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
Q9MYP6 UniProt NPD GO	DHR10_BOVIN	Dehydrogenase/reductase SDR family member 10 (EC 1.1.-.-) (Retinal short-chain dehydrogenase/reducta ...	0.03	-	cyt	0					270
Q3ZBV9 UniProt NPD GO	DHR11_BOVIN	Dehydrogenase/reductase SDR family member 11 precursor (EC 1.-.-.-)	0.03	-	end	0	Secreted protein (Potential)				255
O81931 UniProt NPD GO	FAD12_CREAL	Delta(12) fatty acid dehydrogenase (EC 1.14.99.33) (Crepenynate synthase) (Delta-12 fatty acid acety ...	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				375
Q7SY23 UniProt NPD GO	AL4A1_BRARE	Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (EC 1.5.1.12) (P5C dehydrogen ...	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				556
Q9Y8H5 UniProt NPD GO	FAD12_MORAP	Delta-12 fatty acid desaturase (EC 1.14.19.-)	0.03	-	end	4	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			400
P59668 UniProt NPD GO	FAD12_MORIS	Delta-12 fatty acid desaturase (EC 1.14.19.-)	0.03	-	end	4	Membrane; multi-pass membrane protein (Potential)				400
P13716 UniProt NPD GO	HEM2_HUMAN	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (Porphobilinogen synthase) (ALADH)	0.03	-	cyt	0			125270	1PV8	330
Q5R971 UniProt NPD GO	HEM2_PONPY	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (Porphobilinogen synthase) (ALADH)	0.03	-	cyt	0					330
P05373 UniProt NPD GO	HEM2_YEAST	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (Porphobilinogen synthase) (ALADH)	0.03	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1YLV	342
P83258 UniProt NPD GO	TXDP3_PARLU	Delta-palutoxin IT3 (Delta-paluIT3)	0.03	-	nuc	0	Secreted protein	extracellular region [NAS]			36
P13403 UniProt NPD GO	GRA1_TOXGO	Dense granule protein 1 precursor (Protein GRA 1) (Major antigen p24)	0.03	-	exc	0	Secreted protein. Located in dense granules of tachyzoites				190
Q9AXQ9 UniProt NPD GO	DHYS_MUSAC	Deoxyhypusine synthase (EC 2.5.1.46)	0.03	-	cyt	0					376
Q9QZK8 UniProt NPD GO	DNS2A_RAT	Deoxyribonuclease-2-alpha precursor (EC 3.1.22.1) (Deoxyribonuclease II alpha) (DNase II alpha) (Aci ...	0.03	-	exc	0	Lysosome (By similarity)				350
Q6BRN7 UniProt NPD GO	DUT_DEBHA	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.03	-	cyt	0					160
P20690 UniProt NPD GO	DEPA_ASTAM	Depactin	0.03	-	cyt	0					150
O93455 UniProt NPD GO	DMS5_PACDA	Dermaseptin PD-3-7 precursor	0.03	-	exc	0	Secreted protein				66
P81485 UniProt NPD GO	DMS3_PHYBI	Dermaseptin-B3 precursor (Dermaseptin BIII)	0.03	-	exc	0	Secreted protein				74
P81486 UniProt NPD GO	DMS4_PHYBI	Dermaseptin-B4 precursor (Dermaseptin BIV)	0.03	-	exc	0	Secreted protein				76
O09035 UniProt NPD GO	DBIL5_MOUSE	Diazepam-binding inhibitor-like 5 (Endozepine-like peptide) (ELP)	0.03	-	nuc	0	Cytoplasm				87
P51107 UniProt NPD GO	DFRA_LYCES	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase)	0.03	-	cyt	0					379
P51108 UniProt NPD GO	DFRA_MAIZE	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase)	0.03	-	nuc	0					357
P00377 UniProt NPD GO	DYR_PIG	Dihydrofolate reductase (EC 1.5.1.3)	0.03	-	cyt	0					186
P90597 UniProt NPD GO	DLDH_TRYCR	Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase)	0.03	-	mit	0					477
Q6CTX8 UniProt NPD GO	PYRD2_KLULA	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				445
Q6SZS6 UniProt NPD GO	PYRD2_KLUMA	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				446
Q75CE1 UniProt NPD GO	PYRD_ASHGO	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.03	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				444
