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
Q9FY42 UniProt NPD GO	HBL_MAIZE	Non-symbiotic hemoglobin (Hbm) (ZEAma GLB1)	0.02	-	cyt	0					165
Q9M593 UniProt NPD GO	HBL_ZEAMP	Non-symbiotic hemoglobin (Hbt) (ZEAmp GLB1)	0.02	-	cyt	0					165
Q9M630 UniProt NPD GO	HBL0_PHYPA	Non-symbiotic hemoglobin 0 (Non-vascular plant hemoglobin Glb0)	0.02	-	cyt	0					180
O24520 UniProt NPD GO	HBL1_ARATH	Non-symbiotic hemoglobin 1 (Hb1) (ARAth GLB1)	0.02	-	cyt	0					160
O04986 UniProt NPD GO	HBL1_ORYSA	Non-symbiotic hemoglobin 1 (rHb1) (ORYsa GLB1a)	0.02	-	cyt	0				2GNW	166
Q941P9 UniProt NPD GO	HBL2_LYCES	Non-symbiotic hemoglobin 2 (Hb2) (SOLly GLB2)	0.02	-	cyt	0					156
Q94FT8 UniProt NPD GO	HBL3_ORYSA	Non-symbiotic hemoglobin 3 (rHb3) (ORYsa GLB1c)	0.02	-	cyt	0					169
O77463 UniProt NPD GO	NTXP_TITSE	Non-toxic protein NTxP precursor (TsNTxP)	0.02	-	mit	0	Secreted protein				84
P80551 UniProt NPD GO	RNAS2_PIG	Nonsecretory ribonuclease (EC 3.1.27.5) (Eosinophil-derived neurotoxin) (Fragment)	0.02	-		0	Lysosome (Probable). Matrix of eosinophil's large specific granule				20
P83434 UniProt NPD GO	NLTP1_PHAAU	Nonspecific lipid-transfer protein 1 (LTP 1) (NS-LTP1)	0.02	-	nuc	0				1SIY	91
Q42614 UniProt NPD GO	NLTP1_BRANA	Nonspecific lipid-transfer protein 1 precursor (LTP 1)	0.02	-	nuc	0					117
P93224 UniProt NPD GO	NLTP1_LYCES	Nonspecific lipid-transfer protein 1 precursor (LTP 1)	0.02	-	cyt	0					114
Q42952 UniProt NPD GO	NLTP1_TOBAC	Nonspecific lipid-transfer protein 1 precursor (LTP 1) (Pathogenesis-related protein 14) (PR-14)	0.02	-	exc	0				1T12	114
Q42615 UniProt NPD GO	NLTP2_BRANA	Nonspecific lipid-transfer protein 2 precursor (LTP 2)	0.02	-	nuc	0					117
P27056 UniProt NPD GO	NLTP2_LYCES	Nonspecific lipid-transfer protein 2 precursor (LTP 2)	0.02	-	mit	0					114
P83210 UniProt NPD GO	NLTPX_ORYSA	Nonspecific lipid-transfer protein 2 precursor (nsLTP2) (7 kDa lipid transfer protein)	0.02	-	end	1 *				1L6H	96
Q42616 UniProt NPD GO	NLTP3_BRANA	Nonspecific lipid-transfer protein 3 precursor (LTP 3)	0.02	-	nuc	0					117
Q43019 UniProt NPD GO	NLTP3_PRUDU	Nonspecific lipid-transfer protein 3 precursor (LTP 3)	0.02	-	nuc	0					123
Q42641 UniProt NPD GO	NLTPA_BRAOT	Nonspecific lipid-transfer protein A precursor (LTP A) (Wax-associated protein 9A)	0.02	-	nuc	0					118
Q42642 UniProt NPD GO	NLTPB_BRAOT	Nonspecific lipid-transfer protein B precursor (LTP B) (Wax-associated protein 9B)	0.02	-	nuc	0					117
Q42762 UniProt NPD GO	NLTP1_GOSHI	Nonspecific lipid-transfer protein precursor (LTP)	0.02	-	exc	0					116
Q39794 UniProt NPD GO	NLTP_GERHY	Nonspecific lipid-transfer protein precursor (LTP)	0.02	-	exc	0					116
Q41073 UniProt NPD GO	NLTP_PINTA	Nonspecific lipid-transfer protein precursor (LTP)	0.02	-	mit	1 *					123
P27631 UniProt NPD GO	NLTP_DAUCA	Nonspecific lipid-transfer protein precursor (LTP) (Extracellular protein 2)	0.02	-	mit	0					120
Q43129 UniProt NPD GO	NLTP2_GOSHI	Nonspecific lipid-transfer protein precursor (LTP) (GH3)	0.02	-	exc	0					120
P48817 UniProt NPD GO	NDK_BRUMA	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.02	-	cyt	0	Cytoplasm (By similarity)				153
