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
P46869 UniProt NPD GO	FLA10_CHLRE	Kinesin-like protein FLA10 (Protein KHP1)	0.61	-	nuc	0					786
Q5IS44 UniProt NPD GO	LHX1_PANTR	LIM/homeobox protein Lhx1 (LIM homeobox protein 1)	0.61	+	nuc	0	Nucleus (Probable)				406
Q5IS89 UniProt NPD GO	LHX1_SAIBB	LIM/homeobox protein Lhx1 (LIM homeobox protein 1)	0.61	+	nuc	0	Nucleus (Probable)				406
P63006 UniProt NPD GO	LHX1_MOUSE	LIM/homeobox protein Lhx1 (LIM homeobox protein 1) (Homeobox protein Lim-1)	0.61	+	nuc	0	Nucleus (Probable)				406
P63008 UniProt NPD GO	LHX1_MESAU	LIM/homeobox protein Lhx1 (LIM homeobox protein 1) (Homeobox protein Lim-1) (Homeobox protein LMX-2) ...	0.61	+	nuc	0	Nucleus (Probable)				406
P63007 UniProt NPD GO	LHX1_RAT	LIM/homeobox protein Lhx1 (LIM homeobox protein 1) (Homeobox protein Lim-1) (Rlim)	0.61	+	nuc	0	Nucleus (Probable)				406
P52889 UniProt NPD GO	LHX5_BRARE	LIM/homeobox protein Lhx5 (Homeobox protein LIM-5)	0.61	+	nuc	0	Nucleus (Probable)				399
Q5T5A8 UniProt NPD GO	LCE3C_HUMAN	Late cornified envelope protein 3C (Late envelope protein 15) (Small proline-rich-like epidermal dif ...	0.61	-	nuc	0					94
Q8K4G1 UniProt NPD GO	LTBP4_MOUSE	Latent-transforming growth factor beta-binding protein 4 precursor (LTBP-4)	0.61	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [ISS]			1666
Q80TS3 UniProt NPD GO	LPHN3_MOUSE	Latrophilin-3 (Lectomedin-3) (Fragment)	0.61	-	end	7	Membrane; multi-pass membrane protein				1189
Q9HAR2 UniProt NPD GO	LPHN3_HUMAN	Latrophilin-3 precursor (Calcium-independent alpha-latrotoxin receptor 3) (Lectomedin-3)	0.61	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [NAS]			1447
Q24332 UniProt NPD GO	NT56_DROVI	Lethal(2)neighbour of Tid protein (NOT58)	0.61	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				526
Q04081 UniProt NPD GO	LCMT1_YEAST	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.61	-	nuc	0				1RJG	328
Q4R747 UniProt NPD GO	LRC46_MACFA	Leucine-rich repeat-containing protein 46	0.61	-	nuc	0					321
Q6AXZ2 UniProt NPD GO	LRC46_RAT	Leucine-rich repeat-containing protein 46	0.61	-	nuc	0					323
Q75WE7 UniProt NPD GO	LHR2A_RAT	Loss of heterozygosity 11 chromosomal region 2 gene A protein homolog (Mast cell surface antigen 1) ...	0.61	-	nuc	0					822
Q67FQ3 UniProt NPD GO	ARHB_XENLA	Low density lipoprotein receptor adapter protein 1-B (Autosomal recessive hypercholesterolemia prote ...	0.61	-	nuc	0	Cytoplasm (By similarity)				309
O09159 UniProt NPD GO	MA2B1_MOUSE	Lysosomal alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase, alpha B) (Lysosomal acid alpha-man ...	0.61	-	cyt	0	Lysosome				1013
Q43776 UniProt NPD GO	SYK_LYCES	Lysyl-tRNA synthetase (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.61	-	nuc	0	Cytoplasm				588
Q9WV34 UniProt NPD GO	MPP2_MOUSE	MAGUK p55 subfamily member 2 (Protein MPP2) (Dlgh2 protein)	0.61	-	cyt	0		membrane [ISS]			552
Q3UMW7 UniProt NPD GO	MAPK3_MOUSE	MAP kinase-activated protein kinase 3 (EC 2.7.11.1) (MAPK-activated protein kinase 3) (MAPKAP kinase ...	0.61	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Predominantly located in the nucleus, when activ ...				384
