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
Q6XZ78 UniProt NPD GO	SCRK2_MAIZE	Fructokinase-2 (EC 2.7.1.4) (ZmFRK2)	0.01	-	cyt	0					335
Q9C2U0 UniProt NPD GO	ALF_KLULA	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.01	-	cyt	0					361
Q8J0N6 UniProt NPD GO	ALF_PARBR	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.01	-	cyt	0					363
Q42690 UniProt NPD GO	ALFC_CHLRE	Fructose-bisphosphate aldolase 1, chloroplast precursor (EC 4.1.2.13)	0.01	-	mit	0	Plastid; chloroplast				374
O65735 UniProt NPD GO	ALF_CICAR	Fructose-bisphosphate aldolase, cytoplasmic isozyme (EC 4.1.2.13)	0.01	-	cyt	0	Cytoplasm				359
P04158 UniProt NPD GO	SC1_SCHCO	Fruiting body protein SC1 precursor (Hydrophobin SC1)	0.01	-	end	0	Cell wall. Secreted protein. Secreted in aqueous environment				109
P16933 UniProt NPD GO	SC3_SCHCO	Fruiting body protein SC3 precursor (Hydrophobin SC3)	0.01	-	end	1 *	Cell wall. Cell wall of aerial hyphae. Secreted protein. Abundantly secreted from the tips of submer ...				136
P16934 UniProt NPD GO	SC4_SCHCO	Fruiting body protein SC4 precursor (Hydrophobin SC4)	0.01	-	end	0	Cell wall. Secreted protein. Abundantly secreted in aqueous environment				111
Q7SIC1 UniProt NPD GO	FUCL_ANGAN	Fucolectin	0.01	-	nuc	0	Secreted protein (By similarity)			1K12	158
Q40297 UniProt NPD GO	FCPA_MACPY	Fucoxanthin-chlorophyll a-c binding protein A, chloroplast precursor	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				217
Q42395 UniProt NPD GO	FCP_ODOSI	Fucoxanthin-chlorophyll a-c binding protein, chloroplast precursor (FCP)	0.01	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane. FCPs are probably transported across the endop ...				203
P80347 UniProt NPD GO	FUC1_RAT	Fuctinin-1 (Fucosyltransferase inhibitor 1) (Fragment)	0.01	-	nuc	0	Cytoplasm				22
P80348 UniProt NPD GO	FUC2_RAT	Fuctinin-2 (Fucosyltransferase inhibitor 2) (Fragment)	0.01	-	cyt	0	Cytoplasm				22
P56600 UniProt NPD GO	GAL10_CANMA	GAL10 bifunctional protein [Includes: UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase); Aldos ...	0.01	-	cyt	0					153
P83337 UniProt NPD GO	OFUT1_CRIGR	GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O-FucT-1) ( ...	0.01	-	cyt	0	Endoplasmic reticulum (By similarity)				61
Q9U6Y3 UniProt NPD GO	GFPL_CLASP	GFP-like fluorescent chromoprotein cFP484	0.01	-	exc	0					266
Q9U6Y7 UniProt NPD GO	GFPL_DISST	GFP-like fluorescent chromoprotein dsFP483	0.01	-	cyt	0					232
Q95P04 UniProt NPD GO	NFCP_GONTE	GFP-like non-fluorescent chromoprotein (gtCP)	0.01	-	cyt	0		host [ISS]			221
Q4ILH3 UniProt NPD GO	MCD4_GIBZE	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.01	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				981
Q6C7Q6 UniProt NPD GO	GPI7_YARLI	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.01	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				860
Q5B7W0 UniProt NPD GO	GPI14_EMENI	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.01	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				443
Q6C216 UniProt NPD GO	GPI18_YARLI	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.01	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				357
Q290J8 UniProt NPD GO	PIGV_DROPS	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Protein vegetable)	0.01	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				452
Q6CAB8 UniProt NPD GO	GPI10_YARLI	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.01	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				510
