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
P34926 UniProt NPD GO	MAP1A_RAT	Microtubule-associated protein 1A (MAP 1A) [Contains: MAP1 light chain LC2]	0.79	+	nuc	0		microtubule associated complex [IDA]			2774
Q7RZA2 UniProt NPD GO	GEM1_NEUCR	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.79	+	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				629
P26865 UniProt NPD GO	RT03_MARPO	Mitochondrial ribosomal protein S3	0.79	-	nuc	0	Mitochondrion				430
Q9NYL2 UniProt NPD GO	MLTK_HUMAN	Mitogen-activated protein kinase kinase kinase MLT (EC 2.7.11.25) (MLK-like mitogen-activated protei ...	0.79	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]	609479		800
Q924I2 UniProt NPD GO	M4K3_RAT	Mitogen-activated protein kinase kinase kinase kinase 3 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.79	-	nuc	0					862
O44514 UniProt NPD GO	PMK3_CAEEL	Mitogen-activated protein kinase pmk-3 (EC 2.7.11.24) (p38 MAP kinase 3) (Stress-activated protein k ...	0.79	-	nuc	0	Nucleus	nucleus [IEP]			474
O43683 UniProt NPD GO	BUB1_HUMAN	Mitotic checkpoint serine/threonine-protein kinase BUB1 (EC 2.7.11.1) (hBUB1) (BUB1A)	0.79	-	nuc	0	Nucleus (By similarity). Nuclear in interphase cells. Kinetochore localization is required for norma ...	kinetochore [TAS] spindle pole body [TAS]	602452		1085
P31732 UniProt NPD GO	OV71_ONCVO	Muscle cell intermediate filament protein OV71 (Fragment)	0.79	-	nuc	0					432
P80073 UniProt NPD GO	MYB2_PHYPA	Myb-related protein Pp2	0.79	+	nuc	0	Nucleus (Potential)				421
P29331 UniProt NPD GO	MYOD1_SHEEP	Myoblast determination protein 1	0.79	+	nuc	0	Nucleus				319
Q25413 UniProt NPD GO	MYOM_LYMST	Myomodulin neuropeptides precursor [Contains: GLQMLRL-amide; QIPMLRL-amide; SMSMLRL-amide; SLSMLRL-a ...	0.79	-	nuc	0	Secreted protein				350
Q923E4 UniProt NPD GO	SIRT1_MOUSE	NAD-dependent deacetylase sirtuin-1 (EC 3.5.1.-) (SIR2alpha) (mSIR2a) (Sir2) (SIR2-like protein 1)	0.79	+	nuc	0	Nucleus (By similarity). Recruited to the nuclear bodies via its interaction with PML (By similarity ...	nucleus [IDA]			737
Q61122 UniProt NPD GO	NAB1_MOUSE	NGFI-A-binding protein 1 (EGR-1-binding protein 1)	0.79	-	nuc	0	Nucleus (By similarity)				486
O35589 UniProt NPD GO	NAB1_MESAU	NGFI-A-binding protein 1 (EGR-1-binding protein 1) (Transcriptional repressor TA16)	0.79	-	nuc	0	Nucleus (By similarity)				485
Q8S3M3 UniProt NPD GO	NOIL_ELAOL	NOI-like protein	0.79	-	nuc	0					228
P23250 UniProt NPD GO	RPI1_YEAST	Negative RAS protein regulator protein	0.79	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			407
P43146 UniProt NPD GO	DCC_HUMAN	Netrin receptor DCC precursor (Tumor suppressor protein DCC) (Colorectal cancer suppressor)	0.79	-	nuc	2 *	Membrane; single-pass type I membrane protein		120470		1447
