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
P18845 UniProt NPD GO	ACHA3_CARAU	Neuronal acetylcholine receptor protein subunit alpha-3 precursor (GF-alpha-3)	0.01	-	end	4	Membrane; multi-pass membrane protein				512
P35803 UniProt NPD GO	GPM6B_MOUSE	Neuronal membrane glycoprotein M6-b (M6b)	0.01	-	end	4	Membrane; multi-pass membrane protein				328
P83570 UniProt NPD GO	GWA_SEPOF	Neuropeptide GWa	0.01	-		0	Secreted protein				2
P97295 UniProt NPD GO	NPY2R_MOUSE	Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor)	0.01	-	end	7	Membrane; multi-pass membrane protein				385
P79211 UniProt NPD GO	NPY2R_SHEEP	Neuropeptide Y receptor type 2 (NPY2-R) (NPY-Y2 receptor) (Fragment)	0.01	-	end	3 *	Membrane; multi-pass membrane protein				146
P50391 UniProt NPD GO	NPY4R_HUMAN	Neuropeptide Y receptor type 4 (NPY4-R) (Pancreatic polypeptide receptor 1) (PP1)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601790		375
Q9VV28 UniProt NPD GO	NPLP3_DROME	Neuropeptide-like 3 precursor [Contains: SHA-peptide; VVI-amide peptide]	0.01	-	mit	0	Secreted protein	extracellular region [NAS]			90
Q71DC3 UniProt NPD GO	NPLP3_DROYA	Neuropeptide-like 3 precursor [Contains: SHA-peptide; VVI-amide peptide]	0.01	-	mit	0	Secreted protein (By similarity)	extracellular region [ISS]			86
P60277 UniProt NPD GO	SCX1_MESTA	Neurotoxin	0.01	-	cyt	0	Secreted protein			2A7T	64
P01493 UniProt NPD GO	SCX2_CENSC	Neurotoxin 2 precursor (CsEv2) (CsE v2)	0.01	-	exc	1 *	Secreted protein			1JZB	87
P01484 UniProt NPD GO	SCX2_ANDAU	Neurotoxin 2 precursor (Neurotoxin II) (AaH II) (AaHII) (AaH2)	0.01	-	exc	0	Secreted protein			1SEG	85
P01480 UniProt NPD GO	SCX3_ANDAU	Neurotoxin 3 precursor (Neurotoxin III) (AaH III) (AaHIII) (AaH3)	0.01	-	mit	0	Secreted protein				84
P45658 UniProt NPD GO	SCX4_ANDAU	Neurotoxin 4 precursor (Neurotoxin IV) (AaH IV) (AaHIV) (AaH4)	0.01	-	exc	0	Secreted protein				84
P58779 UniProt NPD GO	SCX5_CENSC	Neurotoxin 5 (CsEv5) (CsE v5)	0.01	-	nuc	0	Secreted protein			1NH5	59
P04097 UniProt NPD GO	SCX5_BUTOC	Neurotoxin 5 (Neurotoxin V) (Fragment)	0.01	-	nuc	0	Secreted protein				24
P04098 UniProt NPD GO	SCX8_BUTOC	Neurotoxin 8 (Neurotoxin VIII) (Fragment)	0.01	-	nuc	0	Secreted protein				36
Q86M31 UniProt NPD GO	AEP2_MESMA	Neurotoxin AEP2 precursor	0.01	-	exc	0	Secreted protein				85
Q9NJQ2 UniProt NPD GO	TXAE1_ACTEQ	Neurotoxin Ae I precursor (Toxin Ae I) (AeNa)	0.01	-	exc	0	Secreted protein (By similarity). Found in nematocyst (By similarity)				82
Q9UAC9 UniProt NPD GO	SCAS_MESMA	Neurotoxin BmK AS precursor	0.01	-	vac	0	Secreted protein				85
Q9UAC8 UniProt NPD GO	SCAT_MESMA	Neurotoxin BmK AS-1 precursor	0.01	-	end	1 *	Secreted protein				85
P59360 UniProt NPD GO	SCX2_MESMA	Neurotoxin BmK-II (BmK II) (BmKII) (BmK2)	0.01	-	nuc	0	Secreted protein				64
P15227 UniProt NPD GO	SCX3_MESMA	Neurotoxin BmK-III (BmKIII) (BmK III) (BmK3) (BmK-M3) (Bmk M3)	0.01	-	cyt	0	Secreted protein				65
P45698 UniProt NPD GO	SCX9_MESMA	Neurotoxin BmK-IX precursor (BmK9) (BmK-M9) (Bmk M9)	0.01	-	vac	0	Secreted protein			1SN4	79
