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
O81646 UniProt NPD GO	COMT1_CAPCH	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	nuc	0					359
O23760 UniProt NPD GO	COMT1_CLABR	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	cyt	0					370
Q8LL87 UniProt NPD GO	COMT1_COFCA	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	nuc	0					350
Q06509 UniProt NPD GO	COMT1_MAIZE	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	cyt	0					364
P28002 UniProt NPD GO	COMT1_MEDSA	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	cyt	0				1KYZ	365
Q43609 UniProt NPD GO	COMT1_PRUDU	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	cyt	0					365
Q8GU25 UniProt NPD GO	COMT1_ROSCH	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	cyt	0					365
O82054 UniProt NPD GO	COMT1_SACOF	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	cyt	0					362
Q43239 UniProt NPD GO	COMT1_ZINEL	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	cyt	0					354
Q9SWC2 UniProt NPD GO	COMT1_EUCGL	Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) (S-adenosysl-L-methionine:caffeic acid 3-O-methyltr ...	0.00	-	mit	0					313
Q43237 UniProt NPD GO	CAMT_VITVI	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCOAMT) ...	0.00	-	nuc	0					242
Q40313 UniProt NPD GO	CAMT_MEDSA	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.00	-	cyt	0				1SUS	247
Q43095 UniProt NPD GO	CAMT_POPTM	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.00	-	cyt	0					247
O65862 UniProt NPD GO	CAMT1_POPTR	Caffeoyl-CoA O-methyltransferase 1 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 1) (CCoA ...	0.00	-	cyt	0					247
O24144 UniProt NPD GO	CAMT1_TOBAC	Caffeoyl-CoA O-methyltransferase 1 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 1) (CCoA ...	0.00	-	cyt	0					239
O24150 UniProt NPD GO	CAMT3_TOBAC	Caffeoyl-CoA O-methyltransferase 3 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 3) (CCoA ...	0.00	-	nuc	0					242
O24151 UniProt NPD GO	CAMT4_TOBAC	Caffeoyl-CoA O-methyltransferase 4 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase 4) (CCoA ...	0.00	-	cyt	0					242
P30880 UniProt NPD GO	CALCA_PIG	Calcitonin gene-related peptide (CGRP)	0.00	-	cyt	0	Secreted protein				37
P42529 UniProt NPD GO	CBP1_DICDI	Calcium-binding protein 1	0.00	-	nuc	0					156
Q967W0 UniProt NPD GO	CAB2_ECHGR	Calcium-binding protein 2 (Calcium-binding protein II) (CaBP-II) (EgCaBPII)	0.00	-	cyt	0					70
P09485 UniProt NPD GO	LPS1A_LYTPI	Calcium-binding protein LPS1-alpha	0.00	-	cyt	0					321
P54657 UniProt NPD GO	CAD1_DICDI	Calcium-dependent cell adhesion molecule 1 (DdCAD-1) (GP24)	0.00	-	cyt	0	Cell membrane. Associated with the ecto-surface of the plasma membrane. May be transported to the pl ...			1YHP	213
P82978 UniProt NPD GO	S100_LEPPA	Calhepatin	0.00	-	cyt	0					75
P41841 UniProt NPD GO	ALL5_CALVO	Callatostatin-5 (Met-callatostatin-1) ([Hyp3]Met-callatostatin)	0.00	-		0	Secreted protein				8
