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
O97438 UniProt NPD GO	CBK_GIALA	Carbamate kinase (EC 2.7.2.2)	0.03	-	vac	0					317
P84783 UniProt NPD GO	CABM1_MACCH	Carbamoylase-1 (EC 3.-.-.-) (Carbamoylase I) (Fragment)	0.03	-		0					17
P26322 UniProt NPD GO	AQN1_PIG	Carbohydrate-binding protein AQN-1 (Zona pellucida-binding protein AQN-1) (Spermadhesin AQN-1)	0.03	-	nuc	0	Secreted protein				111
P00915 UniProt NPD GO	CAH1_HUMAN	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I)	0.03	-	nuc	0	Cytoplasm		114800	2FOY	260
P48282 UniProt NPD GO	CAH1_SHEEP	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I)	0.03	-	nuc	0	Cytoplasm				260
P16015 UniProt NPD GO	CAH3_MOUSE	Carbonic anhydrase 3 (EC 4.2.1.1) (Carbonic anhydrase III) (Carbonate dehydratase III) (CA-III)	0.03	-	cyt	0	Cytoplasm				259
P27141 UniProt NPD GO	CAHC_TOBAC	Carbonic anhydrase, chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase)	0.03	-	mit	0	Plastid; chloroplast; chloroplast stroma				321
P35219 UniProt NPD GO	CAH8_HUMAN	Carbonic anhydrase-related protein (CARP) (CA-VIII)	0.03	-	cyt	0			114815		289
Q5PPN4 UniProt NPD GO	CAH8_RAT	Carbonic anhydrase-related protein (CARP) (CA-VIII)	0.03	-	cyt	0					289
Q9W716 UniProt NPD GO	CXH5_NAJAT	Cardiotoxin 5V precursor (CTX5V)	0.03	-	nuc	0	Secreted protein				83
Q9NQ79 UniProt NPD GO	CRAC1_HUMAN	Cartilage acidic protein 1 precursor (Chondrocyte expressed protein 68 kDa) (CEP-68) (ASPIC)	0.03	-	exc	0	Secreted protein (Probable)		606276		661
P07688 UniProt NPD GO	CATB_BOVIN	Cathepsin B precursor (EC 3.4.22.1) (BCSB) [Contains: Cathepsin B light chain; Cathepsin B heavy cha ...	0.03	-	exc	0	Lysosome			2DCD	335
P10605 UniProt NPD GO	CATB_MOUSE	Cathepsin B precursor (EC 3.4.22.1) (Cathepsin B1) [Contains: Cathepsin B light chain; Cathepsin B h ...	0.03	-	end	0	Lysosome	mitochondrion [IDA]			339
P92132 UniProt NPD GO	CATB2_GIALA	Cathepsin B-like CP2 precursor (EC 3.4.22.-) (Cathepsin B-like protease B2)	0.03	-	exc	0	Vacuole				300
P92133 UniProt NPD GO	CATB3_GIALA	Cathepsin B-like CP3 precursor (EC 3.4.22.-) (Cathepsin B-like protease B3)	0.03	-	exc	0	Vacuole				299
P43508 UniProt NPD GO	CPR4_CAEEL	Cathepsin B-like cysteine proteinase 4 precursor (EC 3.4.22.-) (Cysteine protease-related 4)	0.03	-	exc	0					335
P25796 UniProt NPD GO	CATE_CAVPO	Cathepsin E precursor (EC 3.4.23.34)	0.03	-	exc	0	Endosome (By similarity). The proenzyme is localized to the endoplasmic reticulum and Golgi apparatu ...	endosome [ISS]			391
Q10991 UniProt NPD GO	CATL_SHEEP	Cathepsin L (EC 3.4.22.15) [Contains: Cathepsin L heavy chain; Cathepsin L light chain]	0.03	-	cyt	0	Lysosome				217
P32656 UniProt NPD GO	CHAC_YEAST	Cation transport regulator-like protein	0.03	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			232
Q94051 UniProt NPD GO	CAV1_CAEEL	Caveolin-1	0.03	-	end	2	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				235
P83661 UniProt NPD GO	C125_CYPDO	Cd-125 peptide	0.03	-		0	Secreted protein	extracellular space [IDA]			8
P14956 UniProt NPD GO	CECB_DROME	Cecropin-B precursor	0.03	-	vac	1 *	Secreted protein	extracellular region [IDA]			63
P67791 UniProt NPD GO	CECB_DROSE	Cecropin-B precursor	0.03	-	vac	1 *	Secreted protein	extracellular region [ISS]			63
P67792 UniProt NPD GO	CECB_DROSI	Cecropin-B precursor	0.03	-	vac	1 *	Secreted protein	extracellular region [ISS]			63
P13863 UniProt NPD GO	CDC2_CHICK	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.03	-	cyt	0	Nucleus (By similarity)				303
