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
Q80Z29 UniProt NPD GO	NAMPT_RAT	Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) (NAmPRTase) (Nampt) (Pre-B-cell colony-enhancin ...	0.10	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			491
O15118 UniProt NPD GO	NPC1_HUMAN	Niemann-Pick C1 protein precursor	0.10	-	end	12	Endosome; late endosome; late endosomal membrane; single-pass membrane protein. Lysosome; lysosomal ...	endoplasmic reticulum [IDA] integral to plasma membrane [IDA] lysosome [TAS] nuclear envelope [IDA] perinuclear region [IDA]	607623		1278
P56941 UniProt NPD GO	NPC1_PIG	Niemann-Pick C1 protein precursor	0.10	-	end	12	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...	endoplasmic reticulum [ISS] integral to plasma membrane [ISS] lysosome [ISS] nuclear envelope [ISS] perinuclear region [ISS]			1277
Q93W77 UniProt NPD GO	NIFU1_ARATH	NifU-like protein 1, chloroplast precursor (AtCNfu1) (AtCnfUIV-b)	0.10	-	mit	0	Plastid; chloroplast; chloroplast stroma				231
P39871 UniProt NPD GO	NIA2_MAIZE	Nitrate reductase [NAD(P)H] (EC 1.7.1.2) (NR) (Fragment)	0.10	-	cyt	0					231
P59866 UniProt NPD GO	BS10_BUTSI	Non-cysteinic peptide Bs 10 (Bs10)	0.10	-	nuc	0	Secreted protein				34
P83893 UniProt NPD GO	TX16_PHORI	Non-toxic venom protein PRTx16C0	0.10	-	nuc	0	Secreted protein				64
Q07598 UniProt NPD GO	NLTP_CHICK	Nonspecific lipid-transfer protein (EC 2.3.1.176) (Propanoyl-CoA C-acyltransferase) (NSL-TP) (Sterol ...	0.10	-	pox	0	Cytoplasm. Mitochondrion. Isoform SCP-X: Peroxisome. Cytoplasmic in the liver and also associated wi ...				547
Q9LDB4 UniProt NPD GO	NLTP6_ARATH	Nonspecific lipid-transfer protein 6 precursor (LTP 6)	0.10	-	exc	0					113
O65888 UniProt NPD GO	NLTP_STRHE	Nonspecific lipid-transfer protein precursor (LTP) (Fragment)	0.10	-	exc	0					118
P19656 UniProt NPD GO	NLTP_MAIZE	Nonspecific lipid-transfer protein precursor (LTP) (Phospholipid transfer protein) (PLTP) (Allergen ...	0.10	-	exc	1 *				1MZM	120
Q298S5 UniProt NPD GO	NDC1_DROPS	Nucleoporin Ndc1	0.10	-	end	5 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...				579
Q96DE0 UniProt NPD GO	NUD16_HUMAN	Nucleoside diphosphate-linked moiety X motif 16 (EC 3.6.1.-) (Nudix motif 16)	0.10	-	vac	0					195
Q9SZ63 UniProt NPD GO	NUD14_ARATH	Nudix hydrolase 14, mitochondrial precursor (EC 3.6.1.-) (AtNUDT14)	0.10	-	mit	0	Mitochondrion (Potential)				309
Q8L7W2 UniProt NPD GO	NUDT8_ARATH	Nudix hydrolase 8 (EC 3.6.1.-) (AtNUDT8)	0.10	-	cyt	0					369
Q27709 UniProt NPD GO	OBL_OBELO	Obelin precursor (OBL)	0.10	-	nuc	0				2F8P	195
P81924 UniProt NPD GO	OR85E_DROME	Odorant receptor 85e	0.10	-	end	4	Membrane; multi-pass membrane protein (Potential)				467
P29529 UniProt NPD GO	OLEO_HELAN	Oleosin (Fragment)	0.10	-	end	3 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				181
Q43804 UniProt NPD GO	OLEO1_PRUDU	Oleosin 1	0.10	-	end	2 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				148
Q8NGC4 UniProt NPD GO	O10G3_HUMAN	Olfactory receptor 10G3 (Olfactory receptor OR14-40)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				313
Q8NGX5 UniProt NPD GO	O10K1_HUMAN	Olfactory receptor 10K1	0.10	-	end	7 *	Membrane; multi-pass membrane protein				313
Q60895 UniProt NPD GO	OL150_MOUSE	Olfactory receptor 150 (Olfactory receptor 7I) (Olfactory receptor 171-18) (Odorant receptor M93)	0.10	-	end	8 *	Membrane; multi-pass membrane protein				312
Q9GZK4 UniProt NPD GO	OR2H1_HUMAN	Olfactory receptor 2H1 (Hs6M1-16) (Olfactory receptor 6-2) (OR6-2) (OLFR42A-9004.14/9026.2)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				316
O95918 UniProt NPD GO	OR2H2_HUMAN	Olfactory receptor 2H2 (Hs6M1-12) (Olfactory receptor-like protein FAT11)	0.10	-	end	7 *	Membrane; multi-pass membrane protein		600578		312
