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
P41376 UniProt NPD GO	IF4A1_ARATH	Eukaryotic initiation factor 4A-1 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-1) (eIF-4A-1) (DEAD ...	0.42	-	cyt	0	Cytoplasm (By similarity)				412
Q3SZ54 UniProt NPD GO	IF4A1_BOVIN	Eukaryotic initiation factor 4A-I (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-1) (eIF4A-I) (eIF-4 ...	0.42	-	nuc	0					406
P60842 UniProt NPD GO	IF4A1_HUMAN	Eukaryotic initiation factor 4A-I (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-1) (eIF4A-I) (eIF-4 ...	0.42	-	nuc	0			602641	2G9N	406
P60843 UniProt NPD GO	IF4A1_MOUSE	Eukaryotic initiation factor 4A-I (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-1) (eIF4A-I) (eIF-4 ...	0.42	-	nuc	0					406
P30822 UniProt NPD GO	XPO1_YEAST	Exportin-1 (Chromosome region maintenance protein 1)	0.42	-	nuc	0	Nucleus. Cytoplasm; perinuclear region. Localized in the nucleus and at its periphery	nucleus [IDA]			1084
O14980 UniProt NPD GO	XPO1_HUMAN	Exportin-1 (Exp1) (Chromosome region maintenance 1 protein homolog)	0.42	-	cyt	0	Cytoplasm. Nucleus; nucleoplasm. Nucleus; nucleoplasm; Cajal body. Nucleus; nucleolus. Located in th ...	cytoplasm [TAS] nuclear envelope [TAS] nucleoplasm [TAS]	602559	1W9C	1071
Q923V4 UniProt NPD GO	FBX6_RAT	F-box only protein 6 (F-box only protein 6b) (F-box/G-domain protein 2)	0.42	-	cyt	0					284
O74854 UniProt NPD GO	POF6_SCHPO	F-box protein pof6	0.42	-	mit	0		barrier septum [IDA] cell tip [IDA] nucleolus [IDA] nucleus [IDA]			872
Q96IG2 UniProt NPD GO	FXL20_HUMAN	F-box/LRR-repeat protein 20 (F-box and leucine-rich repeat protein 20) (F-box/LRR-repeat protein 2-l ...	0.42	-	mit	0	Cytoplasm (By similarity)		609086		436
Q9CZV8 UniProt NPD GO	FXL20_MOUSE	F-box/LRR-repeat protein 20 (F-box and leucine-rich repeat protein 20) (F-box/LRR-repeat protein 2-l ...	0.42	-	mit	0	Cytoplasm (By similarity)				436
Q8BIA4 UniProt NPD GO	FBXW8_MOUSE	F-box/WD repeat protein 8 (F-box and WD-40 domain protein 8)	0.42	+	cyt	0					598
Q756V1 UniProt NPD GO	FKBP3_ASHGO	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.42	-	nuc	0	Nucleus; nucleolus (By similarity)				418
Q9S7Q7 UniProt NPD GO	FLC_ARATH	FLOWERING LOCUS C protein (MADS-box protein FLOWERING LOCUS F)	0.42	-	nuc	0	Nucleus (Probable)				196
Q00558 UniProt NPD GO	F8I2_MOUSE	Factor VIII intron 22 protein (CpG island protein)	0.42	-	cyt	0					380
O19104 UniProt NPD GO	FANCC_BOVIN	Fanconi anemia group C protein homolog (Protein FACC)	0.42	-	cyt	0	Nucleus (By similarity). Major form. Cytoplasm (By similarity). Minor form				567
P15368 UniProt NPD GO	FAS2_PENPA	Fatty acid synthase subunit alpha (EC 2.3.1.86) [Includes: Acyl carrier; 3-oxoacyl-[acyl-carrier-pro ...	0.42	+	nuc	0					1857
Q8VI82 UniProt NPD GO	FGF23_RAT	Fibroblast growth factor 23 precursor (FGF-23)	0.42	-	exc	0	Secreted protein (Potential)				251
P50608 UniProt NPD GO	FMOD_MOUSE	Fibromodulin precursor (FM) (Collagen-binding 59 kDa protein) (Keratan sulfate proteoglycan fibromod ...	0.42	-	exc	0	Secreted protein; extracellular space; extracellular matrix				376
Q9Y893 UniProt NPD GO	FOLE_CANAL	Folylpolyglutamate synthase (EC 6.3.2.17) (Folylpoly-gamma-glutamate synthetase) (FPGS) (Tetrahydrof ...	0.42	-	nuc	0					514
P78423 UniProt NPD GO	X3CL1_HUMAN	Fractalkine precursor (CX3CL1) (Neurotactin) (CX3C membrane-anchored chemokine) (Small inducible cyt ...	0.42	-	nuc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein. Also exists as ...	cell surface [IDA] extracellular region [IDA] integral to membrane [IDA]	601880	1F2L	397
P35922 UniProt NPD GO	FMR1_MOUSE	Fragile X mental retardation protein 1 homolog (Protein FMR-1) (FMRP) (mFmr1p)	0.42	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [IDA]			614
