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
P32300 UniProt NPD GO	OPRD_MOUSE	Delta-type opioid receptor (DOR-1) (K56) (MSL-2)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IDA] membrane fraction [IDA]			372
P33533 UniProt NPD GO	OPRD_RAT	Delta-type opioid receptor (DOR-1) (Opioid receptor A)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				372
P00983 UniProt NPD GO	IVBIB_DENPO	Dendrotoxin-B (Venom basic protease inhibitor B)	0.05	-	nuc	1 *	Secreted protein				57
P00984 UniProt NPD GO	IVBIE_DENPO	Dendrotoxin-E (Venom basic protease inhibitor E)	0.05	-	nuc	0	Secreted protein				59
Q6CNG7 UniProt NPD GO	DHYS_KLULA	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.05	-	cyt	0					379
P24336 UniProt NPD GO	SIX2_BUTJU	Depressant insect toxin 2 precursor (IT-2) (BjIT2)	0.05	-	exc	0	Secreted protein				85
Q8BNI4 UniProt NPD GO	DERL2_MOUSE	Derlin-2 (Degradation in endoplasmic reticulum protein 2) (Der1-like protein 2) (F-LANa)	0.05	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [ISS]			239
O93222 UniProt NPD GO	DMS2_AGAAN	Dermaseptin AA-2-5 precursor	0.05	-	exc	0	Secreted protein				73
Q9PT75 UniProt NPD GO	DERB_PHYBI	Dermatoxin precursor	0.05	-	exc	0	Secreted protein				77
Q920D2 UniProt NPD GO	DYR_RAT	Dihydrofolate reductase (EC 1.5.1.3)	0.05	-	mit	0					186
Q86XF0 UniProt NPD GO	DYRL1_HUMAN	Dihydrofolate reductase-like protein 1	0.05	-	cyt	0					187
P31023 UniProt NPD GO	DLDH_PEA	Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (Glycine cleavage system L protein ...	0.05	-	mit	0	Mitochondrion; mitochondrial matrix			1DXL	501
P10515 UniProt NPD GO	ODP2_HUMAN	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochond ...	0.05	-	mit	0	Mitochondrion; mitochondrial matrix	pyruvate dehydrogenase complex (sensu Eukar... [NAS]	608770	1Y8P	614
O04904 UniProt NPD GO	PYRC_ARATH	Dihydroorotase, mitochondrial precursor (EC 3.5.2.3) (DHOase)	0.05	-	cyt	0	Mitochondrion (Potential)				377
P07670 UniProt NPD GO	PYRD_DICDI	Dihydroorotate dehydrogenase (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (DHODase) (DHOD)	0.05	-	cyt	0					369
Q874I4 UniProt NPD GO	PYRD_CANAL	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				444
Q8SPQ7 UniProt NPD GO	FMO3_MACMU	Dimethylaniline monooxygenase [N-oxide-forming] 3 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.05	-	end	1	Microsome				531
Q9EQ76 UniProt NPD GO	FMO3_RAT	Dimethylaniline monooxygenase [N-oxide-forming] 3 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.05	-	nuc	0	Microsome (By similarity)				531
P31512 UniProt NPD GO	FMO4_HUMAN	Dimethylaniline monooxygenase [N-oxide-forming] 4 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.05	-	nuc	1	Microsome	microsome [NAS]	136131		557
P97872 UniProt NPD GO	FMO5_MOUSE	Dimethylaniline monooxygenase [N-oxide-forming] 5 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.05	-	end	1	Microsome				532
P22412 UniProt NPD GO	DPEP1_PIG	Dipeptidase 1 precursor (EC 3.4.13.19) (Microsomal dipeptidase) (Renal dipeptidase)	0.05	-	end	0	Cell membrane; lipid-anchor; GPI-anchor. Brush border membrane				409
P31428 UniProt NPD GO	DPEP1_MOUSE	Dipeptidase 1 precursor (EC 3.4.13.19) (Microsomal dipeptidase) (Renal dipeptidase) (Membrane-bound ...	0.05	-	end	0	Cell membrane; lipid-anchor; GPI-anchor. Brush border membrane				410
Q8J1M3 UniProt NPD GO	DPP5_ARTBE	Dipeptidyl-peptidase 5 precursor (EC 3.4.14.-) (Dipeptidyl-peptidase V) (DPP V) (DppV) (Allergen Tri ...	0.05	-	exc	0	Secreted protein (By similarity)				726
Q6CGE7 UniProt NPD GO	DPH2_YARLI	Diphthamide biosynthesis protein 2	0.05	-	mit	0	Cytoplasm (By similarity)				481
