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
Q9LLX1 UniProt NPD GO	ISAP1_ORYSA	Multiple stress-responsive zinc-finger protein ISAP1 (Stress-associated protein 1) (OsISAP1)	0.49	-	nuc	0					164
Q863A3 UniProt NPD GO	MYOC_MACFA	Myocilin precursor (Trabecular meshwork-induced glucocorticoid response protein)	0.49	-	nuc	0	Located preferentially in the ciliary rootlet and basal body of the connecting cilium of photorecept ...				491
Q9R1J4 UniProt NPD GO	MYOC_RAT	Myocilin precursor (Trabecular meshwork-induced glucocorticoid response protein)	0.49	-	nuc	0	Located preferentially in the ciliary rootlet and basal body of the connecting cilium of photorecept ...				502
P10568 UniProt NPD GO	MYO1A_BOVIN	Myosin Ia (Brush border myosin I) (BBM-I) (BBMI) (Myosin I heavy chain) (MIHC) (Brush border 110 kDa ...	0.49	-	cyt	0					1043
Q5E9V3 UniProt NPD GO	MYOZ2_BOVIN	Myozenin-2 (Calsarcin-1)	0.49	-	nuc	0	Colocalizes with ACTN1 and PPP3CA at the Z-line of heart and skeletal muscle (By similarity)				264
O95544 UniProt NPD GO	NADK_HUMAN	NAD kinase (EC 2.7.1.23) (Poly(P)/ATP NAD kinase)	0.49	-	cyt	0		cytosol [IEP]			446
P03906 UniProt NPD GO	NU4M_PANTR	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.49	-	end	12 *					459
P60323 UniProt NPD GO	NANO3_HUMAN	Nanos homolog 3	0.49	-	nuc	0			608229		173
O43847 UniProt NPD GO	NRDC_HUMAN	Nardilysin precursor (EC 3.4.24.61) (N-arginine dibasic convertase) (NRD convertase) (NRD-C)	0.49	-	mit	0		cell surface [TAS] cytosol [TAS]	602651		1150
Q761X5 UniProt NPD GO	UNC5C_RAT	Netrin receptor UNC5C precursor (Unc-5 homolog C) (Unc-5 homolog 3)	0.49	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				931
O15943 UniProt NPD GO	CADN_DROME	Neural-cadherin precursor (Cadherin-N protein) (DN-cadherin)	0.49	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	intercellular junction [IDA] plasma membrane [TAS]			3097
Q8N2Q7 UniProt NPD GO	NLGN1_HUMAN	Neuroligin-1 precursor	0.49	-	cyt	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Enriched in synaptic plasma memb ...	integral to plasma membrane [ISS] synapse [ISS]	600568		840
O97512 UniProt NPD GO	NK3R_RABIT	Neuromedin K receptor (NKR) (Neurokinin B receptor) (NK-3 receptor) (NK-3R) (Tachykinin receptor 3)	0.49	-	end	7	Membrane; multi-pass membrane protein				467
Q9Y639 UniProt NPD GO	NPTN_HUMAN	Neuroplastin precursor (Stromal cell-derived receptor 1) (SDR-1)	0.49	+	exc	1	Cell membrane; single-pass type I membrane protein (Potential)	integral to membrane of membrane fraction [ISS] postsynaptic membrane [ISS] presynaptic membrane [ISS]			282
O42622 UniProt NPD GO	TREB_MAGGR	Neutral trehalase (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.49	+	cyt	0	Cytoplasm (By similarity)				736
Q4PBZ9 UniProt NPD GO	NHP6_USTMA	Nonhistone chromosomal protein 6	0.49	-	nuc	0	Nucleus (By similarity)				99
Q9H1B4 UniProt NPD GO	NXF5_HUMAN	Nuclear RNA export factor 5 (TAP-like protein 1) (TAPL-1)	0.49	-	nuc	0	Cytoplasm. Mainly localized in the cytoplasm of cells and more particularly in the cell body and neu ...	cytoplasm [IDA] nucleus [IDA]	300319		397
P32588 UniProt NPD GO	PUB1_YEAST	Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 (ARS consensus-binding protein ACBP- ...	0.49	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] heterogeneous nuclear ribonucleoprotein com... [IDA] nucleus [IDA]			452
P19838 UniProt NPD GO	NFKB1_HUMAN	Nuclear factor NF-kappa-B p105 subunit (DNA-binding factor KBF1) (EBP-1) [Contains: Nuclear factor N ...	0.49	+	nuc	0	Nucleus. Cytoplasm. Nuclear, but also found in the cytoplasm in an inactive form complexed to an inh ...	cytoplasm [IDA] nucleus [IDA]	164011	1SVC	968
O17928 UniProt NPD GO	NHR52_CAEEL	Nuclear hormone receptor family member nhr-52	0.49	-	nuc	0	Nucleus (Potential)				338
Q9WTK0 UniProt NPD GO	NUPR1_MOUSE	Nuclear protein 1 (Protein p8)	0.49	+	nuc	0	Nucleus (By similarity)				80
Q9D1X0 UniProt NPD GO	NOL3_MOUSE	Nucleolar protein 3	0.49	-	nuc	0	Nucleus (By similarity)	mitochondrion [IDA] sarcoplasm [IDA]			220
Q8I4N3 UniProt NPD GO	NDC1_CAEEL	Nucleoporin ndc-1	0.49	-	end	5	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...				588
P36991 UniProt NPD GO	OV17_ONCVO	OV-17 antigen precursor (Immunodominant hypodermal antigen)	0.49	-	exc	0					164
