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
P82739 UniProt NPD GO	LCR25_ARATH	Putative low-molecular-weight cysteine-rich protein LCR25 precursor	0.02	-	mit	1 *					77
Q9M0F1 UniProt NPD GO	LCR27_ARATH	Putative low-molecular-weight cysteine-rich protein LCR27	0.02	-	nuc	0					61
P82743 UniProt NPD GO	LCR28_ARATH	Putative low-molecular-weight cysteine-rich protein LCR28 precursor	0.02	-	cyt	0					59
P82746 UniProt NPD GO	LCR31_ARATH	Putative low-molecular-weight cysteine-rich protein LCR31 precursor	0.02	-	mit	1 *					81
P82762 UniProt NPD GO	LCR47_ARATH	Putative low-molecular-weight cysteine-rich protein LCR47 precursor	0.02	-	mit	1 *					77
P82794 UniProt NPD GO	LCR85_ARATH	Putative low-molecular-weight cysteine-rich protein LCR85 precursor	0.02	-	exc	1 *					86
O74556 UniProt NPD GO	YCZ2_SCHPO	Putative mannan endo-1,6-alpha-mannosidase C970.02 precursor (EC 3.2.1.101) (Endo-alpha-1->6-D-manna ...	0.02	-	exc	0					442
Q9M2P2 UniProt NPD GO	MTPC3_ARATH	Putative metal tolerance protein C3 (AtMTPc3)	0.02	-	end	4	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				390
Q10248 UniProt NPD GO	YD1K_SCHPO	Putative mitochondrial carrier C4G9.20c	0.02	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				302
O74369 UniProt NPD GO	NSMA_SCHPO	Putative neutral sphingomyelinase (EC 3.1.4.12)	0.02	-	end	2	Membrane; multi-pass membrane protein (Potential)				424
Q9UT28 UniProt NPD GO	NNT1_SCHPO	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.02	-	cyt	0	Cytoplasm (By similarity)				255
Q9VHQ7 UniProt NPD GO	OR85B_DROME	Putative odorant receptor 85b	0.02	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			390
Q9SS98 UniProt NPD GO	OLEO5_ARATH	Putative oleosin 5	0.02	-	end	3 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface (By similarity)				183
Q09851 UniProt NPD GO	YAEB_SCHPO	Putative oxidoreductase C23D3.11 (EC 1.-.-.-)	0.02	-	cyt	0					296
O65456 UniProt NPD GO	PEL16_ARATH	Putative pectate lyase 16 precursor (EC 4.2.2.2)	0.02	-	exc	0					394
P15973 UniProt NPD GO	PHXR1_MOUSE	Putative per-hexamer repeat protein 1	0.02	-	mit	0					60
P15972 UniProt NPD GO	PHXR2_MOUSE	Putative per-hexamer repeat protein 2	0.02	-	cyt	0					65
O14313 UniProt NPD GO	PMP20_SCHPO	Putative peroxiredoxin pmp20 (EC 1.11.1.15) (Thioredoxin reductase) (Peroxisomal membrane protein pm ...	0.02	-	mit	0	Peroxisome (Potential)				156
Q9ZW82 UniProt NPD GO	PIRL2_ARATH	Putative pirin-like protein At2g43120	0.02	-	cyt	0	Nucleus (By similarity)				296
Q9LX45 UniProt NPD GO	PIRL4_ARATH	Putative pirin-like protein At3g59260	0.02	-	cyt	0	Nucleus (By similarity)				271
Q9SHZ0 UniProt NPD GO	DEGP4_ARATH	Putative protease Do-like 4, mitochondrial precursor (EC 3.4.21.-)	0.02	-	mit	1 *	Mitochondrion; mitochondrial membrane (Potential)				518
Q9TZH6 UniProt NPD GO	PHS_CAEEL	Putative pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropte ...	0.02	-	cyt	0					98
Q09737 UniProt NPD GO	PDC1_SCHPO	Putative pyruvate decarboxylase C13A11.06 (EC 4.1.1.1)	0.02	-	cyt	0					571
Q53FA7 UniProt NPD GO	QORX_HUMAN	Putative quinone oxidoreductase (EC 1.-.-.-) (Tumor protein p53-inducible protein 3) (p53-induced pr ...	0.02	-	cyt	0			605171		332
Q9U3N5 UniProt NPD GO	SELT1_CAEEL	Putative selT-like protein C35C5.3 precursor	0.02	-	end	0					247
