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
Q9D5R2 UniProt NPD GO	WDR20_MOUSE	WD repeat protein 20	0.34	-	nuc	0					567
Q8BND3 UniProt NPD GO	WDR35_MOUSE	WD repeat protein 35	0.34	-	nuc	0					1181
Q5R9T6 UniProt NPD GO	WDR55_PONPY	WD repeat protein 55	0.34	-	cyt	0					383
P43582 UniProt NPD GO	YFB0_YEAST	WW domain-containing protein YFL010C	0.34	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			211
P29181 UniProt NPD GO	TXW7_NAJNA	Weak neurotoxin 7	0.34	-	nuc	0	Secreted protein			1LQ3	65
Q9LLL8 UniProt NPD GO	XSP1_ARATH	Xylem serine proteinase 1 precursor (EC 3.4.21.-) (AtXSP1) (Cucumisin-like protein)	0.34	-	exc	0					749
P06675 UniProt NPD GO	ZEA4_MAIZE	Zein-alpha 19B1 precursor (19 kDa zein 19B1)	0.34	-	exc	0					234
P08416 UniProt NPD GO	ZEA5_MAIZE	Zein-alpha GZ19AB11 precursor (19 kDa zein GZ19AB11)	0.34	-	exc	0					234
P04704 UniProt NPD GO	ZEA2_MAIZE	Zein-alpha ZG99 precursor (19 kDa zein ZG99)	0.34	-	exc	0					235
O70418 UniProt NPD GO	ZN179_RAT	Zinc finger protein 179 (Brain finger protein)	0.34	-	nuc	2					631
Q9ULX5 UniProt NPD GO	ZN179_HUMAN	Zinc finger protein 179 (Brain finger protein) (RING finger protein 112)	0.34	-	nuc	2			601237		632
Q7TNU6 UniProt NPD GO	ZN250_MOUSE	Zinc finger protein 250 (Zinc finger protein 647)	0.34	-	nuc	0	Nucleus (Probable)				535
Q9Y508 UniProt NPD GO	ZN313_HUMAN	Zinc finger protein 313 (RING finger protein 114)	0.34	-	nuc	0					228
Q96BR6 UniProt NPD GO	ZN669_HUMAN	Zinc finger protein 669	0.34	-	nuc	0	Nucleus (Probable)				464
Q20176 UniProt NPD GO	NAS39_CAEEL	Zinc metalloproteinase nas-39 precursor (EC 3.4.24.21) (Nematode astacin 39)	0.34	-	end	1 *	Secreted protein (Potential)				951
Q07287 UniProt NPD GO	ZP4_PIG	Zona pellucida sperm-binding protein 4 precursor (Zona pellucida sperm-binding protein B) (Zona pell ...	0.34	-	exc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				536
Q96UX3 UniProt NPD GO	KAPR_ASPFU	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.34	-	nuc	0					413
Q28055 UniProt NPD GO	ARP19_BOVIN	cAMP-regulated phosphoprotein 19 (ARPP-19)	0.34	-	nuc	0	Cytoplasm				111
Q13976 UniProt NPD GO	KGP1A_HUMAN	cGMP-dependent protein kinase 1, alpha isozyme (EC 2.7.11.12) (CGK 1 alpha) (cGKI-alpha)	0.34	-	cyt	0			176894	1ZXA	670
O77676 UniProt NPD GO	KGP1A_RABIT	cGMP-dependent protein kinase 1, alpha isozyme (EC 2.7.11.12) (CGK 1 alpha) (cGKI-alpha)	0.34	-	cyt	0					670
Q6CKU1 UniProt NPD GO	YTH1_KLULA	mRNA 3'-end-processing protein YTH1	0.34	-	nuc	0	Nucleus (By similarity)				210
Q9UBP6 UniProt NPD GO	TRMB_HUMAN	tRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) (tRNA(m7G46)-methyltransferase) (Methyltransfer ...	0.34	-	cyt	0			604466		276
P15455 UniProt NPD GO	12S1_ARATH	12S seed storage protein CRA1 precursor [Contains: 12S seed storage protein CRA1 alpha chain (12S se ...	0.33	-	exc	0					472
Q5PRD0 UniProt NPD GO	143BB_BRARE	14-3-3 protein beta/alpha-B	0.33	-	nuc	0	Cytoplasm (By similarity)				244
Q9C5W6 UniProt NPD GO	14312_ARATH	14-3-3-like protein GF14 iota (General regulatory factor 12)	0.33	-	nuc	0					268
O14126 UniProt NPD GO	PRS6A_SCHPO	26S protease regulatory subunit 6A	0.33	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				438
