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
Q9ET64 UniProt NPD GO	NSMA_RAT	Sphingomyelin phosphodiesterase 2 (EC 3.1.4.12) (Neutral sphingomyelinase) (nSMase) (N-SMase) (Lyso- ...	0.01	-	end	2	Membrane; multi-pass membrane protein				422
Q7M485 UniProt NPD GO	SMAD_LOXRE	Sphingomyelinase D (EC 3.1.4.41) (Mammalian toxin) (Fragment)	0.01	-	cyt	0	Secreted protein				35
P10917 UniProt NPD GO	SPORA_IPOBA	Sporamin A precursor	0.01	-	end	0	Vacuole				219
P10965 UniProt NPD GO	SPORB_IPOBA	Sporamin B precursor	0.01	-	end	0	Vacuole				216
P12671 UniProt NPD GO	HAPS_PHYPO	Sporulation-specific hydrophobic abundant protein precursor (HAP-S)	0.01	-	end	2 *	Membrane				163
P32476 UniProt NPD GO	ERG1_YEAST	Squalene monooxygenase (EC 1.14.99.7) (Squalene epoxidase) (SE)	0.01	-	end	2 *	Microsome; microsomal membrane; multi-pass membrane protein	lipid particle [IDA]			496
O65403 UniProt NPD GO	ERG13_ARATH	Squalene monooxygenase 2 (EC 1.14.99.7) (Squalene epoxidase 2) (SE 2)	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				516
P78589 UniProt NPD GO	FDFT_CANAL	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				448
P14533 UniProt NPD GO	CABO_LOLPE	Squidulin (Optic lobe calcium-binding protein) (SCABP)	0.01	-	cyt	0					149
Q9NSY2 UniProt NPD GO	STAR5_HUMAN	StAR-related lipid transfer protein 5 (StARD5) (START domain-containing protein 5)	0.01	-	cyt	0			607050		213
Q5R8P9 UniProt NPD GO	STAR5_PONPY	StAR-related lipid transfer protein 5 (StARD5) (START domain-containing protein 5)	0.01	-	cyt	0					213
P61807 UniProt NPD GO	SNN_MOUSE	Stannin	0.01	-	mit	1 *					88
P61808 UniProt NPD GO	SNN_RAT	Stannin	0.01	-	mit	1 *					88
O75324 UniProt NPD GO	SNN_HUMAN	Stannin (AG8_1)	0.01	-	mit	1 *			603032	1ZZA	88
P43649 UniProt NPD GO	STC_ONCNE	Stanniocalcin (STC) (Corpuscles of Stannius protein) (CS) (Hypocalcin) (Teleocalcin) (Fragment)	0.01	-	nuc	0	Secreted protein				40
Q43654 UniProt NPD GO	SSY1_WHEAT	Starch synthase 1, chloroplast precursor (EC 2.4.1.21) (SS I) (Starch synthase I-2) (SS I-2)	0.01	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Soluble (By similarity)				647
P35174 UniProt NPD GO	CYT2_MOUSE	Stefin 2	0.01	-	cyt	0	Cytoplasm (By similarity)				103
P10742 UniProt NPD GO	S25K_SOYBN	Stem 31 kDa glycoprotein precursor (Vegetative storage protein VSP25) (Fragment)	0.01	-	exc	0					291
O14321 UniProt NPD GO	ERG6_SCHPO	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.01	-	cyt	0					378
P53199 UniProt NPD GO	ERG26_YEAST	Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating (EC 1.1.1.170)	0.01	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [IDA] endoplasmic reticulum membrane [IDA]			349
Q9SW93 UniProt NPD GO	SCA_LILLO	Stigma/stylar cysteine-rich adhesin precursor (Lipid transfer protein)	0.01	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				113
P18612 UniProt NPD GO	KIN1_ARATH	Stress-induced KIN1 protein	0.01	-	nuc	0					66
P19991 UniProt NPD GO	SUGA_ACHDO	Suboesophageal ganglion pentapeptide	0.01	-		0					5
P42989 UniProt NPD GO	TKN4_PSEGU	Substance P-like peptide 1 (PG-SPI)	0.01	-		0	Secreted protein				11
P81726 UniProt NPD GO	ICI2_CANLI	Subtilisin inhibitor CLSI-II [Contains: Subtilisin inhibitor CLSI-III]	0.01	-	cyt	0	Secreted protein				190
Q9P7X0 UniProt NPD GO	DHSD_SCHPO	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.01	+	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				186