O23264 UniProt NPD GO	SBP_ARATH	Putative selenium-binding protein	0.02	-	cyt	0					490
Q22682 UniProt NPD GO	EAA4_CAEEL	Putative sodium-dependent excitatory amino acid transporter glt-4	0.02	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				499
Q00675 UniProt NPD GO	STCI_EMENI	Putative sterigmatocystin biosynthesis lipase/esterase stcI	0.02	-	cyt	0					286
O17795 UniProt NPD GO	DHBX_CAEEL	Putative steroid dehydrogenase F11A5.12 (EC 1.1.1.-)	0.02	-	end	1 *					315
P91247 UniProt NPD GO	THT1_CAEEL	Putative thiosulfate sulfurtransferase F11G11.9 (EC 2.8.1.1)	0.02	-	nuc	2					277
Q12305 UniProt NPD GO	YO285_YEAST	Putative thiosulfate sulfurtransferase YOR285W (EC 2.8.1.1)	0.02	-	nuc	0	Mitochondrion	endoplasmic reticulum [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			139
Q95P90 UniProt NPD GO	LP2_MESMA	Putative toxin BmKTXLP2 precursor	0.02	-	mit	1 *	Secreted protein				94
Q8VCL5 UniProt NPD GO	CT059_MOUSE	Putative transporter C20orf59 homolog	0.02	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				439
Q10072 UniProt NPD GO	YAN6_SCHPO	Putative transporter C3H1.06c	0.02	-	end	13	Membrane; multi-pass membrane protein (Potential)				589
O74829 UniProt NPD GO	YN2F_SCHPO	Putative transporter C530.15c	0.02	-	end	12	Membrane; multi-pass membrane protein (Potential)				516
Q42330 UniProt NPD GO	ITI1_ARATH	Putative trypsin inhibitor At1g47540 precursor	0.02	-	cyt	0	Secreted protein (Potential)				98
P31379 UniProt NPD GO	YAB8_YEAST	Putative uncharacterized protein YAL018C	0.02	-	end	5	Membrane; multi-pass membrane protein (Potential)				325
P53089 UniProt NPD GO	YGV4_YEAST	Putative uncharacterized protein YGL204C	0.02	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				101
P53069 UniProt NPD GO	YGY9_YEAST	Putative uncharacterized protein YGL239C	0.02	-	nuc	0					104
P53056 UniProt NPD GO	YGZE_YEAST	Putative uncharacterized protein YGL260W	0.02	-	cyt	0					76
P53975 UniProt NPD GO	YNB9_YEAST	Putative uncharacterized protein YNL019C precursor	0.02	-	end	2 *					284
Q08560 UniProt NPD GO	YO186_YEAST	Putative uncharacterized protein YOR186W	0.02	-	nuc	1	Membrane; single-pass membrane protein (Potential)				144
Q9SV61 UniProt NPD GO	XTH1_ARATH	Putative xyloglucan endotransglucosylase/hydrolase protein 1 precursor (EC 2.4.1.207) (At-XTH1) (XTH ...	0.02	-	mit	0	Secreted protein; extracellular space; apoplast (Probable)				295
Q42963 UniProt NPD GO	PMT1_TOBAC	Putrescine N-methyltransferase 1 (EC 2.1.1.53) (PMT 1) (A411)	0.02	-	cyt	0					375
Q66HC4 UniProt NPD GO	PHOP2_RAT	Pyridoxal phosphate phosphatase PHOSPHO2 (EC 3.1.3.74)	0.02	-	nuc	0					241
O59905 UniProt NPD GO	PDX1_CERNC	Pyridoxine biosynthesis protein PDX1 (Singlet oxygen resistance protein 1)	0.02	-	cyt	0					343
P43534 UniProt NPD GO	THI5_YEAST	Pyrimidine precursor biosynthesis enzyme THI5	0.02	-	mit	0					340
P84357 UniProt NPD GO	PPK_MUSDO	Pyrokinin (Musdo-PK) (FXPRL-amide)	0.02	-		0	Secreted protein				15
P84356 UniProt NPD GO	PPK_SARBU	Pyrokinin (Neobu-PK) (FXPRL-amide)	0.02	-		0	Secreted protein				15
P84369 UniProt NPD GO	PPK4_CELBM	Pyrokinin-4 (Cel-PK-4) (YXPRL-amide)	0.02	-		0	Secreted protein				12

You are viewing entries 85451 to 85500 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.