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
P12812 UniProt NPD GO	P40_SCHMA	Major egg antigen (p40)	0.19	-	cyt	0					354
Q5UJG1 UniProt NPD GO	PRIO_ANTCE	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				264
Q5UAF1 UniProt NPD GO	PRIO_BISBI	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				264
Q5UJH0 UniProt NPD GO	PRIO_BOSGA	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				264
Q5UJI7 UniProt NPD GO	PRIO_BOSIN	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				264
Q95M08 UniProt NPD GO	PRIO_BUDTA	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				256
P52113 UniProt NPD GO	PRIO_CAPHI	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor				256
P67987 UniProt NPD GO	PRIO_CEREL	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				256
P67986 UniProt NPD GO	PRIO_CEREN	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)			1XYW	256
O18754 UniProt NPD GO	PRIO_FELCA	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor			1XYJ	256
Q68G95 UniProt NPD GO	PRIO_MOSCH	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				256
P47852 UniProt NPD GO	PRIO_ODOHE	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				256
Q7JIH3 UniProt NPD GO	PRIO_OVICA	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				256
Q7JIY2 UniProt NPD GO	PRIO_OVIMO	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				256
Q7JK02 UniProt NPD GO	PRIO_OVIMU	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				256
P13852 UniProt NPD GO	PRIO_RAT	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [TAS] cell surface [TAS]			254
Q5XVM4 UniProt NPD GO	PRIO_RUPRU	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				256
Q5UJG3 UniProt NPD GO	PRIO_TRAIM	Major prion protein precursor (PrP) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				264
P10279 UniProt NPD GO	PRIO_BOVIN	Major prion protein precursor (PrP) (Major scrapie-associated fibril protein 1) (CD230 antigen)	0.19	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor			1SKH	264
P40249 UniProt NPD GO	PRIO_CEBAP	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.19	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				252
P40244 UniProt NPD GO	PRIO_MUSVI	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.19	-	nuc	2 *	Cell membrane; lipid-anchor; GPI-anchor				257
P40258 UniProt NPD GO	PRIO_SAISC	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.19	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				260
Q96AM1 UniProt NPD GO	MRGRF_HUMAN	Mas-related G-protein coupled receptor member F (Mas-related gene F protein) (G-protein coupled rece ...	0.19	-	end	6 *	Membrane; multi-pass membrane protein		607233		343
P01365 UniProt NPD GO	MTAL1_YEAST	Mating-type protein ALPHA1 (MATalpha1 protein) (Alpha-1 activator)	0.19	-	nuc	0	Nucleus (Potential)				175
O42401 UniProt NPD GO	MATN3_CHICK	Matrilin-3 precursor	0.19	-	mit	0	Secreted protein				452
O15232 UniProt NPD GO	MATN3_HUMAN	Matrilin-3 precursor	0.19	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]	608728		486
O89029 UniProt NPD GO	MATN4_MOUSE	Matrilin-4 precursor (MAT-4)	0.19	-	nuc	0	Secreted protein				624
