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
Q9W4Y2 UniProt NPD GO	PDFR_DROME	PDF receptor (Protein groom-of-PDF)	0.39	-	end	7	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]			669
Q16633 UniProt NPD GO	OBF1_HUMAN	POU domain class 2-associating factor 1 (B-cell-specific coactivator OBF-1) (OCT-binding factor 1) ( ...	0.39	-	nuc	0	Nucleus		601206	1CQT	256
Q12006 UniProt NPD GO	PFA4_YEAST	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.39	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				378
Q9UQ90 UniProt NPD GO	SPG7_HUMAN	Paraplegin (EC 3.4.24.-) (Spastic paraplegia protein 7)	0.39	+	cyt	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrion [TAS]	607259		795
Q27384 UniProt NPD GO	API_DIRIM	Pepsin inhibitor Dit33 precursor	0.39	+	nuc	0	Secreted protein				234
Q718F4 UniProt NPD GO	KB1_MESMA	Peptide BmKb1 precursor (Anti-microbial peptide-like protein) (BmKb1*) (BmKb1') (Toxin peptide 6)	0.39	-	end	1 *	Secreted protein				74
O60683 UniProt NPD GO	PEX10_HUMAN	Peroxisome assembly protein 10 (Peroxin-10) (Peroxisome biogenesis factor 10) (RING finger protein 6 ...	0.39	-	cyt	1	Peroxisome; peroxisomal membrane; peripheral membrane protein (Potential)	peroxisomal membrane [NAS]	602859		326
O18971 UniProt NPD GO	PPARG_BOVIN	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.39	+	cyt	0	Nucleus				505
P57797 UniProt NPD GO	PPARG_CRIGR	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.39	+	cyt	0	Nucleus				475
Q9W1V6 UniProt NPD GO	PRPA3_DROME	Phenoloxidase subunit A3 precursor (EC 1.14.18.1) (Tyrosinase A3) (PO A3)	0.39	-	cyt	0	Secreted protein (By similarity)	extracellular region [IDA]			683
Q9SLX9 UniProt NPD GO	VPS_PSINU	Phloroisovalerophenone synthase (EC 2.3.1.156) (Valerophenone synthase) (3-methyl-1-(trihydroxypheny ...	0.39	-	cyt	0					406
P37822 UniProt NPD GO	AROG_SOLTU	Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplast precursor (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.39	-	mit	0	Plastid; chloroplast				511
P04711 UniProt NPD GO	CAPP1_MAIZE	Phosphoenolpyruvate carboxylase 1 (EC 4.1.1.31) (PEPCase 1) (PEPC 1)	0.39	-	nuc	0	Cytoplasm			1JQO	970
P15804 UniProt NPD GO	CAPP3_SORBI	Phosphoenolpyruvate carboxylase 3 (EC 4.1.1.31) (PEPCase 3) (PEPC 3) (CP46)	0.39	-	nuc	0	Cytoplasm				960
O08589 UniProt NPD GO	PLM_RAT	Phospholemman precursor (FXYD domain-containing ion transport regulator 1)	0.39	-	exc	1 *	Membrane; single-pass type I membrane protein	integral to membrane [TAS]			92
P12401 UniProt NPD GO	PRP2_BOVIN	Placental prolactin-related protein 2 precursor (PRC-II) (bPRCII)	0.39	-	mit	0	Secreted protein				267
P12402 UniProt NPD GO	PRP3_BOVIN	Placental prolactin-related protein 3 precursor (PRC-III) (bPRCIII)	0.39	-	exc	0	Secreted protein				213
P34768 UniProt NPD GO	RK2_ASTLO	Plastid 50S ribosomal protein L2	0.39	-	mit	0	Plastid				274
Q9TJR5 UniProt NPD GO	RK32_PROWI	Plastid 50S ribosomal protein L32	0.39	-	nuc	0	Plastid				47
Q9LFV0 UniProt NPD GO	RRP32_ARATH	Plastid-specific 30S ribosomal protein 3-2, chloroplast precursor (PSRP-3 2)	0.39	-	mit	0	Plastid; chloroplast (By similarity)				183
Q9Y5J5 UniProt NPD GO	PHLA3_HUMAN	Pleckstrin homology-like domain family A member 3 (TDAG51/Ipl homolog 1)	0.39	-	nuc	0			607054		127
Q9WV95 UniProt NPD GO	PHLA3_MOUSE	Pleckstrin homology-like domain family A member 3 (TDAG51/Ipl homolog 1)	0.39	-	nuc	0					125
Q9M9E1 UniProt NPD GO	PDR12_ARATH	Pleiotropic drug resistance protein 12	0.39	-	end	13	Cell membrane; multi-pass membrane protein	plasma membrane [IDA]			1423
Q91ZV7 UniProt NPD GO	PXDC1_MOUSE	Plexin domain-containing protein 1 precursor (Tumor endothelial marker 7)	0.39	-	end	1	Membrane; single-pass type I membrane protein (Potential)				500
O88554 UniProt NPD GO	PARP2_MOUSE	Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30) (PARP-2) (NAD(+) ADP-ribosyltransferase 2) (Poly[ADP-ri ...	0.39	-	nuc	0	Nucleus	nucleus [IDA]		1GS0	559
P34678 UniProt NPD GO	GALT3_CAEEL	Polypeptide N-acetylgalactosaminyltransferase 3 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.39	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				612
