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
P32462 UniProt NPD GO	ERG24_YEAST	Delta(14)-sterol reductase (EC 1.3.1.70) (C-14 sterol reductase) (Sterol C14-reductase)	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				438
Q9P8I0 UniProt NPD GO	PUT2_EMENI	Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (EC 1.5.1.12) (P5C dehydrogen ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				572
P30038 UniProt NPD GO	AL4A1_HUMAN	Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (EC 1.5.1.12) (P5C dehydrogen ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [TAS]	606811		563
P18511 UniProt NPD GO	CXDA_CONTE	Delta-conotoxin TxVIA precursor (TxIA) (Conotoxin King-Kong 0) (KK-0)	0.02	-	exc	0	Secreted protein			1FU3	78
P41143 UniProt NPD GO	OPRD_HUMAN	Delta-type opioid receptor (DOR-1)	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	165195	1OZC	372
Q9FI94 UniProt NPD GO	DHYS_ARATH	Deoxyhypusine synthase (EC 2.5.1.46)	0.02	-	cyt	0					368
Q6RJS2 UniProt NPD GO	DHYS_BRANA	Deoxyhypusine synthase (EC 2.5.1.46)	0.02	-	cyt	0					368
Q9AXQ8 UniProt NPD GO	DHYS_DIACA	Deoxyhypusine synthase (EC 2.5.1.46)	0.02	-	cyt	0					373
Q9SC14 UniProt NPD GO	DHYS_SENVE	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.02	-	cyt	0					371
P40115 UniProt NPD GO	PHR1_SINAL	Deoxyribodipyrimidine photo-lyase (EC 4.1.99.3) (DNA photolyase) (Photoreactivating enzyme)	0.02	-	nuc	0					501
Q9D1G0 UniProt NPD GO	DNSL2_MOUSE	Deoxyribonuclease I-like 2 precursor (EC 3.1.21.-) (DNase I-like 2)	0.02	-	cyt	1 *	Secreted protein (Potential)				278
P49183 UniProt NPD GO	DNAS1_MOUSE	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.02	-	end	0	Secretory protein, stored in zymogen granules and found in the nuclear envelope (By similarity)				284
P24855 UniProt NPD GO	DNAS1_HUMAN	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I) (Dornase alfa)	0.02	-	end	1 *	Secretory protein, stored in zymogen granules and found in the nuclear envelope	extracellular region [TAS]	125505		282
Q6MVL2 UniProt NPD GO	DUT_NEUCR	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.02	-	cyt	0					165
Q9Y1U3 UniProt NPD GO	SIXC_MESMA	Depressant insect neurotoxin BmK ITc precursor	0.02	-	mit	0	Secreted protein (By similarity)				85
Q9VQ57 UniProt NPD GO	DERL1_DROME	Derlin-1 (DER1-like protein 1)	0.02	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS]			245
P83640 UniProt NPD GO	DDSM_PHYDS	Dermadistinctin-M (DD M)	0.02	-	cyt	0	Secreted protein				31
P24302 UniProt NPD GO	DMS1_PHYSA	Dermaseptin-1 (DS I)	0.02	-	cyt	0	Secreted protein				34
P80278 UniProt NPD GO	DMS2_PHYSA	Dermaseptin-2 (DS II)	0.02	-	cyt	0	Secreted protein				34
P79712 UniProt NPD GO	DHH_DANKE	Desert hedgehog protein (DHH) (Fragment)	0.02	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
P79853 UniProt NPD GO	DHH_PUNTE	Desert hedgehog protein (DHH) (Fragment)	0.02	-	nuc	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				58
P22242 UniProt NPD GO	DRPE_CRAPL	Desiccation-related protein PCC13-62 precursor	0.02	-	vac	1 *					313
P55039 UniProt NPD GO	DRG2_HUMAN	Developmentally-regulated GTP-binding protein 2 (DRG 2)	0.02	-	cyt	0	Cytoplasm		602986		364
Q9QXB9 UniProt NPD GO	DRG2_MOUSE	Developmentally-regulated GTP-binding protein 2 (DRG 2)	0.02	-	cyt	0	Cytoplasm (By similarity)				364
Q8AXL1 UniProt NPD GO	SAT1_CHICK	Diamine acetyltransferase 1 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 1) (SSAT) (SSA ...	0.02	-	cyt	0	Cytoplasm (By similarity)				171
