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
P82084 UniProt NPD GO	DYS6_LIMSA	Dynastin-6	0.01	-		0	Secreted protein				10
P82085 UniProt NPD GO	DYS7_LIMSA	Dynastin-7	0.01	-		0	Secreted protein				12
Q6FUJ0 UniProt NPD GO	DYL1_CANGA	Dynein light chain 1, cytoplasmic	0.01	-	cyt	0	Cytoplasm (By similarity)				86
Q6BZF8 UniProt NPD GO	DYL1_DEBHA	Dynein light chain 1, cytoplasmic	0.01	-	cyt	0	Cytoplasm (By similarity)				91
P63171 UniProt NPD GO	DYLT1_BOVIN	Dynein light chain Tctex-type 1 (T-complex testis-specific protein 1 homolog)	0.01	-	cyt	0		cytoplasmic dynein complex [NAS]			113
Q9Z336 UniProt NPD GO	DYLT1_RAT	Dynein light chain Tctex-type 1 (T-complex testis-specific protein 1 homolog)	0.01	-	cyt	0					113
P63172 UniProt NPD GO	DYLT1_HUMAN	Dynein light chain Tctex-type 1 (T-complex testis-specific protein 1 homolog) (Protein CW-1)	0.01	-	cyt	0		cytoplasmic dynein complex [ISS]	601554		113
P51807 UniProt NPD GO	DYLT1_MOUSE	Dynein light chain Tctex-type 1 (T-complex testis-specific protein 1) (TCTEX-1)	0.01	-	cyt	0		axonemal dynein complex [TAS] cytoplasmic dynein complex [TAS] Golgi apparatus [IDA]			113
P48583 UniProt NPD GO	ERD2_CAEEL	ER lumen protein retaining receptor	0.01	-	end	5 *	Membrane; multi-pass membrane protein				213
O76767 UniProt NPD GO	ERD2_DROME	ER lumen protein retaining receptor	0.01	-	end	5 *	Membrane; multi-pass membrane protein				212
Q9CQM2 UniProt NPD GO	ERD22_MOUSE	ER lumen protein retaining receptor 2 (KDEL receptor 2) (KDEL endoplasmic reticulum protein retentio ...	0.01	-	nuc	4 *	Membrane; multi-pass membrane protein (By similarity)				212
Q5U305 UniProt NPD GO	ERD22_RAT	ER lumen protein retaining receptor 2 (KDEL receptor 2) (KDEL endoplasmic reticulum protein retentio ...	0.01	-	nuc	4 *	Membrane; multi-pass membrane protein (By similarity)				212
P33947 UniProt NPD GO	ERD22_HUMAN	ER lumen protein retaining receptor 2 (KDEL receptor 2) (KDEL endoplasmic reticulum protein retentio ...	0.01	-	nuc	4 *	Membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] Golgi apparatus [TAS] integral to membrane [TAS]	609024		212
P30042 UniProt NPD GO	ES1_HUMAN	ES1 protein homolog, mitochondrial precursor (Protein KNP-I) (Protein GT335)	0.01	-	mit	0	Mitochondrion (Potential)		601659		268
P55959 UniProt NPD GO	NO40_PEA	Early nodulin 40	0.01	-		0					13
P55960 UniProt NPD GO	NO40_SOYBN	Early nodulin 40	0.01	-		0					12
Q8LC95 UniProt NPD GO	ENL3_ARATH	Early nodulin-like protein 3 precursor (Phytocyanin-like protein)	0.01	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				186
Q07892 UniProt NPD GO	ECLH_DROME	Eclosion hormone precursor (Ecdysis activator) (EH)	0.01	-	cyt	1 *	Secreted protein				97
P49343 UniProt NPD GO	ECAA_ECTTU	Ectatomin subunit A (EA)	0.01	-	cyt	0	Secreted protein			1ECI	37
O75356 UniProt NPD GO	ENP5_HUMAN	Ectonucleoside triphosphate diphosphohydrolase 5 precursor (EC 3.6.1.6) (NTPDase5) (Nucleoside dipho ...	0.01	-	exc	2 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)		603162		428
Q9WUZ9 UniProt NPD GO	ENP5_MOUSE	Ectonucleoside triphosphate diphosphohydrolase 5 precursor (EC 3.6.1.6) (NTPDase5) (Nucleoside dipho ...	0.01	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum lumen				427
Q01383 UniProt NPD GO	ELYS_HALSO	Egg-lysin precursor (Sperm-lysin)	0.01	-	end	0					154
Q23982 UniProt NPD GO	PEB2_DROME	Ejaculatory bulb-specific protein 2 precursor (Ejaculatory bulb-specific protein II) (PEB-meII)	0.01	-	mit	0	Secreted protein (Potential)	extracellular region [NAS]			66
P09093 UniProt NPD GO	ELA3A_HUMAN	Elastase-3A precursor (EC 3.4.21.70) (Elastase IIIA) (Protease E)	0.01	-	exc	0					270
