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
P34264 UniProt NPD GO	RM11_CAEEL	Probable 39S ribosomal protein L11, mitochondrial precursor	0.14	-	mit	0	Mitochondrion (By similarity)				195
P55844 UniProt NPD GO	RL14_PEA	Probable 60 ribosomal protein L14 (Hydroxyproline-rich glycoprotein HRGP1)	0.14	-	mit	0					133
O14069 UniProt NPD GO	YFF6_SCHPO	Probable 60S ribosomal protein C1687.06c	0.14	-	nuc	0					134
Q9SHU5 UniProt NPD GO	ARF4_ARATH	Probable ADP-ribosylation factor At2g15310	0.14	-	mit	0					204
Q49SQ2 UniProt NPD GO	GPR33_PANPA	Probable G-protein coupled receptor 33	0.14	-	end	7 *	Membrane; multi-pass membrane protein				333
Q49SQ3 UniProt NPD GO	GPR33_PANTR	Probable G-protein coupled receptor 33	0.14	-	end	7 *	Membrane; multi-pass membrane protein				333
Q03566 UniProt NPD GO	YLD1_CAEEL	Probable G-protein coupled receptor C38C10.1	0.14	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				374
P83118 UniProt NPD GO	MTH11_DROME	Probable G-protein coupled receptor Mth-like 11 precursor (Protein methuselah-like 11)	0.14	-	end	7	Membrane; multi-pass membrane protein (Potential)				510
Q9N2W7 UniProt NPD GO	NDUAC_CAEEL	Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (EC 1.6.5.3) (EC 1.6.99.3) (N ...	0.14	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				146
Q852M1 UniProt NPD GO	ALDO2_ORYSA	Probable aldehyde oxidase 2 (EC 1.2.3.1) (AO-2)	0.14	-	cyt	0					1355
Q852M2 UniProt NPD GO	ALDO3_ORYSA	Probable aldehyde oxidase 3 (EC 1.2.3.1) (AO-3)	0.14	-	cyt	0					1356
Q9Y7S9 UniProt NPD GO	AMY4_SCHPO	Probable alpha-amylase C63.02c precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.14	-	exc	1 *					564
Q6NSR8 UniProt NPD GO	PEPL1_MOUSE	Probable aminopeptidase NPEPL1 (EC 3.4.11.-) (Aminopeptidase-like 1)	0.14	+	cyt	0					524
P90747 UniProt NPD GO	YE56_CAEEL	Probable cation-transporting ATPase C10C6.6 in chromosome IV (EC 3.6.3.-)	0.14	-	end	9 *	Membrane; multi-pass membrane protein				1178
Q75E61 UniProt NPD GO	ATG4_ASHGO	Probable cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.14	-	end	0	Cytoplasm (By similarity)				521
Q9V399 UniProt NPD GO	CP303_DROME	Probable cytochrome P450 303a1 (EC 1.14.-.-) (CYPCCCIIIA1)	0.14	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				503
Q9VFP1 UniProt NPD GO	CP6D5_DROME	Probable cytochrome P450 6d5 (EC 1.14.-.-) (CYPVID5)	0.14	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				508
Q9XVV5 UniProt NPD GO	DPM3_CAEEL	Probable dolichol-phosphate mannosyltransferase subunit 3 (Dolichol-phosphate mannose synthase subun ...	0.14	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				95
Q22618 UniProt NPD GO	ADR2_CAEEL	Probable double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) (DRADA)	0.14	-	cyt	0	Nucleus (Potential)				495
O74742 UniProt NPD GO	FOLE_SCHPO	Probable folylpolyglutamate synthase (EC 6.3.2.17) (Folylpoly-gamma-glutamate synthetase) (FPGS) (Te ...	0.14	-	nuc	0	Cytoplasm	cytoplasm [IDA]			505
O94509 UniProt NPD GO	GATH_SCHPO	Probable glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial precursor (EC 6.3.5.-) (Glu-AD ...	0.14	-	cyt	0					471
Q03557 UniProt NPD GO	GATH_YEAST	Probable glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial precursor (EC 6.3.5.-) (Glu-AD ...	0.14	-	cyt	0	Mitochondrion	mitochondrion [IDA]			464
P49954 UniProt NPD GO	NIT3_YEAST	Probable hydrolase NIT3 (EC 3.5.-.-)	0.14	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]		1F89	291
Q5NAZ7 UniProt NPD GO	GH33_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.3 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.14	-	mit	0					462
Q6I581 UniProt NPD GO	GH35_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.5 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.14	-	cyt	0					581
