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
Q36425 UniProt NPD GO	NU6M_LOCMI	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.14	-	end	4 *					173
P50126 UniProt NPD GO	NCPR_CANMA	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.14	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				680
Q6P8D9 UniProt NPD GO	UBC12_XENTR	NEDD8-conjugating enzyme Ubc12 (EC 6.3.2.-) (Ubiquitin-conjugating enzyme E2 M) (NEDD8 protein ligas ...	0.14	-	nuc	0					183
Q9GZT8 UniProt NPD GO	NIF3L_HUMAN	NIF3-like protein 1 (Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 1 protein)	0.14	-	mit	0	Cytoplasm		605778		350
O82264 UniProt NPD GO	NPL42_ARATH	NPL4-like protein 2	0.14	-	cyt	0					413
Q06942 UniProt NPD GO	FL3H_MALDO	Naringenin,2-oxoglutarate 3-dioxygenase (EC 1.14.11.9) (Flavonone-3-hydroxylase) (F3H) (FHT)	0.14	-	cyt	0					364
P27811 UniProt NPD GO	KLRBA_MOUSE	Natural killer cell surface protein P1-2 (NKR-P1 2) (NKR-P1.7)	0.14	-	nuc	1 *	Membrane; single-pass type II membrane protein				227
Q8WMJ7 UniProt NPD GO	NXPH4_MACMU	Neurexophilin-4 (Fragment)	0.14	-	nuc	0	Secreted protein (Potential)				77
Q58CW4 UniProt NPD GO	NMUR2_BOVIN	Neuromedin U receptor 2 (NMU-R2)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				407
Q5IS76 UniProt NPD GO	ACHA6_PANTR	Neuronal acetylcholine receptor protein subunit alpha-6 precursor	0.14	-	end	4	Membrane; multi-pass membrane protein (By similarity)				494
P12391 UniProt NPD GO	ACHB3_RAT	Neuronal acetylcholine receptor protein subunit beta-3 precursor	0.14	-	end	4 *	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]			464
O70340 UniProt NPD GO	NPTX2_MOUSE	Neuronal pentraxin-2 precursor (NP2) (Neuronal pentraxin II) (NP-II)	0.14	-	nuc	0	Secreted protein (By similarity)				429
Q9GZQ6 UniProt NPD GO	NPFF1_HUMAN	Neuropeptide FF receptor 1 (G-protein coupled receptor 147) (RFamide-related peptide receptor OT7T02 ...	0.14	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	607448		430
O76201 UniProt NPD GO	TX32_PHONI	Neurotoxin Tx3-2 precursor	0.14	-	exc	0	Secreted protein				82
P84716 UniProt NPD GO	TXL1_CAURH	Neurotoxin-like protein 1	0.14	-	nuc	0	Secreted protein				61
P34131 UniProt NPD GO	NT5_RAT	Neurotrophin-5 precursor (NT-5) (Neutrophic factor 5) (Neurotrophin-4) (NT-4) (Neutrophic factor 4)	0.14	-	exc	0	Secreted protein				209
P46076 UniProt NPD GO	NPII_ASPOR	Neutral protease 2 precursor (EC 3.4.24.39) (Neutral protease II) (NPII) (Deuterolysin)	0.14	-	mit	0				1EB6	352
O77775 UniProt NPD GO	NCF2_BOVIN	Neutrophil cytosol factor 2 (NCF-2) (Neutrophil NADPH oxidase factor 2) (67 kDa neutrophil oxidase f ...	0.14	-	cyt	0	Cytoplasm				527
P11832 UniProt NPD GO	NIA1_ARATH	Nitrate reductase [NADH] 1 (EC 1.7.1.1) (NR1)	0.14	-	cyt	0					917
P36842 UniProt NPD GO	NIA_LEPMC	Nitrate reductase [NADPH] (EC 1.7.1.3) (NR)	0.14	-	cyt	0					893
P80450 UniProt NPD GO	NLTP_AMACA	Nonspecific lipid-transfer protein (LTP) (Phospholipid transfer protein) (PLTP)	0.14	-	nuc	0					94
P83167 UniProt NPD GO	NLTP1_AMAHP	Nonspecific lipid-transfer protein 1 (LTP 1) (NS-LTP1)	0.14	-	nuc	0					94
P82900 UniProt NPD GO	NLT2G_WHEAT	Nonspecific lipid-transfer protein 2G (LTP2G) (Lipid transfer protein 2 isoform 1) (LTP2-1) (7 kDa l ...	0.14	-	nuc	0				1TUK	67
P82901 UniProt NPD GO	NLT2P_WHEAT	Nonspecific lipid-transfer protein 2P (LTP2P) (Lipid transfer protein 2 isoform 2) (LTP2-2) (7 kDa l ...	0.14	-	nuc	0					67
