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
P41856 UniProt NPD GO	FAR1_CALVO	CalliFMRFamide-1	0.07	-		0	Secreted protein				9
P23286 UniProt NPD GO	CALM_CANAL	Calmodulin (CaM)	0.07	-	cyt	0					149
Q39752 UniProt NPD GO	CALM_FAGSY	Calmodulin (CaM)	0.07	-	cyt	0					147
P62203 UniProt NPD GO	CALM_PLAF7	Calmodulin (CaM)	0.07	-	cyt	0					148
P24044 UniProt NPD GO	CALM_PLAFA	Calmodulin (CaM)	0.07	-	cyt	0					148
P02597 UniProt NPD GO	CALMS_CHICK	Calmodulin, striated muscle	0.07	-	cyt	0					148
P27482 UniProt NPD GO	CALL3_HUMAN	Calmodulin-like protein 3 (Calmodulin-related protein NB-1) (CaM-like protein) (CLP)	0.07	-	cyt	0			114184	1GGZ	148
P07221 UniProt NPD GO	CASQ1_RABIT	Calsequestrin-1 precursor (Calsequestrin, skeletal muscle isoform) (Aspartactin) (Laminin-binding pr ...	0.07	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen. This isoform of calsequestrin occurs in the sa ...			1A8Y	395
P28872 UniProt NPD GO	CARP1_CANAL	Candidapepsin-1 precursor (EC 3.4.23.24) (Aspartate protease 1) (ACP 1) (Secreted aspartic protease ...	0.07	-	exc	0	Secreted protein				391
P56971 UniProt NPD GO	CNR1_POEGU	Cannabinoid receptor 1 (CB1) (CB-R)	0.07	-	end	7	Membrane; multi-pass membrane protein				473
Q9PUI7 UniProt NPD GO	CNR1_TARGR	Cannabinoid receptor 1 (CB1) (CB-R)	0.07	-	end	7	Membrane; multi-pass membrane protein				473
P00916 UniProt NPD GO	CAH1_MACMU	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I)	0.07	-	nuc	0	Cytoplasm				260
P35217 UniProt NPD GO	CAH1_MACNE	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I)	0.07	-	nuc	0	Cytoplasm				260
Q8UWA5 UniProt NPD GO	CAH2_TRIHK	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonic anhydrase II) (Carbonate dehydratase II) (CA-II)	0.07	-	nuc	0	Cytoplasm (By similarity)				259
P40880 UniProt NPD GO	CAHC_HORVU	Carbonic anhydrase, chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast stroma (By similarity)				324
P37892 UniProt NPD GO	CBPE_LOPAM	Carboxypeptidase E precursor (EC 3.4.17.10) (CPE) (Carboxypeptidase H) (CPH) (Enkephalin convertase) ...	0.07	-	exc	0					454
P30574 UniProt NPD GO	CBPY_CANAL	Carboxypeptidase Y precursor (EC 3.4.16.5) (Carboxypeptidase YSCY)	0.07	-	exc	0	Vacuole. Lysosome-like vacuoles				542
P52710 UniProt NPD GO	CBPY_PICPA	Carboxypeptidase Y precursor (EC 3.4.16.5) (Carboxypeptidase YSCY)	0.07	-	vac	0	Vacuole. Lysosome-like vacuoles				523
Q8S4R4 UniProt NPD GO	CRTSO_LYCES	Carotenoid isomerase, chloroplast precursor (EC 5.-.-.-) (CrtISO) (Protein tangerine)	0.07	-	cyt	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Probable)				615
P38087 UniProt NPD GO	YMC2_YEAST	Carrier protein YMC2, mitochondrial precursor	0.07	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				329
P05195 UniProt NPD GO	3DHQ_NEUCR	Catabolic 3-dehydroquinase (EC 4.2.1.10) (3-dehydroquinate dehydratase)	0.07	-	mit	0					173
P43233 UniProt NPD GO	CATB_CHICK	Cathepsin B precursor (EC 3.4.22.1) (Cathepsin B1) [Contains: Cathepsin B light chain; Cathepsin B h ...	0.07	-	exc	0	Lysosome				340
P07339 UniProt NPD GO	CATD_HUMAN	Cathepsin D precursor (EC 3.4.23.5) [Contains: Cathepsin D light chain; Cathepsin D heavy chain]	0.07	-	mit	0	Lysosome	extracellular region [NAS] lysosome [NAS]	116840	1LYW	412
P14091 UniProt NPD GO	CATE_HUMAN	Cathepsin E precursor (EC 3.4.23.34)	0.07	-	exc	0	Endosome. The proenzyme is localized to the endoplasmic reticulum and Golgi apparatus, while the mat ...	endosome [IDA]	116890	1LCG	401
P70269 UniProt NPD GO	CATE_MOUSE	Cathepsin E precursor (EC 3.4.23.34)	0.07	-	exc	0	Endosome. The proenzyme is localized to the endoplasmic reticulum and Golgi apparatus, while the mat ...	endosome [IDA]			397
