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
Q86QU4 UniProt NPD GO	KGX49_CENSC	Potassium channel toxin gamma-KTx 4.9 (Ergtoxin-like protein 3) (ErgTx3) (CsErg3) (CsErgTx3)	0.10	-	nuc	0	Secreted protein				43
P82850 UniProt NPD GO	KKX11_HETFU	Potassium channel toxin kappa-KTx 1.1 (Kappa-hefutoxin-1) (Kappa-HfTx1)	0.10	-	nuc	0	Secreted protein			1HP9	22
P82851 UniProt NPD GO	KKX12_HETFU	Potassium channel toxin kappa-KTx 1.2 (Kappa-hefutoxin-2) (Kappa-HfTx2)	0.10	-	nuc	0	Secreted protein				23
Q9Y6H6 UniProt NPD GO	KCNE3_HUMAN	Potassium voltage-gated channel subfamily E member 3 (Minimum potassium ion channel-related peptide ...	0.10	-	nuc	1	Membrane; single-pass type I membrane protein		604433		103
Q9WTW2 UniProt NPD GO	KCNE3_MOUSE	Potassium voltage-gated channel subfamily E member 3 (Minimum potassium ion channel-related peptide ...	0.10	-	nuc	1	Membrane; single-pass type I membrane protein				103
P18597 UniProt NPD GO	ATP4B_RABIT	Potassium-transporting ATPase subunit beta (Proton pump beta chain) (Gastric H(+)/K(+) ATPase beta s ...	0.10	-	mit	1 *	Membrane; single-pass type II membrane protein				291
Q8ITY4 UniProt NPD GO	PM14_CAEEL	Pre-mRNA branch site p14-like protein	0.10	-	cyt	0	Nucleus (Potential)				138
P83203 UniProt NPD GO	PAG57_SHEEP	Pregnancy-associated glycoprotein 57 (EC 3.4.23.-) (ovPAG-57) (Fragment)	0.10	-		0	Secreted protein				20
Q6BKZ1 UniProt NPD GO	PAM17_DEBHA	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.10	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				177
Q02465 UniProt NPD GO	DD31_DICDI	Prespore protein Dd31	0.10	-	end	4	Associated with the inner face of spore coat				269
P12729 UniProt NPD GO	PSA_DICDI	Prespore-specific cell surface antigen PsA precursor (D19 protein)	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				168
P69155 UniProt NPD GO	MCH2_ONCKE	Pro-MCH 2 precursor [Contains: Neuropeptide-glutamic acid-valine (NEV) (Neuropeptide E-V); Melanin-c ...	0.10	-	exc	1 *					132
P69157 UniProt NPD GO	MCH2_ONCMY	Pro-MCH 2 precursor [Contains: Neuropeptide-glutamic acid-valine (NEV) (Neuropeptide E-V); Melanin-c ...	0.10	-	exc	1 *					132
P69156 UniProt NPD GO	MCH2_ONCTS	Pro-MCH 2 precursor [Contains: Neuropeptide-glutamic acid-valine (NEV) (Neuropeptide E-V); Melanin-c ...	0.10	-	exc	1 *					132
Q03677 UniProt NPD GO	MTND_YEAST	Probable 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-)	0.10	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Nucleus	cytoplasm [IDA] nucleus [IDA]			179
P34439 UniProt NPD GO	HCDH1_CAEEL	Probable 3-hydroxyacyl-CoA dehydrogenase F54C8.1 (EC 1.1.1.35)	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				298
P48334 UniProt NPD GO	YCXD_CYAPA	Probable ABC transporter ATP-binding protein in ycf23-apcF intergenic region (ORF244)	0.10	-	cyt	0	Plastid; cyanelle				244
Q9ZPX1 UniProt NPD GO	ARF5_ARATH	Probable ADP-ribosylation factor At2g18390	0.10	-	nuc	0					185
Q9XVH6 UniProt NPD GO	RPO2J_CAEEL	Probable DNA-directed RNA polymerase II subunit J (EC 2.7.7.6)	0.10	-	cyt	0	Nucleus (By similarity)				122
Q4YZZ7 UniProt NPD GO	RPO2J_PLABA	Probable DNA-directed RNA polymerase II subunit J (EC 2.7.7.6)	0.10	-	nuc	0	Nucleus (By similarity)				126
Q8TDV0 UniProt NPD GO	GP151_HUMAN	Probable G-protein coupled receptor 151 (G-protein coupled receptor PGR7) (GPCR-2037)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				419
Q7TSN6 UniProt NPD GO	GP151_MOUSE	Probable G-protein coupled receptor 151 protein (G-protein coupled receptor PGR7) (GPCR-2037)	0.10	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				422
Q9I918 UniProt NPD GO	GP173_BRARE	Probable G-protein coupled receptor 173 (Super conserved receptor expressed in brain 3)	0.10	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				387
Q9BXC1 UniProt NPD GO	GP174_HUMAN	Probable G-protein coupled receptor 174	0.10	-	end	7 *	Membrane; multi-pass membrane protein				333
O00155 UniProt NPD GO	GPR25_HUMAN	Probable G-protein coupled receptor 25	0.10	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602174		361
