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
Q03280 UniProt NPD GO	TOM1_YEAST	E3 ubiquitin protein ligase TOM1 (EC 6.3.2.-) (Temperature-dependent organization in mitotic nucleus ...	0.90	-	end	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			3268
O13834 UniProt NPD GO	PTR1_SCHPO	E3 ubiquitin protein ligase ptr1 (EC 6.3.2.-) (Poly(A)+ RNA transport protein 1)	0.90	-	end	0	Nucleus				3227
P46934 UniProt NPD GO	NEDD4_HUMAN	E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-)	0.90	-	mit	0	Cytoplasm (By similarity)		602278		1000
P17686 UniProt NPD GO	ELH2_APLPA	ELH type 2 precursor [Contains: Alpha-bag cell peptide (Alpha-BCP); Beta-bag cell peptide (Beta-BCP) ...	0.90	+	exc	0	Secreted protein				252
P11536 UniProt NPD GO	E74EB_DROME	Ecdysone-induced protein 74EF isoform B (ETS-related protein E74B)	0.90	-	mit	0	Nucleus				883
O08719 UniProt NPD GO	EVL_RAT	Ena/VASP-like protein (Ena/vasodilator-stimulated phosphoprotein-like)	0.90	-	nuc	0	Cytoplasm. Targeted to the leading edge of lamellipodia and the dital tip of stress fibers through i ...	cytoplasm [ISS] focal adhesion [ISS] lamellipodium [ISS]			393
Q9LD55 UniProt NPD GO	IF3A_ARATH	Eukaryotic translation initiation factor 3 subunit 10 (eIF-3 theta) (Eukaryotic translation initiati ...	0.90	+	nuc	0					987
Q80XI3 UniProt NPD GO	IF4G3_MOUSE	Eukaryotic translation initiation factor 4 gamma 3 (eIF-4-gamma 3) (eIF-4G 3) (eIF4G 3) (eIF-4-gamma ...	0.90	-	nuc	0					1579
Q5R9G4 UniProt NPD GO	XPO7_PONPY	Exportin-7 (Exp7)	0.90	-	cyt	0	Cytoplasm. Nucleus. Nucleus; nuclear envelope; nuclear pore complex. Shuttles between the nucleus an ...				1086
P52734 UniProt NPD GO	FGD1_MOUSE	FYVE, RhoGEF and PH domain-containing protein 1 (Faciogenital dysplasia 1 protein homolog) (Zinc fin ...	0.90	-	nuc	0	Cytoplasm. Associated with membrane ruffles and lamellipodia	cytoplasm [IDA] Golgi apparatus [IDA] lamellipodium [IDA] ruffle [IDA]			960
P98174 UniProt NPD GO	FGD1_HUMAN	FYVE, RhoGEF and PH domain-containing protein 1 (Faciogenital dysplasia 1 protein) (Zinc finger FYVE ...	0.90	-	nuc	0	Cytoplasm (By similarity). Associated with membrane ruffles and lamellipodia (By similarity)	cytoplasm [ISS] Golgi apparatus [ISS] lamellipodium [ISS] ruffle [ISS]	305400		961
Q8K0X8 UniProt NPD GO	FEZ1_MOUSE	Fasciculation and elongation protein zeta 1 (Zygin-1) (Zygin I)	0.90	+	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocated from the plasma membrane to t ...	centrosome [IDA] cytoplasm [IDA]			392
Q12950 UniProt NPD GO	FOXD4_HUMAN	Forkhead box protein D4 (Forkhead-related protein FKHL9) (Forkhead-related transcription factor 5) ( ...	0.90	-	nuc	0	Nucleus	nucleus [NAS]	601092		439
Q28HT3 UniProt NPD GO	FOXI2_XENTR	Forkhead box protein I2	0.90	+	nuc	0	Nucleus (Potential)				368
Q63ZH2 UniProt NPD GO	FXI2B_XENLA	Forkhead box protein I2-B (XlFoxI2-B)	0.90	+	nuc	0	Nucleus (Potential)				367
Q9JL04 UniProt NPD GO	FMN2_MOUSE	Formin-2	0.90	-	nuc	0					1567
Q8L4M6 UniProt NPD GO	GATA3_ARATH	GATA transcription factor 3 (AtGATA-3)	0.90	-	nuc	0	Nucleus (Probable)				269
Q9UEY8 UniProt NPD GO	ADDG_HUMAN	Gamma-adducin (Adducin-like protein 70)	0.90	+	nuc	0		membrane [TAS]	601568		706
Q16666 UniProt NPD GO	IF16_HUMAN	Gamma-interferon-inducible protein Ifi-16 (Interferon-inducible myeloid differentiation transcriptio ...	0.90	+	nuc	0	Nucleus	nucleolus [IDA] nucleoplasm [IDA] nucleus [IDA]	147586		785
O14367 UniProt NPD GO	GTI1_SCHPO	Gluconate transport inducer 1	0.90	-	nuc	0					720
Q75AF5 UniProt NPD GO	IMH1_ASHGO	Golgin IMH1	0.90	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				887
Q5XJW2 UniProt NPD GO	G45IP_RAT	Growth arrest and DNA-damage-inducible proteins-interacting protein 1	0.90	+	mit	0	Nucleus (By similarity)				228
Q9WVI4 UniProt NPD GO	GCYA2_RAT	Guanylate cyclase soluble subunit alpha-2 (EC 4.6.1.2) (GCS-alpha-2)	0.90	-	mit	0	Cytoplasm (By similarity)				730
Q13601 UniProt NPD GO	HRB2_HUMAN	HIV-1 Rev-binding protein 2 (Rev-interacting protein 1) (Rip-1)	0.90	+	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [ISS]			380
