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
Q8MZR5 UniProt NPD GO	HYEP2_CTEFE	Juvenile hormone epoxide hydrolase 2 (EC 3.3.2.3) (Juvenile hormone epoxide hydrolase II) (Juvenile ...	0.07	-	mit	1 *	Microsome; microsomal membrane; single-pass membrane protein				465
P30809 UniProt NPD GO	JHEA_TRINI	Juvenile hormone esterase, isoform A (EC 3.1.1.59) (JH esterase) (JHE-A) (Fragments)	0.07	-	nuc	0					109
P00757 UniProt NPD GO	K1KB4_MOUSE	Kallikrein 1-related peptidase-like b4 precursor (7S nerve growth factor alpha chain) (Alpha-NGF)	0.07	-	vac	0				1SGF	256
Q9Y5K2 UniProt NPD GO	KLK4_HUMAN	Kallikrein-4 precursor (EC 3.4.21.-) (Prostase) (Kallikrein-like protein 1) (KLK-L1) (Enamel matrix ...	0.07	-	cyt	1 *	Secreted protein	extracellular region [TAS]	603767		254
P49862 UniProt NPD GO	KLK7_HUMAN	Kallikrein-7 precursor (EC 3.4.21.-) (hK7) (Stratum corneum chymotryptic enzyme) (hSCCE)	0.07	-	exc	0	Secreted protein. In ovarian carcinoma, secreted and also observed at the apical membrane and in cyt ...		604438		253
P41144 UniProt NPD GO	OPRK_CAVPO	Kappa-type opioid receptor (KOR-1)	0.07	-	end	7	Membrane; multi-pass membrane protein				380
Q9Y2U9 UniProt NPD GO	KLDC2_HUMAN	Kelch domain-containing protein 2 (Hepatocellular carcinoma-associated antigen 33) (Host cell factor ...	0.07	-	cyt	0					406
Q8R179 UniProt NPD GO	KBTB4_MOUSE	Kelch repeat and BTB domain-containing protein 4 (BTB and kelch domain-containing protein 4)	0.07	-	nuc	0					534
Q96CT2 UniProt NPD GO	KBTB9_HUMAN	Kelch repeat and BTB domain-containing protein 9	0.07	-	cyt	0					655
Q80T74 UniProt NPD GO	KBTB9_MOUSE	Kelch repeat and BTB domain-containing protein 9	0.07	-	cyt	0					655
P60329 UniProt NPD GO	KR124_HUMAN	Keratin-associated protein 12-4 (Keratin-associated protein 12.4) (High sulfur keratin-associated pr ...	0.07	-	exc	0					112
Q6L8H1 UniProt NPD GO	KRA54_HUMAN	Keratin-associated protein 5-4 (Keratin-associated protein 5.4) (Ultrahigh sulfur keratin-associated ...	0.07	-	nuc	0					288
P48808 UniProt NPD GO	FGF7_SHEEP	Keratinocyte growth factor precursor (KGF) (Fibroblast growth factor 7) (FGF-7) (HBGF-7)	0.07	-	mit	0					194
Q5RL79 UniProt NPD GO	KCP2_MOUSE	Keratinocytes-associated protein 2 (KCP-2)	0.07	-	end	4	Membrane; multi-pass membrane protein				220
Q02974 UniProt NPD GO	KHK_RAT	Ketohexokinase (EC 2.7.1.3) (Hepatic fructokinase)	0.07	-	cyt	0					298
Q00948 UniProt NPD GO	TOXK_WILSA	Killer toxin precursor	0.07	-	exc	0	Secreted protein (By similarity)				124
Q9U518 UniProt NPD GO	ASPG_DIRIM	L-asparaginase (EC 3.5.1.1) (L-asparagine amidohydrolase) (DiAsp)	0.07	-	mit	0					590
P30362 UniProt NPD GO	ASPG_LUPAR	L-asparaginase precursor (EC 3.5.1.1) (L-asparagine amidohydrolase) [Contains: L-asparaginase subuni ...	0.07	-	cyt	0					306
Q7M429 UniProt NPD GO	CYTL_TACTR	L-cystatin precursor	0.07	-	cyt	1 *	Large granules of hemocytes				133
P93052 UniProt NPD GO	LDH_BOTBR	L-lactate dehydrogenase (EC 1.1.1.27) (LDH)	0.07	-	nuc	0					316
Q03966 UniProt NPD GO	LAC1_CRYPA	Laccase precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase)	0.07	-	exc	0	Secreted protein (Potential)				591
Q8SPX7 UniProt NPD GO	CRYL1_BOVIN	Lambda-crystallin homolog	0.07	-	nuc	0					320
Q01635 UniProt NPD GO	LAMB1_CHICK	Laminin beta-1 chain (Laminin beta-1-1 chain) (Fragment)	0.07	-	cyt	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component				303
P02874 UniProt NPD GO	LEC_ONOVI	Lectin	0.07	-	cyt	0					236
P81517 UniProt NPD GO	LECA_CRAFL	Lectin alpha chain [Contains: Lectin beta chain; Lectin gamma chain]	0.07	-	nuc	0				2D3R	236
Q9Y5L5 UniProt NPD GO	LENEP_HUMAN	Lens epithelial cell protein LEP503	0.07	-	cyt	0			607377		61
Q9BY71 UniProt NPD GO	LRRC3_HUMAN	Leucine-rich repeat-containing protein 3 precursor	0.07	-	end	1					257
