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
Q21974 UniProt NPD GO	UNC8_CAEEL	Degenerin unc-8 (Uncoordinated protein 8)	0.84	-	nuc	1	Membrane; multi-pass membrane protein				777
O01635 UniProt NPD GO	DEGY_CAEEL	Degenerin-like protein asic-1 (Acid-sensing/amiloride-sensitive ion channel protein 1)	0.84	+	nuc	1	Membrane; multi-pass membrane protein				795
Q5PYH6 UniProt NPD GO	DLG1_BRARE	Disks large homolog 1 (Synapse-associated protein 97A) (SAP-97A)	0.84	-	nuc	0	Membrane; peripheral membrane protein (By similarity)	basolateral plasma membrane [ISS] intercellular junction [ISS] plasma membrane [ISS]			873
Q3TTA7 UniProt NPD GO	CBLB_MOUSE	E3 ubiquitin-protein ligase CBL-B (EC 6.3.2.-) (Signal transduction protein CBL-B) (SH3-binding prot ...	0.84	-	nuc	0	Cytoplasm. In adipocytes, translocates to the plasma membrane upon insulin stimulation				982
Q9CXC9 UniProt NPD GO	ETV5_MOUSE	ETS translocation variant 5	0.84	-	nuc	0	Nucleus (By similarity)	nucleus [IC]			510
Q15075 UniProt NPD GO	EEA1_HUMAN	Early endosome antigen 1 (Endosome-associated protein p162) (Zinc finger FYVE domain-containing prot ...	0.84	-	nuc	0	Cytoplasm. Endosome; early endosome; early endosomal membrane; peripheral membrane protein	cytoplasm [TAS] cytosol [IDA] early endosome [IDA] extrinsic to plasma membrane [IDA] membrane fraction [TAS]	605070	1JOC	1411
O01991 UniProt NPD GO	EF2K_CAEEL	Elongation factor 2 kinase (EC 2.7.11.20) (eEF-2 kinase) (eEF-2K) (Calcium/calmodulin-dependent euka ...	0.84	-	nuc	0					768
Q765Z5 UniProt NPD GO	EDN2_RABIT	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2)	0.84	-	nuc	0	Secreted protein				178
Q9D952 UniProt NPD GO	EVPL_MOUSE	Envoplakin (p210) (210 kDa cornified envelope precursor protein)	0.84	-	nuc	0	Cell membrane; cell-cell junction; desmosome (By similarity). Colocalized with DSP at desmosomes and ...				2035
P79944 UniProt NPD GO	EOMES_XENLA	Eomesodermin	0.84	+	exc	0	Nucleus (Potential)				692
Q8R5F8 UniProt NPD GO	ES8L1_MOUSE	Epidermal growth factor receptor kinase substrate 8-like protein 1 (Epidermal growth factor receptor ...	0.84	-	nuc	0	Cytoplasm (By similarity)				716
Q3B7T1 UniProt NPD GO	EDRF1_HUMAN	Erythroid differentiation-related factor 1	0.84	-	nuc	0	Nucleus (Probable)				1238
Q9W6M2 UniProt NPD GO	ESR2_SPAAU	Estrogen receptor beta (ER-beta)	0.84	+	nuc	0	Nucleus				559
P57783 UniProt NPD GO	ESR3_MICUN	Estrogen receptor gamma (ER-gamma)	0.84	+	nuc	0	Nucleus				565
Q76E23 UniProt NPD GO	IF4G1_ARATH	Eukaryotic translation initiation factor 4G (Protein synthesis initiation factor 4G) (Cucumovirus mu ...	0.84	-	nuc	0					1725
P39730 UniProt NPD GO	IF2P_YEAST	Eukaryotic translation initiation factor 5B (eIF-5B) (Translation initiation factor IF-2)	0.84	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA] mitochondrion [IDA]			1002
P56960 UniProt NPD GO	EXOSX_MOUSE	Exosome component 10 (Polymyositis/scleroderma autoantigen 2 homolog) (Autoantigen PM/Scl 2 homolog) ...	0.84	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)	nucleolus [TAS]			887
Q5ZLT0 UniProt NPD GO	XPO7_CHICK	Exportin-7	0.84	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1087
Q8HZQ5 UniProt NPD GO	EZRI_RABIT	Ezrin (p81) (Cytovillin) (Villin-2)	0.84	+	nuc	0	Cell membrane; peripheral membrane protein. Localizes to cell extensions and peripheral processes of ...	actin cytoskeleton [ISS]			585
Q8TCJ0 UniProt NPD GO	FBX25_HUMAN	F-box only protein 25	0.84	+	cyt	0		ubiquitin ligase complex [NAS]	609098		367
Q756A7 UniProt NPD GO	SPT16_ASHGO	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16)	0.84	-	nuc	0	Nucleus (By similarity)				1031
Q8C0V9 UniProt NPD GO	FRMD6_MOUSE	FERM domain-containing protein 6	0.84	-	nuc	0					622
P41870 UniProt NPD GO	FAR2_HELAS	FMRFamide-related peptides type HF-1 precursor (TetraFaRP) [Contains: QFYRF-amide; FLRF-amide; FMRF- ...	0.84	-	exc	0	Secreted protein				346
Q91ZT5 UniProt NPD GO	FGD4_MOUSE	FYVE, RhoGEF and PH domain-containing protein 4 (Actin filament-binding protein frabin) (FGD1-relate ...	0.84	+	nuc	0	Cytoplasm (By similarity). Concentrated in filopodia and poorly detected at lamellipodia. Binds alon ...	filopodium [IDA] lamellipodium [IDA]			766
