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
P30292 UniProt NPD GO	AMY_ASPSH	Alpha-amylase precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.01	-	end	0					499
P17654 UniProt NPD GO	AMY1_ORYSA	Alpha-amylase precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Isozyme 1B)	0.01	-	exc	1 *					434
P56641 UniProt NPD GO	CXA3_CONAL	Alpha-conotoxin AuIC	0.01	-		0	Secreted protein				16
Q9U619 UniProt NPD GO	CX2A_CONIM	Alpha-conotoxin ImIIA precursor	0.01	-	exc	1 *	Secreted protein (By similarity)				62
Q6PTD1 UniProt NPD GO	CX11_CONMR	Alpha-conotoxin Mr1.1 precursor	0.01	-	end	1 *	Secreted protein				65
Q9LNU3 UniProt NPD GO	EXP11_ARATH	Alpha-expansin 11 precursor (AtEXPA11) (At-EXP11) (AtEx11) (Ath-ExpAlpha-1.14)	0.01	-	exc	0	Cell wall; peripheral membrane protein				252
Q9UVD6 UniProt NPD GO	MEL_TORDE	Alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase) (MELt ...	0.01	-	mit	0					474
P01545 UniProt NPD GO	THNA_HORVU	Alpha-hordothionin precursor (Purothionin II) [Contains: Alpha-hordothionin; Acidic protein]	0.01	-	nuc	0	Secreted protein				127
P13488 UniProt NPD GO	SCX3_BUTOM	Alpha-like neurotoxin III (Bom III) (BomIII) (Bom3)	0.01	-	cyt	0	Secreted protein				66
P59354 UniProt NPD GO	SCX4_BUTOM	Alpha-like neurotoxin IV (Bom IV) (BomIV) (Bom4)	0.01	-	nuc	0	Secreted protein				65
Q86SE1 UniProt NPD GO	SCX1_ANDAM	Alpha-neurotoxin 1 precursor (AamH1)	0.01	-	exc	0	Secreted protein				83
P69391 UniProt NPD GO	PMTXA_ANOSM	Alpha-pompilidotoxin (Alpha-PMTX)	0.01	-		0	Secreted protein				13
P82535 UniProt NPD GO	AMC_RABIT	Alveolar macrophage chemotactic factor (Neutrophil chemotactic protein) (NPC)	0.01	-	mit	0	Secreted protein				76
O62816 UniProt NPD GO	SCNNB_SHEEP	Amiloride-sensitive sodium channel subunit beta (Epithelial Na+ channel subunit beta) (Beta ENaC) (N ...	0.01	-	end	0	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				221
P56560 UniProt NPD GO	AOFB_BOVIN	Amine oxidase [flavin-containing] B (EC 1.4.3.4) (Monoamine oxidase type B) (MAO-B)	0.01	-	cyt	1	Mitochondrion; mitochondrial outer membrane				519
P19643 UniProt NPD GO	AOFB_RAT	Amine oxidase [flavin-containing] B (EC 1.4.3.4) (Monoamine oxidase type B) (MAO-B)	0.01	-	cyt	1	Mitochondrion; mitochondrial outer membrane				519
Q03154 UniProt NPD GO	ACY1_HUMAN	Aminoacylase-1 (EC 3.5.1.14) (N-acyl-L-amino-acid amidohydrolase) (ACY-1)	0.01	-	cyt	0	Cytoplasm	cytosol [TAS]	104620	1Q7L	408
Q9ZPJ8 UniProt NPD GO	AMT12_ARATH	Ammonium transporter 1 member 2 (AtAMT1;2)	0.01	-	end	11	Membrane; multi-pass membrane protein (Probable)				514
Q9SQH9 UniProt NPD GO	AMT13_ARATH	Ammonium transporter 1 member 3 (AtAMT1;3)	0.01	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				519
Q9SVT8 UniProt NPD GO	AMT14_ARATH	Ammonium transporter 1 member 4 (AtAMT1;4)	0.01	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				504
Q6KCA4 UniProt NPD GO	ICP1_ENTHI	Amoebiasin-1 (Cysteine protease inhibitor 1) (ICP1) (EhICP1)	0.01	-	cyt	0	Cytoplasm				102
P29261 UniProt NPD GO	AH3_PRUSE	Amygdalin beta-glucosidase 2 (EC 3.2.1.117) (Amygdalin beta-glucosidase II) (Amygdalin hydrolase iso ...	0.01	-		0					10
P33588 UniProt NPD GO	VSP1_AGKBI	Ancrod (EC 3.4.21.74) (Venombin A) (Protein C activator) (ACC-C) (Fragment)	0.01	-		0	Secreted protein (Potential)				20
P80899 UniProt NPD GO	VSP3_AGKHP	Ancrod (EC 3.4.21.74) (Venombin A) (Protein C activator) (ACC-C) (Fragment)	0.01	-		0	Secreted protein				15
Q9D8B1 UniProt NPD GO	AIG1_MOUSE	Androgen-induced protein 1 (AIG-1)	0.01	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				262
P84761 UniProt NPD GO	ACI_TRIGI	Angiotensin-1-converting enzyme inhibitory peptide	0.01	-		0					3