O96102 UniProt NPD GO	CALM_PHYPO	Calmodulin (CaM)	0.00	-	cyt	0					148
P27166 UniProt NPD GO	CALM_STYLE	Calmodulin (CaM)	0.00	-	cyt	0					148
Q6F332 UniProt NPD GO	CALM2_ORYSA	Calmodulin-2 (CaM-2)	0.00	-	cyt	0					148
Q41420 UniProt NPD GO	CALM3_SOLTU	Calmodulin-3 (CaM-3) (Fragment)	0.00	-	cyt	0					124
Q9JM83 UniProt NPD GO	CALM4_MOUSE	Calmodulin-4 (Calcium-binding protein Dd112)	0.00	-	cyt	0		soluble fraction [IDA]			148
Q9SRP5 UniProt NPD GO	CALL2_ARATH	Calmodulin-like protein 2	0.00	-	nuc	0				1TIZ	131
P28490 UniProt NPD GO	CALR_CANFA	Calreticulin (CRP55) (Calregulin) (HACBP) (ERp60) (Fragment)	0.00	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen				24
P31832 UniProt NPD GO	CALR_RANES	Calreticulin (Major microsomal calcium-binding protein) (Fragment)	0.00	-		0	Endoplasmic reticulum; endoplasmic reticulum lumen				13
Q25088 UniProt NPD GO	CLSS_HAEMA	Calsensin (LAN3-6 antigen)	0.00	-	nuc	0	Cytoplasm			1YX8	83
P19633 UniProt NPD GO	CASQ1_RAT	Calsequestrin-1 (Calsequestrin, skeletal muscle isoform) (Aspartactin) (Laminin-binding protein) (Fr ...	0.00	-		0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...				20
P81783 UniProt NPD GO	CADO_BUNCA	Candoxin precursor	0.00	-	mit	0	Secreted protein			1JGK	87
P07258 UniProt NPD GO	CARA_YEAST	Carbamoyl-phosphate synthase arginine-specific small chain (EC 6.3.5.5) (Arginine-specific carbamoyl ...	0.00	-	nuc	0	Cytoplasm				411
Q5S1S4 UniProt NPD GO	CAH3_PIG	Carbonic anhydrase 3 (EC 4.2.1.1) (Carbonic anhydrase III) (Carbonate dehydratase III) (CA-III)	0.00	-	cyt	0	Cytoplasm (By similarity)				259
P55749 UniProt NPD GO	PEP1_ASPNG	Carboxypeptidase 1 (EC 3.4.16.-) (Carboxypeptidase I) (CPD-I) (Fragment)	0.00	-	cyt	0	Secreted protein				24
Q61400 UniProt NPD GO	CEAMA_MOUSE	Carcinoembryonic antigen-related cell adhesion molecule 10 precursor (CEA-related cell adhesion mole ...	0.00	-	end	0	Secreted protein; extracellular space				265
P81813 UniProt NPD GO	ALL10_CARMA	Carcinustatin-10	0.00	-		0	Secreted protein				9
P81814 UniProt NPD GO	ALL11_CARMA	Carcinustatin-11	0.00	-		0	Secreted protein				9
P81815 UniProt NPD GO	ALL12_CARMA	Carcinustatin-12	0.00	-		0	Secreted protein				8
P81820 UniProt NPD GO	ALL17_CARMA	Carcinustatin-17	0.00	-		0	Secreted protein				8
P81821 UniProt NPD GO	ALL18_CARMA	Carcinustatin-18	0.00	-		0	Secreted protein				8
P81822 UniProt NPD GO	ALL19_CARMA	Carcinustatin-19	0.00	-		0	Secreted protein				10
P81807 UniProt NPD GO	ALL4_CARMA	Carcinustatin-4	0.00	-		0	Secreted protein				7
P58649 UniProt NPD GO	OCP3_OCTMI	Cardioactive peptides Ocp-3/Ocp-4	0.00	-		0	Secreted protein				4
O93471 UniProt NPD GO	CTX1_NAJSP	Cardiotoxin 1 precursor (CTX-1) (Ctx1)	0.00	-	mit	0	Secreted protein				81
Q98957 UniProt NPD GO	CX1A_NAJAT	Cardiotoxin 1a precursor	0.00	-	nuc	0	Secreted protein				81
Q98956 UniProt NPD GO	CX1B_NAJAT	Cardiotoxin 1b precursor	0.00	-	mit	0	Secreted protein				81

You are viewing entries 93001 to 93050 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.