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
Q9M9P0 UniProt NPD GO	EXP13_ARATH	Alpha-expansin 13 precursor (AtEXPA13) (At-EXP13) (AtEx13) (Ath-ExpAlpha-1.22)	0.03	-	exc	0	Cell wall; peripheral membrane protein				266
Q9SZM1 UniProt NPD GO	EXP20_ARATH	Alpha-expansin 20 precursor (AtEXPA20) (At-EXP20) (AtEx20) (Ath-ExpAlpha-1.23)	0.03	-	cyt	0	Cell wall; peripheral membrane protein				256
P51569 UniProt NPD GO	AGAL_MOUSE	Alpha-galactosidase A precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase) (Al ...	0.03	-	mit	0	Lysosome	cytoplasm [ISS] extracellular region [ISS] Golgi apparatus [ISS] lysosome [ISS]			419
P07458 UniProt NPD GO	LALBA_MACRG	Alpha-lactalbumin (Lactose synthase B protein)	0.03	-	cyt	0	Secreted protein				121
P18137 UniProt NPD GO	LALBA_PIG	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.03	-	exc	0	Secreted protein				141
P00716 UniProt NPD GO	LALBA_RABIT	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.03	-	exc	0	Secreted protein				141
P00714 UniProt NPD GO	LALBA_RAT	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.03	-	exc	0	Secreted protein				159
O96569 UniProt NPD GO	L2AM_DROLE	Alpha-methyldopa hypersensitive protein (EC 4.1.1.-) (Fragment)	0.03	-	cyt	0					439
P60257 UniProt NPD GO	SCXC_BUTOM	Alpha-neurotoxin Bom alpha-6c	0.03	-	nuc	0	Secreted protein				66
P84646 UniProt NPD GO	SCX1_ODODO	Alpha-toxin OD1	0.03	-	nuc	0	Secreted protein	extracellular region [IDA]			65
Q16515 UniProt NPD GO	ACCN1_HUMAN	Amiloride-sensitive cation channel 1, neuronal (Amiloride-sensitive brain sodium channel) (Amiloride ...	0.03	-	cyt	0	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane of neur ...	integral to plasma membrane [TAS]	601784		512
P27338 UniProt NPD GO	AOFB_HUMAN	Amine oxidase [flavin-containing] B (EC 1.4.3.4) (Monoamine oxidase type B) (MAO-B)	0.03	-	cyt	1	Mitochondrion; mitochondrial outer membrane	mitochondrial envelope [TAS]	309860	2C76	519
Q6PLK3 UniProt NPD GO	AOFB_PIG	Amine oxidase [flavin-containing] B (EC 1.4.3.4) (Monoamine oxidase type B) (MAO-B)	0.03	-	cyt	1	Mitochondrion; mitochondrial outer membrane (By similarity)				519
Q5RE98 UniProt NPD GO	AOFB_PONPY	Amine oxidase [flavin-containing] B (EC 1.4.3.4) (Monoamine oxidase type B) (MAO-B)	0.03	-	cyt	1	Mitochondrion; mitochondrial outer membrane (By similarity)				519
Q9USX1 UniProt NPD GO	APE1_SCHPO	Aminopeptidase 1 (EC 3.4.11.-) (Aminopeptidase I)	0.03	-	nuc	0					882
Q9M6N7 UniProt NPD GO	AMT2_ARATH	Ammonium transporter 2 (AtAMT2)	0.03	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				475
P29260 UniProt NPD GO	AH2_PRUSE	Amygdalin beta-glucosidase I' (EC 3.2.1.117) (Amygdalin hydrolase isozyme I') (AH I') (Fragment)	0.03	-		0					15
P80884 UniProt NPD GO	ANAN_ANACO	Ananain precursor (EC 3.4.22.31)	0.03	-	exc	1 *					345
Q5R8C8 UniProt NPD GO	ANR46_PONPY	Ankyrin repeat domain-containing protein 46	0.03	-	nuc	1	Membrane; single-pass membrane protein (Potential)				228
Q8BTZ5 UniProt NPD GO	ANR46_MOUSE	Ankyrin repeat domain-containing protein 46 (Ankyrin repeat small protein) (ANK-S)	0.03	-	cyt	1	Membrane; single-pass membrane protein (Potential)				228
P24804 UniProt NPD GO	TA29_TOBAC	Anther-specific protein TA-29	0.03	-	exc	1 *					321
Q43716 UniProt NPD GO	UFOG_PETHY	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase) (UDP-glucose ...	0.03	-	mit	0					473
P19664 UniProt NPD GO	LEC_LOTTE	Anti-H(O) lectin (LTA)	0.03	-	cyt	0					240
P22972 UniProt NPD GO	LEC1_ULEEU	Anti-H(O) lectin 1 (Anti-H(O) lectin I) (UEA-I)	0.03	-	nuc	0				1JXN	243
