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
O93295 UniProt NPD GO	ENP1_CHICK	Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) (NTPDase1) (Ecto-ATP diphosphohydrolas ...	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				493
P81130 UniProt NPD GO	COEC_SCYCA	Egg case collagen (Fragments)	0.00	-	cyt	0					209
P04552 UniProt NPD GO	ELYS_HALRU	Egg-lysin precursor (Sperm-lysin)	0.00	-	end	0				2LYN	154
P19957 UniProt NPD GO	ELAF_HUMAN	Elafin precursor (Elastase-specific inhibitor) (ESI) (Skin-derived antileukoproteinase) (SKALP) (WAP ...	0.00	-	mit	1 *	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]	182257	2REL	117
P32197 UniProt NPD GO	ELAS_GADMO	Elastase (EC 3.4.21.-) (Fragment)	0.00	-		0					20
P82096 UniProt NPD GO	EI01_LITRU	Electrin-1	0.00	-		0	Secreted protein				6
P82097 UniProt NPD GO	EI21_LITRU	Electrin-2.1	0.00	-		0	Secreted protein				13
P82101 UniProt NPD GO	EI05_LITRU	Electrin-5	0.00	-		0	Secreted protein				7
P81266 UniProt NPD GO	EF1A_MICCR	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.00	-		0	Cytoplasm				15
P55823 UniProt NPD GO	EF2_RABIT	Elongation factor 2 (EF-2) (Fragment)	0.00	-	cyt	0	Cytoplasm				34
P35450 UniProt NPD GO	EFGC_PEA	Elongation factor G, chloroplast (EF-G) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				141
P54835 UniProt NPD GO	EFTU_CANFA	Elongation factor Tu, mitochondrial (EF-Tu) (Fragment)	0.00	-		0	Mitochondrion				14
Q9BY08 UniProt NPD GO	EBPL_HUMAN	Emopamil-binding protein-like (Emopamil-binding-related protein)	0.00	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				206
Q9D0P0 UniProt NPD GO	EBPL_MOUSE	Emopamil-binding protein-like (Emopamil-binding-related protein)	0.00	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				206
P56588 UniProt NPD GO	XYNA_PENSI	Endo-1,4-beta-xylanase (EC 3.2.1.8) (Xylanase) (1,4-beta-D-xylan xylanohydrolase)	0.00	-	nuc	0	Secreted protein			1BG4	302
P55328 UniProt NPD GO	XYN1_ASPAW	Endo-1,4-beta-xylanase I precursor (EC 3.2.1.8) (Xylanase I) (1,4-beta-D-xylan xylanohydrolase I)	0.00	-	cyt	0					211
P55329 UniProt NPD GO	XYN1_ASPNG	Endo-1,4-beta-xylanase I precursor (EC 3.2.1.8) (Xylanase I) (1,4-beta-D-xylan xylanohydrolase I)	0.00	-	cyt	0				1UKR	211
P55331 UniProt NPD GO	XYN1_ASPTU	Endo-1,4-beta-xylanase I precursor (EC 3.2.1.8) (Xylanase I) (1,4-beta-D-xylan xylanohydrolase I)	0.00	-	cyt	0					211
P84195 UniProt NPD GO	XYNA_GLOTR	Endo-1,4-beta-xylanase Xyn10A (EC 3.2.1.8) (EC 3.2.1.4) (Fragments)	0.00	-	cyt	0	Secreted protein; extracellular space	extracellular region [IDA]			45
O59859 UniProt NPD GO	XYNA_ASPAC	Endo-1,4-beta-xylanase precursor (EC 3.2.1.8) (Xylanase) (1,4-beta-D-xylan xylanohydrolase) (FIA-xyl ...	0.00	-	end	0	Secreted protein (By similarity)				327
P81179 UniProt NPD GO	PGLR_DIAAB	Endo-polygalacturonase (PG) (EC 3.2.1.15) (Fragment)	0.00	-		0					9
P21225 UniProt NPD GO	CHI1_PEA	Endochitinase A1 (EC 3.2.1.14) (Fragment)	0.00	-		0					15
P27054 UniProt NPD GO	CHI4_PHAVU	Endochitinase PR4 precursor (EC 3.2.1.14)	0.00	-	cyt	0					270
Q7M4F0 UniProt NPD GO	CUD9_SCHGR	Endocuticle structural glycoprotein SgAbd-9	0.00	-	cyt	0					129
P21834 UniProt NPD GO	GUN2_SCLSC	Endoglucanase 2 (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase) (EG2) (Fragment)	0.00	-	cyt	0					31
P84196 UniProt NPD GO	GUNB_GLOTR	Endoglucanase Cel12A (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase) (Fragments)	0.00	-	cyt	0	Secreted protein; extracellular space	extracellular region [IDA]			36
P84194 UniProt NPD GO	GUNA_GLOTR	Endoglucanase Cel5A (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase) (Fragments)	0.00	-	cyt	0	Secreted protein; extracellular space	extracellular region [IDA]			56