P18691 UniProt NPD GO	ACI_THUAL	Angiotensin-converting enzyme inhibitor	0.01	-		0					8
Q10581 UniProt NPD GO	ANGT1_BOTJA	Angiotensin-like peptide 1 (Fragment)	0.01	-		0					10
P01017 UniProt NPD GO	ANGT_BOVIN	Angiotensinogen [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotensin II) (An ...	0.01	-		0	Secreted protein			3ER5	10
P67885 UniProt NPD GO	ANGT_CHICK	Angiotensinogen [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotensin II) (An ...	0.01	-		0	Secreted protein				10
P67886 UniProt NPD GO	ANGT_COTJA	Angiotensinogen [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotensin II) (An ...	0.01	-		0	Secreted protein				10
Q29463 UniProt NPD GO	TRY2_BOVIN	Anionic trypsin precursor (EC 3.4.21.4)	0.01	-	exc	0	Secreted protein; extracellular space	extracellular matrix [ISS] extracellular region [ISS] extracellular space [ISS]			247
P06872 UniProt NPD GO	TRY2_CANFA	Anionic trypsin precursor (EC 3.4.21.4)	0.01	-	exc	0	Secreted protein; extracellular space	extracellular matrix [ISS] extracellular region [ISS] extracellular space [ISS]			247
P00762 UniProt NPD GO	TRY1_RAT	Anionic trypsin-1 precursor (EC 3.4.21.4) (Anionic trypsin I) (Pretrypsinogen I)	0.01	-	exc	0	Secreted protein; extracellular space				246
P07146 UniProt NPD GO	TRY2_MOUSE	Anionic trypsin-2 precursor (EC 3.4.21.4) (Anionic trypsin II) (Pretrypsinogen II)	0.01	-	exc	0	Secreted protein; extracellular space	extracellular matrix [ISS] extracellular region [ISS] extracellular space [ISS]			246
P00763 UniProt NPD GO	TRY2_RAT	Anionic trypsin-2 precursor (EC 3.4.21.4) (Anionic trypsin II) (Pretrypsinogen II)	0.01	-	exc	0	Secreted protein; extracellular space	extracellular matrix [ISS] extracellular region [ISS] extracellular space [ISS]		3TGK	246
Q3SZE4 UniProt NPD GO	ASB11_BOVIN	Ankyrin repeat and SOCS box protein 11 (ASB-11)	0.01	-	nuc	1 *					323
Q8VBX0 UniProt NPD GO	ASB13_MOUSE	Ankyrin repeat and SOCS box protein 13 (ASB-13)	0.01	-	cyt	0					278
Q9H765 UniProt NPD GO	ASB8_HUMAN	Ankyrin repeat and SOCS box protein 8 (ASB-8)	0.01	-	cyt	0	Cytoplasm				288
P46683 UniProt NPD GO	YAR1_YEAST	Ankyrin repeat-containing protein YAR1	0.01	-	cyt	0		cytoplasm [IDA]			200
P58705 UniProt NPD GO	FFKA_ANTEL	Antho-KAamide	0.01	-		0	Secreted protein				4
Q96493 UniProt NPD GO	UFOG_GENTR	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase) (UDP-glucose ...	0.01	-	cyt	0					453
Q9ZWR8 UniProt NPD GO	ANTA_GENTR	Anthocyanin 5-aromatic acyltransferase (EC 2.3.1.153) (5AT)	0.01	-	cyt	0	Cytoplasm				469
P01531 UniProt NPD GO	TXAB_ANTXA	Anthopleurin-B (Toxin AP-B)	0.01	-	nuc	0	Secreted protein. Found in nematocyst			1APF	49
P23032 UniProt NPD GO	LEC3_ULEEU	Anti-H(O) lectin 3 (Anti-H(O) lectin III) (UEA-III) (Fragment)	0.01	-	cyt	0					35
Q03383 UniProt NPD GO	ACH1_BOMMO	Antichymotrypsin-1 precursor (Antichymotrypsin I) (ACHY-I)	0.01	-	exc	0	Secreted protein				400
P80034 UniProt NPD GO	ACH2_BOMMO	Antichymotrypsin-2 (Antichymotrypsin II) (ACHY-II)	0.01	-	mit	0	Secreted protein				375
P83109 UniProt NPD GO	ADFB_TENMO	Antidiuretic factor B (ADFb)	0.01	-		0	Secreted protein				13
P36370 UniProt NPD GO	TAP1_RAT	Antigen peptide transporter 1 (APT1) (Peptide transporter TAP1) (ATP-binding cassette sub-family B m ...	0.01	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. The transmembran ...	cytosol [ISS] endoplasmic reticulum lumen [ISS] TAP complex [IPI]			725
P84387 UniProt NPD GO	XT1_XENTR	Antimicrobial peptide 1 (XT-1)	0.01	-	mit	0	Secreted protein	extracellular region [IDA]			27

You are viewing entries 86701 to 86750 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.