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
Q8VD53 UniProt NPD GO	ASA3L_MOUSE	Alkaline ceramidase 2 (EC 3.5.1.23) (AlkCDase 2) (maCER2) (Acylsphingosine deacylase 3-like) (N-acyl ...	0.05	-	end	7 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				275
P09230 UniProt NPD GO	AEP_YARLI	Alkaline extracellular protease precursor (EC 3.4.21.-) (AEP)	0.05	-	vac	0	Secreted protein				454
Q28133 UniProt NPD GO	ALL2_BOVIN	Allergen Bos d 2 precursor (Dander major allergen BDA20) (Dermal allergen BDA20)	0.05	-	exc	0	Secreted protein			1BJ7	172
P28556 UniProt NPD GO	PHAB_AGLNE	Allophycocyanin beta chain	0.05	-	cyt	0	Plastid; chloroplast				161
P00319 UniProt NPD GO	PHAB_GALSU	Allophycocyanin beta chain	0.05	-	cyt	0	Plastid; chloroplast				161
P59857 UniProt NPD GO	PHAB_PORYE	Allophycocyanin beta chain	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen. Phycobilisome core			1KN1	161
O94213 UniProt NPD GO	TPS1_PICAN	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] (EC 2.4.1.15) (Trehalose-6-phosphate synthase ...	0.05	-	cyt	0					475
Q6FL34 UniProt NPD GO	ALG10_CANGA	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.05	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				522
P80607 UniProt NPD GO	UPTG_MAIZE	Alpha-1,4-glucan-protein synthase [UDP-forming] (EC 2.4.1.112) (UDP-glucose:protein transglucosylase ...	0.05	-	cyt	0	Cell wall. Cell wall; cell-cell junction; plasmodesma. Cell wall-associated, with highest concentrat ...				364
P39091 UniProt NPD GO	A1BG_HORSE	Alpha-1B-glycoprotein (Alpha-1-B glycoprotein) (Plasma protein XK) (Fragment)	0.05	-	cyt	0	Secreted protein				41
P80191 UniProt NPD GO	FETUA_RABIT	Alpha-2-HS-glycoprotein precursor (Fetuin-A) (Haemonectin) (Fragment)	0.05	-	vac	0	Secreted protein	extracellular space [ISS]			360
P15326 UniProt NPD GO	IAMY_COILA	Alpha-amylase inhibitor/endochitinase (EC 3.2.1.14) (Fragments)	0.05	-	nuc	0					133
P00693 UniProt NPD GO	AMY1_HORVU	Alpha-amylase type A isozyme precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (AMY1) (Lo ...	0.05	-	exc	1 *	Secreted protein; extracellular space			1RPK	438
O77020 UniProt NPD GO	AMYR_DROAV	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.05	-	cyt	0	Secreted protein (Probable)				494
O77019 UniProt NPD GO	AMYR_DROBA	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.05	-	cyt	0	Secreted protein (Probable)				494
O77021 UniProt NPD GO	AMYR_DRODO	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.05	-	pox	0	Secreted protein (Probable)				494
O76262 UniProt NPD GO	AMYR_DROLN	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.05	-	cyt	0	Secreted protein (Probable)				494
O77022 UniProt NPD GO	AMYR_DROPN	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.05	-	cyt	0	Secreted protein (Probable)				494
O18420 UniProt NPD GO	AMYR_DROSU	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.05	-	pox	0	Secreted protein (Probable)				494
O18344 UniProt NPD GO	AMYR_DROAN	Alpha-amylase-related protein precursor (EC 3.2.1.1) (Amy c6)	0.05	-	cyt	0	Secreted protein (Probable)				493
P29421 UniProt NPD GO	IAAS_ORYSA	Alpha-amylase/subtilisin inhibitor precursor (RASI)	0.05	-	exc	0					200
P16850 UniProt NPD GO	IAAC1_WHEAT	Alpha-amylase/trypsin inhibitor CM1 precursor (Chloroform/methanol-soluble protein CM1)	0.05	-	exc	1 *	Secreted protein				145
P69658 UniProt NPD GO	CXA1_CONPU	Alpha-conotoxin PIA precursor (Fragment)	0.05	-	nuc	0	Secreted protein (By similarity)				40
Q9LDR9 UniProt NPD GO	EXP10_ARATH	Alpha-expansin 10 precursor (AtEXPA10) (At-EXP10) (AtEx10) (Ath-ExpAlpha-1.1)	0.05	-	cyt	1 *	Cell wall; peripheral membrane protein				249
Q38864 UniProt NPD GO	EXPA5_ARATH	Alpha-expansin 5 precursor (AtEXPA5) (At-EXP5) (AtEx5) (Ath-ExpAlpha-1.4)	0.05	-	mit	1 *	Cell wall; peripheral membrane protein				255
