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
Q96L73 UniProt NPD GO	NSD1_HUMAN	Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific (EC 2.1.1.43) (H3-K36-HMT ...	0.98	+	nuc	0	Nucleus	histone methyltransferase complex [ISS]	606681		2696
Q9IA16 UniProt NPD GO	HXD12_HETFR	Homeobox protein Hox-D12	0.98	+	nuc	0	Nucleus (By similarity)				272
P24343 UniProt NPD GO	HXD12_CHICK	Homeobox protein Hox-D12 (Chox-4.7) (Chox-4F)	0.98	+	nuc	0	Nucleus				266
P42583 UniProt NPD GO	NKX25_XENLA	Homeobox protein Nkx-2.5 (Homeobox protein NK-2 homolog E) (XNkx-2.5)	0.98	+	nuc	0	Nucleus (Probable)				299
P41934 UniProt NPD GO	HM18_CAEEL	Homeobox protein ceh-18	0.98	+	nuc	0	Nucleus	nucleus [IDA]			542
P10180 UniProt NPD GO	CUT_DROME	Homeobox protein cut	0.98	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			2175
P39880 UniProt NPD GO	CUTL1_HUMAN	Homeobox protein cut-like 1 (CCAAT displacement protein) (CDP)	0.98	-	nuc	0	Nucleus		116896		1505
Q00383 UniProt NPD GO	YCF1_EPIVI	Hypothetical 208 kDa protein ycf1 (ORF 1738)	0.98	+	end	6 *	Plastid				1738
P56785 UniProt NPD GO	YCF1_ARATH	Hypothetical 213.7 kDa protein ycf1	0.98	+	end	6 *	Plastid; chloroplast				1786
Q9MTH5 UniProt NPD GO	YCF1_OENHO	Hypothetical 287.9 kDa protein ycf1	0.98	+	nuc	6 *	Plastid; chloroplast				2434
P36103 UniProt NPD GO	YKC3_YEAST	Hypothetical 32.3 kDa protein in URA6-CDC16 intergenic region	0.98	+	nuc	0		cytoplasm [IDA]			277
Q9LME2 UniProt NPD GO	Y1226_ARATH	Hypothetical protein At1g22260	0.98	-	nuc	0					871
P61430 UniProt NPD GO	Y1275_ARATH	Hypothetical protein At1g22275	0.98	+	nuc	0					856
P46012 UniProt NPD GO	YKI5_CAEEL	Hypothetical protein C01G6.5	0.98	-	nuc	0					952
O13796 UniProt NPD GO	YKY1_SCHPO	Hypothetical protein C1142.01 in chromosome I	0.98	+	nuc	0					667
O13803 UniProt NPD GO	YE06_SCHPO	Hypothetical protein C17H9.06c in chromosome I	0.98	+	nuc	0		nucleus [IDA]			601
Q9USR9 UniProt NPD GO	YOW1_SCHPO	Hypothetical protein C1861.01c in chromosome II	0.98	-	nuc	0		condensed nuclear chromosome kinetochore [IDA]			643
Q09505 UniProt NPD GO	YQI4_CAEEL	Hypothetical protein C45G9.4	0.98	+	nuc	0					292
O14207 UniProt NPD GO	YDT2_SCHPO	Hypothetical protein C6B12.02c in chromosome I	0.98	+	end	0					1888
Q09950 UniProt NPD GO	YSR2_CAEEL	Hypothetical protein F59B10.2	0.98	+	nuc	0					482
Q21653 UniProt NPD GO	YNG2_CAEEL	Hypothetical protein R02F2.2	0.98	-	nuc	0					1182
Q8R0S2 UniProt NPD GO	IQEC1_MOUSE	IQ motif and Sec7 domain-containing protein 1	0.98	-	nuc	0					961
Q6DN90 UniProt NPD GO	IQEC1_HUMAN	IQ motif and Sec7 domain-containing protein 1 (ADP-ribosylation factors guanine nucleotide-exchange ...	0.98	-	nuc	0	Cytoplasm. At steady state, may be preferentially cytosolic. Nucleus		610166		963
Q8C1D8 UniProt NPD GO	IWS1_MOUSE	IWS1 homolog (IWS1-like protein)	0.98	-	nuc	0	Nucleus (By similarity)				766
Q3SWT4 UniProt NPD GO	IWS1_RAT	IWS1 homolog (IWS1-like protein)	0.98	-	nuc	0	Nucleus (By similarity)				764
Q6DE96 UniProt NPD GO	IWS1A_XENLA	IWS1 homolog A (IWS1-like protein A)	0.98	+	nuc	0	Nucleus (By similarity)				836
P38283 UniProt NPD GO	SLI15_YEAST	Inner centromere protein-related protein SLI15 (INCENP-related protein SLI15)	0.98	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	kinetochore microtubule [IDA] spindle midzone [IDA]			698
Q8BVK9 UniProt NPD GO	IPR1_MOUSE	Intracellular pathogen resistance protein 1	0.98	+	nuc	0	Nucleus (Potential)			1UFN	445
