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
P45880 UniProt NPD GO	VDAC2_HUMAN	Voltage-dependent anion-selective channel protein 2 (VDAC-2) (hVDAC2) (Outer mitochondrial membrane ...	0.07	-	cyt	0	Mitochondrion; mitochondrial outer membrane	mitochondrial outer membrane [TAS]	193245		347
O70410 UniProt NPD GO	V2RX_MOUSE	Vomeronasal type-2 receptor X precursor (Putative pheromone receptor V2RX)	0.07	-	end	7	Membrane; multi-pass membrane protein (Potential)				912
Q29126 UniProt NPD GO	WAP3_PIG	WAP-3 protein precursor	0.07	-	cyt	0					144
Q9Y484 UniProt NPD GO	WIPI4_HUMAN	WD repeat domain phosphoinositide-interacting protein 4 (WIPI-4) (WD repeat protein 45)	0.07	-	mit	0			300526		360
Q91VM3 UniProt NPD GO	WIPI4_MOUSE	WD repeat domain phosphoinositide-interacting protein 4 (WIPI-4) (WD repeat protein 45) (WD repeat d ...	0.07	-	cyt	0					360
Q95JL5 UniProt NPD GO	WDR16_MACFA	WD repeat protein 16	0.07	-	mit	0	Cytoplasm (By similarity)				571
O22467 UniProt NPD GO	MSI1_ARATH	WD-40 repeat protein MSI1 (Protein MULTICOPY SUPPRESSOR OF IRA 1) (Protein medicis)	0.07	-	cyt	0	Nucleus (By similarity)				424
O22469 UniProt NPD GO	MSI3_ARATH	WD-40 repeat protein MSI3	0.07	-	cyt	0	Nucleus (By similarity)				424
P25677 UniProt NPD GO	TXW3_NAJHA	Weak toxin CM-3	0.07	-	nuc	0	Secreted protein				60
Q9NQW7 UniProt NPD GO	XPP1_HUMAN	Xaa-Pro aminopeptidase 1 (EC 3.4.11.9) (X-Pro aminopeptidase 1) (X-prolyl aminopeptidase 1, soluble) ...	0.07	-	mit	0	Cytoplasm (By similarity)	cytoplasm [ISS]	602443		622
Q6P1B1 UniProt NPD GO	XPP1_MOUSE	Xaa-Pro aminopeptidase 1 (EC 3.4.11.9) (X-Pro aminopeptidase 1) (X-prolyl aminopeptidase 1, soluble) ...	0.07	-	mit	0	Cytoplasm (By similarity)	cytoplasm [ISS]			623
O54975 UniProt NPD GO	XPP1_RAT	Xaa-Pro aminopeptidase 1 (EC 3.4.11.9) (X-Pro aminopeptidase 1) (X-prolyl aminopeptidase 1, soluble) ...	0.07	-	mit	0	Cytoplasm	cytoplasm [IDA] cytosol [IDA]			623
P24806 UniProt NPD GO	XTH24_ARATH	Xyloglucan endotransglucosylase/hydrolase protein 24 precursor (EC 2.4.1.207) (At-XTH24) (XTH-24) (M ...	0.07	-	vac	0	Secreted protein; extracellular space; apoplast (Probable)				269
Q9SE20 UniProt NPD GO	ZDS_LYCES	Zeta-carotene desaturase, chloroplast precursor (EC 1.14.99.30) (Carotene 7,8-desaturase)	0.07	-	mit	0	Plastid; chloroplast. Plastid; chromoplast				588
Q9VL86 UniProt NPD GO	CBPA1_DROME	Zinc carboxypeptidase A 1 precursor (EC 3.4.17.-)	0.07	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			430
P80944 UniProt NPD GO	ZFX_PIG	Zinc finger X-chromosomal protein (Fragment)	0.07	-	nuc	0	Nucleus				148
Q29419 UniProt NPD GO	ZFY_PIG	Zinc finger Y-chromosomal protein (Fragment)	0.07	-	nuc	0	Nucleus				148
P17016 UniProt NPD GO	ZNF13_HUMAN	Zinc finger protein 13 (Zinc finger protein KOX5) (Fragment)	0.07	-	nuc	0	Nucleus (Potential)		194554		56
P84587 UniProt NPD GO	ZN326_RAT	Zinc finger protein 326 (Fragments)	0.07	-	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity)				22
O04089 UniProt NPD GO	ZIP4_ARATH	Zinc transporter 4, chloroplast precursor (ZRT/IRT-like protein 4)	0.07	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Potential)				374
Q92504 UniProt NPD GO	KE4_HUMAN	Zinc transporter SLC39A7 (Solute carrier family 39 member 7) (Histidine-rich membrane protein Ke4)	0.07	-	end	7 *	Membrane; multi-pass membrane protein (Probable)	membrane fraction [TAS]	601416		469
Q5RFD5 UniProt NPD GO	KE4_PONPY	Zinc transporter SLC39A7 (Solute carrier family 39 member 7) (Histidine-rich membrane protein Ke4)	0.07	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				469
Q6X782 UniProt NPD GO	ZPBP2_RAT	Zona pellucida-binding protein 2 precursor	0.07	-	exc	0	Secreted protein (By similarity)				326
P54923 UniProt NPD GO	ADPRH_MOUSE	[Protein ADP-ribosylarginine] hydrolase (EC 3.2.2.19) (ADP-ribosylarginine hydrolase) (ADP-ribose-L- ...	0.07	-	cyt	0					362
P49673 UniProt NPD GO	KAPC_ASCSU	cAMP-dependent protein kinase catalytic subunit (EC 2.7.11.11) (PKA C)	0.07	-	cyt	0					337
