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
Q95195 UniProt NPD GO	DRD5_MACMU	D(1B) dopamine receptor (D(5) dopamine receptor) (Fragment)	0.08	-	end	2	Membrane; multi-pass membrane protein				147
Q6TLJ0 UniProt NPD GO	DRD4_MUSPF	D(4) dopamine receptor (Dopamine D4 receptor)	0.08	+	end	7 *	Membrane; multi-pass membrane protein				357
Q8CIM3 UniProt NPD GO	D2HDH_MOUSE	D-2-hydroxyglutarate dehydrogenase, mitochondrial precursor (EC 1.1.99.-)	0.08	-	mit	0	Mitochondrion (By similarity)				535
P84850 UniProt NPD GO	D2HDH_RAT	D-2-hydroxyglutarate dehydrogenase, mitochondrial precursor (EC 1.1.99.-)	0.08	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			535
P40054 UniProt NPD GO	SERA_YEAST	D-3-phosphoglycerate dehydrogenase 1 (EC 1.1.1.95) (3-PGDH 1)	0.08	-	cyt	0		cytoplasm [IDA]			469
O35078 UniProt NPD GO	OXDA_RAT	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.08	-	nuc	0	Peroxisome				346
Q6CSY3 UniProt NPD GO	ALO_KLULA	D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) (ALO) (L-galactono-gamma-lactone oxidase)	0.08	-	cyt	0	Mitochondrion; mitochondrial membrane (By similarity). Membrane-embedded (By similarity)				525
Q922Z0 UniProt NPD GO	OXDD_MOUSE	D-aspartate oxidase (EC 1.4.3.1) (DASOX) (DDO)	0.08	-	cyt	1 *	Peroxisome (By similarity)				341
Q75E95 UniProt NPD GO	DAD1_ASHGO	DASH complex subunit DAD1 (Outer kinetochore protein DAD1)	0.08	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				114
Q56XG6 UniProt NPD GO	RH15_ARATH	DEAD-box ATP-dependent RNA helicase 15 (EC 3.6.1.-)	0.08	-	cyt	0					427
O61305 UniProt NPD GO	DBP80_DROME	DEAD-box helicase Dbp80 (EC 3.6.1.-)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side (By sim ...				460
Q6E7D1 UniProt NPD GO	DDB1_LYCCS	DNA damage-binding protein 1 (UV-damaged DNA-binding protein 1)	0.08	-	end	0	Nucleus (By similarity)				1095
Q6QNU4 UniProt NPD GO	DDB1_LYCES	DNA damage-binding protein 1 (UV-damaged DNA-binding protein 1) (High pigmentation protein 1)	0.08	-	vac	0	Nucleus (By similarity)				1090
P41135 UniProt NPD GO	ID1_RAT	DNA-binding protein inhibitor ID-1 (Inhibitor of DNA binding 1)	0.08	-	cyt	0	Nucleus				164
O15160 UniProt NPD GO	RPA5_HUMAN	DNA-directed RNA polymerase I 40 kDa polypeptide (EC 2.7.7.6) (RPA40) (RPA39)	0.08	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [TAS]			346
P97304 UniProt NPD GO	RPO1D_MOUSE	DNA-directed RNA polymerase I subunit D (EC 2.7.7.6) (DNA-directed RNA polymerase I 16 kDa polypepti ...	0.08	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [IDA]			133
Q9VC49 UniProt NPD GO	RPB10_DROME	DNA-directed RNA polymerase II 7.6 kDa polypeptide (EC 2.7.7.6) (RPB10) (RPB7.6)	0.08	-	cyt	0	Nucleus				67
Q8SRS6 UniProt NPD GO	RPB10_ENCCU	DNA-directed RNA polymerases I/II/III subunit 10 (EC 2.7.7.6)	0.08	-	cyt	0	Nucleus (By similarity)				72
P38307 UniProt NPD GO	DER1_YEAST	Degradation in the endoplasmic reticulum protein 1	0.08	-	cyt	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA]			211
Q13268 UniProt NPD GO	DHRS2_HUMAN	Dehydrogenase/reductase SDR family member 2 (EC 1.1.-.-) (HEP27 protein) (Protein D)	0.08	-	mit	0	Nucleus	nucleus [IDA]			257
Q9CXR1 UniProt NPD GO	DHRS7_MOUSE	Dehydrogenase/reductase SDR family member 7 precursor (EC 1.1.-.-) (Retinal short-chain dehydrogenas ...	0.08	-	mit	1 *					338
Q8CHT0 UniProt NPD GO	AL4A1_MOUSE	Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (EC 1.5.1.12) (P5C dehydrogen ...	0.08	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			562
P83256 UniProt NPD GO	TXDP1_PARLU	Delta-palutoxin IT1 (Delta-paluIT1)	0.08	-	nuc	0	Secreted protein	extracellular region [NAS]		1V90	37
P13404 UniProt NPD GO	GRA2_TOXGO	Dense granule protein 2 precursor (Protein GRA 2) (28 kDa antigen) (GP28.5)	0.08	-	cyt	0	Located in dense granules of tachyzoites. Upon infection, secreted, in a Ca(2+)-dependent manner, in ...				185
