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
P22284 UniProt NPD GO	MPA91_POAPR	Pollen allergen KBG 31 precursor (Pollen allergen Poa p 9) (Poa p IX)	0.01	-	cyt	0					373
P14946 UniProt NPD GO	MPAL1_LOLPR	Pollen allergen Lol p 1 precursor (Lol p I) (Allergen R7)	0.01	-	end	1 *	Secreted protein				263
P14948 UniProt NPD GO	MPAL3_LOLPR	Pollen allergen Lol p 3 (Lol p III)	0.01	-	cyt	0	Secreted protein				97
P83466 UniProt NPD GO	MPAO2_ORYSA	Pollen allergen Ory s 2-A (Fragment)	0.01	-		0					15
P43213 UniProt NPD GO	MPAP1_PHLPR	Pollen allergen Phl p 1 precursor (Phl p I)	0.01	-	exc	1 *	Secreted protein			1N10	263
P43214 UniProt NPD GO	MPAP2_PHLPR	Pollen allergen Phl p 2 precursor (Phl p II)	0.01	-	exc	1 *	Secreted protein			1WHP	122
P69341 UniProt NPD GO	PARN_BOVIN	Poly(A)-specific ribonuclease PARN (EC 3.1.13.4) (Polyadenylate-specific ribonuclease) (Deadenylatin ...	0.01	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Some nuclear fraction is nucleolar (By similarit ...				54
P82415 UniProt NPD GO	PCG2_PACGO	Ponericin-G2	0.01	-	cyt	0	Secreted protein				30
P82418 UniProt NPD GO	PCG5_PACGO	Ponericin-G5	0.01	-	cyt	0	Secreted protein				30
P82426 UniProt NPD GO	PCW4_PACGO	Ponericin-W4	0.01	-	cyt	0	Secreted protein				26
Q9HAB3 UniProt NPD GO	PEVR1_HUMAN	Porcine endogenous retrovirus A receptor 1 precursor (PERV-A receptor 1) (Protein GPR172A)	0.01	-	end	11 *	Membrane; multi-pass membrane protein		607882		445
Q9NWF4 UniProt NPD GO	PEVR2_HUMAN	Porcine endogenous retrovirus A receptor 2 precursor (PERV-A receptor 2) (Protein GPR172B)	0.01	-	end	11 *	Membrane; multi-pass membrane protein		607883		448
Q863Y8 UniProt NPD GO	PEVR2_PAPHA	Porcine endogenous retrovirus A receptor 2 precursor (PERV-A receptor 2) (Protein GPR172B)	0.01	-	end	11 *	Membrane; multi-pass membrane protein				448
Q9Y2U2 UniProt NPD GO	KCNK7_HUMAN	Potassium channel subfamily K member 7	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Potential)		603940		307
Q9Z2T1 UniProt NPD GO	KCNK7_MOUSE	Potassium channel subfamily K member 7 (Putative potassium channel DP3) (Double-pore K(+) channel 3) ...	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				307
P0C182 UniProt NPD GO	KAX1B_CENNO	Potassium channel toxin alpha-KTx 1.11 (Slotoxin) (SloTx)	0.01	-	cyt	0	Secreted protein				37
P59848 UniProt NPD GO	KAX19_CENLM	Potassium channel toxin alpha-KTx 1.9 (Hongotoxin-2) (HgTX2) (Fragment)	0.01	-	nuc	0	Secreted protein				36
P60164 UniProt NPD GO	KA111_PARVI	Potassium channel toxin alpha-KTx 11.1 (Parabutoxin-1) (PBTx1)	0.01	-	nuc	0	Secreted protein	extracellular region [IDA]			37
Q6WGI9 UniProt NPD GO	KA113_PARGR	Potassium channel toxin alpha-KTx 11.3 (Parabutoxin-10) (PBTx10)	0.01	-	nuc	0	Secreted protein	extracellular region [IDA]			36
Q95NK7 UniProt NPD GO	KA142_MESMA	Potassium channel toxin alpha-KTx 14.2 precursor (Toxin Kk2) (BmKK2) (BmTXKS3) (Neurotoxin BmP07) (P ...	0.01	-	vac	1 *	Secreted protein			1PVZ	54
Q9BKB4 UniProt NPD GO	KA144_MESMA	Potassium channel toxin alpha-KTx 14.4 precursor (Neurotoxin SKTx1) (BmSKTx1)	0.01	-	vac	1 *	Secreted protein				54
Q9NBG9 UniProt NPD GO	KA162_MESMA	Potassium channel toxin alpha-KTx 16.2 precursor (Martentoxin) (BmK 622) (BmTx3B) [Contains: Martent ...	0.01	-	exc	1 *	Secreted protein			1M2S	59
Q8MQL0 UniProt NPD GO	KA163_MESMA	Potassium channel toxin alpha-KTx 16.3 precursor (Charybdotoxin-like toxin 1) (Kchtx1) (KTX1)	0.01	-	exc	1 *	Secreted protein				59
P0C164 UniProt NPD GO	KAX2B_CENEL	Potassium channel toxin alpha-KTx 2.11 (Toxin Ce4)	0.01	-	nuc	0	Secreted protein				39
P59849 UniProt NPD GO	KAX26_CENLM	Potassium channel toxin alpha-KTx 2.6 (Hongotoxin-3) (HgTX3) (Fragment)	0.01	-	nuc	0	Secreted protein				34
P45630 UniProt NPD GO	KAX27_CENLL	Potassium channel toxin alpha-KTx 2.7 (Toxin II) (Toxin II.10.9.2) (CllTx2) (Fragment)	0.01	-	nuc	0	Secreted protein				36
