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
P98088 UniProt NPD GO	MUC5A_HUMAN	Mucin-5AC (Mucin-5 subtype AC, tracheobronchial) (Tracheobronchial mucin) (TBM) (Major airway glycop ...	0.47	-	mit	0	Secreted protein	fibril [IDA]			1233
Q8LPT1 UniProt NPD GO	MDR6_ARATH	Multidrug resistance protein 6 (P-glycoprotein 6)	0.47	-	end	13	Membrane; multi-pass membrane protein (Potential)				1407
O75095 UniProt NPD GO	MEGF6_HUMAN	Multiple epidermal growth factor-like domains 6 precursor (EGF-like domain-containing protein 3) (Mu ...	0.47	-	nuc	0			604266		1229
Q4JL76 UniProt NPD GO	MYBA2_ORYSA	Myb-related protein MYBAS2	0.47	-	nuc	0	Nucleus (By similarity)				242
O08839 UniProt NPD GO	BIN1_RAT	Myc box-dependent-interacting protein 1 (Bridging integrator 1) (Amphiphysin-like protein) (Amphiphy ...	0.47	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	synaptic vesicle [IDA]		1BB9	588
Q28824 UniProt NPD GO	MYLK_BOVIN	Myosin light chain kinase, smooth muscle (EC 2.7.11.18) (MLCK) (Telokin)	0.47	-	nuc	0					1176
Q13496 UniProt NPD GO	MTM1_HUMAN	Myotubularin (EC 3.1.3.48)	0.47	-	nuc	0			310400		603
Q9JJW5 UniProt NPD GO	MYOZ2_MOUSE	Myozenin-2 (Calsarcin-1) (FATZ-related protein 2)	0.47	-	nuc	0	Colocalizes with ACTN1 and PPP3CA at the Z-line of heart and skeletal muscle	actin cytoskeleton [IDA] Z disc [IDA]			264
P30009 UniProt NPD GO	MARCS_RAT	Myristoylated alanine-rich C-kinase substrate (MARCKS) (Protein kinase C substrate 80 kDa protein)	0.47	+	nuc	0					308
Q7GCL7 UniProt NPD GO	NAC74_ORYSA	NAC domain-containing protein 74 (ONAC074)	0.47	-	nuc	1	Nucleus (Probable)				489
Q9MTP4 UniProt NPD GO	NUKC_OENHO	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.47	-	nuc	0	Plastid; chloroplast				247
O96000 UniProt NPD GO	NDUBA_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.47	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side		603843		171
Q9T9W6 UniProt NPD GO	NU4M_PANPA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.47	-	end	12 *					459
O79677 UniProt NPD GO	NU4M_PELSU	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.47	-	end	12 *					459
Q9Z0H5 UniProt NPD GO	NCTR1_RAT	Natural cytotoxicity triggering receptor 1 precursor (Natural killer cell p46-related protein) (NKp4 ...	0.47	-	end	1	Membrane; single-pass type I membrane protein (Potential)				325
P11627 UniProt NPD GO	L1CAM_MOUSE	Neural cell adhesion molecule L1 precursor (N-CAM L1) (CD171 antigen)	0.47	-	end	1	Membrane; single-pass type I membrane protein	cell surface [IDA] presynaptic membrane [IDA] terminal button [IDA]			1260
P29120 UniProt NPD GO	NEC1_HUMAN	Neuroendocrine convertase 1 precursor (EC 3.4.21.93) (NEC 1) (PC1) (Prohormone convertase 1) (Propro ...	0.47	+	mit	0	Secretory vesicle. Localized in the secretion granules		600955		753
P06837 UniProt NPD GO	NEUM_MOUSE	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43) (Calmodulin-binding pro ...	0.47	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of growth cone and ...	axon [IDA]			227
Q8MI35 UniProt NPD GO	NPW_PIG	Neuropeptide W precursor (Preproprotein L8) (PPL8) [Contains: Neuropeptide W-23 (NPW23) (L8); Neurop ...	0.47	-	mit	1 *	Secreted protein				152
O19114 UniProt NPD GO	NOS2_RABIT	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.47	-	cyt	0					496
Q14961 UniProt NPD GO	NOS2C_HUMAN	Nitric-oxide synthase IIC (EC 1.14.13.39) (NOS type II C) (NOSIIc) (Fragment)	0.47	-	cyt	0			600720		69
P79942 UniProt NPD GO	NOCT_XENLA	Nocturnin (Rhythmic message 1) (RM1)	0.47	-	nuc	0					388
P43021 UniProt NPD GO	NODAL_MOUSE	Nodal precursor	0.47	-	mit	0	Secreted protein (By similarity)				354
Q9IAK4 UniProt NPD GO	NOE1_CHICK	Noelin precursor (Neuronal olfactomedin-related ER localized protein) (Olfactomedin-1) (Pancortin)	0.47	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				485
Q99ML2 UniProt NPD GO	TNK1_MOUSE	Non-receptor tyrosine-protein kinase TNK1 (EC 2.7.10.2) (Kinase of embryonic stem cells)	0.47	-	nuc	0	Membrane (By similarity). Cytoplasm	cytosol [IDA]			666
Q5KEP6 UniProt NPD GO	NHP6_CRYNE	Nonhistone chromosomal protein 6	0.47	-	nuc	0	Nucleus (By similarity)				116
