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
Q9VQ66 UniProt NPD GO	NPLP4_DROME	Neuropeptide-like 4 precursor (YSY peptide)	0.02	-	exc	1 *	Secreted protein	extracellular region [NAS]			64
P49681 UniProt NPD GO	NPBW1_MOUSE	Neuropeptides B/W receptor type 1 (G-protein coupled receptor 7) (Fragment)	0.02	-	end	1 *	Membrane; multi-pass membrane protein				146
Q9JLD2 UniProt NPD GO	NEUS_RAT	Neuroserpin precursor (Serpin I1) (Protease inhibitor 17)	0.02	-	end	0	Secreted protein (By similarity)				410
P83920 UniProt NPD GO	TX13B_CUPSA	Neurotoxic enhancer CSTX-13 B chain	0.02	-	nuc	0	Secreted protein				29
Q8MTX1 UniProt NPD GO	TXCA_CAEEX	Neurotoxic peptide caeron precursor	0.02	-	nuc	1 *	Secreted protein (Probable)				102
P45666 UniProt NPD GO	SCX1_CENLL	Neurotoxin 1 (Toxin II.8.4.3) (Cll1m)	0.02	-	cyt	0	Secreted protein				66
P01492 UniProt NPD GO	SCX1_CENSC	Neurotoxin 1 precursor (CsEv1) (CsE v1)	0.02	-	end	0	Secreted protein			1VNB	87
P01483 UniProt NPD GO	SCX2_BUTOC	Neurotoxin 2 (Neurotoxin II) (Bot II) (BotII)	0.02	-	nuc	0	Secreted protein				65
P01494 UniProt NPD GO	SCX3_CENSC	Neurotoxin 3 precursor (CsEv3) (CsE v3)	0.02	-	exc	1 *	Secreted protein			2SN3	87
P84027 UniProt NPD GO	32C7_ANCSP	Neurotoxin ANC32C7 (Fragment)	0.02	-	nuc	0	Secreted protein				37
P84028 UniProt NPD GO	45C1_ANCSP	Neurotoxin ANC45C1	0.02	-	nuc	0	Secreted protein				47
Q9BJW4 UniProt NPD GO	SCCX_MESMA	Neurotoxin Bm12-b precursor	0.02	-	exc	1 *	Secreted protein				59
Q7M463 UniProt NPD GO	SCK6_MESMA	Neurotoxin BmK A3-6	0.02	-	nuc	0	Secreted protein				29
P59854 UniProt NPD GO	SCX7_MESMA	Neurotoxin BmK-M7 (Bmk M7) (BmKM7)	0.02	-	nuc	0	Secreted protein			1KV0	66
P54135 UniProt NPD GO	SCX8_MESMA	Neurotoxin BmK-VIII (BmKVIII) (BmK8) (BmK-M8) (Bmk M8)	0.02	-	nuc	0	Secreted protein			1SNB	64
Q9UAD0 UniProt NPD GO	SCCT_MESMA	Neurotoxin BmKCT precursor (Cl-channel toxin) (CT neurotoxin) (Short-chain toxin KCT) (BmKCL1) (TXCL ...	0.02	-	end	1 *	Secreted protein				59
P61509 UniProt NPD GO	TX1_EURCA	Neurotoxin ESTx1	0.02	-	nuc	0	Secreted protein				39
P61510 UniProt NPD GO	TX2_EURCA	Neurotoxin ESTx2	0.02	-	nuc	0	Secreted protein				39
P83905 UniProt NPD GO	TX20_PHOKE	Neurotoxin PKTx20C2	0.02	-	nuc	0	Secreted protein				50
P31010 UniProt NPD GO	TX3_PHONI	Neurotoxin Tx3 (Fragment)	0.02	-		0	Secreted protein				19
Q7YXD3 UniProt NPD GO	SCX8_ANDMA	Neurotoxin VIII precursor (Amm VIII) (P4)	0.02	-	exc	0	Secreted protein				85
P83561 UniProt NPD GO	TXMG5_MACGS	Neurotoxin magi-5 precursor	0.02	-	exc	0	Secreted protein				79
P10454 UniProt NPD GO	TXA2_ANTFU	Neurotoxin-2 (Toxin AFII) (Toxin AFT-II)	0.02	-	cyt	0	Secreted protein. Found in nematocyst				48
P09949 UniProt NPD GO	TXA3_PARAC	Neurotoxin-3 homolog (Neurotoxin III homolog) (PA-TX)	0.02	-	nuc	0	Secreted protein. Found in nematocyst				31
P01479 UniProt NPD GO	SCX1_ANDAU	Neurotoxins precursor [Contains: Neurotoxin-1'' (Neurotoxin I'') (AaH I'') (AaHI''); Neurotoxin-1/1' ...	0.02	-	exc	0	Secreted protein				83
Q58DA5 UniProt NPD GO	NTRI_BOVIN	Neurotrimin precursor	0.02	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				345
Q99PJ0 UniProt NPD GO	NTRI_MOUSE	Neurotrimin precursor	0.02	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				344
Q62718 UniProt NPD GO	NTRI_RAT	Neurotrimin precursor (GP65)	0.02	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				344
Q9P121 UniProt NPD GO	NTRI_HUMAN	Neurotrimin precursor (hNT)	0.02	-	end	0	Cell membrane; lipid-anchor; GPI-anchor		607938		344
