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
P50637 UniProt NPD GO	BZRP_MOUSE	Peripheral-type benzodiazepine receptor (PBR) (PKBS) (Mitochondrial benzodiazepine receptor)	0.00	-	mit	5 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				169
P16257 UniProt NPD GO	BZRP_RAT	Peripheral-type benzodiazepine receptor (PBR) (PKBS) (Mitochondrial benzodiazepine receptor)	0.00	-	cyt	5 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrion [TAS]			169
P84442 UniProt NPD GO	PVK_PHYMO	Periviscerokinin	0.00	-		0	Secreted protein				10
P83382 UniProt NPD GO	PVK_LOCMI	Periviscerokinin (Lom-PVK-1)	0.00	-		0	Secreted protein	extracellular region [IDA]			10
P41837 UniProt NPD GO	PVK1_PERAM	Periviscerokinin-1 (Pea-PVK-1)	0.00	-		0	Secreted protein				11
P15984 UniProt NPD GO	PERX_WHEAT	Peroxidase (EC 1.11.1.7) (Fragment)	0.00	-	cyt	0					80
O22711 UniProt NPD GO	TPX2_ARATH	Peroxiredoxin TPx2 (EC 1.11.1.15) (Thioredoxin reductase)	0.00	-	cyt	0					162
Q9Y7F0 UniProt NPD GO	TSA1_CANAL	Peroxiredoxin TSA1 (EC 1.11.1.15) (Thioredoxin peroxidase) (Thiol-specific antioxidant protein)	0.00	-	mit	1 *	Cytoplasm				196
O08709 UniProt NPD GO	PRDX6_MOUSE	Peroxiredoxin-6 (EC 1.11.1.15) (Antioxidant protein 2) (1-Cys peroxiredoxin) (1-Cys PRX) (Acidic cal ...	0.00	-	cyt	0	Cytoplasm (By similarity). Lysosome (By similarity). Also found in lung secretory organelles (By sim ...	cytosol [IDA]			223
Q9BY49 UniProt NPD GO	PECR_HUMAN	Peroxisomal trans-2-enoyl-CoA reductase (EC 1.3.1.38) (TERP) (HPDHase) (pVI-ARL) (2,4-dienoyl-CoA re ...	0.00	-	mit	0	Peroxisome		605843	1YXM	303
P40935 UniProt NPD GO	PNMT_MOUSE	Phenylethanolamine N-methyltransferase (EC 2.1.1.28) (PNMTase) (Noradrenaline N-methyltransferase)	0.00	-	cyt	0					295
P10937 UniProt NPD GO	PNMT_RAT	Phenylethanolamine N-methyltransferase (EC 2.1.1.28) (PNMTase) (Noradrenaline N-methyltransferase)	0.00	-	cyt	0					285
P83568 UniProt NPD GO	ILME_SEPOF	Pheromone peptide ILME	0.00	-		0	Secreted protein				4
P34178 UniProt NPD GO	PBP_ORGPS	Pheromone-binding protein (PBP) (Fragment)	0.00	-	nuc	0					35
Q95VE9 UniProt NPD GO	PBP1_EPIPO	Pheromone-binding protein 1 precursor (PBP 1)	0.00	-	end	0					164
P34177 UniProt NPD GO	PBP2_LYMDI	Pheromone-binding protein 2 (PBP2) (Fragment)	0.00	-	cyt	0					35
Q27388 UniProt NPD GO	PBP_HELVI	Pheromone-binding protein precursor (PBP)	0.00	-	exc	0					163
P54194 UniProt NPD GO	PBP4_DROME	Pheromone-binding protein-related protein 4 precursor (PBPRP-4)	0.00	-	exc	0	Secreted protein (Potential). Secreted in the lumen of olfactory hairs (Potential)				175
P25271 UniProt NPD GO	PHPT_PSESE	Pheromonotropin (Pss-PT)	0.00	-		0	Secreted protein				18
P10891 UniProt NPD GO	DEFI_PROTE	Phormicin precursor (Insect defensin A/B)	0.00	-	exc	1 *	Secreted protein			1ICA	94
P40614 UniProt NPD GO	MPCP_CAEEL	Phosphate carrier protein, mitochondrial precursor (PTP)	0.00	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				340
Q5A8A2 UniProt NPD GO	NPC2_CANAL	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.00	-	exc	0					192
Q5KIR9 UniProt NPD GO	NPC2_CRYNE	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.00	-	mit	0					180
Q52FS9 UniProt NPD GO	NPC2_MAGGR	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.00	-	exc	0					178
Q7RZ85 UniProt NPD GO	NPC2_NEUCR	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.00	-	exc	0					177
Q9C0X9 UniProt NPD GO	NPC2_SCHPO	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.00	-	mit	1 *					188
