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
P84756 UniProt NPD GO	TOX2_OXYLI	Oxytoxin-2 (OxyTx2)	0.11	-	nuc	0	Secreted protein				55
Q9D8I2 UniProt NPD GO	P2Y13_MOUSE	P2Y purinoceptor 13 (P2Y13) (G-protein coupled receptor 86)	0.11	-	end	7 *	Membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			337
O00151 UniProt NPD GO	PDLI1_HUMAN	PDZ and LIM domain protein 1 (Elfin) (LIM domain protein CLP-36) (C-terminal LIM domain protein 1)	0.11	-	nuc	0	Cytoplasm (By similarity). Associates with the actin stress fibers (By similarity)		605900	1X62	328
Q5T2W1 UniProt NPD GO	PDZD1_HUMAN	PDZ domain-containing protein 1 (CFTR-associated protein of 70 kDa) (Na/Pi cotransporter C-terminal- ...	0.11	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with pe ...		603831		519
Q9EP80 UniProt NPD GO	PICK1_RAT	PRKCA-binding protein (Protein kinase C-alpha-binding protein) (Protein interacting with C kinase 1) ...	0.11	-	cyt	0	Cytoplasm; perinuclear region. Membrane; peripheral membrane protein. Also membrane-associated, pres ...	cytoplasm [ISS] Golgi apparatus [ISS] perinuclear region [ISS] plasma membrane [ISS] postsynaptic density [IDA] presynaptic membrane [ISS] synapse [IDA] synaptosome [IDA]			416
Q2VL61 UniProt NPD GO	PAX9_MACMU	Paired box protein Pax-9	0.11	-	nuc	0	Nucleus				341
Q2VL62 UniProt NPD GO	PAX9_PANTR	Paired box protein Pax-9	0.11	-	nuc	0	Nucleus				341
Q20390 UniProt NPD GO	PPT1_CAEEL	Palmitoyl-protein thioesterase 1 precursor (EC 3.1.2.22) (PPT-1) (Palmitoyl-protein hydrolase 1)	0.11	-	end	0					298
Q5KP49 UniProt NPD GO	AKR1_CRYNE	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.11	-	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				776
Q09701 UniProt NPD GO	AKR1_SCHPO	Palmitoyltransferase akr1 (EC 2.3.1.-) (Ankyrin repeat-containing protein akr1)	0.11	-	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				642
P01302 UniProt NPD GO	PAHO_BOVIN	Pancreatic prohormone precursor (Pancreatic polypeptide) (PP) [Contains: Pancreatic hormone; C-termi ...	0.11	-	exc	1 *	Secreted protein			1V1D	131
P19218 UniProt NPD GO	GP2_RAT	Pancreatic secretory granule membrane major glycoprotein GP2 precursor (Pancreatic zymogen granule m ...	0.11	-	end	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein. Secreted after cleavage in the pancreatic ...				530
Q9Z0K8 UniProt NPD GO	VNN1_MOUSE	Pantetheinase precursor (EC 3.5.1.92) (Pantetheine hydrolase) (Vascular non-inflammatory molecule 1) ...	0.11	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				512
P07743 UniProt NPD GO	PSP_MOUSE	Parotid secretory protein precursor (PSP)	0.11	-	mit	0	Secreted protein	extracellular region [TAS]			235
Q9VJS7 UniProt NPD GO	PBURS_DROME	Partner of bursicon precursor (Bursicon subunit beta)	0.11	-	nuc	0	Secreted protein	extracellular region [IDA]			141
P07745 UniProt NPD GO	PAT0_SOLTU	Patatin precursor (Potato tuber protein)	0.11	-	exc	1 *					386
P40973 UniProt NPD GO	PEL_LILLO	Pectate lyase precursor (EC 4.2.2.2)	0.11	-	vac	0					434
P20141 UniProt NPD GO	PEP3_THUTO	Pepsin-3 precursor (EC 3.4.23.-) (Fragment)	0.11	-	nuc	0					60
P29203 UniProt NPD GO	PYY_CHICK	Peptide YY-like (PYY)	0.11	-	nuc	0	Secreted protein				37
Q9PT99 UniProt NPD GO	PYY_DICLA	Peptide YY-like precursor (PYY)	0.11	-	nuc	0	Secreted protein				99
Q765P2 UniProt NPD GO	PGRP3_HOLDI	Peptidoglycan-recognition protein 3 precursor (Hd-PGRP-3)	0.11	-	vac	1 *	Secreted protein (By similarity)				187
Q4WIF3 UniProt NPD GO	PPID_ASPFU	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.11	-	cyt	0	Cytoplasm (By similarity)				377
Q5B5W1 UniProt NPD GO	PIN4_EMENI	Peptidyl-prolyl cis-trans isomerase pin4 (EC 5.2.1.8) (PPIase pin4) (Parvulin pin4)	0.11	-	nuc	0					128
Q95UE8 UniProt NPD GO	PE55_LUCCU	Peritrophin-55 precursor	0.11	-	exc	0					220
Q9SUT2 UniProt NPD GO	PER39_ARATH	Peroxidase 39 precursor (EC 1.11.1.7) (Atperox P39) (ATP19a)	0.11	-	exc	0	Secreted protein (By similarity)				326
