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
O47157 UniProt NPD GO	MATK_ERITE	Maturase K (Intron maturase)	0.70	-	nuc	0	Plastid; chloroplast				506
Q5J308 UniProt NPD GO	MATK_GOMHA	Maturase K (Intron maturase)	0.70	-	nuc	0	Plastid; chloroplast				505
Q7YKQ3 UniProt NPD GO	MATK_GRAOF	Maturase K (Intron maturase)	0.70	-	pox	0	Plastid; chloroplast				510
Q95G88 UniProt NPD GO	MATK_JURCY	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				506
Q8MCR9 UniProt NPD GO	MATK_LATSA	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				506
O62992 UniProt NPD GO	MATK_LEDPA	Maturase K (Intron maturase)	0.70	-	nuc	0	Plastid; chloroplast				506
Q85XY8 UniProt NPD GO	MATK_MIMPU	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				506
Q95DR3 UniProt NPD GO	MATK_NICGL	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				509
Q8WJN9 UniProt NPD GO	MATK_PURTR	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				503
Q5J2W0 UniProt NPD GO	MATK_SILOT	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				505
O94356 UniProt NPD GO	MEU6_SCHPO	Meiotic expression up-regulated protein 6	0.70	-	nuc	0					651
P55162 UniProt NPD GO	HEM_DROME	Membrane-associated protein Hem (dHem-2)	0.70	+	end	0					1126
P28825 UniProt NPD GO	MEP1A_MOUSE	Meprin A subunit alpha precursor (EC 3.4.24.18) (Endopeptidase-2) (MEP-1)	0.70	-	end	1	Membrane; single-pass type I membrane protein			1IAF	747
Q8N108 UniProt NPD GO	MIER1_HUMAN	Mesoderm induction early response protein 1 (Mi-er1) (hmi-er1) (Early response 1) (Er1)	0.70	+	exc	0	Isoform 1, isoform 2, isoform 3: Nucleus. Isoform 4, isoform 5, isoform 6: Cytoplasm				536
P46821 UniProt NPD GO	MAP1B_HUMAN	Microtubule-associated protein 1B (MAP 1B) [Contains: MAP1 light chain LC1]	0.70	+	nuc	0		microtubule associated complex [TAS]	157129		2468
Q8VII8 UniProt NPD GO	MCR_MOUSE	Mineralocorticoid receptor (MR)	0.70	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Endoplasmic reticulum; endoplasmic reticulum mem ...				978
Q9CR88 UniProt NPD GO	RT14_MOUSE	Mitochondrial 28S ribosomal protein S14 (S14mt) (MRP-S14)	0.70	+	nuc	0	Mitochondrion	mitochondrion [IDA]			128
P46740 UniProt NPD GO	RT03_PROWI	Mitochondrial ribosomal protein S3	0.70	-	nuc	0	Mitochondrion				500
Q6L5F7 UniProt NPD GO	MPK17_ORYSA	Mitogen-activated protein kinase 17 (EC 2.7.11.24) (MAP kinase 17)	0.70	-	nuc	0					582
O80397 UniProt NPD GO	M2K4_ARATH	Mitogen-activated protein kinase kinase 4 (EC 2.7.12.2) (MAP kinase kinase 4) (AtMKK4)	0.70	-	mit	0		cytoplasm [IDA] nucleus [IDA]			366
O14029 UniProt NPD GO	SEC16_SCHPO	Multidomain vesicle coat protein	0.70	-	nuc	0	Endoplasmic reticulum (By similarity). On the endoplasmic reticulum and on vesicles which bud from i ...				1995
Q6CEW9 UniProt NPD GO	MRD1_YARLI	Multiple RNA-binding domain-containing protein 1	0.70	-	cyt	0	Nucleus (By similarity)				828
P08912 UniProt NPD GO	ACM5_HUMAN	Muscarinic acetylcholine receptor M5	0.70	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	118496		532
Q8TDH9 UniProt NPD GO	MUTED_HUMAN	Muted protein homolog	0.70	-	nuc	0			607289		187
O13493 UniProt NPD GO	MYB1_NEUCR	Myb-like DNA-binding protein myb-1	0.70	-	nuc	0	Nucleus (By similarity)				324
Q10656 UniProt NPD GO	EGL15_CAEEL	Myoblast growth factor receptor egl-15 precursor (EC 2.7.10.1) (Egg-laying defective protein 15)	0.70	-	end	2	Membrane; single-pass type I membrane protein	cell [IDA]			1040
Q03479 UniProt NPD GO	MYOE_DICDI	Myosin IE heavy chain	0.70	-	cyt	0				1LKX	1003
