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
P43210 UniProt NPD GO	HEM2_SOYBN	Delta-aminolevulinic acid dehydratase, chloroplast precursor (EC 4.2.1.24) (Porphobilinogen synthase ...	0.14	-	mit	0	Plastid; chloroplast				412
P24493 UniProt NPD GO	HEM2_SPIOL	Delta-aminolevulinic acid dehydratase, chloroplast precursor (EC 4.2.1.24) (Porphobilinogen synthase ...	0.14	-	nuc	0	Plastid; chloroplast				433
P83259 UniProt NPD GO	TXDP4_PARLU	Delta-palutoxin IT4 (Delta-paluIT4)	0.14	-	nuc	0	Secreted protein	extracellular region [NAS]			37
Q01931 UniProt NPD GO	DS22_CRAPL	Desiccation stress protein DSP-22, chloroplast precursor	0.14	-	nuc	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				199
Q03763 UniProt NPD GO	DSG1_BOVIN	Desmoglein-1 precursor (Desmosomal glycoprotein 1) (DG1) (DGI) (Pemphigus foliaceus antigen)	0.14	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				1043
Q01459 UniProt NPD GO	DIAC_HUMAN	Di-N-acetylchitobiase precursor (EC 3.2.1.-)	0.14	-	exc	0	Lysosome		600873		385
Q5E9W3 UniProt NPD GO	PYRD_BOVIN	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.14	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				395
Q02127 UniProt NPD GO	PYRD_HUMAN	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.14	-	mit	1 *	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [NAS]	126064	2B0M	395
Q16555 UniProt NPD GO	DPYL2_HUMAN	Dihydropyrimidinase-related protein 2 (DRP-2) (Collapsin response mediator protein 2) (CRMP-2) (N2A3 ...	0.14	-	cyt	0	Cytoplasm (Potential)		602463		572
Q90635 UniProt NPD GO	DPYL2_CHICK	Dihydropyrimidinase-related protein 2 (DRP-2) (Collapsin response mediator protein CRMP-62)	0.14	-	cyt	0	Cytoplasm (Potential)				572
O02675 UniProt NPD GO	DPYL2_BOVIN	Dihydropyrimidinase-related protein 2 (DRP-2) (Neural-specific protein NSP60)	0.14	-	cyt	0	Cytoplasm (Potential)				572
P47942 UniProt NPD GO	DPYL2_RAT	Dihydropyrimidinase-related protein 2 (DRP-2) (Turned on after division, 64 kDa protein) (TOAD-64) ( ...	0.14	-	cyt	0	Membrane; peripheral membrane protein. Tightly, but noncovalently, associated with membranes	growth cone [IDA]			572
O08553 UniProt NPD GO	DPYL2_MOUSE	Dihydropyrimidinase-related protein 2 (DRP-2) (ULIP 2 protein)	0.14	-	cyt	0	Cytoplasm (Potential)	axon [IDA] cell soma [IDA] dendrite [IDA] mitochondrion [IDA]			572
Q58DK4 UniProt NPD GO	DAK_BOVIN	Dihydroxyacetone kinase (EC 2.7.1.29) (Glycerone kinase) (DHA kinase)	0.14	+	cyt	0					578
O15228 UniProt NPD GO	GNPAT_HUMAN	Dihydroxyacetone phosphate acyltransferase (EC 2.3.1.42) (DHAP-AT) (DAP-AT) (Glycerone-phosphate O-a ...	0.14	-	pox	0	Peroxisome; peroxisomal membrane; matrix side (By similarity). Exclusively localized to the lumenal ...	peroxisome [TAS]	602744		680
Q9ES71 UniProt NPD GO	GNPAT_RAT	Dihydroxyacetone phosphate acyltransferase (EC 2.3.1.42) (DHAP-AT) (DAP-AT) (Glycerone-phosphate O-a ...	0.14	-	mit	0	Peroxisome; peroxisomal membrane; matrix side (By similarity). Exclusively localized to the lumenal ...	peroxisomal membrane [TAS]			678
Q9UI17 UniProt NPD GO	M2GD_HUMAN	Dimethylglycine dehydrogenase, mitochondrial precursor (EC 1.5.99.2) (ME2GLYDH)	0.14	-	mit	0	Mitochondrion	mitochondrion [TAS]	605850		866
Q9ET22 UniProt NPD GO	DPP2_MOUSE	Dipeptidyl-peptidase 2 precursor (EC 3.4.14.2) (Dipeptidyl-peptidase II) (DPP II) (Dipeptidyl aminop ...	0.14	-	end	0	Lysosome (By similarity)				506
Q757B6 UniProt NPD GO	DPH2_ASHGO	Diphthamide biosynthesis protein 2	0.14	-	cyt	0	Cytoplasm (By similarity)				582
Q7S5C0 UniProt NPD GO	DPH2_NEUCR	Diphthamide biosynthesis protein 2	0.14	-	mit	0	Cytoplasm (By similarity)				602
P17497 UniProt NPD GO	DISI_BITAR	Disintegrin bitan (Platelet aggregation activation inhibitor) (Bitistatin) (Venom protein CM-2) (Ari ...	0.14	-	nuc	0	Secreted protein				83
P31982 UniProt NPD GO	DISI_CROCC	Disintegrin cerastin (Platelet aggregation activation inhibitor)	0.14	-	nuc	0	Secreted protein				73
P68520 UniProt NPD GO	DISI_CROAT	Disintegrin crotatroxin (Platelet aggregation activation inhibitor)	0.14	-	nuc	0	Secreted protein				72
P68521 UniProt NPD GO	DISI_CRODD	Disintegrin durissin (Platelet aggregation activation inhibitor)	0.14	-	nuc	0	Secreted protein				72
