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
P11686 UniProt NPD GO	PSPC_HUMAN	Pulmonary surfactant-associated protein C precursor (SP-C) (SP5) (Pulmonary surfactant-associated pr ...	0.02	-	gol	1 *	Secreted protein; extracellular space		265120		197
P80684 UniProt NPD GO	CUC1B_TENMO	Pupal cuticle protein C1B (TM-C1B) (TM-PCP C1B)	0.02	-	mit	0					161
Q05788 UniProt NPD GO	PNPH_YEAST	Purine nucleoside phosphorylase (EC 2.4.2.1) (Inosine phosphorylase) (PNP)	0.02	-	cyt	0					311
Q12119 UniProt NPD GO	FCY22_YEAST	Purine-cytosine permease FCY22 (PCP FCY22) (Cytosine/purine transport protein FCY22) (Fluorocytosine ...	0.02	-	end	12	Membrane; multi-pass membrane protein (Probable)				530
P01543 UniProt NPD GO	THNB_WHEAT	Purothionin A-1 precursor (Purothionin A-I) (Beta-purothionin) [Contains: Purothionin A-1; Acidic pr ...	0.02	-	nuc	0	Secreted protein			1BHP	136
Q95Y72 UniProt NPD GO	SEM1_CAEEL	Putative 26 proteasome complex subunit sem1	0.02	-	cyt	0		proteasome complex (sensu Eukaryota) [ISS]			82
O49227 UniProt NPD GO	DHBK_SOYBN	Putative 3,4-dihydroxy-2-butanone kinase (EC 2.7.1.-) (Fragment)	0.02	-	cyt	0					82
O13931 UniProt NPD GO	ATP18_SCHPO	Putative ATP synthase J chain, mitochondrial (EC 3.6.3.14)	0.02	-	mit	1 *					60
Q99622 UniProt NPD GO	C10_HUMAN	Putative C10 protein	0.02	-	cyt	0					126
Q84VZ5 UniProt NPD GO	UGPI2_ARATH	Putative GPI-anchored protein At5g19240 precursor	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				199
Q9D0P8 UniProt NPD GO	RAYL_MOUSE	Putative GTP-binding protein RAY-like (Rab-like protein 4)	0.02	-	cyt	0					186
Q9XXD4 UniProt NPD GO	NOLA2_CAEEL	Putative H/ACA ribonucleoprotein complex subunit 2-like protein	0.02	+	nuc	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			163
Q9DCQ2 UniProt NPD GO	ASPD_MOUSE	Putative L-aspartate dehydrogenase (EC 1.4.1.21)	0.02	-	cyt	0					287
Q5I0J9 UniProt NPD GO	ASPD_RAT	Putative L-aspartate dehydrogenase (EC 1.4.1.21)	0.02	-	mit	0					297
P29188 UniProt NPD GO	NEUAX_RAT	Putative N-acylneuraminate cytidylyltransferase (EC 2.7.7.43) (CMP-N-acetylneuraminic acid synthetas ...	0.02	-		0	Nucleus				20
P84721 UniProt NPD GO	PS5_PINST	Putative NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase PS5 (EC 1.2.1.-) (Fragments)	0.02	-	cyt	0					40
O64749 UniProt NPD GO	ARAE2_ARATH	Putative UDP-arabinose 4-epimerase 2 (EC 5.1.3.5) (UDP-D-xylose 4-epimerase 2)	0.02	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Potential) ...				417
P08105 UniProt NPD GO	YZ_SHEEP	Putative Z protein	0.02	-	mit	2 *					79
Q6YZX6 UniProt NPD GO	ACOC_ORYSA	Putative aconitate hydratase (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.02	-	cyt	0					898
Q8RYC2 UniProt NPD GO	ACT5_ARATH	Putative actin-5	0.02	-	cyt	0	Cytoplasm				378
Q9US40 UniProt NPD GO	YFZ1_SCHPO	Putative amino-acid permease C1039.01	0.02	-	end	10	Membrane; multi-pass membrane protein (Potential)				567
O74543 UniProt NPD GO	YCV4_SCHPO	Putative amino-acid permease C777.04	0.02	-	end	11	Membrane; multi-pass membrane protein (Potential)				521
O59813 UniProt NPD GO	YCT3_SCHPO	Putative amino-acid permease C794.03	0.02	-	end	12	Membrane; multi-pass membrane protein (Potential)				554
Q9UT18 UniProt NPD GO	YFYA_SCHPO	Putative amino-acid permease C9.10	0.02	-	end	12	Membrane; multi-pass membrane protein (Potential)				591
Q9C6T0 UniProt NPD GO	NIP31_ARATH	Putative aquaporin NIP3.1 (NOD26-like intrinsic protein 3.1)	0.02	-	end	5 *	Membrane; multi-pass membrane protein (Probable)				269