P15018 UniProt NPD GO	LIF_HUMAN	Leukemia inhibitory factor precursor (LIF) (Differentiation-stimulating factor) (D factor) (Melanoma ...	0.07	-	mit	0	Secreted protein		159540	1PVH	202
Q9NPC1 UniProt NPD GO	LT4R2_HUMAN	Leukotriene B4 receptor 2 (LTB4-R2) (Seven transmembrane receptor BLTR2) (Leukotriene B4 receptor BL ...	0.07	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	605773		389
P11543 UniProt NPD GO	LIG5_PHACH	Ligninase LG5 precursor (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase)	0.07	-	exc	0					371
Q803C7 UniProt NPD GO	LMBRL_BRARE	Limb region 1 homolog-like protein	0.07	-	end	9 *	Cell membrane; multi-pass membrane protein (By similarity)				491
P32946 UniProt NPD GO	LIP2_CANRU	Lipase 2 precursor (EC 3.1.1.3)	0.07	-	exc	0				1GZ7	548
Q9P8V9 UniProt NPD GO	LIP8_CANAL	Lipase 8 precursor (EC 3.1.1.3)	0.07	-	exc	0	Secreted protein				460
P41365 UniProt NPD GO	LIPB_CANAR	Lipase B precursor (EC 3.1.1.3) (CALB)	0.07	-	end	0				1TCC	342
Q7KNS3 UniProt NPD GO	LIS1_DROME	Lissencephaly-1 homolog (Lissencephaly1) (Dlis1) (DLis-1)	0.07	-	nuc	0	Cytoplasm. Localizes to the plus end of microtubules. Also localizes to the mitotic spindle poles fr ...	axon [IDA] cell soma [IDA] dendrite [IDA]			411
Q08731 UniProt NPD GO	LIT2_MOUSE	Lithostathine 2 precursor (Pancreatic stone protein 2) (PSP) (Pancreatic thread protein 2) (PTP) (Is ...	0.07	-	exc	0					173
P10959 UniProt NPD GO	EST1_RAT	Liver carboxylesterase 1 precursor (EC 3.1.1.1) (Carboxyesterase ES-1) (E1) (ES-THET) (Esterase-2)	0.07	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...				549
Q63010 UniProt NPD GO	EST5_RAT	Liver carboxylesterase B-1 precursor (EC 3.1.1.1) (Liver microsomal carboxylesterase)	0.07	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...				561
P01388 UniProt NPD GO	NXL2_NAJME	Long neurotoxin 2 (Neurotoxin B)	0.07	-	nuc	0	Secreted protein				71
P80156 UniProt NPD GO	NXL4_OPHHA	Long neurotoxin 4 (Alpha-neurotoxin)	0.07	-	nuc	0	Secreted protein				72
P80965 UniProt NPD GO	NXL5_OPHHA	Long neurotoxin OH-5 (Alpha-neurotoxin)	0.07	-	nuc	0	Secreted protein				72
Q8TDL5 UniProt NPD GO	LPLC1_HUMAN	Long palate, lung and nasal epithelium carcinoma-associated protein 1 precursor (Von Ebner minor sal ...	0.07	-	exc	1 *	Secreted protein (By similarity)				484
Q60HI0 UniProt NPD GO	ACADL_MACFA	Long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.13) (LCAD)	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				430
Q8JZR0 UniProt NPD GO	ACSL5_MOUSE	Long-chain-fatty-acid--CoA ligase 5 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 5) (LACS 5)	0.07	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...	mitochondrial inner membrane [IDA] mitochondrion [IDA]			683
Q63203 UniProt NPD GO	FCGR2_RAT	Low affinity immunoglobulin gamma Fc region receptor II precursor (Fc-gamma RII) (FcRII) (IgG Fc rec ...	0.07	-	mit	1	Membrane; single-pass type I membrane protein				285
Q41914 UniProt NPD GO	LCR70_ARATH	Low-molecular-weight cysteine-rich protein LCR70 precursor	0.07	-	vac	1 *	Secreted protein (Potential)				77
Q27757 UniProt NPD GO	LUCI_PHOPE	Luciferin 4-monooxygenase (EC 1.13.12.7) (Luciferase)	0.07	-	mit	0	Peroxisome (By similarity)				545
Q8HZR9 UniProt NPD GO	LSHB_AILFU	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.07	-	mit	0	Secreted protein				141
Q32LD3 UniProt NPD GO	LYPD4_BOVIN	Ly6/PLAUR domain-containing protein 4 precursor	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				246
Q90890 UniProt NPD GO	LY86_CHICK	Lymphocyte antigen 86 precursor (MD-1 protein)	0.07	-	exc	0	Secreted protein; extracellular space (By similarity). Associated with CD180 at the cell surface (By ...				160

You are viewing entries 70301 to 70350 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.