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
Q3TNA1 UniProt NPD GO	XYLB_MOUSE	Xylulose kinase (EC 2.7.1.17) (Xylulokinase)	0.09	-	mit	0					551
Q9Y330 UniProt NPD GO	ZBT12_HUMAN	Zinc finger and BTB domain-containing protein 12 (Protein G10)	0.09	-	cyt	0	Nucleus (Potential)				459
Q62941 UniProt NPD GO	ZNT2_RAT	Zinc transporter 2 (ZnT-2) (Solute carrier family 30 member 2)	0.09	-	end	6	Endosome; endosomal membrane; multi-pass membrane protein (Probable)	cytoplasmic membrane-bound vesicle [IDA]			359
Q05996 UniProt NPD GO	ZP2_HUMAN	Zona pellucida sperm-binding protein 2 precursor (Zona pellucida glycoprotein ZP2) (Zona pellucida p ...	0.09	-	nuc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...		182888		745
P48832 UniProt NPD GO	ZP3_FELCA	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3) (Sperm receptor) ...	0.09	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				424
P48830 UniProt NPD GO	ZP3_BOVIN	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3B) (Sperm receptor) ...	0.09	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				421
Q02589 UniProt NPD GO	ADPRH_RAT	[Protein ADP-ribosylarginine] hydrolase (EC 3.2.2.19) (ADP-ribosylarginine hydrolase) (ADP-ribose-L- ...	0.09	-	cyt	0					362
P84773 UniProt NPD GO	BRK_AMICA	[Trp5]-bradykinin	0.09	-		0	Secreted protein	extracellular space [IDA]			9
P84774 UniProt NPD GO	BRK_LEPOS	[Trp5]-bradykinin	0.09	-		0	Secreted protein	extracellular space [IDA]			9
P63248 UniProt NPD GO	IPKA_MOUSE	cAMP-dependent protein kinase inhibitor alpha (PKI-alpha) (cAMP-dependent protein kinase inhibitor, ...	0.09	-	nuc	0				1PVK	75
P63249 UniProt NPD GO	IPKA_RAT	cAMP-dependent protein kinase inhibitor alpha (PKI-alpha) (cAMP-dependent protein kinase inhibitor, ...	0.09	-	nuc	0					75
P22612 UniProt NPD GO	KAPCG_HUMAN	cAMP-dependent protein kinase, gamma-catalytic subunit (EC 2.7.11.11) (PKA C-gamma)	0.09	-	nuc	0			176893		350
Q9D2C9 UniProt NPD GO	SNPC3_MOUSE	snRNA-activating protein complex subunit 3 (SNAPc subunit 3) (snRNA-activating protein complex 50 kD ...	0.09	-	cyt	0	Nucleus (By similarity)				407
Q6CCT1 UniProt NPD GO	GLGB_YARLI	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.08	-	nuc	0					691
Q8K4X7 UniProt NPD GO	PLCD_MOUSE	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (EC 2.3.1.51) (1-AGP acyltransferase 4) (1-AGPA ...	0.08	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				378
Q924S1 UniProt NPD GO	PLCD_RAT	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (EC 2.3.1.51) (1-AGP acyltransferase 4) (1-AGPA ...	0.08	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				378
Q86UL3 UniProt NPD GO	PLCF_HUMAN	1-acyl-sn-glycerol-3-phosphate acyltransferase zeta precursor (EC 2.3.1.51) (1-AGP acyltransferase 6 ...	0.08	-	vac	3 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [ISS] integral to endoplasmic reticulum membrane [ISS]	608143		456
Q5R6J7 UniProt NPD GO	PLCF_PONPY	1-acyl-sn-glycerol-3-phosphate acyltransferase zeta precursor (EC 2.3.1.51) (1-AGP acyltransferase 6 ...	0.08	-	vac	3 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [ISS] integral to endoplasmic reticulum membrane [ISS]			456
P31531 UniProt NPD GO	1A1C_SOYBN	1-aminocyclopropane-1-carboxylate synthase (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methionine met ...	0.08	-	cyt	0					484
P93206 UniProt NPD GO	14331_LYCES	14-3-3 protein 1	0.08	-	cyt	0					249
Q84J55 UniProt NPD GO	14331_ORYSA	14-3-3-like protein GF14-A (G-box factor 14-3-3 homolog A)	0.08	-	cyt	0					264
Q9ERR7 UniProt NPD GO	SEP15_MOUSE	15 kDa selenoprotein precursor	0.08	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity). The association with UGCGL1/UGTR ...	endoplasmic reticulum lumen [ISS]			162
Q08275 UniProt NPD GO	HSP23_MAIZE	17.0 kDa class II heat shock protein (HSP 18)	0.08	-	cyt	0	Cytoplasm				154
P46516 UniProt NPD GO	HSP21_HELAN	17.9 kDa class II heat shock protein	0.08	-	nuc	0	Cytoplasm (Potential)				160
