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
Q7TSF0 UniProt NPD GO	DSG1C_MOUSE	Desmoglein-1 gamma precursor (Dsg1-gamma) (Desmoglein-6)	0.24	-	end	0	Membrane; single-pass type I membrane protein (By similarity)	desmosome [IDA]			911
P32748 UniProt NPD GO	PYRD_DROME	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.24	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane				405
Q28943 UniProt NPD GO	DPYD_PIG	Dihydropyrimidine dehydrogenase [NADP+] precursor (EC 1.3.1.2) (DPD) (DHPDHase) (Dihydrouracil dehyd ...	0.24	-	nuc	0	Cytoplasm			1H7X	1025
Q9JI46 UniProt NPD GO	NUDT3_MOUSE	Diphosphoinositol polyphosphate phosphohydrolase 1 (EC 3.6.1.52) (DIPP-1) (muDIPP1) (Diadenosine 5', ...	0.24	-	nuc	0	Cytoplasm (Probable)	intracellular [ISS]			168
Q9NZJ9 UniProt NPD GO	NUDT4_HUMAN	Diphosphoinositol polyphosphate phosphohydrolase 2 (EC 3.6.1.52) (DIPP-2) (Diadenosine 5',5'''-P1,P6 ...	0.24	-	nuc	0	Cytoplasm	intracellular [ISS]	609229		180
Q5RAF0 UniProt NPD GO	NUDT4_PONPY	Diphosphoinositol polyphosphate phosphohydrolase 2 (EC 3.6.1.52) (DIPP-2) (Diadenosine 5',5'''-P1,P6 ...	0.24	-	nuc	0	Cytoplasm (By similarity)				180
Q58CW0 UniProt NPD GO	NUD11_BOVIN	Diphosphoinositol polyphosphate phosphohydrolase 3 beta (EC 3.6.1.52) (DIPP-3 beta) (DIPP3 beta) (Di ...	0.24	-	cyt	0	Cytoplasm (By similarity)				164
Q96G61 UniProt NPD GO	NUD11_HUMAN	Diphosphoinositol polyphosphate phosphohydrolase 3 beta (EC 3.6.1.52) (DIPP-3 beta) (DIPP3 beta) (hD ...	0.24	-	cyt	0	Cytoplasm	intracellular [ISS]	300528		164
P53602 UniProt NPD GO	ERG19_HUMAN	Diphosphomevalonate decarboxylase (EC 4.1.1.33) (Mevalonate pyrophosphate decarboxylase) (Mevalonate ...	0.24	-	cyt	0			603236		400
Q9FW44 UniProt NPD GO	ADR1_ARATH	Disease resistance protein ADR1 (Activated disease resistance protein 1)	0.24	-	cyt	0					787
P82014 UniProt NPD GO	DIUH1_HYLLI	Diuretic hormone 1 (DH-1) (Diuretic peptide 1) (DP-1) (DH(41))	0.24	-	nuc	0	Secreted protein				41
Q05610 UniProt NPD GO	DON1_YEAST	Donuts protein 1	0.24	-	nuc	0	Localizes to prospore membrane. Towards the end of meosis I, or early stages of meiosis II, it forms ...	prospore membrane [IDA] spindle [IDA]			365
Q9Z0Y1 UniProt NPD GO	DCTN3_MOUSE	Dynactin subunit 3 (Dynactin light chain p24)	0.24	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Kinetochore (By similarity). Spindle (By simi ...	dynactin complex [ISS] perinuclear region [ISS]			186
Q9NP97 UniProt NPD GO	DLC2A_HUMAN	Dynein light chain 2A, cytoplasmic (Dynein-associated protein Km23) (Bithoraxoid-like protein) (BLP) ...	0.24	-	nuc	0	Cytoplasm	cytoplasm [ISS] cytoplasmic dynein complex [NAS]	607167	2B95	95
P30569 UniProt NPD GO	EC1_WHEAT	EC protein I/II (Zinc-metallothionein class II)	0.24	-	nuc	0					80
P30570 UniProt NPD GO	EC3_WHEAT	EC protein III (Zinc-metallothionein class II)	0.24	-	nuc	0					80
Q61549 UniProt NPD GO	EMR1_MOUSE	EGF-like module-containing mucin-like hormone receptor-like 1 precursor (Cell surface glycoprotein E ...	0.24	-	end	7	Membrane; multi-pass membrane protein	external side of plasma membrane [IDA]			931
O35474 UniProt NPD GO	EDIL3_MOUSE	EGF-like repeat and discoidin I-like domain-containing protein 3 precursor (EGF-like repeats and dis ...	0.24	-	vac	0	Secreted protein				480
P16329 UniProt NPD GO	NO75_PEA	Early nodulin 75 protein (N-75) (NGM-75) (Fragment)	0.24	-	nuc	0					112
P79784 UniProt NPD GO	ENP2_CHICK	Ectonucleoside triphosphate diphosphohydrolase 2 (EC 3.6.1.-) (NTPDase2) (Ecto-ATPase) (CD39 antigen ...	0.24	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				494
P80594 UniProt NPD GO	ELH_THETS	Egg-laying-like hormone (L-ELH)	0.24	-	nuc	0					36
P28996 UniProt NPD GO	EF2_CHLKE	Elongation factor 2 (EF-2)	0.24	-	cyt	0	Cytoplasm				845
Q02855 UniProt NPD GO	EFTS_ANTSP	Elongation factor Ts (EF-Ts) (Fragment)	0.24	-	nuc	0	Plastid; chloroplast				87
P43897 UniProt NPD GO	EFTS_HUMAN	Elongation factor Ts, mitochondrial precursor (EF-Ts) (EF-TsMt)	0.24	-	mit	0	Mitochondrion	mitochondrion [TAS]	604723	2CP9	325
