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
O15218 UniProt NPD GO	ADMR_HUMAN	Adrenomedullin receptor (AM-R)	0.03	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]	605307		404
P18675 UniProt NPD GO	LECB1_MACPO	Agglutinin beta-1 chain (MPA)	0.03	-	nuc	0					21
Q9BYV1 UniProt NPD GO	AGT2_HUMAN	Alanine--glyoxylate aminotransferase 2, mitochondrial precursor (EC 2.6.1.44) ((R)-3-amino-2-methylp ...	0.03	-	mit	0	Mitochondrion (Potential)				514
Q9FRT9 UniProt NPD GO	ALB1_PHAAN	Albumin-1 precursor (A1) [Contains: Albumin-1 chain b (A1b) (Leginsulin); Albumin-1 chain a (A1a)] ( ...	0.03	-	nuc	0					90
P25406 UniProt NPD GO	ADH1B_UROHA	Alcohol dehydrogenase 1B (EC 1.1.1.1) (Alcohol dehydrogenase I-B) (ADH IB)	0.03	-	nuc	0	Cytoplasm				375
Q17334 UniProt NPD GO	ADH1_CAEEL	Alcohol dehydrogenase K12G11.3 (EC 1.1.1.1)	0.03	-	cyt	0					349
Q09008 UniProt NPD GO	ADHR_DROMD	Alcohol dehydrogenase-related 31 kDa protein	0.03	-	cyt	0					279
Q24640 UniProt NPD GO	ADHR_DROSU	Alcohol dehydrogenase-related 31 kDa protein	0.03	-	cyt	0					279
Q64057 UniProt NPD GO	AL7A1_RAT	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin-1) (Fragment)	0.03	-	mit	0					228
P16116 UniProt NPD GO	ALDR_BOVIN	Aldose reductase (EC 1.1.1.21) (AR) (Aldehyde reductase) (20-alpha-hydroxysteroid dehydrogenase) (EC ...	0.03	-	cyt	0	Cytoplasm			2GO6	315
Q04895 UniProt NPD GO	DAL4_YEAST	Allantoin permease (Allantoin transport protein)	0.03	-	end	11	Membrane; multi-pass membrane protein				635
O60024 UniProt NPD GO	ALL4_ASPFU	Allergen Asp f 4 precursor	0.03	-	end	0	Secreted protein (Probable)				322
P28555 UniProt NPD GO	PHAA_AGLNE	Allophycocyanin alpha chain	0.03	-	cyt	0	Plastid; chloroplast				160
O59921 UniProt NPD GO	TPS1_EMENI	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] (EC 2.4.1.15) (Trehalose-6-phosphate synthase ...	0.03	-	cyt	0					504
O74932 UniProt NPD GO	TPS1_YARLI	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] (EC 2.4.1.15) (Trehalose-6-phosphate synthase ...	0.03	-	cyt	0					469
Q5RET3 UniProt NPD GO	P34_PONPY	Alpha- and gamma-adaptin-binding protein p34	0.03	-	vac	0					315
Q6CEA5 UniProt NPD GO	ALG10_YARLI	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.03	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				522
Q09174 UniProt NPD GO	GMA12_SCHPO	Alpha-1,2-galactosyltransferase (EC 2.4.1.-)	0.03	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi membrane [IDA]			375
P38027 UniProt NPD GO	A1AT_MACEU	Alpha-1-antiproteinase (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor) (Fragments)	0.03	-	nuc	0	Secreted protein				46
P12725 UniProt NPD GO	A1AT_SHEEP	Alpha-1-antiproteinase precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor)	0.03	-	end	0	Secreted protein				416
Q5RCW5 UniProt NPD GO	A1AT_PONPY	Alpha-1-antitrypsin precursor (Alpha-1 protease inhibitor) (Alpha-1-antiproteinase)	0.03	-	end	0	Secreted protein (By similarity)				418
P01010 UniProt NPD GO	A1AT_PAPAN	Alpha-1-antitrypsin precursor (Alpha-1 protease inhibitor) (Alpha-1-antiproteinase) (AAT) (Fragment) ...	0.03	-	end	0	Secreted protein				409
O00394 UniProt NPD GO	A1AT_CERAE	Alpha-1-antitrypsin precursor (Alpha-1 protease inhibitor) (Alpha-1-antiproteinase) (Fragment)	0.03	-	mit	0	Secreted protein (By similarity)				396
O54762 UniProt NPD GO	ALLT_SPETR	Alpha-1-antitrypsin-like protein GS55-LT precursor	0.03	-	exc	0	Secreted protein (By similarity)				413
P01544 UniProt NPD GO	THN1_WHEAT	Alpha-1-purothionin precursor (Purothionin A-II) [Contains: Alpha-1-purothionin; Acidic protein] (Fr ...	0.03	-	nuc	0	Secreted protein			2PLH	126
O77621 UniProt NPD GO	ADA1A_CANFA	Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1A-adrenoreceptor) (Alpha-1C adrenergic ...	0.03	-	end	6 *	Membrane; multi-pass membrane protein				295