P48363 UniProt NPD GO	PFD3_YEAST	Prefoldin subunit 3 (Genes involved in microtubule biogenesis protein 2) (Gim complex subunit 2) (Gi ...	0.39	-	nuc	0		cytoplasm [IDA] prefoldin complex [IPI]			199
Q01570 UniProt NPD GO	SECA_PAVLU	Preprotein translocase secA subunit	0.39	-	mit	0	Plastid; chloroplast				891
Q5AEM8 UniProt NPD GO	PAM17_CANAL	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.39	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				185
Q8NDV2 UniProt NPD GO	GPR26_HUMAN	Probable G-protein coupled receptor 26	0.39	-	end	6 *	Membrane; multi-pass membrane protein		604847		337
Q9BY21 UniProt NPD GO	GPR87_HUMAN	Probable G-protein coupled receptor 87 (G-protein coupled receptor 95)	0.39	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	606379		358
P90789 UniProt NPD GO	NDUB7_CAEEL	Probable NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 (EC 1.6.5.3) (EC 1.6.99.3)	0.39	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side				123
Q94A82 UniProt NPD GO	NUD19_ARATH	Probable NADH pyrophosphatase NUDT19, chloroplast precursor (EC 3.6.1.22) (Nudix hydrolase 19) (AtNU ...	0.39	-	mit	0	Plastid; chloroplast (Potential)				438
Q9SCQ7 UniProt NPD GO	AN32_ARATH	Probable acidic leucine-rich nuclear phosphoprotein 32-related protein (ANP32/acidic nuclear phospho ...	0.39	-	cyt	0					447
Q27533 UniProt NPD GO	YH2M_CAEEL	Probable cation-transporting ATPase W08D2.5 in chromosome IV (EC 3.6.3.-)	0.39	-	end	11 *	Membrane; multi-pass membrane protein				1256
Q9V8M2 UniProt NPD GO	C12B2_DROME	Probable cytochrome P450 12b2, mitochondrial precursor (EC 1.14.-.-) (CYPXIIB2)	0.39	-	mit	0	Mitochondrion (Potential)				561
Q9VMS8 UniProt NPD GO	C4AC2_DROME	Probable cytochrome P450 4ac2 (EC 1.14.-.-) (CYPIVAC2)	0.39	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				497
Q95KJ0 UniProt NPD GO	DIMH_MACFA	Probable dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N',N'-adenosyl(rRNA) dim ...	0.39	-	nuc	0	Nucleus; nucleolus (By similarity)				313
Q9S825 UniProt NPD GO	IF5Z_ARATH	Probable eukaryotic translation initiation factor 5-2 (eIF-5 2)	0.39	+	nuc	0					437
Q9SJP2 UniProt NPD GO	FUT4_ARATH	Probable fucosyltransferase 4 (EC 2.4.1.-) (AtFUT4)	0.39	-	end	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				503
Q22949 UniProt NPD GO	PLSB_CAEEL	Probable glycerol-3-phosphate acyltransferase, mitochondrial precursor (EC 2.3.1.15) (GPAT)	0.39	-	nuc	0	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				718
Q1SU99 UniProt NPD GO	H2B3_MEDTR	Probable histone H2B.3	0.39	+	nuc	0	Nucleus (By similarity)				137
O02161 UniProt NPD GO	TIM44_CAEEL	Probable import inner membrane translocase subunit TIM44, mitochondrial precursor	0.39	-	mit	0	Mitochondrion; mitochondrial inner membrane (Potential)				425
Q753W9 UniProt NPD GO	SPC24_ASHGO	Probable kinetochore protein SPC24	0.39	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				204
Q10175 UniProt NPD GO	FKBPH_SCHPO	Probable peptidyl-prolyl cis-trans isomerase C27F1.06c (EC 5.2.1.8) (PPIase) (Rotamase)	0.39	-	nuc	0					362
P98198 UniProt NPD GO	AT8B2_HUMAN	Probable phospholipid-transporting ATPase ID (EC 3.6.3.1) (ATPase class I type 8B member 2)	0.39	-	end	9	Membrane; multi-pass membrane protein		605867		1209
P98199 UniProt NPD GO	AT8B2_MOUSE	Probable phospholipid-transporting ATPase ID (EC 3.6.3.1) (ATPase class I type 8B member 2) (Fragmen ...	0.39	-	end	6 *	Membrane; multi-pass membrane protein				347
Q9NY28 UniProt NPD GO	GALT8_HUMAN	Probable polypeptide N-acetylgalactosaminyltransferase 8 (EC 2.4.1.41) (Protein-UDP acetylgalactosam ...	0.39	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		606250		637
P43293 UniProt NPD GO	NAK_ARATH	Probable serine/threonine-protein kinase NAK (EC 2.7.11.1)	0.39	-	nuc	0					389
Q9NQC7 UniProt NPD GO	CYLD_HUMAN	Probable ubiquitin carboxyl-terminal hydrolase CYLD (EC 3.1.2.15) (Ubiquitin thioesterase CYLD) (Ubi ...	0.39	-	cyt	0	Cytoplasm; perinuclear region	cytoskeleton [NAS]	132700	1WHM	956

You are viewing entries 32851 to 32900 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.