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
Q16570 UniProt NPD GO	DUFFY_HUMAN	Duffy antigen/chemokine receptor (Fy glycoprotein) (GpFy) (Glycoprotein D) (Plasmodium vivax recepto ...	0.03	-	end	7	Membrane; multi-pass membrane protein	plasma membrane [TAS]	110700		336
O00399 UniProt NPD GO	DCTN6_HUMAN	Dynactin subunit 6 (Dynactin subunit p27) (WS-3 protein)	0.03	-	nuc	0		mitochondrion [ISS]			190
Q94758 UniProt NPD GO	DYL1_SCHMA	Dynein light chain	0.03	-	cyt	0	Cytoplasm (By similarity)				89
Q32KN5 UniProt NPD GO	DNAL4_BOVIN	Dynein light chain 4, axonemal	0.03	-	cyt	0					105
O96015 UniProt NPD GO	DNAL4_HUMAN	Dynein light chain 4, axonemal	0.03	-	cyt	0		axonemal dynein complex [NAS]			105
Q9DCM4 UniProt NPD GO	DNAL4_MOUSE	Dynein light chain 4, axonemal	0.03	-	cyt	0					105
Q9UTS6 UniProt NPD GO	DYLT_SCHPO	Dynein light chain Tctex-type (TCTEX-1 protein homolog)	0.03	-	cyt	0		cortical microtubule cytoskeleton [IDA] dynein complex [TAS]			111
P35402 UniProt NPD GO	ERD2_ARATH	ER lumen protein retaining receptor (HDEL receptor)	0.03	-	end	5 *	Membrane; multi-pass membrane protein				215
P38312 UniProt NPD GO	ERV15_YEAST	ER-derived vesicles protein ERV15	0.03	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				142
P93328 UniProt NPD GO	NO16_MEDTR	Early nodulin 16 precursor (N-16)	0.03	-	end	1					180
O22426 UniProt NPD GO	NO40_LOTJA	Early nodulin 40	0.03	-		0					12
P25331 UniProt NPD GO	ECLH_BOMMO	Eclosion hormone precursor (Ecdysis activator) (EH)	0.03	-	mit	1 *	Secreted protein				88
P11919 UniProt NPD GO	ECLH_MANSE	Eclosion hormone precursor (Ecdysis activator) (EH)	0.03	-	mit	1 *	Secreted protein				88
P01363 UniProt NPD GO	EGGR_APLCA	Egg-releasing peptide	0.03	-	cyt	0					34
P19469 UniProt NPD GO	EGG2_SCHJA	Eggshell protein 2A precursor	0.03	+	exc	0					207
P06649 UniProt NPD GO	EGG1_SCHMA	Eggshell protein precursor (Chorion protein)	0.03	-	vac	0					173
P12796 UniProt NPD GO	EGG2_SCHMA	Eggshell protein precursor (Chorion protein)	0.03	-	vac	0					177
P13396 UniProt NPD GO	EGG3_SCHMA	Eggshell protein precursor (Chorion protein)	0.03	-	vac	0					177
P16895 UniProt NPD GO	IELA_ANESU	Elastase inhibitor	0.03	-	nuc	0				1Y1C	48
P00772 UniProt NPD GO	ELA1_PIG	Elastase-1 precursor (EC 3.4.21.36)	0.03	-	exc	0	Secreted protein			9EST	266
P07916 UniProt NPD GO	ELN_CHICK	Elastin precursor (Tropoelastin) (Fragment)	0.03	-	cyt	0	Secreted protein; extracellular space; extracellular matrix. Extracellular matrix of elastic fibers				750
P55931 UniProt NPD GO	ETFD_PIG	Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (EC 1.5.5.1) (ETF- ...	0.03	-	mit	1	Mitochondrion; mitochondrial inner membrane (By similarity)				607
Q96WZ1 UniProt NPD GO	EF1A_COCIM	Elongation factor 1-alpha (EF-1-alpha)	0.03	-	cyt	0	Cytoplasm				460
P27634 UniProt NPD GO	EF1A_RHYAM	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.03	-	cyt	0	Cytoplasm				412
O74173 UniProt NPD GO	EF1B_SCHPO	Elongation factor 1-beta (EF-1-beta)	0.03	-	pox	0					214
P19457 UniProt NPD GO	EFTU_GUITH	Elongation factor Tu (EF-Tu)	0.03	-	cyt	0	Plastid; chloroplast				408
Q9TKZ5 UniProt NPD GO	EFTU_NEPOL	Elongation factor Tu (EF-Tu)	0.03	-	cyt	0	Plastid; chloroplast				410
