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
Q6PP78 UniProt NPD GO	MATK_VIGUN	Maturase K (Intron maturase)	0.58	-	nuc	0	Plastid; chloroplast				504
P34765 UniProt NPD GO	MEC3_CAEVU	Mechanosensory protein 3	0.58	+	nuc	0	Nucleus				320
P31423 UniProt NPD GO	MGR4_RAT	Metabotropic glutamate receptor 4 precursor (mGluR4)	0.58	-	end	7 *	Membrane; multi-pass membrane protein	active zone presynaptic plasma membrane [IDA] dendritic shaft [IDA] terminal button [IDA]			912
Q14831 UniProt NPD GO	MGR7_HUMAN	Metabotropic glutamate receptor 7 precursor (mGluR7)	0.58	-	end	6	Membrane; multi-pass membrane protein	active zone presynaptic plasma membrane [TAS] integral to plasma membrane [TAS] postsynaptic membrane [TAS]	604101		915
Q9D9H3 UniProt NPD GO	MB3L1_MOUSE	Methyl-CpG-binding domain protein 3-like 1 (MBD3-like 1)	0.58	-	nuc	0	Nucleus (By similarity). Nuclear, in large foci (By similarity)				186
Q5ZKK1 UniProt NPD GO	MARE2_CHICK	Microtubule-associated protein RP/EB family member 2	0.58	-	nuc	0	Cytoplasm (By similarity). Associated with the microtubule network (By similarity)				338
Q15555 UniProt NPD GO	MARE2_HUMAN	Microtubule-associated protein RP/EB family member 2 (APC-binding protein EB2) (End-binding protein ...	0.58	-	nuc	0	Cytoplasm. Associated with the microtubule network. Accumulates at the plus end of microtubules		605789		327
O94624 UniProt NPD GO	TIM54_SCHPO	Mitochondrial import inner membrane translocase subunit tim54	0.58	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				347
Q62760 UniProt NPD GO	TOM20_RAT	Mitochondrial import receptor subunit TOM20 homolog (Mitochondrial 20 kDa outer membrane protein) (O ...	0.58	+	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (Potential)	mitochondrial outer membrane translocase co... [NAS]		2CUV	145
Q96033 UniProt NPD GO	RT12_HELAN	Mitochondrial ribosomal protein S12	0.58	-	nuc	0	Mitochondrion				125
Q5SN53 UniProt NPD GO	MPK8_ORYSA	Mitogen-activated protein kinase 8 (EC 2.7.11.24) (MAP kinase 8) (OsWJUMK1) (Wound- and JA-uninducib ...	0.58	-	nuc	0					569
Q9V3Q6 UniProt NPD GO	M3K7_DROME	Mitogen-activated protein kinase kinase kinase 7 (EC 2.7.11.25) (TGF-beta-activated kinase 1) (dTAK1 ...	0.58	-	nuc	0					678
Q571K4 UniProt NPD GO	TAB3_MOUSE	Mitogen-activated protein kinase kinase kinase 7-interacting protein 3 (TAK1-binding protein 3)	0.58	-	nuc	0					716
Q8N5C8 UniProt NPD GO	TAB3_HUMAN	Mitogen-activated protein kinase kinase kinase 7-interacting protein 3 (TAK1-binding protein 3) (NF- ...	0.58	-	nuc	0			300480		712
Q7ZXH3 UniProt NPD GO	TAB3_XENLA	Mitogen-activated protein kinase kinase kinase 7-interacting protein 3 homolog	0.58	-	nuc	0					692
Q9CWP6 UniProt NPD GO	MSPD2_MOUSE	Motile sperm domain-containing protein 2	0.58	-	nuc	1				1WIC	518
O01704 UniProt NPD GO	EXT1_CAEEL	Multiple exostoses homolog 1 (Related to mammalian RIB protein 1)	0.58	-	cyt	0					378
Q6PDN3 UniProt NPD GO	MYLK_MOUSE	Myosin light chain kinase, smooth muscle (EC 2.7.11.18) (MLCK) (Telokin) (Kinase-related protein) (K ...	0.58	-	cyt	0	Cytoplasm. Tagged isoform 1 colocalizes with stress fibers. Tagged Smooth muscle isoform is found th ...				1941
P53685 UniProt NPD GO	HST1_YEAST	NAD-dependent deacetylase HST1 (EC 3.5.1.-) (Homologous to SIR2 protein 1)	0.58	-	nuc	0	Nucleus. But not nucleolar, and cytoplasmic	histone deacetylase complex [IDA] nucleus [TAS]			503
P18939 UniProt NPD GO	NU4M_CHICK	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.58	-	end	11 *					459
O88995 UniProt NPD GO	IKBL_MOUSE	NF-kappa-B inhibitor-like protein 1 (Inhibitor of kappa B-like) (I-kappa-B-like) (IkappaBL) (Nuclear ...	0.58	-	nuc	0					381
P26717 UniProt NPD GO	NKG2C_HUMAN	NKG2-C type II integral membrane protein (NKG2-C-activating NK receptor) (NK cell receptor C) (CD159 ...	0.58	-	nuc	1	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	602891		231
Q9BZM4 UniProt NPD GO	N2DL3_HUMAN	NKG2D ligand 3 precursor (NKG2D ligand 3) (NKG2DL3) (N2DL-3) (ALCAN-gamma) (Retinoic acid early tran ...	0.58	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor	membrane [NAS]	605699	1KCG	244
Q8C567 UniProt NPD GO	NCTR1_MOUSE	Natural cytotoxicity triggering receptor 1 precursor (Natural killer cell p46-related protein) (NKp4 ...	0.58	-	end	1	Membrane; single-pass type I membrane protein (Potential)				325