Q9UUJ6 UniProt NPD GO	NED1_SCHPO	Nuclear elongation and deformation protein 1	0.47	-	nuc	0					656
O17927 UniProt NPD GO	NHR51_CAEEL	Nuclear hormone receptor family member nhr-51	0.47	-	cyt	0	Nucleus (Potential)				371
Q9QZ86 UniProt NPD GO	NOP5_RAT	Nucleolar protein NOP5 (Nucleolar protein 5) (Nopp140-associated protein)	0.47	+	cyt	0	Nucleus; nucleolus	nucleolus [ISS] small nucleolar ribonucleoprotein complex [IDA]			534
Q68FY1 UniProt NPD GO	NUP53_RAT	Nucleoporin NUP53 (Nuclear pore complex protein Nup53) (Nucleoporin Nup35) (35 kDa nucleoporin)	0.47	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Tightly associated with the nuclear ...				325
Q8NFH5 UniProt NPD GO	NUP53_HUMAN	Nucleoporin NUP53 (Nuclear pore complex protein Nup53) (Nucleoporin Nup35) (35 kDa nucleoporin) (Mit ...	0.47	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex. Tightly associated with the nuclear membrane and la ...		608140		326
Q12445 UniProt NPD GO	POM34_YEAST	Nucleoporin POM34 (Nuclear pore protein POM34) (Pore membrane protein POM34)	0.47	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...	nuclear pore [IDA]			299
Q96EE3 UniProt NPD GO	SEH1L_HUMAN	Nucleoporin SEH1-like (SEC13-like protein)	0.47	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex				421
P18739 UniProt NPD GO	ZO10_XENLA	Oocyte zinc finger protein XLCOF10 (Fragment)	0.47	-	nuc	0	Nucleus (Potential)				214
P18742 UniProt NPD GO	ZO19_XENLA	Oocyte zinc finger protein XLCOF19 (Fragment)	0.47	-	nuc	0	Nucleus (Potential)				168
P83860 UniProt NPD GO	OX26_RAT	Orexigenic neuropeptide QRFP precursor (P518) [Contains: QRF-amide (Pyroglutamylated arginine-phenyl ...	0.47	-	exc	0	Secreted protein				124
Q9N1U7 UniProt NPD GO	OTC_BOVIN	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.47	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				354
O19072 UniProt NPD GO	OTC_PIG	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.47	-	cyt	0	Mitochondrion; mitochondrial matrix				328
Q60674 UniProt NPD GO	NR1D2_MOUSE	Orphan nuclear receptor NR1D2 (Rev-erb-beta) (Orphan nuclear receptor RVR)	0.47	-	nuc	0	Nucleus (By similarity)			1EFJ	576
Q6AYD6 UniProt NPD GO	PDLI2_RAT	PDZ and LIM domain protein 2	0.47	-	nuc	0	Cytoplasm. Cytoskeleton. Localizes at the cytoskeleton. Colocalizes with beta-1 integrin (ITGB1) and ...				349
Q5AGV7 UniProt NPD GO	PFA4_CANAL	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.47	+	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				446
Q6BP97 UniProt NPD GO	PFA5_DEBHA	Palmitoyltransferase PFA5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.47	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				411
Q6BWH6 UniProt NPD GO	CWC27_DEBHA	Peptidyl-prolyl isomerase CWC27 (EC 5.2.1.8)	0.47	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				327
P43884 UniProt NPD GO	PLIN_RAT	Perilipin (PERI) (Lipid droplet-associated protein)	0.47	-	nuc	0	Lipid droplet surface-associated				517
Q6FW67 UniProt NPD GO	PEX6_CANGA	Peroxisomal biogenesis factor 6 (Peroxin-6)	0.47	-	cyt	0					1017
P37234 UniProt NPD GO	PPARG_XENLA	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.47	+	nuc	0	Nucleus				477
Q6NVD9 UniProt NPD GO	BFSP2_MOUSE	Phakinin (Beaded filament structural protein 2) (Lens fiber cell beaded filament protein CP 49) (CP4 ...	0.47	-	mit	0	Membrane (By similarity). Cytoplasm (By similarity). Membrane- and cytoskeleton-associated (By simil ...				416
Q6P268 UniProt NPD GO	PDCL3_BRARE	Phosducin-like protein 3 (Viral IAP-associated factor 1 homolog)	0.47	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			239
Q64143 UniProt NPD GO	P55G_MOUSE	Phosphatidylinositol 3-kinase regulatory subunit gamma (PI3-kinase p85-subunit gamma) (PtdIns-3-kina ...	0.47	-	nuc	0		phosphoinositide 3-kinase complex [IPI]			461
P53306 UniProt NPD GO	GPI1_YEAST	Phosphatidylinositol N-acetylglucosaminyltransferase subunit GPI1 (EC 2.4.1.198)	0.47	-	end	6	Membrane; multi-pass membrane protein (Potential)	glycosylphosphatidylinositol-N-acetylglucos... [TAS] membrane [TAS]			609

You are viewing entries 27101 to 27150 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.