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
Q93W20 UniProt NPD GO	NIFU2_ARATH	NifU-like protein 2, chloroplast precursor (AtCNfu2) (AtCnfU-V)	0.13	-	mit	0	Plastid; chloroplast; chloroplast stroma				235
P11035 UniProt NPD GO	NIA2_ARATH	Nitrate reductase [NADH] 2 (EC 1.7.1.1) (NR2)	0.13	-	nuc	0					917
P39867 UniProt NPD GO	NIA1_BRANA	Nitrate reductase [NADH], clone PBNBR1405 (EC 1.7.1.1) (NR)	0.13	-	nuc	0					911
P32961 UniProt NPD GO	NRL1_ARATH	Nitrilase 1 (EC 3.5.5.1)	0.13	-	cyt	0					346
Q7TQ94 UniProt NPD GO	NIT1_RAT	Nitrilase homolog 1 (EC 3.5.-.-)	0.13	-	cyt	0					292
Q5NE24 UniProt NPD GO	NSP2_MEDTR	Nodulation signaling pathway 2 protein	0.13	-	cyt	0	Nucleus; nuclear membrane. Mainly localized to the nuclear envelope. Endoplasmic reticulum. Also fou ...				508
P08960 UniProt NPD GO	NO20_SOYBN	Nodulin 20 precursor (N-20)	0.13	-	exc	0	Peribacteroid membrane or peribacteroid space (Potential)				185
Q42978 UniProt NPD GO	NLTP2_ORYSA	Nonspecific lipid-transfer protein 2 precursor (LTP 2)	0.13	-	exc	1 *					118
Q42976 UniProt NPD GO	NLTP3_ORYSA	Nonspecific lipid-transfer protein 3 precursor (LTP 3)	0.13	-	exc	0					121
P53060 UniProt NPD GO	YGZA_YEAST	Nuclear protein YGL250W	0.13	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			241
P53370 UniProt NPD GO	NUDT6_HUMAN	Nucleoside diphosphate-linked moiety X motif 6 (Nudix motif 6) (Protein GFG) (GFG-1) (Antisense basi ...	0.13	-	mit	0			606261		316
O22951 UniProt NPD GO	NUD22_ARATH	Nudix hydrolase 22, chloroplast precursor (EC 3.6.1.-) (AtNUDT22)	0.13	-	nuc	0	Plastid; chloroplast (Potential)				302
Q8WTE7 UniProt NPD GO	OR1_ANOGA	Odorant receptor Or1 (AgOr1)	0.13	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			417
Q60890 UniProt NPD GO	OLF11_MOUSE	Olfactory receptor 11 (Olfactory receptor 256-11) (Odorant receptor M49)	0.13	+	end	7 *	Membrane; multi-pass membrane protein				313
Q8NGG0 UniProt NPD GO	OR8J3_HUMAN	Olfactory receptor 8J3	0.13	-	end	7 *	Membrane; multi-pass membrane protein				315
Q8WMX5 UniProt NPD GO	S15A1_CANFA	Oligopeptide transporter, small intestine isoform (Peptide transporter 1) (Intestinal H(+)/peptide c ...	0.13	-	end	12 *	Membrane; multi-pass membrane protein				708
P36836 UniProt NPD GO	S15A1_RABIT	Oligopeptide transporter, small intestine isoform (Peptide transporter 1) (Intestinal H(+)/peptide c ...	0.13	-	end	11 *	Membrane; multi-pass membrane protein				707
Q6C6S3 UniProt NPD GO	RFT1_YARLI	Oligosaccharide translocation protein RFT1	0.13	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				673
Q39287 UniProt NPD GO	FAD6E_BRAJU	Omega-6 fatty acid desaturase, endoplasmic reticulum (EC 1.14.19.-) (Delta-12 desaturase)	0.13	-	mit	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				384
P30288 UniProt NPD GO	TOG4A_AGEAP	Omega-agatoxin-4A (Omega-agatoxin IVA) (Omega-Aga-IVA)	0.13	-	nuc	0	Secreted protein			1OAW	48
P05485 UniProt NPD GO	CXO7B_CONMA	Omega-conotoxin MVIIb (SNX-159)	0.13	-	nuc	0	Secreted protein				25
P05150 UniProt NPD GO	OTC_YEAST	Ornithine carbamoyltransferase (EC 2.1.3.3) (OTCase) (Ornithine transcarbamylase)	0.13	-	cyt	0	Cytoplasm	cytosol [IDA]			338
Q751H1 UniProt NPD GO	OAZ_ASHGO	Ornithine decarboxylase antizyme	0.13	-	cyt	0					254
Q9HF68 UniProt NPD GO	PYRF_SOLCC	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.13	-	nuc	0					280
Q12709 UniProt NPD GO	PYRF_TRIAT	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.13	-	mit	0					379
Q62422 UniProt NPD GO	OSTF1_MOUSE	Osteoclast-stimulating factor 1 (SH3 domain protein 3)	0.13	-	cyt	0	Cytoplasm (Probable)				215
