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
Q75D66 UniProt NPD GO	CARB_ASHGO	Carbamoyl-phosphate synthase arginine-specific large chain (EC 6.3.5.5) (Arginine-specific carbamoyl ...	0.09	-	cyt	0	Cytoplasm (By similarity)				1113
Q9D5J6 UniProt NPD GO	CARKL_MOUSE	Carbohydrate kinase-like protein (EC 2.7.1.-)	0.09	-	mit	0	Cytoplasm (Potential)				476
Q5ZIE4 UniProt NPD GO	CHSTA_CHICK	Carbohydrate sulfotransferase 10 (EC 2.8.2.-) (HNK-1 sulfotransferase) (HNK1ST) (HNK-1ST)	0.09	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				358
P07452 UniProt NPD GO	CAH1_RABIT	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I) (Fragment) ...	0.09	-	nuc	0	Cytoplasm				235
P24258 UniProt NPD GO	CAH2_CHLRE	Carbonic anhydrase 2 precursor (EC 4.2.1.1) (Carbonate dehydratase 2) (CA2) [Contains: Carbonic anhy ...	0.09	-	cyt	0	Periplasm				380
P16303 UniProt NPD GO	CES3_RAT	Carboxylesterase 3 precursor (EC 3.1.1.1) (Liver carboxylesterase 10) (Carboxyesterase ES-10) (pI 6. ...	0.09	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				565
P83852 UniProt NPD GO	CBPD_LOPSP	Carboxypeptidase D (Metallocarboxypeptidase D) (EC 3.4.17.22) (CPD-2) (Fragment)	0.09	-	cyt	0		integral to membrane [ISS]		1QMU	380
P81823 UniProt NPD GO	ALL20_CARMA	Carcinustatin-20	0.09	-	cyt	0	Secreted protein				27
Q52QW3 UniProt NPD GO	CRTS1_ONCHC	Carotenoid isomerase 1, chloroplast precursor (EC 5.-.-.-) (CrtISO1) (OcrtISO22)	0.09	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (By similarity)				587
Q8R555 UniProt NPD GO	CRAC1_MOUSE	Cartilage acidic protein 1 precursor (CRTAC1-B protein) (Chondrocyte expressed protein 68 kDa) (CEP- ...	0.09	-	vac	0	Secreted protein (Probable)				646
O96863 UniProt NPD GO	CSK2C_DROME	Casein kinase II subunit beta' (CK II beta')	0.09	-	cyt	0					219
P55212 UniProt NPD GO	CASP6_HUMAN	Caspase-6 precursor (EC 3.4.22.-) (CASP-6) (Apoptotic protease Mch-2) [Contains: Caspase-6 subunit p ...	0.09	-	cyt	0	Cytoplasm		601532	1MI9	293
O08738 UniProt NPD GO	CASP6_MOUSE	Caspase-6 precursor (EC 3.4.22.-) (CASP-6) (Apoptotic protease Mch-2) [Contains: Caspase-6 subunit p ...	0.09	-	cyt	0	Cytoplasm				276
P55307 UniProt NPD GO	CATA1_HORVU	Catalase isozyme 1 (EC 1.11.1.6)	0.09	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
P55308 UniProt NPD GO	CATA2_HORVU	Catalase isozyme 2 (EC 1.11.1.6)	0.09	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				494
Q9C168 UniProt NPD GO	CAT1_NEUCR	Catalase-1 (EC 1.11.1.6)	0.09	-	cyt	0	Cell wall. Principally associated with the cell wall of conidia	spore wall (sensu Fungi) [IDA]		1SY7	736
P24268 UniProt NPD GO	CATD_RAT	Cathepsin D precursor (EC 3.4.23.5) [Contains: Cathepsin D 12 kDa light chain; Cathepsin D 9 kDa lig ...	0.09	-	end	0	Lysosome	lysosome [IDA]			407
P43159 UniProt NPD GO	CATE_RABIT	Cathepsin E precursor (EC 3.4.23.34)	0.09	-	mit	0	Endosome (By similarity). The proenzyme is localized to the endoplasmic reticulum and Golgi apparatu ...	endosome [ISS]			396
Q9GLE3 UniProt NPD GO	CATK_PIG	Cathepsin K precursor (EC 3.4.22.38)	0.09	-	end	0	Lysosome. Secreted protein				330
P07154 UniProt NPD GO	CATL_RAT	Cathepsin L precursor (EC 3.4.22.15) (Major excreted protein) (MEP) (Cyclic protein 2) (CP-2) [Conta ...	0.09	-	exc	0	Procathepsin L: Secreted protein. Cathepsin L: Lysosome	lysosome [IDA]			334
Q7ZT99 UniProt NPD GO	CRVP_CROAT	Catrin-1/2 precursor	0.09	-	exc	0	Secreted protein				240
Q9QWZ1 UniProt NPD GO	RAD1_MOUSE	Cell cycle checkpoint protein RAD1 (EC 3.1.11.2) (DNA repair exonuclease rad1 homolog) (Rad1-like DN ...	0.09	-	cyt	0	Nucleus (By similarity)	nucleus [ISS]			280
O96821 UniProt NPD GO	CDC2H_PLAKH	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23)	0.09	-	cyt	0	Cytoplasm (By similarity)				288
