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
Q6EIK1 UniProt NPD GO	MATK_PENDO	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				504
Q95E84 UniProt NPD GO	MATK_SCHTR	Maturase K (Intron maturase)	0.63	-	nuc	0	Plastid; chloroplast				509
Q5YK01 UniProt NPD GO	MATK_SPAJU	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				506
Q9TKD3 UniProt NPD GO	MATK_THRSA	Maturase K (Intron maturase)	0.63	-	nuc	0	Plastid; chloroplast				503
Q8MCN1 UniProt NPD GO	MATK_TRIHI	Maturase K (Intron maturase)	0.63	-	nuc	0	Plastid; chloroplast				506
Q8MCM8 UniProt NPD GO	MATK_TRILP	Maturase K (Intron maturase)	0.63	-	nuc	0	Plastid; chloroplast				506
Q8MCJ4 UniProt NPD GO	MATK_VICVI	Maturase K (Intron maturase)	0.63	-	mit	0	Plastid; chloroplast				503
Q499Q5 UniProt NPD GO	MKS1_RAT	Meckel syndrome type 1 protein homolog	0.63	-	cyt	0					561
Q6FW79 UniProt NPD GO	MSC6_CANGA	Meiotic sister-chromatid recombination protein 6, mitochondrial precursor	0.63	-	mit	0	Mitochondrion (By similarity)				709
O15480 UniProt NPD GO	MAGB3_HUMAN	Melanoma-associated antigen B3 (MAGE-B3 antigen)	0.63	-	nuc	0			300152		346
Q8TD91 UniProt NPD GO	MAGC3_HUMAN	Melanoma-associated antigen C3 (MAGE-C3 antigen) (Hepatocellular carcinoma-associated antigen 2)	0.63	-	end	0			300469		643
Q9UNF1 UniProt NPD GO	MAGD2_HUMAN	Melanoma-associated antigen D2 (MAGE-D2 antigen) (MAGE-D) (Breast cancer-associated gene 1 protein) ...	0.63	-	nuc	0			300470		606
Q96JG8 UniProt NPD GO	MAGD4_HUMAN	Melanoma-associated antigen D4 (MAGE-D4 antigen) (MAGE-E1 antigen)	0.63	-	nuc	0					741
Q9FK28 UniProt NPD GO	MEM12_ARATH	Membrin 12 (AtMEMB12) (Golgi SNAP receptor complex member 2-2)	0.63	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (Potential)				219
Q9QUS6 UniProt NPD GO	TRIM1_MOUSE	Midline-2 (Midline defect 2) (Tripartite motif-containing protein 1)	0.63	-	nuc	0	Cytoplasm. Microtubule-associated				685
Q9D0G0 UniProt NPD GO	RT30_MOUSE	Mitochondrial 28S ribosomal protein S30 (S30mt) (MRP-S30)	0.63	+	mit	0	Mitochondrion (By similarity)				442
Q5ABR2 UniProt NPD GO	GEM1_CANAL	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.63	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				644
P50892 UniProt NPD GO	RT12_RAPSA	Mitochondrial ribosomal protein S12	0.63	-	nuc	0	Mitochondrion				125
Q99717 UniProt NPD GO	SMAD5_HUMAN	Mothers against decapentaplegic homolog 5 (SMAD 5) (Mothers against DPP homolog 5) (Smad5) (hSmad5) ...	0.63	-	nuc	0	Cytoplasm. In the cytoplasm in the absence of ligand. Nucleus. Migration to the nucleus when complex ...	integral to membrane [NAS] intracellular [NAS] nucleus [NAS]	603110		465
P97454 UniProt NPD GO	SMAD5_MOUSE	Mothers against decapentaplegic homolog 5 (SMAD 5) (Mothers against DPP homolog 5) (Smad5) (mSmad5) ...	0.63	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	integral to membrane [ISS] intracellular [ISS] nucleus [ISS]			465
Q17295 UniProt NPD GO	MYOD1_CAEBR	Myoblast determination protein 1 homolog (MyoD protein 1)	0.63	+	nuc	0	Nucleus				329
Q13614 UniProt NPD GO	MTMR2_HUMAN	Myotubularin-related protein 2 (EC 3.1.3.-)	0.63	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Partly associated with membranes	cytoplasm [IDA] nucleus [IDA]	601382	1ZVR	643
Q9Y216 UniProt NPD GO	MTMR7_HUMAN	Myotubularin-related protein 7 (EC 3.1.3.-)	0.63	-	nuc	0			603562		660
Q4PS85 UniProt NPD GO	MYOZ1_PIG	Myozenin-1 (Calsarcin-2) (Calcineurin-interacting protein 2)	0.63	-	nuc	0	Localized to the nucleus and pseudopodia of undifferentiated cells and detected throughout the myotu ...				298
Q9NP98 UniProt NPD GO	MYOZ1_HUMAN	Myozenin-1 (Calsarcin-2) (Filamin-, actinin- and telethonin-binding protein) (Protein FATZ)	0.63	-	nuc	0	Localized to the nucleus and pseudopodia of undifferentiated cells and detected throughout the myotu ...		605603		299
Q8VDP3 UniProt NPD GO	MICA1_MOUSE	NEDD9-interacting protein with calponin homology and LIM domains (Molecule interacting with CasL pro ...	0.63	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS] intermediate filament [ISS]		2C4C	1048
Q9MZK6 UniProt NPD GO	NKG2C_MACMU	NKG2-C type II integral membrane protein (NKG2-C-activating NK receptor) (NK cell receptor C) (CD159 ...	0.63	-	nuc	1	Membrane; single-pass type II membrane protein				231
