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
P01175 UniProt NPD GO	NEU1_BOVIN	Oxytocin-neurophysin 1 precursor (OT-NPI) [Contains: Oxytocin (Ocytocin); Neurophysin 1]	0.10	-	exc	0	Secreted protein			1XY2	125
P13389 UniProt NPD GO	NEU1_SHEEP	Oxytocin-neurophysin 1 precursor (OT-NPI) [Contains: Oxytocin (Ocytocin); Neurophysin 1]	0.10	-	exc	0				1XY2	125
P51575 UniProt NPD GO	P2RX1_HUMAN	P2X purinoceptor 1 (ATP receptor) (P2X1) (Purinergic receptor)	0.10	-	end	2 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600845		399
O70400 UniProt NPD GO	PDLI1_MOUSE	PDZ and LIM domain protein 1 (Elfin) (LIM domain protein CLP-36) (C-terminal LIM domain protein 1)	0.10	-	nuc	0	Cytoplasm. Associates with the actin stress fibers	transcription factor complex [IDA]			326
O75915 UniProt NPD GO	PRAF3_HUMAN	PRA1 family protein 3 (ARL-6-interacting protein 5) (ADP-ribosylation-like factor 6-interacting prot ...	0.10	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	integral to membrane [ISS]	605709		188
Q62083 UniProt NPD GO	PICK1_MOUSE	PRKCA-binding protein (Protein kinase C-alpha-binding protein) (Protein interacting with C kinase 1) ...	0.10	-	cyt	0	Cytoplasm; perinuclear region. Also present at excitatory synapses	cytoplasm [IDA] Golgi apparatus [IDA] mitochondrion [IDA] perinuclear region [IDA] plasma membrane [ISS] presynaptic membrane [ISS] synapse [IDA]			416
Q2VL53 UniProt NPD GO	PAX9_DAUMA	Paired box protein Pax-9	0.10	-	nuc	0	Nucleus				341
Q2VL52 UniProt NPD GO	PAX9_LEMCA	Paired box protein Pax-9	0.10	-	nuc	0	Nucleus				341
Q2VL51 UniProt NPD GO	PAX9_LEPED	Paired box protein Pax-9	0.10	-	nuc	0	Nucleus				341
Q9YGJ2 UniProt NPD GO	VSP1_AGKHP	Pallabin precursor (EC 3.4.21.-)	0.10	-	exc	0	Secreted protein				260
Q6BP80 UniProt NPD GO	AKR1_DEBHA	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.10	-	end	6	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				821
Q875S9 UniProt NPD GO	AKR1_SACKL	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.10	-	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				737
Q9C0W9 UniProt NPD GO	PFA5_SCHPO	Palmitoyltransferase PFA5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.10	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				312
Q4X251 UniProt NPD GO	AKR1_ASPFU	Palmitoyltransferase akr1 (EC 2.3.1.-) (Ankyrin repeat-containing protein akr1)	0.10	-	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				738
Q5BC23 UniProt NPD GO	SWF1_EMENI	Palmitoyltransferase swf1 (EC 2.3.1.-)	0.10	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				412
O60069 UniProt NPD GO	SWF1_SCHPO	Palmitoyltransferase swf1 (EC 2.3.1.-)	0.10	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				356
P06305 UniProt NPD GO	PAHO_ALLMI	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.10	-	cyt	0	Secreted protein				36
P68249 UniProt NPD GO	PAHO_MELGA	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.10	-	nuc	0	Secreted protein			2BF9	36
P54317 UniProt NPD GO	LIPR2_HUMAN	Pancreatic lipase-related protein 2 precursor (EC 3.1.1.3)	0.10	-	exc	0	Secreted protein	extracellular region [TAS]	604423		469
P55259 UniProt NPD GO	GP2_HUMAN	Pancreatic secretory granule membrane major glycoprotein GP2 precursor (Pancreatic zymogen granule m ...	0.10	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity). Secreted protein (By similarity). Secreted ...		602977		527
P81634 UniProt NPD GO	IPK1_HORSE	Pancreatic secretory trypsin inhibitor	0.10	-	nuc	0	Secreted protein				56
Q64425 UniProt NPD GO	LIPP_MYOCO	Pancreatic triacylglycerol lipase precursor (EC 3.1.1.3) (Pancreatic lipase) (PL) (Fragment)	0.10	-	nuc	0	Secreted protein				457
Q96RD7 UniProt NPD GO	PANX1_HUMAN	Pannexin-1	0.10	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		608420		426
