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
P69033 UniProt NPD GO	CR23_LITSP	Splendipherin	0.00	-	cyt	0	Secreted protein				25
O13306 UniProt NPD GO	ERG1_CANGA	Squalene monooxygenase (EC 1.14.99.7) (Squalene epoxidase) (SE)	0.00	-	end	3 *	Microsome; microsomal membrane; multi-pass membrane protein (By similarity)				489
P35175 UniProt NPD GO	CYT3_MOUSE	Stefin 3	0.00	-	cyt	0	Cytoplasm (By similarity)				97
P15490 UniProt NPD GO	VSPA_SOYBN	Stem 28 kDa glycoprotein precursor (Vegetative storage protein A)	0.00	-	cyt	1 *					254
P10743 UniProt NPD GO	VSPB_SOYBN	Stem 31 kDa glycoprotein precursor (Vegetative storage protein B)	0.00	-	mit	1 *					254
P83897 UniProt NPD GO	SIP_HUMAN	Steroidogenesis-inducing protein (Fragments)	0.00	-	cyt	0					39
Q759S7 UniProt NPD GO	ERG6_ASHGO	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.00	-	cyt	0					373
Q8T9R8 UniProt NPD GO	STMX_STOCA	Stomoxyn precursor	0.00	-	end	1 *	Secreted protein	extracellular region [TAS]		1ZRX	67
P31169 UniProt NPD GO	KIN2_ARATH	Stress-induced KIN2 protein (Cold-induced COR6.6 protein)	0.00	-	nuc	0					66
P26987 UniProt NPD GO	SAM22_SOYBN	Stress-induced protein SAM22 (Starvation-associated message 22) (Allergen Gly m 4)	0.00	-	cyt	0					158
P31082 UniProt NPD GO	HSP7S_CUCMA	Stromal 70 kDa heat shock-related protein, chloroplast (Fragment)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast stroma				34
O35982 UniProt NPD GO	SMR2B_MOUSE	Submaxillary gland androgen-regulated protein 2, isoform beta precursor (Salivary protein MSG2, isof ...	0.00	-	cyt	1 *	Secreted protein				41
P42990 UniProt NPD GO	TKN5_PSEGU	Substance P-like peptide 2 (PG-SPII)	0.00	-		0	Secreted protein				11
P16062 UniProt NPD GO	ICIA_HORVU	Subtilisin-chymotrypsin inhibitor CI-1A	0.00	-	nuc	0					83
P01054 UniProt NPD GO	ICIC_HORVU	Subtilisin-chymotrypsin inhibitor CI-1C	0.00	-	cyt	0	Secreted protein				77
Q95123 UniProt NPD GO	DHSD_BOVIN	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.00	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				158
O14521 UniProt NPD GO	DHSD_HUMAN	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.00	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial envelope [TAS] mitochondrial inner membrane [IDA] mitochondrion [TAS]	602690		159
Q9CXV1 UniProt NPD GO	DHSD_MOUSE	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.00	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				159
Q5RC29 UniProt NPD GO	DHSD_PONPY	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.00	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				159
P54323 UniProt NPD GO	DHSD_CHOCR	Succinate dehydrogenase membrane anchor subunit (Succinate dehydrogenase, subunit IV)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				84
Q03184 UniProt NPD GO	SUCB_TRIVA	Succinyl-CoA ligase [GDP-forming] beta-chain, hydrogenosomal precursor (EC 6.2.1.4) (Succinyl-CoA sy ...	0.00	-	cyt	0	Hydrogenosome				407
Q9LT15 UniProt NPD GO	STP10_ARATH	Sugar transport protein 10 (Hexose transporter 10)	0.00	-	end	12 *	Membrane; multi-pass membrane protein				514
Q9FMX3 UniProt NPD GO	STP11_ARATH	Sugar transport protein 11 (Hexose transporter 11)	0.00	-	end	12 *	Cell membrane; multi-pass membrane protein				514
Q39228 UniProt NPD GO	STP4_ARATH	Sugar transport protein 4 (Hexose transporter 4)	0.00	-	end	11 *	Membrane; multi-pass membrane protein				514
Q6CIG2 UniProt NPD GO	CCS1_KLULA	Superoxide dismutase 1 copper chaperone	0.00	-	cyt	0	Cytoplasm (By similarity)				245
P24704 UniProt NPD GO	SODC_ARATH	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				151
Q8X1S6 UniProt NPD GO	SODC_ASPFL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				152
Q9Y8D9 UniProt NPD GO	SODC_ASPFU	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				153
Q877B5 UniProt NPD GO	SODC_ASPOR	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				153
Q52RN5 UniProt NPD GO	SODC_BOSMU	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				151
P00442 UniProt NPD GO	SODC_BOVIN	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm			3SOD	151
P09678 UniProt NPD GO	SODC_BRAOC	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				151
O73872 UniProt NPD GO	SODC_BRARE	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				154
O59924 UniProt NPD GO	SODC_CANAL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				153
Q5FB29 UniProt NPD GO	SODC_CAPHI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				151
O65768 UniProt NPD GO	SODC_CARPA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	vac	0	Cytoplasm				152
P28755 UniProt NPD GO	SODC_CERCA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				152
Q07182 UniProt NPD GO	SODC_CHYAM	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				152
Q96VL0 UniProt NPD GO	SODC_CLAPU	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				153
Q9U4X4 UniProt NPD GO	SODC_DROER	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				152
P61853 UniProt NPD GO	SODC_DROMA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				152
P61851 UniProt NPD GO	SODC_DROME	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				152
Q9U4X5 UniProt NPD GO	SODC_DROOR	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				152
Q95086 UniProt NPD GO	SODC_DROPS	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				151
P61854 UniProt NPD GO	SODC_DROSE	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				152
P61852 UniProt NPD GO	SODC_DROSI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				152
Q9U4X2 UniProt NPD GO	SODC_DROTE	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				152
P10791 UniProt NPD GO	SODC_DROVI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				152
Q9U4X3 UniProt NPD GO	SODC_DROYA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				152
Q9HEY7 UniProt NPD GO	SODC_EMENI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				153

You are viewing entries 98101 to 98150 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.