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
Q99JZ7 UniProt NPD GO	ERRFI_MOUSE	ERBB receptor feedback inhibitor 1 (Mitogen-inducible gene 6 protein homolog) (Mig-6)	0.66	-	nuc	0	Cytoplasm (By similarity)				461
P05432 UniProt NPD GO	ERRFI_RAT	ERBB receptor feedback inhibitor 1 (Mitogen-inducible gene 6 protein homolog) (Mig-6) (Gene 33 polyp ...	0.66	-	nuc	0	Cytoplasm (By similarity)				459
Q9ZQX6 UniProt NPD GO	ETOL1_ARATH	ETO1-like protein 1 (Ethylene overproducer 1-like protein 1)	0.66	-	mit	0					888
P32519 UniProt NPD GO	ELF1_HUMAN	ETS-related transcription factor Elf-1 (E74-like factor 1)	0.66	+	nuc	0	Nucleus	nucleus [NAS]	189973		619
Q60775 UniProt NPD GO	ELF1_MOUSE	ETS-related transcription factor Elf-1 (E74-like factor 1)	0.66	+	nuc	0	Nucleus				612
Q6DEY7 UniProt NPD GO	EPAB_XENTR	Embryonic polyadenylate-binding protein (Embryonic poly(A)-binding protein) (ePABP)	0.66	-	nuc	0	Cytoplasm. Associated with polysomes (By similarity)	cytoplasm [ISS]			629
Q6GR16 UniProt NPD GO	EPABB_XENLA	Embryonic polyadenylate-binding protein-B (Embryonic poly(A)-binding protein-B) (ePABP-B) (ePAB-B) ( ...	0.66	-	nuc	0	Cytoplasm. Associated with polysomes (By similarity)	cytoplasm [ISS]			629
Q6FMQ0 UniProt NPD GO	PPN1_CANGA	Endopolyphosphatase (EC 3.6.1.10)	0.66	+	gol	1 *	Vacuole; vacuolar membrane; single-pass type II membrane protein				663
P22387 UniProt NPD GO	EDN1_MOUSE	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1)	0.66	-	nuc	0	Secreted protein	extracellular space [IDA]			202
Q9UTE5 UniProt NPD GO	E2AK2_SCHPO	Eukaryotic translation initiation factor 2-alpha kinase 2 (EC 2.7.11.1) (Heme-regulated eukaryotic i ...	0.66	-	nuc	0					639
Q9VDE6 UniProt NPD GO	EXOC6_DROME	Exocyst complex component 6 (Exocyst complex component Sec15)	0.66	-	cyt	0		exocyst [NAS]		2A2F	766
Q8IYI6 UniProt NPD GO	EXOC8_HUMAN	Exocyst complex component 8 (Exocyst complex 84 kDa subunit)	0.66	-	nuc	0	Cytoplasm. Redistributes to growing neurites and growth cones during cell differentiation (By simila ...				725
O54924 UniProt NPD GO	EXOC8_RAT	Exocyst complex component 8 (Exocyst complex 84 kDa subunit)	0.66	-	nuc	0	Cytoplasm. Binds lipids with phosphatidylinositol-3,4,5-trisphosphate groups (By similarity). Perinu ...	exocyst [IDA]		1ZC4	716
Q9QY96 UniProt NPD GO	CASR_MOUSE	Extracellular calcium-sensing receptor precursor (CaSR) (Parathyroid Cell calcium-sensing receptor)	0.66	-	end	7	Membrane; multi-pass membrane protein				1079
Q86XX4 UniProt NPD GO	FRAS1_HUMAN	Extracellular matrix protein FRAS1 precursor	0.66	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)		607830		4007
Q641X7 UniProt NPD GO	FBX25_RAT	F-box only protein 25	0.66	+	cyt	0					357
Q55VJ3 UniProt NPD GO	SPT16_CRYNE	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16)	0.66	+	cyt	0	Nucleus (By similarity)				1035
Q4HYB8 UniProt NPD GO	SPT16_GIBZE	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16)	0.66	+	cyt	0	Nucleus (By similarity)				1034
Q9JLN9 UniProt NPD GO	FRAP_MOUSE	FKBP12-rapamycin complex-associated protein (FK506-binding protein 12-rapamycin complex-associated p ...	0.66	-	end	0					2549
P42346 UniProt NPD GO	FRAP_RAT	FKBP12-rapamycin complex-associated protein (FK506-binding protein 12-rapamycin complex-associated p ...	0.66	-	end	0					2549
P16463 UniProt NPD GO	F801_SCHMA	Female-specific protein 800 (FS800)	0.66	-	nuc	1 *					238
O60258 UniProt NPD GO	FGF17_HUMAN	Fibroblast growth factor 17 precursor (FGF-17)	0.66	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	603725		216
Q805B2 UniProt NPD GO	FG17A_BRARE	Fibroblast growth factor 17a precursor (FGF-17a)	0.66	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			212
Q12948 UniProt NPD GO	FOXC1_HUMAN	Forkhead box protein C1 (Forkhead-related protein FKHL7) (Forkhead-related transcription factor 3) ( ...	0.66	+	nuc	0	Nucleus	nucleus [NAS]	604229		553
Q63251 UniProt NPD GO	FOXD1_RAT	Forkhead box protein D1 (Brain factor 2) (HFH-BF-2) (Fragment)	0.66	-	nuc	0	Nucleus (Potential)				101