P43236 UniProt NPD GO	CATK_RABIT	Cathepsin K precursor (EC 3.4.22.38) (OC-2 protein)	0.07	-	cyt	0	Lysosome (By similarity)			2F7D	329
P80528 UniProt NPD GO	CATL4_FASHE	Cathepsin L-like cysteine proteinase (EC 3.4.22.-) (Newly excysted juvenile protein 4) (Fragment)	0.07	-		0	Lysosome (Potential)				20
P22196 UniProt NPD GO	PER2_ARAHY	Cationic peroxidase 2 precursor (EC 1.11.1.7) (PNPC2)	0.07	-	exc	1 *	Secreted protein (By similarity)				330
P06871 UniProt NPD GO	TRY1_CANFA	Cationic trypsin precursor (EC 3.4.21.4)	0.07	-	exc	0	Secreted protein; extracellular space				246
P84222 UniProt NPD GO	CECC_DROER	Cecropin-C precursor	0.07	-	vac	1 *	Secreted protein				63
P84019 UniProt NPD GO	CECC_DROMA	Cecropin-C precursor	0.07	-	vac	1 *	Secreted protein	extracellular region [ISS]			63
O16829 UniProt NPD GO	CECC_DROME	Cecropin-C precursor	0.07	-	vac	1 *	Secreted protein	extracellular region [IDA]			63
P84223 UniProt NPD GO	CECC_DROOR	Cecropin-C precursor	0.07	-	vac	1 *	Secreted protein				63
P84020 UniProt NPD GO	CECC_DROSE	Cecropin-C precursor	0.07	-	vac	1 *	Secreted protein	extracellular region [ISS]			63
P84021 UniProt NPD GO	CECC_DROSI	Cecropin-C precursor	0.07	-	vac	1 *	Secreted protein	extracellular region [ISS]			63
P84225 UniProt NPD GO	CECC_DROTE	Cecropin-C precursor	0.07	-	vac	1 *	Secreted protein				63
P84224 UniProt NPD GO	CECC_DROTK	Cecropin-C precursor	0.07	-	vac	1 *	Secreted protein				63
P84226 UniProt NPD GO	CECC_DROYA	Cecropin-C precursor	0.07	-	vac	1 *	Secreted protein				63
P48734 UniProt NPD GO	CDC2_BOVIN	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.07	-	cyt	0	Nucleus (By similarity)				297
Q38775 UniProt NPD GO	CDC2D_ANTMA	Cell division control protein 2 homolog D (EC 2.7.11.22) (EC 2.7.11.23)	0.07	-	cyt	0					312
Q9HF56 UniProt NPD GO	CDC42_ASHGO	Cell division control protein 42	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				191
Q90694 UniProt NPD GO	CDC42_CHICK	Cell division control protein 42 homolog (G25K GTP-binding protein)	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	adherens junction [ISS] cytoplasm [ISS] filopodium [ISS] plasma membrane [ISS]			191
P11802 UniProt NPD GO	CDK4_HUMAN	Cell division protein kinase 4 (EC 2.7.11.22) (Cyclin-dependent kinase 4) (PSK-J3)	0.07	-	cyt	0			123829	1LD2	303
P38907 UniProt NPD GO	CHL4_YEAST	Central kinetochore subunit CHL4 (Chromosome loss protein 4) (Chromosome transmission fidelity prote ...	0.07	-	cyt	0	Nucleus. Associated with kinetochores	outer kinetochore of condensed nuclear chro... [IDA]			458
P38265 UniProt NPD GO	IML3_YEAST	Central kinetochore subunit IML3 (Increased minichromosome loss protein 3) (Minichromosome maintenan ...	0.07	-	cyt	0	Nucleus. Associated with kinetochores	outer kinetochore of condensed nuclear chro... [IDA]			245
Q9NSP4 UniProt NPD GO	CENPM_HUMAN	Centromere protein M (CENP-M) (Proliferation-associated nuclear element protein 1)	0.07	-	cyt	0	Nucleus (By similarity). Nuclear in non-confluent cells and cytoplasmic in confluent or dividing cel ...				180
P23419 UniProt NPD GO	CHS2_LYCES	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.07	-	nuc	0					389
Q43188 UniProt NPD GO	CHS2_SOLTU	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.07	-	nuc	0					389
P22928 UniProt NPD GO	CHSJ_PETHY	Chalcone synthase J (EC 2.3.1.74) (Naringenin-chalcone synthase J)	0.07	-	nuc	0					389
Q8L7B5 UniProt NPD GO	CH60B_ARATH	Chaperonin CPN60-like 1, mitochondrial precursor (HSP60-like 1)	0.07	-	mit	0	Mitochondrion	mitochondrion [IDA]			585

You are viewing entries 69651 to 69700 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.