P56219 UniProt NPD GO	KAX42_TITSE	Potassium channel toxin alpha-KTx 4.2 precursor (Neurotoxin Ts-kappa) (TsKapa) (TsK)	0.01	-	cyt	1 *	Secreted protein			1TSK	57
P59925 UniProt NPD GO	KAX43_TITDI	Potassium channel toxin alpha-KTx 4.3 (Toxin TdK1)	0.01	-	nuc	0	Secreted protein				37
Q6XLL6 UniProt NPD GO	KAX69_OPICA	Potassium channel toxin alpha-KTx 6.9 precursor (OcKTx4)	0.01	-	exc	0	Secreted protein (By similarity)				61
P56215 UniProt NPD GO	KAX81_ANDMA	Potassium channel toxin alpha-KTx 8.1 (Neurotoxin P01) (AmP01)	0.01	-	nuc	0	Secreted protein			1ACW	29
Q9NJP7 UniProt NPD GO	KAX91_MESMA	Potassium channel toxin alpha-KTx 9.1 precursor (Neurotoxin BmP02) (Potassium ion channel blocker P0 ...	0.01	-	mit	0	Secreted protein			1DU9	56
Q9U8D1 UniProt NPD GO	KAX92_MESMA	Potassium channel toxin alpha-KTx 9.2 precursor (Neurotoxin BmP03) (Potassium ion channel blocker P0 ...	0.01	-	mit	0	Secreted protein			1WM8	56
P80669 UniProt NPD GO	KAX93_LEIQH	Potassium channel toxin alpha-KTx 9.3 (Leiuropeptide-1) (Leiuropeptide I) (LpI)	0.01	-	nuc	0	Secreted protein				28
P60209 UniProt NPD GO	KAX94_MESTA	Potassium channel toxin alpha-KTx 9.4 (Toxin BTK-2) (Bt BTK-2)	0.01	-	nuc	0	Secreted protein				32
P84744 UniProt NPD GO	KAX95_BUTOC	Potassium channel toxin alpha-KTx 9.5 (Neurotoxin Kbot1)	0.01	-	nuc	0	Secreted protein	extracellular region [NAS]			28
Q9NJC6 UniProt NPD GO	KBX3_MESMA	Potassium channel toxin beta-KTx 3 precursor (Toxin BmTX K-beta) (BmTXKbeta) (BmKLK)	0.01	-	mit	0	Secreted protein (By similarity)				90
Q9TWG1 UniProt NPD GO	TXKS_ANESU	Potassium channel toxin kaliseptin (Kaliseptine) (AsKS)	0.01	-	nuc	0	Secreted protein. Found in nematocyst				36
O97531 UniProt NPD GO	KCNQ1_FELCA	Potassium voltage-gated channel subfamily KQT member 1 (Voltage-gated potassium channel subunit Kv7. ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein				172
P80935 UniProt NPD GO	PAG55_CAPHI	Pregnancy-associated glycoprotein 55 (EC 3.4.23.-) (PAG 55) (Fragment)	0.01	-	cyt	0					27
P02877 UniProt NPD GO	HEVE_HEVBR	Pro-hevein precursor (Major hevein) [Contains: Hevein (Allergen Hev b 6); Win-like protein]	0.01	-	exc	0				1T0W	204
Q9URX3 UniProt NPD GO	1A1D_SCHPO	Probable 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) (ACC deaminase) (ACCD)	0.01	-	mit	0					338
Q9M9K1 UniProt NPD GO	PMG2_ARATH	Probable 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 2 (EC 5.4.2.1) (Phosphoglycerom ...	0.01	-	cyt	0	Cytoplasm (By similarity)				560
O24412 UniProt NPD GO	PSD7_ARATH	Probable 26S proteasome non-ATPase regulatory subunit 7 (26S proteasome regulatory subunit rpn8) (MO ...	0.01	-	nuc	0					308
Q9NV35 UniProt NPD GO	NUD15_HUMAN	Probable 7,8-dihydro-8-oxoguanine triphosphatase NUDT15 (EC 3.1.6.-) (8-oxo-dGTPase NUDT15) (Nucleos ...	0.01	-	cyt	0					164
Q9VSH3 UniProt NPD GO	BI1_DROME	Probable Bax inhibitor 1 (BI-1)	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				245
Q7SBB6 UniProt NPD GO	ERG3_NEUCR	Probable C-5 sterol desaturase (EC 1.3.3.-) (Sterol-C5-desaturase) (Ergosterol delta 5,6 desaturase) ...	0.01	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				344
P84066 UniProt NPD GO	DTD_LEIMA	Probable D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.01	-	cyt	0	Cytoplasm (By similarity)			1TC5	181
Q9VGG8 UniProt NPD GO	MTH5_DROME	Probable G-protein coupled receptor Mth-like 5 (Protein methuselah-like 5)	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				496
Q9W0R6 UniProt NPD GO	MTH9_DROME	Probable G-protein coupled receptor Mth-like 9 precursor (Protein methuselah-like 9)	0.01	-	end	7	Membrane; multi-pass membrane protein (Potential)				513
Q99LE2 UniProt NPD GO	GP146_MOUSE	Probable G-protein-coupled receptor 146	0.01	-	end	6 *	Membrane; multi-pass membrane protein				333

You are viewing entries 90651 to 90700 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.