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
Q92060 UniProt NPD GO	MAOX_CHICK	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME) (Fragment)	0.03	-		0	Cytoplasm				15
P18819 UniProt NPD GO	DHE4_EMENI	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.03	-	cyt	0					459
Q96UJ9 UniProt NPD GO	DHE4_HEBCY	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.03	-	cyt	0					450
Q9HGU4 UniProt NPD GO	DHE4_NEUIN	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.03	-	cyt	0					453
Q9URS1 UniProt NPD GO	DHE4_PENCH	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.03	-	cyt	0					461
P36587 UniProt NPD GO	NCPR_SCHPO	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.03	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				678
P87039 UniProt NPD GO	XYL2_CANTR	NADPH-dependent D-xylose reductase II,III (EC 1.1.1.-) (XR)	0.03	-	cyt	0					324
P38715 UniProt NPD GO	GRE3_YEAST	NADPH-dependent aldose reductase GRE3 (EC 1.1.1.21) (NADPH-dependent aldo-keto reductase GRE3) (NADP ...	0.03	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			327
Q6DGP4 UniProt NPD GO	NFIP1_BRARE	NEDD4 family-interacting protein 1	0.03	-	vac	3	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				210
Q5U2S1 UniProt NPD GO	NFIP1_RAT	NEDD4 family-interacting protein 1	0.03	-	end	3	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				221
Q9BT67 UniProt NPD GO	NFIP1_HUMAN	NEDD4 family-interacting protein 1 (NEDD4 WW domain-binding protein 5) (Putative MAPK-activating pro ...	0.03	-	end	3	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				221
Q8CEC5 UniProt NPD GO	KBRS1_MOUSE	NF-kappa-B inhibitor-interacting Ras-like protein 1 (I-kappa-B-interacting Ras-like protein 1) (Kapp ...	0.03	-	cyt	0	Cytoplasm (By similarity)				192
Q5RD30 UniProt NPD GO	NPAL3_PONPY	NIPA-like protein 3	0.03	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				406
Q8MJ02 UniProt NPD GO	NCTR3_MACMU	Natural cytotoxicity triggering receptor 3 precursor (Natural killer cell p30-related protein) (NKp3 ...	0.03	-	end	0	Membrane; single-pass type I membrane protein (Potential)				201
P61484 UniProt NPD GO	NCTR3_PANTR	Natural cytotoxicity triggering receptor 3 precursor (Natural killer cell p30-related protein) (NKp3 ...	0.03	-	end	0	Membrane; single-pass type I membrane protein (Potential)				201
O14931 UniProt NPD GO	NCTR3_HUMAN	Natural cytotoxicity triggering receptor 3 precursor (Natural killer cell p30-related protein) (NKp3 ...	0.03	-	end	0	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]			201
P05419 UniProt NPD GO	CALN_CHICK	Neo-calmodulin (NeoCaM) (Fragment)	0.03	-	cyt	0					131
Q8WMH2 UniProt NPD GO	NLGN3_MACMU	Neuroligin-3 (Gliotactin homolog) (Fragment)	0.03	-	mit	0	Membrane; single-pass type I membrane protein (Potential)				202
P04757 UniProt NPD GO	ACHA3_RAT	Neuronal acetylcholine receptor protein subunit alpha-3 precursor	0.03	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]			499
P26152 UniProt NPD GO	ACHA5_CHICK	Neuronal acetylcholine receptor protein subunit alpha-5 precursor	0.03	-	end	4	Membrane; multi-pass membrane protein				454
P43679 UniProt NPD GO	ACHB3_CHICK	Neuronal acetylcholine receptor protein subunit beta-3 precursor	0.03	-	end	4	Membrane; multi-pass membrane protein				455
Q9W6V2 UniProt NPD GO	NEGR1_CHICK	Neuronal growth regulator 1 precursor (Neurotractin)	0.03	-	vac	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				352