P32496 UniProt NPD GO	RPN12_YEAST	26S proteasome regulatory subunit RPN12 (Nuclear integrity protein 1)	0.33	-	nuc	0		proteasome regulatory particle, lid subcomp... [IPI]			273
P34135 UniProt NPD GO	HMDH1_DICDI	3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (EC 1.1.1.34) (HMG-CoA reductase 1)	0.33	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				552
P52410 UniProt NPD GO	KASC1_ARATH	3-oxoacyl-[acyl-carrier-protein] synthase I, chloroplast precursor (EC 2.3.1.41) (Beta-ketoacyl-ACP ...	0.33	-	mit	0	Plastid; chloroplast				473
Q3T0V4 UniProt NPD GO	RS11_BOVIN	40S ribosomal protein S11	0.33	-	cyt	0					157
P62280 UniProt NPD GO	RS11_HUMAN	40S ribosomal protein S11	0.33	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	180471		157
P61270 UniProt NPD GO	RS11_MACFA	40S ribosomal protein S11	0.33	-	cyt	0					157
P62281 UniProt NPD GO	RS11_MOUSE	40S ribosomal protein S11	0.33	-	cyt	0					157
P62282 UniProt NPD GO	RS11_RAT	40S ribosomal protein S11	0.33	-	cyt	0					157
Q56JU9 UniProt NPD GO	RS24_BOVIN	40S ribosomal protein S24	0.33	-	nuc	0					131
Q5RAQ8 UniProt NPD GO	RS24_PONPY	40S ribosomal protein S24	0.33	-	nuc	0					131
Q94G66 UniProt NPD GO	RS25_AMACR	40S ribosomal protein S25	0.33	-	nuc	0					114
Q3E792 UniProt NPD GO	RS25A_YEAST	40S ribosomal protein S25-A precursor (S31) (YS23) (RP45)	0.33	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			108
P27923 UniProt NPD GO	RS27A_MAIZE	40S ribosomal protein S27a	0.33	+	nuc	0					79
P61246 UniProt NPD GO	RS3A_FELCA	40S ribosomal protein S3a (Fragment)	0.33	+	cyt	0					260
P48155 UniProt NPD GO	RS7_MANSE	40S ribosomal protein S7	0.33	-	nuc	0					190
Q9UGI9 UniProt NPD GO	AAKG3_HUMAN	5'-AMP-activated protein kinase subunit gamma-3 (AMPK gamma-3 chain) (AMPK gamma3)	0.33	-	end	0			604976		489
P17643 UniProt NPD GO	TYRP1_HUMAN	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (EC 1.14.18.-) (DHICA oxidase) (Tyrosinase-r ...	0.33	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (Potential)	melanosome [ISS]	278400		537
O42385 UniProt NPD GO	5HT1A_FUGRU	5-hydroxytryptamine 1A-alpha receptor (5-HT-1A-alpha) (Serotonin receptor 1A-alpha) (5-HT1A-alpha) ( ...	0.33	-	end	7 *	Membrane; multi-pass membrane protein				423
P35404 UniProt NPD GO	5HT1B_DIDMA	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B)	0.33	-	end	7 *	Membrane; multi-pass membrane protein				388
P35563 UniProt NPD GO	5HT3R_RAT	5-hydroxytryptamine 3 receptor precursor (5-HT-3) (Serotonin-gated ion channel receptor) (5-HT3R)	0.33	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			483
P49163 UniProt NPD GO	RK22_MEDSA	50S ribosomal protein L22, chloroplast precursor (CL22)	0.33	-	nuc	0	Plastid; chloroplast				200
O80360 UniProt NPD GO	RK3_TOBAC	50S ribosomal protein L3, chloroplast precursor (Fragment)	0.33	-	mit	0	Plastid; chloroplast (Potential)				259
Q9HGZ1 UniProt NPD GO	K6PF1_ASPOR	6-phosphofructokinase subunit alpha (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (6PF-1 ...	0.33	+	cyt	0	Cytoplasm (By similarity)				785
Q95307 UniProt NPD GO	RL13A_PIG	60S ribosomal protein L13a (Fragment)	0.33	-	cyt	0					137

You are viewing entries 37251 to 37300 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.