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
Q9Z0N1 UniProt NPD GO	IF2G_MOUSE	Eukaryotic translation initiation factor 2 subunit 3, X-linked (Eukaryotic translation initiation fa ...	0.02	-	cyt	0					471
O96719 UniProt NPD GO	IF2G_ENCCU	Eukaryotic translation initiation factor 2 subunit gamma (eIF-2-gamma)	0.02	-	mit	0					439
O73777 UniProt NPD GO	IF4G2_CHICK	Eukaryotic translation initiation factor 4 gamma 2 (eIF-4-gamma 2) (eIF-4G 2) (eIF4G 2) (p97) (Fragm ...	0.02	-	cyt	0					73
Q75AV8 UniProt NPD GO	IF4E_ASHGO	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.02	-	cyt	0					211
Q9P975 UniProt NPD GO	IF4E_CANAL	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.02	-	cyt	0					209
O45551 UniProt NPD GO	IF4E1_CAEEL	Eukaryotic translation initiation factor 4E-1 (eIF4E-1) (eIF-4E-1) (mRNA cap-binding protein) (eIF-4 ...	0.02	-	cyt	0	Cytoplasm. When associated with pgl-1				212
Q26571 UniProt NPD GO	IF5A_SCHMA	Eukaryotic translation initiation factor 5A (eIF-5A) (Fragment)	0.02	-	nuc	0					52
Q9XI91 UniProt NPD GO	IF5A1_ARATH	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1)	0.02	-	nuc	0					158
P56289 UniProt NPD GO	IF5A1_SCHPO	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1)	0.02	-	mit	0					157
P10160 UniProt NPD GO	IF5A1_RABIT	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-5A1) (Eukaryotic initiation factor 5A ...	0.02	-	mit	0					153
Q9UST4 UniProt NPD GO	IF5A2_SCHPO	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2)	0.02	-	mit	0					157
Q9GZV4 UniProt NPD GO	IF5A2_HUMAN	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2) (eIF-5A2) (Eukaryotic initiation factor 5A ...	0.02	-	cyt	0			605782		152
Q8BGY2 UniProt NPD GO	IF5A2_MOUSE	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2) (eIF-5A2) (Eukaryotic initiation factor 5A ...	0.02	-	cyt	0					152
Q5R898 UniProt NPD GO	IF5A2_PONPY	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2) (eIF-5A2) (Eukaryotic initiation factor 5A ...	0.02	-	cyt	0					152
O62106 UniProt NPD GO	IF6_CAEEL	Eukaryotic translation initiation factor 6 (eIF-6)	0.02	-	cyt	0					246
O94476 UniProt NPD GO	IF6_SCHPO	Eukaryotic translation initiation factor 6 (eIF-6)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				244
Q9XYP3 UniProt NPD GO	IF6_TRYCR	Eukaryotic translation initiation factor 6 (eIF-6) (Fragment)	0.02	-	cyt	0					114
Q95135 UniProt NPD GO	EAA3_BOVIN	Excitatory amino acid transporter 3 (Sodium-dependent glutamate/aspartate transporter 3) (Excitatory ...	0.02	-	end	8 *	Membrane; multi-pass membrane protein				524
O35544 UniProt NPD GO	EAA4_MOUSE	Excitatory amino acid transporter 4 (Sodium-dependent glutamate/aspartate transporter) (High-affinit ...	0.02	-	end	8	Membrane; multi-pass membrane protein				561
O35921 UniProt NPD GO	EAA4_RAT	Excitatory amino acid transporter 4 (Sodium-dependent glutamate/aspartate transporter) (High-affinit ...	0.02	-	end	7	Membrane; multi-pass membrane protein				561
P49063 UniProt NPD GO	PGLR2_ARATH	Exopolygalacturonase clone GBGA483 precursor (EC 3.2.1.67) (ExoPG) (Pectinase) (Galacturan 1,4-alpha ...	0.02	-	exc	1 *	Secreted protein				444
Q9LZT4 UniProt NPD GO	EXPL1_ARATH	Expansin-like 1 precursor (AtEXPL1) (At-EXPL1) (Ath-ExpBeta-2.1)	0.02	-	exc	2 *					265
Q9SVE5 UniProt NPD GO	EXPL2_ARATH	Expansin-like 2 precursor (AtEXPL2) (At-EXPL2) (Ath-ExpBeta-2.2)	0.02	-	exc	0					265
Q9LZT5 UniProt NPD GO	EXPL3_ARATH	Expansin-like 3 precursor (AtEXPL3) (At-EXPL3) (Ath-ExpBeta-2.3)	0.02	-	exc	0					263
P11069 UniProt NPD GO	GLB3_LUMTE	Extracellular globin-3 precursor (Extracellular globin III) (Erythrocruorin) (Globin C)	0.02	-	exc	0				1X9F	170
