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
P50985 UniProt NPD GO	CXAB_CONPE	Alpha-conotoxin PnIB precursor	0.00	-	exc	1 *	Secreted protein			1AKG	61
O80622 UniProt NPD GO	EXP15_ARATH	Alpha-expansin 15 precursor (AtEXPA15) (At-EXP15) (AtEx15) (Ath-ExpAlpha-1.3)	0.00	-	end	0	Cell wall; peripheral membrane protein				248
Q9FL79 UniProt NPD GO	EXP23_ARATH	Alpha-expansin 23 precursor (AtEXPA23) (At-EXP23) (AtEx23) (Ath-ExpAlpha-1.17)	0.00	-	mit	0	Cell wall; peripheral membrane protein				269
P37154 UniProt NPD GO	LALBA_FELCA	Alpha-lactalbumin (Lactose synthase B protein) (Fragment)	0.00	-	cyt	0	Secreted protein				24
Q9TSR4 UniProt NPD GO	LALBA_BOSMU	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.00	-	exc	0	Secreted protein				142
Q9TSN6 UniProt NPD GO	LALBA_BUBBU	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.00	-	exc	0	Secreted protein				142
P00712 UniProt NPD GO	LALBA_CAPHI	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.00	-	exc	0	Secreted protein			1HMK	142
P09462 UniProt NPD GO	LALBA_SHEEP	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.00	-	exc	0	Secreted protein				142
P00711 UniProt NPD GO	LALBA_BOVIN	Alpha-lactalbumin precursor (Lactose synthase B protein) (Allergen Bos d 4)	0.00	-	exc	0	Secreted protein			1HFZ	142
P49125 UniProt NPD GO	TXALA_LATMA	Alpha-latrotoxin-associated LMWP precursor	0.00	-	exc	1 *	Secreted protein				88
P45697 UniProt NPD GO	SCX1_MESMA	Alpha-like neurotoxin BmK-I precursor (BmK I) (BmKI) (BmK1) (BmK-M1) (Bmk M1) (BmKM1)	0.00	-	vac	0	Secreted protein			1ZYW	84
P58328 UniProt NPD GO	SCX4_MESMA	Alpha-like neurotoxin BmK-IV (BmK4) (BmK-M4) (Bmk M4) (BmKM4)	0.00	-	nuc	0	Secreted protein			1SN4	64
P56678 UniProt NPD GO	SCL3_LEIQH	Alpha-like neurotoxin Lqh III (LqhIII) (Lqh3)	0.00	-	mit	0	Secreted protein			1FH3	67
P59356 UniProt NPD GO	SCL6_LEIQH	Alpha-like neurotoxin Lqh VI (LqhVI) (Lqh6)	0.00	-	mit	0	Secreted protein				64
P59357 UniProt NPD GO	SCL7_LEIQH	Alpha-like neurotoxin Lqh VII (LqhVII) (Lqh7)	0.00	-	cyt	0	Secreted protein				66
Q86SE0 UniProt NPD GO	SCX2_ANDAM	Alpha-neurotoxin 2 precursor (AamH2)	0.00	-	exc	0	Secreted protein				86
Q86SD9 UniProt NPD GO	SCX3_ANDAM	Alpha-neurotoxin 3 precursor (AamH3)	0.00	-	mit	0	Secreted protein				86
P60255 UniProt NPD GO	SCXA_BUTOM	Alpha-neurotoxin Bom alpha-6a	0.00	-	nuc	0	Secreted protein				66
P60256 UniProt NPD GO	SCXB_BUTOM	Alpha-neurotoxin Bom alpha-6b	0.00	-	nuc	0	Secreted protein				66
Q9NJC5 UniProt NPD GO	SC10_MESMA	Alpha-neurotoxin TX10 precursor (BmKalphaTx10) (Toxin KT2)	0.00	-	cyt	0	Secreted protein				85
Q9GQW3 UniProt NPD GO	SC12_MESMA	Alpha-neurotoxin TX12 precursor (BmKalphaTx12) (Alpha-neurotoxin IT01) (BmKalphaIT01) (BmKalphaIT1)	0.00	-	nuc	0	Secreted protein			1OMY	85
Q9NJC8 UniProt NPD GO	SC13_MESMA	Alpha-neurotoxin TX13 precursor (BmKalphaTx13)	0.00	-	cyt	0	Secreted protein				84
Q9GNG8 UniProt NPD GO	SC15_MESMA	Alpha-neurotoxin TX15 precursor (BmKalphaTx15)	0.00	-	mit	0	Secreted protein				85
Q9GQV6 UniProt NPD GO	SC16_MESMA	Alpha-neurotoxin TX16 precursor (BmKalphaTx16)	0.00	-	vac	0	Secreted protein				84
