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
P13473 UniProt NPD GO	LAMP2_HUMAN	Lysosome-associated membrane glycoprotein 2 precursor (LAMP-2) (CD107b antigen)	0.01	-	end	1 *	Cell membrane; single-pass type I membrane protein. Endosome; endosomal membrane; single-pass type I ...	late endosome [IDA] lysosomal membrane [IDA] membrane fraction [IDA] platelet dense granule membrane [IDA]	309060		410
P21776 UniProt NPD GO	LYSC_PSEPE	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C) (Fragment)	0.01	-	nuc	0					49
P37712 UniProt NPD GO	LYSC_CAMDR	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.01	-	cyt	0					130
P61631 UniProt NPD GO	LYSC_COLAN	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	cyt	0					148
P61632 UniProt NPD GO	LYSC_COLGU	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	cyt	0					148
Q659U0 UniProt NPD GO	LYSC_LEPWE	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	exc	0					148
P79811 UniProt NPD GO	LYSC_NASLA	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	end	0					148
P79847 UniProt NPD GO	LYSC_PYGNE	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	end	0					148
P67977 UniProt NPD GO	LYSC_SEMEN	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	end	0					148
P67980 UniProt NPD GO	LYSC_TRAFR	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	end	0					148
P67979 UniProt NPD GO	LYSC_TRAOB	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	end	0					148
P67978 UniProt NPD GO	LYSC_TRAVT	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	end	0					148
P37713 UniProt NPD GO	LYSC1_CAPHI	Lysozyme C-1 (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C-1)	0.01	-	cyt	0					129
P17607 UniProt NPD GO	LYSC1_SHEEP	Lysozyme C-1 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	cyt	0					147
P37714 UniProt NPD GO	LYSC2_CAPHI	Lysozyme C-2 (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C-2)	0.01	-	cyt	0					129
P12068 UniProt NPD GO	LYSC2_PIG	Lysozyme C-2 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	end	0					146
P12069 UniProt NPD GO	LYSC3_PIG	Lysozyme C-3 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.01	-	exc	0					148
P37161 UniProt NPD GO	LYSX_DROME	Lysozyme X precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase X)	0.01	-	exc	0					142
Q9DA11 UniProt NPD GO	LYZL6_MOUSE	Lysozyme-like protein 6 precursor (EC 3.2.1.17)	0.01	-	mit	0	Secreted protein (Probable)				148
Q18785 UniProt NPD GO	MIF2_CAEEL	MIF-like protein mif-2	0.01	-	cyt	0					120
Q9SSK9 UniProt NPD GO	MLP28_ARATH	MLP-like protein 28	0.01	-	cyt	0					335
Q941R6 UniProt NPD GO	MLP31_ARATH	MLP-like protein 31	0.01	-	cyt	0					162
Q9ZVF3 UniProt NPD GO	ML328_ARATH	MLP-like protein 328	0.01	-	cyt	0					151
Q9SSK5 UniProt NPD GO	MLP43_ARATH	MLP-like protein 43	0.01	-	nuc	0					158
Q6UL01 UniProt NPD GO	MORN2_MOUSE	MORN repeat-containing protein 2 (MORN motif protein in testis)	0.01	-	cyt	0					79
Q02960 UniProt NPD GO	MIF_CHICK	Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1)	0.01	-	cyt	0					114
