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
P97594 UniProt NPD GO	MCPT8_RAT	Mast cell protease 8 precursor (EC 3.4.21.-) (Mast cell protease VIII) (rMCP-VIII) (rMCP-8)	0.00	-	end	0	Secretory granules				248
P17238 UniProt NPD GO	MAST_VESOR	Mastoparan (Histamine-releasing peptide I) (HR-I)	0.00	-		0	Secreted protein				14
P69034 UniProt NPD GO	MAST1_PROEX	Mastoparan-1 (Mastoparan I) (MP-I)	0.00	-		0	Secreted protein				14
P69036 UniProt NPD GO	MAST3_PROEX	Mastoparan-3 (Mastoparan III) (MP-III)	0.00	-		0	Secreted protein				14
P21654 UniProt NPD GO	MAST_VESBA	Mastoparan-B	0.00	-		0	Secreted protein				14
P01516 UniProt NPD GO	MAST_VESCR	Mastoparan-C	0.00	-		0	Secreted protein				14
P01514 UniProt NPD GO	MAST_VESLE	Mastoparan-L	0.00	-		0	Secreted protein			1D7N	14
P04205 UniProt NPD GO	MAST_VESMA	Mastoparan-M (Mast cell-degranulating peptide)	0.00	-		0	Secreted protein				14
P0C1Q7 UniProt NPD GO	MAST_VESTR	Mastoparan-T	0.00	-		0	Secreted protein				14
P58547 UniProt NPD GO	MER23_EUPRA	Mating pheromone Er-23 (Euplomone R23)	0.00	-	nuc	0	Secreted protein			1HA8	51
Q02594 UniProt NPD GO	BAP13_SCHCO	Mating-type pheromone BAP1(3) precursor	0.00	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				50
P78743 UniProt NPD GO	BB12_SCHCO	Mating-type pheromone BBP1(2) precursor	0.00	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				65
P80728 UniProt NPD GO	MAVI_CUCPE	Mavicyanin	0.00	-	nuc	0				1WS8	108
P83086 UniProt NPD GO	MHT_BOMMX	Maximin-Ht (Maximin-7)	0.00	-		0	Secreted protein				20
P83087 UniProt NPD GO	MHU_BOMMX	Maximin-Hu (Maximin-8)	0.00	-		0	Secreted protein				20
Q09150 UniProt NPD GO	REC14_SCHPO	Meiotic recombination protein rec14	0.00	-	cyt	0					302
P33033 UniProt NPD GO	MC3R_MOUSE	Melanocortin receptor 3 (MC3-R)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				323
Q61865 UniProt NPD GO	MIA_MOUSE	Melanoma-derived growth regulatory protein precursor (Melanoma inhibitory activity) (Cartilage-deriv ...	0.00	-	exc	0	Secreted protein	extracellular region [TAS]			130
Q62946 UniProt NPD GO	MIA_RAT	Melanoma-derived growth regulatory protein precursor (Melanoma inhibitory activity) (Cartilage-deriv ...	0.00	-	exc	0	Secreted protein				130
Q62953 UniProt NPD GO	MTR1L_RAT	Melatonin-related receptor (G protein-coupled receptor 50) (H9) (Fragment)	0.00	-	end	2 *	Membrane; multi-pass membrane protein				119
P21376 UniProt NPD GO	MELG_MELGA	Meleagrin	0.00	-	nuc	0					40
P56924 UniProt NPD GO	MLP_RANTE	Melittin-like peptide (MLP)	0.00	-	mit	0	Secreted protein				22
P11022 UniProt NPD GO	P8A7_DICDI	Membrane protein P8A7	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				138
Q12116 UniProt NPD GO	TMS1_YEAST	Membrane protein TMS1	0.00	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)	vacuolar membrane [IDA]			473
Q96PG1 UniProt NPD GO	M4A4E_HUMAN	Membrane-spanning 4-domains subfamily A member 4E (Fragment)	0.00	-	mit	0	Membrane; multi-pass membrane protein (By similarity)		608401		34
