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
P20013 UniProt NPD GO	LIGC_TRAVE	Ligninase C precursor (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase)	0.21	-	exc	0					372
Q26422 UniProt NPD GO	LFC_CARRO	Limulus clotting factor C precursor (EC 3.4.21.84) (FC) [Contains: Limulus clotting factor C heavy c ...	0.21	-	nuc	0	Secreted protein. Secreted in hemolymph				1019
O54957 UniProt NPD GO	LAT_MOUSE	Linker for activation of T-cells family member 1 (36 kDa phospho-tyrosine adapter protein) (pp36) (p ...	0.21	-	nuc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts	immunological synapse [IDA] integral to plasma membrane [TAS]			242
Q9SXP7 UniProt NPD GO	LIPB_ARATH	Lipoate-protein ligase (EC 6.-.-.-) (Lipoate biosynthesis protein) (Lipoyl ligase)	0.21	-	mit	0					235
P93647 UniProt NPD GO	LONH1_MAIZE	Lon protease homolog 1, mitochondrial precursor (EC 3.4.21.-)	0.21	-	pox	0	Mitochondrion; mitochondrial matrix (Potential)				885
P93648 UniProt NPD GO	LONH2_MAIZE	Lon protease homolog 2, mitochondrial precursor (EC 3.4.21.-)	0.21	-	cyt	0	Mitochondrion; mitochondrial matrix (Potential)				964
P25668 UniProt NPD GO	NXL1_NAJNA	Long neurotoxin 1 (Toxin A)	0.21	-	nuc	0	Secreted protein				71
P01386 UniProt NPD GO	NXL2_OPHHA	Long neurotoxin 2 (Neurotoxin B)	0.21	-	nuc	0	Secreted protein			1TXB	73
P25671 UniProt NPD GO	NXL3_NAJNA	Long neurotoxin 3 (Toxin C)	0.21	-	nuc	0	Secreted protein			2CTX	71
P08101 UniProt NPD GO	FCGR2_MOUSE	Low affinity immunoglobulin gamma Fc region receptor II precursor (Fc-gamma RII) (FcRII) (IgG Fc rec ...	0.21	-	nuc	1	Cell membrane; single-pass type I membrane protein. Isoform IIB1: Cytoskeleton. Isoform IIB1 binds t ...	external side of plasma membrane [IDA] integral to plasma membrane [IC]			330
O46483 UniProt NPD GO	LSHB_MACRU	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B) (Fragment ...	0.21	-	exc	0	Secreted protein				138
O23006 UniProt NPD GO	LYM2_ARATH	LysM domain GPI-anchored protein 2 precursor	0.21	-	end	1 *	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			350
O93795 UniProt NPD GO	PLB2_CANAL	Lysophospholipase 2 precursor (EC 3.1.1.5) (Phospholipase B 2) (CaPLB2)	0.21	-	mit	0	Secreted protein (Probable)				608
P11438 UniProt NPD GO	LAMP1_MOUSE	Lysosome-associated membrane glycoprotein 1 precursor (LAMP-1) (LGP-A) (LGP-120) (P2B) (CD107a antig ...	0.21	-	exc	1	Cell membrane; single-pass type I membrane protein. Endosome; endosomal membrane; single-pass type I ...	lysosome [IDA] multivesicular body [IDA] sarcolemma [IDA]			406
P00697 UniProt NPD GO	LYSC1_RAT	Lysozyme C type 1 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.21	-	nuc	0					148
Q15046 UniProt NPD GO	SYK_HUMAN	Lysyl-tRNA synthetase (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.21	-	nuc	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	601421		597
Q8CG85 UniProt NPD GO	MAMC2_MOUSE	MAM domain-containing protein 2 precursor	0.21	-	mit	0	Secreted protein (Potential)				686
Q5PPV3 UniProt NPD GO	MORN3_XENLA	MORN repeat-containing protein 3	0.21	-	cyt	0					238
Q60754 UniProt NPD GO	MARCO_MOUSE	Macrophage receptor MARCO (Macrophage receptor with collagenous structure)	0.21	-	cyt	1 *	Membrane; single-pass type II membrane protein (Probable)				518
P21758 UniProt NPD GO	MSRE_BOVIN	Macrophage scavenger receptor types I and II (Macrophage acetylated LDL receptor I and II)	0.21	-	mit	1	Membrane; single-pass type II membrane protein				453
P16311 UniProt NPD GO	DERF1_DERFA	Major mite fecal allergen Der f 1 precursor (EC 3.4.22.-) (Der f I)	0.21	-	exc	0	Secreted protein				321
P16312 UniProt NPD GO	DERM1_DERMI	Major mite fecal allergen Der m 1 (EC 3.4.22.-) (Der m I) (Fragment)	0.21	-	nuc	0	Secreted protein				30
O76273 UniProt NPD GO	PTP1_ENCHE	Major polar tube protein precursor (Major PTP) (PTP Eh55)	0.21	-	nuc	0	Secreted protein; extracellular space				453
P04156 UniProt NPD GO	PRIO_HUMAN	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (ASCR) (CD230 antigen)	0.21	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor	cytoplasm [TAS] endoplasmic reticulum [ISS] extrinsic to membrane [TAS] Golgi apparatus [ISS] lipid raft [ISS] plasma membrane [ISS]	123400	1QM3	253
P51446 UniProt NPD GO	PRIO_ATEPA	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.21	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				252
