted protein. Found in nematocyst				79
P49127 UniProt NPD GO	TXCL2_CALPA	Calitoxin-2 precursor (CLX-2) (Neurotoxic peptide)	0.01	-	vac	1 *	Secreted protein. Found in nematocyst				79
P41840 UniProt NPD GO	ALL4_CALVO	Callatostatin-4 (Leu-callatostatin-4)	0.01	-		0	Secreted protein				8
P41518 UniProt NPD GO	TKC2_CALVO	Callitachykinin-2 (Callitachykinin II)	0.01	-		0	Secreted protein				11
Q9HFY6 UniProt NPD GO	CALM_BLAEM	Calmodulin (CaM)	0.01	-	cyt	0					148
O82018 UniProt NPD GO	CALM_MOUSC	Calmodulin (CaM)	0.01	-	cyt	0					148
P41041 UniProt NPD GO	CALM_PNECA	Calmodulin (CaM)	0.01	-	cyt	0					151
P04353 UniProt NPD GO	CALM_SPIOL	Calmodulin (CaM)	0.01	-	cyt	0					148
P05935 UniProt NPD GO	CALM_LYTPI	Calmodulin (CaM) (Fragment)	0.01	-	cyt	0					30
P05934 UniProt NPD GO	CALM_STRPU	Calmodulin (CaM) (Fragment)	0.01	-	nuc	0					80
Q05055 UniProt NPD GO	CALM_TETTH	Calmodulin (CaM) (Fragment)	0.01	-		0					12
Q7DMP0 UniProt NPD GO	CALM2_SOLTU	Calmodulin-2/4 (CaM-2/4) (Fragment)	0.01	-	cyt	0					124
P05932 UniProt NPD GO	CALMB_ARBPU	Calmodulin-beta (Cam B) (Fragment)	0.01	-	cyt	0					138
P83003 UniProt NPD GO	CALR_ENTHI	Calreticulin (Fragment)	0.01	-		0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	cytosol [ISS] endoplasmic reticulum lumen [ISS]			19
P30806 UniProt NPD GO	CALR_SPIOL	Calreticulin (Fragment)	0.01	-		0	Endoplasmic reticulum; endoplasmic reticulum lumen				20
P28491 UniProt NPD GO	CALR_PIG	Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (Fragment)	0.01	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				105
P31236 UniProt NPD GO	CASQ1_CANFA	Calsequestrin-1 (Calsequestrin, skeletal muscle isoform) (Fragment)	0.01	-	cyt	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...				56
O18934 UniProt NPD GO	CASQ2_PIG	Calsequestrin-2 (Calsequestrin, cardiac muscle isoform) (Fragment)	0.01	-	cyt	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...				160
P24020 UniProt NPD GO	AQN3_PIG	Carbohydrate-binding protein AQN-3 (Zona pellucida-binding protein AQN-3) (Spermadhesin AQN-3)	0.01	-	mit	0	Secreted protein				116
P54212 UniProt NPD GO	CAH_DUNSA	Carbonic anhydrase (EC 4.2.1.1) (Carbonate dehydratase)	0.01	-	mit	0					589

You are viewing entries 86951 to 87000 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.