P62811 UniProt NPD GO	EXPI_BOVIN	Extracellular peptidase inhibitor precursor (Protein WDNM1)	0.02	-	nuc	1 *	Secreted protein (Probable)				74
P62810 UniProt NPD GO	EXPI_MOUSE	Extracellular peptidase inhibitor precursor (Protein WDNM1)	0.02	-	nuc	1 *	Secreted protein (Probable)				74
P14730 UniProt NPD GO	EXPI_RAT	Extracellular peptidase inhibitor precursor (Protein WDNM1) (Fragment)	0.02	-	nuc	1 *	Secreted protein (Probable)				74
Q07449 UniProt NPD GO	SODE_ONCVO	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD)	0.02	-	nuc	1 *	Secreted protein; extracellular space				201
Q8K3B1 UniProt NPD GO	FBSP1_MOUSE	F-box/SPRY-domain protein 1 (F-box only protein 45)	0.02	-	cyt	0					286
Q4HZB8 UniProt NPD GO	FKBP_GIBZE	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (FkbA) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (R ...	0.02	-	cyt	0	Cytoplasm (By similarity)				111
Q62658 UniProt NPD GO	FKB1A_RAT	FK506-binding protein 1A (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (12 ...	0.02	-	cyt	0	Cytoplasm	microsome [IDA]			107
Q86ZF2 UniProt NPD GO	FKBP2_PODAN	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.02	-	exc	0	Endoplasmic reticulum (By similarity)				185
P69138 UniProt NPD GO	FLRF_HELTI	FLRFamide	0.02	-		0	Secreted protein				4
P69137 UniProt NPD GO	FLRF_HIRME	FLRFamide	0.02	-		0	Secreted protein				4
P18523 UniProt NPD GO	FARP_MANSE	FMRFamide-like neuropeptide	0.02	-		0	Secreted protein				10
P83308 UniProt NPD GO	FARP_CHICK	FMRFamide-like neuropeptide (LPLRF-amide)	0.02	-		0	Secreted protein				5
P83322 UniProt NPD GO	FAR7_PENMO	FMRFamide-like neuropeptide FLP7 (GYRKPPFNGSIF-amide)	0.02	-		0	Secreted protein				12
P83281 UniProt NPD GO	FAR8_MACRS	FMRFamide-like neuropeptide FLP8 (VSHNNFLRF-amide)	0.02	-		0	Secreted protein				9
P41871 UniProt NPD GO	FAR1_HELTI	FMRFamide-like neuropeptide GDPFLRF-amide	0.02	-		0	Secreted protein				7
P42562 UniProt NPD GO	FAR3_HIRME	FMRFamide-like neuropeptide YLRF-amide	0.02	-		0	Secreted protein				4
Q61835 UniProt NPD GO	FXYD3_MOUSE	FXYD domain-containing ion transport regulator 3 precursor (Chloride conductance inducer protein Mat ...	0.02	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				88
Q3MHZ5 UniProt NPD GO	FXYD6_BOVIN	FXYD domain-containing ion transport regulator 6 precursor	0.02	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				95
Q9H0Q3 UniProt NPD GO	FXYD6_HUMAN	FXYD domain-containing ion transport regulator 6 precursor	0.02	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	extracellular space [ISS] integral to membrane [ISS]	606683		95
Q4R566 UniProt NPD GO	FXYD6_MACFA	FXYD domain-containing ion transport regulator 6 precursor	0.02	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				95
Q5RB29 UniProt NPD GO	FXYD6_PONPY	FXYD domain-containing ion transport regulator 6 precursor	0.02	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				95
Q9D164 UniProt NPD GO	FXYD6_MOUSE	FXYD domain-containing ion transport regulator 6 precursor (PLM-like protein)	0.02	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				94
Q91XV6 UniProt NPD GO	FXYD6_RAT	FXYD domain-containing ion transport regulator 6 precursor (Vascular endothelial cell-specific prote ...	0.02	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				94
Q43315 UniProt NPD GO	FPPS2_ARATH	Farnesyl pyrophosphate synthetase 2 (FPP synthetase 2) (FPS 2) (Farnesyl diphosphate synthetase 2) [ ...	0.02	-	cyt	0	Cytoplasm				342
Q8R5H8 UniProt NPD GO	FAIM1_RAT	Fas apoptotic inhibitory molecule 1 (rFAIM)	0.02	-	cyt	0					201

You are viewing entries 83451 to 83500 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.