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
P50543 UniProt NPD GO	S10AB_MOUSE	Protein S100-A11 (S100 calcium-binding protein A11) (Protein S100C) (Calgizzarin) (Endothelial monoc ...	0.16	-	nuc	0		cytoplasm [IDA]			98
P53538 UniProt NPD GO	SSU72_YEAST	Protein SSU72	0.16	-	nuc	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI] nucleus [IGI]			206
Q08553 UniProt NPD GO	SYC1_YEAST	Protein SYC1	0.16	-	nuc	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI] nucleus [IDA]			188
Q84Q83 UniProt NPD GO	TOC75_ORYSA	Protein TOC75, chloroplast precursor (75 kDa translocon at the outer-envelope-membrane of chloroplas ...	0.16	-	end	0	Plastid; chloroplast; chloroplast outer membrane; multi-pass membrane protein (Probable)				817
Q5XJP1 UniProt NPD GO	TSSC1_BRARE	Protein TSSC1	0.16	-	nuc	0					387
Q6DUZ9 UniProt NPD GO	TSSC1_GECJA	Protein TSSC1	0.16	-	cyt	0					387
Q4R571 UniProt NPD GO	TSSC1_MACFA	Protein TSSC1	0.16	-	nuc	0					387
Q8NJR2 UniProt NPD GO	URE2_ASHGO	Protein URE2	0.16	-	cyt	0					354
Q8IUB3 UniProt NPD GO	WF10B_HUMAN	Protein WFDC10B precursor	0.16	-	exc	1 *	Secreted protein (Potential)				73
P49893 UniProt NPD GO	WNT11_XENLA	Protein Wnt-11 precursor (XWnt-11)	0.16	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix				353
Q2IBF4 UniProt NPD GO	WNT2_GORGO	Protein Wnt-2 precursor	0.16	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
Q2QLE7 UniProt NPD GO	WNT2_PANTR	Protein Wnt-2 precursor	0.16	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
Q2IBE2 UniProt NPD GO	WNT2_PONPY	Protein Wnt-2 precursor	0.16	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
P09544 UniProt NPD GO	WNT2_HUMAN	Protein Wnt-2 precursor (IRP protein) (Int-1-related protein)	0.16	-	mit	0	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]	147870		360
P28142 UniProt NPD GO	WNT3A_SCEOC	Protein Wnt-3a (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P28126 UniProt NPD GO	WNT3B_MELGA	Protein Wnt-3b (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P28134 UniProt NPD GO	WNT3B_PLEJO	Protein Wnt-3b (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P28109 UniProt NPD GO	WNT5A_CHECA	Protein Wnt-5a (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
P28145 UniProt NPD GO	WNT6_THUTH	Protein Wnt-6 (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				117
P28111 UniProt NPD GO	WNT7B_CHECA	Protein Wnt-7b (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P28130 UniProt NPD GO	WNT7B_MELGA	Protein Wnt-7b (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P28093 UniProt NPD GO	WNT8_EVATR	Protein Wnt-8 (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				128
P78963 UniProt NPD GO	SKB1_SCHPO	Protein arginine N-methyltransferase skb1 (EC 2.1.1.-) (Shk1 kinase-binding protein 1)	0.16	-	cyt	0	Localizes to cell ends, sites of septation, and nuclei	cell tip [IDA] nucleus [IDA]			645
Q9LX33 UniProt NPD GO	PFTA_ARATH	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.16	-	cyt	0					340
Q01790 UniProt NPD GO	HUNB_SCICO	Protein hunchback (Fragment)	0.16	-	nuc	0	Nucleus (Probable)				50
P17252 UniProt NPD GO	KPCA_HUMAN	Protein kinase C alpha type (EC 2.7.11.13) (PKC-alpha) (PKC-A)	0.16	-	cyt	0		membrane fraction [TAS]	176960		671
P05126 UniProt NPD GO	KPCB_BOVIN	Protein kinase C beta type (EC 2.7.11.13) (PKC-beta) (PKC-B)	0.16	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				672
Q5PU49 UniProt NPD GO	KPCD_CANFA	Protein kinase C delta type (EC 2.7.11.13) (nPKC-delta)	0.16	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				674
Q98864 UniProt NPD GO	PTC1_BRARE	Protein patched homolog 1 (Patched 1) (PTC1)	0.16	-	end	11	Membrane; multi-pass membrane protein				1220
Q5BB40 UniProt NPD GO	PBN1_EMENI	Protein pbn1	0.16	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				440