Q86VD9 UniProt NPD GO	PIGZ_HUMAN	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV) (Phosphatidylinosito ...	0.01	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				548
P52885 UniProt NPD GO	SAR1_TOBAC	GTP-binding protein SAR1	0.01	-	cyt	0					198
Q9Y6B6 UniProt NPD GO	SAR1B_HUMAN	GTP-binding protein SAR1b (GTBPB)	0.01	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity). ...		607692		198
Q9QVY3 UniProt NPD GO	SAR1B_CRIGR	GTP-binding protein SAR1b (Sar1) (GTBPB)	0.01	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Golgi apparatus; ...			1F6B	198
Q39571 UniProt NPD GO	YPTC1_CHLRE	GTP-binding protein YPTC1	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
Q01475 UniProt NPD GO	SAR1_SCHPO	GTP-binding protein sar1	0.01	-	cyt	0		endoplasmic reticulum membrane [TAS]			190
P52886 UniProt NPD GO	SAR1_ASPNG	GTP-binding protein sarA	0.01	-	cyt	0					189
P33723 UniProt NPD GO	YPT1_NEUCR	GTP-binding protein ypt1	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
P80396 UniProt NPD GO	GGN2_RANRU	Gaegurin-2	0.01	-	nuc	0	Secreted protein				33
P80397 UniProt NPD GO	GGN3_RANRU	Gaegurin-3	0.01	-	nuc	0	Secreted protein				33
P04385 UniProt NPD GO	GAL1_YEAST	Galactokinase (EC 2.7.1.6) (Galactose kinase)	0.01	-	nuc	0				2AJ4	527
P06294 UniProt NPD GO	IGAO_DACDE	Galactose oxidase inhibitor	0.01	-		0					7
P33889 UniProt NPD GO	AGI_EUPMA	Galactose-inhibitable lectin [Contains: Galactose-inhibitable lectin isoform Ala-1 del] (Fragment)	0.01	-		0					18
O77486 UniProt NPD GO	FUT2_GORGO	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.01	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				343
O77485 UniProt NPD GO	FUT2_PANTR	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.01	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				343
P47215 UniProt NPD GO	GALA_ALLMI	Galanin	0.01	-	cyt	0	Secreted protein				29
P30802 UniProt NPD GO	GALA_CHICK	Galanin	0.01	-	cyt	0	Secreted protein				29
P82447 UniProt NPD GO	LEG1_PODHI	Galectin-1 (Fragment)	0.01	-	cyt	0					58
Q49I35 UniProt NPD GO	LEG1_PIG	Galectin-1 (Lectin galactoside-binding soluble 1)	0.01	-	cyt	0					134
P48538 UniProt NPD GO	LEG1_CRIGR	Galectin-1 (Lectin galactoside-binding soluble 1) (Beta-galactoside-binding lectin L-14-I) (Lactose- ...	0.01	-	cyt	0	Cytoplasm				134
P16045 UniProt NPD GO	LEG1_MOUSE	Galectin-1 (Lectin galactoside-binding soluble 1) (Beta-galactoside-binding lectin L-14-I) (Lactose- ...	0.01	-	cyt	0		extracellular space [IDA]			134
O54891 UniProt NPD GO	LEG6_MOUSE	Galectin-6	0.01	-	cyt	0					301
P46158 UniProt NPD GO	GLL2_CHICK	Gallinacin-2 precursor (Gal-2)	0.01	-	exc	0	Cytoplasmic granule				64
O57391 UniProt NPD GO	ENOG_CHICK	Gamma-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Neural enolase) (NSE)	0.01	-	cyt	0	Cytoplasm				434
P09104 UniProt NPD GO	ENOG_HUMAN	Gamma-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Neural enolase) (Neuron-specific en ...	0.01	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Can translocate to the plasma membrane in ...		131360	2AKZ	433
P17183 UniProt NPD GO	ENOG_MOUSE	Gamma-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Neural enolase) (Neuron-specific en ...	0.01	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Can translocate to the plasma membrane in ...				433

You are viewing entries 88351 to 88400 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.