Q5KP86 UniProt NPD GO	DPH3_CRYNE	Diphthamide biosynthesis protein 3	0.05	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				153
P02888 UniProt NPD GO	DIS1D_DICDI	Discoidin I, D chain (Fragment)	0.05	-	cyt	0	Cytoplasm				149
Q16983 UniProt NPD GO	DIHR_ACHDO	Diuretic hormone receptor precursor (DH-R)	0.05	-	end	6	Membrane; multi-pass membrane protein				441
Q5RCP4 UniProt NPD GO	DCJ15_PONPY	DnaJ homolog subfamily C member 15	0.05	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				150
Q8VDB2 UniProt NPD GO	ALG12_MOUSE	Dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl-alpha-1,6-mannosyltransferase (EC 2.4.1.-) (Mannosyltrans ...	0.05	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				483
Q00665 UniProt NPD GO	NO12B_PEA	Early nodulin 12B precursor (N-12B)	0.05	-	exc	1 *	Cell wall (Potential)				86
Q41705 UniProt NPD GO	NO5_VICSA	Early nodulin 5 precursor (N-5) (Fragment)	0.05	-	nuc	1					124
P06027 UniProt NPD GO	LECE_ANTCR	Echinoidin	0.05	-	cyt	0	Secreted protein				147
O55026 UniProt NPD GO	ENP2_MOUSE	Ectonucleoside triphosphate diphosphohydrolase 2 (EC 3.6.1.-) (NTPDase2) (Ecto-ATPase) (CD39 antigen ...	0.05	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	basal lamina [IDA]			495
Q9QYC8 UniProt NPD GO	ENP5_MESAU	Ectonucleoside triphosphate diphosphohydrolase 5 precursor (EC 3.6.1.6) (NTPDase5) (Nucleoside dipho ...	0.05	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				469
P59722 UniProt NPD GO	EGLN1_RAT	Egl nine homolog 1 (EC 1.14.11.-) (Hypoxia-inducible factor prolyl hydroxylase 2) (HIF-prolyl hydrox ...	0.05	-	cyt	0					222
Q867B0 UniProt NPD GO	ELA1_CANFA	Elastase-1 precursor (EC 3.4.21.36)	0.05	-	cyt	0	Secreted protein				258
Q9UNI1 UniProt NPD GO	ELA1_HUMAN	Elastase-1 precursor (EC 3.4.21.36)	0.05	-	cyt	0	Secreted protein		130120		258
Q28153 UniProt NPD GO	ELA1_BOVIN	Elastase-1 precursor (EC 3.4.21.36) (Elastase I)	0.05	-	exc	0	Secreted protein				266
P05208 UniProt NPD GO	ELA2A_MOUSE	Elastase-2A precursor (EC 3.4.21.71) (Elastase-2)	0.05	-	exc	0	Secreted protein				271
P08218 UniProt NPD GO	ELA2B_HUMAN	Elastase-2B precursor (EC 3.4.21.71)	0.05	-	exc	0	Secreted protein	extracellular region [TAS]	609444		269
Q921G7 UniProt NPD GO	ETFD_MOUSE	Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (EC 1.5.5.1) (ETF- ...	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)	electron transfer flavoprotein complex (sen... [TAS] mitochondrial inner membrane [IDA] mitochondrion [IDA]			616
Q6UPE1 UniProt NPD GO	ETFD_RAT	Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (EC 1.5.5.1) (ETF- ...	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				616
Q9Y713 UniProt NPD GO	EF1A_ASPOR	Elongation factor 1-alpha (EF-1-alpha)	0.05	-	cyt	0	Cytoplasm				460
P16017 UniProt NPD GO	EF1A_CANAL	Elongation factor 1-alpha (EF-1-alpha)	0.05	-	cyt	0	Cytoplasm				458
O42671 UniProt NPD GO	EF1A_CRYNE	Elongation factor 1-alpha (EF-1-alpha)	0.05	-	cyt	0	Cytoplasm				459
P27592 UniProt NPD GO	EF1A_ONCVO	Elongation factor 1-alpha (EF-1-alpha)	0.05	-	cyt	0	Cytoplasm				464
Q41011 UniProt NPD GO	EF1A_PEA	Elongation factor 1-alpha (EF-1-alpha)	0.05	-	cyt	0	Cytoplasm				447
P32186 UniProt NPD GO	EF1A_PUCGR	Elongation factor 1-alpha (EF-1-alpha)	0.05	-	cyt	0	Cytoplasm				463
P41166 UniProt NPD GO	EF1A_TRYBB	Elongation factor 1-alpha (EF-1-alpha)	0.05	-	cyt	0	Cytoplasm				449
P50522 UniProt NPD GO	EF1A1_SCHPO	Elongation factor 1-alpha-A (EF-1-alpha-A)	0.05	-	cyt	0	Cytoplasm				460

You are viewing entries 74301 to 74350 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.