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
Q8K2X3 UniProt NPD GO	OBFC1_MOUSE	Oligonucleotide/oligosaccharide-binding fold-containing protein 1	0.29	-	cyt	0				1WJ5	371
P01522 UniProt NPD GO	CXO6_CONGE	Omega-conotoxin GVIA precursor (Shaker peptide) (SNX-124) [Contains: Omega-conotoxin GVIB; Omega-con ...	0.29	-	exc	1 *	Secreted protein			2CCO	73
Q9XZL4 UniProt NPD GO	CXS61_CONST	Omega-conotoxin SVIA mutant 1 precursor	0.29	-	exc	1 *	Secreted protein				72
P60253 UniProt NPD GO	SCX2_OPICA	Opicalcin-2 precursor (Opicalcine-2)	0.29	-	nuc	1 *	Secreted protein				66
Q6U736 UniProt NPD GO	OPN5_HUMAN	Opsin-5 (Neuropsin) (G-protein coupled receptor 136) (G-protein coupled receptor PGR12) (Transmembra ...	0.29	+	end	7 *	Membrane; multi-pass membrane protein		609042		353
Q9Y267 UniProt NPD GO	ORCT4_HUMAN	Organic-cation transporter-like 4 (Solute carrier family 22 member 14)	0.29	-	end	12	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS] membrane fraction [TAS]	604048		594
Q9Z0L3 UniProt NPD GO	OC90_MOUSE	Otoconin 90 precursor (Oc90) (Otoconin-95) (Oc95)	0.29	-	exc	0	Secreted protein (By similarity)	extracellular matrix (sensu Metazoa) [IDA]			485
Q7S4P1 UniProt NPD GO	OXR1_NEUCR	Oxidation resistance protein 1	0.29	-	nuc	0	Mitochondrion (By similarity)				355
P12301 UniProt NPD GO	PSBQ_SPIOL	Oxygen-evolving enhancer protein 3, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolving ...	0.29	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex			1VYK	232
P38755 UniProt NPD GO	OSH7_YEAST	Oxysterol-binding protein homolog 7	0.29	-	cyt	0					437
Q9EPX4 UniProt NPD GO	P2Y12_RAT	P2Y purinoceptor 12 (P2Y12) (P2Y12 platelet ADP receptor)	0.29	-	end	7 *	Membrane; multi-pass membrane protein				343
P41231 UniProt NPD GO	P2RY2_HUMAN	P2Y purinoceptor 2 (P2Y2) (P2U purinoceptor 1) (P2U1) (ATP receptor) (Purinergic receptor)	0.29	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600041		377
P35383 UniProt NPD GO	P2RY2_MOUSE	P2Y purinoceptor 2 (P2Y2) (P2U purinoceptor 1) (P2U1) (ATP receptor) (Purinergic receptor)	0.29	-	end	6 *	Membrane; multi-pass membrane protein				373
P41232 UniProt NPD GO	P2RY2_RAT	P2Y purinoceptor 2 (P2Y2) (P2U purinoceptor 1) (P2U1) (ATP receptor) (Purinergic receptor)	0.29	-	end	6 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] basolateral plasma membrane [IDA]			374
Q9PU47 UniProt NPD GO	PDLI3_CHICK	PDZ and LIM domain protein 3 (Alpha-actinin-associated LIM protein)	0.29	-	nuc	0	Isoform 1 colocalizes with alpha-actinin along actin stress fibers and lammellipodia of spreading fi ...				315
Q3SX40 UniProt NPD GO	PDLI7_BOVIN	PDZ and LIM domain protein 7	0.29	-	nuc	0	Cytoplasm (By similarity). Colocalizes with RET to the cell periphery and in some cytoskeletal compo ...				424
Q9NR12 UniProt NPD GO	PDLI7_HUMAN	PDZ and LIM domain protein 7 (LIM mineralization protein) (LMP) (Protein enigma)	0.29	-	nuc	0	Cytoplasm (By similarity). Colocalizes with RET to the cell periphery and in some cytoskeletal compo ...		605903		457
Q9Z254 UniProt NPD GO	GIPC1_RAT	PDZ domain-containing protein GIPC1 (RGS19-interacting protein 1) (GAIP C-terminus-interacting prote ...	0.29	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				333
P07765 UniProt NPD GO	PF2L_PLAFP	PPF2L antigen (Fragment)	0.29	-	nuc	0					70
Q59QL0 UniProt NPD GO	ERFB_CANAL	Palmitoyltransferase ERF2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein ERF2) (Ras prot ...	0.29	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				382
Q8TE04 UniProt NPD GO	PANK1_HUMAN	Pantothenate kinase 1 (EC 2.7.1.33) (Pantothenic acid kinase 1) (hPanK1) (hPanK)	0.29	-	cyt	0	Cytoplasm		606160		598
P20962 UniProt NPD GO	PTMS_HUMAN	Parathymosin	0.29	-	nuc	0		nucleus [TAS]	168440		101
Q43062 UniProt NPD GO	PME_PRUPE	Pectinesterase PPE8B precursor (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.29	-	exc	0					522
Q9P7R0 UniProt NPD GO	ARO1_SCHPO	Pentafunctional AROM polypeptide [Includes: 3-dehydroquinate synthase (EC 4.2.3.4); 3-dehydroquinate ...	0.29	-	nuc	1	Cytoplasm (By similarity)				1573
