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
P54115 UniProt NPD GO	ALDH6_YEAST	Magnesium-activated aldehyde dehydrogenase, cytosolic (EC 1.2.1.3) (Mg(2+)-activated acetaldehyde de ...	0.00	-	nuc	0	Cytoplasm	cytoplasm [IMP] mitochondrion [IDA]			499
P82947 UniProt NPD GO	ALL50_SOYBN	Major Gly 50 kDa allergen (Fragment)	0.00	-		0					17
P49372 UniProt NPD GO	ALL1_APIGR	Major allergen Api g 1 (Api g 1.0101) (Api g I)	0.00	-	cyt	0				2BK0	154
P92918 UniProt NPD GO	ALL2_APIGR	Major allergen Api g 2 (Api g 1.0201)	0.00	-	cyt	0					159
P83508 UniProt NPD GO	AVP2_CAVPO	Major allergen Cav p 2 (Fragment)	0.00	-		0	Secreted protein				15
P83340 UniProt NPD GO	EPIP1_EPIPU	Major allergen Epi p 1 (EC 3.4.21.-) (EpI n I4625*) (Fragments)	0.00	-		0					18
P30438 UniProt NPD GO	FEL1A_FELCA	Major allergen I polypeptide chain 1 precursor (Allergen Fel d 1-A) (Fel d I-A) (Allergen Cat-1) (Fe ...	0.00	-	exc	0	Secreted protein			1PUO	92
Q40280 UniProt NPD GO	MAL12_MALDO	Major allergen Mal d 1 (Mal d I) (AP15)	0.00	-	cyt	0					158
O50001 UniProt NPD GO	PRU1_PRUAR	Major allergen Pru ar 1	0.00	-	cyt	0					160
P83148 UniProt NPD GO	MEFP_MYTED	Major extrapallial fluid protein (EP protein) (Fragment)	0.00	-		0					20
Q06394 UniProt NPD GO	ML146_PAPSO	Major latex protein 146 (MLP 146)	0.00	-	cyt	0	Vacuole. Cytoplasmic vesicle. Central vacuole of developing laticifers and membrane-bound vesicles o ...				159
P19825 UniProt NPD GO	MLP15_PAPSO	Major latex protein 15 (MLP 15) (gMLP15)	0.00	-	cyt	0	Vacuole. Cytoplasmic vesicle. Central vacuole of developing laticifers and membrane-bound vesicles o ...				159
Q41020 UniProt NPD GO	MLP22_PAPSO	Major latex protein 22 (MLP 22) (gMLP22)	0.00	-	cyt	0	Vacuole. Cytoplasmic vesicle. Central vacuole of developing laticifers and membrane-bound vesicles o ...				158
P45431 UniProt NPD GO	BEV1B_BETVE	Major pollen allergen Bet v 1-B (Bet v I-B)	0.00	-	cyt	0	Cytoplasm				159
P43176 UniProt NPD GO	BEV1C_BETVE	Major pollen allergen Bet v 1-C (Bet v I-C)	0.00	-	cyt	0	Cytoplasm				159
P43184 UniProt NPD GO	BEV1K_BETVE	Major pollen allergen Bet v 1-K (Bet v I-K)	0.00	-	cyt	0	Cytoplasm				159
P43186 UniProt NPD GO	BEV1M_BETVE	Major pollen allergen Bet v 1-M/N (Bet v I-M/N)	0.00	-	cyt	0	Cytoplasm				159
P38950 UniProt NPD GO	MPAC2_CARBE	Major pollen allergen Car b 1 isoform 2 (Car b I)	0.00	-	cyt	0					159
P38949 UniProt NPD GO	MPAC1_CARBE	Major pollen allergen Car b 1 isoforms 1A and 1B (Car B I)	0.00	-	cyt	0					159
Q08407 UniProt NPD GO	MPAC1_CORAV	Major pollen allergen Cor a 1 isoforms 5, 6, 11 and 16 (Cor a I)	0.00	-	cyt	0					159
Q9SCG9 UniProt NPD GO	MPAC1_CUPAR	Major pollen allergen Cup a 1	0.00	-	cyt	0					346
P82946 UniProt NPD GO	MPAG4_DACGL	Major pollen allergen Dac g 4 (Fragments)	0.00	-	cyt	0					55
Q9LLT1 UniProt NPD GO	MPAJ1_JUNVI	Major pollen allergen Jun v 1 precursor	0.00	-	exc	0					367
P80741 UniProt NPD GO	ALL4_OLEEU	Major pollen allergen Ole e 4 (Ole e IV) (Fragments)	0.00	-	cyt	0					24
Q6PAB3 UniProt NPD GO	MDHC_XENLA	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Cytosolic malate dehydrogenase)	0.00	-	cyt	0	Cytoplasm (By similarity)				334
Q6DIY9 UniProt NPD GO	MDHC_XENTR	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Cytosolic malate dehydrogenase)	0.00	-	cyt	0	Cytoplasm (By similarity)				334
Q6BN12 UniProt NPD GO	MPG1_DEBHA	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (ATP-mannose-1-phosphate guanylyltransferase) (G ...	0.00	-	cyt	0	Cytoplasm (By similarity)				362
