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
Q60902 UniProt NPD GO	EP15R_MOUSE	Epidermal growth factor receptor substrate 15-like 1 (Eps15-related protein) (Eps15R) (Epidermal gro ...	0.85	-	nuc	0	Cell membrane; peripheral membrane protein. Nucleus. Localized to plasma menbrane coated pits				907
Q9PVZ9 UniProt NPD GO	ESR1_SPAAU	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.85	-	nuc	0	Nucleus				579
Q9IAL9 UniProt NPD GO	ESRB2_CARAU	Estrogen receptor beta-2 (ER-beta-2)	0.85	-	nuc	0	Nucleus				610
Q8BGD9 UniProt NPD GO	IF4B_MOUSE	Eukaryotic translation initiation factor 4B (eIF-4B)	0.85	-	nuc	0					611
P38261 UniProt NPD GO	EXO84_YEAST	Exocyst complex component EXO84 (Exocyst complex protein of 84 kDa) (U1 SNP1-associating protein 3)	0.85	-	nuc	0	Secretory vesicle. Bud. Bud neck. Cell periphery, bud and bud neck. The polarization of EXO84 requir ...	bud neck [IDA] bud tip [IDA] exocyst [IPI] incipient bud site [IDA]		2D2S	753
O14226 UniProt NPD GO	EXO84_SCHPO	Exocyst complex component exo84	0.85	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				578
Q12149 UniProt NPD GO	RRP6_YEAST	Exosome complex exonuclease RRP6 (EC 3.1.13.-) (Ribosomal RNA-processing protein 6)	0.85	+	nuc	0	Nucleus; nucleolus (Potential)	nuclear exosome (RNase complex) [IDA]		1M0Y	733
Q01780 UniProt NPD GO	EXOSX_HUMAN	Exosome component 10 (Polymyositis/scleroderma autoantigen 2) (Autoantigen PM/Scl 2) (Polymyositis/s ...	0.85	+	nuc	0	Cytoplasm. Nucleus; nucleolus	nucleolus [TAS]	605960	2CPR	885
P41876 UniProt NPD GO	FMRF_DROVI	FMRFamide-related peptides precursor [Contains: SLQDNFMHF-amide; DPKQDFMRF-amide; APPSDFMRF-amide; A ...	0.85	-	nuc	0	Secreted protein				339
Q5R5T1 UniProt NPD GO	FGD3_PONPY	FYVE, RhoGEF and PH domain-containing protein 3	0.85	-	nuc	0	Cytoplasm (Probable)				737
Q5JSP0 UniProt NPD GO	FGD3_HUMAN	FYVE, RhoGEF and PH domain-containing protein 3 (Zinc finger FYVE domain-containing protein 5)	0.85	-	nuc	0	Cytoplasm (Probable)	cytoplasm [ISS] Golgi apparatus [ISS] lamellipodium [ISS] ruffle [ISS]		2COC	725
Q96M96 UniProt NPD GO	FGD4_HUMAN	FYVE, RhoGEF and PH domain-containing protein 4 (Actin filament-binding protein frabin) (FGD1-relate ...	0.85	+	nuc	0	Cytoplasm (By similarity). Concentrated in filopodia and poorly detected at lamellipodia. Binds alon ...	cytoplasm [ISS] Golgi apparatus [ISS] lamellipodium [ISS] ruffle [ISS]			766
Q06001 UniProt NPD GO	FAR10_YEAST	Factor arrest protein 10	0.85	+	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	endoplasmic reticulum [IDA]			478
Q24761 UniProt NPD GO	TRSF_DROVI	Female-specific protein transformer	0.85	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Speckled subnuclear compartment (By similarit ...				199
Q8WU20 UniProt NPD GO	FRS2_HUMAN	Fibroblast growth factor receptor substrate 2 (FGFR substrate 2) (Suc1-associated neurotrophic facto ...	0.85	-	nuc	0	Intracytoplasmic membrane. Cytoplasmic, membrane-bound	integral to plasma membrane [TAS] membrane fraction [TAS]	607743	1XR0	511
P42776 UniProt NPD GO	GBF3_ARATH	G-box-binding factor 3 (AtbZIP55)	0.85	+	nuc	0	Nucleus				382
Q5BCB9 UniProt NPD GO	GPI10_EMENI	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.85	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				663
Q99PF6 UniProt NPD GO	GAB1_MESAU	GRB2-associated-binding protein 1 (GRB2-associated binder 1)	0.85	-	nuc	0					694
Q8BHN1 UniProt NPD GO	TXLNG_MOUSE	Gamma-taxilin	0.85	-	nuc	0					524
P06537 UniProt NPD GO	GCR_MOUSE	Glucocorticoid receptor (GR)	0.85	+	nuc	0	Cytoplasm. Nucleus. Cytoplasmic in the absence of ligand; nuclear after ligand-binding. The hormone- ...	nucleus [IDA]			783
P59667 UniProt NPD GO	GCR_RABIT	Glucocorticoid receptor (GR)	0.85	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				772
P06536 UniProt NPD GO	GCR_RAT	Glucocorticoid receptor (GR)	0.85	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...	nucleus [TAS]		2GDA	795
Q61543 UniProt NPD GO	GSLG1_MOUSE	Golgi apparatus protein 1 precursor (Golgi sialoglycoprotein MG-160) (E-selectin ligand 1) (ESL-1) ( ...	0.85	-	nuc	1	Cell membrane; single-pass type I membrane protein. Golgi apparatus; Golgi membrane; single-pass typ ...				1175
