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
O55208 UniProt NPD GO	FIGLA_MOUSE	Factor in the germline alpha (Transcription factor FIGa) (FIGalpha)	0.53	-	nuc	0	Nucleus (Probable)				194
P02672 UniProt NPD GO	FIBA_BOVIN	Fibrinogen alpha chain precursor [Contains: Fibrinopeptide A]	0.53	-	exc	0	Secreted protein			2BAF	615
P12034 UniProt NPD GO	FGF5_HUMAN	Fibroblast growth factor 5 precursor (FGF-5) (HBGF-5) (Smag-82)	0.53	-	exc	0		extracellular space [TAS]	165190		268
P37237 UniProt NPD GO	FGF8_MOUSE	Fibroblast growth factor 8 precursor (FGF-8) (HBGF-8) (Androgen-induced growth factor) (AIGF)	0.53	-	exc	0	Secreted protein				268
P13605 UniProt NPD GO	FMOD_BOVIN	Fibromodulin precursor (FM) (Collagen-binding 59 kDa protein) (Keratan sulfate proteoglycan fibromod ...	0.53	-	exc	0	Secreted protein; extracellular space; extracellular matrix				375
P12759 UniProt NPD GO	RSP3_CHLRE	Flagellar radial spoke protein 3	0.53	-	cyt	0	Radial spoke				516
P39749 UniProt NPD GO	FEN1_MOUSE	Flap endonuclease 1 (EC 3.1.-.-) (Flap structure-specific endonuclease 1) (FEN-1)	0.53	-	nuc	0	Nucleus (Probable)	nucleus [TAS]			378
Q8NB78 UniProt NPD GO	AOF1_HUMAN	Flavin-containing amine oxidase domain-containing protein 1 (EC 1.-.-.-)	0.53	-	cyt	0					823
Q12947 UniProt NPD GO	FOXF2_HUMAN	Forkhead box protein F2 (Forkhead-related protein FKHL6) (Forkhead-related transcription factor 2) ( ...	0.53	-	nuc	0	Nucleus	nucleus [TAS] transcription factor complex [TAS]	603250		444
P26323 UniProt NPD GO	FLI1_MOUSE	Friend leukemia integration 1 transcription factor (Retroviral integration site protein Fli-1)	0.53	-	nuc	0	Nucleus	nucleus [IDA]			452
P25693 UniProt NPD GO	PCL2_YEAST	G1/S-specific cyclin PCL2 (Cyclin HCS26 homolog)	0.53	-	nuc	0		cyclin-dependent protein kinase holoenzyme ... [TAS]			308
Q6UXV0 UniProt NPD GO	GFRAL_HUMAN	GDNF family receptor alpha-like precursor	0.53	-	cyt	1	Membrane; single-pass membrane protein (Potential)				394
Q5PR73 UniProt NPD GO	DIRA2_MOUSE	GTP-binding protein Di-Ras2 (Distinct subgroup of the Ras family member 2)	0.53	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				199
Q9Z137 UniProt NPD GO	B3GA2_RAT	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.53	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to membrane [NAS]			324
P28471 UniProt NPD GO	GBRA4_RAT	Gamma-aminobutyric-acid receptor alpha-4 subunit precursor (GABA(A) receptor)	0.53	-	exc	4 *	Membrane; multi-pass membrane protein				552
P56476 UniProt NPD GO	GBRR2_MOUSE	Gamma-aminobutyric-acid receptor rho-2 subunit precursor (GABA(A) receptor)	0.53	-	end	4	Membrane; multi-pass membrane protein	axon [TAS]			465
P18714 UniProt NPD GO	ZG20_XENLA	Gastrula zinc finger protein XFG20-1 (XLCGF20.1)	0.53	-	nuc	0	Nucleus (Potential)				675
P06100 UniProt NPD GO	NOT2_YEAST	General negative regulator of transcription subunit 2	0.53	-	cyt	0	Cytoplasm. Nucleus	CCR4-NOT core complex [IPI] cytoplasm [IDA] nucleus [IDA]			191
P41541 UniProt NPD GO	VDP_BOVIN	General vesicular transport factor p115 (Transcytosis-associated protein) (TAP) (Vesicle docking pro ...	0.53	-	nuc	0	Cytoplasm; cytosol. Golgi apparatus; Golgi membrane; peripheral membrane protein. Recycles between t ...				961
Q39110 UniProt NPD GO	GAOX1_ARATH	Gibberellin 20 oxidase 1 (EC 1.14.11.-) (Gibberellin C-20 oxidase 1) (GA 20-oxidase 1) (AtGA20ox)	0.53	-	nuc	0					377
Q28115 UniProt NPD GO	GFAP_BOVIN	Glial fibrillary acidic protein, astrocyte (GFAP)	0.53	-	mit	0	Cytoplasm (By similarity). Associated with intermediate filaments (By similarity)				428
P47819 UniProt NPD GO	GFAP_RAT	Glial fibrillary acidic protein, astrocyte (GFAP)	0.53	-	mit	0	Cytoplasm (By similarity). Associated with intermediate filaments (By similarity)	intermediate filament [TAS]			430
