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
P60982 UniProt NPD GO	DEST_PIG	Destrin (Actin-depolymerizing factor) (ADF)	0.26	+	cyt	0				1AK7	164
Q9QUN9 UniProt NPD GO	DKK3_MOUSE	Dickkopf-related protein 3 precursor (Dkk-3) (Dickkopf-3) (mDkk-3)	0.26	-	exc	0	Secreted protein				349
P14740 UniProt NPD GO	DPP4_RAT	Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen C ...	0.26	-	cyt	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists i ...	membrane fraction [IDA] soluble fraction [IDA]			767
P0C027 UniProt NPD GO	NUD10_MOUSE	Diphosphoinositol polyphosphate phosphohydrolase 3 alpha (EC 3.6.1.52) (DIPP-3 alpha) (DIPP3 alpha) ...	0.26	-	cyt	0	Cytoplasm (By similarity)				164
P0C028 UniProt NPD GO	NUD11_MOUSE	Diphosphoinositol polyphosphate phosphohydrolase 3 beta (EC 3.6.1.52) (DIPP-3 beta) (DIPP3 beta) (Di ...	0.26	-	cyt	0	Cytoplasm (By similarity)				164
Q91ZV2 UniProt NPD GO	DCBD2_RAT	Discoidin, CUB and LCCL domain-containing protein 2 precursor (Endothelial and smooth muscle cell-de ...	0.26	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	cell surface [ISS] integral to plasma membrane [ISS]			769
P83043 UniProt NPD GO	DIS8A_CERCE	Disintegrin CC8A	0.26	-	nuc	0	Secreted protein				65
P31987 UniProt NPD GO	DISI_CROVV	Disintegrin viridin (Platelet aggregation activation inhibitor)	0.26	-	nuc	0	Secreted protein				71
Q9QYI7 UniProt NPD GO	DNJB8_MOUSE	DnaJ homolog subfamily B member 8 (mDJ6)	0.26	-	cyt	0					227
P25303 UniProt NPD GO	SCJ1_YEAST	DnaJ-related protein SCJ1	0.26	-	mit	1 *	Mitochondrion. Endoplasmic reticulum	endoplasmic reticulum lumen [IDA]			404
Q05754 UniProt NPD GO	DOPO_RAT	Dopamine beta-hydroxylase precursor (EC 1.14.17.1) (Dopamine beta-monooxygenase)	0.26	-	exc	1 *	Exists as both a soluble and membrane-bound form in chromaffin granules (the membrane-bound form may ...			1ZHB	620
Q8GY31 UniProt NPD GO	CDC25_ARATH	Dual specificity phosphatase Cdc25 (EC 3.1.3.48) (Arath;CDC25)	0.26	-	mit	0	Nucleus (Probable)			1T3K	146
Q09019 UniProt NPD GO	DMWD_HUMAN	Dystrophia myotonica WD repeat-containing protein (Dystrophia myotonica-containing WD repeat motif p ...	0.26	-	nuc	0			609857		553
P43401 UniProt NPD GO	EC_MAIZE	EC protein homolog (Zinc-metallothionein class II)	0.26	-	nuc	0					76
Q9HBW9 UniProt NPD GO	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain-containing protein 1 precursor (EGF-TM7-latrophilin- ...	0.26	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]			690
Q923X1 UniProt NPD GO	ELTD1_MOUSE	EGF, latrophilin seven transmembrane domain-containing protein 1 precursor	0.26	-	end	7	Membrane; multi-pass membrane protein				739
Q9HAT1 UniProt NPD GO	LMA1L_HUMAN	ERGIC-53-like protein precursor (ERGIC53-like protein) (Lectin, mannose-binding 1-like) (LMAN1-like ...	0.26	-	end	0	Membrane; single-pass type I membrane protein (Potential)		609548		526
Q8R4A1 UniProt NPD GO	ERO1A_RAT	ERO1-like protein alpha precursor (EC 1.8.4.-) (ERO1-Lalpha) (Oxidoreductin-1-Lalpha) (Endoplasmic o ...	0.26	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				464
Q86YB8 UniProt NPD GO	ERO1B_HUMAN	ERO1-like protein beta precursor (EC 1.8.4.-) (ERO1-Lbeta) (Oxidoreductin-1-Lbeta) (Endoplasmic oxid ...	0.26	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side. Th ...	endoplasmic reticulum [TAS]			467
P26634 UniProt NPD GO	EGR2_DUSTH	Early growth response protein 2 (EGR-2) (Krox-20 protein) (Fragment)	0.26	-	nuc	0	Nucleus				62
Q05544 UniProt NPD GO	NO551_SOYBN	Early nodulin 55-1 (N-55-1) (Fragment)	0.26	-	nuc	0	Peribacteroid membrane (Potential)				137
Q7M427 UniProt NPD GO	ELH_APLBR	Egg-laying hormone (ELH)	0.26	-	nuc	0	Secreted protein				36
O01971 UniProt NPD GO	EMR1_CAEEL	Emerin homolog 1 (Ce-emerin)	0.26	-	nuc	1	Nucleus; nuclear inner membrane; single-pass membrane protein; nucleoplasmic side. Lmn-1 is required ...	integral to nuclear inner membrane [IDA]			166
Q9ULC0 UniProt NPD GO	MUCEN_HUMAN	Endomucin precursor (Endomucin-2) (Gastric cancer antigen Ga34)	0.26	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 1: Membrane; single-pass type ...		608350		261
Q14249 UniProt NPD GO	NUCG_HUMAN	Endonuclease G, mitochondrial precursor (EC 3.1.30.-) (Endo G)	0.26	-	mit	0	Mitochondrion		600440		297
