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
O44662 UniProt NPD GO	NLP31_CAEEL	Neuropeptide-like protein 31 precursor [Contains: QWGYGGY-amide; GYGGYGGY-amide; GYGGY-amide; GMYGGY ...	0.04	-	vac	1 *	Secreted protein (Potential)				75
Q90935 UniProt NPD GO	NEUS_CHICK	Neuroserpin precursor (Axonin-2)	0.04	-	end	0	Secreted protein				410
Q99574 UniProt NPD GO	NEUS_HUMAN	Neuroserpin precursor (Serpin I1) (Protease inhibitor 12)	0.04	-	end	0	Secreted protein		604218		410
P01486 UniProt NPD GO	SCXB_BUTOC	Neurotoxin 11 (Neurotoxin XI) (BotXI)	0.04	-	cyt	0	Secreted protein				65
P01485 UniProt NPD GO	SCX3_BUTOC	Neurotoxin 3 (Neurotoxin III) (Bot III) (BotIII)	0.04	-	nuc	0	Secreted protein				64
Q95WD1 UniProt NPD GO	SCX8_CENSC	Neurotoxin 8 precursor (CsE8)	0.04	-	exc	0	Secreted protein				85
Q3HM34 UniProt NPD GO	SCXKI_MESMA	Neurotoxin KITx precursor (BmKITx)	0.04	-	mit	1 *	Secreted protein				95
P84012 UniProt NPD GO	TX36_PHOKE	Neurotoxin PKTx36C1	0.04	-	nuc	0	Secreted protein				54
P81793 UniProt NPD GO	TX3A_PHONI	Neurotoxin Pn3A precursor	0.04	-	exc	0	Secreted protein				80
P81791 UniProt NPD GO	TX35_PHONI	Neurotoxin Tx3-5 (Fragment)	0.04	-	nuc	0	Secreted protein				36
P80950 UniProt NPD GO	SCXL_ANDAU	Neurotoxin-like protein STR1 (Anatoxin AaH STR1) (AaHSTR1)	0.04	-	cyt	0	Secreted protein				66
Q5W7F1 UniProt NPD GO	ASAH2_BRARE	Neutral ceramidase (EC 3.5.1.23) (NCDase) (N-CDase) (Acylsphingosine deacylase 2) (N-acylsphingosine ...	0.04	-	end	1 *	Cell membrane; single-pass type II membrane protein	apical plasma membrane [IDA] endoplasmic reticulum membrane [IDA] Golgi membrane [IDA]			743
Q9JHE3 UniProt NPD GO	ASAH2_MOUSE	Neutral ceramidase (EC 3.5.1.23) (NCDase) (N-CDase) (Acylsphingosine deacylase 2) (N-acylsphingosine ...	0.04	-	end	1 *	Cell membrane; single-pass type II membrane protein. The neutral ceramidase soluble form is a secret ...	membrane fraction [IDA]			756
Q29C43 UniProt NPD GO	NCASE_DROPS	Neutral ceramidase precursor (EC 3.5.1.23) (NCDase) (N-CDase) (Acylsphingosine deacylase) (N-acylsph ...	0.04	-	end	1 *	Secreted protein (By similarity)				704
P19877 UniProt NPD GO	NAP4_HUMAN	Neutrophil-activating protein 4 (NAP-4) (Fragment)	0.04	-	cyt	0	Secreted protein				31
Q9XFB7 UniProt NPD GO	NAS9_HORVU	Nicotianamine synthase 9 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-m ...	0.04	-	mit	0					340
O55239 UniProt NPD GO	NNMT_MOUSE	Nicotinamide N-methyltransferase (EC 2.1.1.1)	0.04	-	cyt	0	Cytoplasm				264
P43619 UniProt NPD GO	NADC_YEAST	Nicotinate-nucleotide pyrophosphorylase [carboxylating] (EC 2.4.2.19) (Quinolinate phosphoribosyltra ...	0.04	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			295
P08460 UniProt NPD GO	NID1_RAT	Nidogen-1 (Entactin) (Fragment)	0.04	-	cyt	0	Secreted protein; extracellular space; extracellular matrix; basement membrane				324
P36841 UniProt NPD GO	NIA_VOLCA	Nitrate reductase [NADH] (EC 1.7.1.1) (NR)	0.04	-	cyt	0					864
P97270 UniProt NPD GO	NOS3_CAVPO	Nitric-oxide synthase, endothelial (EC 1.14.13.39) (EC-NOS) (NOS type III) (NOSIII) (Endothelial NOS ...	0.04	-	nuc	0					100
Q26241 UniProt NPD GO	NP2_RHOPR	Nitrophorin-2 precursor (NP2) (Prolixin-S)	0.04	-	nuc	0	Secreted protein			2ACP	202
P55791 UniProt NPD GO	PNOC_PIG	Nociceptin (Orphanin FQ)	0.04	-		0	Secreted protein				17
P16313 UniProt NPD GO	NO21_SOYBN	Nodulin 21 (N-21)	0.04	-	end	4					206
Q947C5 UniProt NPD GO	HBL1_GOSHI	Non-symbiotic hemoglobin 1 (Hb1) (GOShi GLB1)	0.04	-	cyt	0					163
