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
Q98958 UniProt NPD GO	CX1D_NAJAT	Cardiotoxin 1d/1e precursor	0.00	-	mit	0	Secreted protein				81
Q9PST4 UniProt NPD GO	CTX2A_NAJSP	Cardiotoxin 2a precursor (CTX-2a) (Ctx2a)	0.00	-	mit	0	Secreted protein				81
O93472 UniProt NPD GO	CTX2C_NAJSP	Cardiotoxin 2c precursor (CTX-2c) (Ctx2c)	0.00	-	mit	0	Secreted protein				81
P60302 UniProt NPD GO	CTX3_NAJSP	Cardiotoxin 3 precursor (CTX-3) (Ctx3)	0.00	-	mit	0	Secreted protein				81
Q98959 UniProt NPD GO	CX3A_NAJAT	Cardiotoxin 3a precursor (Cardiotoxin-31) (Ctx-31)	0.00	-	mit	0	Secreted protein			1I02	81
Q98960 UniProt NPD GO	CX3B_NAJAT	Cardiotoxin 3b precursor	0.00	-	mit	0	Secreted protein				81
Q98962 UniProt NPD GO	CX3D_NAJAT	Cardiotoxin 3d precursor	0.00	-	mit	0	Secreted protein				81
O93473 UniProt NPD GO	CTX4A_NAJSP	Cardiotoxin 4a precursor (CTX-4a) (Ctx4a)	0.00	-	mit	0	Secreted protein				81
O73856 UniProt NPD GO	CTX4B_NAJSP	Cardiotoxin 4b precursor (CTX-4b) (Ctx4b)	0.00	-	mit	0	Secreted protein				81
Q98961 UniProt NPD GO	CX5_NAJAT	Cardiotoxin 5 precursor	0.00	-	mit	0	Secreted protein				81
O73857 UniProt NPD GO	CTX5A_NAJSP	Cardiotoxin 5a precursor (CTX-5a) (Ctx5a)	0.00	-	mit	0	Secreted protein				81
P60310 UniProt NPD GO	CTX5B_NAJSP	Cardiotoxin 5b precursor (CTX-5b) (Ctx5b)	0.00	-	mit	0	Secreted protein				81
Q91136 UniProt NPD GO	CX15_NAJAT	Cardiotoxin I-like T-15 precursor	0.00	-	mit	0	Secreted protein				81
Q91124 UniProt NPD GO	CTX8_NAJAT	Cardiotoxin VIII precursor	0.00	-	mit	0	Secreted protein				81
Q02454 UniProt NPD GO	CTX_NAJSP	Cardiotoxin precursor	0.00	-	mit	0	Secreted protein				81
P55738 UniProt NPD GO	CCAC_AMPCA	Caroteno-chlorophyll a-c-binding protein (Fragment)	0.00	-	nuc	1	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				102
P05147 UniProt NPD GO	3DHQ_EMENI	Catabolic 3-dehydroquinase (EC 4.2.1.10) (3-dehydroquinate dehydratase)	0.00	-	cyt	0					153
P83205 UniProt NPD GO	CATB_SHEEP	Cathepsin B (EC 3.4.22.1) (Cathepsin B1) (Fragment)	0.00	-		0	Lysosome (By similarity)				10
P25773 UniProt NPD GO	CATL_FELCA	Cathepsin L (EC 3.4.22.15) (Progesterone-dependent protein) (PDP) (Fragment)	0.00	-	cyt	0	Lysosome				139
P79132 UniProt NPD GO	CAV1_BOVIN	Caveolin-1	0.00	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	caveolar membrane [ISS]			178
P35431 UniProt NPD GO	CAV1_CHICK	Caveolin-1	0.00	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side. Membrane protein of ...				178
Q9YGM8 UniProt NPD GO	CAV1_FUGRU	Caveolin-1	0.00	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	caveolar membrane [ISS]			181
Q6B3Y2 UniProt NPD GO	CAV1_SHEEP	Caveolin-1	0.00	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				178
Q2QLG7 UniProt NPD GO	CAV2_CALJA	Caveolin-2	0.00	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
Q2QLC2 UniProt NPD GO	CAV2_CALMO	Caveolin-2	0.00	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
Q2QL91 UniProt NPD GO	CAV2_MICMU	Caveolin-2	0.00	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
Q9WVC3 UniProt NPD GO	CAV2_MOUSE	Caveolin-2	0.00	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	caveolar membrane [IDA] lipid raft [ISS]			162
Q2QLH8 UniProt NPD GO	CAV2_OTOGA	Caveolin-2	0.00	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
