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
O46379 UniProt NPD GO	LUM_RABIT	Lumican (Keratan sulfate proteoglycan lumican) (KSPG lumican) (Fragment)	0.13	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				192
Q9LKR3 UniProt NPD GO	BIP1_ARATH	Luminal-binding protein 1 precursor (BiP1) (AtBP1)	0.13	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				669
Q39043 UniProt NPD GO	BIP2_ARATH	Luminal-binding protein 2 precursor (BiP2) (AtBP2)	0.13	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				668
O42790 UniProt NPD GO	PLB_NEUCR	Lysophospholipase precursor (EC 3.1.1.5) (Phospholipase B)	0.13	-	exc	0	Secreted protein (Probable)				653
P16973 UniProt NPD GO	LYSC_RABIT	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.13	-	nuc	0					130
P11376 UniProt NPD GO	LYSC1_HORSE	Lysozyme C, milk isozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.13	-	nuc	0				2EQL	129
P00717 UniProt NPD GO	LYG_CYGAT	Lysozyme g (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase) (Goose-type lysozyme)	0.13	-	cyt	0	Secreted protein			1LSP	185
Q4R842 UniProt NPD GO	MORN3_MACFA	MORN repeat-containing protein 3	0.13	-	cyt	0					240
Q09734 UniProt NPD GO	MIP_TRYCR	Macrophage infectivity potentiator precursor (Peptidyl-prolyl cis-trans isomerase) (EC 5.2.1.8) (PPI ...	0.13	-	exc	1 *	Secreted protein; extracellular space			1JVW	196
P56304 UniProt NPD GO	CHLI_CHLVU	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.13	-	cyt	0	Plastid; chloroplast				354
O77061 UniProt NPD GO	MRJP2_APIME	Major royal jelly protein 2 precursor (MRJP-2) (Bee-milk protein)	0.13	-	exc	0	Secreted protein				452
Q03185 UniProt NPD GO	TS11_GIALA	Major surface trophozoite antigen 11 precursor	0.13	-	nuc	1	Cell membrane; single-pass type I membrane protein				667
Q02216 UniProt NPD GO	MASY_CANTR	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.13	-	cyt	0	Glyoxysome				551
P17815 UniProt NPD GO	MASY_RICCO	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.13	-	cyt	0	Glyoxysome				567
P45458 UniProt NPD GO	MASY_SOYBN	Malate synthase, glyoxysomal (EC 2.3.3.9) (MS) (Fragment)	0.13	-	pox	0	Glyoxysome				564
Q75DG6 UniProt NPD GO	DCW1_ASHGO	Mannan endo-1,6-alpha-mannosidase DCW1 precursor (EC 3.2.1.101) (Endo-alpha-1->6-D-mannanase DCW1) ( ...	0.13	-	end	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				451
Q5H7P5 UniProt NPD GO	EBM_LILLO	Mannosylglycoprotein endo-beta-mannosidase (EC 3.2.1.152) (Endo-beta-mannosidase) [Contains: Mannosy ...	0.13	-	cyt	0					952
P54070 UniProt NPD GO	KTR6_YEAST	Mannosyltransferase KTR6 (EC 2.4.1.131) (Mannosylphosphate transferase MNN6)	0.13	-	cyt	1 *	Membrane; single-pass type II membrane protein (Probable)				446
Q91ZB8 UniProt NPD GO	MRGRD_MOUSE	Mas-related G-protein coupled receptor member D (Beta-alanine receptor) (G-protein coupled receptor ...	0.13	+	end	6 *	Membrane; multi-pass membrane protein				321
P28716 UniProt NPD GO	MER4_EUPOC	Mating pheromone 4 precursor	0.13	-	mit	0	Secreted protein				127
P41245 UniProt NPD GO	MMP9_MOUSE	Matrix metalloproteinase-9 precursor (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gel ...	0.13	-	exc	0		extracellular space [ISS]			730
P83080 UniProt NPD GO	M1H1_BOMMX	Maximins 1/H1 precursor [Contains: Maximin-1; Maximin-H1 (Maximin-6)]	0.13	-	exc	0	Secreted protein				144