Q9M4W3 UniProt NPD GO	ISPF_CATRO	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplast precursor (EC 4.6.1.12) (MECPS) ( ...	0.08	-	end	0	Plastid; chloroplast				236
Q9FPW3 UniProt NPD GO	DBBT_TAXCU	2-alpha-hydroxytaxane 2-O-benzoyltransferase (EC 2.3.1.166) (TBT) (2-debenzoyl-7,13-diacetylbaccatin ...	0.08	-	pox	0					440
Q8TDX5 UniProt NPD GO	ACMSD_HUMAN	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45)	0.08	-	cyt	1		cytosol [NAS]	608889		336
P80774 UniProt NPD GO	CWP15_PHAVU	22 kDa cell wall protein (Fragment)	0.08	-		0	Cell wall				18
P54814 UniProt NPD GO	PRS8_MANSE	26S protease regulatory subunit 8 (18-56 protein)	0.08	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				402
O76577 UniProt NPD GO	PSDE_CAEEL	26S proteasome non-ATPase regulatory subunit 14 (26S proteasome regulatory subunit rpn11)	0.08	-	cyt	0					312
Q9V3H2 UniProt NPD GO	PSDE_DROME	26S proteasome non-ATPase regulatory subunit 14 (26S proteasome regulatory subunit rpn11) (26S prote ...	0.08	-	cyt	0		proteasome regulatory particle (sensu Eukar... [IDA]			308
O00487 UniProt NPD GO	PSDE_HUMAN	26S proteasome non-ATPase regulatory subunit 14 (26S proteasome regulatory subunit rpn11) (26S prote ...	0.08	-	cyt	0		proteasome complex (sensu Eukaryota) [TAS]	607173		310
O35593 UniProt NPD GO	PSDE_MOUSE	26S proteasome non-ATPase regulatory subunit 14 (26S proteasome regulatory subunit rpn11) (MAD1)	0.08	-	cyt	0					310
P51665 UniProt NPD GO	PSD7_HUMAN	26S proteasome non-ATPase regulatory subunit 7 (26S proteasome regulatory subunit rpn8) (26S proteas ...	0.08	-	end	0		proteasome regulatory particle (sensu Eukar... [TAS]	157970		324
Q6FMD8 UniProt NPD GO	RPN8_CANGA	26S proteasome regulatory subunit RPN8	0.08	-	cyt	0					329
P42126 UniProt NPD GO	D3D2_HUMAN	3,2-trans-enoyl-CoA isomerase, mitochondrial precursor (EC 5.3.3.8) (Dodecenoyl-CoA isomerase) (Delt ...	0.08	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]	600305	1SG4	302
P04035 UniProt NPD GO	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.08	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Peroxisome; pero ...	endoplasmic reticulum membrane [TAS]	142910	1HWL	888
Q10283 UniProt NPD GO	HMDH_SCHPO	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.08	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				1053
P34136 UniProt NPD GO	HMDH2_DICDI	3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 (EC 1.1.1.34) (HMG-CoA reductase 2) (Fragment)	0.08	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				481
Q9XHL5 UniProt NPD GO	HMDH3_ORYSA	3-hydroxy-3-methylglutaryl-coenzyme A reductase 3 (EC 1.1.1.34) (HMG-CoA reductase 3)	0.08	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				561
P47096 UniProt NPD GO	3HAO_YEAST	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.08	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA]		1ZVF	177
Q07510 UniProt NPD GO	FABH_SPIOL	3-oxoacyl-[acyl-carrier-protein] synthase III, chloroplast precursor (EC 2.3.1.41) (Beta-ketoacyl-AC ...	0.08	-	mit	0	Plastid; chloroplast				405
P34755 UniProt NPD GO	PHYB_ASPAW	3-phytase B precursor (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase B) (pH 2.5 optimum ...	0.08	-	exc	0				1QFX	479
Q04836 UniProt NPD GO	ROC3_ARATH	31 kDa ribonucleoprotein, chloroplast precursor (RNA-binding protein RNP-T) (RNA-binding protein 1/2 ...	0.08	-	mit	0	Plastid; chloroplast				329
Q872T7 UniProt NPD GO	HPPD_NEUCR	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase)	0.08	-	cyt	0					412
P27072 UniProt NPD GO	RS13_MUSDO	40S ribosomal protein S13 (Fragment)	0.08	-	mit	0					114
Q876B4 UniProt NPD GO	RS16_SACEX	40S ribosomal protein S16	0.08	-	cyt	0					142
P24494 UniProt NPD GO	RS19G_ASCSU	40S ribosomal protein S19G (Eliminated protein NO. 1)	0.08	-	cyt	0					148
P39698 UniProt NPD GO	RS19S_ASCSU	40S ribosomal protein S19S	0.08	-	cyt	0					150
P05764 UniProt NPD GO	RS21_SCHPO	40S ribosomal protein S21 (S28)	0.08	-	cyt	0		small ribosomal subunit [TAS]			87

You are viewing entries 67351 to 67400 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.