P24033 UniProt NPD GO	CDC2B_XENLA	Cell division control protein 2-B (EC 2.7.11.22) (EC 2.7.11.23) (Cell division control protein 2 hom ...	0.03	-	cyt	0	Nucleus (By similarity)				302
Q75A37 UniProt NPD GO	CD123_ASHGO	Cell division cycle protein 123	0.03	-	cyt	0	Cytoplasm (By similarity)				355
O55076 UniProt NPD GO	CDK2_CRIGR	Cell division protein kinase 2 (EC 2.7.11.22)	0.03	-	cyt	0					298
P48963 UniProt NPD GO	CDK2_MESAU	Cell division protein kinase 2 (EC 2.7.11.22)	0.03	-	cyt	0					298
P23437 UniProt NPD GO	CDK2_XENLA	Cell division protein kinase 2 (EC 2.7.11.22) (CDC2 homolog Eg1 protein kinase)	0.03	-	cyt	0					297
P56553 UniProt NPD GO	CGR1_CANAL	Cell growth protein CGR1	0.03	-	cyt	0					340
Q06991 UniProt NPD GO	YL414_YEAST	Cell membrane protein YLR414C precursor	0.03	-	end	4 *	Cell membrane; multi-pass membrane protein (Potential)	bud [IDA] cytoplasm [IDA]			263
Q9UR09 UniProt NPD GO	PSU1_SCHPO	Cell wall synthesis protein psu1 precursor	0.03	-	end	0	Cell wall (Potential)	cell surface [TAS]			417
P62966 UniProt NPD GO	RABP1_RAT	Cellular retinoic acid-binding protein 1 (Cellular retinoic acid-binding protein I) (CRABP-I) (Retin ...	0.03	-	cyt	0	Cytoplasm				33
P63181 UniProt NPD GO	CBLN1_PIG	Cerebellin	0.03	-		0	Secreted protein				16
P63182 UniProt NPD GO	CBLN1_RAT	Cerebellin	0.03	-		0	Secreted protein				16
P51080 UniProt NPD GO	CHS7_MEDSA	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase) (Fragment)	0.03	-	cyt	0					265
P51079 UniProt NPD GO	CHS6_MEDSA	Chalcone synthase 6-4 (EC 2.3.1.74) (Naringenin-chalcone synthase 6-4) (Fragment)	0.03	-	nuc	0					285
Q9MB41 UniProt NPD GO	CHS2_IPOBA	Chalcone synthase LF2 (EC 2.3.1.74) (Naringenin-chalcone synthase LF2)	0.03	-	cyt	0					393
O65333 UniProt NPD GO	CFI_ELAUM	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.03	-	cyt	0					256
Q39727 UniProt NPD GO	CH60_EUGGR	Chaperonin CPN60, mitochondrial precursor (HSP 60)	0.03	-	mit	0	Mitochondrion				569
O35786 UniProt NPD GO	CML1_RAT	Chemokine receptor-like 1 (G-protein coupled receptor DEZ) (G-protein coupled chemoattractant-like r ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein				371
P30579 UniProt NPD GO	CHS1_AJEDE	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-I chitin synth ...	0.03	-	cyt	0	Cell membrane; multi-pass membrane protein				188
P30590 UniProt NPD GO	CHS1_PHAEX	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Fragment)	0.03	-	cyt	0	Cell membrane; multi-pass membrane protein				189
P30604 UniProt NPD GO	CHS2_XYLBA	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2) (Class-II chitin synt ...	0.03	-	cyt	0	Cell membrane; multi-pass membrane protein				189
P30586 UniProt NPD GO	CHS2_EXOJE	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2) (Fragment)	0.03	-	cyt	0	Cell membrane; multi-pass membrane protein				188
Q9D7Q1 UniProt NPD GO	CHIT1_MOUSE	Chitotriosidase-1 precursor (EC 3.2.1.14) (Chitinase-1)	0.03	-	cyt	0	Secreted protein (By similarity). Lysosome (By similarity). A small proportion is lysosomal (By simi ...				396
Q9WUB6 UniProt NPD GO	CLCKB_MOUSE	Chloride channel protein ClC-Kb (Chloride channel Kb) (ClC-K2)	0.03	-	end	8 *	Membrane; multi-pass membrane protein				687
P36494 UniProt NPD GO	CB4_SPIOL	Chlorophyll a-b binding protein CP24, chloroplast precursor	0.03	-	cyt	2	Plastid; chloroplast				261
O46913 UniProt NPD GO	RR11_GUITH	Chloroplast 30S ribosomal protein S11	0.03	-	mit	0	Plastid; chloroplast				130

You are viewing entries 79351 to 79400 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.