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
Q6FXA5 UniProt NPD GO	LCMT2_CANGA	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.59	-	nuc	0					674
Q8K4Y5 UniProt NPD GO	LGI1_RAT	Leucine-rich glioma-inactivated protein 1 precursor	0.59	-	mit	0	Secreted protein (Potential)	extracellular space [NAS]			557
Q9HB75 UniProt NPD GO	PIDD_HUMAN	Leucine-rich repeat and death domain-containing protein (p53-induced protein with a death domain)	0.59	-	nuc	0	Cytoplasm. Nucleus		605247		910
Q6YXP4 UniProt NPD GO	CHLN_PHYPA	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.59	+	cyt	0	Plastid; chloroplast				474
Q5XI07 UniProt NPD GO	LPP_RAT	Lipoma-preferred partner homolog	0.59	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Cell membrane; cell-cell junction (By similarity ...				632
P06734 UniProt NPD GO	FCER2_HUMAN	Low affinity immunoglobulin epsilon Fc receptor (Lymphocyte IgE receptor) (Fc-epsilon-RII) (BLAST-2) ...	0.59	-	nuc	1 *	Cell membrane; single-pass type II membrane protein. Secreted protein. Also exists as a soluble excr ...	integral to plasma membrane [TAS]	151445	2H2T	321
Q8SPV8 UniProt NPD GO	FCG2A_PANTR	Low affinity immunoglobulin gamma Fc region receptor II-a precursor (Fc-gamma RII-a) (FcRII-a) (IgG ...	0.59	-	nuc	1	Membrane; single-pass type I membrane protein				316
Q8VI56 UniProt NPD GO	LRP4_MOUSE	Low-density lipoprotein receptor-related protein 4 precursor (LDLR dan)	0.59	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1905
Q9QYP1 UniProt NPD GO	LRP4_RAT	Low-density lipoprotein receptor-related protein 4 precursor (Multiple epidermal growth factor-like ...	0.59	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				1905
Q60787 UniProt NPD GO	LCP2_MOUSE	Lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76 kDa) (SLP-76 tyrosine ...	0.59	-	nuc	0	Cytoplasm (Probable)			2EU0	533
Q9UJ55 UniProt NPD GO	MAGL2_HUMAN	MAGE-like protein 2 (Necdin-like protein 1) (Protein nM15)	0.59	-	nuc	0			605283		529
Q66H84 UniProt NPD GO	MAPK3_RAT	MAP kinase-activated protein kinase 3 (EC 2.7.11.1) (MAPK-activated protein kinase 3) (MAPKAP kinase ...	0.59	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Predominantly located in the nucleus, when activ ...				384
Q60764 UniProt NPD GO	MKRN3_MOUSE	Makorin-3 (Zinc finger protein 127)	0.59	-	nuc	0					544
Q6WRX6 UniProt NPD GO	MATMC_SCHKA	Mating-type M-specific polypeptide Mc (mat-Mc)	0.59	-	nuc	0	Nucleus (Potential)				181
P01366 UniProt NPD GO	MATA1_YEAST	Mating-type protein A1 (MATa1 protein)	0.59	-	nuc	0	Nucleus	nucleus [IDA]		1YRN	126
Q9UW19 UniProt NPD GO	MTAL1_CANAL	Mating-type-like protein ALPHA1 (MTLalpha1 protein)	0.59	-	nuc	0	Nucleus (By similarity)				193
Q9MV51 UniProt NPD GO	MATK_ABIFI	Maturase K (Intron maturase)	0.59	-	nuc	0	Plastid; chloroplast				509
Q9MV46 UniProt NPD GO	MATK_ABIHL	Maturase K (Intron maturase)	0.59	-	nuc	0	Plastid; chloroplast				509
Q9GHE4 UniProt NPD GO	MATK_ALICA	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				512
Q6PSE2 UniProt NPD GO	MATK_AMPBR	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				507
Q8MDT1 UniProt NPD GO	MATK_ARAHE	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				507
Q67BD8 UniProt NPD GO	MATK_BETPA	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				504
Q6LA17 UniProt NPD GO	MATK_BOWVO	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				511
Q6QHD9 UniProt NPD GO	MATK_BRACM	Maturase K (Intron maturase)	0.59	-	mit	0	Plastid; chloroplast				502
Q6QHE0 UniProt NPD GO	MATK_BRAOL	Maturase K (Intron maturase)	0.59	-	mit	0	Plastid; chloroplast				502
Q5YB04 UniProt NPD GO	MATK_BROPL	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				511
Q9MVW5 UniProt NPD GO	MATK_CALDE	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				507
Q7YJY7 UniProt NPD GO	MATK_CALFE	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				505
Q6QUL7 UniProt NPD GO	MATK_CALFL	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				505
Q5F4M7 UniProt NPD GO	MATK_CALOC	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				505
P68749 UniProt NPD GO	MATK_CARBE	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				504
P68748 UniProt NPD GO	MATK_CAROR	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				504
Q8MEY4 UniProt NPD GO	MATK_CERME	Maturase K (Intron maturase)	0.59	-	nuc	0	Plastid; chloroplast				499
Q859W3 UniProt NPD GO	MATK_FAGTA	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				507
Q8MEC7 UniProt NPD GO	MATK_FILMA	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				512
Q7YM28 UniProt NPD GO	MATK_GALBE	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				509
Q9GHV0 UniProt NPD GO	MATK_LINBE	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				507
Q9MDX7 UniProt NPD GO	MATK_LIRCH	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				507
Q7J1C8 UniProt NPD GO	MATK_LIRTU	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				507
O47125 UniProt NPD GO	MATK_LYOLU	Maturase K (Intron maturase)	0.59	-	nuc	0	Plastid; chloroplast				507
Q9TNB2 UniProt NPD GO	MATK_MAIDI	Maturase K (Intron maturase)	0.59	-	nuc	0	Plastid; chloroplast				520
Q9MVD8 UniProt NPD GO	MATK_MICFI	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				507
Q8HV04 UniProt NPD GO	MATK_MUSLA	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				511
Q9MTQ1 UniProt NPD GO	MATK_OENHO	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				512
Q8M924 UniProt NPD GO	MATK_PRIVE	Maturase K (Intron maturase)	0.59	-	nuc	0	Plastid; chloroplast				511
Q75VB5 UniProt NPD GO	MATK_QUECE	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				504
Q75VB1 UniProt NPD GO	MATK_QUELY	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				504
Q75VA8 UniProt NPD GO	MATK_QUEPE	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				504
Q8M920 UniProt NPD GO	MATK_QUERO	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				504
Q75VA5 UniProt NPD GO	MATK_QUESU	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				504

You are viewing entries 19651 to 19700 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.