P81629 UniProt NPD GO	ERP29_TRIVU	Endoplasmic reticulum protein ERp29 (Fragment)	0.00	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen				32
P81623 UniProt NPD GO	ERP29_BOVIN	Endoplasmic reticulum protein ERp29 (Fragments)	0.00	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen				31
P30040 UniProt NPD GO	ERP29_HUMAN	Endoplasmic reticulum protein ERp29 precursor (ERp31) (ERp28)	0.00	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS]	602287		261
Q4HY20 UniProt NPD GO	ERV25_GIBZE	Endoplasmic reticulum vesicle protein 25 precursor	0.00	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				214
Q6NS19 UniProt NPD GO	ERGI1_XENLA	Endoplasmic reticulum-Golgi intermediate compartment protein 1 (ER-Golgi intermediate compartment 32 ...	0.00	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Endoplasmic reti ...				290
Q28468 UniProt NPD GO	EDNRB_MACFA	Endothelin B receptor (ET-B) (Endothelin receptor non-selective type) (Fragment)	0.00	-	cyt	2 *	Membrane; multi-pass membrane protein				99
Q27655 UniProt NPD GO	ENO_FASHE	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.00	-	cyt	0	Cytoplasm				431
P84208 UniProt NPD GO	ENO_IMPCY	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Fragment ...	0.00	-	cyt	0	Cytoplasm (By similarity)				32
P97400 UniProt NPD GO	LPPL_MOUSE	Eosinophil lysophospholipase (EC 3.1.1.5) (Charcot-Leyden crystal protein homolog) (Lysolecithin acy ...	0.00	-	cyt	0	Localized in granules from where it may be secreted or transported to other locations in the cell (B ...				68
P06911 UniProt NPD GO	ERBP_RAT	Epididymal retinoic acid-binding protein precursor (E-RABP) (Androgen-dependent epididymal 18.5 kDa ...	0.00	-	cyt	0				1EPB	188
O18994 UniProt NPD GO	GPX5_PIG	Epididymal secretory glutathione peroxidase precursor (EC 1.11.1.9) (Epididymis-specific glutathione ...	0.00	-	end	0	Secreted protein				219
P35578 UniProt NPD GO	ESP4_LACVV	Epididymal secretory protein 4 precursor (Epididymal secretory protein IV) (LESP IV) (C731)	0.00	-	cyt	0	Secreted protein; extracellular space				172
Q28895 UniProt NPD GO	NPC2_CANFA	Epididymal secretory protein E1 precursor (Niemann Pick type C2 protein homolog) (cE1)	0.00	-	end	0	Secreted protein (Potential)				149
P62502 UniProt NPD GO	LCN6_HUMAN	Epididymal-specific lipocalin-6 precursor (Lipocalin-5)	0.00	-	exc	0	Secreted protein. Located on the head and tail of spermatozoa with the highest concentration on the ...		609379		163
P47801 UniProt NPD GO	EMP1_MOUSE	Epithelial membrane protein 1 (EMP-1) (Tumor-associated membrane protein)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				160
Q9JIM1 UniProt NPD GO	S29A1_MOUSE	Equilibrative nucleoside transporter 1 (Equilibrative nitrobenzylmercaptopurine riboside-sensitive n ...	0.00	-	end	10 *	Membrane; multi-pass membrane protein				459
Q80WK7 UniProt NPD GO	S29A3_RAT	Equilibrative nucleoside transporter 3 (Solute carrier family 29 member 3)	0.00	-	end	11	Membrane; multi-pass membrane protein				475
P0C1H0 UniProt NPD GO	ACTP1_ACTEQ	Equinatoxin-1 (Equinatoxin I') (Equinatoxin I'') (Fragment)	0.00	-		0	Secreted protein. Found in nematocyst				20
P0C1H1 UniProt NPD GO	ACTPP_ACTEQ	Equinatoxin-1'' (Equinatoxin I'') (Fragment)	0.00	-		0	Secreted protein. Found in nematocyst				20
P0C1H2 UniProt NPD GO	ACTP3_ACTEQ	Equinatoxin-3 (Equinatoxin III) (EqTIII) (EqT-III) (Fragment)	0.00	-		0	Secreted protein. Found in nematocyst				20
O74820 UniProt NPD GO	ERG28_SCHPO	Ergosterol biosynthetic protein 28	0.00	-	mit	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				136
P02728 UniProt NPD GO	GLEM_HUMAN	Erythrocyte membrane glycopeptide	0.00	-		0					10
P40843 UniProt NPD GO	ES1A_RANES	Esculentin-1A	0.00	-	cyt	0	Secreted protein				46

You are viewing entries 94401 to 94450 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.