P55316 UniProt NPD GO	FOXGA_HUMAN	Forkhead box protein G1A (Forkhead-related protein FKHL2) (Transcription factor BF-2) (Brain factor ...	0.84	+	nuc	0	Nucleus (Potential)		600779		469
P30432 UniProt NPD GO	FUR2_DROME	Furin-like protease 2 precursor (EC 3.4.21.75) (Furin-2)	0.84	-	mit	1					1679
P48479 UniProt NPD GO	NIM1_NEUCR	G2-specific protein kinase nim-1 (EC 2.7.11.1)	0.84	-	nuc	0	Nucleus (Probable)				779
Q5FVG8 UniProt NPD GO	GRAM3_RAT	GRAM domain-containing protein 3	0.84	-	nuc	1					445
Q6GYQ0 UniProt NPD GO	GRIPE_HUMAN	GTPase-activating Rap/Ran-GAP domain-like 1 (GAP-related-interacting partner to E12) (GRIPE) (Tuberi ...	0.84	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated to the nucleus, when associated wit ...		608884		2036
Q5RA17 UniProt NPD GO	ZG14_PONPY	Gastric cancer antigen Zg14 homolog	0.84	+	nuc	0					280
P18733 UniProt NPD GO	ZG66_XENLA	Gastrula zinc finger protein XLCGF66.1 (Fragment)	0.84	-	nuc	0	Nucleus (Potential)				606
P79686 UniProt NPD GO	GCR_AOTNA	Glucocorticoid receptor (GR)	0.84	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				777
Q08379 UniProt NPD GO	GOGA2_HUMAN	Golgin subfamily A member 2 (Cis-Golgi matrix protein GM130) (Gm130 autoantigen) (Golgin-95)	0.84	+	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein	Golgi apparatus [IDA]	602580		990
P43027 UniProt NPD GO	GDF5_MOUSE	Growth/differentiation factor 5 precursor (GDF-5)	0.84	-	exc	0	Secreted protein (By similarity)				495
Q9GK68 UniProt NPD GO	GDF9_BOVIN	Growth/differentiation factor 9 precursor (GDF-9)	0.84	-	exc	0	Secreted protein (By similarity)				453
O15068 UniProt NPD GO	MCF2L_HUMAN	Guanine nucleotide exchange factor DBS (DBL's big sister) (MCF2-transforming sequence-like protein) ...	0.84	-	nuc	0			609499		1108
Q6DRP2 UniProt NPD GO	GNL3_BRARE	Guanine nucleotide-binding protein-like 3 (Nucleostemin-like protein)	0.84	+	nuc	0	Nucleus (By similarity)	nucleolus [ISS] nucleus [ISS]			561
Q9N2M8 UniProt NPD GO	HDC_DROME	Headcase protein [Contains: Headcase short protein]	0.84	-	mit	0	Cytoplasm	cytoplasm [IDA]			1080
Q64279 UniProt NPD GO	HAND1_MOUSE	Heart- and neural crest derivatives-expressed protein 1 (Extraembryonic tissues, heart, autonomic ne ...	0.84	-	nuc	0		nucleus [IDA]			216
Q9UBC0 UniProt NPD GO	HNF6_HUMAN	Hepatocyte nuclear factor 6 (HNF-6) (One cut domain family member 1)	0.84	-	nuc	0	Nucleus	nucleus [NAS]	604164		465
O08755 UniProt NPD GO	HNF6_MOUSE	Hepatocyte nuclear factor 6 (HNF-6) (One cut domain family member 1)	0.84	-	nuc	0	Nucleus	nucleus [IDA]		1S7E	465
P70512 UniProt NPD GO	HNF6_RAT	Hepatocyte nuclear factor 6 (HNF-6) (One cut domain family member 1)	0.84	-	nuc	0	Nucleus	nucleus [IPI]			465
Q24537 UniProt NPD GO	HMG2_DROME	High mobility group protein DSP1 (Protein dorsal switch 1)	0.84	+	nuc	0	Nucleus	nucleus [NAS]			393
Q9M364 UniProt NPD GO	ATX3_ARATH	Histone-lysine N-methyltransferase ATX3 (EC 2.1.1.43) (Trithorax-homolog protein 3) (TRX-homolog pro ...	0.84	-	nuc	0	Nucleus (By similarity)				902
Q9C5X4 UniProt NPD GO	ATX1_ARATH	Histone-lysine N-methyltransferase, H3 lysine-4 specific ATX1 (EC 2.1.1.43) (H3-K4-HMTase) (Trithora ...	0.84	+	nuc	0	Nucleus. Cytoplasm. Shifts from nucleus to cytoplasm as PIP5 levels increase. When in the nucleus, a ...				1062
Q2YDW7 UniProt NPD GO	SETD8_MOUSE	Histone-lysine N-methyltransferase, H4 lysine-20 specific (EC 2.1.1.43) (Histone H4-K20 methyltransf ...	0.84	-	nuc	0	Nucleus (By similarity). Associates with silent chromatin on euchromatic arms. No association with c ...				349
Q9IA27 UniProt NPD GO	HXA10_HETFR	Homeobox protein Hox-A10	0.84	+	nuc	0	Nucleus (By similarity)				271
Q6JIY5 UniProt NPD GO	HXCDA_BRARE	Homeobox protein Hox-C13a	0.84	+	nuc	0	Nucleus (By similarity)				306
Q90470 UniProt NPD GO	HXDBA_BRARE	Homeobox protein Hox-D11a (Hox-D11) (Hox-C11)	0.84	+	nuc	0	Nucleus (By similarity)				263
P19601 UniProt NPD GO	SAX1_CHICK	Homeobox protein SAX-1 (CHOX-3) (Fragment)	0.84	+	nuc	0	Nucleus (Probable)				232

You are viewing entries 6951 to 7000 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.