P11799 UniProt NPD GO	MYLK_CHICK	Myosin light chain kinase, smooth muscle (EC 2.7.11.18) (MLCK) (Telokin)	0.70	+	cyt	0	Cytoplasm; cytosol. Membrane. Telokin is cytosolic and can translocate to the membrane upon stimulat ...			1VRK	1906
Q8K296 UniProt NPD GO	MTMR3_MOUSE	Myotubularin-related protein 3 (EC 3.1.3.48)	0.70	-	nuc	0					1075
Q9Z2C9 UniProt NPD GO	MTMR7_MOUSE	Myotubularin-related protein 7 (EC 3.1.3.-)	0.70	-	nuc	0		cytosol [IDA] membrane fraction [IDA]			660
O15049 UniProt NPD GO	N4BP3_HUMAN	NEDD4-binding protein 3 (N4BP3)	0.70	-	nuc	0	Cytoplasmic vesicle; cytoplasmic vesicle membrane; peripheral membrane protein				544
O75161 UniProt NPD GO	NPHP4_HUMAN	Nephrocystin-4 (Nephroretinin)	0.70	-	cyt	0		membrane [IC]	607215		1426
Q61391 UniProt NPD GO	NEP_MOUSE	Neprilysin (EC 3.4.24.11) (Neutral endopeptidase) (NEP) (Enkephalinase) (Neutral endopeptidase 24.11 ...	0.70	-	mit	1 *	Membrane; single-pass type II membrane protein	membrane [IDA]			749
P21263 UniProt NPD GO	NEST_RAT	Nestin	0.70	-	nuc	0					1805
P54846 UniProt NPD GO	NRL_MOUSE	Neural retina-specific leucine zipper protein (NRL)	0.70	-	nuc	0	Nucleus				237
P54845 UniProt NPD GO	NRL_HUMAN	Neural retina-specific leucine zipper protein (NRL) (D14S46E)	0.70	-	nuc	0	Nucleus	nucleus [TAS]	162080		237
Q15784 UniProt NPD GO	NDF2_HUMAN	Neurogenic differentiation factor 2 (NeuroD2) (NeuroD-related factor) (NDRF)	0.70	+	nuc	0	Nucleus (Probable)		601725		382
P21519 UniProt NPD GO	MAM_DROME	Neurogenic protein mastermind	0.70	+	nuc	0	Nucleus	nucleus [IDA]			1594
Q92886 UniProt NPD GO	NGN1_HUMAN	Neurogenin 1 (Neurogenic differentiation factor 3) (NeuroD3) (Neurogenic basic-helix-loop-helix prot ...	0.70	+	nuc	0	Nucleus (Probable)		601726		237
P70595 UniProt NPD GO	NGN1_RAT	Neurogenin 1 (Neurogenic differentiation factor 3) (NeuroD3) (Neurogenic basic-helix-loop-helix prot ...	0.70	+	nuc	0	Nucleus (Probable)				244
P17691 UniProt NPD GO	NEUM_CARAU	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43)	0.70	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of growth cone and ...				213
Q22127 UniProt NPD GO	NHR40_CAEEL	Nuclear hormone receptor family member nhr-40	0.70	+	nuc	0	Nucleus (Potential)				455
Q99567 UniProt NPD GO	NUP88_HUMAN	Nuclear pore complex protein Nup88 (Nucleoporin Nup88) (88 kDa nuclear pore complex protein)	0.70	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex	nuclear pore [TAS]	602552		741
O60356 UniProt NPD GO	NUPR1_HUMAN	Nuclear protein 1 (Protein p8) (Candidate of metastasis 1)	0.70	+	nuc	0	Nucleus	nucleus [IDA]			82
P53254 UniProt NPD GO	UTP22_YEAST	Nucleolar protein UTP22	0.70	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA] small nucleolar ribonucleoprotein complex [IPI]			1237
Q95KA2 UniProt NPD GO	OPTN_MACFA	Optineurin	0.70	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Golgi apparatus (By similarity). Found in the perinuc ...				571
Q10067 UniProt NPD GO	ORC3_SCHPO	Origin recognition complex subunit 3	0.70	-	cyt	0	Nucleus	nuclear origin of replication recognition c... [IDA]			690
O43114 UniProt NPD GO	ORC5_SCHPO	Origin recognition complex subunit 5	0.70	+	cyt	0	Nucleus	nuclear origin of replication recognition c... [IDA]			455
Q4V8B0 UniProt NPD GO	OXR1_RAT	Oxidation resistance protein 1 (Protein C7)	0.70	-	nuc	0	Mitochondrion (By similarity)				758
P42201 UniProt NPD GO	LYAM3_BOVIN	P-selectin precursor (Granule membrane protein 140) (GMP-140) (PADGEM) (Leukocyte-endothelial cell a ...	0.70	-	nuc	1	Membrane; single-pass type I membrane protein				646

You are viewing entries 13851 to 13900 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.