P50378 UniProt NPD GO	EFTU_GONPE	Elongation factor Tu (EF-Tu) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast				235
O63930 UniProt NPD GO	EFTU_GYMST	Elongation factor Tu (EF-Tu) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast				363
P50380 UniProt NPD GO	EFTU_PANMO	Elongation factor Tu (EF-Tu) (Fragment)	0.03	-	nuc	0	Plastid; chloroplast				234
Q9EQC4 UniProt NPD GO	ELOV4_MOUSE	Elongation of very long chain fatty acids protein 4	0.03	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				312
Q751F9 UniProt NPD GO	ELOC_ASHGO	Elongin-C	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				100
Q00177 UniProt NPD GO	XYNC_EMENI	Endo-1,4-beta-xylanase C precursor (EC 3.2.1.8) (Xylanase C) (1,4-beta-D-xylan xylanohydrolase C) (3 ...	0.03	-	exc	0	Secreted protein			1TA3	327
P55330 UniProt NPD GO	XYN2_ASPNG	Endo-1,4-beta-xylanase II precursor (EC 3.2.1.8) (Xylanase II) (1,4-beta-D-xylan xylanohydrolase II) ...	0.03	-	vac	0					225
Q06015 UniProt NPD GO	CHI3_ARAHY	Endochitinase 3 (EC 3.2.1.14) (CHIT 3) (Fragment)	0.03	-	nuc	0					46
Q06016 UniProt NPD GO	CHI4_ARAHY	Endochitinase 4 (EC 3.2.1.14) (CHIT 4) (Fragment)	0.03	-	nuc	0					46
P29030 UniProt NPD GO	CHIT_BRUMA	Endochitinase precursor (EC 3.2.1.14) (MF1 antigen)	0.03	-	mit	1 *					504
P56561 UniProt NPD GO	CUD5_LOCMI	Endocuticle structural glycoprotein ABD-5	0.03	-	cyt	0					82
P56562 UniProt NPD GO	CUD5_SCHGR	Endocuticle structural glycoprotein SgAbd-5	0.03	-	cyt	0					82
P16347 UniProt NPD GO	IAAS_WHEAT	Endogenous alpha-amylase/subtilisin inhibitor (WASI)	0.03	-	cyt	0					180
Q863Y7 UniProt NPD GO	PEVRA_PIG	Endogenous retrovirus A receptor precursor	0.03	-	end	11 *	Membrane; multi-pass membrane protein				446
P22669 UniProt NPD GO	GUN_ASPAC	Endoglucanase-1 precursor (EC 3.2.1.4) (Endoglucanase I) (Endo-1,4-beta-glucanase) (Cellulase) (FI-C ...	0.03	-	exc	0	Secreted protein				237
O14405 UniProt NPD GO	GUN4_TRIRE	Endoglucanase-4 precursor (EC 3.2.1.4) (Endoglucanase IV) (Endo-1,4-beta-glucanase IV) (Cellulase IV ...	0.03	-	mit	0	Secreted protein	extracellular region [IDA]			344
P57759 UniProt NPD GO	ERP29_MOUSE	Endoplasmic reticulum protein ERp29 precursor	0.03	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				262
P52555 UniProt NPD GO	ERP29_RAT	Endoplasmic reticulum protein ERp29 precursor (ERp31)	0.03	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS] endoplasmic reticulum lumen [TAS] transport vesicle [IDA]		1G7E	260
Q6C503 UniProt NPD GO	ERV25_YARLI	Endoplasmic reticulum vesicle protein 25 precursor	0.03	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				211
Q96VP4 UniProt NPD GO	ENO_CURLU	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.03	-	cyt	0	Cytoplasm (By similarity)				440
O02654 UniProt NPD GO	ENO_LOLPE	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.03	-	nuc	0	Cytoplasm				434
P42896 UniProt NPD GO	ENO_RICCO	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.03	-	nuc	0	Cytoplasm				445
Q12007 UniProt NPD GO	ERR1_YEAST	Enolase-related protein 1/2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hy ...	0.03	-	cyt	0					437

You are viewing entries 79801 to 79850 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.