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
Q754Q7 UniProt NPD GO	RFT1_ASHGO	Oligosaccharide translocation protein RFT1	0.17	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				552
P46975 UniProt NPD GO	STT3_CAEEL	Oligosaccharyl transferase subunit STT3 homolog	0.17	+	end	12 *	Membrane; multi-pass membrane protein				757
P32063 UniProt NPD GO	STAD_CORSA	Omega-12 acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP ...	0.17	-	mit	0	Plastid; chloroplast. In green tissue, found in chloroplasts. Plastid. In non-photosynthetic tissue, ...				385
P56207 UniProt NPD GO	TOT1A_HADVE	Omega-atracotoxin-Hv1a (Omega-AcTx-Hv1a) (AcTx-Hv1)	0.17	+	nuc	0	Secreted protein			1HVW	37
P83588 UniProt NPD GO	TOM1A_MISBR	Omega-missulenatoxin-Mb1a (Omega-MSTX-Mb1a)	0.17	-	nuc	0	Secreted protein	extracellular region [NAS]			39
P83862 UniProt NPD GO	OX26_BOVIN	Orexigenic neuropeptide QRFP precursor [Contains: QRF-amide (Pyroglutamylated arginine-phenylalanine ...	0.17	-	exc	0	Secreted protein				134
O55241 UniProt NPD GO	OREX_MOUSE	Orexin precursor (Hypocretin) (Hcrt) [Contains: Orexin-A (Hypocretin-1) (Hcrt1); Orexin-B (Hypocreti ...	0.17	-	exc	1 *	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Associated with perikaryal rough ...				130
P21846 UniProt NPD GO	PYRE_TRIRE	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.17	-	cyt	0					236
P01177 UniProt NPD GO	NEU1_PIG	Oxytocin-neurophysin 1 precursor (OT-NPI) [Contains: Oxytocin (Ocytocin); Neurophysin 1]	0.17	-	exc	0				1XY2	125
P83952 UniProt NPD GO	OWAP_OXYMI	Oxywaprin	0.17	-	nuc	0	Secreted protein				50
Q60945 UniProt NPD GO	MTCPB_MOUSE	P13 MTCP-1 protein (Mature T-cell proliferation-1 type B1) (MTCP-1 type B1) (P13MTCP1)	0.17	-	cyt	0					107
Q15077 UniProt NPD GO	P2RY6_HUMAN	P2Y purinoceptor 6 (P2Y6)	0.17	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602451		328
Q9W1W9 UniProt NPD GO	PAP21_DROME	PAP21-like protein precursor	0.17	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			196
Q5EBL8 UniProt NPD GO	PDZ11_HUMAN	PDZ domain-containing protein 11	0.17	-	cyt	0	Isoform 2: Secreted protein (Potential)				140
Q6BLY8 UniProt NPD GO	PFA4_DEBHA	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.17	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				402
P39659 UniProt NPD GO	PAHO_TAPPI	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.17	-	nuc	0	Secreted protein				36
P68248 UniProt NPD GO	PAHO_CHICK	Pancreatic hormone precursor (Pancreatic polypeptide) (PP)	0.17	-	exc	0	Secreted protein				80
P10601 UniProt NPD GO	PAHO_MOUSE	Pancreatic prohormone precursor (Pancreatic polypeptide) (PP) [Contains: Pancreatic hormone; C-termi ...	0.17	-	vac	1 *	Secreted protein				100
P50903 UniProt NPD GO	LIPP_CAVPO	Pancreatic triacylglycerol lipase precursor (EC 3.1.1.3) (Pancreatic lipase) (PL)	0.17	-	vac	0	Secreted protein				465
P41593 UniProt NPD GO	PTHR1_MOUSE	Parathyroid hormone/parathyroid hormone-related peptide receptor precursor (PTH/PTHr receptor) (PTH/ ...	0.17	-	end	7	Membrane; multi-pass membrane protein				591
P25961 UniProt NPD GO	PTHR1_RAT	Parathyroid hormone/parathyroid hormone-related peptide receptor precursor (PTH/PTHr receptor) (PTH/ ...	0.17	-	end	7	Membrane; multi-pass membrane protein				591
P41247 UniProt NPD GO	PLPL4_HUMAN	Patatin-like phospholipase domain-containing protein 4 (Protein GS2) (DXS1283E)	0.17	-	cyt	0			300102		253
P83218 UniProt NPD GO	PME_DAUCA	Pectinesterase (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.17	-	nuc	0				1GQ8	319
P29205 UniProt NPD GO	PYY_AMICA	Peptide YY-like (PYY)	0.17	-	nuc	0	Secreted protein				36
P84005 UniProt NPD GO	PYF1_PENMO	Peptide tyrosine phenylalanine 1 (Pem-PYF1)	0.17	-		0	Secreted protein				6