Q16534 UniProt NPD GO	HLF_HUMAN	Hepatic leukemia factor	0.90	+	nuc	0	Nucleus (Probable)	nucleus [TAS]	142385		295
Q64709 UniProt NPD GO	HLF_RAT	Hepatic leukemia factor	0.90	+	nuc	0	Nucleus (Probable)				295
P02257 UniProt NPD GO	H1_ECHCR	Histone H1, gonadal (Fragment)	0.90	+	nuc	0	Nucleus				171
Q6DN03 UniProt NPD GO	H2B2C_HUMAN	Histone H2B type 2-C (H2.t) (H2B/t)	0.90	+	nuc	0	Nucleus				192
P97440 UniProt NPD GO	SLBP_MOUSE	Histone RNA hairpin-binding protein (Histone stem-loop-binding protein)	0.90	-	nuc	0	Cytoplasm. Nucleus. Polyribosome-associated	cytoplasm [IDA] nucleus [IDA] ribonucleoprotein complex [IDA]			275
Q5RBG4 UniProt NPD GO	TIP60_PONPY	Histone acetyltransferase HTATIP (EC 2.3.1.48) (EC 2.3.1.-) (60 kDa Tat interactive protein) (Tip60) ...	0.90	-	nuc	0	Nucleus. Cytoplasm; perinuclear region. Upon stimulation with EDN1, it is exported from the nucleus ...				461
Q15047 UniProt NPD GO	SETB1_HUMAN	Histone-lysine N-methyltransferase, H3 lysine-9 specific 4 (EC 2.1.1.43) (Histone H3-K9 methyltransf ...	0.90	-	nuc	0	Nucleus. Associated with non-pericentromeric regions of chromatin. Excluded from nucleoli and island ...		604396		1291
Q9VFK6 UniProt NPD GO	SETD8_DROME	Histone-lysine N-methyltransferase, H4 lysine-20 specific (EC 2.1.1.43) (Histone H4-K20 methyltransf ...	0.90	+	nuc	0	Nucleus. Associates to chromatin-dense and transcriptionally silent euchromatic regions	polytene chromosome [IDA]			691
Q26656 UniProt NPD GO	HMX_STRPU	Homeobox protein Hmx (SpHmx) (H6-like) (Fragment)	0.90	+	nuc	0	Nucleus (By similarity)				405
P31272 UniProt NPD GO	HXB9_XENLA	Homeobox protein Hox-B9 (XlHbox-6)	0.90	+	nuc	0	Nucleus				232
P42584 UniProt NPD GO	LOX10_HELTR	Homeobox protein LOX10 (Fragment)	0.90	-	nuc	0	Nucleus (Probable)				184
P43697 UniProt NPD GO	NKX22_MESAU	Homeobox protein Nkx-2.2 (Homeobox protein NK-2 homolog B)	0.90	+	nuc	0	Nucleus (By similarity)				273
Q90788 UniProt NPD GO	NKX25_CHICK	Homeobox protein Nkx-2.5 (Homeobox protein NK-2 homolog E) (cNKX-2.5)	0.90	+	nuc	0	Nucleus (Probable)				294
Q9GZN2 UniProt NPD GO	TGIF2_HUMAN	Homeobox protein TGIF2 (TGFB-induced factor 2) (5'-TG-3'-interacting factor 2) (TGF(beta)-induced tr ...	0.90	-	nuc	0	Nucleus. Excluded from nucleoli	nucleus [TAS]	607294		237
P27610 UniProt NPD GO	HMIN_BOMMO	Homeobox protein invected	0.90	+	nuc	0	Nucleus (Potential)				476
Q9NJB5 UniProt NPD GO	ONEC_DROME	Homeobox protein onecut	0.90	-	nuc	0	Nucleus				1081
P18264 UniProt NPD GO	ROUGH_DROVI	Homeobox protein rough	0.90	+	nuc	0	Nucleus (Probable)				339
P22808 UniProt NPD GO	VND_DROME	Homeobox protein vnd (Protein ventral nervous system defective) (Homeobox protein NK-2)	0.90	+	nuc	0	Nucleus (Probable)			1VND	723
Q96ED9 UniProt NPD GO	HOOK2_HUMAN	Hook homolog 2 (h-hook2) (hHK2)	0.90	-	nuc	0	Cytoplasm. Associates with discrete punctate structure that correspond to neither early or late endo ...		607824		719
O60229 UniProt NPD GO	HAPIP_HUMAN	Huntingtin-associated protein-interacting protein (Protein Duo)	0.90	-	nuc	0	Cytoplasm (By similarity)		604605		1663
P47171 UniProt NPD GO	YJ9H_YEAST	Hypothetical 191.7 kDa protein in HOM6-PMT4 intergenic region	0.90	-	nuc	0	Membrane; multi-pass membrane protein (Potential)	nucleus [IDA]			1648
P40470 UniProt NPD GO	YIM7_YEAST	Hypothetical 23.8 kDa protein in MET18-STH1 intergenic region	0.90	+	nuc	0		nucleolus [IDA]			206
P35194 UniProt NPD GO	YBA4_YEAST	Hypothetical 287.5 kDa protein in PDR3-HTA2 intergenic region	0.90	+	end	0		cytoplasm [IDA] nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI]			2493
P53866 UniProt NPD GO	YNW4_YEAST	Hypothetical 86.9 kDa protein in URE2-SSU72 intergenic region	0.90	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			767
Q09871 UniProt NPD GO	YAG7_SCHPO	Hypothetical protein C12G12.07c in chromosome I	0.90	-	nuc	0					412
Q10483 UniProt NPD GO	YDFB_SCHPO	Hypothetical protein C17C9.11c in chromosome I	0.90	+	nuc	0					240

You are viewing entries 4151 to 4200 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.