P29700 UniProt NPD GO	FETUA_PIG	Alpha-2-HS-glycoprotein precursor (Fetuin-A) (Fragment)	0.03	-	mit	0	Secreted protein	extracellular space [ISS]			362
P24090 UniProt NPD GO	FETUA_RAT	Alpha-2-HS-glycoprotein precursor (Fetuin-A) (Glycoprotein PP63) (59 kDa bone sialic acid-containing ...	0.03	-	exc	0	Secreted protein	extracellular space [ISS]			352
P20737 UniProt NPD GO	A2M_HOMAM	Alpha-2-macroglobulin homolog (Alpha-2-M) (Fragments)	0.03	-	cyt	0	Secreted protein				38
P32032 UniProt NPD GO	THN2_WHEAT	Alpha-2-purothionin precursor [Contains: Alpha-2-purothionin; Acidic protein]	0.03	-	nuc	0	Secreted protein				136
P42254 UniProt NPD GO	ABFA_ASPNG	Alpha-N-arabinofuranosidase A precursor (EC 3.2.1.55) (Arabinosidase A) (ABF A)	0.03	-	exc	0					628
P56634 UniProt NPD GO	AMY_TENMO	Alpha-amylase (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.03	-	pox	0				1TMQ	471
Q23835 UniProt NPD GO	AMY1_DROAN	Alpha-amylase 1 precursor (EC 3.2.1.1)	0.03	-	pox	0					494
Q01117 UniProt NPD GO	AMY1_LIPKO	Alpha-amylase 1 precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase 1)	0.03	-	nuc	2 *	Secreted protein				624
O18345 UniProt NPD GO	AMY2_DROAN	Alpha-amylase 2 precursor (EC 3.2.1.1)	0.03	-	pox	0					494
Q23834 UniProt NPD GO	AM4N_DROAN	Alpha-amylase 4N precursor (EC 3.2.1.1)	0.03	-	exc	0					495
P08117 UniProt NPD GO	AMY3_WHEAT	Alpha-amylase AMY3 precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.03	-	exc	1 *					413
P16968 UniProt NPD GO	IAA1_HORVU	Alpha-amylase inhibitor BMAI-1 precursor (Allergen Hor v 1) (Alpha-amylase flour inhibitor) (Fragmen ...	0.03	-	cyt	0	Secreted protein				146
P10846 UniProt NPD GO	IAA3_WHEAT	Alpha-amylase inhibitor WDAI-3 (Fragment)	0.03	-	nuc	0	Secreted protein				44
O76264 UniProt NPD GO	AMYR_DROYA	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.03	-	end	0	Secreted protein (Probable)				493
P07596 UniProt NPD GO	IAAS_HORVU	Alpha-amylase/subtilisin inhibitor precursor (BASI)	0.03	-	mit	0				1AVA	203
P15471 UniProt NPD GO	CXAS1_CONST	Alpha-conotoxin SI precursor (S1)	0.03	-	exc	1 *	Secreted protein				64
P06733 UniProt NPD GO	ENOA_HUMAN	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Non-neural enolase) (NNE) (Enolase ...	0.03	-	mit	0	Cytoplasm. Cell membrane. Can translocate to the plasma membrane in either the homodimeric (alpha/al ...		172430		433
Q9XSJ4 UniProt NPD GO	ENOA_BOVIN	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Non-neural enolase) (NNE) (Enolase ...	0.03	-	mit	0	Cytoplasm (By similarity). Cell membrane (By similarity). Can translocate to the plasma membrane in ...				433
P51913 UniProt NPD GO	ENOA_CHICK	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Phosphopyruvate hydratase)	0.03	-	nuc	0	Cytoplasm			2GUA	433
Q9W7L0 UniProt NPD GO	ENOA_PYTRG	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Phosphopyruvate hydratase)	0.03	-	nuc	0	Cytoplasm				433
Q9W7L2 UniProt NPD GO	ENOA_SCEUN	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Phosphopyruvate hydratase)	0.03	-	nuc	0	Cytoplasm				433
P19140 UniProt NPD GO	ENOA_ANAPL	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Tau-crystallin)	0.03	-	nuc	0	Cytoplasm				433
Q05524 UniProt NPD GO	ENO1B_HUMAN	Alpha-enolase, lung specific (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Non-neural enolase) ...	0.03	-	mit	0	Cytoplasm (Potential)		607098		458
Q9C554 UniProt NPD GO	EXPA1_ARATH	Alpha-expansin 1 precursor (AtEXPA1) (At-EXP1) (AtEx1) (Ath-ExpAlpha-1.2)	0.03	-	cyt	0	Cell wall; peripheral membrane protein				250

You are viewing entries 79101 to 79150 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.