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
Q7Z1Y7 UniProt NPD GO	SMAD_LOXAR	Sphingomyelinase D precursor (EC 3.1.4.41) (SMase D) (Dermonecrotic enzyme)	0.02	-	cyt	0	Secreted protein				320
Q05567 UniProt NPD GO	SGPL_YEAST	Sphingosine-1-phosphate lyase (EC 4.1.2.27) (SP-lyase) (ySPL) (Sphingosine-1-phosphate aldolase) (Be ...	0.02	-	nuc	0		endoplasmic reticulum [IDA]			589
P14715 UniProt NPD GO	SPOR1_IPOBA	Sporamin A precursor (Clone PIM0335)	0.02	-	end	0	Vacuole				219
P14716 UniProt NPD GO	SPOR2_IPOBA	Sporamin B precursor (Clone PIM0535)	0.02	-	end	0	Vacuole				216
P52750 UniProt NPD GO	DEWA_EMENI	Spore-wall fungal hydrophobin dewA precursor	0.02	-	mit	0	Secreted protein. Spore wall				135
Q75F69 UniProt NPD GO	ERG1_ASHGO	Squalene monooxygenase (EC 1.14.99.7) (Squalene epoxidase) (SE)	0.02	-	vac	2 *	Microsome; microsomal membrane; multi-pass membrane protein (By similarity)				497
Q9EPQ7 UniProt NPD GO	STAR5_MOUSE	StAR-related lipid transfer protein 5 (StARD5) (START domain-containing protein 5)	0.02	-	cyt	0					213
P00302 UniProt NPD GO	STEL_RHUVE	Stellacyanin	0.02	-	cyt	0					107
Q6FRZ7 UniProt NPD GO	ERG6_CANGA	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.02	-	cyt	0					372
Q6C2D9 UniProt NPD GO	ERG6_YARLI	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.02	-	cyt	0					381
Q9R1J0 UniProt NPD GO	NSDHL_MOUSE	Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating (EC 1.1.1.170)	0.02	-	cyt	1					362
P15589 UniProt NPD GO	STS_RAT	Steryl-sulfatase precursor (EC 3.1.6.2) (Steroid sulfatase) (Steryl-sulfate sulfohydrolase) (Arylsul ...	0.02	-	end	2	Microsome; microsomal membrane; multi-pass membrane protein. The sequence shows several membrane-spa ...				577
P20077 UniProt NPD GO	THS2_ARAHY	Stilbene synthase 2 (EC 2.3.1.95) (Resveratrol synthase 2) (RS2) (Trihydroxystilbene synthase 2) (Fr ...	0.02	-	nuc	0	Cytoplasm				313
Q8CI66 UniProt NPD GO	STML1_MOUSE	Stomatin-like protein 1 (SLP-1)	0.02	-	nuc	1	Membrane; single-pass type III membrane protein (Potential)				399
Q6PE84 UniProt NPD GO	STML3_MOUSE	Stomatin-like protein 3 (Stomatin-related olfactory protein)	0.02	-	end	1 *	Cell membrane; single-pass type III membrane protein. Detected in lipid rafts, in apical dendrites a ...	lipid raft [IDA]			287
P48723 UniProt NPD GO	STCH_HUMAN	Stress 70 protein chaperone microsome-associated 60 kDa protein precursor (Microsomal stress 70 prot ...	0.02	-	mit	1 *	Microsome	microsome [TAS]	601100		471
P68175 UniProt NPD GO	STSY_RAUSE	Strictosidine synthase precursor (EC 4.3.3.2)	0.02	-	vac	1 *	Vacuole			2FPC	344
P68174 UniProt NPD GO	STSY_RAUMA	Strictosidine synthase precursor (EC 4.3.3.2) (Fragment)	0.02	-	vac	1 *	Vacuole				342
P81469 UniProt NPD GO	STYA_STYCL	Styelin-A (Fragment)	0.02	-		0	Secreted protein				20
P81470 UniProt NPD GO	STYB_STYCL	Styelin-B (Fragment)	0.02	-		0	Secreted protein				20
O35961 UniProt NPD GO	SMR2E_MOUSE	Submaxillary gland androgen-regulated protein 2, isoform epsilon precursor (Salivary protein MSG2, i ...	0.02	-	cyt	0	Secreted protein				40
P67932 UniProt NPD GO	TKNA_CAVPO	Substance P	0.02	-		0	Secreted protein				11
P67933 UniProt NPD GO	TKNA_HORSE	Substance P	0.02	-		0	Secreted protein				11
P41333 UniProt NPD GO	TKNA_SCYCA	Substance P	0.02	-		0	Secreted protein				11
P08820 UniProt NPD GO	ICIS_VICFA	Subtilisin inhibitor (Fragment)	0.02	-	cyt	0	Secreted protein				62
P82977 UniProt NPD GO	ICIW_WHEAT	Subtilisin-chymotrypsin inhibitor WSCI	0.02	-	cyt	0					72