P11915 UniProt NPD GO	NLTP_RAT	Nonspecific lipid-transfer protein (EC 2.3.1.176) (Propanoyl-CoA C-acyltransferase) (NSL-TP) (Sterol ...	0.04	-	pox	0	Cytoplasm. Mitochondrion. Isoform SCP-X: Peroxisome. Cytoplasmic in the liver and also associated wi ...				547
P82534 UniProt NPD GO	NLTP1_PRUDO	Nonspecific lipid-transfer protein 1 (LTP 1) (Major allergen Pru d 3)	0.04	-	nuc	0					91
P81402 UniProt NPD GO	NLTP1_PRUPE	Nonspecific lipid-transfer protein 1 (LTP 1) (Major allergen Pru p 3) (Pru p 1)	0.04	-	nuc	0				2B5S	91
Q9LLR7 UniProt NPD GO	NLTP3_ARATH	Nonspecific lipid-transfer protein 3 precursor (LTP 3)	0.04	-	exc	0					115
Q43875 UniProt NPD GO	NLT42_HORVU	Nonspecific lipid-transfer protein 4.2 precursor (LTP 4.2) (Low-temperature-responsive protein 4.9)	0.04	-	mit	1 *					115
Q42842 UniProt NPD GO	NLT43_HORVU	Nonspecific lipid-transfer protein 4.3 precursor (LTP 4.3)	0.04	-	exc	1 *					115
P10975 UniProt NPD GO	NLTPC_RICCO	Nonspecific lipid-transfer protein C, cotyledon-specific isoform precursor (NS-LTP C) (Phospholipid ...	0.04	-	exc	1 *					116
Q43748 UniProt NPD GO	NLTP_BETVU	Nonspecific lipid-transfer protein precursor (LTP)	0.04	-	exc	0					117
O23758 UniProt NPD GO	NLTP_CICAR	Nonspecific lipid-transfer protein precursor (LTP)	0.04	-	exc	1 *					116
Q9M5X8 UniProt NPD GO	NLTP_PRUAV	Nonspecific lipid-transfer protein precursor (LTP) (Allergen Pru av 3)	0.04	-	exc	1 *					117
Q39950 UniProt NPD GO	NLTP_HELAN	Nonspecific lipid-transfer protein precursor (LTP) (NsLTP) (SDI-9)	0.04	-	nuc	0					116
Q8LGU7 UniProt NPD GO	RNZN_ARATH	Nuclear ribonuclease Z (EC 3.1.26.11) (RNase Z) (tRNase Z) (tRNA 3 endonuclease) (Zinc phosphodieste ...	0.04	-	cyt	0	Nucleus (Probable)				280
Q9XJ54 UniProt NPD GO	NTF2_ORYSA	Nuclear transport factor 2 (NTF-2)	0.04	-	cyt	0	Cytoplasm (By similarity)				122
Q9ZU95 UniProt NPD GO	NUD17_ARATH	Nudix hydrolase 17, mitochondrial precursor (EC 3.6.1.-) (AtNUDT17)	0.04	-	mit	0	Mitochondrion (Potential)				182
P81922 UniProt NPD GO	OR47B_DROME	Odorant receptor 47b	0.04	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			412
P29528 UniProt NPD GO	OLEO7_GOSHI	Oleosin 16.4 kDa	0.04	-	end	3 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface (By similarity)				154
Q8VGR8 UniProt NPD GO	O1052_MOUSE	Olfactory receptor 1052 (Olfactory receptor 172-1)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312
Q9H207 UniProt NPD GO	O10A5_HUMAN	Olfactory receptor 10A5 (HP3) (Olfactory receptor-like protein JCG6)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				317
Q8NH74 UniProt NPD GO	O10A6_HUMAN	Olfactory receptor 10A6	0.04	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NH19 UniProt NPD GO	O10AG_HUMAN	Olfactory receptor 10AG1 (Olfactory receptor OR11-160)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				301
Q8NGC3 UniProt NPD GO	O10G2_HUMAN	Olfactory receptor 10G2	0.04	-	end	7 *	Membrane; multi-pass membrane protein				310
O60403 UniProt NPD GO	O10H2_HUMAN	Olfactory receptor 10H2	0.04	-	end	7 *	Membrane; multi-pass membrane protein				315
P34985 UniProt NPD GO	OL143_MOUSE	Olfactory receptor 143 (Olfactory receptor 7A) (Olfactory receptor 170-6) (Odorant receptor K18)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				313
Q8VFX2 UniProt NPD GO	O1444_MOUSE	Olfactory receptor 1444 (Olfactory receptor 202-4)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				319
Q9TU93 UniProt NPD GO	OR1D2_GORGO	Olfactory receptor 1D2	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312

You are viewing entries 77701 to 77750 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.