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
Q6IE40 UniProt NPD GO	WFD12_RAT	WAP four-disulfide core domain protein 12 precursor	0.02	-	vac	0	Secreted protein (Potential)	extracellular space [ISS]			78
Q9Y6I7 UniProt NPD GO	WSB1_HUMAN	WD repeat and SOCS box-containing protein 1 (WSB-1) (SOCS box-containing WD protein SWiP-1)	0.02	-	cyt	0					421
O93277 UniProt NPD GO	WDR1_CHICK	WD repeat protein 1 (Actin-interacting protein 1) (AIP1)	0.02	-	cyt	0					609
O88342 UniProt NPD GO	WDR1_MOUSE	WD repeat protein 1 (Actin-interacting protein 1) (AIP1)	0.02	-	cyt	0					605
Q12788 UniProt NPD GO	TBL3_HUMAN	WD repeat protein SAZD (Transducin beta-like 3 protein)	0.02	-	mit	0	Nucleus; nucleolus		605915		519
O22468 UniProt NPD GO	MSI2_ARATH	WD-40 repeat protein MSI2	0.02	-	cyt	0	Nucleus (By similarity)				415
Q01482 UniProt NPD GO	WIR1A_WHEAT	WIR1A protein	0.02	-	gol	1 *	Membrane; single-pass type II membrane protein (Probable)				88
Q01481 UniProt NPD GO	WIR1B_WHEAT	WIR1B protein	0.02	-	cyt	1 *	Membrane; single-pass type II membrane protein (Probable)				85
P35921 UniProt NPD GO	WWA3_ACHFU	WWamide-3	0.02	-		0					7
P29179 UniProt NPD GO	TXW5_NAJNA	Weak neurotoxin 5	0.02	-	nuc	0	Secreted protein			1LN7	62
Q02243 UniProt NPD GO	WIN_SOYBN	Wound-induced protein (Fragment)	0.02	-	cyt	0					102
Q5GH62 UniProt NPD GO	XKR9_MOUSE	XK-related protein 9	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				373
Q8L5C6 UniProt NPD GO	XIP1_WHEAT	Xylanase inhibitor protein 1 precursor (Class III chitinase homolog) (XIP-I protein)	0.02	-	exc	1 *	Secreted protein (Potential)			1TE1	304
Q76BW5 UniProt NPD GO	XTH8_ORYSA	Xyloglucan endotransglycosylase/hydrolase protein 8 precursor (EC 2.4.1.207) (End-xyloglucan transfe ...	0.02	-	exc	1 *	Secreted protein; extracellular space; apoplast (Probable)				290
Q9UM01 UniProt NPD GO	YLA1_HUMAN	Y+L amino acid transporter 1 (y(+)L-type amino acid transporter 1) (y+LAT-1) (Y+LAT1) (Monocyte amin ...	0.02	-	end	13 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	603593		511
O80813 UniProt NPD GO	YC20L_ARATH	Ycf20-like protein	0.02	-	end	3 *					121
Q38893 UniProt NPD GO	ZDS_ARATH	Zeta-carotene desaturase, chloroplast precursor (EC 1.14.99.30) (Carotene 7,8-desaturase)	0.02	-	mit	0	Plastid; chloroplast. Plastid; chromoplast				558
Q9NZ45 UniProt NPD GO	ZCD1_HUMAN	Zinc finger CDGSH domain-containing protein 1	0.02	-	mit	1 *		mitochondrion [ISS]			108
Q94EG9 UniProt NPD GO	ZIP11_ARATH	Zinc transporter 11 precursor (ZRT/IRT-like protein 11)	0.02	-	end	9 *	Cell membrane; multi-pass membrane protein (Potential)				326
Q9BRI3 UniProt NPD GO	ZNT2_HUMAN	Zinc transporter 2 (ZnT-2) (Solute carrier family 30 member 2)	0.02	-	end	4	Vacuole; vacuolar membrane; multi-pass membrane protein		609617		323
Q9LTH9 UniProt NPD GO	ZIP2_ARATH	Zinc transporter 2 precursor (ZRT/IRT-like protein 2)	0.02	-	end	9 *	Cell membrane; multi-pass membrane protein (Potential)				353
Q9QZ03 UniProt NPD GO	S39A1_MOUSE	Zinc transporter ZIP1 (Zinc-iron-regulated transporter-like) (Solute carrier family 39 member 1)	0.02	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				324
P32804 UniProt NPD GO	ZRT1_YEAST	Zinc-regulated transporter 1 (High-affinity zinc transport protein ZRT1)	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [IMP]			376
Q12436 UniProt NPD GO	ZRT2_YEAST	Zinc-regulated transporter 2 (Low-affinity zinc transport protein ZRT2)	0.02	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IMP]			422
P39713 UniProt NPD GO	YAG1_YEAST	Zinc-type alcohol dehydrogenase-like protein YAL061W	0.02	-	mit	0		cytoplasm [IDA] nucleus [IDA]			417
Q8K0C5 UniProt NPD GO	ZG16_MOUSE	Zymogen granule membrane protein 16 precursor (Zymogen granule protein 16) (Secretory lectin ZG16)	0.02	-	exc	0	Secreted protein. Stored in zymogen granules (By similarity)				167
O95455 UniProt NPD GO	TGDS_HUMAN	dTDP-D-glucose 4,6-dehydratase (EC 4.2.1.46)	0.02	-	cyt	0					350