Q61060 UniProt NPD GO	FOXD3_MOUSE	Forkhead box protein D3 (HNF3/FH transcription factor genesis) (Hepatocyte nuclear factor 3 forkhead ...	0.66	-	nuc	0	Nucleus (Probable)	nucleus [IC] transcription factor complex [TAS]			465
Q61575 UniProt NPD GO	FOXN1_MOUSE	Forkhead box protein N1 (Transcription factor winged-helix nude) (Hepatocyte nuclear factor 3 forkhe ...	0.66	-	nuc	0	Nucleus				648
Q8VEB1 UniProt NPD GO	GRK5_MOUSE	G protein-coupled receptor kinase 5 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK5)	0.66	+	nuc	0					590
P20237 UniProt NPD GO	GBRA4_BOVIN	Gamma-aminobutyric-acid receptor alpha-4 subunit precursor (GABA(A) receptor)	0.66	-	end	5 *	Membrane; multi-pass membrane protein				556
P18735 UniProt NPD GO	ZG7_XENLA	Gastrula zinc finger protein XLCGF7.1 (Fragment)	0.66	-	nuc	0	Nucleus (Potential)				168
Q99N64 UniProt NPD GO	GMCL2_MOUSE	Germ cell-less protein-like 2 (mGclh)	0.66	-	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity)				498
Q8BZM1 UniProt NPD GO	GLMN_MOUSE	Glomulin (FKBP-associated protein) (FK506-binding protein-associated protein) (FAP)	0.66	-	cyt	0		intracellular [ISS]			596
P35439 UniProt NPD GO	NMDZ1_RAT	Glutamate [NMDA] receptor subunit zeta 1 precursor (N-methyl-D-aspartate receptor subunit NR1) (NMD- ...	0.66	+	end	3	Cell membrane; multi-pass membrane protein (By similarity). Enriched in post-synaptic plasma membran ...	dendrite [ISS] growth cone [ISS] N-methyl-D-aspartate selective glutamate re... [ISS] synapse [IDA]		2A5T	938
Q8CIX8 UniProt NPD GO	GLUD1_MOUSE	Glutamate--ammonia ligase domain-containing protein 1 (Lengsin) (Lens glutamine synthase-like)	0.66	-	nuc	0					563
O75311 UniProt NPD GO	GLRA3_HUMAN	Glycine receptor alpha-3 chain precursor	0.66	-	end	4	Membrane; multi-pass membrane protein	glycine-gated chloride channel complex [ISS] integral to membrane [NAS]	600421		465
P04405 UniProt NPD GO	GLYG2_SOYBN	Glycinin G2 precursor [Contains: Glycinin A2 subunit; Glycinin B1a subunit]	0.66	-	exc	0					485
Q8BKV1 UniProt NPD GO	GPC2_MOUSE	Glypican-2 precursor	0.66	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				579
P51653 UniProt NPD GO	GPC2_RAT	Glypican-2 precursor (Cerebroglycan) (HSPG M13)	0.66	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor	extracellular matrix (sensu Metazoa) [TAS]			579
Q5M7R9 UniProt NPD GO	GRHL2_XENTR	Grainyhead-like protein 2 homolog (Transcription factor CP2-like 3)	0.66	-	nuc	0	Nucleus (By similarity)				619
Q8MT08 UniProt NPD GO	GAS8_DROME	Growth-arrest-specific protein 8 homolog	0.66	-	nuc	0	Cytoplasm (Probable)	cytoplasm [NAS]			479
O16118 UniProt NPD GO	GNAS_HOMAM	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.66	-	nuc	0					379
P27584 UniProt NPD GO	GPA1_SCHPO	Guanine nucleotide-binding protein alpha-1 subunit (GP1-alpha)	0.66	-	nuc	0					406
P27601 UniProt NPD GO	GNA13_MOUSE	Guanine nucleotide-binding protein alpha-13 subunit (G alpha-13)	0.66	-	mit	0	Membrane; lipid-anchor	heterotrimeric G-protein complex [TAS]		1ZCB	377
O73819 UniProt NPD GO	GNA14_XENLA	Guanine nucleotide-binding protein alpha-14 subunit	0.66	-	cyt	0					354
P54111 UniProt NPD GO	GPA2_KLULA	Guanine nucleotide-binding protein alpha-2 subunit (GP2-alpha)	0.66	-	nuc	0					554
Q08886 UniProt NPD GO	GPB1_YEAST	Guanine nucleotide-binding protein subunit beta 1 (Gbeta mimic kelch protein 1)	0.66	-	nuc	0	Cytoplasm	cytoplasm [IDA] plasma membrane [IGI]			897
P63130 UniProt NPD GO	GAK12_HUMAN	HERV-K_1q22 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K102 Gag protein) (HERV-K(III ...	0.66	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				665
Q10061 UniProt NPD GO	YAM6_SCHPO	Heat shock protein 70 homolog precursor	0.66	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				848
P34058 UniProt NPD GO	HS90B_RAT	Heat shock protein HSP 90-beta (HSP 84)	0.66	-	cyt	0	Cytoplasm				723
Q9QYK5 UniProt NPD GO	H6ST1_MOUSE	Heparan-sulfate 6-O-sulfotransferase 1 (EC 2.8.2.-) (HS6ST-1) (mHS6ST-1)	0.66	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				411

You are viewing entries 15751 to 15800 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.