Q7PCJ8 UniProt NPD GO	SAT2_BOVIN	Diamine acetyltransferase 2 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 2) (Polyamine ...	0.02	-	cyt	0	Intracellular organelles (By similarity)				170
Q8T0W8 UniProt NPD GO	DIAP_GASAT	Diapausin precursor	0.02	-	vac	0	Secreted protein	extracellular region [TAS]			65
Q9MZG3 UniProt NPD GO	DBIL5_BOVIN	Diazepam-binding inhibitor-like 5 (Endozepine-like peptide) (ELP)	0.02	-	nuc	0	Cytoplasm (By similarity)				87
P13277 UniProt NPD GO	CYSP1_HOMAM	Digestive cysteine proteinase 1 precursor (EC 3.4.22.-)	0.02	-	exc	0					322
Q39535 UniProt NPD GO	DAPA_COILA	Dihydrodipicolinate synthase, chloroplast precursor (EC 4.2.1.52) (DHDPS)	0.02	-	mit	0	Plastid; chloroplast				377
P26259 UniProt NPD GO	DAPA_MAIZE	Dihydrodipicolinate synthase, chloroplast precursor (EC 4.2.1.52) (DHDPS)	0.02	-	mit	0	Plastid; chloroplast				380
P51103 UniProt NPD GO	DFRA_CALCH	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase)	0.02	-	cyt	0					364
P51109 UniProt NPD GO	DFRA_MEDSA	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase) (Fragment)	0.02	-	nuc	0					217
P00376 UniProt NPD GO	DYR_BOVIN	Dihydrofolate reductase (EC 1.5.1.3)	0.02	-	cyt	0					186
P00374 UniProt NPD GO	DYR_HUMAN	Dihydrofolate reductase (EC 1.5.1.3)	0.02	-	cyt	0			126060	2DHF	186
P04753 UniProt NPD GO	DYR_MESAU	Dihydrofolate reductase (EC 1.5.1.3)	0.02	-	mit	0					186
P81896 UniProt NPD GO	ODO2_SOLTU	Dihydrolipoamide-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex (EC 2 ...	0.02	-		0	Mitochondrion; mitochondrial membrane				20
P20285 UniProt NPD GO	ODP2_NEUCR	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochond ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				458
Q90512 UniProt NPD GO	ODO2_FUGRU	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, m ...	0.02	-	mit	0	Mitochondrion (By similarity)				409
P31301 UniProt NPD GO	PYRC_USTMA	Dihydroorotase (EC 3.5.2.3) (DHOase)	0.02	-	mit	0					391
Q7Z894 UniProt NPD GO	PYRD_SACBA	Dihydroorotate dehydrogenase (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (DHODase) (DHOD)	0.02	-	cyt	0	Cytoplasm (By similarity)				314
Q7Z893 UniProt NPD GO	PYRD_SACMI	Dihydroorotate dehydrogenase (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (DHODase) (DHOD)	0.02	-	cyt	0	Cytoplasm (By similarity)				314
Q8BVI4 UniProt NPD GO	DHPR_MOUSE	Dihydropteridine reductase (EC 1.5.1.34) (HDHPR) (Quinoid dihydropteridine reductase)	0.02	-	cyt	0					241
Q8MJ30 UniProt NPD GO	DHPR_PIG	Dihydropteridine reductase (EC 1.5.1.34) (HDHPR) (Quinoid dihydropteridine reductase)	0.02	-	cyt	0					243
P11348 UniProt NPD GO	DHPR_RAT	Dihydropteridine reductase (EC 1.5.1.34) (HDHPR) (Quinoid dihydropteridine reductase)	0.02	-	cyt	0				1DIR	241
Q60Q85 UniProt NPD GO	DHP1_CAEBR	Dihydropyrimidinase 1 (EC 3.5.2.2)	0.02	-	nuc	0	Nucleus (By similarity)				489
O93884 UniProt NPD GO	DAS_CANBO	Dihydroxyacetone synthase (EC 2.2.1.3) (DHAS) (Formaldehyde transketolase) (Glycerone synthase)	0.02	-	cyt	0	Peroxisome (By similarity)				705
Q01740 UniProt NPD GO	FMO1_HUMAN	Dimethylaniline monooxygenase [N-oxide-forming] 1 (EC 1.14.13.8) (Fetal hepatic flavin-containing mo ...	0.02	-	nuc	0	Microsome		136130		531
P97501 UniProt NPD GO	FMO3_MOUSE	Dimethylaniline monooxygenase [N-oxide-forming] 3 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.02	-	nuc	1	Microsome				534
Q3E840 UniProt NPD GO	DPH3_YEAST	Diphthamide biosynthesis protein 3 (Kluyveromyces lactis toxin-insensitive protein 11)	0.02	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]		1YOP	82

You are viewing entries 83301 to 83350 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.