Q8LAH8 UniProt NPD GO	NDK4_ARATH	Nucleoside diphosphate kinase IV, chloroplast/mitochondrial precursor (EC 2.7.4.6) (NDK IV) (NDP kin ...	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen (By similarity). Mitochondrion; mitochondrial inte ...				237
Q9R060 UniProt NPD GO	NUBP1_MOUSE	Nucleotide-binding protein 1 (NBP 1)	0.02	-	cyt	0					320
Q9R061 UniProt NPD GO	NUBP2_MOUSE	Nucleotide-binding protein 2 (NBP 2)	0.02	-	cyt	0					275
Q9LHK1 UniProt NPD GO	NUD16_ARATH	Nudix hydrolase 16, mitochondrial precursor (EC 3.6.1.-) (AtNUDT16)	0.02	-	nuc	0	Mitochondrion (Potential)				180
O13326 UniProt NPD GO	CYSD_SCHPO	O-acetylhomoserine (thiol)-lyase (EC 2.5.1.49) (O-acetylhomoserine sulfhydrylase) (OAH sulfhydrylase ...	0.02	-	cyt	0					429
Q5E972 UniProt NPD GO	ORML2_BOVIN	ORM1-like protein 2	0.02	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q9CQZ0 UniProt NPD GO	ORML2_MOUSE	ORM1-like protein 2	0.02	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q53FV1 UniProt NPD GO	ORML2_HUMAN	ORM1-like protein 2 (Adoplin-2)	0.02	-	cyt	1 *	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum		610074		153
Q8N138 UniProt NPD GO	ORML3_HUMAN	ORM1-like protein 3	0.02	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum		610075		153
Q5R570 UniProt NPD GO	ORML3_PONPY	ORM1-like protein 3	0.02	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q6QI25 UniProt NPD GO	ORML3_RAT	ORM1-like protein 3 (Liver regeneration-related protein LRRGT00183)	0.02	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
P31729 UniProt NPD GO	OV16_ONCVO	OV-16 antigen precursor	0.02	-	mit	0					197
Q9Y5M6 UniProt NPD GO	TISR_HUMAN	Oculomedin (Trabecular meshwork-inducible stretch response protein) (TISR)	0.02	-	mit	1 *			604301		44
Q43284 UniProt NPD GO	OLEO3_ARATH	Oleosin 14.9 kDa	0.02	-	end	2 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface (By similarity)				141
P29526 UniProt NPD GO	OLEOC_BRANA	Oleosin C98 (Fragment)	0.02	-	end	3 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				183
Q8NGN2 UniProt NPD GO	O10S1_HUMAN	Olfactory receptor 10S1	0.02	-	end	6 *	Membrane; multi-pass membrane protein				322
Q8NGI7 UniProt NPD GO	O10V1_HUMAN	Olfactory receptor 10V1	0.02	-	end	7 *	Membrane; multi-pass membrane protein				309
Q8NGY0 UniProt NPD GO	O10X1_HUMAN	Olfactory receptor 10X1 (Olfactory receptor OR1-14)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				309
Q60894 UniProt NPD GO	OLF12_MOUSE	Olfactory receptor 12 (Odorant receptor M76)	0.02	-	end	8 *	Membrane; multi-pass membrane protein				333
Q60891 UniProt NPD GO	OL139_MOUSE	Olfactory receptor 139 (Olfactory receptor 1) (Olfactory receptor 255-2) (Odorant receptor M5)	0.02	-	end	6 *	Membrane; multi-pass membrane protein				315
Q8NGS9 UniProt NPD GO	O13C2_HUMAN	Olfactory receptor 13C2	0.02	-	end	7 *	Membrane; multi-pass membrane protein				318
Q8NGS7 UniProt NPD GO	O13C8_HUMAN	Olfactory receptor 13C8	0.02	-	end	8 *	Membrane; multi-pass membrane protein				320
Q8NGT0 UniProt NPD GO	O13C9_HUMAN	Olfactory receptor 13C9	0.02	-	end	7 *	Membrane; multi-pass membrane protein				318
Q9TU92 UniProt NPD GO	OR1A1_GORGO	Olfactory receptor 1A1	0.02	-	end	6 *	Membrane; multi-pass membrane protein				309

You are viewing entries 84651 to 84700 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.