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
P30599 UniProt NPD GO	CHS2_USTMA	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2)	0.74	-	end	7	Cell membrane; multi-pass membrane protein				1074
Q9HC52 UniProt NPD GO	CBX8_HUMAN	Chromobox protein homolog 8 (Polycomb 3 homolog) (Pc3) (hPc3) (Rectachrome 1)	0.74	+	nuc	0	Nucleus				389
Q8K1A6 UniProt NPD GO	CCD1A_MOUSE	Coiled-coil and C2 domain-containing protein 1A (Five repressor element under dual repression-bindin ...	0.74	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				943
Q59NG5 UniProt NPD GO	MUS81_CANAL	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.74	-	nuc	0	Nucleus (By similarity)				614
O15320 UniProt NPD GO	CTGE5_HUMAN	Cutaneous T-cell lymphoma-associated antigen 5 (cTAGE-5 protein) (cTAGE family member 5) (Meningioma ...	0.74	-	nuc	1 *			602132		804
Q9Y2D1 UniProt NPD GO	ATF5_HUMAN	Cyclic AMP-dependent transcription factor ATF-5 (Activating transcription factor 5) (Transcription f ...	0.74	+	nuc	0	Cytoplasm. Nucleus		606398		282
P14579 UniProt NPD GO	CP4A5_RABIT	Cytochrome P450 4A5 precursor (EC 1.14.15.3) (CYPIVA5) (Lauric acid omega-hydroxylase)	0.74	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				511
Q8N118 UniProt NPD GO	CP4X1_HUMAN	Cytochrome P450 4X1 (EC 1.14.14.1) (CYPIVX1)	0.74	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				509
Q5APC8 UniProt NPD GO	DAM1_CANAL	DASH complex subunit DAM1 (Outer kinetochore protein DAM1)	0.74	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				277
Q99J72 UniProt NPD GO	ABEC3_MOUSE	DNA dC->dU-editing enzyme APOBEC-3 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing complex 3) (Arp3) (CE ...	0.74	-	nuc	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				429
Q6FNX0 UniProt NPD GO	LCD1_CANGA	DNA damage checkpoint protein LCD1	0.74	+	end	0	Cytoplasm (By similarity). Nucleus (By similarity)				667
P04053 UniProt NPD GO	TDT_HUMAN	DNA nucleotidylexotransferase (EC 2.7.7.31) (Terminal addition enzyme) (Terminal deoxynucleotidyltra ...	0.74	-	cyt	0	Nucleus		187410	2COE	509
P33609 UniProt NPD GO	DPOLA_MOUSE	DNA polymerase alpha catalytic subunit (EC 2.7.7.7)	0.74	+	cyt	0	Nucleus				1465
P27727 UniProt NPD GO	DPOLA_TRYBB	DNA polymerase alpha catalytic subunit (EC 2.7.7.7) (DNA polymerase I)	0.74	-	nuc	0	Nucleus				1339
P97283 UniProt NPD GO	DPOD1_MESAU	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.74	+	cyt	0	Nucleus				1103
P54358 UniProt NPD GO	DPOD_DROME	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.74	-	cyt	0	Nucleus				1092
P30316 UniProt NPD GO	DPOD_SCHPO	DNA polymerase delta catalytic subunit (EC 2.7.7.7) (DNA polymerase III)	0.74	+	cyt	0	Nucleus	delta DNA polymerase complex [TAS]			1086
Q6FSK8 UniProt NPD GO	DPB2_CANGA	DNA polymerase epsilon subunit B (EC 2.7.7.7) (DNA polymerase II subunit B)	0.74	-	nuc	0	Nucleus (By similarity)				719
Q756F4 UniProt NPD GO	RAD52_ASHGO	DNA repair and recombination protein RAD52	0.74	-	nuc	0	Nucleus (By similarity)				435
P14746 UniProt NPD GO	REC1_USTMA	DNA repair exonuclease REC1 (EC 3.1.11.2)	0.74	-	nuc	0	Nucleus (Potential)				522
Q38861 UniProt NPD GO	XPB1_ARATH	DNA repair helicase XPB1 (EC 3.6.1.-) (XPB homolog 1) (ERCC3 homolog 1) (RAD25 homolog 1) (AtXPB1) ( ...	0.74	-	nuc	0	Nucleus (Probable)				767
Q01320 UniProt NPD GO	TOP2A_MOUSE	DNA topoisomerase 2-alpha (EC 5.99.1.3) (DNA topoisomerase II, alpha isozyme)	0.74	+	nuc	0	Nucleus	condensed chromosome [IDA] nucleolus [IDA]			1528
P42698 UniProt NPD GO	DR111_ARATH	DNA-damage-repair/toleration protein DRT111, chloroplast precursor	0.74	-	nuc	0	Plastid; chloroplast				387
P91875 UniProt NPD GO	RPA1_DROME	DNA-directed RNA polymerase I largest subunit (EC 2.7.7.6)	0.74	-	cyt	0	Nucleus				1642