Q07008 UniProt NPD GO	NOTC1_RAT	Neurogenic locus notch homolog protein 1 precursor (Notch 1) [Contains: Notch 1 extracellular trunca ...	0.79	+	exc	0	Cell membrane; single-pass type I membrane protein (By similarity). NICD: Nucleus (By similarity). F ...			1YMP	2531
Q8TDF5 UniProt NPD GO	NETO1_HUMAN	Neuropilin and tolloid-like protein 1 precursor (Brain-specific transmembrane protein containing 2 C ...	0.79	-	nuc	1	Isoform 2, isoform 3: Cell membrane; single-pass type I membrane protein (Potential). Isoform 1: Sec ...		607973		533
Q09014 UniProt NPD GO	NCF1_MOUSE	Neutrophil cytosol factor 1 (NCF-1) (Neutrophil NADPH oxidase factor 1) (47 kDa neutrophil oxidase f ...	0.79	-	nuc	0	Cytoplasm	cytoplasm [IDA] cytosol [TAS]			390
P26343 UniProt NPD GO	DAL80_YEAST	Nitrogen regulatory protein DAL80 (Regulatory protein UGA43)	0.79	-	nuc	0	Nucleus	nucleus [IDA]			269
Q99K48 UniProt NPD GO	NONO_MOUSE	Non-POU domain-containing octamer-binding protein (NonO protein)	0.79	+	nuc	0	Nucleus (By similarity)			2CPJ	473
Q5FVM4 UniProt NPD GO	NONO_RAT	Non-POU domain-containing octamer-binding protein (NonO protein)	0.79	+	nuc	0	Nucleus (By similarity)				476
Q56A27 UniProt NPD GO	NCBP1_RAT	Nuclear cap-binding protein subunit 1	0.79	+	mit	0	Nucleus (By similarity)	nucleus [ISS]			790
Q8BVZ5 UniProt NPD GO	NFHEV_MOUSE	Nuclear factor from high endothelial venules (NF-HEV)	0.79	-	nuc	0	Nucleus (By similarity)				266
Q92621 UniProt NPD GO	NU205_HUMAN	Nuclear pore complex protein Nup205 (Nucleoporin Nup205) (205 kDa nucleoporin)	0.79	-	end	0	Nucleus; nuclear envelope; nuclear pore complex (Potential)	nuclear pore [NAS]			2012
Q8CEC0 UniProt NPD GO	NUP88_MOUSE	Nuclear pore complex protein Nup88 (Nucleoporin Nup88) (88 kDa nuclear pore complex protein)	0.79	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity)				753
Q9UND3 UniProt NPD GO	NPIP_HUMAN	Nuclear pore complex-interacting protein (NPIP)	0.79	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex. Colocalizes with nuclear pore complex protein NUP62 ...		606406		350
P51450 UniProt NPD GO	RORG_MOUSE	Nuclear receptor ROR-gamma (Nuclear receptor RZR-gamma) (Thymus orphan receptor) (TOR)	0.79	-	nuc	0	Nucleus (Probable)				516
Q9U6A9 UniProt NPD GO	NOG1_TRYBB	Nucleolar GTP-binding protein 1	0.79	-	nuc	0	Nucleus; nucleolus				655
Q6NRY2 UniProt NPD GO	NOL6_XENLA	Nucleolar protein 6	0.79	-	cyt	0	Nucleus; nucleolus (By similarity)				1147
P13483 UniProt NPD GO	DATI_YEAST	Oligo(A)/oligo(T)-binding protein (Datin)	0.79	-	nuc	0		nucleus [IDA]			248
O75469 UniProt NPD GO	PXR_HUMAN	Orphan nuclear receptor PXR (Pregnane X receptor) (Orphan nuclear receptor PAR1) (Steroid and xenobi ...	0.79	-	cyt	0	Nucleus (By similarity)		603065	1SKX	434
Q07084 UniProt NPD GO	SSK1_YEAST	Osomolarity two-component system protein SSK1	0.79	-	nuc	0	Cytoplasm (Potential)	cytoplasm [TAS]			712