P51912 UniProt NPD GO	AAAT_MOUSE	Neutral amino acid transporter B (Insulin-activated amino acid transporter) (ASC-like Na(+)-dependen ...	0.02	-	end	9	Membrane; multi-pass membrane protein				553
Q95JC7 UniProt NPD GO	AAAT_BOVIN	Neutral amino acid transporter B(0) (ATB(0)) (Sodium-dependent neutral amino acid transporter type 2 ...	0.02	-	end	9	Membrane; multi-pass membrane protein				539
O19105 UniProt NPD GO	AAAT_RABIT	Neutral amino acid transporter B(0) (ATB(0)) (Sodium-dependent neutral amino acid transporter type 2 ...	0.02	-	end	9	Membrane; multi-pass membrane protein				541
Q15758 UniProt NPD GO	AAAT_HUMAN	Neutral amino acid transporter B(0) (ATB(0)) (Sodium-dependent neutral amino acid transporter type 2 ...	0.02	-	end	9	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	109190		541
Q9VA70 UniProt NPD GO	NCASE_DROME	Neutral ceramidase precursor (EC 3.5.1.23) (NCDase) (N-CDase) (Neutral acylsphingosine deacylase) (N ...	0.02	-	exc	1 *	Secreted protein				704
P82317 UniProt NPD GO	DEF2_MACMU	Neutrophil defensin 2 (RMAD-2)	0.02	-	cyt	0	Secreted protein				30
Q9ZQV9 UniProt NPD GO	NAS1_HORVU	Nicotianamine synthase 1 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-m ...	0.02	-	nuc	0					327
Q9SXQ7 UniProt NPD GO	NAS1_ORYSA	Nicotianamine synthase 1 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-m ...	0.02	-	nuc	0					332
Q9XFB6 UniProt NPD GO	NAS8_HORVU	Nicotianamine synthase 8 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-m ...	0.02	-	nuc	0					329
P40261 UniProt NPD GO	NNMT_HUMAN	Nicotinamide N-methyltransferase (EC 2.1.1.1)	0.02	-	cyt	0	Cytoplasm		600008		264
Q3T063 UniProt NPD GO	NADC_BOVIN	Nicotinate-nucleotide pyrophosphorylase [carboxylating] (EC 2.4.2.19) (Quinolinate phosphoribosyltra ...	0.02	-	cyt	0					299
Q15274 UniProt NPD GO	NADC_HUMAN	Nicotinate-nucleotide pyrophosphorylase [carboxylating] (EC 2.4.2.19) (Quinolinate phosphoribosyltra ...	0.02	-	mit	0			606248		297
Q91X91 UniProt NPD GO	NADC_MOUSE	Nicotinate-nucleotide pyrophosphorylase [carboxylating] (EC 2.4.2.19) (Quinolinate phosphoribosyltra ...	0.02	-	cyt	0					299
Q5I0M2 UniProt NPD GO	NADC_RAT	Nicotinate-nucleotide pyrophosphorylase [carboxylating] (EC 2.4.2.19) (Quinolinate phosphoribosyltra ...	0.02	-	cyt	0					299
Q9H1K1 UniProt NPD GO	NIFUN_HUMAN	NifU-like N-terminal domain-containing protein, mitochondrial precursor (NifU-like protein) (Iron-su ...	0.02	-	mit	0	Isoform 1: Mitochondrion. Isoform 2: Cytoplasm. Nucleus	cytoplasm [IDA] mitochondrion [IDA]			167
Q9D7P6 UniProt NPD GO	NIFUN_MOUSE	NifU-like N-terminal domain-containing protein, mitochondrial precursor (NifU-like protein) (Iron-su ...	0.02	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]		1WFZ	168
Q05085 UniProt NPD GO	CHL1_ARATH	Nitrate/chlorate transporter	0.02	-	end	11	Membrane; multi-pass membrane protein				590
P23233 UniProt NPD GO	NO16_SOYBN	Nodulin 16 precursor (N-16)	0.02	-	exc	1 *	Peribacteroid membrane (Potential)				109
P08961 UniProt NPD GO	NO22_SOYBN	Nodulin 22 precursor (N-22)	0.02	-	exc	0	Peribacteroid membrane or peribacteroid space (Potential)				215
P04145 UniProt NPD GO	NO24_SOYBN	Nodulin 24 precursor (N-24)	0.02	-	vac	1 *	Integral part of the peribacteroid membrane, a compartment essential for effective symbiotic nitroge ...				147
P08864 UniProt NPD GO	NO27_SOYBN	Nodulin 27 precursor (N-27)	0.02	-	exc	0					213

You are viewing entries 84601 to 84650 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.