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
Q99518 UniProt NPD GO	FMO2_HUMAN	Dimethylaniline monooxygenase [N-oxide-forming] 2 (EC 1.14.13.8) (Pulmonary flavin-containing monoox ...	0.09	-	end	1	Microsome		603955		534
Q7LZT4 UniProt NPD GO	DISI2_AGKCA	Disintegrin ussuristatin-2 (US-2)	0.09	-	nuc	0	Secreted protein				71
P40350 UniProt NPD GO	ALG5_YEAST	Dolichyl-phosphate beta-glucosyltransferase (EC 2.4.1.117) (DolP-glucosyltransferase)	0.09	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Its int ...	endoplasmic reticulum membrane [IDA]			334
P46971 UniProt NPD GO	PMT4_YEAST	Dolichyl-phosphate-mannose--protein mannosyltransferase 4 (EC 2.4.1.109)	0.09	-	end	11	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [TAS]			762
Q6AXW7 UniProt NPD GO	DUS18_RAT	Dual specificity protein phosphatase 18 (EC 3.1.3.48) (EC 3.1.3.16)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				204
P27766 UniProt NPD GO	DYI3_CHLRE	Dynein, 70 kDa intermediate chain, flagellar outer arm (IC69) (IC70)	0.09	-	cyt	0					567
Q6GUQ1 UniProt NPD GO	EGFL8_MOUSE	EGF-like domain-containing protein 8 precursor (Epidermal growth factor-like protein 8) (Multiple EG ...	0.09	-	mit	0	Secreted protein (Potential)				293
Q6MG84 UniProt NPD GO	EGFL8_RAT	EGF-like domain-containing protein 8 precursor (Epidermal growth factor-like protein 8) (Multiple EG ...	0.09	-	cyt	0	Secreted protein (Potential)				291
Q15717 UniProt NPD GO	ELAV1_HUMAN	ELAV-like protein 1 (Hu-antigen R) (HuR)	0.09	-	cyt	0			603466		326
Q8IZ81 UniProt NPD GO	ELMD2_HUMAN	ELMO domain-containing protein 2	0.09	-	cyt	0					293
P81017 UniProt NPD GO	ECHA_ECHCA	Echicetin subunit alpha	0.09	-	cyt	0	Secreted protein				133
O18956 UniProt NPD GO	ENP1_BOVIN	Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) (NTPDase1) (Ecto-ATP diphosphohydrolas ...	0.09	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				513
O35795 UniProt NPD GO	ENP2_RAT	Ectonucleoside triphosphate diphosphohydrolase 2 (EC 3.6.1.-) (NTPDase2) (Ecto-ATPase) (CD39 antigen ...	0.09	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				495
Q5EZ72 UniProt NPD GO	ENPP7_RAT	Ectonucleotide pyrophosphatase/phosphodiesterase 7 precursor (EC 3.1.4.12) (E-NPP7) (NPP-7) (Alkalin ...	0.09	-	end	1 *	Membrane; single-pass type I membrane protein (Potential). Localized at the surface of the microvill ...				439
P08861 UniProt NPD GO	ELA3B_HUMAN	Elastase-3B precursor (EC 3.4.21.70) (Elastase IIIB) (Protease E)	0.09	-	gol	0		extracellular region [NAS]			270
P14963 UniProt NPD GO	EF1A_EUGGR	Elongation factor 1-alpha (EF-1-alpha)	0.09	-	cyt	0	Cytoplasm				445
Q01372 UniProt NPD GO	EF1A_NEUCR	Elongation factor 1-alpha (EF-1-alpha)	0.09	-	cyt	0	Cytoplasm				460
Q09069 UniProt NPD GO	EF1A_SORMA	Elongation factor 1-alpha (EF-1-alpha)	0.09	-	cyt	0	Cytoplasm				460
P34825 UniProt NPD GO	EF1A_TRIRE	Elongation factor 1-alpha (EF-1-alpha)	0.09	-	cyt	0	Cytoplasm				460
P17506 UniProt NPD GO	EF1A1_XENLA	Elongation factor 1-alpha (EF-1-alpha) (42Sp50) (Thesaurin A)	0.09	-	cyt	0	Cytoplasm				463
P68103 UniProt NPD GO	EF1A1_BOVIN	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 A-1) (eEF1A-1) (Elongation factor Tu ...	0.09	-	cyt	0	Cytoplasm (By similarity)				462
P62629 UniProt NPD GO	EF1A1_CRIGR	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 A-1) (eEF1A-1) (Elongation factor Tu ...	0.09	-	cyt	0	Cytoplasm (By similarity)				462
Q66RN5 UniProt NPD GO	EF1A1_FELCA	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 A-1) (eEF1A-1) (Elongation factor Tu ...	0.09	-	cyt	0	Cytoplasm (By similarity)				462
P68104 UniProt NPD GO	EF1A1_HUMAN	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 A-1) (eEF1A-1) (Elongation factor Tu ...	0.09	-	cyt	0	Cytoplasm		130590	1SYW	462
P10126 UniProt NPD GO	EF1A1_MOUSE	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 A-1) (eEF1A-1) (Elongation factor Tu ...	0.09	-	cyt	0	Cytoplasm	cytoplasm [IDA]			462