Q8K202 UniProt NPD GO	RPF53_MOUSE	DNA-directed RNA polymerase I-associated factor 53 kDa subunit (EC 2.7.7.6) (RNA polymerase I-associ ...	0.74	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			482
Q9XPS8 UniProt NPD GO	RPOC1_WHEAT	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.74	-	cyt	0	Plastid; chloroplast				683
Q8R1A4 UniProt NPD GO	DOCK7_MOUSE	Dedicator of cytokinesis protein 7 (Fragment)	0.74	-	mit	0					727
Q9SVX5 UniProt NPD GO	DRE2F_ARATH	Dehydration-responsive element-binding protein 2F (DREB2F protein)	0.74	-	nuc	0	Nucleus (Probable)				277
Q01583 UniProt NPD GO	DGK1_DROME	Diacylglycerol kinase 1 (EC 2.7.1.107) (Diglyceride kinase 1) (DGK 1) (DAG kinase 1)	0.74	-	nuc	0					1020
Q09790 UniProt NPD GO	APS1_SCHPO	Diphosphoinositol polyphosphate phosphohydrolase aps1 (EC 3.6.1.52) (Diadenosine 5',5'''-P1,P6-hexap ...	0.74	+	nuc	0					210
O75165 UniProt NPD GO	DNJCD_HUMAN	DnaJ homolog subfamily C member 13 (Required for receptor-mediated endocytosis 8)	0.74	-	mit	0					2243
Q5ZI13 UniProt NPD GO	DNJC3_CHICK	DnaJ homolog subfamily C member 3	0.74	-	nuc	0					503
Q7ZW47 UniProt NPD GO	STAU2_BRARE	Double-stranded RNA-binding protein Staufen homolog 2	0.74	-	nuc	0					606
O60469 UniProt NPD GO	DSCAM_HUMAN	Down syndrome cell adhesion molecule precursor (CHD2)	0.74	-	exc	1	Isoform Long: Cell membrane; single-pass type I membrane protein (Potential). Isoform Short: Secrete ...	integral to plasma membrane [TAS] membrane fraction [TAS] plasma membrane [TAS]	602523		2012
P78716 UniProt NPD GO	DYHC_FUSSO	Dynein heavy chain, cytosolic (DYHC)	0.74	-	nuc	0	Cytoplasm				4349
Q8CFI0 UniProt NPD GO	NED4L_MOUSE	E3 ubiquitin-protein ligase NEDD4-like protein (EC 6.3.2.-) (Nedd4-2) (NEDD4.2)	0.74	-	nuc	0	Cytoplasm			1WR7	1004
P34021 UniProt NPD GO	ECR_DROME	Ecdysone receptor (Ecdysteroid receptor) (20-hydroxy-ecdysone receptor) (20E receptor) (EcRH)	0.74	-	nuc	0	Nucleus	cytoplasm [IDA] ecdysone receptor holocomplex [TAS] nucleus [IDA]		1R0O	878
O18531 UniProt NPD GO	ECR_LUCCU	Ecdysone receptor (Ecdysteroid receptor) (20-hydroxy-ecdysone receptor) (20E receptor) (EcRH)	0.74	-	nuc	0	Nucleus				757
P17671 UniProt NPD GO	E75BC_DROME	Ecdysone-induced protein 75B isoforms C/D (E75-A)	0.74	-	nuc	0	Nucleus (Potential)				1199
Q28470 UniProt NPD GO	EDN2_MACFA	Endothelin-2 (ET-2) (Preproendothelin-2) (PPET2) (Fragment)	0.74	-	mit	0	Secreted protein				79
Q5NRQ0 UniProt NPD GO	EDN2_FELCA	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2)	0.74	-	exc	0	Secreted protein (By similarity)				178
Q4I5V3 UniProt NPD GO	EPL1_GIBZE	Enhancer of polycomb-like protein 1	0.74	-	mit	0	Nucleus (By similarity)				644
Q01071 UniProt NPD GO	ESMD_DROME	Enhancer of split mdelta protein (E(spl)mdelta) (HLH-mdelta) (Split locus enhancer protein mC)	0.74	-	nuc	0	Nucleus (Probable)				173
Q8R0W0 UniProt NPD GO	EPIPL_MOUSE	Epiplakin	0.74	-	nuc	0		cytoplasm [IDA]			6548
P49884 UniProt NPD GO	ESR1_BOVIN	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.74	+	nuc	0	Nucleus				596
P03372 UniProt NPD GO	ESR1_HUMAN	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.74	+	nuc	0	Nucleus	chromatin remodeling complex [NAS] membrane [NAS]	133430	3ERT	595
P06211 UniProt NPD GO	ESR1_RAT	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.74	+	nuc	0	Nucleus	nucleus [IMP]			600
Q04660 UniProt NPD GO	ERB1_YEAST	Eukaryotic ribosome biogenesis protein 1	0.74	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			807
P20042 UniProt NPD GO	IF2B_HUMAN	Eukaryotic translation initiation factor 2 subunit 2 (Eukaryotic translation initiation factor 2 sub ...	0.74	+	nuc	0		eukaryotic translation initiation factor 2 ... [TAS]	603908		333
P41035 UniProt NPD GO	IF2B_RABIT	Eukaryotic translation initiation factor 2 subunit 2 (Eukaryotic translation initiation factor 2 sub ...	0.74	+	nuc	0					333

You are viewing entries 11751 to 11800 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.