P35693 UniProt NPD GO	FPR1_PODAN	MAT+ sexual cell fertilization-promoting factor	0.61	-	nuc	0	Nucleus (Potential)				402
P50539 UniProt NPD GO	MXI1_HUMAN	MAX-interacting protein 1 (Protein MXI1)	0.61	-	nuc	0	Nucleus	nucleus [TAS]	600020		228
Q9GHE2 UniProt NPD GO	MATK_COLSP	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				516
Q8VWJ4 UniProt NPD GO	MATK_CURLO	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				515
Q5YK00 UniProt NPD GO	MATK_CYTSC	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				506
Q8W8E6 UniProt NPD GO	MATK_FAGCR	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				504
Q8WKE6 UniProt NPD GO	MATK_FAGHA	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				504
Q4H1A5 UniProt NPD GO	MATK_GLAPA	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				522
Q4H195 UniProt NPD GO	MATK_LAPNE	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				522
Q8WJM5 UniProt NPD GO	MATK_LIQOR	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				503
Q9TKI5 UniProt NPD GO	MATK_MEDSA	Maturase K (Intron maturase)	0.61	-	nuc	0	Plastid; chloroplast				506
Q5YJU1 UniProt NPD GO	MATK_PEA	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				506
Q4H186 UniProt NPD GO	MATK_PILTE	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				522
Q75VA9 UniProt NPD GO	MATK_QUEPA	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				504
Q7YM14 UniProt NPD GO	MATK_QUERU	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				504
Q5YJV6 UniProt NPD GO	MATK_TRIBE	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				506
Q8MCM9 UniProt NPD GO	MATK_TRIIC	Maturase K (Intron maturase)	0.61	-	nuc	0	Plastid; chloroplast				506
Q8MCM2 UniProt NPD GO	MATK_TRISO	Maturase K (Intron maturase)	0.61	-	nuc	0	Plastid; chloroplast				506
Q8MCL8 UniProt NPD GO	MATK_TRIWI	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				506
Q8MCL7 UniProt NPD GO	MATK_TRIWO	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				506
Q8MEW9 UniProt NPD GO	MATK_WELMI	Maturase K (Intron maturase)	0.61	-	cyt	0	Plastid; chloroplast				524
Q9TKP6 UniProt NPD GO	MATK_WISFR	Maturase K (Intron maturase)	0.61	-	mit	0	Plastid; chloroplast				506
Q8MEX4 UniProt NPD GO	MATK_ZAMFL	Maturase K (Intron maturase)	0.61	-	nuc	0	Plastid; chloroplast				514
Q9GHE5 UniProt NPD GO	MATK_ZANAE	Maturase K (Intron maturase)	0.61	-	nuc	0	Plastid; chloroplast				512
P78956 UniProt NPD GO	RE114_SACPA	Meiotic recombination protein REC114	0.61	-	nuc	0					432
Q8TD90 UniProt NPD GO	MAGE2_HUMAN	Melanoma-associated antigen E2 (MAGE-E2 antigen) (Hepatocellular carcinoma-associated protein 3)	0.61	-	cyt	0					523
Q14696 UniProt NPD GO	MESD2_HUMAN	Mesoderm development candidate 2 (NY-REN-61 antigen)	0.61	+	exc	0			607783		234
Q8INK9 UniProt NPD GO	MSRB_DROME	Methionine-R-sulfoxide reductase (EC 1.8.4.-) (Selenoprotein R)	0.61	-	mit	0					207
P27816 UniProt NPD GO	MAP4_HUMAN	Microtubule-associated protein 4 (MAP 4)	0.61	-	nuc	0		microtubule associated complex [TAS]	157132		1152

You are viewing entries 18551 to 18600 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.