Q5R1X2 UniProt NPD GO	EF1A1_PANTR	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 A-1) (eEF1A-1) (Elongation factor Tu ...	0.09	-	cyt	0	Cytoplasm (By similarity)				462
Q5R4R8 UniProt NPD GO	EF1A1_PONPY	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 A-1) (eEF1A-1) (Elongation factor Tu ...	0.09	-	cyt	0	Cytoplasm (By similarity)				462
P68105 UniProt NPD GO	EF1A1_RABIT	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 A-1) (eEF1A-1) (Elongation factor Tu ...	0.09	-	cyt	0	Cytoplasm				462
P62630 UniProt NPD GO	EF1A1_RAT	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor 1 A-1) (eEF1A-1) (Elongation factor Tu ...	0.09	-	cyt	0	Cytoplasm				462
Q90835 UniProt NPD GO	EF1A_CHICK	Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor Tu) (EF-Tu)	0.09	-	cyt	0	Cytoplasm	cytoplasm [ISS]			462
Q9ZRI7 UniProt NPD GO	EF1G1_ORYSA	Elongation factor 1-gamma 1 (EF-1-gamma 1) (eEF-1B gamma 1)	0.09	-	cyt	0					418
Q6YW46 UniProt NPD GO	EF1G2_ORYSA	Elongation factor 1-gamma 2 (EF-1-gamma 2) (eEF-1B gamma 2)	0.09	-	cyt	0					418
P34811 UniProt NPD GO	EFGC_SOYBN	Elongation factor G, chloroplast precursor (EF-G)	0.09	-	mit	0	Plastid; chloroplast				788
P35019 UniProt NPD GO	EFTS_GALSU	Elongation factor Ts (EF-Ts)	0.09	-	cyt	0	Plastid; chloroplast				199
P50371 UniProt NPD GO	EFTU_CHACO	Elongation factor Tu (EF-Tu)	0.09	-	cyt	0	Plastid; chloroplast				408
P55334 UniProt NPD GO	XYN1_HUMIN	Endo-1,4-beta-xylanase 1 precursor (EC 3.2.1.8) (Xylanase 1) (1,4-beta-D-xylan xylanohydrolase 1)	0.09	-	vac	0					227
Q7M4T0 UniProt NPD GO	NEG1_NEUCR	Endo-1,6-beta-D-glucanase precursor (EC 3.2.1.75) (Beta-1,6-glucanase Neg1) (Glucan endo-1,6-beta-gl ...	0.09	-	exc	0	Secreted protein				480
P29022 UniProt NPD GO	CHIA_MAIZE	Endochitinase A precursor (EC 3.2.1.14) (Seed chitinase A)	0.09	-	vac	0					280
P21227 UniProt NPD GO	CHIB_PEA	Endochitinase B (EC 3.2.1.14) (Fragment)	0.09	-	nuc	0					23
Q12624 UniProt NPD GO	GUN3_HUMIN	Endoglucanase 3 precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase 3) (Cellulase 3)	0.09	-	mit	0					388
Q9CQE7 UniProt NPD GO	ERGI3_MOUSE	Endoplasmic reticulum-Golgi intermediate compartment protein 3 (Serologically defined breast cancer ...	0.09	-	end	2 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				383
P26214 UniProt NPD GO	PGLR2_ASPNG	Endopolygalacturonase-2 precursor (EC 3.2.1.15) (Endopolygalacturonase II) (EPG-II) (PG-II) (Pectina ...	0.09	-	end	0				1CZF	362
Q96AP7 UniProt NPD GO	ESAM_HUMAN	Endothelial cell-selective adhesion molecule precursor	0.09	-	exc	1	Cell membrane; cell-cell junction; adherens junction; single-pass type I membrane protein (By simila ...				390
P28088 UniProt NPD GO	EDNRB_BOVIN	Endothelin B receptor precursor (ET-B) (Endothelin receptor Non-selective type)	0.09	-	end	8 *	Membrane; multi-pass membrane protein				441
P56497 UniProt NPD GO	EDNRB_CANFA	Endothelin B receptor precursor (ET-B) (Endothelin receptor Non-selective type)	0.09	-	end	7	Membrane; multi-pass membrane protein				442
P24530 UniProt NPD GO	EDNRB_HUMAN	Endothelin B receptor precursor (ET-B) (Endothelin receptor Non-selective type)	0.09	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	600501		442
P48302 UniProt NPD GO	EDNRB_MOUSE	Endothelin B receptor precursor (ET-B) (Endothelin receptor Non-selective type)	0.09	-	end	8 *	Membrane; multi-pass membrane protein				442
O60883 UniProt NPD GO	ETBR2_HUMAN	Endothelin B receptor-like protein 2 precursor (ETBR-LP-2) (G-protein coupled receptor 37-like 1)	0.09	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			481
O97176 UniProt NPD GO	ESM1_DROME	Enhancer of split M1 protein precursor (E(spl)m1)	0.09	-	exc	0					156
Q8NKC2 UniProt NPD GO	ENO12_SCHPO	Enolase 1-2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 1-2) (2-phospho-D-glycerate hydro-lyase 1- ...	0.09	-	cyt	0	Cytoplasm (By similarity)				440

You are viewing entries 66051 to 66100 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.