O44663 UniProt NPD GO	NLP30_CAEEL	Neuropeptide-like protein 30 precursor [Contains: QWGYGGY-amide; GYGGYGGY-amide; GYGGY-amide; GMW-am ...	0.03	-	vac	1 *	Secreted protein (Potential)				69
O35684 UniProt NPD GO	NEUS_MOUSE	Neuroserpin precursor (Serpin I1) (Protease inhibitor 17)	0.03	-	mit	0	Secreted protein			1JJO	410
P31745 UniProt NPD GO	NEUT_TRIVU	Neurotensin (NT)	0.03	-		0	Secreted protein				13
P18926 UniProt NPD GO	SCX1_CENLI	Neurotoxin 1 (Clt1)	0.03	-	cyt	0	Secreted protein				66
P01488 UniProt NPD GO	SCX1_BUTOC	Neurotoxin 1 (Neurotoxin I) (Bot I) (BotI)	0.03	-	nuc	0	Secreted protein				65
P58778 UniProt NPD GO	SCX4_CENSC	Neurotoxin 4 (CsEv4) (CsE v4)	0.03	-	nuc	0	Secreted protein				66
P58488 UniProt NPD GO	SCM2_MESMA	Neurotoxin BmK-M2 (BmK M2) (BmKM2)	0.03	-	nuc	0	Secreted protein			1CHZ	64
P01491 UniProt NPD GO	SCXI_CENSC	Neurotoxin I precursor (CsEI) (CsE-I)	0.03	-	vac	1 *	Secreted protein			2B3C	86
P09982 UniProt NPD GO	SCXE_BUTEU	Neurotoxin M14 (BeM14)	0.03	-	nuc	0	Secreted protein				66
P84062 UniProt NPD GO	TX1A_PHOKE	Neurotoxin PKTx1A (Fragment)	0.03	-	nuc	0	Secreted protein				78
P84063 UniProt NPD GO	TX1B_PHOKE	Neurotoxin PKTx1B (Fragment)	0.03	-	nuc	0	Secreted protein				78
P83910 UniProt NPD GO	TX32_PHOKE	Neurotoxin PKTx32C4	0.03	-	mit	0	Secreted protein				36
P29424 UniProt NPD GO	TX25_PHONI	Neurotoxin Tx2-5	0.03	-	nuc	0	Secreted protein				49
P29426 UniProt NPD GO	TX29_PHONI	Neurotoxin Tx2-9	0.03	-	nuc	0	Secreted protein				32
P81789 UniProt NPD GO	TX33_PHONI	Neurotoxin Tx3-3 (Fragment)	0.03	-	nuc	0	Secreted protein				34
Q17254 UniProt NPD GO	SCXE_BUTOC	Neurotoxin XIV precursor (Bot14) (BotXIV)	0.03	-	nuc	0	Secreted protein				85
P01528 UniProt NPD GO	TXA2_ANESU	Neurotoxin-2 (Toxin ATX-II) (Toxin II)	0.03	-	nuc	0	Secreted protein. Found in nematocyst				47
P01529 UniProt NPD GO	TXA5_ANESU	Neurotoxin-5 (Toxin ATX-V) (Toxin V)	0.03	-	nuc	0	Secreted protein. Found in nematocyst				46
Q800Y3 UniProt NPD GO	NXLX_BUNMU	Neurotoxin-like protein pMD18-NTL3 precursor	0.03	-	exc	0	Secreted protein				86
P25436 UniProt NPD GO	NT4_VIPLE	Neurotrophin-4 (NT-4) (Fragment)	0.03	-	nuc	0					43
P34180 UniProt NPD GO	PA2N_VIPAA	Neutral phospholipase A2 precursor (EC 3.1.1.4) (Ammodytin I2) (Phosphatidylcholine 2-acylhydrolase) ...	0.03	-	end	1 *	Secreted protein				137
Q9XGI7 UniProt NPD GO	NAS_LYCES	Nicotianamine synthase (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-met ...	0.03	-	cyt	0					317
P53184 UniProt NPD GO	PNC1_YEAST	Nicotinamidase (EC 3.5.1.19) (Nicotine deamidase) (NAMase)	0.03	-	cyt	0		cytoplasm [IDA] nucleus [IDA] peroxisome [IDA]			216
Q84LK7 UniProt NPD GO	NIFU1_ORYSA	NifU-like protein 1, chloroplast precursor (OsNifu1)	0.03	-	mit	0	Plastid; chloroplast; chloroplast stroma (By similarity)			1TH5	226
Q92982 UniProt NPD GO	NINJ1_HUMAN	Ninjurin-1 (Nerve injury-induced protein 1)	0.03	-	end	2	Membrane; multi-pass membrane protein		602062		152
P22152 UniProt NPD GO	CRNA_EMENI	Nitrate transporter (Nitrate permease)	0.03	-	end	12 *	Membrane; multi-pass membrane protein				507
P79290 UniProt NPD GO	NOS2_PIG	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.03	-	cyt	0					215
P79209 UniProt NPD GO	NOS3_SHEEP	Nitric-oxide synthase, endothelial (EC 1.14.13.39) (EC-NOS) (NOS type III) (NOSIII) (Endothelial NOS ...	0.03	-	cyt	0					99

You are viewing entries 80751 to 80800 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.