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
Q60760 UniProt NPD GO	GRB10_MOUSE	Growth factor receptor-bound protein 10 (GRB10 adaptor protein)	0.89	-	nuc	0		cytosol [TAS]			621
Q6HA10 UniProt NPD GO	GDF6_RAT	Growth/differentiation factor 6 precursor (GDF-6) (Growth/differentiation factor 16)	0.89	+	nuc	0	Secreted protein (Probable)				452
Q03933 UniProt NPD GO	HSF2_HUMAN	Heat shock factor protein 2 (HSF 2) (Heat shock transcription factor 2) (HSTF 2)	0.89	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic during normal growth and moves to the nucleus upon activation		140581		536
P38533 UniProt NPD GO	HSF2_MOUSE	Heat shock factor protein 2 (HSF 2) (Heat shock transcription factor 2) (HSTF 2)	0.89	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic during normal growth and moves to the nucleus upon activation	cytoplasm [IDA] nucleus [IDA]			535
P41894 UniProt NPD GO	DEI_DROME	Helix-loop-helix protein delilah	0.89	+	nuc	0	Nucleus (Probable)				384
Q9ERZ0 UniProt NPD GO	HEMGN_MOUSE	Hemogen (Hemopoietic gene protein) (Negative differentiation regulator protein) (mNDR)	0.89	+	nuc	0	Nucleus	nucleoplasm [IDA]			503
Q6AZ54 UniProt NPD GO	HEMGN_RAT	Hemogen (Hemopoietic gene protein) (Protein RP59)	0.89	+	nuc	0	Nucleus (By similarity)				514
O88974 UniProt NPD GO	SETB1_MOUSE	Histone-lysine N-methyltransferase, H3 lysine-9 specific 4 (EC 2.1.1.43) (Histone H3-K9 methyltransf ...	0.89	-	exc	0	Nucleus (By similarity). Associated with non-pericentromeric regions of chromatin (By similarity)	nucleus [IDA]			1307
Q9H9B1 UniProt NPD GO	EHMT1_HUMAN	Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) (Histone H3-K9 methyltransf ...	0.89	+	nuc	0	Nucleus. Associates with euchromatic regions	nucleus [IC]	607001		1267
Q61412 UniProt NPD GO	CHX10_MOUSE	Homeobox protein CHX10 (Ceh-10 homeodomain-containing homolog)	0.89	+	nuc	0	Nucleus				361
Q04996 UniProt NPD GO	HAT31_ARATH	Homeobox protein HAT3.1	0.89	+	nuc	0	Nucleus				661
P31258 UniProt NPD GO	HXA11_CHICK	Homeobox protein Hox-A11 (Ghox-1I) (Chox-1.9)	0.89	+	nuc	0	Nucleus				297
P23812 UniProt NPD GO	HXD12_MOUSE	Homeobox protein Hox-D12 (Hox-4.7) (Hox-5.6)	0.89	+	nuc	0	Nucleus				279
Q38796 UniProt NPD GO	LUMI_ARATH	Homeobox protein LUMINIDEPENDENS	0.89	-	nuc	0	Nucleus				953
O15522 UniProt NPD GO	NKX28_HUMAN	Homeobox protein Nkx-2.8 (Homeobox protein NK-2 homolog H)	0.89	-	nuc	0	Nucleus (Probable)		603245		239
Q99801 UniProt NPD GO	NKX31_HUMAN	Homeobox protein Nkx-3.1	0.89	+	nuc	0	Nucleus	nucleus [NAS]	602041		234
P97436 UniProt NPD GO	NKX31_MOUSE	Homeobox protein Nkx-3.1	0.89	+	nuc	0	Nucleus (By similarity)				237
P34522 UniProt NPD GO	HM26_CAEEL	Homeobox protein ceh-26	0.89	-	nuc	0	Nucleus (Potential)				586
P53545 UniProt NPD GO	GSC_CHICK	Homeobox protein goosecoid	0.89	+	nuc	0	Nucleus				245
P53544 UniProt NPD GO	GSC_BRARE	Homeobox protein goosecoid (ZGSC)	0.89	+	nuc	0	Nucleus				240
P46640 UniProt NPD GO	KNAT2_ARATH	Homeobox protein knotted-1-like 2 (KNAT2) (ATK1)	0.89	-	nuc	0	Nucleus (Probable)				310
P48002 UniProt NPD GO	KNAT5_ARATH	Homeobox protein knotted-1-like 5 (KNAT5) (Homeodomain-containing protein 1)	0.89	+	nuc	0	Nucleus (Probable)				383
P29506 UniProt NPD GO	UNC4_CAEEL	Homeobox protein unc-4 (Homeobox protein ceh-4) (Uncoordinated protein 4)	0.89	+	nuc	0	Nucleus (Probable)	nucleus [NAS]			252
Q8BJA3 UniProt NPD GO	HMBX1_MOUSE	Homeobox-containing protein 1	0.89	-	nuc	0	Nucleus (Potential)				419