Q60879 UniProt NPD GO	OLF3_MOUSE	Olfactory receptor 3 (Olfactory receptor 136-14) (Odorant receptor K10)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				313
Q8NGJ8 UniProt NPD GO	O51S1_HUMAN	Olfactory receptor 51S1	0.10	-	end	7 *	Membrane; multi-pass membrane protein				323
Q8NGC0 UniProt NPD GO	O5AU1_HUMAN	Olfactory receptor 5AU1	0.10	-	end	8 *	Membrane; multi-pass membrane protein				311
Q8NGY5 UniProt NPD GO	OR6N1_HUMAN	Olfactory receptor 6N1	0.10	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NGN1 UniProt NPD GO	OR6T1_HUMAN	Olfactory receptor 6T1	0.10	-	end	7 *	Membrane; multi-pass membrane protein				323
Q98914 UniProt NPD GO	OLF9_CHICK	Olfactory receptor-like protein COR9 (Fragment)	0.10	-	nuc	2 *	Membrane; multi-pass membrane protein				131
P46059 UniProt NPD GO	S15A1_HUMAN	Oligopeptide transporter, small intestine isoform (Peptide transporter 1) (Intestinal H(+)/peptide c ...	0.10	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	600544		708
Q9JIP7 UniProt NPD GO	S15A1_MOUSE	Oligopeptide transporter, small intestine isoform (Peptide transporter 1) (Intestinal H(+)/peptide c ...	0.10	-	end	9 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			709
P38206 UniProt NPD GO	RFT1_YEAST	Oligosaccharide translocation protein RFT1 (Requiring fifty-three protein 1)	0.10	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA]			574
P81599 UniProt NPD GO	TOT1F_HADVE	Omega-atracotoxin-Hv1f (Omega-AcTx-Hv1f)	0.10	-	nuc	0	Secreted protein				37
P81790 UniProt NPD GO	TOP2A_PHONI	Omega-phonetoxin-2A (Omega-phonetoxin-IIA) (Omega-Ptx-IIA) (Neurotoxin Tx3-4)	0.10	-	nuc	0	Secreted protein				76
O35508 UniProt NPD GO	ONCO_CAVPO	Oncomodulin (OM) (Parvalbumin beta) (CBP-15)	0.10	-	cyt	0					108
O76082 UniProt NPD GO	S22A5_HUMAN	Organic cation/carnitine transporter 2 (Solute carrier family 22 member 5) (High-affinity sodium-dep ...	0.10	-	end	12 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]	603377		557
Q00291 UniProt NPD GO	OTC_ASPTE	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.10	-	mit	0	Mitochondrion; mitochondrial matrix				361
Q5J2D0 UniProt NPD GO	PYRF_ASPAW	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.10	-	mit	0					277
P21593 UniProt NPD GO	PYRF_PHYBL	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.10	-	cyt	0					267
Q9UVZ5 UniProt NPD GO	PYRF_SACFI	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.10	-	nuc	0					265
P50701 UniProt NPD GO	OS13_SOLCO	Osmotin-like protein OSML13 precursor (PA13)	0.10	-	exc	1 *					246
P39056 UniProt NPD GO	OSTC_RABIT	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.10	-	nuc	0	Secreted protein				49
P04640 UniProt NPD GO	OSTC_RAT	Osteocalcin precursor (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.10	-	exc	0	Secreted protein	extracellular region [ISS]			99
Q92882 UniProt NPD GO	OSTF1_HUMAN	Osteoclast-stimulating factor 1	0.10	-	cyt	0	Cytoplasm (Probable)	intracellular [TAS]		1ZLM	214
Q8MJ49 UniProt NPD GO	OSTF1_PIG	Osteoclast-stimulating factor 1	0.10	-	cyt	0	Cytoplasm (By similarity)				214
Q7ZYG4 UniProt NPD GO	OSTF1_XENLA	Osteoclast-stimulating factor 1	0.10	-	cyt	0	Cytoplasm (By similarity)				214
P42057 UniProt NPD GO	VDAC_MAIZE	Outer plastidial membrane protein porin (Voltage-dependent anion-selective channel protein) (VDAC)	0.10	-	cyt	0	Plastid; plastid outer membrane. Found in non-photosynthetic root plastids only				277
O49344 UniProt NPD GO	PSBP2_ARATH	Oxygen-evolving enhancer protein 2-2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolvin ...	0.10	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				265
Q28756 UniProt NPD GO	OXYR_SHEEP	Oxytocin receptor (OT-R)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				391

You are viewing entries 64851 to 64900 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.