P41940 UniProt NPD GO	MPG1_YEAST	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (ATP-mannose-1-phosphate guanylyltransferase) (G ...	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA]			361
Q70SJ2 UniProt NPD GO	MPG1_KLULA	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.00	-	cyt	0	Cytoplasm (By similarity)				361
Q9P8N0 UniProt NPD GO	MPG1_PICAN	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.00	-	cyt	0	Cytoplasm (By similarity)				364
Q6CCU3 UniProt NPD GO	MPG1_YARLI	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.00	-	cyt	0	Cytoplasm (By similarity)				363
Q76IQ2 UniProt NPD GO	MANA_CANGA	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.00	-	cyt	0	Cytoplasm (By similarity)				429
O75352 UniProt NPD GO	MPU1_HUMAN	Mannose-P-dolichol utilization defect 1 protein (Suppressor of Lec15 and Lec35 glycosylation mutatio ...	0.00	-	end	5 *	Membrane; multi-pass membrane protein (Potential)		609180		247
Q9R0Q9 UniProt NPD GO	MPU1_MOUSE	Mannose-P-dolichol utilization defect 1 protein (Suppressor of Lec15 and Lec35 glycosylation mutatio ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				247
Q9VMW8 UniProt NPD GO	MPU1_DROME	Mannose-P-dolichol utilization defect 1 protein homolog	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				252
P82953 UniProt NPD GO	LEC_HORVU	Mannose-specific lectin (Agglutinin) (Fragments)	0.00	-	cyt	0	Secreted protein; extracellular space; apoplast				77
P12306 UniProt NPD GO	LEC1_LATOC	Mannose/glucose-specific lectin alpha 1 chain (Lol I)	0.00	-	cyt	0				1LOG	53
P12307 UniProt NPD GO	LEC2_LATOC	Mannose/glucose-specific lectin alpha 2 chain (Lol II)	0.00	-	cyt	0				1LGC	53
P12308 UniProt NPD GO	LECA_LATSA	Mannose/glucose-specific lectin alpha chain	0.00	-	cyt	0					55
P02868 UniProt NPD GO	LECA_VICCR	Mannose/glucose-specific lectin alpha chain	0.00	-	cyt	0					53
Q91WW5 UniProt NPD GO	MRGA1_MOUSE	Mas-related G-protein coupled receptor member A1 (RF-amide G-protein coupled receptor)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				304
Q91WW3 UniProt NPD GO	MRGA3_MOUSE	Mas-related G-protein coupled receptor member A3	0.00	-	end	7 *	Membrane; multi-pass membrane protein				302
Q91WW2 UniProt NPD GO	MRGA4_MOUSE	Mas-related G-protein coupled receptor member A4 (RF-amide G-protein coupled receptor)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				313
Q91ZC7 UniProt NPD GO	MRGA5_MOUSE	Mas-related G-protein coupled receptor member A5	0.00	-	end	7 *	Membrane; multi-pass membrane protein				304
Q91ZC5 UniProt NPD GO	MRGA7_MOUSE	Mas-related G-protein coupled receptor member A7	0.00	-	end	7 *	Membrane; multi-pass membrane protein				305
Q7TN40 UniProt NPD GO	MRGRE_RAT	Mas-related G-protein coupled receptor member E	0.00	-	end	7 *	Membrane; multi-pass membrane protein				309
Q91ZB7 UniProt NPD GO	MRGRE_MOUSE	Mas-related G-protein coupled receptor member E (Evolutionary breakpoint transcript 3 protein)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				310
Q91ZB5 UniProt NPD GO	MRGRG_MOUSE	Mas-related G-protein coupled receptor member G (Evolutionary breakpoint transcript 2 protein)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
Q86SM5 UniProt NPD GO	MRGRG_HUMAN	Mas-related G-protein coupled receptor member G (G-protein coupled receptor 169) (Fragment)	0.00	-	mit	1 *	Membrane; multi-pass membrane protein		607234		54
P97592 UniProt NPD GO	MCPT4_RAT	Mast cell protease 4 precursor (EC 3.4.21.-) (Mast cell protease IV) (rMCP-IV) (rMCP-4)	0.00	-	exc	0	Secretory granules				246

You are viewing entries 95551 to 95600 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.