Q9TSX8 UniProt NPD GO	VNN1_CANFA	Pantetheinase precursor (EC 3.5.1.92) (Pantetheine hydrolase) (Vascular non-inflammatory molecule 1) ...	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				514
P40459 UniProt NPD GO	PANC_YEAST	Pantoate--beta-alanine ligase (EC 6.3.2.1) (Pantothenate synthetase) (Pantoate-activating enzyme)	0.10	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			309
P15477 UniProt NPD GO	PAT2_SOLTU	Patatin B2 precursor (Potato tuber protein)	0.10	-	exc	0					386
O59939 UniProt NPD GO	PELB_COLGL	Pectate lyase B precursor (EC 4.2.2.2)	0.10	-	mit	0	Secreted protein (Potential)				331
Q9LUV1 UniProt NPD GO	PMEI2_ARATH	Pectinmethylesterase inhibitor 2 precursor (AtPMEI2)	0.10	-	nuc	0					173
Q963D0 UniProt NPD GO	PEN3D_PENVA	Penaeidin-3d precursor (Pen-3d)	0.10	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				82
Q963C7 UniProt NPD GO	PEN3G_PENVA	Penaeidin-3g precursor (Pen-3g)	0.10	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				82
Q963C6 UniProt NPD GO	PEN3H_PENVA	Penaeidin-3h precursor (Pen-3h)	0.10	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				82
Q963C5 UniProt NPD GO	PEN3I_PENVA	Penaeidin-3i precursor (Pen-3i)	0.10	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				82
Q90WP7 UniProt NPD GO	PLR_RANPI	Peptide leucine arginine precursor (pLR)	0.10	-	exc	0	Secreted protein	extracellular region [IDA]			62
P08761 UniProt NPD GO	MSRA_DROME	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Methionine-S-sulfoxide reductase) (Ecdysone-ind ...	0.10	-	cyt	0					246
P12890 UniProt NPD GO	AMD2_XENLA	Peptidyl-glycine alpha-amidating monooxygenase 2 precursor (EC 1.14.17.3) (Peptidyl-glycine alpha-am ...	0.10	-	end	1					875
Q2U0E0 UniProt NPD GO	PPID_ASPOR	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.10	-	cyt	0	Cytoplasm (By similarity)				371
Q9NI62 UniProt NPD GO	CYPE_DICDI	Peptidyl-prolyl cis-trans isomerase cypE (EC 5.2.1.8) (Cyclophilin cypE)	0.10	-	cyt	0	Cytoplasm. Nucleus				156
Q5KHA8 UniProt NPD GO	PPIL3_CRYNE	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase)	0.10	-	cyt	0					167
Q03293 UniProt NPD GO	PER_DROAN	Period circadian protein (Fragment)	0.10	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				125
P82595 UniProt NPD GO	PLS_HALLA	Perlustrin	0.10	-	nuc	0					84
Q9SK52 UniProt NPD GO	PER18_ARATH	Peroxidase 18 precursor (EC 1.11.1.7) (Atperox P18)	0.10	-	end	0	Secreted protein (By similarity)				329
Q43731 UniProt NPD GO	PER50_ARATH	Peroxidase 50 precursor (EC 1.11.1.7) (Atperox P50) (PRXR2) (ATP9a)	0.10	-	exc	0	Secreted protein (By similarity)				329
Q05855 UniProt NPD GO	PER1_WHEAT	Peroxidase precursor (EC 1.11.1.7) (WP2)	0.10	-	exc	0	Secreted protein (By similarity)				312
Q5E947 UniProt NPD GO	PRDX1_BOVIN	Peroxiredoxin-1 (EC 1.11.1.15)	0.10	-	cyt	0	Cytoplasm (By similarity)				199
O08807 UniProt NPD GO	PRDX4_MOUSE	Peroxiredoxin-4 (EC 1.11.1.15) (Prx-IV) (Thioredoxin peroxidase AO372) (Thioredoxin-dependent peroxi ...	0.10	-	mit	0	Cytoplasm (By similarity)	mitochondrion [IDA]			274
Q9NA25 UniProt NPD GO	NDX8_CAEEL	Peroxisomal coenzyme A diphosphatase ndx-8 (EC 3.6.1.-) (Nudix hydrolase 8)	0.10	-	nuc	1	Peroxisome				234
Q6CLU6 UniProt NPD GO	PEX22_KLULA	Peroxisome assembly protein 22 (Peroxin-22)	0.10	-	mit	1 *	Peroxisome; peroxisomal membrane; single-pass membrane protein (By similarity)				156
Q9UW82 UniProt NPD GO	PEX22_PICPA	Peroxisome assembly protein 22 (Peroxin-22)	0.10	-	exc	1 *	Peroxisome; peroxisomal membrane; single-pass membrane protein				187
Q42609 UniProt NPD GO	PALY_BROFI	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.10	-	nuc	0	Cytoplasm (Probable)				703
P02720 UniProt NPD GO	PPCT_BOVIN	Phosphatidylcholine transfer protein (PC-TP) (StAR-related lipid transfer protein 2) (StARD2) (START ...	0.10	-	cyt	0	Cytoplasm				213

You are viewing entries 64901 to 64950 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.