Q96FX8 UniProt NPD GO	PERP_HUMAN	p53 apoptosis effector related to PMP-22 (Keratinocytes-associated protein 1) (KCP-1) (P53-induced p ...	0.02	-	end	4 *	Cell membrane; cell-cell junction; desmosome; multi-pass membrane protein (By similarity). Associate ...		609301		193
Q6CUG3 UniProt NPD GO	PALI2_KLULA	pH-response regulator palI/RIM9 homolog 2	0.02	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity)				225
Q6FU42 UniProt NPD GO	PALI_CANGA	pH-response regulator protein palI/RIM9	0.02	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity)				246
Q96FX7 UniProt NPD GO	TRM61_HUMAN	tRNA (adenine-N(1)-)-methyltransferase catalytic subunit TRM61 (EC 2.1.1.36) (tRNA(m1A58)-methyltran ...	0.02	-	cyt	0	Nucleus (By similarity)				289
Q80XC2 UniProt NPD GO	TRM61_MOUSE	tRNA (adenine-N(1)-)-methyltransferase catalytic subunit TRM61 (EC 2.1.1.36) (tRNA(m1A58)-methyltran ...	0.02	-	mit	0	Nucleus (By similarity)				290
Q6AY46 UniProt NPD GO	TRM61_RAT	tRNA (adenine-N(1)-)-methyltransferase catalytic subunit TRM61 (EC 2.1.1.36) (tRNA(m1A58)-methyltran ...	0.02	-	cyt	0	Nucleus (By similarity)				290
O04385 UniProt NPD GO	IEMT_CLABR	(Iso)eugenol O-methyltransferase (EC 2.1.1.146) (S-adenosysl-L-methionine:(Iso)eugenol O-methyltrans ...	0.01	-	cyt	0					368
O64899 UniProt NPD GO	C80B1_ESCCA	(S)-N-methylcoclaurine 3'-hydroxylase isozyme 1 (EC 1.14.13.71) (Cytochrome P450 80B1) (Fragment)	0.01	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				487
O64900 UniProt NPD GO	C80B2_ESCCA	(S)-N-methylcoclaurine 3'-hydroxylase isozyme 2 (EC 1.14.13.71) (Cytochrome P450 80B2)	0.01	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				488
P52705 UniProt NPD GO	HNL_MANES	(S)-acetone-cyanohydrin lyase (EC 4.1.2.39) ((S)-hydroxynitrile lyase) ((S)-hydroxynitrilase) (Oxyni ...	0.01	-	nuc	0				1EB9	257
Q8GXE2 UniProt NPD GO	ARD2_ARATH	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 2 (EC 1.13.-.-) (Aci-reductone dioxygenase 2)	0.01	-	cyt	0					192
Q9HFV5 UniProt NPD GO	HIS4_CANAL	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase ( ...	0.01	-	cyt	0	Cytoplasm (By similarity)				279
Q6BUV9 UniProt NPD GO	HIS4_DEBHA	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase ( ...	0.01	-	cyt	0	Cytoplasm (By similarity)				276
Q7RXQ8 UniProt NPD GO	HIS4_NEUCR	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase ( ...	0.01	-	cyt	0	Cytoplasm (By similarity)				257
Q09052 UniProt NPD GO	ACCO1_BRAJU	1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming enzyme) (EF ...	0.01	-	cyt	0					320
Q9MB94 UniProt NPD GO	ACCO_PRUMU	1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming enzyme) (EF ...	0.01	-	nuc	0					319
Q08506 UniProt NPD GO	ACCO1_PETHY	1-aminocyclopropane-1-carboxylate oxidase 1 (EC 1.14.17.4) (ACC oxidase 1) (Ethylene-forming enzyme) ...	0.01	-	cyt	0				1WA6	319
Q04644 UniProt NPD GO	ACCO1_CUCME	1-aminocyclopropane-1-carboxylate oxidase 1 (EC 1.14.17.4) (ACC oxidase 1) (Ethylene-forming enzyme) ...	0.01	-	cyt	0					318
P05116 UniProt NPD GO	ACCO1_LYCES	1-aminocyclopropane-1-carboxylate oxidase 1 (EC 1.14.17.4) (ACC oxidase 1) (Ethylene-forming enzyme) ...	0.01	-	cyt	0					315
P54847 UniProt NPD GO	ACCO3_CUCME	1-aminocyclopropane-1-carboxylate oxidase 3 (EC 1.14.17.4) (ACC oxidase 3) (Ethylene-forming enzyme) ...	0.01	-	cyt	0					320
Q08507 UniProt NPD GO	ACCO3_PETHY	1-aminocyclopropane-1-carboxylate oxidase 3 (EC 1.14.17.4) (ACC oxidase 3) (Ethylene-forming enzyme) ...	0.01	-	cyt	0					320
P38910 UniProt NPD GO	CH10_YEAST	10 kDa heat shock protein, mitochondrial (HSP10) (10 kDa chaperonin)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			106
P61603 UniProt NPD GO	CH10_BOVIN	10 kDa heat shock protein, mitochondrial (Hsp10) (10 kDa chaperonin) (CPN10)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [ISS]			101

You are viewing entries 86251 to 86300 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.