P55067 UniProt NPD GO	CSPG3_RAT	Neurocan core protein precursor (Chondroitin sulfate proteoglycan 3) (245 kDa early postnatal core g ...	0.58	-	nuc	0		extracellular matrix (sensu Metazoa) [IPI]			1257
Q810U3 UniProt NPD GO	NFASC_MOUSE	Neurofascin precursor	0.58	-	exc	2 *	Membrane; single-pass type I membrane protein	axon [IDA] plasma membrane [IDA]			1240
P12839 UniProt NPD GO	NFM_RAT	Neurofilament triplet M protein (160 kDa neurofilament protein) (Neurofilament medium polypeptide) ( ...	0.58	-	nuc	0		cytoskeleton [IDA]			845
P12760 UniProt NPD GO	NEUU_RAT	Neuromedin U-23 precursor (NmU-23)	0.58	+	exc	0	Secreted protein				174
O62729 UniProt NPD GO	NPY5R_CANFA	Neuropeptide Y receptor type 5 (NPY5-R) (NPY-Y5 receptor) (Y5 receptor) (NPYY5)	0.58	-	end	7 *	Membrane; multi-pass membrane protein				446
P20068 UniProt NPD GO	NEUT_RAT	Neurotensin/neuromedin N precursor [Contains: Large neuromedin N (NmN-125); Neuromedin N (NmN) (NN); ...	0.58	-	exc	0	Secreted protein. Packaged within secretory vesicles				169
P35228 UniProt NPD GO	NOS2A_HUMAN	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.58	-	mit	0		cytoplasm [TAS] cytosol [ISS]	163730	4NOS	1153
Q75B82 UniProt NPD GO	NHP6_ASHGO	Nonhistone chromosomal protein 6	0.58	-	nuc	0	Nucleus (By similarity)				94
Q5B995 UniProt NPD GO	NHP6_EMENI	Nonhistone chromosomal protein 6	0.58	-	nuc	0	Nucleus (By similarity)				106
Q9N1Q6 UniProt NPD GO	SP100_GORGO	Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein) (Fragment)	0.58	+	nuc	0	Nucleus (By similarity). Found in the nuclear body, a nucleoplasmic structure of punctate shape, whi ...				225
Q7SXI6 UniProt NPD GO	NDL1A_BRARE	Nuclear distribution protein nudE-like 1-A	0.58	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				344
O97863 UniProt NPD GO	NFHEV_CANFA	Nuclear factor from high endothelial venules (NF-HEV) (DVS27 protein)	0.58	-	nuc	0	Nucleus (By similarity)				263
P41999 UniProt NPD GO	NHR10_CAEEL	Nuclear hormone receptor family member nhr-10	0.58	-	cyt	0	Nucleus (Potential)				395
Q18192 UniProt NPD GO	NHR31_CAEEL	Nuclear hormone receptor family member nhr-31	0.58	-	nuc	0	Nucleus (Potential)				583
O17933 UniProt NPD GO	NHR53_CAEEL	Nuclear hormone receptor family member nhr-53	0.58	-	cyt	0	Nucleus (Potential)				364
O45460 UniProt NPD GO	NHR54_CAEEL	Nuclear hormone receptor family member nhr-54	0.58	-	nuc	0	Nucleus (Potential)				422
Q99P88 UniProt NPD GO	NU155_MOUSE	Nuclear pore complex protein Nup155 (Nucleoporin Nup155) (155 kDa nucleoporin)	0.58	-	end	0	Nucleus; nuclear envelope; nuclear pore complex; peripheral membrane protein; cytoplasmic side (By s ...				1391
Q96F24 UniProt NPD GO	NRBF2_HUMAN	Nuclear receptor-binding factor 2 (NRBF-2) (Comodulator of PPAR and RXR)	0.58	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				287
Q02892 UniProt NPD GO	NOG1_YEAST	Nucleolar GTP-binding protein 1	0.58	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			647
Q8JZU0 UniProt NPD GO	NUD13_MOUSE	Nucleoside diphosphate linked moiety X motif 13 (EC 3.-.-.-) (Nudix motif 13)	0.58	-	mit	0					352
Q61146 UniProt NPD GO	OCLN_MOUSE	Occludin	0.58	-	end	5	Membrane; multi-pass membrane protein	plasma membrane [IDA] tight junction [IDA]			521
Q6PFG8 UniProt NPD GO	OLIG3_MOUSE	Oligodendrocyte transcription factor 3 (Oligo3) (Oligodendrocyte-specific bHLH transcription factor ...	0.58	-	nuc	0	Nucleus				273
P53049 UniProt NPD GO	YOR1_YEAST	Oligomycin resistance ATP-dependent permease YOR1	0.58	-	end	11	Membrane; multi-pass membrane protein	plasma membrane [IDA]			1477
Q9QUS1 UniProt NPD GO	NR1I3_RAT	Orphan nuclear receptor NR1I3 (Constitutive androstane receptor) (CAR)	0.58	-	cyt	0	Nucleus (By similarity)				358
Q26622 UniProt NPD GO	SHR2_STRPU	Orphan steroid hormone receptor 2 (SpSHR2)	0.58	-	nuc	0	Cytoplasm. Nucleus. The subcellular location of isoform 1 alters throughout development; in the unfe ...	apical part of cell [IDA] cytoplasm [IDA] nuclear lamina [IDA] nucleus [IDA] perinuclear region [IDA]			583
Q6ZZF5 UniProt NPD GO	OXR1_PICJA	Oxidation resistance protein 1 (Fragment)	0.58	-	nuc	0	Mitochondrion (By similarity)				176

You are viewing entries 20301 to 20350 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.