P83469 UniProt NPD GO	DISI_VIPLO	Disintegrin obustatin	0.14	-	mit	0	Secreted protein			1MPZ	41
Q805F5 UniProt NPD GO	DISA_AGKPI	Disintegrin piscivostatin alpha precursor	0.14	-	nuc	0	Secreted protein				111
P17495 UniProt NPD GO	DISB_TRIGA	Disintegrin trigramin-beta-2 (Platelet aggregation activation inhibitor) [Contains: Disintegrin trig ...	0.14	-	nuc	0	Secreted protein				73
P20048 UniProt NPD GO	SEC59_YEAST	Dolichol kinase (EC 2.7.1.108)	0.14	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane (Probable)	endoplasmic reticulum membrane [IDA]			519
P81482 UniProt NPD GO	IPSG_MARMT	Double-headed protease inhibitor, submandibular gland	0.14	-	nuc	0	Secreted protein				122
P81262 UniProt NPD GO	IPSG_UNCUN	Double-headed protease inhibitor, submandibular gland	0.14	-	nuc	0	Secreted protein				122
P08479 UniProt NPD GO	IPSG_VULVU	Double-headed protease inhibitor, submandibular gland	0.14	-	nuc	0	Secreted protein				115
P84615 UniProt NPD GO	DCAL1_DRONO	Dromaiocalcin-1 (DCA-1)	0.14	-	cyt	0	Eggshell matrix				142
P36193 UniProt NPD GO	DROS_DROME	Drosocin precursor	0.14	-	mit	1 *	Secreted protein	extracellular region [IDA]			64
Q6XMH8 UniProt NPD GO	DROS_DROSI	Drosocin precursor	0.14	-	mit	1 *	Secreted protein	extracellular region [ISS]			64
Q9QXT1 UniProt NPD GO	DAPP1_MOUSE	Dual adapter for phosphotyrosine and 3-phosphotyrosine and 3-phosphoinositide (mDAPP1) (B cell adapt ...	0.14	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Membrane-associate ...				280
Q9WVS7 UniProt NPD GO	MP2K5_MOUSE	Dual specificity mitogen-activated protein kinase kinase 5 (EC 2.7.12.2) (MAP kinase kinase 5) (MAPK ...	0.14	-	cyt	0	Cytoplasm (By similarity)	spindle [IDA]		1WI0	448
Q9UII6 UniProt NPD GO	DUS13_HUMAN	Dual specificity protein phosphatase 13 (EC 3.1.3.48) (EC 3.1.3.16) (Testis- and skeletal-muscle-spe ...	0.14	-	cyt	0					198
Q60900 UniProt NPD GO	ELAV3_MOUSE	ELAV-like protein 3 (Hu-antigen C) (HuC)	0.14	-	cyt	0				1FNX	367
Q92611 UniProt NPD GO	EDEM1_HUMAN	ER degradation-enhancing alpha-mannosidase-like 1	0.14	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (Potenti ...	integral to endoplasmic reticulum membrane [ISS]	607673		657
Q925U4 UniProt NPD GO	EDEM1_MOUSE	ER degradation-enhancing alpha-mannosidase-like 1	0.14	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (Potenti ...	integral to endoplasmic reticulum membrane [IDA]			652
Q9XZE6 UniProt NPD GO	ECLH_ROMGU	Eclosion hormone (Ecdysis activator) (EH) (Fragment)	0.14	-	nuc	0	Secreted protein (By similarity)				55
P55772 UniProt NPD GO	ENP1_MOUSE	Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) (NTPDase1) (Ecto-ATP diphosphohydrolas ...	0.14	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	basal lamina [IDA]			510
Q9MYU4 UniProt NPD GO	ENP1_PIG	Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) (NTPDase1) (Ecto-ATP diphosphohydrolas ...	0.14	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				510
Q6UWR7 UniProt NPD GO	ENPP6_HUMAN	Ectonucleotide pyrophosphatase/phosphodiesterase 6 precursor (EC 3.1.-.-) (E-NPP6) (NPP-6) [Contains ...	0.14	-	exc	0	Cell membrane; single-pass type I membrane protein (Probable). A minor secreted form also exists				440
Q9U6L5 UniProt NPD GO	PEB1_DROME	Ejaculatory bulb-specific protein 1 precursor (Ejaculatory bulb-specific protein I) (PEB-me)	0.14	-	exc	0	Secreted protein	extracellular region [IDA]			377
O88775 UniProt NPD GO	EMB_RAT	Embigin precursor	0.14	-	end	1 *	Membrane; single-pass type I membrane protein				328
P22503 UniProt NPD GO	GUN_PHAVU	Endoglucanase precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Abscission cellulase)	0.14	-	exc	0					496
P46237 UniProt NPD GO	GUNC_FUSOX	Endoglucanase type C precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase) (Endoglucanase I) ...	0.14	-	exc	0				4OVW	429
O62709 UniProt NPD GO	EDNRB_HORSE	Endothelin B receptor precursor (ET-B) (Endothelin receptor Non-selective type)	0.14	-	end	8 *	Membrane; multi-pass membrane protein				443
O97179 UniProt NPD GO	ESM6_DROME	Enhancer of split m6 protein (E(spl)m6)	0.14	-	nuc	0					70

You are viewing entries 58251 to 58300 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.