P01053 UniProt NPD GO	ICI2_HORVU	Subtilisin-chymotrypsin inhibitor-2A (CI-2A)	0.02	-	cyt	0				3CI2	83
P70097 UniProt NPD GO	C560_CRIGR	Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (Integral membrane protein ...	0.02	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				169
Q9CZB0 UniProt NPD GO	C560_MOUSE	Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (Integral membrane protein ...	0.02	-	end	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrion [IDA]			169
P35720 UniProt NPD GO	C560_BOVIN	Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (Integral membrane protein ...	0.02	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				169
Q99643 UniProt NPD GO	C560_HUMAN	Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (Integral membrane protein ...	0.02	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to membrane [TAS] mitochondrion [TAS] respiratory chain complex II [TAS]	605373		169
P80482 UniProt NPD GO	DHSD_RECAM	Succinate dehydrogenase membrane anchor subunit (Succinate dehydrogenase, subunit IV)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				120
P99507 UniProt NPD GO	SUCB1_CANFA	Succinyl-CoA ligase [ADP-forming] beta-chain, mitochondrial (EC 6.2.1.5) (Succinyl-CoA synthetase, b ...	0.02	-		0	Mitochondrion (By similarity)				20
Q94AZ2 UniProt NPD GO	STP13_ARATH	Sugar transport protein 13 (Hexose transporter 13) (Multicopy suppressor of snf4 deficiency protein ...	0.02	-	end	12 *	Cell membrane; multi-pass membrane protein (Probable)				526
Q9LNV3 UniProt NPD GO	STP2_ARATH	Sugar transport protein 2 (Hexose transporter 2)	0.02	-	end	11 *	Membrane; multi-pass membrane protein				522
Q60FC6 UniProt NPD GO	SAT_PORYE	Sulfate adenylyltransferase (EC 2.7.7.4) (Sulfate adenylate transferase) (SAT) (ATP-sulfurylase)	0.02	-	cyt	0					419
P82205 UniProt NPD GO	SODC_BOMMO	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm (By similarity)				153
Q6FWL5 UniProt NPD GO	SODC_CANGA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	end	0	Cytoplasm (By similarity)				153
O22373 UniProt NPD GO	SODC_CAPAN	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	exc	0	Cytoplasm				152
P00441 UniProt NPD GO	SODC_HUMAN	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm		105400	4SOD	153
Q6CPE2 UniProt NPD GO	SODC_KLULA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm (By similarity)				155
Q8HXQ1 UniProt NPD GO	SODC_MACFA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm (By similarity)				153
Q8HXQ2 UniProt NPD GO	SODC_MACFU	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm (By similarity)				153
Q8HXQ0 UniProt NPD GO	SODC_MACMU	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm (By similarity)				153
P60052 UniProt NPD GO	SODC_PANTR	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm (By similarity)				153
P24669 UniProt NPD GO	SODC_PINSY	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm				154
Q8HXQ4 UniProt NPD GO	SODC_PONPY	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm (By similarity)				154
Q6C662 UniProt NPD GO	SODC_YARLI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm (By similarity)				153
O49044 UniProt NPD GO	SODC2_MESCR	Superoxide dismutase [Cu-Zn] 2 (EC 1.15.1.1)	0.02	-	cyt	0	Cytoplasm				156
P28759 UniProt NPD GO	SODF_SOYBN	Superoxide dismutase [Fe], chloroplast precursor (EC 1.15.1.1)	0.02	-	cyt	0	Plastid; chloroplast				248

You are viewing entries 85801 to 85850 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.