Q767J3 UniProt NPD GO	DNAS1_CANFA	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.08	-	end	1 *	Secretory protein, stored in zymogen granules and found in the nuclear envelope (By similarity)				284
Q4AEE3 UniProt NPD GO	DNAS1_HORSE	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.08	-	end	1 *	Secretory protein, stored in zymogen granules and found in the nuclear envelope (By similarity)				282
O62855 UniProt NPD GO	DNS2A_PIG	Deoxyribonuclease-2-alpha precursor (EC 3.1.22.1) (Deoxyribonuclease II alpha) (DNase II alpha) (Aci ...	0.08	-	exc	0	Lysosome				364
P70583 UniProt NPD GO	DUT_RAT	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase) (PPA ...	0.08	-	mit	0	Cytoplasm. Nucleus. Binding to PPAR induces translocation to the nucleus	cytoplasm [IEP] nucleus [IEP]			205
Q05521 UniProt NPD GO	DPP1_YEAST	Diacylglycerol pyrophosphate phosphatase 1 (EC 3.1.3.-) (DGPP phosphatase) (Phosphatidate phosphatas ...	0.08	-	end	5 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane (sensu Fungi) [IDA]			289
P36957 UniProt NPD GO	ODO2_HUMAN	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, m ...	0.08	-	mit	0	Mitochondrion		126063		453
Q01205 UniProt NPD GO	ODO2_RAT	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, m ...	0.08	-	mit	0	Mitochondrion				454
Q9N0F1 UniProt NPD GO	ODO2_PIG	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, m ...	0.08	-	mit	0	Mitochondrion				455
Q7Z895 UniProt NPD GO	PYD1_KLULA	Dihydroorotate dehydrogenase (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (DHODase) (DHOD)	0.08	-	cyt	0	Cytoplasm (By similarity)				315
Q6SZS5 UniProt NPD GO	PYRD_CANGA	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				439
O35098 UniProt NPD GO	DPYL4_MOUSE	Dihydropyrimidinase-related protein 4 (DRP-4) (Collapsin response mediator protein 3) (CRMP-3) (UNC3 ...	0.08	-	cyt	0	Cytoplasm (Potential)				572
O74192 UniProt NPD GO	DAK_PICPA	Dihydroxyacetone kinase (EC 2.7.1.29) (Glycerone kinase) (DHA kinase)	0.08	-	mit	0	Cytoplasm				608
O74215 UniProt NPD GO	DAK2_SCHPO	Dihydroxyacetone kinase 2 (EC 2.7.1.29) (Glycerone kinase 2) (DHA kinase 2)	0.08	-	cyt	0					591
P78697 UniProt NPD GO	DIM1_KLULA	Dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltra ...	0.08	-	cyt	0					320
Q8HZ69 UniProt NPD GO	FMO2_GORGO	Dimethylaniline monooxygenase [N-oxide-forming] 2 (EC 1.14.13.8) (Pulmonary flavin-containing monoox ...	0.08	-	end	1	Microsome				534
Q28505 UniProt NPD GO	FMO2_MACMU	Dimethylaniline monooxygenase [N-oxide-forming] 2 (EC 1.14.13.8) (Pulmonary flavin-containing monoox ...	0.08	-	end	1	Microsome				534
P31429 UniProt NPD GO	DPEP1_RABIT	Dipeptidase 1 precursor (EC 3.4.13.19) (Microsomal dipeptidase) (43 kDa renal band 3-related protein ...	0.08	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Brush border membrane				410
P13240 UniProt NPD GO	DR206_PEA	Disease resistance response protein 206	0.08	-	vac	1 *					184
P81630 UniProt NPD GO	DIS3A_ECHCA	Disintegrin EC3A	0.08	-	nuc	0	Secreted protein				67
P81631 UniProt NPD GO	DIS3B_ECHCA	Disintegrin EC3B	0.08	-	nuc	0	Secreted protein				67
P81742 UniProt NPD GO	DI10A_ERIMA	Disintegrin EMF10A (Platelet aggregation activation inhibitor) (EMF-10A)	0.08	-	nuc	0	Secreted protein				69
Q7ZZM2 UniProt NPD GO	DISS_TRIJE	Disintegrin jerdostatin precursor	0.08	-	nuc	0	Secreted protein (By similarity)				110
Q7LZI5 UniProt NPD GO	DISI1_AGKCA	Disintegrin ussuristatin-1 (US-1)	0.08	-	nuc	0	Secreted protein				71
Q9Y5T4 UniProt NPD GO	DCJ15_HUMAN	DnaJ homolog subfamily C member 15 (Methylation-controlled J protein) (MCJ)	0.08	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				150
Q9USW6 UniProt NPD GO	DPM2_SCHPO	Dolichol phosphate-mannose biosynthesis regulatory protein	0.08	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				72
P54856 UniProt NPD GO	DPM1_USTMA	Dolichol-phosphate mannosyltransferase (EC 2.4.1.83) (Dolichol-phosphate mannose synthase) (Dolichyl ...	0.08	-	nuc	1					294

You are viewing entries 67901 to 67950 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.