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
P84423 UniProt NPD GO	PVK22_PERBR	Periviscerokinin-2.2 (Lem-PVK-2-like peptide)	0.01	-		0	Secreted protein				11
P84425 UniProt NPD GO	PVK22_PERFU	Periviscerokinin-2.2 (Lem-PVK-2-like peptide)	0.01	-		0	Secreted protein				11
P84434 UniProt NPD GO	PVK22_PSEBJ	Periviscerokinin-2.2 (Lem-PVK-2-like peptide)	0.01	-		0	Secreted protein				11
P84427 UniProt NPD GO	PVK22_SHELA	Periviscerokinin-2.2 (Lem-PVK-2-like peptide)	0.01	-		0	Secreted protein				11
Q9SZH2 UniProt NPD GO	PER43_ARATH	Peroxidase 43 precursor (EC 1.11.1.7) (Atperox P43)	0.01	-	cyt	0	Secreted protein (By similarity)				326
Q9LXG3 UniProt NPD GO	PER56_ARATH	Peroxidase 56 precursor (EC 1.11.1.7) (Atperox P56) (ATP33)	0.01	-	mit	1 *	Secreted protein (By similarity)				329
P84752 UniProt NPD GO	PERA_ALOVR	Peroxidase A (EC 1.11.1.7) (Fragments)	0.01	-	end	2	Secreted protein (By similarity)				361
Q9URB1 UniProt NPD GO	PEM5_PHACH	Peroxidase manganese-dependent H5 (EC 1.11.1.13) (Fragment)	0.01	-		0	Secreted protein				20
P34760 UniProt NPD GO	TSA1_YEAST	Peroxiredoxin TSA1 (EC 1.11.1.15) (Thioredoxin peroxidase) (Cytoplasmic thiol peroxidase 1) (cTPx 1) ...	0.01	-	mit	1 *	Cytoplasm	cytoplasm [IDA]			195
Q04120 UniProt NPD GO	TSA2_YEAST	Peroxiredoxin TSA2 (EC 1.11.1.15) (Thioredoxin peroxidase 2) (Cytoplasmic thiol peroxidase 2) (cTPx ...	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA]			195
P38013 UniProt NPD GO	AHP1_YEAST	Peroxiredoxin type-2 (EC 1.11.1.15) (Peroxiredoxin type II) (Peroxisomal alkyl hydroperoxide reducta ...	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA]			175
Q9BGI3 UniProt NPD GO	PRDX2_BOVIN	Peroxiredoxin-2 (EC 1.11.1.15)	0.01	-	cyt	0	Cytoplasm (By similarity)				199
Q61171 UniProt NPD GO	PRDX2_MOUSE	Peroxiredoxin-2 (EC 1.11.1.15) (Thioredoxin peroxidase 1) (Thioredoxin-dependent peroxide reductase ...	0.01	-	cyt	0	Cytoplasm				197
P35704 UniProt NPD GO	PRDX2_RAT	Peroxiredoxin-2 (EC 1.11.1.15) (Thioredoxin peroxidase 1) (Thioredoxin-dependent peroxide reductase ...	0.01	-	cyt	0	Cytoplasm				197
P52552 UniProt NPD GO	PRDX2_PIG	Peroxiredoxin-2 (EC 1.11.1.15) (Thioredoxin peroxidase 1) (Thioredoxin-dependent peroxide reductase ...	0.01	-	cyt	0	Cytoplasm (By similarity)				127
P32119 UniProt NPD GO	PRDX2_HUMAN	Peroxiredoxin-2 (EC 1.11.1.15) (Thioredoxin peroxidase 1) (Thioredoxin-dependent peroxide reductase ...	0.01	-	cyt	0	Cytoplasm	cytoplasm [TAS]	600538	1QMV	197
Q9R063 UniProt NPD GO	PRDX5_RAT	Peroxiredoxin-5, mitochondrial precursor (EC 1.11.1.15) (Prx-V) (Peroxisomal antioxidant enzyme) (PL ...	0.01	-	mit	0	Mitochondrion (By similarity). Cytoplasm (By similarity). Peroxisome (By similarity)				213
P30041 UniProt NPD GO	PRDX6_HUMAN	Peroxiredoxin-6 (EC 1.11.1.15) (Antioxidant protein 2) (1-Cys peroxiredoxin) (1-Cys PRX) (Acidic cal ...	0.01	-	cyt	0	Cytoplasm (By similarity). Lysosome (By similarity). Cytoplasmic vesicle (By similarity). And also f ...	cytosol [NAS]	602316	1PRX	223
O35244 UniProt NPD GO	PRDX6_RAT	Peroxiredoxin-6 (EC 1.11.1.15) (Antioxidant protein 2) (1-Cys peroxiredoxin) (1-Cys PRX) (Acidic cal ...	0.01	-	cyt	0	Cytoplasm. Lysosome. Also found in lung secretory organelles				223
P05414 UniProt NPD GO	GOX_SPIOL	Peroxisomal (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) (Glycolate oxidase) (GOX) (Short chain alpha-hy ...	0.01	-	cyt	0	Peroxisome			1GYL	369
Q9WV68 UniProt NPD GO	DECR2_MOUSE	Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) (2,4-dienoyl-CoA reductase 2)	0.01	-	pox	0	Peroxisome				292
Q9Z2M4 UniProt NPD GO	DECR2_RAT	Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) (2,4-dienoyl-CoA reductase 2) (DCR-AKL) (pVI-AKL ...	0.01	-	pox	0	Peroxisome				292
Q6QHF9 UniProt NPD GO	PAOX_HUMAN	Peroxisomal N1-acetyl-spermine/spermidine oxidase (EC 1.5.3.11) (Polyamine oxidase)	0.01	-	nuc	0	Peroxisome (By similarity). Cytoplasm (By similarity)				648