Q2IBD6 UniProt NPD GO	CAV2_PONPY	Caveolin-2	0.00	-	end	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				162
Q3ZDQ5 UniProt NPD GO	CAV3_PIG	Caveolin-3	0.00	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				151
P51638 UniProt NPD GO	CAV3_RAT	Caveolin-3	0.00	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	integral to membrane [TAS] plasma membrane [IDA]			151
P56539 UniProt NPD GO	CAV3_HUMAN	Caveolin-3 (M-caveolin)	0.00	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	dystrophin-associated glycoprotein complex [TAS]	607801		151
P51637 UniProt NPD GO	CAV3_MOUSE	Caveolin-3 (M-caveolin)	0.00	-	mit	1	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...	caveola [TAS] membrane fraction [IDA]			151
Q8MUF3 UniProt NPD GO	CECC_ANOGA	Cecropin-C precursor	0.00	-	end	1 *	Secreted protein (By similarity)				59
P01511 UniProt NPD GO	CECD_ANTPE	Cecropin-D	0.00	-	nuc	0	Secreted protein				36
P01510 UniProt NPD GO	CECD_HYACE	Cecropin-D precursor	0.00	-	end	0	Secreted protein				62
Q9W739 UniProt NPD GO	CDC2_RANDY	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase)	0.00	-	cyt	0	Nucleus (By similarity)				302
P38155 UniProt NPD GO	DAN3_YEAST	Cell wall protein DAN3 precursor	0.00	-	exc	0					120
Q5PXY7 UniProt NPD GO	RABP2_BOVIN	Cellular retinoic acid-binding protein 2 (Cellular retinoic acid-binding protein II) (CRABP-II) (Ret ...	0.00	-	cyt	0	Cytoplasm (By similarity)				137
P29373 UniProt NPD GO	RABP2_HUMAN	Cellular retinoic acid-binding protein 2 (Cellular retinoic acid-binding protein II) (CRABP-II) (Ret ...	0.00	-	cyt	0	Cytoplasm		180231	3CBS	137
P11935 UniProt NPD GO	EXPA_CEPAC	Cephalosporin biosynthesis expandase/hydroxylase [Includes: Deacetoxycephalosporin C synthetase (EC ...	0.00	-	cyt	0					332
Q16739 UniProt NPD GO	CEGT_HUMAN	Ceramide glucosyltransferase (EC 2.4.1.80) (Glucosylceramide synthase) (GCS) (UDP-glucose:N-acylsphi ...	0.00	-	nuc	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	membrane fraction [TAS]	602874		394
O88693 UniProt NPD GO	CEGT_MOUSE	Ceramide glucosyltransferase (EC 2.4.1.80) (Glucosylceramide synthase) (GCS) (UDP-glucose:N-acylsphi ...	0.00	-	nuc	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				394
Q9R0E0 UniProt NPD GO	CEGT_RAT	Ceramide glucosyltransferase (EC 2.4.1.80) (Glucosylceramide synthase) (GCS) (UDP-glucose:N-acylsphi ...	0.00	-	nuc	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				394
P18692 UniProt NPD GO	VSPA_CERVI	Cerastobin (EC 3.4.21.-) (Venom serine protease) (Fragment)	0.00	-	cyt	0	Secreted protein				35
P81702 UniProt NPD GO	CEPL_CERFI	Cerato-platanin	0.00	-	cyt	0	Secreted protein				120
P36191 UniProt NPD GO	CTXB_CERCA	Ceratotoxin-B	0.00	-	nuc	0	Secreted protein				29
Q6UW01 UniProt NPD GO	CBLN3_HUMAN	Cerebellin-3 precursor	0.00	-	exc	0	Secreted protein (Potential)				205
Q9JHG0 UniProt NPD GO	CBLN3_MOUSE	Cerebellin-3 precursor	0.00	-	exc	0	Secreted protein (Potential)				197
Q966X9 UniProt NPD GO	CHAG_TRYCR	Chagasin	0.00	-	cyt	0	Flagellar pocket and cytoplasmic vesicles of trypomastigotes and to the cell surface of amastigotes			2FO8	110

You are viewing entries 93051 to 93100 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.