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
Q9UKK6 UniProt NPD GO	NXT1_HUMAN	NTF2-related export protein 1 (p15)	0.38	+	cyt	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm	cytoplasm [TAS] nuclear pore [TAS]	605811	1JN5	140
P01091 UniProt NPD GO	2SS1_BRANA	Napin-1 precursor (1.7S seed storage protein) [Contains: Napin-1 small chain; Napin-1 large chain] ( ...	0.38	-	nuc	0					133
P01090 UniProt NPD GO	2SS2_BRANA	Napin-2 precursor (1.7S seed storage protein) [Contains: Napin-2 small chain; Napin-2 large chain]	0.38	-	exc	1 *					178
O76036 UniProt NPD GO	NCTR1_HUMAN	Natural cytotoxicity triggering receptor 1 precursor (Natural killer cell p46-related protein) (NKp4 ...	0.38	+	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [NAS] SWI/SNF complex [ISS]	604530	1P6F	304
Q9Y113 UniProt NPD GO	NELFB_DROME	Negative elongation factor B homolog	0.38	-	mit	0	Nucleus (By similarity)	transcriptional repressor complex [ISS]			594
Q6ZN44 UniProt NPD GO	UNC5A_HUMAN	Netrin receptor UNC5A precursor (Unc-5 homolog A) (Unc-5 homolog 1)	0.38	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). The interaction with PRKCABP reg ...		607869		842
Q05695 UniProt NPD GO	L1CAM_RAT	Neural cell adhesion molecule L1 precursor (N-CAM L1) (Nerve-growth factor-inducible large external ...	0.38	-	end	1	Membrane; single-pass type I membrane protein				1259
Q61200 UniProt NPD GO	NXPH1_MOUSE	Neurexophilin-1 precursor	0.38	-	nuc	0	Secreted protein (Potential)				271
P16177 UniProt NPD GO	NK3R_RAT	Neuromedin K receptor (NKR) (Neurokinin B receptor) (NK-3 receptor) (NK-3R) (Tachykinin receptor 3)	0.38	-	end	7	Membrane; multi-pass membrane protein				452
P09482 UniProt NPD GO	ACHA4_CHICK	Neuronal acetylcholine receptor protein subunit alpha-4 precursor	0.38	-	end	4	Membrane; multi-pass membrane protein				622
Q8LKZ1 UniProt NPD GO	NORK_PEA	Nodulation receptor kinase precursor (EC 2.7.11.1)	0.38	-	end	2 *					924
P04144 UniProt NPD GO	NO23_SOYBN	Nodulin 23 precursor (N-23)	0.38	-	exc	0					220
Q96PB7 UniProt NPD GO	NOE3_HUMAN	Noelin-3 precursor (Olfactomedin-3) (Optimedin)	0.38	-	mit	0	Secreted protein (By similarity)		607567		478
O60443 UniProt NPD GO	DFNA5_HUMAN	Non-syndromic hearing impairment protein 5 (Inversely correlated with estrogen receptor expression 1 ...	0.38	+	nuc	0			600994		496
Q9LRP1 UniProt NPD GO	NPS13_ARATH	Novel plant SNARE 13 (AtNPSN13)	0.38	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				269
Q21701 UniProt NPD GO	NHR12_CAEEL	Nuclear hormone receptor family member nhr-12	0.38	-	cyt	0	Nucleus (Potential)				453
O16354 UniProt NPD GO	NH133_CAEEL	Nuclear hormone receptor family member nhr-133	0.38	-	nuc	0	Nucleus (Potential)				406
O17930 UniProt NPD GO	NH268_CAEEL	Nuclear hormone receptor family member nhr-268	0.38	-	mit	0	Nucleus (Potential)				355
Q17905 UniProt NPD GO	NHR28_CAEEL	Nuclear hormone receptor family member nhr-28	0.38	-	cyt	0	Nucleus (Potential)				437
Q6P6X9 UniProt NPD GO	NUP53_BRARE	Nucleoporin NUP53 (Nuclear pore complex protein Nup53) (Nucleoporin Nup35) (35 kDa nucleoporin)	0.38	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity)				308
Q9Z2G8 UniProt NPD GO	NP1L1_RAT	Nucleosome assembly protein 1-like 1 (NAP-1-related protein)	0.38	+	cyt	0	Nucleus (By similarity)				390
Q8VY81 UniProt NPD GO	NUD21_ARATH	Nudix hydrolase 21, chloroplast precursor (EC 3.6.1.-) (AtNUDT21)	0.38	-	cyt	0	Plastid; chloroplast (Potential)				198
Q8NGX1 UniProt NPD GO	O2T34_HUMAN	Olfactory receptor 2T34 (Olfactory receptor OR1-63)	0.38	-	end	7 *	Membrane; multi-pass membrane protein				318
Q56K12 UniProt NPD GO	OAZ1_BOVIN	Ornithine decarboxylase antizyme (ODC-Az)	0.38	-	mit	0					226
O77742 UniProt NPD GO	OMD_BOVIN	Osteomodulin precursor (Osteoadherin) (OSAD) (Keratan sulfate proteoglycan osteomodulin) (KSPG osteo ...	0.38	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				422
O18641 UniProt NPD GO	PBAN_HELAU	PBAN-type neuropeptides precursor [Contains: Diapause hormone homolog (DH); Alpha-SG neuropeptide; B ...	0.38	-	exc	0	Secreted protein				194