P05132 UniProt NPD GO	KAPCA_MOUSE	cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) (PKA C-alpha)	0.07	-	cyt	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...	cytoplasm [IDA] mitochondrion [IDA]		2ERZ	350
P33766 UniProt NPD GO	FPR1_MOUSE	fMet-Leu-Phe receptor (fMLP receptor) (N-formyl peptide receptor) (FPR) (N-formylpeptide chemoattrac ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				364
Q7S302 UniProt NPD GO	MRT4_NEUCR	mRNA turnover protein 4 homolog	0.07	-	cyt	0	Nucleus; nucleolus (By similarity)				252
P52707 UniProt NPD GO	MDL3_PRUSE	(R)-mandelonitrile lyase 3 precursor (EC 4.1.2.10) (Hydroxynitrile lyase 3) ((R)-oxynitrilase 3)	0.06	-	mit	0	Protein body (By similarity). Primarily found within protein bodies of the cotyledonary parenchyma c ...				573
Q7XEJ5 UniProt NPD GO	ARD4_ORYSA	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 4 (EC 1.13.-.-) (Aci-reductone dioxygenase 4)	0.06	-	cyt	0					184
Q6FJV0 UniProt NPD GO	GLGB_CANGA	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.06	-	cyt	0					706
Q41745 UniProt NPD GO	LPAT_MAIZE	1-acyl-sn-glycerol-3-phosphate acyltransferase PLS1 (EC 2.3.1.51) (Phospholipid synthesis protein 1) ...	0.06	-	end	3 *	Membrane; multi-pass membrane protein (Probable)				374
Q9FEX0 UniProt NPD GO	OPRL_LYCES	12-oxophytodienoate reductase-like protein (EC 1.3.1.-) (LeOPR2)	0.06	-	mit	0	Cytoplasm				355
Q15332 UniProt NPD GO	C11X_HUMAN	13.2 kDa protein in chromosome 11	0.06	-	nuc	0					126
P84746 UniProt NPD GO	VVP1_BOTJR	1370.6 Da venom vasodilator peptide	0.06	-		0	Secreted protein				12
P84747 UniProt NPD GO	VVP1_BOTMO	1370.6 Da venom vasodilator peptide	0.06	-		0	Secreted protein				12
Q07167 UniProt NPD GO	SM16_SCHMA	16 kDa calcium-binding protein (Egg antigen SME16)	0.06	-	cyt	0					143
P24631 UniProt NPD GO	HSP21_MAIZE	17.5 kDa class II heat shock protein	0.06	-	cyt	0	Cytoplasm				161
P27880 UniProt NPD GO	HSP12_MEDSA	18.2 kDa class I heat shock protein	0.06	-	cyt	0	Cytoplasm				158
P80402 UniProt NPD GO	DHBD_ASPOR	2,3-dihydroxybenzoic acid decarboxylase (EC 4.1.1.46) (DHBD) (o-pyrocatechuate decarboxylase) (2,3-D ...	0.06	-	cyt	0					338
P26270 UniProt NPD GO	PSD7_DROME	26S proteasome non-ATPase regulatory subunit 7 (26S proteasome regulatory subunit rpn8) (26S proteas ...	0.06	-	mit	0		proteasome regulatory particle, lid subcomp... [NAS]			337
Q9DCA2 UniProt NPD GO	RT11_MOUSE	28S ribosomal protein S11, mitochondrial precursor (S11mt) (MRP-S11)	0.06	-	mit	0	Mitochondrion				191
Q9N119 UniProt NPD GO	3BHS_PIG	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase (3Beta-HSD) [Includes: 3-beta-hydroxy-delt ...	0.06	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
P26150 UniProt NPD GO	3BHS3_MOUSE	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type III (3Beta-HSD III) [Includes: 3-beta ...	0.06	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...	mitochondrial inner membrane [IDA]			372
P23457 UniProt NPD GO	DIDH_RAT	3-alpha-hydroxysteroid dehydrogenase (EC 1.1.1.213) (3-alpha-HSD) (Hydroxyprostaglandin dehydrogenas ...	0.06	-	cyt	0	Cytoplasm			1RAL	322
P52841 UniProt NPD GO	SUHB_CAVPO	3-beta-hydroxysteroid sulfotransferase (EC 2.8.2.2) (Alcohol sulfotransferase) (Pregnenolone sulfotr ...	0.06	-	cyt	0	Cytoplasm				286
P09610 UniProt NPD GO	HMDH_MESAU	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.06	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				887
O64966 UniProt NPD GO	HMDH1_GOSHI	3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (EC 1.1.1.34) (HMG-CoA reductase 1)	0.06	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Mitochondrion; m ...				585
Q6PY58 UniProt NPD GO	LEU3_CANMI	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.06	-	cyt	0	Cytoplasm				363
Q6B458 UniProt NPD GO	LEU3_DEBHA	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.06	-	cyt	0	Cytoplasm				382

You are viewing entries 71301 to 71350 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.