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
P54963 UniProt NPD GO	EP65_HUMAN	Erythrocyte 65 kDa protein (P65) (Fragment)	0.04	-		0	Cytoplasm	cytoplasm [NAS]			13
P12264 UniProt NPD GO	41_CHICK	Erythroid protein 4.1 (Band 4.1) (Fragment)	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				90
Q02025 UniProt NPD GO	ESCA_LITFO	Escargot/snail protein homolog (Fragment)	0.04	-	nuc	0	Nucleus (Probable)				46
P81011 UniProt NPD GO	ESTB_SCHGA	Esterase 56 kDa subunit (EC 3.1.1.1) (Carboxylic-ester hydrolase) (Fragment)	0.04	-		0	Cytoplasm				15
P35501 UniProt NPD GO	ESTE_MYZPE	Esterase E4 precursor (EC 3.1.1.1) (Carboxylic-ester hydrolase)	0.04	-	vac	1 *					552
P35502 UniProt NPD GO	ESTF_MYZPE	Esterase FE4 precursor (EC 3.1.1.1) (Carboxylic-ester hydrolase)	0.04	-	vac	1 *					564
O16173 UniProt NPD GO	EST5A_DROPE	Esterase-5A precursor (EC 3.1.1.1) (Est-5A) (Carboxylic-ester hydrolase 5A) (Carboxylesterase-5A)	0.04	-	mit	0	Secreted protein				548
P19217 UniProt NPD GO	ST1E1_BOVIN	Estrogen sulfotransferase (EC 2.8.2.4) (Sulfotransferase, estrogen-preferring) (ST1E1)	0.04	-	mit	0	Cytoplasm				295
P49890 UniProt NPD GO	ST1E6_RAT	Estrogen sulfotransferase, isoform 6 (EC 2.8.2.4) (EST-6) (Sulfotransferase, estrogen-preferring) (E ...	0.04	-	cyt	0	Cytoplasm				295
Q9HBU6 UniProt NPD GO	EKI1_HUMAN	Ethanolamine kinase 1 (EC 2.7.1.82) (EKI 1)	0.04	-	mit	1	Cytoplasm	cytoplasm [NAS]	609858		452
P22140 UniProt NPD GO	EPT1_YEAST	Ethanolaminephosphotransferase (EC 2.7.8.1) (ETHPT)	0.04	-	end	7 *	Microsome; microsomal membrane; multi-pass membrane protein				391
P31597 UniProt NPD GO	EAA3_RABIT	Excitatory amino acid transporter 3 (Sodium-dependent glutamate/aspartate transporter 3) (Excitatory ...	0.04	-	end	8 *	Membrane; multi-pass membrane protein				524
O00341 UniProt NPD GO	EAA5_HUMAN	Excitatory amino acid transporter 5 (Retinal glutamate transporter)	0.04	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604471		560
P83488 UniProt NPD GO	CHXI_ASPFL	Exochitosanase (EC 3.2.1.-) (Exo-beta-D-glucosaminidase) (Fragment)	0.04	-		0					17
P49075 UniProt NPD GO	GUX3_AGABI	Exoglucanase 3 precursor (EC 3.2.1.91) (Exocellobiohydrolase 3) (1,4-beta-cellobiohydrolase 3)	0.04	-	exc	0					438
P26216 UniProt NPD GO	PGLR1_MAIZE	Exopolygalacturonase precursor (EC 3.2.1.67) (ExoPG) (Pectinase) (Galacturan 1,4-alpha-galacturonida ...	0.04	-	exc	0	Secreted protein				410
P35338 UniProt NPD GO	PGLR2_MAIZE	Exopolygalacturonase precursor (EC 3.2.1.67) (ExoPG) (Pectinase) (Galacturan 1,4-alpha-galacturonida ...	0.04	-	vac	0	Secreted protein				410
Q15024 UniProt NPD GO	EXOS7_HUMAN	Exosome complex exonuclease RRP42 (EC 3.1.13.-) (Ribosomal RNA-processing protein 42) (Exosome compo ...	0.04	-	cyt	0	Nucleus; nucleolus	exosome (RNase complex) [TAS]	606488		291
O23547 UniProt NPD GO	EXPR1_ARATH	Expansin-related protein 1 precursor (AtEXPR1) (At-EXPR1) (Ath-ExpBeta-3.1)	0.04	-	end	0					250
Q9ZV52 UniProt NPD GO	EXPR3_ARATH	Expansin-related protein 3 precursor (AtEXPR3) (Ath-ExpGamma-1.2)	0.04	-	cyt	0					130
P02219 UniProt NPD GO	GLB1_TYLHE	Extracellular globin-1 (Extracellular globin I) (Erythrocruorin)	0.04	-	cyt	0	Secreted protein				139
P09966 UniProt NPD GO	GLB2_TYLHE	Extracellular globin-2A (Globin IIA) (Erythrocruorin)	0.04	-	cyt	0					146
P28870 UniProt NPD GO	FKBP_CANAL	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.04	-	cyt	0	Cytoplasm				124
