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
O42768 UniProt NPD GO	HEM2_CANGA	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (Porphobilinogen synthase) (ALADH)	0.07	-	cyt	0					340
Q60HH9 UniProt NPD GO	HEM2_MACFA	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (Porphobilinogen synthase) (ALADH)	0.07	-	mit	0					330
Q9PS09 UniProt NPD GO	TXDB_DENAN	Dendrotoxin B (DTX-B) (Fragment)	0.07	-	nuc	0	Secreted protein				30
P90661 UniProt NPD GO	GRA1_NEOCA	Dense granule protein 1 precursor (NcDG1) (Antigen Nc4.1)	0.07	-	end	2 *	Secreted protein (Potential)				217
Q9SC80 UniProt NPD GO	DHYS_TOBAC	Deoxyhypusine synthase (EC 2.5.1.46)	0.07	-	cyt	0					379
P56542 UniProt NPD GO	DNS2A_MOUSE	Deoxyribonuclease-2-alpha precursor (EC 3.1.22.1) (Deoxyribonuclease II alpha) (DNase II alpha) (Aci ...	0.07	-	exc	0	Lysosome	lysosome [TAS]			353
Q96Q80 UniProt NPD GO	DERL3_HUMAN	Derlin-3 (Degradation in endoplasmic reticulum protein 3) (Der1-like protein 3) (DERtrin-3)	0.07	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [IDA]			235
O93224 UniProt NPD GO	DMS4_AGAAN	Dermaseptin AA-3-3 precursor	0.07	-	exc	0	Secreted protein				72
O93226 UniProt NPD GO	DMS6_AGAAN	Dermaseptin AA-3-6 precursor	0.07	-	exc	0	Secreted protein				80
P25782 UniProt NPD GO	CYSP2_HOMAM	Digestive cysteine proteinase 2 precursor (EC 3.4.22.-)	0.07	-	mit	0					323
O59816 UniProt NPD GO	ODP2_SCHPO	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochond ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix				483
Q6V3W9 UniProt NPD GO	PYRD_SACKL	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.07	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				446
Q62951 UniProt NPD GO	DPYL4_RAT	Dihydropyrimidinase-related protein 4 (DRP-4) (Collapsin response mediator protein 3) (CRMP-3) (UNC3 ...	0.07	-	cyt	0	Cytoplasm (Potential)				564
P39522 UniProt NPD GO	ILV3_YEAST	Dihydroxy-acid dehydratase, mitochondrial precursor (EC 4.2.1.9) (DAD) (2,3-dihydroxy acid hydrolyas ...	0.07	-	mit	0	Mitochondrion	mitochondrion [IDA]			585
Q8VC30 UniProt NPD GO	DAK_MOUSE	Dihydroxyacetone kinase (EC 2.7.1.29) (Glycerone kinase) (DHA kinase)	0.07	+	cyt	0					578
P43550 UniProt NPD GO	DAK2_YEAST	Dihydroxyacetone kinase 2 (EC 2.7.1.29) (Glycerone kinase 2) (DHA kinase 2)	0.07	-	cyt	0					591
Q6C7H6 UniProt NPD GO	DIM1_YARLI	Dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltra ...	0.07	-	cyt	0					317
Q6IRI9 UniProt NPD GO	FMO2_RAT	Dimethylaniline monooxygenase [N-oxide-forming] 2 (EC 1.14.13.8) (Pulmonary flavin-containing monoox ...	0.07	-	cyt	1	Microsome (By similarity)				534
P16444 UniProt NPD GO	DPEP1_HUMAN	Dipeptidase 1 precursor (EC 3.4.13.19) (Microsomal dipeptidase) (Renal dipeptidase) (hRDP) (Dehydrop ...	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Brush border membrane		179780	1ITU	411
Q9VHR8 UniProt NPD GO	DPP3_DROME	Dipeptidyl-peptidase 3 (EC 3.4.14.4) (Dipeptidyl-peptidase III) (DPP III) (Dipeptidyl aminopeptidase ...	0.07	-	mit	0	Cell membrane; multi-pass membrane protein. Cytoplasm				786
Q752D7 UniProt NPD GO	DPH4_ASHGO	Diphthamide biosynthesis protein 4	0.07	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				156
Q6FWM1 UniProt NPD GO	DPH4_CANGA	Diphthamide biosynthesis protein 4	0.07	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				175
P82466 UniProt NPD GO	DIS6B_ECHCS	Disintegrin EC6B	0.07	-	nuc	0	Secreted protein				69
P35464 UniProt NPD GO	DIHR_MANSE	Diuretic hormone receptor (DH-R)	0.07	-	end	7	Membrane; multi-pass membrane protein				395
