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
P37116 UniProt NPD GO	NCPR_PHAAU	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.07	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...				690
Q9LK88 UniProt NPD GO	NQR_ARATH	NADPH:quinone oxidoreductase (EC 1.6.5.2)	0.07	-	cyt	0					196
Q4V786 UniProt NPD GO	NFIP1_XENTR	NEDD4 family-interacting protein 1	0.07	-	vac	3	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				211
Q6C9W0 UniProt NPD GO	UBC12_YARLI	NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-) (RUB1-conjugating enzyme) (RUB1-protein ligase) (Ubiquit ...	0.07	-	cyt	0					179
Q91WC7 UniProt NPD GO	NPAL2_MOUSE	NIPA-like protein 2	0.07	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				383
P83350 UniProt NPD GO	FMRF1_SARBU	Neb-FMRFamide-1	0.07	-		0	Secreted protein				9
Q6WZ19 UniProt NPD GO	NGB_BOVIN	Neuroglobin	0.07	-	cyt	0					151
Q6WZ18 UniProt NPD GO	NGB_CANFA	Neuroglobin	0.07	-	cyt	0					151
Q68RJ7 UniProt NPD GO	ACH92_ONCMY	Neuronal acetylcholine receptor protein subunit alpha-9-II precursor (Nicotinic acetylcholine recept ...	0.07	-	end	4	Membrane; multi-pass membrane protein (Probable)				550
Q8BMN3 UniProt NPD GO	ACHB3_MOUSE	Neuronal acetylcholine receptor protein subunit beta-3 precursor	0.07	-	end	4	Membrane; multi-pass membrane protein				464
P13908 UniProt NPD GO	ACHN2_CARAU	Neuronal acetylcholine receptor protein subunit non-alpha-2 precursor (GFN-alpha-2)	0.07	-	end	4 *	Membrane; multi-pass membrane protein				462
Q7Z3B1 UniProt NPD GO	NEGR1_HUMAN	Neuronal growth regulator 1 precursor	0.07	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				354
Q5R603 UniProt NPD GO	GPM6B_PONPY	Neuronal membrane glycoprotein M6-b (M6b)	0.07	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				265
Q07475 UniProt NPD GO	NP311_MOUSE	Neuronal protein 3.1 (p311 protein)	0.07	-	cyt	0					68
Q62649 UniProt NPD GO	NNAT_RAT	Neuronatin	0.07	-	mit	1 *					81
P49146 UniProt NPD GO	NPY2R_HUMAN	Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor)	0.07	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	162642		381
Q9GK74 UniProt NPD GO	NPY2R_MACMU	Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor)	0.07	-	end	7	Membrane; multi-pass membrane protein				381
Q5IS62 UniProt NPD GO	NPY2R_PANTR	Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor)	0.07	-	end	7	Membrane; multi-pass membrane protein (By similarity)				381
P15444 UniProt NPD GO	NEU1_STRCA	Neurophysin 1	0.07	-	nuc	0					93
P83895 UniProt NPD GO	TX19_PHOKE	Neurotoxin PKTx19C5	0.07	-	nuc	0	Secreted protein				46
P83998 UniProt NPD GO	TX22_PHONI	Neurotoxin PNTx22A0C1	0.07	-	nuc	0	Secreted protein				35
P84017 UniProt NPD GO	TX24_PHONI	Neurotoxin PNTx24A0C3	0.07	-	nuc	0	Secreted protein				31
O76200 UniProt NPD GO	TX31_PHONI	Neurotoxin Tx3-1 precursor	0.07	-	exc	0	Secreted protein				83
P01481 UniProt NPD GO	SCX5_LEIQU	Neurotoxin V (Lqq V) (Lqq5)	0.07	-	nuc	0	Secreted protein				64
P30831 UniProt NPD GO	TXA1_RADMA	Neurotoxin-1 (Toxin RTX-I)	0.07	-	nuc	0	Secreted protein. Found in nematocyst				48
P01535 UniProt NPD GO	TXA3_ANESU	Neurotoxin-3 (Neurotoxin III) (Toxin ATX-III)	0.07	-	nuc	0	Secreted protein. Found in nematocyst			1ANS	27
P08380 UniProt NPD GO	TXA3_RADPA	Neurotoxin-3 (Neurotoxin-III) (Toxin RpIII) (Sodium channel toxin III)	0.07	-	nuc	0	Secreted protein. Found in nematocyst				48
P30832 UniProt NPD GO	TXA3_RADMA	Neurotoxin-3 (Toxin RTX-III)	0.07	-	nuc	0	Secreted protein. Found in nematocyst				48