P37298 UniProt NPD GO	DHSD_YEAST	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.01	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	respiratory chain complex II (sensu Eukaryota) [TAS]		1PB4	181
P92507 UniProt NPD GO	DHSD_ASCSU	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.01	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				156
Q6PCT8 UniProt NPD GO	DHSD_RAT	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.01	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				159
P35721 UniProt NPD GO	C560_MARPO	Succinate dehydrogenase cytochrome b560 subunit (Succinate dehydrogenase, subunit III)	0.01	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				137
P80481 UniProt NPD GO	C560_RECAM	Succinate dehydrogenase cytochrome b560 subunit (Succinate dehydrogenase, subunit III)	0.01	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				144
Q9BXA5 UniProt NPD GO	SUCR1_HUMAN	Succinate receptor 1 (G-protein coupled receptor 91) (P2Y purinoceptor 1-like)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	606381		330
P38067 UniProt NPD GO	UGA2_YEAST	Succinate-semialdehyde dehydrogenase [NADP+] (EC 1.2.1.16) (SSDH)	0.01	-	cyt	0		cytoplasm [IDA]			497
P53587 UniProt NPD GO	SUCB_NEOFR	Succinyl-CoA ligase [GDP-forming] beta-chain, hydrogenosomal precursor (EC 6.2.1.4) (Succinyl-CoA sy ...	0.01	-	mit	0	Hydrogenosome				437
Q6K9N6 UniProt NPD GO	SUCB_ORYSA	Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA syn ...	0.01	-	mit	0	Mitochondrion (By similarity)				422
Q9SX48 UniProt NPD GO	STP9_ARATH	Sugar transport protein 9 (Hexose transporter 9)	0.01	-	end	12 *	Membrane; multi-pass membrane protein				517
P18632 UniProt NPD GO	SBP_CRYJA	Sugi basic protein precursor (SBP) (Major allergen Cry j 1) (Cry j I)	0.01	-	cyt	0					374
P47733 UniProt NPD GO	LOSK_LOCMI	Sulfakinin (Lom-SK)	0.01	-		0					12
P84547 UniProt NPD GO	SAT_POPEU	Sulfate adenylyltransferase (EC 2.7.7.4) (Sulfate adenylate transferase) (SAT) (ATP-sulfurylase) (Fr ...	0.01	-		0					11
P41930 UniProt NPD GO	SSU1_YEAST	Sulfite sensitivity protein SSU1	0.01	-	end	9 *		plasma membrane [IDA]			458
Q6FU61 UniProt NPD GO	CCS1_CANGA	Superoxide dismutase 1 copper chaperone	0.01	-	cyt	0	Cytoplasm (By similarity)				239
P40202 UniProt NPD GO	CCS1_YEAST	Superoxide dismutase 1 copper chaperone	0.01	-	cyt	0	Cytoplasm. A small percentage (around 1-5 percent) localizes to the mitochondrial intermembrane spac ...	cytosol [IDA] mitochondrial inner membrane [IDA]		1QUP	249
Q9SQL5 UniProt NPD GO	SODC_ANACO	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm (By similarity)				152
Q70Q35 UniProt NPD GO	SODC_BOTCI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm (By similarity)				153
P41962 UniProt NPD GO	SODC_BRUPA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				158
P34697 UniProt NPD GO	SODC_CAEEL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				158
Q8WNN6 UniProt NPD GO	SODC_CANFA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0					153
P80174 UniProt NPD GO	SODC_CARCR	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	pox	0	Cytoplasm				166
P33431 UniProt NPD GO	SODC_CAVPO	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				152
O46412 UniProt NPD GO	SODC_CEREL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				151

You are viewing entries 91551 to 91600 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.