P81744 UniProt NPD GO	TOG3B_AGEAP	Omega-agatoxin-3B (Omega-agatoxin IIIB) (Omega-Aga-IIIB)	0.49	-	nuc	0	Secreted protein				76
Q90Z16 UniProt NPD GO	OPTN_CHICK	Optineurin (Ag9-C5) (FIP-2)	0.49	-	nuc	0	Cytoplasm. Golgi apparatus				556
Q9ZVH3 UniProt NPD GO	ORC6_ARATH	Origin recognition complex subunit 6	0.49	-	nuc	0	Nucleus (By similarity)				284
P00480 UniProt NPD GO	OTC_HUMAN	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.49	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS] ornithine carbamoyltransferase complex [NAS]	300461	1OTH	354
P00481 UniProt NPD GO	OTC_RAT	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.49	-	mit	0	Mitochondrion; mitochondrial matrix				354
Q63503 UniProt NPD GO	NR1D1_RAT	Orphan nuclear receptor NR1D1 (V-erbA-related protein EAR-1) (Rev-erbA-alpha)	0.49	-	nuc	0	Nucleus (By similarity)				508
P70052 UniProt NPD GO	NR2E1_XENLA	Orphan nuclear receptor NR2E1 (Nuclear receptor TLX) (Tailless homolog) (Tll) (xTLL)	0.49	-	nuc	0	Nucleus (By similarity)				386
P79928 UniProt NPD GO	P2RY4_XENLA	P2Y purinoceptor 4 (P2Y4) (P2Y purinoceptor 8) (P2Y8)	0.49	-	end	6 *	Membrane; multi-pass membrane protein				537
Q8R1G6 UniProt NPD GO	PDLI2_MOUSE	PDZ and LIM domain protein 2 (PDZ-LIM protein mystique)	0.49	-	nuc	0	Cytoplasm. Cytoskeleton. Localizes at the cytoskeleton. Colocalizes with beta-1 integrin (ITGB1) and ...			1VB7	349
Q96HC4 UniProt NPD GO	PDLI5_HUMAN	PDZ and LIM domain protein 5 (Enigma homolog) (Enigma-like PDZ and LIM domains protein)	0.49	-	nuc	0		cytosol [ISS] membrane fraction [ISS]	605904		595
O60809 UniProt NPD GO	PRA10_HUMAN	PRAME family member 10 (Fragment)	0.49	-	nuc	0					459
Q9BZ23 UniProt NPD GO	PANK2_HUMAN	Pantothenate kinase 2, mitochondrial precursor (EC 2.7.1.33) (Pantothenic acid kinase 2) (hPANK2)	0.49	-	mit	0	Cytoplasm. Mitochondrion		607236		570
Q56Z59 UniProt NPD GO	PATL3_ARATH	Patellin-3	0.49	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Mainly membrane-associated. Cytoplasm (By sim ...				490
Q5R7I1 UniProt NPD GO	PAXI_PONPY	Paxillin	0.49	-	nuc	0					591
Q9VXN9 UniProt NPD GO	PGPLE_DROME	Peptidoglycan-recognition protein-LE	0.49	-	nuc	0	Secreted protein. However, no signal sequence are predicted by sequence analysis tools	extracellular region [IDA]		2CB3	345
P22696 UniProt NPD GO	ESS1_YEAST	Peptidyl-prolyl cis-trans isomerase ESS1 (EC 5.2.1.8) (PPIase ESS1) (Processing/termination factor 1 ...	0.49	-	nuc	0	Cytoplasm. Nucleus	nucleus [IPI]			170
Q874C0 UniProt NPD GO	PEX3_YARLI	Peroxisomal biogenesis factor 3 (Peroxin-3)	0.49	-	mit	1 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein				431
Q01495 UniProt NPD GO	PEX5_PICAN	Peroxisomal targeting signal receptor (Peroxisomal protein PAH2) (Peroxin-5) (PTS1 receptor)	0.49	-	nuc	0	Cytoplasm. Peroxisome; peroxisomal membrane; peripheral membrane protein. Its distribution appears t ...				569
Q9SLG9 UniProt NPD GO	PI5K5_ARATH	Phosphatidylinositol-4-phosphate 5-kinase 5 (EC 2.7.1.68) (AtPIP5K5) (1-phosphatidylinositol-4-phosp ...	0.49	-	nuc	0					772
Q9SLZ0 UniProt NPD GO	PEPCK_MAIZE	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49) (PEP carboxykinase) (Phosphoenolpyruvate carbo ...	0.49	-	nuc	0	Cytoplasm (Probable)				666
Q9W6R1 UniProt NPD GO	KPB2_FUGRU	Phosphorylase b kinase regulatory subunit alpha, liver isoform (Phosphorylase kinase alpha L subunit ...	0.49	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1229
P30733 UniProt NPD GO	PHYA_SOLTU	Phytochrome A	0.49	-	mit	0					1123
O18400 UniProt NPD GO	PITX1_DROME	Pituitary homeobox 1 homolog (D-PTX1)	0.49	+	nuc	0	Nucleus				509
Q9DAS4 UniProt NPD GO	PRLC3_MOUSE	Placental prolactin-like protein C3 precursor (PRL-like protein C3) (PLP-C3) (Prolactin-like protein ...	0.49	-	mit	0	Secreted protein (By similarity)				241
Q29485 UniProt NPD GO	PLMN_ERIEU	Plasminogen precursor (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Activation peptide; Plasmin he ...	0.49	-	exc	0	Secreted protein				810
P34769 UniProt NPD GO	RK20_ASTLO	Plastid 50S ribosomal protein L20	0.49	+	nuc	0	Plastid				117

You are viewing entries 25751 to 25800 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.