Q60468 UniProt NPD GO	PRIO_CRIMI	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.21	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor				254
P40252 UniProt NPD GO	PRIO_GORGO	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.21	-	exc	2	Cell membrane; lipid-anchor; GPI-anchor				253
P04273 UniProt NPD GO	PRIO_MESAU	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.21	-	nuc	2	Cell membrane; lipid-anchor; GPI-anchor			1B10	254
P40255 UniProt NPD GO	PRIO_MANSP	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.21	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				241
O95822 UniProt NPD GO	DCMC_HUMAN	Malonyl-CoA decarboxylase, mitochondrial precursor (EC 4.1.1.9) (MCD)	0.21	-	pox	0	Mitochondrion. Cytoplasm. Peroxisome	cytoplasm [TAS] peroxisome [TAS]	606761		493
Q99J39 UniProt NPD GO	DCMC_MOUSE	Malonyl-CoA decarboxylase, mitochondrial precursor (EC 4.1.1.9) (MCD)	0.21	-	pox	0	Mitochondrion. Cytoplasm. Peroxisome				492
P53625 UniProt NPD GO	MA122_DROME	Mannosyl-oligosaccharide alpha-1,2-mannosidase isoform 2 (EC 3.2.1.113) (Man(9)-alpha-mannosidase)	0.21	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				643
P23749 UniProt NPD GO	MRGRF_RAT	Mas-related G-protein coupled receptor member F (Mas-related gene F protein) (G-protein coupled rece ...	0.21	-	end	6 *	Membrane; multi-pass membrane protein				343
P28717 UniProt NPD GO	MER3_EUPOC	Mating pheromone 3 precursor	0.21	-	nuc	0	Secreted protein				151
O60882 UniProt NPD GO	MMP20_HUMAN	Matrix metalloproteinase-20 precursor (EC 3.4.24.-) (MMP-20) (Enamel metalloproteinase) (Enamelysin) ...	0.21	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular space [TAS]	604629		483
P30659 UniProt NPD GO	MAXA_LUTLO	Maxadilan precursor	0.21	-	exc	1 *	Secreted protein				86
P08503 UniProt NPD GO	ACADM_RAT	Medium-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.3) (MCAD)	0.21	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [ISS] mitochondrion [ISS]			421
P42679 UniProt NPD GO	MATK_HUMAN	Megakaryocyte-associated tyrosine-protein kinase (EC 2.7.10.2) (Tyrosine-protein kinase CTK) (Protei ...	0.21	-	cyt	0	Cytoplasm		600038	1X6G	507
Q01727 UniProt NPD GO	MSHR_MOUSE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.21	-	end	7 *	Membrane; multi-pass membrane protein				315
Q9TTK6 UniProt NPD GO	AOC3_BOVIN	Membrane copper amine oxidase (EC 1.4.3.6) (Semicarbazide-sensitive amine oxidase) (SSAO) (Vascular ...	0.21	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)	cell surface [ISS] integral to membrane [ISS] plasma membrane [ISS]			762
Q96DS6 UniProt NPD GO	M4A6E_HUMAN	Membrane-spanning 4-domains subfamily A member 6E	0.21	-	mit	2 *	Membrane; multi-pass membrane protein		608402		147
Q03646 UniProt NPD GO	MSA2_PLAF2	Merozoite surface antigen 2 precursor (MSA-2)	0.21	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				347
P49068 UniProt NPD GO	MT1A_PIG	Metallothionein-1A (MT-1A) (Metallothionein-IA) (MT-IA)	0.21	-	nuc	0					61
Q2L969 UniProt NPD GO	MTX2_PIG	Metaxin-2	0.21	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				267
Q99MR8 UniProt NPD GO	MCCA_MOUSE	Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial precursor (EC 6.4.1.4) (3-methylcrotony ...	0.21	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial inner membrane [IDA] mitochondrial matrix [ISS] mitochondrion [IDA]			717
O74927 UniProt NPD GO	MTHR2_SCHPO	Methylenetetrahydrofolate reductase 2 (EC 1.5.1.20)	0.21	-	cyt	0					641
Q8HXX1 UniProt NPD GO	MUTA_MACFA	Methylmalonyl-CoA mutase, mitochondrial precursor (EC 5.4.99.2) (MCM) (Methylmalonyl-CoA isomerase)	0.21	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				750
Q8MI68 UniProt NPD GO	MUTA_PIG	Methylmalonyl-CoA mutase, mitochondrial precursor (EC 5.4.99.2) (MCM) (Methylmalonyl-CoA isomerase)	0.21	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				750
P55082 UniProt NPD GO	MFAP3_HUMAN	Microfibril-associated glycoprotein 3 precursor	0.21	-	mit	2 *	Cell membrane; single-pass type I membrane protein (Potential)		600491		362
Q5EA71 UniProt NPD GO	RM49_BOVIN	Mitochondrial 39S ribosomal protein L49 (L49mt) (MRP-L49)	0.21	-	mit	0	Mitochondrion				166

You are viewing entries 49701 to 49750 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.