Q10133 UniProt NPD GO	RHO2_SCHPO	Protein rho2	0.16	-	cyt	0	Cell membrane; lipid-anchor. Found at the growing tips of interphase cells and at the septum prior t ...	cell tip [IDA] medial ring [IDA]			200
Q00991 UniProt NPD GO	PAR1_CRILO	Proteinase-activated receptor 1 precursor (PAR-1) (Thrombin receptor)	0.16	-	end	7	Membrane; multi-pass membrane protein				428
P25116 UniProt NPD GO	PAR1_HUMAN	Proteinase-activated receptor 1 precursor (PAR-1) (Thrombin receptor) (Coagulation factor II recepto ...	0.16	-	end	7	Membrane; multi-pass membrane protein	Golgi apparatus [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	187930	1NRR	425
P14234 UniProt NPD GO	FGR_MOUSE	Proto-oncogene tyrosine-protein kinase FGR (EC 2.7.10.2) (P55-FGR) (C-FGR)	0.16	-	nuc	0					517
Q95KR7 UniProt NPD GO	LCK_SAISC	Proto-oncogene tyrosine-protein kinase LCK (EC 2.7.10.2) (p56-LCK) (Lymphocyte cell-specific protein ...	0.16	-	cyt	0	Cytoplasm (By similarity). Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Present in ...	lipid raft [ISS] pericentriolar material [ISS] plasma membrane [ISS]			508
P06239 UniProt NPD GO	LCK_HUMAN	Proto-oncogene tyrosine-protein kinase LCK (EC 2.7.10.2) (p56-LCK) (Lymphocyte cell-specific protein ...	0.16	-	cyt	0	Cytoplasm. Cell membrane; lipid-anchor; cytoplasmic side. Present in lipid rafts in an unactive form ...	lipid raft [IDA] pericentriolar material [IDA] plasma membrane [NAS]	153390	3LCK	508
Q9UN67 UniProt NPD GO	PCDBA_HUMAN	Protocadherin beta 10 precursor (PCDH-beta10)	0.16	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS]	606336		800
Q5DRD0 UniProt NPD GO	PCDB4_PANTR	Protocadherin beta 4 precursor (PCDH-beta4)	0.16	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				795
Q5DRA4 UniProt NPD GO	PCDGK_PANTR	Protocadherin gamma C3 precursor (PCDH-gamma-C3)	0.16	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				934
Q9UN70 UniProt NPD GO	PCDGK_HUMAN	Protocadherin gamma C3 precursor (PCDH-gamma-C3) (Protocadherin 43) (PC-43) (Protocadherin 2)	0.16	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	membrane [NAS]	604968		934
Q93841 UniProt NPD GO	PLC1_CAEEL	Putative 1-acyl-sn-glycerol-3-phosphate acyltransferase acl-1 (EC 2.3.1.51) (1-AGP acyltransferase) ...	0.16	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				262
Q9FK53 UniProt NPD GO	NLAL2_ARATH	Putative H/ACA ribonucleoprotein complex subunit 1-like protein 2	0.16	+	nuc	0	Nucleus; nucleolus (By similarity)	thylakoid membrane (sensu Viridiplantae) [IDA]			189
P38626 UniProt NPD GO	NCB5R_YEAST	Putative NADH-cytochrome b5 reductase (EC 1.6.2.2) (P35)	0.16	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)	microsome [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			322
Q9VCG3 UniProt NPD GO	OPA32_DROME	Putative OPA3-like protein CG13603	0.16	-	mit	0					255
P15718 UniProt NPD GO	POLB_MAIZE	Putative Pol polyprotein from transposon element Bs1 (ORF 1)	0.16	-	end	2					740
Q9FL42 UniProt NPD GO	ATL5E_ARATH	Putative RING-H2 finger protein ATL5E	0.16	-	nuc	1 *					159
Q9SUN3 UniProt NPD GO	ARAE3_ARATH	Putative UDP-arabinose 4-epimerase 3 (EC 5.1.3.5) (UDP-D-xylose 4-epimerase 3)	0.16	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Potential) ...				411
Q9ZQP2 UniProt NPD GO	ACO12_ARATH	Putative acyl-coenzyme A oxidase 1.2, peroxisomal (EC 1.3.3.6)	0.16	-	pox	0	Peroxisome (Probable)				664
Q11068 UniProt NPD GO	MGAT1_CAEEL	Putative alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.101) (N-gl ...	0.16	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				449
Q8L936 UniProt NPD GO	CAP16_ARATH	Putative clathrin assembly protein At4g40080	0.16	-	nuc	0					365

You are viewing entries 56151 to 56200 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.