Q6WJF5 UniProt NPD GO	SCXBT_MESMA	Neurotoxin BmKBTx precursor	0.01	-	exc	0	Secreted protein				80
Q7Z0H5 UniProt NPD GO	SCKJ_MESMA	Neurotoxin BmKX-A1-S31 precursor	0.01	-	exc	1 *	Secreted protein				55
Q7Z0H4 UniProt NPD GO	SCKI_MESMA	Neurotoxin BmP08 precursor (Short-chain peptide BmKX)	0.01	-	vac	1 *	Secreted protein			1WT8	55
Q94435 UniProt NPD GO	SCXA_CENNO	Neurotoxin Cn10 precursor (CngtVIII) (Fragment)	0.01	-	nuc	0	Secreted protein				81
P58296 UniProt NPD GO	SCXB_CENNO	Neurotoxin Cn11	0.01	-	nuc	0	Secreted protein				63
P63019 UniProt NPD GO	SCX12_CENNO	Neurotoxin Cn12	0.01	-	nuc	0	Secreted protein			1PE4	67
Q95WD3 UniProt NPD GO	SCXX_CENSC	Neurotoxin E1x precursor (CsE1x)	0.01	-	vac	0	Secreted protein				86
P01489 UniProt NPD GO	SCX4_LEIQU	Neurotoxin IV (Lqq IV) (LqqIV) (Lqq4)	0.01	-	nuc	0	Secreted protein				65
P83644 UniProt NPD GO	SCX4_LEIQH	Neurotoxin Lqh IV (LqhIV) (Lqh4)	0.01	-	nuc	0	Secreted protein	extracellular region [NAS]			65
P09981 UniProt NPD GO	SCX9_BUTEU	Neurotoxin M9 (BeM9)	0.01	-	nuc	0	Secreted protein				66
P15225 UniProt NPD GO	SCX3_ORTSC	Neurotoxin Os3 (Os-3)	0.01	-	cyt	0	Secreted protein				67
P59896 UniProt NPD GO	SCXI_BUTOM	Neurotoxin PI (BomPI)	0.01	-	nuc	0	Secreted protein				66
P83999 UniProt NPD GO	TX30_PHONI	Neurotoxin PNTx30C3 (Fragment)	0.01	-	nuc	0	Secreted protein				47
P83892 UniProt NPD GO	TX27_PHORI	Neurotoxin PRTx27C3	0.01	-	cyt	0	Secreted protein				36
O76198 UniProt NPD GO	TX21A_PHONI	Neurotoxin Pn2-1A precursor	0.01	-	exc	0	Secreted protein				115
P29423 UniProt NPD GO	TX21_PHONI	Neurotoxin Tx2-1 precursor	0.01	-	exc	0	Secreted protein				88
Q7Z0F1 UniProt NPD GO	SCKH_MESMA	Neurotoxin X-29S precursor	0.01	-	vac	1 *	Secreted protein				55
P10453 UniProt NPD GO	TXA1_ANTFU	Neurotoxin-1 (Neurotoxin I) (Toxin AFI) (Toxin AFT-I)	0.01	-	cyt	0	Secreted protein. Found in nematocyst				47
P43007 UniProt NPD GO	SATT_HUMAN	Neutral amino acid transporter A (SATT) (Alanine/serine/cysteine/ threonine transporter) (ASCT1)	0.01	-	end	9 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	600229		532
O35874 UniProt NPD GO	SATT_MOUSE	Neutral amino acid transporter A (SATT) (Alanine/serine/cysteine/ threonine transporter) (ASCT1)	0.01	-	end	9 *	Membrane; multi-pass membrane protein				532
P37358 UniProt NPD GO	EL2B_HORSE	Neutrophil elastase 2B (EC 3.4.21.-) (Proteinase 2B) (Fragments)	0.01	-	cyt	0					73
P80526 UniProt NPD GO	NEJ2_FASHE	Newly excysted juvenile protein 2 (Fragment)	0.01	-		0					14
Q9FEG8 UniProt NPD GO	NAS2_ORYSA	Nicotianamine synthase 2 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-m ...	0.01	-	nuc	0					326
P0C008 UniProt NPD GO	NIGR1_RANNI	Nigrocin-1	0.01	-	nuc	0	Secreted protein				33
P0C009 UniProt NPD GO	NIGR2_RANNI	Nigrocin-2	0.01	-	cyt	0	Secreted protein				21
O70131 UniProt NPD GO	NINJ1_MOUSE	Ninjurin-1 (Nerve injury-induced protein 1)	0.01	-	end	2	Membrane; multi-pass membrane protein				152
P70617 UniProt NPD GO	NINJ1_RAT	Ninjurin-1 (Nerve injury-induced protein 1)	0.01	-	end	2	Membrane; multi-pass membrane protein				152

You are viewing entries 89901 to 89950 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.