P39007 UniProt NPD GO	STT3_YEAST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 (EC 2.4.1.119) (Oligosac ...	0.07	-	end	13 *	Membrane; multi-pass membrane protein	oligosaccharyl transferase complex [IPI]			718
Q9DB25 UniProt NPD GO	ALG5_MOUSE	Dolichyl-phosphate beta-glucosyltransferase (EC 2.4.1.117) (DolP-glucosyltransferase)	0.07	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				324
Q39592 UniProt NPD GO	DYL5_CHLRE	Dynein 16 kDa light chain, flagellar outer arm	0.07	-	cyt	0					156
O94270 UniProt NPD GO	ERD2_SCHPO	ER lumen protein retaining receptor	0.07	-	cyt	4 *	Membrane; multi-pass membrane protein				212
P18414 UniProt NPD GO	ERD2_YEAST	ER lumen protein retaining receptor (HDEL receptor)	0.07	-	mit	4	Membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]			219
P37217 UniProt NPD GO	CD69_MOUSE	Early activation antigen CD69	0.07	-	cyt	1 *	Membrane; single-pass type II membrane protein	external side of plasma membrane [IDA]			199
P25226 UniProt NPD GO	NO5_PEA	Early nodulin 5 precursor (N-5)	0.07	-	end	2 *					135
Q8BGN3 UniProt NPD GO	ENPP6_MOUSE	Ectonucleotide pyrophosphatase/phosphodiesterase 6 precursor (EC 3.1.-.-) (E-NPP6) (NPP-6) [Contains ...	0.07	-	exc	0	Cell membrane; single-pass type I membrane protein. A minor secreted form also exists (By similarity ...	plasma membrane [IDA]			440
Q01384 UniProt NPD GO	ELYS_HALWA	Egg-lysin precursor (Sperm-lysin)	0.07	-	exc	0					154
Q9W1C9 UniProt NPD GO	PEB3_DROME	Ejaculatory bulb-specific protein 3 precursor (Ejaculatory bulb-specific protein III) (PEB-meIII)	0.07	-	exc	0	Secreted protein (Potential)	extracellular region [NAS]			126
P00774 UniProt NPD GO	ELA2A_RAT	Elastase-2A precursor (EC 3.4.21.71) (Elastase-2)	0.07	-	exc	0	Secreted protein				271
P06805 UniProt NPD GO	EF1A1_RHIRA	Elongation factor 1-alpha (EF-1-alpha)	0.07	-	cyt	0	Cytoplasm				458
P14864 UniProt NPD GO	EF1A2_RHIRA	Elongation factor 1-alpha (EF-1-alpha)	0.07	-	cyt	0	Cytoplasm				458
P14865 UniProt NPD GO	EF1A3_RHIRA	Elongation factor 1-alpha (EF-1-alpha)	0.07	-	cyt	0	Cytoplasm				457
P41752 UniProt NPD GO	EF1A_ASHGO	Elongation factor 1-alpha (EF-1-alpha)	0.07	-	cyt	0	Cytoplasm				458
Q00251 UniProt NPD GO	EF1A_AURPU	Elongation factor 1-alpha (EF-1-alpha)	0.07	-	cyt	0	Cytoplasm				459
P54959 UniProt NPD GO	EF1A_BLAHO	Elongation factor 1-alpha (EF-1-alpha)	0.07	-	cyt	0	Cytoplasm				434
P53013 UniProt NPD GO	EF1A_CAEEL	Elongation factor 1-alpha (EF-1-alpha)	0.07	-	cyt	0	Cytoplasm				463
O42820 UniProt NPD GO	EF1A_SCHCO	Elongation factor 1-alpha (EF-1-alpha)	0.07	-	cyt	0	Cytoplasm				460
P25698 UniProt NPD GO	EF1A_SOYBN	Elongation factor 1-alpha (EF-1-alpha)	0.07	-	cyt	0	Cytoplasm				447
P08736 UniProt NPD GO	EF11_DROME	Elongation factor 1-alpha (EF-1-alpha) (50 kDa female-specific protein)	0.07	-	cyt	0	Cytoplasm				463
P62631 UniProt NPD GO	EF1A2_MOUSE	Elongation factor 1-alpha 2 (EF-1-alpha-2) (Elongation factor 1 A-2) (eEF1A-2) (Statin S1)	0.07	-	cyt	0	Nucleus	cytoplasm [IDA] eukaryotic translation elongation factor 1 ... [IDA]			463
P62632 UniProt NPD GO	EF1A2_RAT	Elongation factor 1-alpha 2 (EF-1-alpha-2) (Elongation factor 1 A-2) (eEF1A-2) (Statin S1)	0.07	-	cyt	0	Nucleus				463
P17507 UniProt NPD GO	EF1A2_XENLA	Elongation factor 1-alpha, oocyte form (EF-1-alpha-O) (EF-1AO) (42S p48)	0.07	-	cyt	0	Cytoplasm				461
P12262 UniProt NPD GO	EF1B_ARTSA	Elongation factor 1-beta (EF-1-beta)	0.07	-	cyt	0					206
P29546 UniProt NPD GO	EF1B_WHEAT	Elongation factor 1-beta (EF-1-beta) (Elongation factor 1B-alpha 2) (eEF-1B alpha) (Elongation facto ...	0.07	-	cyt	0					215

You are viewing entries 69901 to 69950 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.