P59120 UniProt NPD GO	PER58_ARATH	Peroxidase 58 precursor (EC 1.11.1.7) (Atperox P58) (ATP42)	0.11	-	end	0	Secreted protein (By similarity)				329
Q9LNL0 UniProt NPD GO	PER8_ARATH	Peroxidase 8 precursor (EC 1.11.1.7) (Atperox P8)	0.11	-	exc	0	Secreted protein (By similarity)				310
Q13162 UniProt NPD GO	PRDX4_HUMAN	Peroxiredoxin-4 (EC 1.11.1.15) (Prx-IV) (Thioredoxin peroxidase AO372) (Thioredoxin-dependent peroxi ...	0.11	-	cyt	0	Cytoplasm		606506		271
P14717 UniProt NPD GO	PAL1_ORYSA	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.11	-	nuc	0	Cytoplasm (Probable)				701
P45733 UniProt NPD GO	PAL3_TOBAC	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.11	-	nuc	0	Cytoplasm (Probable)				712
P52777 UniProt NPD GO	PALY_PINTA	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.11	-	cyt	0	Cytoplasm (Probable)				754
P31426 UniProt NPD GO	PAL2_SOLTU	Phenylalanine ammonia-lyase 2 (EC 4.3.1.5) (Fragment)	0.11	-	nuc	0	Cytoplasm (Probable)				590
O49836 UniProt NPD GO	PAL2_LITER	Phenylalanine ammonia-lyase 2 (EC 4.3.1.5) (PAL-2)	0.11	-	cyt	0	Cytoplasm (Probable)				705
P01539 UniProt NPD GO	THN_PHOTO	Phoratoxin	0.11	-	nuc	0	Secreted protein				46
Q9UKL6 UniProt NPD GO	PPCT_HUMAN	Phosphatidylcholine transfer protein (PC-TP) (StAR-related lipid transfer protein 2) (StARD2) (START ...	0.11	-	cyt	0	Cytoplasm (By similarity)	cytosol [NAS]	606055	1LN3	214
P48738 UniProt NPD GO	PIPNA_RABIT	Phosphatidylinositol transfer protein alpha isoform (PtdIns transfer protein alpha) (PtdInsTP) (PI-T ...	0.11	-	cyt	0	Cytoplasm				269
P34725 UniProt NPD GO	AROF_CANAL	Phospho-2-dehydro-3-deoxyheptonate aldolase, phenylalanine-inhibited (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.11	-	nuc	0					368
Q16822 UniProt NPD GO	PPCKM_HUMAN	Phosphoenolpyruvate carboxykinase [GTP], mitochondrial precursor (EC 4.1.1.32) (Phosphoenolpyruvate ...	0.11	-	mit	0	Mitochondrion	mitochondrion [TAS]	261650		640
Q8BH04 UniProt NPD GO	PPCKM_MOUSE	Phosphoenolpyruvate carboxykinase [GTP], mitochondrial precursor (EC 4.1.1.32) (Phosphoenolpyruvate ...	0.11	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			640
Q9D0F9 UniProt NPD GO	PGM1_MOUSE	Phosphoglucomutase-1 (EC 5.4.2.2) (Glucose phosphomutase 1) (PGM 1)	0.11	-	nuc	0	Cytoplasm (By similarity)				561
P07378 UniProt NPD GO	PGKC_TRYBB	Phosphoglycerate kinase, glycosomal (EC 2.7.2.3) (Phosphoglycerate kinase C)	0.11	-	nuc	0	Glycosome			16PK	440
P18669 UniProt NPD GO	PGAM1_HUMAN	Phosphoglycerate mutase 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (Phosphoglycerate mutase isozyme B ...	0.11	-	cyt	0		cytosol [NAS]	172250	1YJX	253
Q5RFB8 UniProt NPD GO	PGAM1_PONPY	Phosphoglycerate mutase 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (Phosphoglycerate mutase isozyme B ...	0.11	-	cyt	0					253
P29601 UniProt NPD GO	PA2H_BUNFA	Phospholipase A2 homolog	0.11	-	nuc	0	Secreted protein				118
P82114 UniProt NPD GO	PA21B_BOTMO	Phospholipase A2 homolog 1 (Myotoxin I) (MjTX-I)	0.11	-	nuc	0	Secreted protein				121
P41485 UniProt NPD GO	PA2H_XENLA	Phospholipase A2 homolog otoconin-22 (Oc22)	0.11	-	nuc	0	Secreted protein (By similarity)				127
P00621 UniProt NPD GO	PA22_BITNA	Phospholipase A2 isozyme CM-II (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.11	-	nuc	0	Secreted protein				119
Q9PUH8 UniProt NPD GO	PA26_AUSSU	Phospholipase A2 isozyme S3-24 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA6) ...	0.11	-	exc	0	Secreted protein (By similarity)				147
Q9PUH0 UniProt NPD GO	PA214_AUSSU	Phospholipase A2 isozyme S8-51 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA14 ...	0.11	-	exc	0	Secreted protein (By similarity)				146
Q8UW08 UniProt NPD GO	PA20_LAPHA	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.11	-	exc	1 *	Secreted protein (By similarity)				146

You are viewing entries 63201 to 63250 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.