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
Q99LY9 UniProt NPD GO	NIPM_MOUSE	NADH-ubiquinone oxidoreductase 15 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-15 kDa) (CI-15 k ...	0.28	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				105
Q42577 UniProt NPD GO	NUKM_ARATH	NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.28	-	mit	0					218
O79881 UniProt NPD GO	NU4M_PIG	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.28	-	end	13 *					459
O21335 UniProt NPD GO	NU5M_DASNO	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.28	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				601
Q95885 UniProt NPD GO	NU5M_PAPHA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.28	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
P11661 UniProt NPD GO	NU5M_RAT	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.28	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				610
O95298 UniProt NPD GO	N4BM_HUMAN	NADH-ubiquinone oxidoreductase subunit B14.5b (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-B14.5b) (CI-B14. ...	0.28	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side		603845		119
P48163 UniProt NPD GO	MAOX_HUMAN	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME) (Malic enzyme 1)	0.28	-	cyt	0	Cytoplasm	cytosol [ISS]	154250	2AW5	572
P56522 UniProt NPD GO	ADRO_RAT	NADPH:adrenodoxin oxidoreductase, mitochondrial precursor (EC 1.18.1.2) (Adrenodoxin reductase) (AR) ...	0.28	-	mit	0	Mitochondrion; mitochondrial matrix				494
Q8C878 UniProt NPD GO	UBA3_MOUSE	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (Ubiquitin-activating enzyme 3) (NEDD8-act ...	0.28	+	cyt	0					462
Q63746 UniProt NPD GO	IKBA_RAT	NF-kappa-B inhibitor alpha (I-kappa-B-alpha) (IkappaBalpha) (IKB-alpha) (RL/IF-1)	0.28	-	nuc	0	Cytoplasm				314
Q99173 UniProt NPD GO	NAH1_ZYGRO	Na(+)/H(+) antiporter 1	0.28	-	end	10 *	Membrane; multi-pass membrane protein				791
P40314 UniProt NPD GO	BTT1_YEAST	Nascent polypeptide-associated complex subunit beta BTT1 (BTF3 homolog BTT1)	0.28	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Predominantly cytoplasmic, may also transiently ...	cytosolic ribosome (sensu Eukaryota) [IC] nascent polypeptide-associated complex [IDA]			149
P32004 UniProt NPD GO	L1CAM_HUMAN	Neural cell adhesion molecule L1 precursor (N-CAM L1) (CD171 antigen)	0.28	-	end	1	Membrane; single-pass type I membrane protein		308840		1257
P58401 UniProt NPD GO	NRX2B_HUMAN	Neurexin-2-beta precursor (Neurexin II-beta)	0.28	-	end	1	Membrane; single-pass type I membrane protein (Potential)		600566		666
O35764 UniProt NPD GO	NPTXR_RAT	Neuronal pentraxin receptor	0.28	-	end	1 *	Membrane; single-pass type II membrane protein (Potential)				494
Q9PW68 UniProt NPD GO	NEUY_TYPNA	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.28	-	exc	1 *	Secreted protein				97
O08762 UniProt NPD GO	NETR_MOUSE	Neurotrypsin precursor (EC 3.4.21.-) (Motopsin) (Brain-specific serine protease 3) (BSSP-3)	0.28	-	exc	0	Secreted protein				761
P56730 UniProt NPD GO	NETR_HUMAN	Neurotrypsin precursor (EC 3.4.21.-) (Motopsin) (Leydin)	0.28	-	end	0	Secreted protein		606709		875
Q62716 UniProt NPD GO	DEF1_RAT	Neutrophil antibiotic peptide NP-1 precursor (Neutrophil defensin 1) (RatNP-1)	0.28	-	exc	0	Secreted protein				94
Q5ZJH2 UniProt NPD GO	NCLN_CHICK	Nicalin precursor (Nicastrin-like protein)	0.28	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				562
O76463 UniProt NPD GO	NFT1_CAEEL	Nitrilase and fragile histidine triad fusion protein NitFhit [Includes: Bis(5'-adenosyl)-triphosphat ...	0.28	-	mit	0				1EMS	440
O18937 UniProt NPD GO	RNAS2_AOTTR	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.28	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule				158
Q6FT66 UniProt NPD GO	NMD4_CANGA	Nonsense-mediated decay protein 4	0.28	-	cyt	0	Cytoplasm (By similarity)				244
Q9VT70 UniProt NPD GO	NDE1_DROME	Nuclear distribution protein nudE homolog	0.28	-	nuc	0					317