Q9JIF5 UniProt NPD GO	PECR_CAVPO	Peroxisomal trans-2-enoyl-CoA reductase (EC 1.3.1.38)	0.01	-	pox	0	Peroxisome	mitochondrion [ISS]			302
Q99MZ7 UniProt NPD GO	PECR_MOUSE	Peroxisomal trans-2-enoyl-CoA reductase (EC 1.3.1.38)	0.01	-	cyt	0	Peroxisome (By similarity)	mitochondrion [IDA]			303
Q9WVK3 UniProt NPD GO	PECR_RAT	Peroxisomal trans-2-enoyl-CoA reductase (EC 1.3.1.38) (RLF98) (Peroxisomal 2,4-dienoyl CoA reductase ...	0.01	-	cyt	0	Peroxisome (By similarity)	mitochondrion [ISS]			303
P42997 UniProt NPD GO	OXYF_SCYCA	Phasvatocin	0.01	-		0	Secreted protein				9
P82609 UniProt NPD GO	SULT_ICTPU	Phenol sulfotransferase (EC 2.8.2.1) (Fragment)	0.01	-		0	Cytoplasm				18
P34176 UniProt NPD GO	PBP1_LYMDI	Pheromone-binding protein 1 (PBP1) (Fragment)	0.01	-	cyt	0					35
Q17077 UniProt NPD GO	PBP1_ANTPE	Pheromone-binding protein 1 precursor (PBP 1) (APR-1)	0.01	-	vac	0					163
Q17078 UniProt NPD GO	PBP2_ANTPE	Pheromone-binding protein 2 precursor (PBP 2) (APR-2)	0.01	-	exc	1 *					164
P20797 UniProt NPD GO	PBP_ANTPO	Pheromone-binding protein precursor (PBP)	0.01	-	exc	0				1TWO	163
P34174 UniProt NPD GO	PBP_BOMMO	Pheromone-binding protein precursor (PBP)	0.01	-	cyt	0				2FJY	164
P18959 UniProt NPD GO	PBP_MANSE	Pheromone-binding protein precursor (PBP)	0.01	-	cyt	0					168
P54191 UniProt NPD GO	PBP1_DROME	Pheromone-binding protein-related protein 1 precursor (PBPRP-1)	0.01	-	end	0	Secreted protein (Potential). Secreted in the lumen of olfactory hairs (Potential)				148
P54192 UniProt NPD GO	PBP2_DROME	Pheromone-binding protein-related protein 2 precursor (PBPRP-2)	0.01	-	vac	0	Secreted protein (Potential). Secreted in the lumen of olfactory hairs (Potential)				150
P54193 UniProt NPD GO	PBP3_DROME	Pheromone-binding protein-related protein 3 precursor (PBPRP-3) (Odorant-binding protein OS-F)	0.01	-	exc	1 *	Secreted protein (Potential). Secreted in the lumen of olfactory hairs (Potential)				154
P54195 UniProt NPD GO	PBP5_DROME	Pheromone-binding protein-related protein 5 precursor (PBPRP-5)	0.01	-	exc	1 *	Secreted protein (Potential). Secreted in the lumen of olfactory hairs (Potential)				143
Q23970 UniProt NPD GO	PBP6_DROME	Pheromone-binding protein-related protein 6 precursor (PBPRP-6) (Odorant-binding protein OS-E)	0.01	-	nuc	0	Secreted protein (Potential). Secreted in the lumen of olfactory hairs (Potential)				141
P15710 UniProt NPD GO	PHO4_NEUCR	Phosphate-repressible phosphate permease	0.01	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				590
O35502 UniProt NPD GO	LCAT_CLEGL	Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) (Lecithin-cholesterol acyltransferase) (Pho ...	0.01	-	cyt	0					291
P18424 UniProt NPD GO	LCAT_RAT	Phosphatidylcholine-sterol acyltransferase precursor (EC 2.3.1.43) (Lecithin-cholesterol acyltransfe ...	0.01	-	exc	1 *					440
Q6FNB1 UniProt NPD GO	NPC2_CANGA	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.01	-	exc	1 *					185
Q4P580 UniProt NPD GO	NPC2_USTMA	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.01	-	exc	0					193
Q05893 UniProt NPD GO	PPCK_ASCSU	Phosphoenolpyruvate carboxykinase [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) (PEPCK)	0.01	-	mit	0					643
P20007 UniProt NPD GO	PPCK_DROME	Phosphoenolpyruvate carboxykinase [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) (PEPCK)	0.01	-	cyt	0					647
O61471 UniProt NPD GO	PGK_APLCA	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	cyt	0	Cytoplasm (By similarity)				412
P46273 UniProt NPD GO	PGK_CANAL	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	cyt	0	Cytoplasm. Cell wall				417
P51903 UniProt NPD GO	PGK_CHICK	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	nuc	0	Cytoplasm (By similarity)				416
Q01604 UniProt NPD GO	PGK_DROME	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	nuc	0	Cytoplasm				415

You are viewing entries 90251 to 90300 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.