Q12408 UniProt NPD GO	NPC2_YEAST	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP) (NPC2 homolog)	0.00	-	exc	1 *	Vacuole	vacuolar lumen (sensu Fungi) [IDA]			173
Q75D30 UniProt NPD GO	ERI1_ASHGO	Phosphatidylinositol N-acetylglucosaminyltransferase ERI1 subunit (Endoplasmic reticulum-associated ...	0.00	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				71
Q3MUY2 UniProt NPD GO	PIGY_HUMAN	Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y (Phosphatidylinositol-glycan biosynth ...	0.00	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA] glycosylphosphatidylinositol-N-acetylglucos... [IDA]			71
P0C1P0 UniProt NPD GO	PIGY_MOUSE	Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y (Phosphatidylinositol-glycan biosynth ...	0.00	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				71
P0C1P1 UniProt NPD GO	PIGY_XENTR	Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y (Phosphatidylinositol-glycan biosynth ...	0.00	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				71
O49730 UniProt NPD GO	MRAY_ARATH	Phospho-N-acetylmuramoyl-pentapeptide-transferase homolog (Translocase I)	0.00	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				326
Q757Q0 UniProt NPD GO	PGK_ASHGO	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	cyt	0	Cytoplasm (By similarity)				415
Q6FKY1 UniProt NPD GO	PGK_CANGA	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	cyt	0	Cytoplasm (By similarity)				416
Q6BLA0 UniProt NPD GO	PGK_DEBHA	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	cyt	0	Cytoplasm (By similarity)				416
P14828 UniProt NPD GO	PGK_KLULA	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	cyt	0	Cytoplasm (By similarity)				416
P38667 UniProt NPD GO	PGK_NEUCR	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	cyt	0	Cytoplasm (By similarity)				418
Q7ZA46 UniProt NPD GO	PGK_PICPA	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	cyt	0	Cytoplasm (By similarity)				416
P27362 UniProt NPD GO	PGK_PLAF7	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	nuc	0				1LTK	416
P41759 UniProt NPD GO	PGK_SCHMA	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	nuc	0					416
O60101 UniProt NPD GO	PGK_SCHPO	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	cyt	0	Cytoplasm (By similarity)				414
P14228 UniProt NPD GO	PGK_TRIRE	Phosphoglycerate kinase (EC 2.7.2.3)	0.00	-	nuc	0	Cytoplasm (By similarity)				416
P50318 UniProt NPD GO	PGKH_ARATH	Phosphoglycerate kinase, chloroplast precursor (EC 2.7.2.3)	0.00	-	mit	0	Plastid; chloroplast				478
P12782 UniProt NPD GO	PGKH_WHEAT	Phosphoglycerate kinase, chloroplast precursor (EC 2.7.2.3)	0.00	-	mit	0	Plastid; chloroplast				480
P29409 UniProt NPD GO	PGKH_SPIOL	Phosphoglycerate kinase, chloroplast precursor (EC 2.7.2.3) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				433
P41760 UniProt NPD GO	PGK1_TRYCO	Phosphoglycerate kinase, cytosolic (EC 2.7.2.3)	0.00	-	cyt	0	Cytoplasm				420
Q42962 UniProt NPD GO	PGKY_TOBAC	Phosphoglycerate kinase, cytosolic (EC 2.7.2.3)	0.00	-	nuc	0	Cytoplasm				401
P83650 UniProt NPD GO	PLMS_SCYCA	Phospholemman-like protein (PLMS) (FXYD domain-containing ion transport regulator) (Fragment)	0.00	-	cyt	0	Membrane; single-pass type I membrane protein (By similarity)				29
P82542 UniProt NPD GO	PLMS_SQUAC	Phospholemman-like protein (PLMS) (Fragment)	0.00	-	cyt	0	Microsome; microsomal membrane; single-pass type I membrane protein				30
Q9U6W0 UniProt NPD GO	PA1_POLAN	Phospholipase A1 (EC 3.1.1.32) (EC 3.1.1.4) (Allergen Pol a 1)	0.00	-	cyt	0					301

You are viewing entries 96351 to 96400 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.