Q02323 UniProt NPD GO	DPSS_PINSY	Dihydropinosylvin synthase (EC 2.3.1.-) (Stilbene synthase) (STS) (Pinosylvin-forming stilbene synth ...	0.03	-	cyt	0	Cytoplasm			1XET	393
Q14117 UniProt NPD GO	DPYS_HUMAN	Dihydropyrimidinase (EC 3.5.2.2) (DHPase) (Hydantoinase) (DHP)	0.03	-	cyt	0			222748		519
Q21773 UniProt NPD GO	DHP1_CAEEL	Dihydropyrimidinase 1 (EC 3.5.2.2) (CeCRMP/DHP-1) (UlipB)	0.03	-	cyt	0	Nucleus	nucleus [IDA]			489
Q61YQ1 UniProt NPD GO	DHP2_CAEBR	Dihydropyrimidinase 2 (EC 3.5.2.2)	0.03	-	nuc	0					518
O60017 UniProt NPD GO	DAK_PICAN	Dihydroxyacetone kinase (EC 2.7.1.29) (Glycerone kinase) (DHA kinase)	0.03	-	cyt	0					609
P06834 UniProt NPD GO	DAS_PICAN	Dihydroxyacetone synthase (EC 2.2.1.3) (DHAS) (Formaldehyde transketolase) (Glycerone synthase)	0.03	-	mit	0	Peroxisome				710
Q7SC15 UniProt NPD GO	DPH3_NEUCR	Diphthamide biosynthesis protein 3	0.03	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				82
Q4P8G2 UniProt NPD GO	DPH3_USTMA	Diphthamide biosynthesis protein 3	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				89
Q7S949 UniProt NPD GO	DPH5_NEUCR	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.03	-	cyt	0	Cytoplasm (By similarity)				287
O74898 UniProt NPD GO	DPH5_SCHPO	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.03	-	cyt	0	Cytoplasm (By similarity)				283
P32469 UniProt NPD GO	DPH5_YEAST	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.03	-	cyt	0	Cytoplasm	cytoplasm [IDA]			300
P10836 UniProt NPD GO	DIPA_PROTE	Diptericin-A	0.03	-	nuc	0					82
P82465 UniProt NPD GO	DIS6A_ECHCS	Disintegrin EC6A	0.03	-	nuc	0	Secreted protein				68
P81743 UniProt NPD GO	DI10B_ERIMA	Disintegrin EMF10B (Platelet aggregation activation inhibitor) (EMF-10B)	0.03	-	nuc	0	Secreted protein				68
P24858 UniProt NPD GO	DIUH2_MANSE	Diuretic hormone 2 (DH-2) (Diuretic peptide 2) (DP-2) (DPII)	0.03	-	nuc	0	Secreted protein				30
P82372 UniProt NPD GO	DIUX_DIPPU	Diuretic hormone class 2 (Diuretic hormone class II) (Diuretic peptide) (DP) (DH(31))	0.03	-	cyt	0	Secreted protein				31
P14020 UniProt NPD GO	DPM1_YEAST	Dolichol-phosphate mannosyltransferase (EC 2.4.1.83) (Dolichol-phosphate mannose synthase) (Dolichyl ...	0.03	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein	endoplasmic reticulum [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA] nuclear envelope-endoplasmic reticulum network [IDA]			266
Q9BV10 UniProt NPD GO	ALG12_HUMAN	Dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl-alpha-1,6-mannosyltransferase (EC 2.4.1.-) (Mannosyltrans ...	0.03	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)		607144		488
Q9JMF7 UniProt NPD GO	DOPP1_MOUSE	Dolichyldiphosphatase 1 (EC 3.6.1.43) (Dolichyl pyrophosphate phosphatase 1) (Protein 2-23)	0.03	-	nuc	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]			238
P59023 UniProt NPD GO	DSC10_PANTR	Down syndrome critical region protein 10	0.03	-	nuc	0					87
O95147 UniProt NPD GO	DUS14_HUMAN	Dual specificity protein phosphatase 14 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinas ...	0.03	-	mit	0			606618		198
Q95LF9 UniProt NPD GO	DUFFY_GORGO	Duffy antigen/chemokine receptor (CD234 antigen)	0.03	-	end	7	Membrane; multi-pass membrane protein				336
Q95LF3 UniProt NPD GO	DUFFY_PANTR	Duffy antigen/chemokine receptor (CD234 antigen)	0.03	-	end	7	Membrane; multi-pass membrane protein				336
Q95LF5 UniProt NPD GO	DUFFY_SAIBB	Duffy antigen/chemokine receptor (CD234 antigen)	0.03	-	end	7	Membrane; multi-pass membrane protein				336

You are viewing entries 79751 to 79800 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.