Q9STX9 UniProt NPD GO	TIP51_ARATH	Putative aquaporin TIP5.1 (Tonoplast intrinsic protein 5.1)	0.02	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				256
Q9LFP6 UniProt NPD GO	PIN5_ARATH	Putative auxin efflux carrier component 5 (AtPIN5)	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				367
Q41160 UniProt NPD GO	LCB3_ROBPS	Putative bark agglutinin LECRPA3 precursor (Fragment)	0.02	-	mit	1 *					272
Q9SHY6 UniProt NPD GO	EXPB2_ARATH	Putative beta-expansin 2 precursor (AtEXPB2) (At-EXPB2) (Ath-ExpBeta-1.4)	0.02	-	exc	1 *	Cell wall; peripheral membrane protein				273
P91375 UniProt NPD GO	YN1I_CAEEL	Putative bolA-like protein K11H12.1	0.02	-	nuc	0					108
Q9LPM8 UniProt NPD GO	BCAT7_ARATH	Putative branched-chain-amino-acid aminotransferase 7 (Atbcat-7)	0.02	-	cyt	0					367
Q9M3H5 UniProt NPD GO	AHM1_ARATH	Putative cadmium/zinc-transporting ATPase HMA1, chloroplast precursor (EC 3.6.3.3) (EC 3.6.3.5)	0.02	-	end	5	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (Potential)				819
Q9SV68 UniProt NPD GO	QORH_ARATH	Putative chloroplastic quinone-oxidoreductase homolog (EC 1.-.-.-)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast inner membrane (By similarity)	thylakoid membrane (sensu Viridiplantae) [IDA]			329
Q9U6Z9 UniProt NPD GO	CX51_CONGL	Putative conotoxin Gm5.1 precursor	0.02	-	exc	0	Secreted protein				63
P55216 UniProt NPD GO	CGL_CAEEL	Putative cystathionine gamma-lyase (EC 4.4.1.1) (Gamma-cystathionase)	0.02	-	cyt	0	Cytoplasm (By similarity)				392
P84733 UniProt NPD GO	PS17_PINST	Putative cytochrome c oxidase subunit II PS17 (Fragments)	0.02	-		0					16
Q6CAB5 UniProt NPD GO	CCPR2_YARLI	Putative cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				285
Q19264 UniProt NPD GO	DEOC_CAEEL	Putative deoxyribose-phosphate aldolase (EC 4.1.2.4) (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) ...	0.02	-	cyt	0					303
Q91YP3 UniProt NPD GO	DEOC_MOUSE	Putative deoxyribose-phosphate aldolase (EC 4.1.2.4) (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) ...	0.02	-	cyt	0					318
O42894 UniProt NPD GO	RRP46_SCHPO	Putative exosome complex exonuclease RRP46 (EC 3.1.13.-) (Ribosomal RNA-processing protein 46)	0.02	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				226
O82616 UniProt NPD GO	SCRK5_ARATH	Putative fructokinase-5 (EC 2.7.1.4)	0.02	-	cyt	0					324
P84675 UniProt NPD GO	PFM_CHAGB	Putative fungistatic metabolite (Fragments)	0.02	-	cyt	0					53
P58952 UniProt NPD GO	GR22C_DROME	Putative gustatory receptor 22c	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			383
P35899 UniProt NPD GO	GU58_RAT	Putative gustatory receptor clone PTE58 (Fragment)	0.02	-	cyt	4 *	Membrane; multi-pass membrane protein				232
Q9T0H7 UniProt NPD GO	H2A8_ARATH	Putative histone H2A.8 (H2A-4) (HTA4)	0.02	-	nuc	0	Nucleus (By similarity)				118
O42885 UniProt NPD GO	YBN1_SCHPO	Putative inorganic phosphate transporter C8E4.01c	0.02	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				572
P84730 UniProt NPD GO	PS14_PINST	Putative leucine-rich repeat protein PS14 (LRR) (Fragments)	0.02	-	cyt	0					32
P82730 UniProt NPD GO	LCR15_ARATH	Putative low-molecular-weight cysteine-rich protein LCR15 precursor	0.02	-	vac	1 *					84
P82734 UniProt NPD GO	LCR20_ARATH	Putative low-molecular-weight cysteine-rich protein LCR20 precursor	0.02	-	exc	0					75
P82737 UniProt NPD GO	LCR23_ARATH	Putative low-molecular-weight cysteine-rich protein LCR23 precursor	0.02	-	nuc	0					77

You are viewing entries 85401 to 85450 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.