O45521 UniProt NPD GO	NH111_CAEEL	Nuclear hormone receptor family member nhr-111	0.28	-	nuc	0	Nucleus (Potential)				311
Q5ZJC7 UniProt NPD GO	NOC4L_CHICK	Nucleolar complex protein 4 homolog (NOC4 protein homolog) (NOC4-like protein) (Nucleolar complex-as ...	0.28	-	nuc	2	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Nucleus; nucleolus (By simil ...				508
Q9JIH2 UniProt NPD GO	NUP50_MOUSE	Nucleoporin 50 kDa (Nuclear pore-associated protein 60 kDa-like)	0.28	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side (By similarity). Localizes to th ...			2C1M	466
Q9QXL8 UniProt NPD GO	NDK7_MOUSE	Nucleoside diphosphate kinase 7 (EC 2.7.4.6) (NDK 7) (NDP kinase 7) (nm23-M7)	0.28	-	mit	0					395
Q6CKV0 UniProt NPD GO	SIL1_KLULA	Nucleotide exchange factor SIL1 precursor	0.28	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				490
Q8BK62 UniProt NPD GO	OLFL3_MOUSE	Olfactomedin-like protein 3 precursor	0.28	-	end	0	Secreted protein (By similarity)				406
Q64288 UniProt NPD GO	OMP_MOUSE	Olfactory marker protein	0.28	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA] cytosol [TAS] nucleus [IDA]		1JOD	162
Q8NGJ9 UniProt NPD GO	O51T1_HUMAN	Olfactory receptor 51T1	0.28	-	end	7 *	Membrane; multi-pass membrane protein				327
P18744 UniProt NPD GO	ZO20_XENLA	Oocyte zinc finger protein XLCOF20 (Fragment)	0.28	-	nuc	0	Nucleus (Potential)				247
P80045 UniProt NPD GO	OMP_LOCMI	Ovary maturating parsin (OMP)	0.28	-	cyt	0					65
Q9XFT3 UniProt NPD GO	PSBQ1_ARATH	Oxygen-evolving enhancer protein 3-1, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolvin ...	0.28	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				223
Q60YJ7 UniProt NPD GO	PCID_CAEBR	PCI domain-containing protein (CSN12-like protein)	0.28	-	cyt	0					413
Q6RIA2 UniProt NPD GO	PAF_RAT	PCNA-associated factor (p15PAF) (HCV NS5A-transactivated protein 9 homolog)	0.28	-	mit	0	Nucleus (By similarity). Mitochondrion (By similarity)				110
Q8WW12 UniProt NPD GO	PCNP_HUMAN	PEST proteolytic signal-containing nuclear protein (PEST-containing nuclear protein) (PCNP)	0.28	-	nuc	0	Nucleus	nucleus [IDA]			178
Q8T0W2 UniProt NPD GO	CVP4_PIMHY	Pacifastin-like protease inhibitor cvp4 precursor (Cysteine-rich venom protein 4)	0.28	-	exc	0	Secreted protein				203
P01300 UniProt NPD GO	PAHO_PIG	Pancreatic hormone precursor (Pancreatic polypeptide) (PP) (Fragment)	0.28	-	nuc	0	Secreted protein				65
P60572 UniProt NPD GO	PANX3_RAT	Pannexin-3	0.28	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	gap junction [IMP]			392
P01269 UniProt NPD GO	PTHY_PIG	Parathyroid hormone precursor (Parathyrin) (PTH)	0.28	-	end	0	Secreted protein				115
O60260 UniProt NPD GO	PRKN2_HUMAN	Parkin (EC 6.3.2.-) (Ubiquitin E3 ligase PRKN) (Parkinson juvenile disease protein 2) (Parkinson dis ...	0.28	-	nuc	0	Cytoplasm. Co-localizes with STY11 in neutrites. Co-localizes with SNCAIP in brainstem Lewy bodies		168600	1IYF	465
Q43143 UniProt NPD GO	PMEU1_LYCES	Pectinesterase U1 precursor (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.28	-	mit	1 *					583
Q9UBV8 UniProt NPD GO	PEF1_HUMAN	Peflin (PEF protein with a long N-terminal hydrophobic domain) (Penta-EF hand domain-containing prot ...	0.28	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein in the presence of Ca(2+)		610033		284
Q9FUZ2 UniProt NPD GO	DEFC_ARATH	Peptide deformylase, chloroplast precursor (EC 3.5.1.88) (PDF) (Polypeptide deformylase)	0.28	-	mit	0	Plastid; chloroplast (Potential)				273
P54150 UniProt NPD GO	MSRA_ARATH	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (Peptide ...	0.28	-	mit	0					258
P81898 UniProt NPD GO	PNAA_PRUDU	Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase A (EC 3.5.1.52) (PNGase A) (Glycopeptide N ...	0.28	-	cyt	0					571
Q9BXM0 UniProt NPD GO	PRAX_HUMAN	Periaxin	0.28	-	nuc	0	Nucleus (By similarity). Isoform 1: Cell membrane (By similarity). Isoform 1 is associated with plas ...		605725		1461

You are viewing entries 42501 to 42550 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.