O04298 UniProt NPD GO	DAU1_DAUCA	Major allergen Dau c 1 (CR16) (Pathogenesis-related protein Gea20)	0.01	-	cyt	0					154
Q95182 UniProt NPD GO	ALL1_HORSE	Major allergen Equ c 1 precursor	0.01	-	exc	0	Secreted protein			1EW3	187
P30440 UniProt NPD GO	FEL1B_FELCA	Major allergen I polypeptide chain 2 precursor (Allergen Fel d 1-B) (Fel d I-B) (Allergen Cat-1) (AG ...	0.01	-	exc	0	Secreted protein			1ZKR	109
Q06395 UniProt NPD GO	ML149_PAPSO	Major latex protein 149 (MLP 149)	0.01	-	cyt	0	Vacuole. Cytoplasmic vesicle. Central vacuole of developing laticifers and membrane-bound vesicles o ...				159
Q08668 UniProt NPD GO	MIAM_SARMU	Major microneme antigen precursor	0.01	-	nuc	1 *	Microneme				241
P38948 UniProt NPD GO	MPAG1_ALNGL	Major pollen allergen Aln g 1 (Aln g I)	0.01	-	cyt	0					159
P15494 UniProt NPD GO	BEV1A_BETVE	Major pollen allergen Bet v 1-A (Bet v I-A)	0.01	-	cyt	0	Cytoplasm			1QMR	159
P43177 UniProt NPD GO	BEV1D_BETVE	Major pollen allergen Bet v 1-D/H (Bet v I-D/H)	0.01	-	cyt	0	Cytoplasm				159
P43178 UniProt NPD GO	BEV1E_BETVE	Major pollen allergen Bet v 1-E (Bet v I-E)	0.01	-	cyt	0	Cytoplasm				159
P43179 UniProt NPD GO	BEV1F_BETVE	Major pollen allergen Bet v 1-F/I (Bet v I-F/I)	0.01	-	cyt	0	Cytoplasm				159
P43180 UniProt NPD GO	BEV1G_BETVE	Major pollen allergen Bet v 1-G (Bet v I-G)	0.01	-	cyt	0	Cytoplasm				159
P43183 UniProt NPD GO	BEV1J_BETVE	Major pollen allergen Bet v 1-J (Bet v I-J)	0.01	-	cyt	0	Cytoplasm				159
P43185 UniProt NPD GO	BEV1L_BETVE	Major pollen allergen Bet v 1-L (Bet v I-L)	0.01	-	cyt	0	Cytoplasm			1FM4	159
Q96385 UniProt NPD GO	MPAC1_CHAOB	Major pollen allergen Cha o 1 precursor	0.01	-	exc	0					375
O04701 UniProt NPD GO	MPAC1_CYNDA	Major pollen allergen Cyn d 1	0.01	-	cyt	0	Secreted protein				246
P43216 UniProt NPD GO	MPAH1_HOLLA	Major pollen allergen Hol l 1 precursor (Hol l I) (Hol l 1.0101 and 1.0102)	0.01	-	exc	1 *	Secreted protein				265
P81294 UniProt NPD GO	MPAJ1_JUNAS	Major pollen allergen Jun a 1 precursor	0.01	-	exc	0				1PXZ	367
P81826 UniProt NPD GO	MPAJ4_JUNVI	Major pollen allergen Jun v 4 (Fragment)	0.01	-		0					5
Q7M1X5 UniProt NPD GO	LOLB_LOLPR	Major pollen allergen Lol p 11 (Lol p XI)	0.01	-	cyt	0	Secreted protein				134
Q41260 UniProt NPD GO	MPAP1_PHAAQ	Major pollen allergen Pha a 1 precursor (Pha a I)	0.01	-	vac	1 *	Secreted protein				269
P56167 UniProt NPD GO	MPA54_PHAAQ	Major pollen allergen Pha a 5.4 (Pha a 5) (Clone 5) (Fragment)	0.01	-	mit	0					175
P13664 UniProt NPD GO	P30_TOXGO	Major surface antigen p30 precursor	0.01	-	nuc	0	Surface of extra- and intracellular tachyzoites and also component of the vesicular network within t ...			1YNT	336
P83507 UniProt NPD GO	MUP_CAVPO	Major urinary protein (MUP) (Allergen Cav p 1) (Fragment)	0.01	-		0	Secreted protein				15
P59853 UniProt NPD GO	MKTX3_MESMA	Makatoxin-3 precursor (Makatoxin III) (MkTx III)	0.01	-	cyt	0	Secreted protein (By similarity)				85

You are viewing entries 89451 to 89500 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.