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
P91613 UniProt NPD GO	PER_DROIN	Period circadian protein (Fragment)	0.23	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				391
P91697 UniProt NPD GO	PER_DROPU	Period circadian protein (Fragment)	0.23	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				396
P91716 UniProt NPD GO	PER_DROTP	Period circadian protein (Fragment)	0.23	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				390
Q9FLC0 UniProt NPD GO	PER52_ARATH	Peroxidase 52 precursor (EC 1.11.1.7) (Atperox P52) (ATP49)	0.23	-	exc	0	Secreted protein (By similarity)				324
P17179 UniProt NPD GO	PER2_ARMRU	Peroxidase C2 precursor (EC 1.11.1.7)	0.23	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				347
P28313 UniProt NPD GO	PER_ARTRA	Peroxidase precursor (EC 1.11.1.7)	0.23	-	cyt	0	Secreted protein			1HSR	364
Q08426 UniProt NPD GO	ECHP_HUMAN	Peroxisomal bifunctional enzyme (PBE) (PBFE) [Includes: Enoyl-CoA hydratase (EC 4.2.1.17); 3,2-trans ...	0.23	-	pox	0	Peroxisome	peroxisome [TAS]	607037		722
O43808 UniProt NPD GO	PM34_HUMAN	Peroxisomal membrane protein PMP34 (34 kDa peroxisomal membrane protein) (Solute carrier family 25 m ...	0.23	-	end	5 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to plasma membrane [TAS] peroxisome [TAS]	606795		307
Q8VC48 UniProt NPD GO	PEX12_MOUSE	Peroxisome assembly protein 12 (Peroxin-12)	0.23	-	cyt	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				359
Q9NSD9 UniProt NPD GO	SYFB_HUMAN	Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chain) (PheRS ...	0.23	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [TAS] soluble fraction [TAS]	609690		589
Q4KLJ8 UniProt NPD GO	PDCL3_RAT	Phosducin-like protein 3	0.23	-	cyt	0	Cytoplasm (By similarity)				240
P53760 UniProt NPD GO	LCAT_CHICK	Phosphatidylcholine-sterol acyltransferase precursor (EC 2.3.1.43) (Lecithin-cholesterol acyltransfe ...	0.23	-	exc	0					413
Q1LZA4 UniProt NPD GO	PIGW_BOVIN	Phosphatidylinositol-glycan biosynthesis class W protein (EC 2.3.-.-) (PIG-W)	0.23	+	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				503
Q9M571 UniProt NPD GO	PEAMT_SPIOL	Phosphoethanolamine N-methyltransferase (EC 2.1.1.103)	0.23	-	cyt	0	Cytoplasm				494
Q9M4G5 UniProt NPD GO	PGMP_SOLTU	Phosphoglucomutase, chloroplast precursor (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.23	-	mit	0	Plastid; chloroplast				632
P14555 UniProt NPD GO	PA2GA_HUMAN	Phospholipase A2, membrane associated precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) ( ...	0.23	-	nuc	1 *	Membrane; peripheral membrane protein	extracellular region [TAS]	172411	2GNY	144
P00614 UniProt NPD GO	PA21B_OXYSC	Phospholipase A2, taipoxin alpha chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.23	-	nuc	0	Secreted protein			1LX1	119
Q9XJ56 UniProt NPD GO	ECP44_DAUCA	Phosphoprotein ECPP44	0.23	-	nuc	1					258
P52422 UniProt NPD GO	PUR3_ARATH	Phosphoribosylglycinamide formyltransferase, chloroplast precursor (EC 2.1.2.2) (GART) (GAR transfor ...	0.23	-	cyt	0	Plastid; chloroplast				292
P00518 UniProt NPD GO	PHKG1_RABIT	Phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (EC 2.7.11.19) (Phosphorylase ...	0.23	-	cyt	0				2PHK	386
P19107 UniProt NPD GO	ARRB_DROME	Phosrestin-1 (Phosrestin I) (Arrestin B) (Arrestin-2) (49 kDa arrestin-like protein)	0.23	-	cyt	0		membrane fraction [IDA] rhabdomere [IDA] soluble fraction [IDA]			401
P19108 UniProt NPD GO	ARRB_DROMI	Phosrestin-1 (Phosrestin I) (Arrestin B) (Arrestin-2) (49 kDa arrestin-like protein)	0.23	-	cyt	0					401
P61843 UniProt NPD GO	YCF3_ARATH	Photosystem I assembly protein ycf3	0.23	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
Q53CF3 UniProt NPD GO	YCF3_BRAJU	Photosystem I assembly protein ycf3	0.23	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