Q04924 UniProt NPD GO	GLU2B_YEAST	Glucosidase 2 subunit beta precursor (Glucosidase II subunit beta) (Alpha-glucosidase II subunit bet ...	0.53	-	exc	0	Endoplasmic reticulum	endoplasmic reticulum lumen [IDA]			702
Q10914 UniProt NPD GO	GLR2_CAEEL	Glutamate receptor 2 precursor	0.53	-	end	3	Membrane; multi-pass membrane protein (Potential)				977
Q93YT1 UniProt NPD GO	GLR32_ARATH	Glutamate receptor 3.2 precursor (Ligand-gated ion channel 3.2) (AtGluR2)	0.53	+	end	3 *	Membrane; multi-pass membrane protein				912
Q8BMF5 UniProt NPD GO	GRIK4_MOUSE	Glutamate receptor, ionotropic kainate 4 precursor	0.53	-	end	4	Membrane; multi-pass membrane protein (Probable)	ionotropic glutamate receptor complex [IC]			956
P19086 UniProt NPD GO	GNAZ_HUMAN	Guanine nucleotide-binding protein G(z) subunit alpha (G(x) alpha chain) (Gz-alpha)	0.53	-	mit	0	Membrane; lipid-anchor	endoplasmic reticulum [TAS] nuclear envelope [TAS] plasma membrane [TAS]	139160		354
P30677 UniProt NPD GO	GNA14_MOUSE	Guanine nucleotide-binding protein alpha-14 subunit	0.53	-	cyt	0					355
O75343 UniProt NPD GO	GCYB2_HUMAN	Guanylate cyclase soluble subunit beta-2 (EC 4.6.1.2) (GCS-beta-2)	0.53	+	cyt	0	Cytoplasm		603695		617
O14007 UniProt NPD GO	CBF5_SCHPO	H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) (Centromere-binding factor 5 homolog)	0.53	+	nuc	0	Nucleus; nucleolus (By similarity)				474
P61576 UniProt NPD GO	REC9_HUMAN	HERV-K_5q13.3 provirus Rec protein (HERV-K104 Rec protein)	0.53	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and the ...				105
P63134 UniProt NPD GO	POK9_HUMAN	HERV-K_5q13.3 provirus ancestral Pol protein (HERV-K104 Pol protein) [Includes: Reverse transcriptas ...	0.53	-	cyt	0					483
Q69QQ6 UniProt NPD GO	HSP82_ORYSA	Heat shock protein 81-2 (HSP81-2) (Heat shock protein 90)	0.53	-	cyt	0	Cytoplasm (Potential)				699
O02192 UniProt NPD GO	HSP83_DROAV	Heat shock protein 83 (HSP 82)	0.53	-	cyt	0	Cytoplasm	centrosome [ISS]			716
P02828 UniProt NPD GO	HSP83_DROME	Heat shock protein 83 (HSP 82)	0.53	-	cyt	0	Cytoplasm	centrosome [ISS]			717
P35582 UniProt NPD GO	HNF3A_MOUSE	Hepatocyte nuclear factor 3-alpha (HNF-3A) (Forkhead box protein A1)	0.53	+	nuc	0	Nucleus	nucleus [IDA]			468
Q3T0D0 UniProt NPD GO	HNRPK_BOVIN	Heterogeneous nuclear ribonucleoprotein K (hnRNP K)	0.53	+	nuc	0	Cytoplasm (By similarity). Nucleus; nucleoplasm (By similarity)				464
P22626 UniProt NPD GO	ROA2_HUMAN	Heterogeneous nuclear ribonucleoproteins A2/B1 (hnRNP A2 / hnRNP B1)	0.53	+	cyt	0	Nucleus. Component of ribonucleosomes	heterogeneous nuclear ribonucleoprotein com... [TAS] nucleus [TAS] spliceosome complex [IDA]	600124	1X4B	353
P31390 UniProt NPD GO	HRH1_RAT	Histamine H1 receptor	0.53	-	end	7 *	Membrane; multi-pass membrane protein				486
Q4HTT2 UniProt NPD GO	H2B_GIBZE	Histone H2B	0.53	-	nuc	0	Nucleus (By similarity)				136
P69069 UniProt NPD GO	H2B_ONCMY	Histone H2B	0.53	+	nuc	0	Nucleus				123
P69070 UniProt NPD GO	H2B_SALTR	Histone H2B	0.53	+	nuc	0	Nucleus				123
Q2M2T1 UniProt NPD GO	H2B1K_BOVIN	Histone H2B type 1-K	0.53	+	nuc	0	Nucleus				125
Q5RCP8 UniProt NPD GO	H2B2E_PONPY	Histone H2B type 2-E	0.53	+	nuc	0	Nucleus				125
P08994 UniProt NPD GO	H2B2_TETTH	Histone H2B.2 (H2B-2)	0.53	-	nuc	0	Nucleus. Macronuclei				121
Q9P427 UniProt NPD GO	H3_AJECA	Histone H3	0.53	-	nuc	0	Nucleus (By similarity)				135
Q9UUK2 UniProt NPD GO	GCN5_SCHPO	Histone acetyltransferase gcn5 (EC 2.3.1.48)	0.53	-	nuc	0	Nucleus (By similarity)				454
Q949T8 UniProt NPD GO	ASHR3_ARATH	Histone-lysine N-methyltransferase ASHR3 precursor (EC 2.1.1.43) (ASH1-related protein 3) (Protein S ...	0.53	+	nuc	0	Nucleus (By similarity)				497
P23683 UniProt NPD GO	EVX1_MOUSE	Homeobox even-skipped homolog protein 1 (EVX-1)	0.53	+	nuc	0	Nucleus				416
Q91617 UniProt NPD GO	ANF2_XENLA	Homeobox protein ANF-2 (XANF-2)	0.53	+	nuc	0	Nucleus (Probable)				183

You are viewing entries 23101 to 23150 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.