Q9FJD2 UniProt NPD GO	OPT9_ARATH	Probable oligopeptide transporter 9 (AtOPT9)	0.14	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				741
Q810M5 UniProt NPD GO	ZDH19_MOUSE	Probable palmitoyltransferase ZDHHC19 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 19) ( ...	0.14	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				347
Q940Q1 UniProt NPD GO	PEL1_ARATH	Probable pectate lyase 1 precursor (EC 4.2.2.2) (Pectate lyase A1)	0.14	-	end	0					431
Q9FXD8 UniProt NPD GO	PEL5_ARATH	Probable pectate lyase 5 precursor (EC 4.2.2.2)	0.14	-	gol	1 *					408
Q9QZW0 UniProt NPD GO	AT11C_MOUSE	Probable phospholipid-transporting ATPase 11C (EC 3.6.3.1) (Fragment)	0.14	-	end	6	Membrane; multi-pass membrane protein				347
O94307 UniProt NPD GO	PFD5_SCHPO	Probable prefoldin subunit 5 (Byr1-binding protein Bob1)	0.14	-	nuc	0					154
P41992 UniProt NPD GO	PFTB_CAEEL	Probable protein farnesyltransferase subunit beta (EC 2.5.1.58) (CAAX farnesyltransferase subunit be ...	0.14	-	nuc	0					335
Q9XI84 UniProt NPD GO	RBCMT_ARATH	Probable ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloropl ...	0.14	-	mit	0	Plastid; chloroplast (By similarity)				482
Q8NBX0 UniProt NPD GO	SCPDH_HUMAN	Probable saccharopine dehydrogenase (EC 1.5.1.9)	0.14	-	nuc	1					429
Q9UUC6 UniProt NPD GO	SMD3_SCHPO	Probable small nuclear ribonucleoprotein Sm D3 (snRNP core protein D3) (Sm-D3)	0.14	-	nuc	0	Nucleus (Potential)				97
Q12608 UniProt NPD GO	STCB_EMENI	Probable sterigmatocystin biosynthesis P450 monooxygenase STCB (EC 1.14.-.-) (Cytochrome P450 62)	0.14	-	cyt	0					435
Q00707 UniProt NPD GO	STCL_EMENI	Probable sterigmatocystin biosynthesis P450 monooxygenase STCL (EC 1.14.-.-) (Cytochrome P450 60B)	0.14	-	cyt	0					500
P28835 UniProt NPD GO	YCF27_PORAE	Probable transcriptional regulator ycf27 (OmpR-like protein)	0.14	-	cyt	0	Plastid; chloroplast				240
Q07904 UniProt NPD GO	YL004_YEAST	Probable transporter YLR004C	0.14	-	end	12					523
Q9ZVN4 UniProt NPD GO	Y1500_ARATH	Probable tyrosine-protein phosphatase At1g05000 (EC 3.1.3.48)	0.14	-	nuc	0				1XRI	215
Q9YGI4 UniProt NPD GO	TXW2_NAJAT	Probable weak neurotoxin NNAM2 precursor (TA-N9)	0.14	-	nuc	1 *	Secreted protein				86
P60814 UniProt NPD GO	TXWI_NAJAT	Probable weak neurotoxin NNAM2I precursor	0.14	-	nuc	1 *	Secreted protein				86
Q9ZVK1 UniProt NPD GO	XTH10_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 10 precursor (EC 2.4.1.207) (At-XTH10) (X ...	0.14	-	exc	1 *	Secreted protein; extracellular space; apoplast (Probable)				299
O80803 UniProt NPD GO	XTH17_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 17 precursor (EC 2.4.1.207) (At-XTH17) (X ...	0.14	-	exc	1 *	Secreted protein; extracellular space; apoplast (Probable)	cell wall (sensu Magnoliophyta) [IDA]			282
Q9M0D2 UniProt NPD GO	XTH18_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 18 precursor (EC 2.4.1.207) (At-XTH18) (X ...	0.14	-	vac	1 *	Secreted protein; extracellular space; apoplast (Probable)				282
Q8LNZ5 UniProt NPD GO	XTHB_PHAAN	Probable xyloglucan endotransglucosylase/hydrolase protein B precursor (EC 2.4.1.207) (VaXTH2)	0.14	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				293
P49921 UniProt NPD GO	GON1_PIG	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.14	-	nuc	1 *	Secreted protein				91
P30973 UniProt NPD GO	GON3_ONCMA	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.14	-	vac	0	Secreted protein				82
P47816 UniProt NPD GO	PDCD2_RAT	Programmed cell death protein 2 (Zinc finger protein Rp-8) (Fragment)	0.14	-	mit	0	Nucleus (Potential)				287
Q9HCJ1 UniProt NPD GO	ANKH_HUMAN	Progressive ankylosis protein homolog (ANK)	0.14	-	end	8 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [IDA] outer membrane [TAS]	605145		492

You are viewing entries 58851 to 58900 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.