O20031 UniProt NPD GO	YCF3_CHLRE	Photosystem I assembly protein ycf3	0.23	-	mit	0	Thylakoid membrane-associated	thylakoid [IDA]			172
P48191 UniProt NPD GO	YCF3_CYAPA	Photosystem I assembly protein ycf3	0.23	-	cyt	0	Plastid; cyanelle; cyanelle thylakoid membrane; peripheral membrane protein (By similarity)				173
P0C160 UniProt NPD GO	YCF3_SACHY	Photosystem I assembly protein ycf3	0.23	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				170
P61844 UniProt NPD GO	YCF3_SINAL	Photosystem I assembly protein ycf3	0.23	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
P27324 UniProt NPD GO	YCF3_MAIZE	Photosystem I assembly protein ycf3 (IRF170)	0.23	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				170
Q6ENG3 UniProt NPD GO	YCF4_ORYNI	Photosystem I assembly protein ycf4	0.23	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
P12206 UniProt NPD GO	YCF4_ORYSA	Photosystem I assembly protein ycf4	0.23	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
P13192 UniProt NPD GO	PSAF_HORVU	Photosystem I reaction center subunit III, chloroplast precursor (Light-harvesting complex I 17 kDa ...	0.23	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				235
P42500 UniProt NPD GO	PHYA_SOYBN	Phytochrome A	0.23	-	mit	0					1131
Q9R006 UniProt NPD GO	PRLPF_RAT	Placental prolactin-like protein F precursor (PRL-like protein F) (PLP-F)	0.23	-	exc	0	Secreted protein (By similarity)				250
Q9QUN5 UniProt NPD GO	PRLPI_MOUSE	Placental prolactin-like protein I precursor (PRL-like protein I) (PLP-I) (Decidualin) (Prolactin-li ...	0.23	-	mit	1 *	Secreted protein (By similarity)				212
Q9JII3 UniProt NPD GO	PRLPM_RAT	Placental prolactin-like protein M precursor (PRL-like protein M) (PLP-M)	0.23	-	nuc	0	Secreted protein (By similarity)				228
P28876 UniProt NPD GO	PMA2_SCHPO	Plasma membrane ATPase 2 (EC 3.6.3.6) (Proton pump 2)	0.23	+	end	9	Cell membrane; multi-pass membrane protein				1010
Q03194 UniProt NPD GO	PMA4_NICPL	Plasma membrane ATPase 4 (EC 3.6.3.6) (Proton pump 4)	0.23	-	end	9	Cell membrane; multi-pass membrane protein				952
Q9R0K7 UniProt NPD GO	AT2B2_MOUSE	Plasma membrane calcium-transporting ATPase 2 (EC 3.6.3.8) (PMCA2) (Plasma membrane calcium pump iso ...	0.23	+	end	8	Cell membrane; multi-pass membrane protein				1198
P30059 UniProt NPD GO	RR11_EPIVI	Plastid 30S ribosomal protein S11	0.23	-	mit	0	Plastid				136
P30055 UniProt NPD GO	RR3_EPIVI	Plastid 30S ribosomal protein S3	0.23	-	cyt	0	Plastid				220
P31209 UniProt NPD GO	PABP_SCHPO	Polyadenylate-binding protein (Poly(A)-binding protein) (PABP)	0.23	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			653
Q75AV4 UniProt NPD GO	PFS2_ASHGO	Polyadenylation factor subunit 2	0.23	-	nuc	0	Nucleus (By similarity)				449
Q6CP71 UniProt NPD GO	PFS2_KLULA	Polyadenylation factor subunit 2	0.23	-	nuc	0	Nucleus (By similarity)				452
Q6CGP9 UniProt NPD GO	PFS2_YARLI	Polyadenylation factor subunit 2	0.23	-	mit	0	Nucleus (By similarity)				532
Q08306 UniProt NPD GO	PPOD_LYCES	Polyphenol oxidase D, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.23	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				591
Q6ICX4 UniProt NPD GO	PTBP3_ARATH	Polypyrimidine tract-binding protein homolog 3	0.23	-	nuc	0	Nucleus (Probable)				432
Q38898 UniProt NPD GO	AKT2_ARATH	Potassium channel AKT2/3	0.23	+	nuc	7	Membrane; multi-pass membrane protein				802
Q9M8S6 UniProt NPD GO	SKOR_ARATH	Potassium channel SKOR (Stelar K(+) outward rectifying channel)	0.23	+	end	5	Membrane; multi-pass membrane protein				828
Q10726 UniProt NPD GO	KAX61_PANIM	Potassium channel toxin alpha-KTx 6.1 (Potassium channel-blocking toxin 1) (Pi1) (Pi-1) (PiTX-K-gamm ...	0.23	-	nuc	0	Secreted protein			1WZ5	35

You are viewing entries 47701 to 47750 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.