Q921C6 UniProt NPD GO	IPR1_MUSCR	Intracellular pathogen resistance protein 1	0.98	+	nuc	0	Nucleus (Potential)				450
P59997 UniProt NPD GO	JHD1A_MOUSE	JmjC domain-containing histone demethylation protein 1A (EC 1.14.11.-) (F-box/LRR-repeat protein 11) ...	0.98	-	nuc	0	Nucleus (By similarity)				1161
Q5U263 UniProt NPD GO	JHD1A_XENTR	JmjC domain-containing histone demethylation protein 1A (EC 1.14.11.-) (F-box/LRR-repeat protein 11) ...	0.98	+	nuc	0	Nucleus (By similarity)				1146
Q6P1G2 UniProt NPD GO	JHD1B_MOUSE	JmjC domain-containing histone demethylation protein 1B (EC 1.14.11.-) (F-box/LRR-repeat protein 10) ...	0.98	-	nuc	0	Nucleus (By similarity)				1309
Q92833 UniProt NPD GO	JARD2_HUMAN	Jumonji protein (Jumonji/ARID domain-containing protein 2)	0.98	-	nuc	0	Nucleus (By similarity)		601594		1246
Q91636 UniProt NPD GO	KCM1_XENLA	Kinesin central motor 1 (XKCM1)	0.98	-	nuc	0	Cytoplasm. Nucleus				730
Q91WD7 UniProt NPD GO	KI18A_MOUSE	Kinesin family member 18A	0.98	-	nuc	0					886
Q29RT6 UniProt NPD GO	KI20A_BOVIN	Kinesin family member 20A	0.98	-	nuc	0	Golgi apparatus (By similarity)				888
O14782 UniProt NPD GO	KIF3C_HUMAN	Kinesin-like protein KIF3C	0.98	+	nuc	0		kinesin complex [TAS]	602845		793
P53086 UniProt NPD GO	KIP3_YEAST	Kinesin-like protein KIP3	0.98	-	nuc	0		cytoplasmic microtubule [IDA] kinesin complex [TAS] nuclear microtubule [IDA]			805
P46867 UniProt NPD GO	KLP68_DROME	Kinesin-like protein KLP68D	0.98	+	nuc	0					784
Q9VAW5 UniProt NPD GO	LARP_DROME	La-related protein (dlarp)	0.98	+	nuc	0	Cytoplasm	cytosol [IDA]			1403
Q6PKG0 UniProt NPD GO	LARP1_HUMAN	La-related protein 1 (La ribonucleoprotein domain family member 1)	0.98	+	nuc	0					1096
P07866 UniProt NPD GO	LTE1_YEAST	Low temperature essential protein	0.98	+	nuc	0		bud [TAS]			1435
Q99698 UniProt NPD GO	LYST_HUMAN	Lysosomal-trafficking regulator (Beige homolog)	0.98	+	end	0	Cytoplasm (Potential)	endosome [TAS] microtubule cytoskeleton [TAS]	606897		3801
Q8C4M7 UniProt NPD GO	MLFIP_MOUSE	MLF1-interacting protein	0.98	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			410
Q9QXZ0 UniProt NPD GO	MACF1_MOUSE	Microtubule-actin crosslinking factor 1 (Actin cross-linking family 7)	0.98	-	nuc	0	Cytoplasm	actin cytoskeleton [IDA] microtubule cytoskeleton [IDA]			5327
Q60592 UniProt NPD GO	MAST2_MOUSE	Microtubule-associated serine/threonine-protein kinase 2 (EC 2.7.11.1)	0.98	-	end	0	Membrane; peripheral membrane protein. Colocalizes with beta 2-syntrophin and utrophin at neuromuscu ...	microtubule cytoskeleton [ISS]			1734
O95819 UniProt NPD GO	M4K4_HUMAN	Mitogen-activated protein kinase kinase kinase kinase 4 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.98	+	nuc	0			604666		1239
P97820 UniProt NPD GO	M4K4_MOUSE	Mitogen-activated protein kinase kinase kinase kinase 4 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.98	+	nuc	0					1233
P47113 UniProt NPD GO	BFA1_YEAST	Mitotic check point protein BFA1 (Cell cycle arrest protein BFA1)	0.98	-	nuc	0	Spindle poles	spindle pole body [IDA]			574
Q96T58 UniProt NPD GO	MINT_HUMAN	Msx2-interacting protein (SPEN homolog) (SMART/HDAC1-associated repressor protein)	0.98	+	nuc	0	Nucleus. Associates with chromatin			1OW1	3664

You are viewing entries 651 to 700 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.