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
O81338 UniProt NPD GO	AMP1_MESCR	Antimicrobial peptide 1 precursor	0.01	-	exc	1 *	Secreted protein				64
P25404 UniProt NPD GO	AMP2_MIRJA	Antimicrobial peptide 2 precursor (AMP2) (MJ-AMP2)	0.01	-	exc	1 *	Secreted protein				63
P84383 UniProt NPD GO	XT3_XENTR	Antimicrobial peptide 3 (XT-3) (Levitide-like peptide)	0.01	-	cyt	0	Secreted protein	extracellular region [IDA]			25
P84386 UniProt NPD GO	XT6_XENTR	Antimicrobial peptide 6 (XT-6)	0.01	-		0	Secreted protein	extracellular region [IDA]			18
P84182 UniProt NPD GO	AP21_EISFO	Antimicrobial peptide OEP3121	0.01	-		0					5
P83477 UniProt NPD GO	APY3_PLECI	Antiviral protein Y3 (Fragment)	0.01	-		0					20
P83481 UniProt NPD GO	APYP3_PLECI	Antiviral protein Yp3 (Fragment)	0.01	-		0					20
P80520 UniProt NPD GO	AP40_HUMAN	Aortic aneurysm-associated antigenic protein 40 (AAAP-40) (Microfibril-associated glycoprotein 3) (M ...	0.01	-	cyt	0		microfibril [NAS]			59
P56595 UniProt NPD GO	APOC1_CANFA	Apolipoprotein C-I precursor (Apo-CI) (ApoC-I)	0.01	-	gol	0	Secreted protein				88
P02654 UniProt NPD GO	APOC1_HUMAN	Apolipoprotein C-I precursor (Apo-CI) (ApoC-I)	0.01	-	gol	0	Secreted protein		107710	1OPP	83
P34929 UniProt NPD GO	APOC1_PAPHA	Apolipoprotein C-I precursor (Apo-CI) (ApoC-I) [Contains: Cholesteryl ester transfer inhibitor prote ...	0.01	-	gol	0	Secreted protein			1EZE	83
P33622 UniProt NPD GO	APOC3_MOUSE	Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III)	0.01	-	exc	0	Secreted protein				99
P05090 UniProt NPD GO	APOD_HUMAN	Apolipoprotein D precursor (Apo-D) (ApoD)	0.01	-	end	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	107740	2APD	189
P51910 UniProt NPD GO	APOD_MOUSE	Apolipoprotein D precursor (Apo-D) (ApoD)	0.01	-	vac	0	Secreted protein				189
O14791 UniProt NPD GO	APOL1_HUMAN	Apolipoprotein-L1 precursor (Apolipoprotein L-I) (Apolipoprotein L) (ApoL-I) (Apo-L) (ApoL)	0.01	-	end	2 *	Secreted protein	extracellular region [NAS] extracellular space [TAS]	603743		398
Q07817 UniProt NPD GO	BCLX_HUMAN	Apoptosis regulator Bcl-X (Bcl-2-like 1 protein)	0.01	-	cyt	1	Mitochondrion; mitochondrial membrane (By similarity). Mitochondrial membranes and perinuclear envel ...	mitochondrial outer membrane [NAS] mitochondrion [TAS]	600039	2B48	233
Q64373 UniProt NPD GO	BCLX_MOUSE	Apoptosis regulator Bcl-X (Bcl-2-like 1 protein)	0.01	-	cyt	1	Isoform Bcl-X(L): Mitochondrion; mitochondrial membrane. Mitochondrial membranes and perinuclear env ...	mitochondrion [IDA]		1PQ1	233
O77737 UniProt NPD GO	BCLX_PIG	Apoptosis regulator Bcl-X (Bcl-2-like 1 protein)	0.01	-	cyt	1	Mitochondrion; mitochondrial membrane (By similarity). Mitochondrial membranes and perinuclear envel ...				233
Q9GL23 UniProt NPD GO	APAF_CANFA	Apoptotic protease-activating factor 1 (Apaf-1) (Fragment)	0.01	-	nuc	0					50
P02657 UniProt NPD GO	APOV1_DRONO	Apovitellenin-1 (Apovitellenin I)	0.01	-	cyt	0					84
P02659 UniProt NPD GO	APOV1_CHICK	Apovitellenin-1 precursor (Apovitellenin I) (Very low density lipoprotein II) (Apo-VLDL-II) (Apo-II) ...	0.01	-	end	0					106
P49271 UniProt NPD GO	TXP7_APTSC	Aptotoxin-7 (Aptotoxin VII) (Paralytic peptide VII) (PP VII)	0.01	-	nuc	0	Secreted protein			1WQB	32
Q9V5Z7 UniProt NPD GO	AQP_DROME	Aquaporin	0.01	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [ISS]			245
Q9SXF8 UniProt NPD GO	PIP13_ORYSA	Aquaporin PIP 1.3 (Plasma membrane intrinsic protein 1.3) (OsPIP1.3) (Water channel protein RWC3) (R ...	0.01	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				288
Q6EU94 UniProt NPD GO	PIP11_ORYSA	Aquaporin PIP1.1 (Plasma membrane intrinsic protein 1a) (PIP1a) (OsPIP1.1) (Water channel protein RW ...	0.01	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				289