P30784 UniProt NPD GO	TXA4_RADMA	Neurotoxin-4 (Toxin RTX-IV)	0.07	-	nuc	0	Secreted protein. Found in nematocyst				48
Q91XT9 UniProt NPD GO	ASAH2_RAT	Neutral ceramidase (EC 3.5.1.23) (NCDase) (N-CDase) (Acylsphingosine deacylase 2) (N-acylsphingosine ...	0.07	-	end	1 *	Cell membrane; single-pass type II membrane protein. The neutral ceramidase soluble form is a secret ...				761
Q9FF79 UniProt NPD GO	NAS1_ARATH	Nicotianamine synthase 1 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-m ...	0.07	-	nuc	0					320
O80483 UniProt NPD GO	NAS3_ARATH	Nicotianamine synthase 3 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-m ...	0.07	-	cyt	0					320
Q9FXW5 UniProt NPD GO	NAS3_ORYSA	Nicotianamine synthase 3 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-m ...	0.07	-	nuc	0					343
Q40987 UniProt NPD GO	LECR_PEA	Nodule lectin precursor (PsNlec-1)	0.07	-	mit	1 *	Peribacteroid space and peribacteroid membrane. Also associates directly or indirectly with the cell ...				270
Q43193 UniProt NPD GO	NLTP1_SORBI	Nonspecific lipid-transfer protein 1 precursor (LTP 1)	0.07	-	exc	1 *					118
Q43194 UniProt NPD GO	NLTP2_SORBI	Nonspecific lipid-transfer protein 2 precursor (LTP 2)	0.07	-	exc	1 *					122
Q9NVX2 UniProt NPD GO	NLE1_HUMAN	Notchless homolog 1	0.07	-	cyt	0	Nucleus; nucleolus				484
Q63369 UniProt NPD GO	NFKB1_RAT	Nuclear factor NF-kappa-B p105 subunit (DNA-binding factor KBF1) (EBP-1) [Contains: Nuclear factor N ...	0.07	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear, but also found in the cytoplasm in an i ...	cytoplasm [IDA] nucleus [TAS]			522
P24021 UniProt NPD GO	NUS1_ASPOR	Nuclease S1 precursor (EC 3.1.30.1) (Endonuclease S1) (Single-stranded-nucleate endonuclease) (Deoxy ...	0.07	-	exc	0					287
Q9CA40 UniProt NPD GO	NUDT1_ARATH	Nudix hydrolase 1 (EC 3.6.1.-) (AtNUDT1) (NADH pyrophosphatase) (EC 3.6.1.22) (DHNTP pyrophosphohydr ...	0.07	-	cyt	0					147
P0C026 UniProt NPD GO	NUD24_ARATH	Nudix hydrolase 24, chloroplast precursor (EC 3.6.1.-) (AtNUDT24)	0.07	-	mit	0	Plastid; chloroplast (Potential)				365
Q9LE73 UniProt NPD GO	NUDT4_ARATH	Nudix hydrolase 4 (EC 3.6.1.-) (AtNUDT4) (ADP-ribose pyrophosphatase) (EC 3.6.1.13) (NADH pyrophosph ...	0.07	-	cyt	0					207
Q01804 UniProt NPD GO	OTUD4_HUMAN	OTU domain-containing protein 4 (HIV-1-induced protein HIN-1)	0.07	-	cyt	0					145
P58181 UniProt NPD GO	O10A3_HUMAN	Olfactory receptor 10A3 (HTPCRX12)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			314
Q8NGY1 UniProt NPD GO	O10Z1_HUMAN	Olfactory receptor 10Z1	0.07	-	end	7 *	Membrane; multi-pass membrane protein				313
Q60884 UniProt NPD GO	OL146_MOUSE	Olfactory receptor 146 (Olfactory receptor 7D) (Olfactory receptor 171-10) (Odorant receptor M15)	0.07	-	end	8 *	Membrane; multi-pass membrane protein				306
P34987 UniProt NPD GO	O1867_RAT	Olfactory receptor 1867 (Gustatory receptor GUST27)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				312
Q96R84 UniProt NPD GO	OR1F2_HUMAN	Olfactory receptor 1F2 (OLFmf2)	0.07	-	end	5 *	Membrane; multi-pass membrane protein				312
Q8NGS3 UniProt NPD GO	OR1J1_HUMAN	Olfactory receptor 1J1 (Olfactory receptor OR9-18)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				322
Q8NH93 UniProt NPD GO	OR1L3_HUMAN	Olfactory receptor 1L3 (Olfactory receptor 9-D) (OR9-D) (Olfactory receptor OR9-28)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				324

You are viewing entries 70551 to 70600 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.