P41946 UniProt NPD GO	MEL5_YEAST	Alpha-galactosidase 5 precursor (EC 3.2.1.22) (Melibiase 5) (Alpha-D-galactoside galactohydrolase 5) ...	0.05	-	mit	0					471
P41947 UniProt NPD GO	MEL6_YEAST	Alpha-galactosidase 6 precursor (EC 3.2.1.22) (Melibiase 6) (Alpha-D-galactoside galactohydrolase 6) ...	0.05	-	mit	0					471
P30805 UniProt NPD GO	LALBA_ORNAN	Alpha-lactalbumin (Lactose synthase B protein)	0.05	-	cyt	0	Secreted protein				126
Q06655 UniProt NPD GO	LALBA_MACEU	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.05	-	exc	0	Secreted protein				140
Q29145 UniProt NPD GO	LALBA_TRIVU	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.05	-	exc	0	Secreted protein				140
P18486 UniProt NPD GO	L2AM_DROME	Alpha-methyldopa hypersensitive protein (EC 4.1.1.-)	0.05	-	cyt	0					510
O03376 UniProt NPD GO	AOX3_SOYBN	Alternative oxidase 3, mitochondrial precursor (EC 1.-.-.-)	0.05	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				326
O93788 UniProt NPD GO	AOX_MAGGR	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-) (MgAOX) (AOXMg)	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				377
Q708S5 UniProt NPD GO	ACCN1_BRARE	Amiloride-sensitive cation channel 1, neuronal (Acid-sensing ion channel 2) (ZASIC2)	0.05	-	mit	0	Cell membrane; multi-pass membrane protein (Probable)				533
Q8BW75 UniProt NPD GO	AOFB_MOUSE	Amine oxidase [flavin-containing] B (EC 1.4.3.4) (Monoamine oxidase type B) (MAO-B)	0.05	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)	mitochondrial inner membrane [IDA]			519
P13090 UniProt NPD GO	ATR1_YEAST	Aminotriazole resistance protein	0.05	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [IMP]			542
Q9BXJ7 UniProt NPD GO	AMNLS_HUMAN	Amnionless protein precursor	0.05	-	end	1	Membrane; single-pass type I membrane protein (Potential)		605799		453
P29262 UniProt NPD GO	AH4_PRUSE	Amygdalin beta-glucosidase II' (EC 3.2.1.117) (Amygdalin hydrolase isozyme II') (AH II') (Fragment)	0.05	-		0					13
P29216 UniProt NPD GO	A4_MACMU	Amyloid beta A4 protein (APP) (ABPP) (Alzheimer disease amyloid A4 protein homolog) (Fragment)	0.05	-	cyt	0	Membrane; single-pass type I membrane protein				76
P09872 UniProt NPD GO	VSP1_AGKCO	Ancrod (EC 3.4.21.74) (Venombin A) (Protein C activator) (ACC-C)	0.05	-	nuc	0	Secreted protein (Potential)			2AIQ	231
Q7YR70 UniProt NPD GO	AAMP_CANFA	Angio-associated migratory cell protein	0.05	-	cyt	0					435
Q13685 UniProt NPD GO	AAMP_HUMAN	Angio-associated migratory cell protein	0.05	-	cyt	0			603488		434
Q5RCG7 UniProt NPD GO	AAMP_PONPY	Angio-associated migratory cell protein	0.05	-	cyt	0					434
Q9TSZ0 UniProt NPD GO	ANGT_CALJA	Angiotensinogen precursor [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotens ...	0.05	-	mit	0	Secreted protein				486
Q5RFS1 UniProt NPD GO	ASB11_PONPY	Ankyrin repeat and SOCS box protein 11 (ASB-11)	0.05	-	nuc	1 *					323
Q9WV71 UniProt NPD GO	ASB4_MOUSE	Ankyrin repeat and SOCS box protein 4 (ASB-4)	0.05	-	mit	0					426
Q2KI79 UniProt NPD GO	ANRA2_BOVIN	Ankyrin repeat family A protein 2	0.05	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				313
P20072 UniProt NPD GO	ANXA7_BOVIN	Annexin A7 (Annexin VII) (Synexin) (Fragment)	0.05	-	nuc	0					61
P52183 UniProt NPD GO	ANNU_SCHAM	Annulin (Protein-glutamine gamma-glutamyltransferase) (EC 2.3.2.13) (Transglutaminase)	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Intracellular and peripherally associated with the in ...				772
O60122 UniProt NPD GO	TRPD_SCHPO	Anthranilate phosphoribosyltransferase (EC 2.4.2.18)	0.05	-	mit	0					354

You are viewing entries 73801 to 73850 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.