P82098 UniProt NPD GO	EI22_LITRU	Electrin-2.2	0.01	-		0	Secreted protein				13
P82100 UniProt NPD GO	EI04_LITRU	Electrin-4	0.01	-		0	Secreted protein				5
Q16134 UniProt NPD GO	ETFD_HUMAN	Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (EC 1.5.5.1) (ETF- ...	0.01	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [NAS]	231680		617
P62933 UniProt NPD GO	TKN_ELECI	Eledoisin	0.01	-		0	Secreted protein			1MXQ	11
P62934 UniProt NPD GO	TKN_ELEMO	Eledoisin	0.01	-		0	Secreted protein			1MXQ	11
P31018 UniProt NPD GO	EF1A_ENTHI	Elongation factor 1-alpha (EF-1-alpha)	0.01	-	cyt	0	Cytoplasm				430
O70251 UniProt NPD GO	EF1B_MOUSE	Elongation factor 1-beta (EF-1-beta)	0.01	-	cyt	0					224
P29412 UniProt NPD GO	EF1B_PIG	Elongation factor 1-beta (EF-1-beta)	0.01	-	cyt	0					224
P32471 UniProt NPD GO	EF1B_YEAST	Elongation factor 1-beta (EF-1-beta) (Translation elongation factor 1B alpha) (Eukaryotic elongation ...	0.01	-	cyt	0		eukaryotic translation elongation factor 1 ... [IMP] ribosome [TAS]		1IJF	205
P50372 UniProt NPD GO	EFTU_CODFR	Elongation factor Tu (EF-Tu)	0.01	-	mit	0	Plastid; chloroplast				410
P50379 UniProt NPD GO	EFTU_MANSQ	Elongation factor Tu (EF-Tu) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				235
P21745 UniProt NPD GO	EA30_VICFA	Embryonic abundant protein VF30.1 precursor	0.01	-	mit	0					268
P33557 UniProt NPD GO	XYN3_ASPKA	Endo-1,4-beta-xylanase 3 precursor (EC 3.2.1.8) (Xylanase 3) (1,4-beta-D-xylan xylanohydrolase 3) (X ...	0.01	-	mit	0	Secreted protein			1BK1	211
P29417 UniProt NPD GO	XYNA_PENCH	Endo-1,4-beta-xylanase precursor (EC 3.2.1.8) (Xylanase) (1,4-beta-D-xylan xylanohydrolase)	0.01	-	end	0	Secreted protein				353
Q06014 UniProt NPD GO	CHI2_ARAHY	Endochitinase 2 (EC 3.2.1.14) (CHIT 2) (Fragment)	0.01	-	nuc	0					46
P81190 UniProt NPD GO	GUN_SCHCO	Endoglucanase (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase) (Fragment)	0.01	-	cyt	0	Cell membrane; lipid-anchor (Probable)				28
P21833 UniProt NPD GO	GUN1_SCLSC	Endoglucanase 1 (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase) (EG1) (Fragment)	0.01	-	cyt	0					34
P23044 UniProt NPD GO	GUN_ROBSP	Endoglucanase 1 (EC 3.2.1.4) (Endoglucanase I) (Endo-1,4-beta-glucanase) (Carboxymethyl-cellulase I) ...	0.01	-	cyt	0					375
Q4V8Y6 UniProt NPD GO	ERGI1_BRARE	Endoplasmic reticulum-Golgi intermediate compartment protein 1 (ER-Golgi intermediate compartment 32 ...	0.01	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Endoplasmic reti ...				290
P56252 UniProt NPD GO	ENO_HOMGA	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.01	-	mit	0	Cytoplasm			1PDZ	433
Q6C1F3 UniProt NPD GO	ENO_YARLI	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.01	-	cyt	0	Cytoplasm (By similarity)				438
O74286 UniProt NPD GO	ENO_CUNEL	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Fragment ...	0.01	-	cyt	0	Cytoplasm (By similarity)				436
Q9HDT3 UniProt NPD GO	ENO_ALTAL	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Major al ...	0.01	-	cyt	0	Cytoplasm (By similarity)				438
P79238 UniProt NPD GO	LPPL_PONPY	Eosinophil lysophospholipase (EC 3.1.1.5) (Charcot-Leyden crystal protein homolog) (Lysolecithin acy ...	0.01	-	cyt	0	Localized in granules from where it may be secreted or transported to other locations in the cell (B ...				68
P02731 UniProt NPD GO	EOSI_HUMAN	Eosinophilotactic peptides	0.01	-		0					4
P38528 UniProt NPD GO	EPD_CYPCA	Ependymin precursor (EPD)	0.01	-	exc	0	Secreted protein				215

You are viewing entries 88151 to 88200 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.