Q9SEC2 UniProt NPD GO	MSRA_LACSA	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (Peptide ...	0.29	-	mit	0					259
Q4WVU5 UniProt NPD GO	PPIL2_ASPFU	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.29	-	nuc	0	Nucleus (By similarity)				579
Q25478 UniProt NPD GO	PER_MANSE	Period circadian protein (Fragment)	0.29	-	cyt	0	Nucleus. Nuclear at specific periods of the day. Interaction with TIM is required for nuclear locali ...				354
Q13610 UniProt NPD GO	PWP1_HUMAN	Periodic tryptophan protein 1 homolog (Keratinocyte protein IEF SSP 9502)	0.29	+	mit	0	Nucleus	nucleus [TAS]			501
Q9LSP0 UniProt NPD GO	PER29_ARATH	Peroxidase 29 precursor (EC 1.11.1.7) (Atperox P29) (ATP40)	0.29	-	exc	0	Secreted protein (By similarity)				339
P00434 UniProt NPD GO	PERP7_BRARA	Peroxidase P7 (EC 1.11.1.7) (TP7)	0.29	-	nuc	0					296
P55100 UniProt NPD GO	ECHP_CAVPO	Peroxisomal bifunctional enzyme (PBE) (PBFE) [Includes: Enoyl-CoA hydratase (EC 4.2.1.17); 3,2-trans ...	0.29	-	pox	0	Peroxisome				725
Q92266 UniProt NPD GO	PEX13_PICPA	Peroxisomal membrane protein PEX13 (Peroxin-13)	0.29	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				380
Q00317 UniProt NPD GO	PX11B_CANBO	Peroxisomal membrane protein PMP30B (PMP32) (Peroxin-11B)	0.29	-	cyt	0	Peroxisome; peroxisomal membrane; peripheral membrane protein				256
P31303 UniProt NPD GO	PRA2_USTMA	Pheromone receptor 2	0.29	+	end	6 *	Membrane; multi-pass membrane protein				346
P32363 UniProt NPD GO	GPI3_YEAST	Phosphatidylinositol N-acetylglucosaminyltransferase GPI3 subunit (EC 2.4.1.198) (GlcNAc-PI synthesi ...	0.29	-	nuc	0		endoplasmic reticulum [IMP] glycosylphosphatidylinositol-N-acetylglucos... [TAS]			461
Q756D4 UniProt NPD GO	GPI19_ASHGO	Phosphatidylinositol N-acetylglucosaminyltransferase subunit GPI19 (EC 2.4.1.198)	0.29	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q4R6N0 UniProt NPD GO	TPTE2_MACFA	Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2 (EC 3.1.3.67)	0.29	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				566
P48426 UniProt NPD GO	PI52A_HUMAN	Phosphatidylinositol-4-phosphate 5-kinase type-2 alpha (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.29	-	mit	0			603140		406
O95394 UniProt NPD GO	AGM1_HUMAN	Phosphoacetylglucosamine mutase (EC 5.4.2.3) (PAGM) (Acetylglucosamine phosphomutase) (N-acetylgluco ...	0.29	-	nuc	0			172100		542
O04865 UniProt NPD GO	PLDA1_VIGUN	Phospholipase D alpha 1 (EC 3.1.4.4) (PLD alpha 1) (Choline phosphatase 1) (Phosphatidylcholine-hydr ...	0.29	-	cyt	0					809
Q9C888 UniProt NPD GO	PLDE1_ARATH	Phospholipase D epsilon (EC 3.1.4.4) (AtPLDepsilon) (PLD epsilon) (PLDalpha3)	0.29	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				762
Q92871 UniProt NPD GO	PMM1_HUMAN	Phosphomannomutase 1 (EC 5.4.2.8) (PMM 1) (PMMH-22)	0.29	-	cyt	0	Cytoplasm		601786	2FUE	262
P35421 UniProt NPD GO	PUR4_DROME	Phosphoribosylformylglycinamidine synthase (EC 6.3.5.3) (FGAM synthase) (FGAMS) (Formylglycinamide r ...	0.29	-	nuc	0					1354
Q2KJ16 UniProt NPD GO	PHKG2_BOVIN	Phosphorylase b kinase gamma catalytic chain, testis/liver isoform (EC 2.7.11.19) (PHK-gamma-T) (Pho ...	0.29	-	cyt	0					406
Q64568 UniProt NPD GO	AT2B3_RAT	Plasma membrane calcium-transporting ATPase 3 (EC 3.6.3.8) (PMCA3) (Plasma membrane calcium pump iso ...	0.29	-	end	6	Cell membrane; multi-pass membrane protein				1258
Q94KU6 UniProt NPD GO	PAP2_BRACM	Plastid lipid-associated protein 2, chloroplast precursor	0.29	-	mit	0	Plastid; chloroplast				319
Q28262 UniProt NPD GO	PAFA_CANFA	Platelet-activating factor acetylhydrolase precursor (EC 3.1.1.47) (PAF acetylhydrolase) (PAF 2-acyl ...	0.29	-	exc	0	Secreted protein; extracellular space				444
P46002 UniProt NPD GO	PTAFR_RAT	Platelet-activating factor receptor (PAF-R)	0.29	-	end	7 *	Membrane; multi-pass membrane protein				341
Q8GU90 UniProt NPD GO	PDR3_ORYSA	Pleiotropic drug resistance protein 3	0.29	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1457
Q8GU89 UniProt NPD GO	PDR4_ORYSA	Pleiotropic drug resistance protein 4	0.29	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1450

You are viewing entries 41551 to 41600 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.