Q28990 UniProt NPD GO	OVGP1_PIG	Oviduct-specific glycoprotein precursor (Oviductal glycoprotein) (Oviductin) (Estrogen-dependent ovi ...	0.13	-	cyt	0	Secretory granules				527
Q6GUG4 UniProt NPD GO	P2Y13_RAT	P2Y purinoceptor 13 (P2Y13)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				336
Q2VL57 UniProt NPD GO	PAX9_LEORO	Paired box protein Pax-9	0.13	-	nuc	0	Nucleus				341
Q2L4T2 UniProt NPD GO	PAX9_RAT	Paired box protein Pax-9	0.13	-	nuc	0	Nucleus				342
Q2VL56 UniProt NPD GO	PAX9_SAGOE	Paired box protein Pax-9	0.13	-	nuc	0	Nucleus				341
Q2VL60 UniProt NPD GO	PAX9_SAIBB	Paired box protein Pax-9	0.13	-	nuc	0	Nucleus				341
Q06551 UniProt NPD GO	ERFB_YEAST	Palmitoyltransferase ERF2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein ERF2) (Ras prot ...	0.13	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA] palmitoyltransferase complex [IPI]			359
Q80TN5 UniProt NPD GO	ZDH17_MOUSE	Palmitoyltransferase ZDHHC17 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 17) (DHHC-17) ...	0.13	-	end	6	Golgi apparatus; Golgi membrane; multi-pass membrane protein (Potential). Cytoplasmic vesicle; cytop ...				632
Q8IUH5 UniProt NPD GO	ZDH17_HUMAN	Palmitoyltransferase ZDHHC17 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 17) (DHHC-17) ...	0.13	-	end	6	Golgi apparatus; Golgi membrane; multi-pass membrane protein (Potential). Cytoplasmic vesicle; cytop ...		607799		632
P00974 UniProt NPD GO	BPT1_BOVIN	Pancreatic trypsin inhibitor precursor (Basic protease inhibitor) (BPI) (BPTI) (Aprotinin)	0.13	-	exc	0	Secreted protein			9PTI	100
Q09673 UniProt NPD GO	PANC_SCHPO	Pantoate--beta-alanine ligase (EC 6.3.2.1) (Pantothenate synthetase) (Pantoate-activating enzyme)	0.13	-	cyt	0					283
P04089 UniProt NPD GO	PTHY_RAT	Parathyroid hormone precursor (Parathyrin) (PTH)	0.13	-	end	0	Secreted protein				115
P25107 UniProt NPD GO	PTHR1_DIDMA	Parathyroid hormone/parathyroid hormone-related peptide receptor precursor (PTH/PTHr receptor) (PTH/ ...	0.13	-	end	7	Membrane; multi-pass membrane protein				585
P11768 UniProt NPD GO	PAT3_SOLTU	Patatin class 1 precursor (Patatin class I) (Potato tuber protein)	0.13	-	exc	0					386
P32045 UniProt NPD GO	PRP2_LYCES	Pathogenesis-related protein P2 precursor	0.13	-	mit	1 *					143
P07052 UniProt NPD GO	PRR2_TOBAC	Pathogenesis-related protein R minor form precursor (PR-R) (PROB12) (Thaumatin-like protein E2)	0.13	-	exc	0	Vacuole				226
Q9NB04 UniProt NPD GO	PATJ_DROME	Patj homolog	0.13	-	cyt	0	Membrane-associated. Localizes to the subapical domain of cells. Sdt is required for its localizatio ...	apical cortex [NAS] apical plasma membrane [IDA] cytoplasm [TAS] nuclear envelope [NAS] plasma membrane [NAS] subapical complex [TAS]			871
P00792 UniProt NPD GO	PEPA_BOVIN	Pepsin A precursor (EC 3.4.23.1)	0.13	-	cyt	0	Secreted protein				372
P27678 UniProt NPD GO	PEPA4_MACFU	Pepsin A-4 precursor (EC 3.4.23.1) (Pepsin I/II)	0.13	-	exc	0	Secreted protein				388
P29206 UniProt NPD GO	PYY_RAJRH	Peptide YY-like (PYY)	0.13	-	nuc	0	Secreted protein				36
P46030 UniProt NPD GO	PTR2_CANAL	Peptide transporter PTR2	0.13	-	end	12	Membrane; multi-pass membrane protein				623
P10731 UniProt NPD GO	AMD_BOVIN	Peptidyl-glycine alpha-amidating monooxygenase precursor (EC 1.14.17.3) (PAM)	0.13	-	end	1	Secretory granules				972
Q26612 UniProt NPD GO	PER_SYRPI	Period circadian protein (Fragment)	0.13	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				109
O23474 UniProt NPD GO	PER40_ARATH	Peroxidase 40 precursor (EC 1.11.1.7) (Atperox P40)	0.13	-	exc	0	Secreted protein (By similarity)				348

You are viewing entries 60101 to 60150 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.