Q3I5G7 UniProt NPD GO	SNCA_PIG	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P61138 UniProt NPD GO	SYUA_ATEGE	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
Q3T0G8 UniProt NPD GO	SYUA_BOVIN	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P61139 UniProt NPD GO	SYUA_ERYPA	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P61140 UniProt NPD GO	SYUA_GORGO	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P61141 UniProt NPD GO	SYUA_LAGLA	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P61142 UniProt NPD GO	SYUA_MACFA	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P61143 UniProt NPD GO	SYUA_MACMU	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P61144 UniProt NPD GO	SYUA_PANPA	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P61145 UniProt NPD GO	SYUA_PANTR	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P61146 UniProt NPD GO	SYUA_PONPA	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P37377 UniProt NPD GO	SYUA_RAT	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA]			140
P61147 UniProt NPD GO	SYUA_SAGLB	Alpha-synuclein	0.00	-	cyt	0	Cytoplasm (By similarity)				140
P37840 UniProt NPD GO	SYUA_HUMAN	Alpha-synuclein (Non-A beta component of AD amyloid) (Non-A4 component of amyloid precursor) (NACP)	0.00	-	cyt	0	Cytoplasm. Membrane. Nucleus. Membrane-bound in dopaminergic neurons. Also found in the nucleus	cytoplasm [TAS]	127750	1XQ8	140
O55042 UniProt NPD GO	SYUA_MOUSE	Alpha-synuclein (Non-A beta component of AD amyloid) (Non-A4 component of amyloid precursor) (NACP)	0.00	-	cyt	0	Cytoplasm (By similarity)	synaptosome [IDA]			140
Q91448 UniProt NPD GO	SYUA_SERCA	Alpha-synuclein (Synelfin)	0.00	-	cyt	0	Cytoplasm (By similarity)				143
Q9GYX2 UniProt NPD GO	SCA1_MESMA	Alpha-toxin 1 precursor (BmKalpha1)	0.00	-	exc	0	Secreted protein				85
P45659 UniProt NPD GO	SCX4_TITSE	Alpha-toxins precursor [Contains: Toxin-5 (Toxin V) (Tityustoxin V) (Ts V) (TsV); Toxin-4 (Toxin IV) ...	0.00	-	end	0	Secreted protein				80
P0C1B5 UniProt NPD GO	ALTI_PARTR	Altitoxin	0.00	-	cyt	0	Secreted protein				58
P84760 UniProt NPD GO	ALVOL_POLAE	Alveolarin (Fragment)	0.00	-		0					9
P12761 UniProt NPD GO	AMEL_RABIT	Amelogenin-like protein (Tooth enamel protein) (Fragment)	0.00	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				29
Q9TRC7 UniProt NPD GO	ABP1_PIG	Amiloride-sensitive amine oxidase [copper-containing] (EC 1.4.3.6) (Diamine oxidase) (DAO) (Amilorid ...	0.00	-		0	Secreted protein; extracellular space (By similarity)				20
P37111 UniProt NPD GO	ACY1_PIG	Aminoacylase-1 (EC 3.5.1.14) (N-acyl-L-amino-acid amidohydrolase) (ACY-1)	0.00	-	cyt	0	Cytoplasm				406
P81731 UniProt NPD GO	AMPN_HELAM	Aminopeptidase N (EC 3.4.11.2) (CryIA(C) receptor) (Fragment)	0.00	-		0					10
P58905 UniProt NPD GO	AMT11_LYCES	Ammonium transporter 1 member 1 (LeAMT1;1)	0.00	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				488
P54144 UniProt NPD GO	AMT11_ARATH	Ammonium transporter 1 member 1 precursor (AtAMT1;1)	0.00	-	mit	9 *	Cell membrane; multi-pass membrane protein (Probable)				501

You are viewing entries 92651 to 92700 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.