Q66HE5 UniProt NPD GO	NUAK2_RAT	NUAK family SNF1-like kinase 2 (EC 2.7.11.1) (SNF1/AMP kinase-related kinase) (SNARK)	0.63	-	nuc	0					630
P07861 UniProt NPD GO	NEP_RAT	Neprilysin (EC 3.4.24.11) (Neutral endopeptidase) (NEP) (Enkephalinase) (Neutral endopeptidase 24.11 ...	0.63	-	mit	1 *	Membrane; single-pass type II membrane protein				749
P55066 UniProt NPD GO	CSPG3_MOUSE	Neurocan core protein precursor (Chondroitin sulfate proteoglycan 3)	0.63	-	exc	0					1268
Q5IS41 UniProt NPD GO	CSPG3_PANTR	Neurocan core protein precursor (Chondroitin sulfate proteoglycan 3)	0.63	+	nuc	0					1321
P28840 UniProt NPD GO	NEC1_RAT	Neuroendocrine convertase 1 precursor (EC 3.4.21.93) (NEC 1) (PC1) (Prohormone convertase 1) (Propro ...	0.63	+	exc	0	Secretory vesicle. Localized in the secretion granules				752
Q9UM47 UniProt NPD GO	NOTC3_HUMAN	Neurogenic locus notch homolog protein 3 precursor (Notch 3) [Contains: Notch 3 extracellular trunca ...	0.63	+	mit	0	Cell membrane; single-pass type I membrane protein. NICD: Nucleus. Following proteolytical processin ...		600276		2321
P29476 UniProt NPD GO	NOS1_RAT	Nitric-oxide synthase, brain (EC 1.14.13.39) (NOS type I) (Neuronal NOS) (N-NOS) (nNOS) (Constitutiv ...	0.63	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein (By similarity). In skeletal muscle, i ...	cytoplasm [IDA] dendrite [IDA] mitochondrial outer membrane [IDA] synapse [IDA]		1ZZU	1429
P16275 UniProt NPD GO	IFEB_HELPO	Non-neuronal cytoplasmic intermediate filament protein B (IFB)	0.63	-	nuc	0	Cytoplasm				450
Q6BDR8 UniProt NPD GO	NSE4_SCHPO	Non-structural maintenance of chromosome element 4 (Non-SMC element 4) (DNA repair protein rad62)	0.63	-	nuc	0	Nucleus	replication fork [TAS] Smc5-Smc6 complex [IDA]			300
P11632 UniProt NPD GO	NHP6A_YEAST	Nonhistone chromosomal protein 6A	0.63	-	nuc	0	Nucleus. Colocalizes with both RNA polymerase II and some regions that are not transcribed on chroma ...	FACT complex [IGI] nuclear chromatin [IPI]		1LWM	93
P18608 UniProt NPD GO	HMGN1_MOUSE	Nonhistone chromosomal protein HMG-14 (High-mobility group nucleosome-binding domain-containing prot ...	0.63	-	nuc	0	Nucleus				95
Q5ZMC9 UniProt NPD GO	NDE1_CHICK	Nuclear distribution protein nudE homolog 1	0.63	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				342
Q66J96 UniProt NPD GO	NDE1A_XENLA	Nuclear distribution protein nudE homolog 1-A (Mitotic phosphoprotein 43) (MP43)	0.63	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				349
Q99383 UniProt NPD GO	HRP1_YEAST	Nuclear polyadenylated RNA-binding protein 4 (Cleavage factor IB) (CFIB)	0.63	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] mRNA cleavage factor complex [IPI] nucleus [IDA]			534
Q8BH74 UniProt NPD GO	NU107_MOUSE	Nuclear pore complex protein Nup107 (Nucleoporin Nup107) (107 kDa nucleoporin)	0.63	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Located on both the cytoplasmic and ...				926
Q8VCQ3 UniProt NPD GO	NRBF2_MOUSE	Nuclear receptor-binding factor 2 (NRBF-2)	0.63	-	nuc	0	Nucleus. Cytoplasm (By similarity)			2CRB	287
Q9JI85 UniProt NPD GO	NUCB2_RAT	Nucleobindin-2 precursor (DNA-binding protein NEFA)	0.63	-	exc	0	Membrane; peripheral membrane protein (By similarity). Cytoplasm (By similarity). Secreted protein ( ...	Golgi medial cisterna [IDA]			420
P36161 UniProt NPD GO	NU133_YEAST	Nucleoporin NUP133 (Nuclear pore protein NUP133)	0.63	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			1157
Q5VST9 UniProt NPD GO	OBSCN_HUMAN	Obscurin (Obscurin-myosin light chain kinase) (Obscurin-MLCK) (Obscurin-RhoGEF)	0.63	-	cyt	0	In differentiating skeletal muscle cells, isoform 3 primarily localizes to the sarcomeric M line and ...		608616	1V1C	7968
Q2YDI2 UniProt NPD GO	ORC4_BOVIN	Origin recognition complex subunit 4	0.63	-	mit	0	Nucleus (By similarity)				436
O43929 UniProt NPD GO	ORC4_HUMAN	Origin recognition complex subunit 4	0.63	-	mit	0	Nucleus	nucleus [TAS]	603056		436
P61364 UniProt NPD GO	OSTN_MOUSE	Osteocrin precursor (Musclin)	0.63	-	nuc	0	Secreted protein (By similarity)	extracellular space [IDA]			130
Q29438 UniProt NPD GO	ODFP_BOVIN	Outer dense fiber protein	0.63	-	nuc	0					262

You are viewing entries 17501 to 17550 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.