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
Q9YI92 UniProt NPD GO	MMHB_AGKHA	Mamushigin beta chain precursor	0.02	-	end	0	Secreted protein				146
P36091 UniProt NPD GO	DCW1_YEAST	Mannan endo-1,6-alpha-mannosidase DCW1 precursor (EC 3.2.1.101) (Endo-alpha-1->6-D-mannanase DCW1) ( ...	0.02	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA] membrane fraction [IDA]			449
Q4U3E8 UniProt NPD GO	MPG1_ASPFU	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.02	-	cyt	0	Cytoplasm (By similarity)				364
Q2UJU5 UniProt NPD GO	MPG1_ASPOR	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.02	-	cyt	0	Cytoplasm (By similarity)				364
Q5B1J4 UniProt NPD GO	MPG1_EMENI	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.02	-	cyt	0	Cytoplasm (By similarity)				351
Q4I1Y5 UniProt NPD GO	MPG1_GIBZE	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.02	-	cyt	0	Cytoplasm (By similarity)				364
Q66WM4 UniProt NPD GO	MANA_ASPFU	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.02	-	cyt	0	Cytoplasm (By similarity)				457
Q60441 UniProt NPD GO	MPU1_CRIGR	Mannose-P-dolichol utilization defect 1 protein (Suppressor of Lec15 and Lec35 glycosylation mutatio ...	0.02	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				247
Q66S54 UniProt NPD GO	MBL2_HYLLA	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.02	-	exc	0					248
Q66S63 UniProt NPD GO	MBL2_PANTR	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.02	-	exc	0					248
Q7TN49 UniProt NPD GO	MRGRA_RAT	Mas-related G-protein coupled receptor member A	0.02	-	end	7 *	Membrane; multi-pass membrane protein				304
Q4QXU6 UniProt NPD GO	MRGX2_BUNHO	Mas-related G-protein coupled receptor member X2	0.02	-	end	7 *	Membrane; multi-pass membrane protein				329
Q4QXU4 UniProt NPD GO	MRGX2_TRAFR	Mas-related G-protein coupled receptor member X2	0.02	-	end	7 *	Membrane; multi-pass membrane protein				330
P11034 UniProt NPD GO	MCPT1_MOUSE	Mast cell protease 1 precursor (EC 3.4.21.-) (MMCP-1)	0.02	-	exc	0	Secretory granules				246
P01517 UniProt NPD GO	MAST_POLJA	Mastoparan-J (Polistes mastoparan)	0.02	-		0	Secreted protein				14
P0C1Q9 UniProt NPD GO	MAST2_VESVU	Mastoparan-V2	0.02	-		0	Secreted protein				15
P32435 UniProt NPD GO	MFAL2_YEAST	Mating factor alpha-2 precursor (Alpha-2 mating pheromone) [Contains: Alpha-2 mating pheromone; Mati ...	0.02	-	exc	0		extracellular region [TAS]			120
P34165 UniProt NPD GO	MFA1_YEAST	Mating hormone A-factor 1 precursor	0.02	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	extracellular region [IDA] soluble fraction [IDA]			36
P78742 UniProt NPD GO	BB11_SCHCO	Mating-type pheromone BBP1(1) precursor	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				76
P41968 UniProt NPD GO	MC3R_HUMAN	Melanocortin receptor 3 (MC3-R)	0.02	-	vac	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	155540		360
P56450 UniProt NPD GO	MC4R_MOUSE	Melanocortin receptor 4 (MC4-R)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				332
Q9MZV8 UniProt NPD GO	MC5R_PIG	Melanocortin receptor 5 (MC5-R) (Fragment)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				294
P43360 UniProt NPD GO	MAGA6_HUMAN	Melanoma-associated antigen 6 (MAGE-6 antigen) (MAGE3B)	0.02	-	cyt	0			300176		314
Q28038 UniProt NPD GO	MIA_BOVIN	Melanoma-derived growth regulatory protein precursor (Melanoma inhibitory activity) (Cartilage-deriv ...	0.02	-	cyt	0	Secreted protein				130
P41989 UniProt NPD GO	MLG_THETS	Melanotropin gamma (Gamma-melanocyte-stimulating hormone) (Gamma-MSH)	0.02	-		0					11