P35845 UniProt NPD GO	OSH1_YEAST	Oxysterol-binding protein homolog 1	0.79	-	nuc	0	Golgi apparatus. Endoplasmic reticulum. Golgi and nucleus-vacuole junction (NVJ), a small subcompart ...	early endosome [IDA] endoplasmic reticulum [IDA] Golgi trans cisterna [IDA]			1188
Q14863 UniProt NPD GO	PO6F1_HUMAN	POU domain, class 6, transcription factor 1 (mPOU homeobox protein) (Brain-specific homeobox/POU dom ...	0.79	+	nuc	0	Nucleus				301
Q9NQV8 UniProt NPD GO	PRDM8_HUMAN	PR domain zinc finger protein 8 (PR domain-containing protein 8)	0.79	-	nuc	0	Nucleus (By similarity)				689
Q925B0 UniProt NPD GO	PAWR_MOUSE	PRKC apoptosis WT1 regulator protein (Prostate apoptosis response 4 protein) (Par-4) (Fragment)	0.79	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Mainly cytoplasmic in absence of apoptosis signa ...	cytoplasm [IDA] nucleus [IDA]			197
Q62627 UniProt NPD GO	PAWR_RAT	PRKC apoptosis WT1 regulator protein (Prostate apoptosis response 4 protein) (Par-4) (Transcriptiona ...	0.79	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Mainly cytoplasmic in absence of apoptosis signa ...				332
Q64305 UniProt NPD GO	PTF1A_RAT	Pancreas transcription factor 1 subunit alpha (Pancreas-specific transcription factor 1a) (bHLH tran ...	0.79	-	nuc	0	Nucleus. Cytoplasm. In the cytoplasm loses its ability to form the PTF1 complex	cytoplasm [IDA] nucleus [IDA] transcription factor complex [IDA]			326
Q8MUF6 UniProt NPD GO	MYSP_BLOTA	Paramyosin (Allergen Blo t 11)	0.79	-	nuc	0	Thick filaments of the myofibrils				875
P21807 UniProt NPD GO	PERI_RAT	Peripherin	0.79	-	mit	0		type III intermediate filament [IDA]			468
Q9JMC1 UniProt NPD GO	PI5PA_RAT	Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (EC 3.1.3.56) (Proline-rich inositol polyphosp ...	0.79	-	nuc	0	Cytoplasm. Predominantly localized to membrane ruffles	ruffle [IDA]			1001
P54677 UniProt NPD GO	PI4K_DICDI	Phosphatidylinositol 4-kinase (EC 2.7.1.67) (PI4-kinase) (PtdIns-4-kinase) (PI4K-alpha)	0.79	-	nuc	0					1093
Q91XR9 UniProt NPD GO	GPX42_MOUSE	Phospholipid hydroperoxide glutathione peroxidase, nuclear (EC 1.11.1.12) (GPX-4)	0.79	+	mit	0	Nucleus	cytosol [IDA] mitochondrial inner membrane [IDA] mitochondrion [IDA] nuclear envelope [IDA] nucleus [IDA]			253
P28561 UniProt NPD GO	APCE_AGLNE	Phycobilisome linker polypeptide (Anchor polypeptide) (PBS-anchor protein)	0.79	-	nuc	0	Plastid; chloroplast				885
P48088 UniProt NPD GO	APCE_CYAPA	Phycobilisome linker polypeptide (Anchor polypeptide) (PBS-anchor protein)	0.79	-	cyt	0	Plastid; cyanelle				883
Q7Z3Z3 UniProt NPD GO	PIWL3_HUMAN	Piwi-like protein 3	0.79	+	nuc	0					882
P34007 UniProt NPD GO	PDGFA_RABIT	Platelet-derived growth factor A chain precursor (PDGF A-chain) (Platelet-derived growth factor alph ...	0.79	+	exc	0					213
Q9D824 UniProt NPD GO	FIP1_MOUSE	Pre-mRNA 3'-end-processing factor FIP1 (FIP1-like 1)	0.79	+	nuc	0	Nucleus (By similarity)				581

You are viewing entries 9451 to 9500 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.