Q58T39 UniProt NPD GO	M1015_BOMMX	Maximins 10/H15 precursor [Contains: Maximin-10; Maximin-H15]	0.13	-	end	0	Secreted protein				144
Q58T89 UniProt NPD GO	M6HV_BOMMX	Maximins 6/Hv precursor [Contains: Maximin-6; Maximin-Hv]	0.13	-	end	0	Secreted protein				144
Q58T94 UniProt NPD GO	MYHV2_BOMMX	Maximins y/Hv type 2 precursor [Contains: Maximin-y; Maximin-Hv]	0.13	-	nuc	0	Secreted protein				142
Q5HYA8 UniProt NPD GO	MKS3_HUMAN	Meckelin (Meckel syndrome type 3 protein) (Transmembrane protein 67)	0.13	-	end	4 *	Cell membrane; multi-pass membrane protein (Potential)		609884		995
O74411 UniProt NPD GO	MEU10_SCHPO	Meiotic expression up-regulated protein 10 precursor	0.13	-	cyt	0	Cytoplasm. Cell wall. And spore wall during sporulation				416
O77616 UniProt NPD GO	MSHR_CANFA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.13	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864K6 UniProt NPD GO	MSHR_HYLCO	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.13	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864J5 UniProt NPD GO	MSHR_MACNG	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.13	-	end	4 *	Membrane; multi-pass membrane protein				317
Q8CIV2 UniProt NPD GO	MBRL_MOUSE	Membralin	0.13	-	end	4	Membrane; multi-pass membrane protein (Potential)				574
P81495 UniProt NPD GO	AMPM_BOMMO	Membrane alanyl aminopeptidase (EC 3.4.11.-) (Aminopeptidase N-like protein) (CryIA(A) receptor) (Fr ...	0.13	-	nuc	0					26
Q865K8 UniProt NPD GO	MPRA_PIG	Membrane progestin receptor alpha (mPR alpha) (Progestin and adipoQ receptor family member VII)	0.13	-	end	6	Membrane; multi-pass membrane protein (By similarity)				350
Q99M02 UniProt NPD GO	MARH2_MOUSE	Membrane-associated RING finger protein 2 (Membrane-associated RING-CH protein II) (MARCH-II)	0.13	+	end	2	Membrane; multi-pass membrane protein (Potential)				246
Q8L725 UniProt NPD GO	MTPC1_ARATH	Metal tolerance protein C1 (AtMTPc1)	0.13	-	mit	0	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				471
P25127 UniProt NPD GO	MT_ESOLU	Metallothionein (MT)	0.13	-	nuc	0					60
Q9IB50 UniProt NPD GO	MT_PAGMA	Metallothionein (MT)	0.13	-	nuc	0					60
Q92044 UniProt NPD GO	MTA_CYPS1	Metallothionein A (MT A)	0.13	-	nuc	0					60
Q9PTG9 UniProt NPD GO	MTB_DICLA	Metallothionein B (MT-B)	0.13	-	nuc	0					60
P68501 UniProt NPD GO	MTB_ONCMY	Metallothionein B (MT-B)	0.13	-	nuc	0					60
P68502 UniProt NPD GO	MTB_SALAL	Metallothionein B (MT-B)	0.13	-	nuc	0					60
P62711 UniProt NPD GO	MTB_CHIHA	Metallothionein B (MT-B) (MT-II)	0.13	-	nuc	0					60
P62679 UniProt NPD GO	MTB_CHIRA	Metallothionein B (MT-B) (MT-II)	0.13	-	nuc	0					60
P62713 UniProt NPD GO	MTB_GYMAC	Metallothionein B (MT-B) (MT-II)	0.13	-	nuc	0					60
P62712 UniProt NPD GO	MTB_MORSA	Metallothionein B (MT-B) (MT-II)	0.13	-	nuc	0					60
P62680 UniProt NPD GO	MTB_NOTCO	Metallothionein B (MT-B) (MT-II)	0.13	-	nuc	0				1M0G	60
P62678 UniProt NPD GO	MTB_PAGBE	Metallothionein B (MT-B) (MT-II)	0.13	-	nuc	0					60
P62681 UniProt NPD GO	MTB_PAGBO	Metallothionein B (MT-B) (MT-II)	0.13	-	nuc	0					60
P62682 UniProt NPD GO	MTB_PARCR	Metallothionein B (MT-B) (MT-II)	0.13	-	nuc	0					60
P41927 UniProt NPD GO	MT1_YARLI	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.13	-	nuc	0					55

You are viewing entries 59951 to 60000 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.