P46280 UniProt NPD GO	EFTU2_SOYBN	Elongation factor Tu, chloroplast precursor (EF-Tu)	0.24	-	mit	0	Plastid; chloroplast				479
Q9Y2C4 UniProt NPD GO	NUCGL_HUMAN	Endonuclease G-like 1 (EC 3.1.30.-) (Endo G-like)	0.24	-	mit	1 *			604051		368
Q4PEJ3 UniProt NPD GO	YSH1_USTMA	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1)	0.24	-	cyt	0	Nucleus (By similarity)				880
Q9JMG1 UniProt NPD GO	EDF1_MOUSE	Endothelial differentiation-related factor 1 (EDF-1) (Multiprotein-bridging factor 1) (MBF1)	0.24	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Also nuclear upon binding to NR5A1 and treatment ...				148
P69736 UniProt NPD GO	EDF1_RAT	Endothelial differentiation-related factor 1 (EDF-1) (Multiprotein-bridging factor 1) (MBF1) (Calmod ...	0.24	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Also nuclear upon binding to NR5A1 and treatment ...				148
P69099 UniProt NPD GO	ERH_ECHMU	Enhancer of rudimentary homolog	0.24	-	cyt	0					102
P69100 UniProt NPD GO	ERH_TAESO	Enhancer of rudimentary homolog	0.24	-	cyt	0					102
P81448 UniProt NPD GO	EMBP_CRIGR	Eosinophil granule major basic protein precursor (MBP)	0.24	-	cyt	0	Matrix of eosinophil's large specific granule (crystalloid core) (By similarity)				206
P98172 UniProt NPD GO	EFNB1_HUMAN	Ephrin-B1 precursor (EPH-related receptor tyrosine kinase ligand 2) (LERK-2) (ELK ligand) (ELK-L)	0.24	-	mit	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] soluble fraction [TAS] synapse [ISS]	304110		346
O73874 UniProt NPD GO	EFNB2_BRARE	Ephrin-B2a precursor	0.24	-	nuc	1	Membrane; single-pass type I membrane protein				332
Q5EG71 UniProt NPD GO	EPGN_CHICK	Epigen precursor (Epithelial mitogen) (EPG)	0.24	-	end	1	Membrane; single-pass type I membrane protein (Probable)				151
Q08662 UniProt NPD GO	EST6_DROSI	Esterase 6 precursor (EC 3.1.1.1) (Est-6) (Carboxylic-ester hydrolase 6) (Carboxylesterase-6)	0.24	-	vac	0	Secreted protein				542
Q9FE67 UniProt NPD GO	ERF9_ARATH	Ethylene-responsive transcription factor 9 (Ethylene-responsive element-binding factor 9) (EREBP-9) ...	0.24	-	cyt	0	Nucleus (Probable)				200
Q5CD97 UniProt NPD GO	ERF1_DIDNA	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.24	-	cyt	0	Cytoplasm (By similarity)				437
Q5E938 UniProt NPD GO	EIF1_BOVIN	Eukaryotic translation initiation factor 1 (eIF1) (Protein translation factor SUI1 homolog)	0.24	-	cyt	0					113
Q5RFF4 UniProt NPD GO	EIF1_PONPY	Eukaryotic translation initiation factor 1 (eIF1) (Protein translation factor SUI1 homolog)	0.24	-	cyt	0					113
P41567 UniProt NPD GO	EIF1_HUMAN	Eukaryotic translation initiation factor 1 (eIF1) (Protein translation factor SUI1 homolog) (Sui1iso ...	0.24	-	cyt	0		cytoplasm [TAS]		2IF1	113
P38912 UniProt NPD GO	IF1A_YEAST	Eukaryotic translation initiation factor 1A (EIF-1A) (EIF-4C)	0.24	-	nuc	0		ribosome [TAS]			153
Q6GVM3 UniProt NPD GO	IF1AY_PANTR	Eukaryotic translation initiation factor 1A, Y-chromosomal (eIF-1A Y isoform) (eIF-4C)	0.24	-	nuc	0					143
Q95RJ9 UniProt NPD GO	EBI_DROME	F-box-like/WD repeat protein ebi	0.24	-	nuc	0	Nucleus	nucleus [IDA]			700
Q8CIG9 UniProt NPD GO	FBXL8_MOUSE	F-box/LRR-repeat protein 8 (F-box and leucine-rich repeat protein 8) (F-box protein FBL8)	0.24	-	nuc	0					374
P57775 UniProt NPD GO	FBXW4_HUMAN	F-box/WD repeat protein 4 (F-box and WD-40 domain protein 4) (Dactylin)	0.24	-	cyt	0		ubiquitin ligase complex [NAS]	608071		412
Q9NYL4 UniProt NPD GO	FKB11_HUMAN	FK506-binding protein 11 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rota ...	0.24	+	end	1					201
P0C1J5 UniProt NPD GO	FKB2B_RHIOR	FK506-binding protein 2B precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rota ...	0.24	-	end	1	Membrane; single-pass membrane protein (Potential)				209
Q7SCN0 UniProt NPD GO	FKBP4_NEUCR	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.24	+	nuc	0	Nucleus; nucleolus (By similarity)				467
P14324 UniProt NPD GO	FPPS_HUMAN	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.24	-	cyt	2	Cytoplasm		134629	2F9K	353

You are viewing entries 46251 to 46300 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.