Q9BZJ7 UniProt NPD GO	GPR62_HUMAN	Probable G-protein coupled receptor 62 (hGPCR8)	0.10	-	end	5 *	Membrane; multi-pass membrane protein		606917		368
Q9W0R5 UniProt NPD GO	MTH10_DROME	Probable G-protein coupled receptor Mth-like 10 precursor (Protein methuselah-like 10)	0.10	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				575
P83119 UniProt NPD GO	MTH12_DROME	Probable G-protein coupled receptor Mth-like 12 precursor (Protein methuselah-like 12)	0.10	-	end	7	Membrane; multi-pass membrane protein (Potential)				488
Q9V818 UniProt NPD GO	MTH3_DROME	Probable G-protein coupled receptor Mth-like 3 precursor (Protein methuselah-like 3)	0.10	-	end	7	Membrane; multi-pass membrane protein (Potential)				511
Q9M9M9 UniProt NPD GO	NDUAC_ARATH	Probable NADH-ubiquinone oxidoreductase subunit B17.2 (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-B17.2) ( ...	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				159
Q941Y8 UniProt NPD GO	NQR2_ORYSA	Probable NADPH:quinone oxidoreductase 2 (EC 1.6.5.2)	0.10	-	nuc	0					203
O59819 UniProt NPD GO	UGPA2_SCHPO	Probable UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) ( ...	0.10	-	mit	0					499
O74548 UniProt NPD GO	ARGD_SCHPO	Probable acetylornithine aminotransferase, mitochondrial precursor (EC 2.6.1.11) (ACOAT)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				441
Q9NHD5 UniProt NPD GO	SAN_DROME	Probable acetyltransferase san (EC 2.3.1.-) (Protein separation anxiety)	0.10	-	cyt	0	Cytoplasm. During interphase, it localizes to the cytoplasm. During the entry into mitosis, it becom ...	cohesin core heterodimer [IDA] cytoplasm [IDA] protein acetyltransferase complex [IPI]			184
P34455 UniProt NPD GO	ACON_CAEEL	Probable aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase) ...	0.10	-	mit	0	Mitochondrion (By similarity)				777
O42918 UniProt NPD GO	AMY2_SCHPO	Probable alpha-amylase meu7 precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Meiotic ex ...	0.10	-	exc	0					774
Q93324 UniProt NPD GO	MANBA_CAEEL	Probable beta-mannosidase precursor (EC 3.2.1.25) (Mannanase) (Mannase)	0.10	-	end	0	Lysosome (Potential)				900
Q23924 UniProt NPD GO	COPB_DICDI	Probable coatomer subunit beta (Beta-coat protein) (Beta-COP) (Fragment)	0.10	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				400
Q9UTH2 UniProt NPD GO	ETFB_SCHPO	Probable electron transfer flavoprotein subunit beta (Beta-ETF)	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				254
P19439 UniProt NPD GO	GLRK_CHICK	Probable glutamate receptor precursor (Kainate-binding protein)	0.10	-	end	3	Membrane; multi-pass membrane protein				487
P91252 UniProt NPD GO	GST6_CAEEL	Probable glutathione S-transferase 6 (EC 2.5.1.18) (GST class-sigma)	0.10	-	cyt	0					206
P50472 UniProt NPD GO	GSTX2_MAIZE	Probable glutathione S-transferase BZ2 (EC 2.5.1.18) (Protein bronze-2)	0.10	-	cyt	0					236
Q8J0P4 UniProt NPD GO	CRF1_ASPFU	Probable glycosidase crf1 precursor (EC 3.2.-.-) (Crh-like protein 1) (Allergen Asp f 9)	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				395
Q9FWA4 UniProt NPD GO	GLTR_ARATH	Probable glycosyltransferase At3g02350 (EC 2.4.1.-)	0.10	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				561
Q8S857 UniProt NPD GO	H2AV2_ORYSA	Probable histone H2A variant 2	0.10	-	mit	0	Nucleus (By similarity)				139
Q84MP7 UniProt NPD GO	H2AV3_ORYSA	Probable histone H2A variant 3	0.10	-	nuc	0	Nucleus (By similarity)				137
Q9LHQ5 UniProt NPD GO	H2A2_ARATH	Probable histone H2A.2 (HTA13)	0.10	-	nuc	0	Nucleus (By similarity)				132
O81826 UniProt NPD GO	H2A3_ARATH	Probable histone H2A.3 (HTA2)	0.10	-	nuc	0	Nucleus (By similarity)				131
Q2QS71 UniProt NPD GO	H2A7_ORYSA	Probable histone H2A.7	0.10	-	cyt	0	Nucleus (By similarity)				135
O94671 UniProt NPD GO	DHOM_SCHPO	Probable homoserine dehydrogenase (EC 1.1.1.3) (HDH)	0.10	-	cyt	1					376

You are viewing entries 65001 to 65050 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.