P53386 UniProt NPD GO	AQY1_YEAST	Aquaporin-1	0.01	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Cell membrane; m ...	plasma membrane [IDA]			327
Q8BHH1 UniProt NPD GO	AQP11_MOUSE	Aquaporin-11 (AQP-11)	0.01	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				271
Q8CHM1 UniProt NPD GO	AQP11_RAT	Aquaporin-11 (AQP-11)	0.01	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				271
O93938 UniProt NPD GO	AQY2_YEAST	Aquaporin-2	0.01	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Cell membrane; m ...				289
O77740 UniProt NPD GO	AQP2_TALEU	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.01	-	end	3 *	Membrane; multi-pass membrane protein				109
Q92482 UniProt NPD GO	AQP3_HUMAN	Aquaporin-3 (AQP-3)	0.01	-	end	6 *	Cell membrane; basolateral cell membrane; multi-pass membrane protein. In collecting ducts of kidney ...		607457		292
Q8R2N1 UniProt NPD GO	AQP3_MOUSE	Aquaporin-3 (AQP-3)	0.01	-	end	6 *	Membrane; multi-pass membrane protein	basolateral plasma membrane [IDA] integral to plasma membrane [TAS]			292
P47862 UniProt NPD GO	AQP3_RAT	Aquaporin-3 (AQP-3) (31.4 kDa water channel protein)	0.01	-	end	6 *	Membrane; multi-pass membrane protein				292
Q13520 UniProt NPD GO	AQP6_HUMAN	Aquaporin-6 (AQP-6) (Aquaporin-2-like) (hKID)	0.01	-	end	5 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	601383	1S6E	282
P56405 UniProt NPD GO	AQP8_RAT	Aquaporin-8 (AQP-8)	0.01	-	end	6 *	Membrane; multi-pass membrane protein	microsome [IDA] plasma membrane [IDA]			263
P56627 UniProt NPD GO	AQP9_RAT	Aquaporin-9 (AQP-9)	0.01	-	end	6 *	Membrane; multi-pass membrane protein	basolateral plasma membrane [IDA]			295
P30356 UniProt NPD GO	FLAP_PIG	Arachidonate 5-lipoxygenase-activating protein (FLAP) (MK-886-binding protein) (Fragment)	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				153
P30357 UniProt NPD GO	FLAP_RABIT	Arachidonate 5-lipoxygenase-activating protein (FLAP) (MK-886-binding protein) (Fragment)	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				153
P20780 UniProt NPD GO	ARA1_ARAHY	Arachin 21 kDa protein	0.01	-	cyt	0					176
P00812 UniProt NPD GO	ARGI_YEAST	Arginase (EC 3.5.3.1)	0.01	-	mit	0					333
P22220 UniProt NPD GO	SPE1_AVESA	Arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC)	0.01	-	cyt	0					607
P83988 UniProt NPD GO	ARIN_CICAR	Arietin (Fragment)	0.01	-		0					20
P05031 UniProt NPD GO	DDC_DROME	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.01	-	cyt	0					510
Q91WU5 UniProt NPD GO	AS3MT_MOUSE	Arsenite methyltransferase (EC 2.1.1.137) (S-adenosyl-L-methionine:arsenic(III) methyltransferase) ( ...	0.01	-	mit	0	Cytoplasm (By similarity)	cytosol [ISS]			376
Q8VHT6 UniProt NPD GO	AS3MT_RAT	Arsenite methyltransferase (EC 2.1.1.137) (S-adenosyl-L-methionine:arsenic(III) methyltransferase) ( ...	0.01	-	mit	0	Cytoplasm	cytosol [IDA] soluble fraction [IDA]			369
Q96EG1 UniProt NPD GO	ARSG_HUMAN	Arylsulfatase G precursor (EC 3.1.6.-) (ASG)	0.01	-	end	0	Endoplasmic reticulum	endoplasmic reticulum [IDA]	610008		525
Q32KJ9 UniProt NPD GO	ARSG_RAT	Arylsulfatase G precursor (EC 3.1.6.-) (ASG)	0.01	-	end	0	Endoplasmic reticulum (By similarity)				526
P14000 UniProt NPD GO	ARS_HEMPU	Arylsulfatase precursor (EC 3.1.6.1) (AS) (Aryl-sulfate sulphohydrolase) (ARS)	0.01	-	vac	0	Cytoplasm. Secreted protein; extracellular space; extracellular matrix				551
P28734 UniProt NPD GO	AATC_DAUCA	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A)	0.01	-	cyt	0	Cytoplasm				405
P23542 UniProt NPD GO	AATC_YEAST	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A)	0.01	-	pox	0	Cytoplasm	cytoplasm [TAS] peroxisome [TAS]		1YAA	417

You are viewing entries 86751 to 86800 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.