P38636 UniProt NPD GO	ATX1_YEAST	Metal homeostasis factor ATX1	0.00	-	cyt	0	Cytoplasm	cytosol [IDA]		1FES	73
P26652 UniProt NPD GO	TIMP3_CHICK	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3) (21 kDa ...	0.00	-	vac	0	Secreted protein; extracellular space; extracellular matrix				212
P26571 UniProt NPD GO	MT1_HORVU	Metallothionein-like protein 1 (MT-1)	0.00	-	nuc	0					74
P69164 UniProt NPD GO	MT2_BRARA	Metallothionein-like protein type 2	0.00	-	nuc	0					80
P30564 UniProt NPD GO	MT2_RICCO	Metallothionein-like protein type 2	0.00	-	nuc	0					80
P69163 UniProt NPD GO	MT22_BRAJU	Metallothionein-like protein type 2, MT2-18	0.00	-	nuc	0					80
P56172 UniProt NPD GO	MT25_BRAJU	Metallothionein-like protein type 2, MT2-28	0.00	-	nuc	0					80
P56168 UniProt NPD GO	MT21_BRAJU	Metallothionein-like protein type 2, MT2-4/MT2-25	0.00	-	nuc	0					80
O24059 UniProt NPD GO	MT3_MALDO	Metallothionein-like protein type 3 (MT-3)	0.00	-	nuc	0					66
Q40256 UniProt NPD GO	MT3_MUSAC	Metallothionein-like protein type 3 (MT-3) (MWMT3)	0.00	-	nuc	0					65
P43389 UniProt NPD GO	MT3_ACTCH	Metallothionein-like protein type 3 PKIWI503	0.00	-	nuc	0					63
P29177 UniProt NPD GO	MGMT_BOVIN	Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (6-O-methylguanine-DNA methyltransf ...	0.00	-		0	Nucleus (Probable)				9
O74827 UniProt NPD GO	CHO1_SCHPO	Methylene-fatty-acyl-phospholipid synthase (EC 2.1.1.16) (Unsaturated phospholipid methyltransferase ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				221
Q26456 UniProt NPD GO	ALL7_DERFA	Mite allergen Der f 7 precursor (Der f VII)	0.00	-	exc	0	Secreted protein				213
P14004 UniProt NPD GO	ALL5_DERPT	Mite allergen Der p 5 (Der P V) (IgE-binding allergen)	0.00	-	mit	0					132
P49273 UniProt NPD GO	ALL7_DERPT	Mite allergen Der p 7 precursor (Der p VII)	0.00	-	end	0	Secreted protein				215
Q9U1G2 UniProt NPD GO	ALL7_LEPDS	Mite allergen Lep d 7 precursor	0.00	-	mit	0	Secreted protein				216
Q00855 UniProt NPD GO	ALL2_DERFA	Mite group 2 allergen Der f 2 precursor (Der f II)	0.00	-	exc	0	Secreted protein			2F08	146
Q9TZZ2 UniProt NPD GO	ALL2_EURMA	Mite group 2 allergen Eur m 2 precursor	0.00	-	exc	0	Secreted protein (By similarity)				145
Q9U5P7 UniProt NPD GO	ALL21_GLYDO	Mite group 2 allergen Gly d 2.01	0.00	-	nuc	0	Secreted protein				128
Q9NFQ4 UniProt NPD GO	ALL22_GLYDO	Mite group 2 allergen Gly d 2.02	0.00	-	cyt	0	Secreted protein				125
P80384 UniProt NPD GO	ALL2_LEPDS	Mite group 2 allergen Lep d 2 precursor (Lep d 1) (Lep d I)	0.00	-	vac	0	Secreted protein				141
Q965E2 UniProt NPD GO	ALL2_PSOOV	Mite group 2 allergen Pso o 2 precursor (Allergen Pso o A)	0.00	-	exc	0	Secreted protein				143
O02380 UniProt NPD GO	ALL2_TYRPU	Mite group 2 allergen Tyr p 2 precursor	0.00	-	end	0	Secreted protein				141
Q9UDX5 UniProt NPD GO	MTP18_HUMAN	Mitochondrial 18 kDa protein (MTP18)	0.00	-	cyt	0	Mitochondrion				166

You are viewing entries 95601 to 95650 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.