O24418 UniProt NPD GO	NLTP6_GOSHI	Nonspecific lipid-transfer protein 6 precursor (LTP)	0.14	-	exc	0					120
Q8NJ52 UniProt NPD GO	NTF2_CLAHE	Nuclear transport factor 2 (NTF-2) (Allergen Cla h ?)	0.14	-	cyt	0	Cytoplasm (By similarity)				125
O00746 UniProt NPD GO	NDKM_HUMAN	Nucleoside diphosphate kinase, mitochondrial precursor (EC 2.7.4.6) (NDP kinase, mitochondrial) (NDK ...	0.14	-	mit	0	Mitochondrion; mitochondrial intermembrane space	mitochondrion [TAS]	601818	1EHW	187
Q6P3D0 UniProt NPD GO	NUD16_MOUSE	Nucleoside diphosphate-linked moiety X motif 16 (EC 3.6.1.-) (Nudix motif 16)	0.14	-	cyt	0					195
Q8TB37 UniProt NPD GO	NUBPL_HUMAN	Nucleotide-binding protein-like	0.14	-	mit	0					319
Q9CQ48 UniProt NPD GO	NUDC2_MOUSE	NudC domain-containing protein 2	0.14	-	cyt	0					157
Q5M823 UniProt NPD GO	NUDC2_RAT	NudC domain-containing protein 2	0.14	-	cyt	0					157
Q8VXZ0 UniProt NPD GO	NUD20_ARATH	Nudix hydrolase 20, chloroplast precursor (EC 3.6.1.-) (AtNUDT20)	0.14	-	mit	0	Plastid; chloroplast (Potential)				374
O49813 UniProt NPD GO	OLEE1_BETVE	Olee1-like protein precursor	0.14	-	exc	0	Secreted protein (Potential)				166
Q8NG85 UniProt NPD GO	OR2L3_HUMAN	Olfactory receptor 2L3	0.14	-	end	7 *	Membrane; multi-pass membrane protein				312
Q9NZP2 UniProt NPD GO	OR6C2_HUMAN	Olfactory receptor 6C2 (HSA3)	0.14	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			312
Q8NGY6 UniProt NPD GO	OR6N2_HUMAN	Olfactory receptor 6N2	0.14	-	end	7 *	Membrane; multi-pass membrane protein				317
Q8NGP2 UniProt NPD GO	OR8J1_HUMAN	Olfactory receptor 8J1	0.14	-	end	7 *	Membrane; multi-pass membrane protein				316
P23274 UniProt NPD GO	OLF15_RAT	Olfactory receptor-like protein I15	0.14	-	end	6 *	Membrane; multi-pass membrane protein				314
Q6AYD2 UniProt NPD GO	OBFC1_RAT	Oligonucleotide/oligosaccharide-binding fold-containing protein 1	0.14	-	cyt	0					408
Q5A6N8 UniProt NPD GO	RFT1_CANAL	Oligosaccharide translocation protein RFT1	0.14	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				561
P58920 UniProt NPD GO	CXO6D_CONCT	Omega-conotoxin CVID precursor (AM336) (AM-336)	0.14	-	exc	1 *	Secreted protein				73
Q9XZK4 UniProt NPD GO	CXSO5_CONST	Omega-type conotoxin SO5 precursor	0.14	-	exc	0	Secreted protein (By similarity)				77
P14995 UniProt NPD GO	OTC_PACTA	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.14	-	mit	0	Mitochondrion; mitochondrial matrix				347
P21594 UniProt NPD GO	PYRF_TRIRE	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.14	-	mit	0					381
P43136 UniProt NPD GO	EAR2_MOUSE	Orphan nuclear receptor EAR-2 (V-erbA-related protein EAR-2)	0.14	-	cyt	0	Nucleus (Potential)				390
O09017 UniProt NPD GO	EAR2_RAT	Orphan nuclear receptor EAR-2 (V-erbA-related protein EAR-2) (Ovalbumin upstream promoter gamma nucl ...	0.14	-	cyt	0	Nucleus (Potential)				390
P21375 UniProt NPD GO	OSM1_YEAST	Osmotic growth protein 1	0.14	-	mit	1 *	Cytoplasm (Probable)	mitochondrion [IDA]			501
Q6P686 UniProt NPD GO	OSTF1_RAT	Osteoclast-stimulating factor 1	0.14	-	cyt	0	Cytoplasm (By similarity)				214
Q9SRH5 UniProt NPD GO	VDAC1_ARATH	Outer mitochondrial membrane protein porin 1 (Voltage-dependent anion-selective channel protein 1) ( ...	0.14	-	cyt	0	Mitochondrion; mitochondrial outer membrane				275
P30559 UniProt NPD GO	OXYR_HUMAN	Oxytocin receptor (OT-R)	0.14	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	167055		389

You are viewing entries 58701 to 58750 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.