P83139 UniProt NPD GO	AFP5_MALPA	Antifungal protein 5 (CW-5) (Fragment)	0.03	-	cyt	0					38
P84794 UniProt NPD GO	AFPJ_SOLTU	Antifungal protein J (AFP-J) (Fragment)	0.03	-		0	Vacuole (By similarity)	vacuole [ISS]			20
P29695 UniProt NPD GO	SVMP_TRIFL	Antihemorragic factor HSF (Metalloproteinase inhibitor)	0.03	-	cyt	0	Secreted protein				323
P11494 UniProt NPD GO	BDS1_ANESU	Antihypertensive protein BDS-1 (BDS-I) (Blood depressing substance I)	0.03	-	nuc	0	Secreted protein. Found in nematocyst			2BDS	43
P25403 UniProt NPD GO	AMP1_MIRJA	Antimicrobial peptide 1 precursor (AMP1) (MJ-AMP1) (Fragment)	0.03	-	exc	1 *	Secreted protein				61
P80915 UniProt NPD GO	AMP1_MACIN	Antimicrobial peptide 1 precursor (AMP1) (MiAMP1)	0.03	-	cyt	1 *	Secreted protein			1C01	102
Q17043 UniProt NPD GO	APLY_APLKU	Aplysianin-A precursor	0.03	-	exc	0					556
P02652 UniProt NPD GO	APOA2_HUMAN	Apolipoprotein A-II precursor (Apo-AII) (ApoA-II) [Contains: Apolipoprotein A-II(1-76)]	0.03	-	exc	0	Secreted protein	extracellular region [NAS]	107670	1L6L	100
P37153 UniProt NPD GO	APOD_RABIT	Apolipoprotein D precursor (Apo-D) (ApoD)	0.03	-	nuc	0	Secreted protein				189
P02660 UniProt NPD GO	APOV1_MELGA	Apovitellenin-1 (Apovitellenin I)	0.03	-	nuc	0					82
Q08733 UniProt NPD GO	PIP13_ARATH	Aquaporin PIP1.3 (Plasma membrane intrinsic protein 1c) (PIP1c) (Transmembrane protein B) (TMP-B)	0.03	-	end	6	Cell membrane; multi-pass membrane protein				286
Q8GRT8 UniProt NPD GO	PIP24_ORYSA	Aquaporin PIP2.4 (Plasma membrane intrinsic protein 2.4) (OsPIP2.4)	0.03	-	end	7 *	Cell membrane; multi-pass membrane protein (By similarity)				286
Q8GRI8 UniProt NPD GO	PIP25_ORYSA	Aquaporin PIP2.5 (Plasma membrane intrinsic protein 2.5) (OsPIP2.5)	0.03	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				283
Q8NBQ7 UniProt NPD GO	AQP11_HUMAN	Aquaporin-11 (AQP-11)	0.03	-	end	5 *	Membrane; multi-pass membrane protein (Potential)		609914		271
Q8IXF9 UniProt NPD GO	AQP12_HUMAN	Aquaporin-12A (AQP-12)	0.03	-	end	0	Membrane; multi-pass membrane protein (Potential)		609789		295
P30353 UniProt NPD GO	FLAP_HORSE	Arachidonate 5-lipoxygenase-activating protein (FLAP) (MK-886-binding protein) (Fragment)	0.03	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				153
P04149 UniProt NPD GO	ARA5_ARAHY	Arachin 25 kDa protein	0.03	-	cyt	0					201
O49046 UniProt NPD GO	ARGI_SOYBN	Arginase (EC 3.5.3.1)	0.03	-	mit	0					350
P30759 UniProt NPD GO	ARGI1_XENLA	Arginase-1 (EC 3.5.3.1) (Type I arginase) (Arginase, hepatic)	0.03	-	cyt	0					316
Q39827 UniProt NPD GO	SPE1_SOYBN	Arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC)	0.03	-	cyt	0					692
Q96A70 UniProt NPD GO	ADC_HUMAN	Arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC) (Ornithine decarboxylase-like protein) (ODC-paral ...	0.03	-	cyt	0			608353		460
P09582 UniProt NPD GO	ESTA_CANFA	Arginine esterase precursor (EC 3.4.21.35)	0.03	-	end	0					260
Q5R4B2 UniProt NPD GO	ARMX1_PONPY	Armadillo repeat-containing X-linked protein 1	0.03	-	mit	1 *					453
Q9P291 UniProt NPD GO	ARMX1_HUMAN	Armadillo repeat-containing X-linked protein 1 (Protein ALEX1) (ARM protein lost in epithelial cance ...	0.03	-	mit	1 *			300362		453
P36576 UniProt NPD GO	ARRC_RAT	Arrestin-C (Cone arrestin) (Fragment)	0.03	-	cyt	0					92
P28513 UniProt NPD GO	ARY1_CALVI	Arylphorin subunit A4 precursor	0.03	-	cyt	0	Secreted protein; extracellular space				759

You are viewing entries 79151 to 79200 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.