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
Q61618 UniProt NPD GO	AA3R_MOUSE	Adenosine A3 receptor (A3AR)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IMP]			319
Q920P6 UniProt NPD GO	ADA_RAT	Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase)	0.06	-	cyt	0					351
P50249 UniProt NPD GO	SAHH_PHASS	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.06	-	nuc	0					485
P40124 UniProt NPD GO	CAP1_MOUSE	Adenylyl cyclase-associated protein 1 (CAP 1)	0.06	-	nuc	0	Cell membrane (By similarity)	cortical actin cytoskeleton [IDA] cytoplasm [IDA]			473
Q12657 UniProt NPD GO	KAPS_PENCH	Adenylyl-sulfate kinase (EC 2.7.1.25) (APS kinase) (Adenosine-5'phosphosulfate kinase) (ATP adenosin ...	0.06	-	mit	0				1M7H	211
P61855 UniProt NPD GO	AKH_DROME	Adipokinetic hormone precursor (dAKH) (Hypertrehalosaemic hormone) (HRTH)	0.06	-	end	1 *	Secreted protein				79
P67788 UniProt NPD GO	AKH_MANSE	Adipokinetic prohormone precursor [Contains: Adipokinetic hormone (AKH)]	0.06	-	exc	1 *	Secreted protein				65
Q27969 UniProt NPD GO	AD50_BOVIN	Adrenal medulla 50 kDa protein	0.06	-	cyt	0					532
Q29297 UniProt NPD GO	ADSV_PIG	Adseverin (Scinderin) (Fragment)	0.06	-	cyt	0					125
P02592 UniProt NPD GO	AEQ2_AEQVI	Aequorin-2 precursor	0.06	-	cyt	0				1UHK	196
P58742 UniProt NPD GO	AAAS_MOUSE	Aladin (Adracalin)	0.06	-	cyt	0					546
P34106 UniProt NPD GO	ALA2_PANMI	Alanine aminotransferase 2 (EC 2.6.1.2) (GPT) (Glutamic--pyruvic transaminase 2) (Glutamic--alanine ...	0.06	-	cyt	0					482
P10593 UniProt NPD GO	ALB3_MAIZE	Albumin b-32 (EC 3.2.2.22) (Protein opaque-6) (rRNA N-glycosidase)	0.06	-	cyt	0	Cytoplasm				303
P62926 UniProt NPD GO	ALB1A_PEA	Albumin-1 A precursor (PA1 A) [Contains: Albumin-1 A chain b (PA1b A) (Leginsulin A); Albumin-1 A ch ...	0.06	-	nuc	0					130
P62928 UniProt NPD GO	ALB1C_PEA	Albumin-1 C precursor (PA1 C) (PsaA1b015) [Contains: Albumin-1 C chain b (PA1b C) (Leginsulin C); Al ...	0.06	-	nuc	0					130
P62929 UniProt NPD GO	ALB1D_PEA	Albumin-1 D precursor (PA1 D) (PsaA1b012) [Contains: Albumin-1 D chain b (PA1b D) (Leginsulin D); Al ...	0.06	-	nuc	0					130
P25139 UniProt NPD GO	ADH_DROAM	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					254
P28483 UniProt NPD GO	ADH_DROER	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					255
Q09009 UniProt NPD GO	ADH_DROGU	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					253
P51549 UniProt NPD GO	ADH_DROHA	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					253
P07162 UniProt NPD GO	ADH_DROMA	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					255
Q09010 UniProt NPD GO	ADH_DROMD	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					253
P00334 UniProt NPD GO	ADH_DROME	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0				1MG5	255
P25721 UniProt NPD GO	ADH_DROMY	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					253
P07159 UniProt NPD GO	ADH_DROOR	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					255
P84328 UniProt NPD GO	ADH_DROPB	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					253
P37473 UniProt NPD GO	ADH_DROPE	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					253
Q6LCE4 UniProt NPD GO	ADH_DROPS	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					253
Q9GN94 UniProt NPD GO	ADH_DROSE	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					255
Q24641 UniProt NPD GO	ADH_DROSI	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					255
Q03384 UniProt NPD GO	ADH_DROSU	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					254
P28484 UniProt NPD GO	ADH_DROTE	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					255
P51550 UniProt NPD GO	ADH_DROTS	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					256
P26719 UniProt NPD GO	ADH_DROYA	Alcohol dehydrogenase (EC 1.1.1.1)	0.06	-	cyt	0					255
P12854 UniProt NPD GO	ADH1_DRONA	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.06	-	cyt	0					253
P30350 UniProt NPD GO	ADH1_ANAPL	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Fragment)	0.06	-	mit	0	Cytoplasm				185
P25720 UniProt NPD GO	ADH2_DROBU	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.06	-	cyt	0					253
P09369 UniProt NPD GO	ADH2_DROMO	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.06	-	cyt	0					253
P07160 UniProt NPD GO	ADH2_DROMU	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.06	-	cyt	0					253
P24267 UniProt NPD GO	ADH2_DROWH	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.06	-	cyt	0					253
Q41247 UniProt NPD GO	AL7A1_BRANA	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin-1) (Brassica turgor-responsive/dr ...	0.06	-	nuc	0					493
Q9DCT1 UniProt NPD GO	AK1E1_MOUSE	Aldo-keto reductase family 1 member E1 (EC 1.1.1.-)	0.06	-	cyt	0	Cytoplasm				301
P07943 UniProt NPD GO	ALDR_RAT	Aldose reductase (EC 1.1.1.21) (AR) (Aldehyde reductase)	0.06	-	cyt	0	Cytoplasm				315
Q9VIP7 UniProt NPD GO	ACASE_DROME	Alkaline ceramidase (EC 3.5.1.23) (AlkCDase) (Alkaline acylsphingosine deacylase) (Alkaline N-acylsp ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				283
P10696 UniProt NPD GO	PPBN_HUMAN	Alkaline phosphatase, placental-like precursor (EC 3.1.3.1) (Nagao isozyme) (Germ-cell alkaline phos ...	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	membrane [NAS]	171810		532
O45218 UniProt NPD GO	ADAS_CAEEL	Alkyldihydroxyacetonephosphate synthase (EC 2.5.1.26) (Alkyl-DHAP synthase) (Alkylglycerone-phosphat ...	0.06	-	cyt	0	Peroxisome				597
P81496 UniProt NPD GO	ALCC_WHEAT	Allergen C-C (Fragment)	0.06	-	nuc	0	Secreted protein				27
Q75AQ8 UniProt NPD GO	ALG10_ASHGO	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.06	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				509
O94738 UniProt NPD GO	ALG2_RHIPU	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.06	-	end	2	Membrane; multi-pass membrane protein				455
O04300 UniProt NPD GO	UPTG_PEA	Alpha-1,4-glucan-protein synthase [UDP-forming] (EC 2.4.1.112) (UDP-glucose:protein transglucosylase ...	0.06	-	cyt	0	Cell wall. Cell wall; cell-cell junction; plasmodesma. Cell wall-associated, with highest concentrat ...				364

You are viewing entries 71501 to 71550 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.