O62685 UniProt NPD GO	MCP_SAISC	Membrane cofactor protein precursor (CD46 antigen) (Fragment)	0.02	-	mit	0	Acrosome; acrosomal inner membrane; single-pass type I membrane protein (By similarity). Inner acros ...				285
Q10659 UniProt NPD GO	SPO14_SCHPO	Membrane glycoprotein spo14 (SEC12-like protein) (Sporulation-specific protein 14)	0.02	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...				395
Q865K9 UniProt NPD GO	MPRB_PIG	Membrane progestin receptor beta (mPR beta) (Progestin and adipoQ receptor family member VIII)	0.02	-	end	6	Membrane; multi-pass membrane protein (By similarity)				354
Q920C4 UniProt NPD GO	MS4A3_MOUSE	Membrane-spanning 4-domains subfamily A member 3 (Hematopoietic-specific transmembrane 4 protein) (H ...	0.02	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			213
Q99N05 UniProt NPD GO	M4A4D_MOUSE	Membrane-spanning 4-domains subfamily A member 4D	0.02	-	end	4 *	Membrane; multi-pass membrane protein				225
Q99N10 UniProt NPD GO	M4A8A_MOUSE	Membrane-spanning 4-domains subfamily A member 8A (CD20 antigen-like 5) (Fragment)	0.02	-	end	4	Membrane; multi-pass membrane protein				287
O97590 UniProt NPD GO	TIMP3_RABIT	Metalloproteinase inhibitor 3 (TIMP-3) (Tissue inhibitor of metalloproteinases 3) (Fragment)	0.02	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				151
P79121 UniProt NPD GO	TIMP3_BOVIN	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3)	0.02	-	exc	0	Secreted protein; extracellular space; extracellular matrix				211
Q9TUL9 UniProt NPD GO	TIMP3_HORSE	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3)	0.02	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				211
P61269 UniProt NPD GO	TIMP3_MACFA	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3)	0.02	-	cyt	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				211
Q5PXZ9 UniProt NPD GO	TIMP3_MACMU	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3)	0.02	-	cyt	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				211
P35625 UniProt NPD GO	TIMP3_HUMAN	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3) (Protein ...	0.02	-	cyt	0	Secreted protein; extracellular space; extracellular matrix		188826		211
P80367 UniProt NPD GO	MT_PARLI	Metallothionein (MT)	0.02	-	nuc	0					65
Q9VDN2 UniProt NPD GO	MT3_DROME	Metallothionein-3 (MT-3) (Metallothionein C)	0.02	-	nuc	0					43
Q26496 UniProt NPD GO	MTB_SPHGR	Metallothionein-B (MTB) (Fragment)	0.02	-	nuc	0					67
P43400 UniProt NPD GO	MT1_WHEAT	Metallothionein-like protein 1 (MT-1)	0.02	-	nuc	0					75
P25860 UniProt NPD GO	MT2A_ARATH	Metallothionein-like protein 2A (MT-2A) (MT-K) (MT-1G)	0.02	-	nuc	0					81
Q99334 UniProt NPD GO	MT1_COLGL	Metallothionein-like protein CAP3	0.02	-	nuc	0					26
P94029 UniProt NPD GO	MT21_ORYSA	Metallothionein-like protein type 2	0.02	-	nuc	0					82
Q43512 UniProt NPD GO	MT2X_LYCES	Metallothionein-like protein type 2	0.02	-	nuc	0					72
Q43513 UniProt NPD GO	MT2Y_LYCES	Metallothionein-like protein type 2	0.02	-	nuc	0					73
Q40157 UniProt NPD GO	MT2A_LYCES	Metallothionein-like protein type 2 A (LeMT(A))	0.02	-	nuc	0					72
P56170 UniProt NPD GO	MT23_BRAJU	Metallothionein-like protein type 2, MT2-22	0.02	-	nuc	0					80
Q96386 UniProt NPD GO	MT3_CARPA	Metallothionein-like protein type 3 (MT-3)	0.02	-	nuc	0					65
Q14805 UniProt NPD GO	MCP33_HUMAN	Metaphase chromosomal protein 1 (33 kDa metaphase chromosomal protein)	0.02	-	cyt	0	Nucleus. During interphase is dispersed in the nucleus and during mitosis it associates exclusively ...	condensed nuclear chromosome [IDA]			290

You are viewing entries 84301 to 84350 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.