Q8BMP6 UniProt NPD GO	GCP60_MOUSE	Golgi resident protein GCP60 (Acyl-CoA-binding domain-containing protein 3) (Golgi phosphoprotein 1) ...	0.85	+	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side. Mitochondrion. Also ...				524
P43028 UniProt NPD GO	GDF6_MOUSE	Growth/differentiation factor 6 precursor (GDF-6) (Growth/differentiation factor 16)	0.85	+	nuc	0	Secreted protein (Probable)				454
Q9ES64 UniProt NPD GO	USH1C_MOUSE	Harmonin (Usher syndrome type-1C protein homolog) (PDZ domain-containing protein)	0.85	-	nuc	0		cilium [IDA] plasma membrane [IDA]		1V6B	910
P38530 UniProt NPD GO	HSF2_CHICK	Heat shock factor protein 2 (HSF 2) (Heat shock transcription factor 2) (HSTF 2) (HSF 3B) (HSTF 3B)	0.85	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic during normal growth and moves to th ...				564
Q960X8 UniProt NPD GO	HRS_DROME	Hepatocyte growth factor-regulated tyrosine kinase substrate	0.85	-	nuc	0	Cytoplasm; cell cortex. Cytoplasm; perinuclear region. Locates to vesicles present in the perinuclea ...	endosome [TAS] synaptic vesicle [NAS]		1DVP	760
P02258 UniProt NPD GO	H5_ANSAN	Histone H5	0.85	+	nuc	0	Nucleus				193
P02259 UniProt NPD GO	H5_CHICK	Histone H5	0.85	+	nuc	0	Nucleus			1HST	189
Q4P3S3 UniProt NPD GO	ESA1_USTMA	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.85	-	nuc	0	Nucleus (By similarity)				565
Q8C2B3 UniProt NPD GO	HDAC7_MOUSE	Histone deacetylase 7a (HD7a)	0.85	-	nuc	0	Nucleus. Cytoplasm. In the nucleus, it associates with distinct subnuclear dot-like structures. Shut ...	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			938
Q9SUE7 UniProt NPD GO	ATX4_ARATH	Histone-lysine N-methyltransferase ATX4 (EC 2.1.1.43) (Trithorax-homolog protein 4) (TRX-homolog pro ...	0.85	+	nuc	1 *	Nucleus (By similarity)				990
Q9NQR1 UniProt NPD GO	SETD8_HUMAN	Histone-lysine N-methyltransferase, H4 lysine-20 specific (EC 2.1.1.43) (Histone H4-K20 methyltransf ...	0.85	-	nuc	1 *	Nucleus (By similarity). Associates with silent chromatin on euchromatic arms. No association with c ...		607240	2BQZ	393
Q61670 UniProt NPD GO	HLX1_MOUSE	Homeobox protein HLX1	0.85	+	nuc	0	Nucleus (Probable)				476
Q14774 UniProt NPD GO	HLX1_HUMAN	Homeobox protein HLX1 (Homeobox protein HB24)	0.85	+	nuc	0	Nucleus (Potential)		142995		488
Q9IA26 UniProt NPD GO	HXA9_HETFR	Homeobox protein Hox-A9	0.85	+	nuc	0	Nucleus (By similarity)				260
Q9YGT5 UniProt NPD GO	HXA9B_BRARE	Homeobox protein Hox-A9b	0.85	+	nuc	0	Nucleus (By similarity)				258
Q8JH55 UniProt NPD GO	HXB8B_BRARE	Homeobox protein Hox-B8b (Hox-A8)	0.85	+	nuc	0	Nucleus (By similarity)				247
P31263 UniProt NPD GO	HXD11_NOTVI	Homeobox protein Hox-D11 (NvHox-2)	0.85	+	nuc	0	Nucleus				277
Q9PWM6 UniProt NPD GO	HXD9A_BRARE	Homeobox protein Hox-D9a (Hox-D9)	0.85	+	nuc	0	Nucleus (By similarity)				262
P50221 UniProt NPD GO	MEOX1_HUMAN	Homeobox protein MOX-1 (Mesenchyme homeobox 1)	0.85	+	nuc	0	Nucleus (Potential)		600147		254
P32443 UniProt NPD GO	MEOX2_MOUSE	Homeobox protein MOX-2 (Mesenchyme homeobox 2)	0.85	+	nuc	0	Nucleus (Potential)				303
Q38874 UniProt NPD GO	STM_ARATH	Homeobox protein SHOOT MERISTEMLESS	0.85	+	nuc	0	Nucleus (Probable)				382
P53147 UniProt NPD GO	TOS8_YEAST	Homeobox protein TOS8 (Target of SBF 8)	0.85	-	nuc	0	Nucleus (Probable)	nucleus [IC]			276
Q94165 UniProt NPD GO	HM34_CAEEL	Homeobox protein ceh-34	0.85	+	nuc	0	Nucleus (Probable)				256
P09532 UniProt NPD GO	HMEN_TRIGR	Homeobox protein engrailed (SU-HB-En) (Fragment)	0.85	+	nuc	0	Nucleus (Probable)				154
O04135 UniProt NPD GO	KNAP2_MALDO	Homeobox protein knotted-1-like 2 (KNAP2)	0.85	-	nuc	0	Nucleus (Probable)				397
Q00466 UniProt NPD GO	HAT7_ARATH	Homeobox-leucine zipper protein HAT7 (HD-ZIP protein 7) (HD-ZIP protein ATHB-3)	0.85	+	nuc	0	Nucleus				314
P13709 UniProt NPD GO	FSH_DROME	Homeotic protein female sterile (Fragile-chorion membrane protein)	0.85	+	nuc	0	Membrane; multi-pass membrane protein (Potential)				2038

You are viewing entries 6501 to 6550 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.