Q6C4C9 UniProt NPD GO	FKBP3_YARLI	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.04	+	cyt	0	Nucleus; nucleolus (By similarity)				407
P38495 UniProt NPD GO	FARP_CALSI	FMRFamide-like neuropeptide	0.04	-		0	Secreted protein				9
P41486 UniProt NPD GO	FAR3_HOMAM	FMRFamide-like neuropeptide 3 (FLI 3) (F2)	0.04	-		0	Secreted protein				8
P83274 UniProt NPD GO	FAR1_MACRS	FMRFamide-like neuropeptide FLP1 (DRNFLRF-amide)	0.04	-		0	Secreted protein				7
P83316 UniProt NPD GO	FAR1_PENMO	FMRFamide-like neuropeptide FLP1 (GDRNFLRF-amide)	0.04	-		0	Secreted protein				8
P83279 UniProt NPD GO	FAR6_MACRS	FMRFamide-like neuropeptide FLP6 (DGGRNFLRF-amide)	0.04	-		0	Secreted protein				9
P81298 UniProt NPD GO	FAR3_HAECO	FMRFamide-like neuropeptide PF3 (KSAYMRF-amide)	0.04	-		0	Secreted protein				7
P41874 UniProt NPD GO	FAR3_PANRE	FMRFamide-like neuropeptide PF3 (KSAYMRF-amide)	0.04	-		0	Secreted protein				7
P82661 UniProt NPD GO	FAR5_PANRE	FMRFamide-like neuropeptide PF5 (AMRNALVRF-amide)	0.04	-		0	Secreted protein				9
P59645 UniProt NPD GO	FXYD3_RAT	FXYD domain-containing ion transport regulator 3 precursor	0.04	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				88
O97797 UniProt NPD GO	FXYD3_PIG	FXYD domain-containing ion transport regulator 3 precursor (Chloride conductance inducer protein Mat ...	0.04	-	mit	1 *	Membrane; single-pass type I membrane protein (Potential)				88
P59648 UniProt NPD GO	FXYD7_MOUSE	FXYD domain-containing ion transport regulator 7	0.04	-	nuc	1 *					80
P59649 UniProt NPD GO	FXYD7_RAT	FXYD domain-containing ion transport regulator 7	0.04	-	nuc	1 *					80
P38777 UniProt NPD GO	FSH1_YEAST	Family of serine hydrolases 1 (EC 3.1.-.-)	0.04	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]		1YCD	243
P49353 UniProt NPD GO	FPPS_MAIZE	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.04	-	cyt	0	Cytoplasm (By similarity)				350
P36189 UniProt NPD GO	FAS_ANSAN	Fatty acid synthase (EC 2.3.1.85) (Fragment)	0.04	-	cyt	0					352
P07855 UniProt NPD GO	FAS_RABIT	Fatty acid synthase (EC 2.3.1.85) (Fragment)	0.04	-	cyt	0					64
P81400 UniProt NPD GO	FABP2_AMBME	Fatty acid-binding protein 2, liver (L-FABP) (Liver basic FABP) (LB-FABP)	0.04	-	cyt	0	Cytoplasm			2FTB	125
Q9BMK3 UniProt NPD GO	FABP2_ECHGR	Fatty acid-binding protein homolog 2	0.04	-	cyt	0					133
O01812 UniProt NPD GO	FABP6_CAEEL	Fatty acid-binding protein homolog 6	0.04	-	cyt	0					135
Q05816 UniProt NPD GO	FABPE_MOUSE	Fatty acid-binding protein, epidermal (E-FABP) (Psoriasis-associated fatty acid-binding protein homo ...	0.04	-	cyt	0	Cytoplasm				134
P80226 UniProt NPD GO	FABPL_CHICK	Fatty acid-binding protein, liver (L-FABP) (Liver basic FABP) (LB-FABP) (Liver bile acid-binding pro ...	0.04	-	cyt	0	Cytoplasm			1ZRY	125
P08335 UniProt NPD GO	KRFT_ANAPL	Feather keratin B-4 (F-ker)	0.04	-	nuc	0					95
P07839 UniProt NPD GO	FER_CHLRE	Ferredoxin, chloroplast precursor	0.04	-	mit	0	Plastid; chloroplast			1FCT	126
P00228 UniProt NPD GO	FER_WHEAT	Ferredoxin, chloroplast precursor	0.04	-	mit	0	Plastid; chloroplast				143
P41343 UniProt NPD GO	FENR_MESCR	Ferredoxin--NADP reductase, chloroplast precursor (EC 1.18.1.2) (FNR)	0.04	-	mit	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				365
Q00598 UniProt NPD GO	FENR_CYAPA	Ferredoxin--NADP reductase, cyanelle precursor (EC 1.18.1.2) (FNR)	0.04	-	cyt	0	Plastid; cyanelle				363

You are viewing entries 76951 to 77000 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.