P11159 UniProt NPD GO	PBAN_HELZE	PBAN-type neuropeptides precursor [Contains: Diapause hormone homolog (DH); Alpha-SG neuropeptide; B ...	0.38	-	exc	0	Secreted protein				194
Q679P3 UniProt NPD GO	PDLI7_CHICK	PDZ and LIM domain protein 7 (LIM mineralization protein)	0.38	-	nuc	0	Cytoplasm. Colocalizes with TPM2 near the Z line in muscle (By similarity). Co-localizes with TBX4 a ...				416
Q7TP40 UniProt NPD GO	PCNP_RAT	PEST proteolytic signal-containing nuclear protein (PEST-containing nuclear protein) (PCNP) (Liver r ...	0.38	-	exc	0	Nucleus (By similarity)	nucleus [ISS]			189
P46892 UniProt NPD GO	CD2L1_RAT	PITSLRE serine/threonine-protein kinase CDC2L1 (EC 2.7.11.22) (Galactosyltransferase-associated prot ...	0.38	+	cyt	0	Cytoplasm. Nucleus; nuclear envelope; peripheral membrane protein. Membrane; perinuclear region; per ...				436
Q6FVE6 UniProt NPD GO	PFA4_CANGA	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.38	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				376
P83948 UniProt NPD GO	PME3_CITSI	Pectinesterase-3 precursor (EC 3.1.1.11) (Pectin methylesterase 3) (PE 3)	0.38	+	mit	1 *	Cell wall				584
P54151 UniProt NPD GO	MSRA_BRANA	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (Peptide ...	0.38	-	mit	0					257
Q70PW6 UniProt NPD GO	PGSB2_DROSI	Peptidoglycan-recognition protein-SB2 precursor (EC 3.5.1.28)	0.38	-	exc	0	Secreted protein (Potential)	extracellular region [ISS]			182
Q8CEC6 UniProt NPD GO	PPWD1_MOUSE	Peptidylprolyl isomerase domain and WD repeat-containing protein 1 (EC 5.2.1.8)	0.38	+	cyt	0					646
Q9QYU1 UniProt NPD GO	PEX19_RAT	Peroxisomal biogenesis factor 19 (Peroxin-19) (Peroxisomal farnesylated protein)	0.38	-	nuc	0	Cytoplasm (By similarity). Mainly (By similarity). Peroxisome; peroxisomal membrane; lipid-anchor; c ...	cytoplasm [IDA] peroxisome [IDA]			299
Q01962 UniProt NPD GO	PEX8_PICPA	Peroxisomal biogenesis factor 8 precursor (Peroxin-8) (Peroxisomal protein PER3)	0.38	-	mit	0	Peroxisome; peroxisomal matrix (Potential)				713
Q00319 UniProt NPD GO	PM47B_CANBO	Peroxisomal membrane protein PMP47B	0.38	-	end	4 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein				419
P19632 UniProt NPD GO	PHOS_BOVIN	Phosducin (PHD) (33 kDa phototransducing protein) (MEKA protein)	0.38	-	nuc	0	Outer and inner segments of the rod cells			1A0R	245
Q9T074 UniProt NPD GO	PEPCK_ARATH	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49) (PEP carboxykinase) (Phosphoenolpyruvate carbo ...	0.38	-	cyt	0	Cytoplasm (Probable)				671
Q29081 UniProt NPD GO	PMVK_PIG	Phosphomevalonate kinase (EC 2.7.4.2) (PMKase) (Fragment)	0.38	-	cyt	0	Peroxisome				129
P84739 UniProt NPD GO	PALST_EUGGR	Photoactivated adenylate cyclase subunit alpha-like protein ST-	0.38	-	mit	0	Flagellum	flagellum [IDA]			1019
Q9ZS62 UniProt NPD GO	PHYB1_LYCES	Phytochrome B1	0.38	-	cyt	0					1131
Q29W19 UniProt NPD GO	PACA_BOVIN	Pituitary adenylate cyclase-activating polypeptide precursor (PACAP) [Contains: PACAP-related peptid ...	0.38	-	nuc	0	Secreted protein (By similarity)				176
O35256 UniProt NPD GO	PRLPA_MOUSE	Placental prolactin-like protein A precursor (PRL-like protein A) (PLP-A)	0.38	-	nuc	0	Secreted protein (By similarity)				227
P09320 UniProt NPD GO	PRLPA_RAT	Placental prolactin-like protein A precursor (PRL-like protein A) (PLP-A)	0.38	-	exc	0	Secreted protein				227
P05155 UniProt NPD GO	IC1_HUMAN	Plasma protease C1 inhibitor precursor (C1 Inh) (C1Inh)	0.38	-	exc	0	Secreted protein	extracellular region [NAS]	106100	1M6Q	500
P58139 UniProt NPD GO	RK14_ASTLO	Plastid 50S ribosomal protein L14	0.38	-	nuc	0	Plastid				122
P51866 UniProt NPD GO	PECA1_BOVIN	Platelet endothelial cell adhesion molecule precursor (PECAM-1) (CD31 antigen)	0.38	-	end	1	Membrane; single-pass type I membrane protein				739
Q9JHK5 UniProt NPD GO	PLEK_MOUSE	Pleckstrin	0.38	-	cyt	0				1UHW	350

You are viewing entries 33601 to 33650 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.