P82869 UniProt NPD GO	CYP37_ARATH	Peptidyl-prolyl cis-trans isomerase CYP37, chloroplast precursor (EC 5.2.1.8) (PPIase CYP37) (Rotama ...	0.17	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				461
Q5B4E7 UniProt NPD GO	PPID_EMENI	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.17	-	cyt	0	Cytoplasm (By similarity)				372
Q5AQL0 UniProt NPD GO	PPIH_EMENI	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H)	0.17	-	cyt	0	Nucleus (By similarity)				183
Q9SJZ2 UniProt NPD GO	PER17_ARATH	Peroxidase 17 precursor (EC 1.11.1.7) (Atperox P17) (ATP25a)	0.17	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				329
P24102 UniProt NPD GO	PER22_ARATH	Peroxidase 22 precursor (EC 1.11.1.7) (Atperox P22) (ATPEa) (Basic peroxidase E)	0.17	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				349
Q9LDA4 UniProt NPD GO	PER38_ARATH	Peroxidase 38 precursor (EC 1.11.1.7) (Atperox P38)	0.17	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				346
Q96512 UniProt NPD GO	PER9_ARATH	Peroxidase 9 precursor (EC 1.11.1.7) (Atperox P9) (ATP18a)	0.17	-	exc	0	Secreted protein (By similarity)				346
Q00925 UniProt NPD GO	PEX8_PICAN	Peroxisomal biogenesis factor 8 precursor (Peroxin-8) (Peroxisomal protein PER1)	0.17	-	mit	0	Peroxisome; peroxisomal matrix				650
P39108 UniProt NPD GO	PEX7_YEAST	Peroxisomal targeting signal 2 receptor (PTS2 receptor) (Peroxisome import protein PAS7) (Peroxin-7) ...	0.17	-	cyt	0	Cytoplasm	cytosol [IDA] peroxisomal matrix [IDA]			375
Q07869 UniProt NPD GO	PPARA_HUMAN	Peroxisome proliferator-activated receptor alpha (PPAR-alpha)	0.17	+	cyt	0	Nucleus	nucleus [TAS]	170998	1KKQ	468
O60542 UniProt NPD GO	PSPN_HUMAN	Persephin precursor (PSP)	0.17	-	exc	0	Secreted protein		602921		156
Q42667 UniProt NPD GO	PALY_CITLI	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.17	-	nuc	0	Cytoplasm (Probable)				722
Q43210 UniProt NPD GO	PALY_WHEAT	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.17	-	nuc	0	Cytoplasm (Probable)				700
P35511 UniProt NPD GO	PAL1_LYCES	Phenylalanine ammonia-lyase (EC 4.3.1.5) (PAL)	0.17	-	cyt	0	Cytoplasm (Probable)				704
P35510 UniProt NPD GO	PAL1_ARATH	Phenylalanine ammonia-lyase 1 (EC 4.3.1.5)	0.17	-	nuc	0	Cytoplasm (Probable)				725
O23865 UniProt NPD GO	PAL1_DAUCA	Phenylalanine ammonia-lyase 1 (EC 4.3.1.5)	0.17	-	nuc	0	Cytoplasm (Probable)				708
P45725 UniProt NPD GO	PAL3_ARATH	Phenylalanine ammonia-lyase 3 (EC 4.3.1.5)	0.17	-	end	0	Cytoplasm (Probable)				694
P45729 UniProt NPD GO	PAL3_PETCR	Phenylalanine ammonia-lyase 3 (EC 4.3.1.5)	0.17	-	nuc	0	Cytoplasm (Probable)				718
P39551 UniProt NPD GO	PRM9_YEAST	Pheromone-regulated membrane protein 9 (DUP240 protein PRM9)	0.17	-	end	2	Cell membrane; multi-pass membrane protein	endoplasmic reticulum [IPI] plasma membrane [IDA]			298
P56079 UniProt NPD GO	CDSA_DROME	Phosphatidate cytidylyltransferase, photoreceptor-specific (EC 2.7.7.41) (CDP-diglyceride synthetase ...	0.17	-	end	7	Membrane; multi-pass membrane protein (Potential)				447
Q00576 UniProt NPD GO	PTSS1_CRIGR	Phosphatidylserine synthase 1 (EC 2.7.8.-) (PtdSer synthase 1) (PSS-1) (Serine-exchange enzyme I)	0.17	-	end	9 *	Membrane; multi-pass membrane protein				471
Q99LH2 UniProt NPD GO	PTSS1_MOUSE	Phosphatidylserine synthase 1 (EC 2.7.8.-) (PtdSer synthase 1) (PSS-1) (Serine-exchange enzyme I)	0.17	-	end	9 *	Membrane; multi-pass membrane protein				473
Q9CYR6 UniProt NPD GO	AGM1_MOUSE	Phosphoacetylglucosamine mutase (EC 5.4.2.3) (PAGM) (Acetylglucosamine phosphomutase) (N-acetylgluco ...	0.17	-	cyt	0				1WJW	542
Q5ZLN1 UniProt NPD GO	PGAM1_CHICK	Phosphoglycerate mutase 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (BPG-dependent PGAM 1)	0.17	-	mit	0					253
P27612 UniProt NPD GO	PLAP_MOUSE	Phospholipase A-2-activating protein (PLAP)	0.17	-	cyt	0					794

You are viewing entries 54651 to 54700 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.