P07548 UniProt NPD GO	DFD_DROME	Homeotic protein deformed	0.89	+	nuc	0	Nucleus				586
P36118 UniProt NPD GO	YK02_YEAST	Hypothetical 36.6 kDa protein in YPT52-DBP7 intergenic region	0.89	-	nuc	0		cytoplasm [IDA] endoplasmic reticulum [IDA] nucleus [IDA]			322
P47015 UniProt NPD GO	YJN1_YEAST	Hypothetical 41.5 kDa protein in MRS3-URA2 intergenic region	0.89	-	nuc	0		mitochondrion [IDA]			356
P36106 UniProt NPD GO	YKA5_YEAST	Hypothetical 67.9 kDa protein RPL14A-AUR1 intergenic region	0.89	+	nuc	0		nucleus [TAS]			594
Q10247 UniProt NPD GO	YD1J_SCHPO	Hypothetical J domain-containing protein C4G9.19	0.89	-	nuc	1					270
P10511 UniProt NPD GO	YPG1_DICSP	Hypothetical plasmid pDG1 103 kDa protein	0.89	-	nuc	0					906
P13740 UniProt NPD GO	YA_ZYGFE	Hypothetical protein A	0.89	+	nuc	0					260
Q10447 UniProt NPD GO	YDEE_SCHPO	Hypothetical protein C12B10.14c	0.89	-	nuc	0					665
Q09560 UniProt NPD GO	YQY1_CAEEL	Hypothetical protein F36G3.1	0.89	-	nuc	0					964
P34428 UniProt NPD GO	YL37_CAEEL	Hypothetical protein F44B9.7	0.89	-	nuc	0					466
P34486 UniProt NPD GO	YMJA_CAEEL	Hypothetical protein F59B2.11 precursor	0.89	-	nuc	0					590
P34572 UniProt NPD GO	YNV9_CAEEL	Hypothetical protein T16H12.9	0.89	-	exc	0					289
Q98SW2 UniProt NPD GO	HIF1A_ONCMY	Hypoxia-inducible factor 1 alpha (HIF-1 alpha) (HIF1 alpha)	0.89	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in normoxia, nuclear translocation i ...				766
P27987 UniProt NPD GO	IP3KB_HUMAN	Inositol-trisphosphate 3-kinase B (EC 2.7.1.127) (Inositol 1,4,5-trisphosphate 3-kinase B) (IP3K B) ...	0.89	-	nuc	0			147522		946
P42335 UniProt NPD GO	IP3KB_RAT	Inositol-trisphosphate 3-kinase B (EC 2.7.1.127) (Inositol 1,4,5-trisphosphate 3-kinase B) (IP3K B) ...	0.89	-	nuc	0				2AQX	934
Q5RJW5 UniProt NPD GO	IRS2B_XENLA	Insulin receptor substrate 2-B (IRS-2-B)	0.89	-	nuc	0					1077
P46402 UniProt NPD GO	IFNG_FELCA	Interferon gamma precursor (IFN-gamma)	0.89	-	nuc	1 *	Secreted protein				167
Q8BKE9 UniProt NPD GO	IFT74_MOUSE	Intraflagellar transport 74 homolog (Coiled-coil domain-containing protein 2) (Capillary morphogenes ...	0.89	+	mit	0	Cytoplasmic vesicle (By similarity). Intracellular vesicular compartment (By similarity)				600
Q6JAN1 UniProt NPD GO	INVS_CANFA	Inversin (Inversion of embryo turning protein) (Nephrocystin-2)	0.89	+	nuc	0	Cytoplasm. Membrane. Spindle. Nucleus. Frequently membrane-associated; membrane localization is depe ...				1081
P41229 UniProt NPD GO	JAD1C_HUMAN	Jumonji/ARID domain-containing protein 1C (SmcX protein) (Xe169 protein)	0.89	-	nuc	0			314690		1560
Q14807 UniProt NPD GO	KIF22_HUMAN	Kinesin-like protein KIF22 (Kinesin-like DNA-binding protein) (Kinesin-like protein 4)	0.89	-	nuc	0	Nucleus	kinetochore [TAS] nucleus [TAS]	603213		665
Q6ZMV9 UniProt NPD GO	KIF6_HUMAN	Kinesin-like protein KIF6	0.89	-	nuc	0					814
O04003 UniProt NPD GO	LG1_MAIZE	LIGULELESS1 protein	0.89	+	nuc	0	Nucleus				399
Q8BWW4 UniProt NPD GO	LARP4_MOUSE	La-related protein 4 (La ribonucleoprotein domain family member 4)	0.89	-	nuc	0					719
O00515 UniProt NPD GO	LAD1_HUMAN	Ladinin 1 (Lad-1) (120 kDa linear IgA bullous dermatosis antigen) (97 kDa linear IgA bullous dermato ...	0.89	-	nuc	0	Secreted protein; extracellular space; extracellular matrix. Localized to anchoring filaments underl ...		602314		517
P14731 UniProt NPD GO	LMNB1_CHICK	Lamin-B1	0.89	-	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side				584

You are viewing entries 4651 to 4700 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.