P41242 UniProt NPD GO	MATK_MOUSE	Megakaryocyte-associated tyrosine-protein kinase (EC 2.7.10.2) (Tyrosine-protein kinase CTK) (Protei ...	0.19	+	mit	0	Cytoplasm				505
O14332 UniProt NPD GO	REM1_SCHPO	Meiosis-specific cyclin rem1	0.19	-	cyt	0					402
P50265 UniProt NPD GO	DLH1_CANAL	Meiotic recombination protein DLH1 (DMC1 homolog)	0.19	-	cyt	0	Nucleus (Potential)				324
P14700 UniProt NPD GO	MAR3_LEIMA	Membrane antigen containing repeating peptides (Clone 39) (Fragment)	0.19	-	cyt	0					53
Q9BY79 UniProt NPD GO	MFRP_HUMAN	Membrane frizzled-related protein (Membrane-type frizzled-related protein)	0.19	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)	integral to membrane [TAS]	609549		579
Q95250 UniProt NPD GO	PGRC1_PIG	Membrane-associated progesterone receptor component 1	0.19	-	nuc	1 *	Microsome; microsomal membrane; single-pass membrane protein				193
Q95KL9 UniProt NPD GO	TIMP1_MACMU	Metalloproteinase inhibitor 1 precursor (TIMP-1)	0.19	-	nuc	0	Secreted protein				207
P01033 UniProt NPD GO	TIMP1_HUMAN	Metalloproteinase inhibitor 1 precursor (TIMP-1) (Erythroid potentiating activity) (EPA) (Tissue inh ...	0.19	-	nuc	0	Secreted protein	extracellular region [NAS]	305370	1UEA	207
Q6J1T3 UniProt NPD GO	MT_SCYTO	Metallothionein (MT)	0.19	-	nuc	0					68
P07215 UniProt NPD GO	MTCU_YEAST	Metallothionein precursor (Cu-MT) (Copper chelatin)	0.19	-	nuc	0		cytosol [IDA]		1RJU	61
P02800 UniProt NPD GO	MT1A_HORSE	Metallothionein-1A (MT-1A) (Metallothionein-IA) (MT-IA)	0.19	-	nuc	0					61
P67983 UniProt NPD GO	MT1A_BOVIN	Metallothionein-1A (MT-1A) (Metallothionein-IA) (MT-IA) (MTC)	0.19	-	nuc	0					61
P67982 UniProt NPD GO	MT1A_SHEEP	Metallothionein-1A (MT-1A) (Metallothionein-IA) (MT-IA) (MTC)	0.19	-	nuc	0					61
P09578 UniProt NPD GO	MT1C_SHEEP	Metallothionein-1C (MT-1C) (Metallothionein-IC) (MT-IC)	0.19	-	nuc	0					61
P79377 UniProt NPD GO	MT1D_PIG	Metallothionein-1D (MT-1D) (Metallothionein-ID) (MT-ID)	0.19	-	nuc	0					61
P47944 UniProt NPD GO	MT4_HUMAN	Metallothionein-4 (MT-4) (Metallothionein-IV) (MT-IV)	0.19	-	nuc	0		cytoplasm [NAS]	606206		62
Q9Y3D2 UniProt NPD GO	MSRB2_HUMAN	Methionine-R-sulfoxide reductase B2 (EC 1.8.4.-)	0.19	-	nuc	0		mitochondrion [ISS]			201
P22033 UniProt NPD GO	MUTA_HUMAN	Methylmalonyl-CoA mutase, mitochondrial precursor (EC 5.4.99.2) (MCM) (Methylmalonyl-CoA isomerase)	0.19	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	609058		750
Q922T2 UniProt NPD GO	MFAP3_MOUSE	Microfibril-associated glycoprotein 3 precursor	0.19	-	end	1 *	Cell membrane; single-pass type I membrane protein (Potential)				349
Q5R9E4 UniProt NPD GO	MFAP3_PONPY	Microfibril-associated glycoprotein 3 precursor	0.19	-	mit	2 *	Cell membrane; single-pass type I membrane protein (Potential)				362
P25780 UniProt NPD GO	EURM1_EURMA	Mite group 1 allergen Eur m 1 precursor (EC 3.4.22.-) (Eur m I)	0.19	-	exc	0	Secreted protein				321
P82663 UniProt NPD GO	RT25_HUMAN	Mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25)	0.19	-	cyt	0	Mitochondrion	mitochondrial small ribosomal subunit [NAS]			173
Q5ZIJ2 UniProt NPD GO	RT06_CHICK	Mitochondrial 28S ribosomal protein S6 (S6mt) (MRP-S6)	0.19	-	nuc	0	Mitochondrion (By similarity)				120

You are viewing entries 52051 to 52100 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.