Q7RM49 UniProt NPD GO	CDC2H_PLAYO	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23)	0.09	-	nuc	0	Cytoplasm (By similarity)				289
Q9DGA5 UniProt NPD GO	CDC2_ORYCU	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.09	-	cyt	0	Nucleus (By similarity)				303
Q9DGA2 UniProt NPD GO	CDC2_ORYJA	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.09	-	cyt	0	Nucleus (By similarity)				303
Q9DGD3 UniProt NPD GO	CDC2_ORYLA	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.09	-	cyt	0	Nucleus (By similarity)				303
Q9DG98 UniProt NPD GO	CDC2_ORYLU	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.09	-	cyt	0	Nucleus (By similarity)				303
P23111 UniProt NPD GO	CDC2_MAIZE	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34cdc2)	0.09	-	cyt	0					294
Q38772 UniProt NPD GO	CDC2A_ANTMA	Cell division control protein 2 homolog A (EC 2.7.11.22) (EC 2.7.11.23)	0.09	-	cyt	0					294
P35426 UniProt NPD GO	CDK4_RAT	Cell division protein kinase 4 (EC 2.7.11.22) (Cyclin-dependent kinase 4) (PSK-J3)	0.09	-	cyt	0					303
P28319 UniProt NPD GO	CWP1_YEAST	Cell wall protein CWP1 precursor	0.09	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			239
Q12282 UniProt NPD GO	YO214_YEAST	Cell wall protein YOR214C precursor	0.09	-	exc	0	Cell wall; lipid-anchor; GPI-anchor. GPI-anchored cell wall protein (GPI-CWP)	cell wall (sensu Fungi) [IDA]			236
Q06153 UniProt NPD GO	CEUL_OPHUL	Cerato-ulmin precursor (Dutch elm disease toxin) (CU)	0.09	-	exc	0					100
P30078 UniProt NPD GO	CHSY_MALDO	Chalcone synthase (EC 2.3.1.74) (Naregenin-chalcone synthase) (Fragment)	0.09	-	cyt	0					232
P06515 UniProt NPD GO	CHSY_ANTMA	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.09	-	mit	0					390
P51075 UniProt NPD GO	CHSY_BETVE	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.09	-	mit	0					395
P30079 UniProt NPD GO	CHSY_PINSY	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.09	-	cyt	0					396
P51090 UniProt NPD GO	CHSY_VITVI	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.09	-	mit	0					393
O23883 UniProt NPD GO	CHS3_PEA	Chalcone synthase 3 (EC 2.3.1.74) (Naregenin-chalcone synthase 3)	0.09	-	mit	0					389
O23884 UniProt NPD GO	CHS5_PEA	Chalcone synthase 5 (EC 2.3.1.74) (Naregenin-chalcone synthase 5)	0.09	-	mit	0					389
P22925 UniProt NPD GO	CHSD_PETHY	Chalcone synthase D (EC 2.3.1.74) (Naringenin-chalcone synthase D)	0.09	-	nuc	0					419
P51076 UniProt NPD GO	CHSY_FRAAN	Chalcone synthase RJ5 (EC 2.3.1.74) (Naringenin-chalcone synthase) (Fragment)	0.09	-	cyt	0					99
Q9DAS1 UniProt NPD GO	CKLF_MOUSE	Chemokine-like factor	0.09	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				152
P30583 UniProt NPD GO	CHS1_EMENI	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-I chitin synth ...	0.09	-	cyt	0	Cell membrane; multi-pass membrane protein				189
Q9W303 UniProt NPD GO	IDGF4_DROME	Chitinase-like protein Idgf4 precursor (Imaginal disk growth factor protein 4)	0.09	-	pox	0	Secreted protein. Secreted in hemolymph. It is probably transported to target tissues via hemolymph	extracellular region [NAS]			442
Q921Q3 UniProt NPD GO	ALG1_MOUSE	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.09	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				438
O70496 UniProt NPD GO	CLCN7_MOUSE	Chloride channel protein 7 (ClC-7)	0.09	-	end	11	Membrane; multi-pass membrane protein				803
P51799 UniProt NPD GO	CLCN7_RAT	Chloride channel protein 7 (ClC-7)	0.09	-	end	11	Membrane; multi-pass membrane protein				803
P51345 UniProt NPD GO	RR1_PORPU	Chloroplast 30S ribosomal protein S1	0.09	-	cyt	0	Plastid; chloroplast				263

You are viewing entries 65851 to 65900 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.