Q8WP15 UniProt NPD GO	GRK7_PIG	G protein-coupled receptor kinase 7 precursor (EC 2.7.11.16) (G protein-coupled receptor kinase GRK7 ...	0.42	+	cyt	0	Membrane; lipid-anchor (By similarity)				553
Q96D09 UniProt NPD GO	GASP2_HUMAN	G-protein coupled receptor-associated sorting protein 2 (GASP-2)	0.42	-	nuc	0					838
Q9DGA3 UniProt NPD GO	CCNB2_ORYCU	G2/mitotic-specific cyclin-B2	0.42	-	cyt	0					388
Q9IBG0 UniProt NPD GO	CCNB2_ORYLA	G2/mitotic-specific cyclin-B2	0.42	-	cyt	0					387
Q9V6X7 UniProt NPD GO	OFUT1_DROME	GDP-fucose protein O-fucosyltransferase 1 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.42	-	exc	0	Endoplasmic reticulum (By similarity)	cytoplasm [IC]			402
Q6CN76 UniProt NPD GO	GPI10_KLULA	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.42	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				601
O93343 UniProt NPD GO	GBP_XENLA	GSK-3-binding protein (GBP)	0.42	-	nuc	0					169
O00178 UniProt NPD GO	GTPB1_HUMAN	GTP-binding protein 1 (G-protein 1) (GP-1) (GP1)	0.42	-	mit	0			602245		584
O08582 UniProt NPD GO	GTPB1_MOUSE	GTP-binding protein 1 (G-protein 1) (GP-1) (GP1)	0.42	-	mit	0				1KJ3	583
O88667 UniProt NPD GO	RAD_MOUSE	GTP-binding protein RAD	0.42	-	cyt	0					308
Q61597 UniProt NPD GO	CRGC_MOUSE	Gamma crystallin C	0.42	-	nuc	0					173
P04730 UniProt NPD GO	GDB3_WHEAT	Gamma-gliadin (Gliadin B-III) (Fragment)	0.42	-	mit	0					244
P80198 UniProt NPD GO	HOG3_HORVU	Gamma-hordein-3	0.42	-	nuc	0	Cytoplasm. Vacuole. Cytoplasmic (as globules) and vacuolar (as protein bodies)				289
Q08602 UniProt NPD GO	PGTA_RAT	Geranylgeranyl transferase type-2 alpha subunit (EC 2.5.1.60) (Geranylgeranyl transferase type II al ...	0.42	-	nuc	0				1LTX	567
P48677 UniProt NPD GO	GFAP_CARAU	Glial fibrillary acidic protein homolog	0.42	-	nuc	0					359
Q9PUR1 UniProt NPD GO	GLUC1_PETMA	Glucagon-1 precursor [Contains: Glucagon-1 (Glucagon I); Glucagon-like peptide 1-I (GLP-1I); Glucago ...	0.42	-	nuc	0	Secreted protein				160
Q7XP59 UniProt NPD GO	GLR31_ORYSA	Glutamate receptor 3.1 precursor (Ligand-gated ion channel 3.1)	0.42	-	end	3	Membrane; multi-pass membrane protein				938
P09812 UniProt NPD GO	PYGM_RAT	Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase)	0.42	-	nuc	0					841
O70310 UniProt NPD GO	NMT1_MOUSE	Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) (Peptide N-myristoyltransferase 1) (Myristo ...	0.42	+	cyt	0	Cytoplasm	cytoplasm [TAS]			496
O35205 UniProt NPD GO	GRAK_MOUSE	Granzyme K precursor (EC 3.4.21.-)	0.42	-	exc	0	Cytoplasmic granule				263
Q8AVB2 UniProt NPD GO	GDF8_COTCO	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.42	+	cyt	0	Secreted protein (By similarity)				375
P20353 UniProt NPD GO	GNAI_DROME	Guanine nucleotide-binding protein G(i) subunit alpha 65A	0.42	-	mit	0		cell cortex [TAS]			355
P04896 UniProt NPD GO	GNAS_BOVIN	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.42	-	mit	0	Cell membrane; lipid anchor (By similarity)			1U0H	394
P63091 UniProt NPD GO	GNAS_CANFA	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.42	-	mit	0	Cell membrane; lipid anchor (By similarity)				394
P63092 UniProt NPD GO	GNAS_HUMAN	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.42	-	mit	0			174800		394
P29797 UniProt NPD GO	GNAS_PIG	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.42	-	mit	0	Cell membrane; lipid anchor (By similarity)				397
P18064 UniProt NPD GO	GPA1_ARATH	Guanine nucleotide-binding protein alpha-1 subunit (GP-alpha-1)	0.42	-	nuc	0					383
P26981 UniProt NPD GO	GPA1_LYCES	Guanine nucleotide-binding protein alpha-1 subunit (GP-alpha-1)	0.42	-	nuc	0					384
P93564 UniProt NPD GO	GPA1_SOLTU	Guanine nucleotide-binding protein alpha-1 subunit (GP-alpha-1)	0.42	-	nuc	0					384

You are viewing entries 30351 to 30400 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.