Q6BMW3 UniProt NPD GO	YSH1_DEBHA	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1)	0.26	-	nuc	0	Nucleus (By similarity)				815
O97178 UniProt NPD GO	ESMA_DROME	Enhancer of split malpha protein (E(spl)malpha)	0.26	-	cyt	0					138
P48298 UniProt NPD GO	CCL11_MOUSE	Eotaxin precursor (Small inducible cytokine A11) (CCL11) (Eosinophil chemotactic protein)	0.26	-	mit	0	Secreted protein				97
Q07496 UniProt NPD GO	EPHA4_CHICK	Ephrin type-A receptor 4 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor CEK8)	0.26	-	end	1	Membrane; single-pass type I membrane protein				986
P54764 UniProt NPD GO	EPHA4_HUMAN	Ephrin type-A receptor 4 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor SEK) (Receptor pr ...	0.26	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	602188		986
Q91735 UniProt NPD GO	EPHB3_XENLA	Ephrin type-B receptor 3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor TCK)	0.26	-	end	1	Membrane; single-pass type I membrane protein				974
O88637 UniProt NPD GO	PCY2_RAT	Ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14) (Phosphorylethanolamine transferase) (CTP: ...	0.26	-	cyt	0					404
Q9NCP1 UniProt NPD GO	ERF1_GIALA	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.26	-	cyt	0	Cytoplasm (By similarity)				457
P47814 UniProt NPD GO	IF1A_RABIT	Eukaryotic translation initiation factor 1A (EIF-1A) (EIF-4C)	0.26	-	nuc	0					143
P68102 UniProt NPD GO	IF2A_BOVIN	Eukaryotic translation initiation factor 2 subunit 1 (Eukaryotic translation initiation factor 2 sub ...	0.26	-	cyt	0					314
Q6ZWX6 UniProt NPD GO	IF2A_MOUSE	Eukaryotic translation initiation factor 2 subunit 1 (Eukaryotic translation initiation factor 2 sub ...	0.26	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			314
P68101 UniProt NPD GO	IF2A_RAT	Eukaryotic translation initiation factor 2 subunit 1 (Eukaryotic translation initiation factor 2 sub ...	0.26	-	cyt	0					314
P06103 UniProt NPD GO	IF39_YEAST	Eukaryotic translation initiation factor 3 90 kDa subunit (eIF3 p90) (eIF3b) (Cell cycle regulation ...	0.26	-	mit	0		cytoplasm [IPI] eukaryotic translation initiation factor 3 ... [IDA] multi-eIF complex [IDA]			763
Q9WUK2 UniProt NPD GO	IF4H_MOUSE	Eukaryotic translation initiation factor 4H (eIF-4H) (Williams-Beuren syndrome chromosome region 1 p ...	0.26	-	nuc	0	Cytoplasm; perinuclear region				247
P38431 UniProt NPD GO	IF5_YEAST	Eukaryotic translation initiation factor 5 (eIF-5)	0.26	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [IPI] multi-eIF complex [IDA]		2FUL	405
P52907 UniProt NPD GO	CAZA1_HUMAN	F-actin capping protein alpha-1 subunit (CapZ alpha-1)	0.26	-	cyt	0		F-actin capping protein complex [TAS]	601580	1MWN	285
P47753 UniProt NPD GO	CAZA1_MOUSE	F-actin capping protein alpha-1 subunit (CapZ alpha-1)	0.26	-	cyt	0					285
Q2USL9 UniProt NPD GO	POB3_ASPOR	FACT complex subunit pob3 (Facilitates chromatin transcription complex subunit pob3)	0.26	-	cyt	0	Nucleus (By similarity)				576
Q9FM65 UniProt NPD GO	FLA1_ARATH	Fasciclin-like arabinogalactan protein 1 precursor	0.26	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			424
Q91775 UniProt NPD GO	FABPI_XENLA	Fatty acid-binding protein, intestinal (I-FABP) (FABPI)	0.26	-	cyt	0	Cytoplasm				131
P17847 UniProt NPD GO	NIR_MAIZE	Ferredoxin--nitrite reductase, chloroplast precursor (EC 1.7.7.1) (Fragment)	0.26	-	cyt	0	Plastid; chloroplast				569
P18685 UniProt NPD GO	FRIH_SHEEP	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.26	-	nuc	0		plasma membrane [ISS]			170
Q6B858 UniProt NPD GO	FANK1_BOVIN	Fibronectin type 3 and ankyrin repeat domains protein 1 (GV14)	0.26	-	cyt	0					345
Q14315 UniProt NPD GO	FLNC_HUMAN	Filamin-C (Gamma-filamin) (Filamin-2) (Protein FLNc) (Actin-binding-like protein) (ABP-L) (ABP-280-l ...	0.26	-	mit	0	Cytoplasm. Membrane; peripheral membrane protein. A small amount localizes at membranes. In striated ...		102565	1V05	2725
P15328 UniProt NPD GO	FOLR1_HUMAN	Folate receptor alpha precursor (FR-alpha) (Folate receptor 1) (Folate receptor, adult) (Adult folat ...	0.26	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein (Probable)	integral to plasma membrane [TAS] membrane fraction [TAS]	136430		257

You are viewing entries 44151 to 44200 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.