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
Q95132 UniProt NPD GO	ICAM1_BOVIN	Intercellular adhesion molecule 1 precursor (ICAM-1)	0.19	-	end	1	Membrane; single-pass type I membrane protein				535
P33729 UniProt NPD GO	ICAM1_CANFA	Intercellular adhesion molecule 1 precursor (ICAM-1) (Fragment)	0.19	-	end	1	Membrane; single-pass type I membrane protein				528
P17181 UniProt NPD GO	INAR1_HUMAN	Interferon-alpha/beta receptor alpha chain precursor (IFN-alpha-REC)	0.19	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	107450		557
O77482 UniProt NPD GO	IL1RA_BOVIN	Interleukin-1 receptor antagonist protein precursor (IL-1ra) (IRAP) (IL1 inhibitor) (IL-1RN)	0.19	-	nuc	0	Secreted protein				174
P43303 UniProt NPD GO	IL1R2_RAT	Interleukin-1 receptor type II precursor (IL-1R-2) (IL-1R-beta) (CD121b antigen)	0.19	-	end	1	Membrane; single-pass type I membrane protein				416
Q9HB29 UniProt NPD GO	ILRL2_HUMAN	Interleukin-1 receptor-like 2 precursor (IL-1Rrp2) (Interleukin-1 receptor-related protein 2) (IL1R- ...	0.19	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604512		575
Q9TSJ4 UniProt NPD GO	IL10_RABIT	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.19	-	exc	0	Secreted protein				178
Q8TAD2 UniProt NPD GO	IL17D_HUMAN	Interleukin-17D precursor (IL-17D) (Interleukin-27) (IL-27)	0.19	-	nuc	0	Secreted protein		607587		202
Q25BC3 UniProt NPD GO	IL2_VULVU	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.19	-	exc	0	Secreted protein				155
Q9JJY8 UniProt NPD GO	IL22B_MOUSE	Interleukin-22b precursor (IL-22b) (IL-10-related T-cell-derived-inducible factor beta) (IL-TIFb) (I ...	0.19	-	exc	1 *	Secreted protein				179
O77762 UniProt NPD GO	IL4_CANFA	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.19	-	nuc	1 *	Secreted protein	extracellular space [ISS]			132
P03877 UniProt NPD GO	SCE3_YEAST	Intron-encoded DNA endonuclease aI3 precursor (DNA endonuclease I-SceIII) [Contains: Truncated, nonf ...	0.19	-	nuc	1 *	Mitochondrion	mitochondrion [TAS]			403
P22889 UniProt NPD GO	IAPP_OCTDE	Islet amyloid polypeptide precursor (Amylin)	0.19	-	exc	0	Secreted protein				91
Q8BIJ6 UniProt NPD GO	SYIM_MOUSE	Isoleucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS)	0.19	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			1012
P58044 UniProt NPD GO	IDI1_MOUSE	Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2) (IPP isomerase 1) (Isopentenyl pyrophosphate ...	0.19	+	cyt	0	Peroxisome (By similarity)				227
Q5BJY4 UniProt NPD GO	JOS1_RAT	Josephin-1 (Josephin domain-containing protein 1)	0.19	-	mit	0					202
P42155 UniProt NPD GO	CASK_BISBO	Kappa-casein (Fragment)	0.19	-	mit	0	Secreted protein				136
Q28400 UniProt NPD GO	CASK_EQUGR	Kappa-casein (Fragment)	0.19	-	mit	0	Secreted protein				135
P02444 UniProt NPD GO	KRA33_SHEEP	Keratin, high sulfur matrix protein, IIIB3	0.19	-	nuc	0					98
Q3SZ72 UniProt NPD GO	KCP3_BOVIN	Keratinocytes-associated protein 3 (KCP-3)	0.19	-	end	4 *	Membrane; multi-pass membrane protein				240
Q14954 UniProt NPD GO	KI2S1_HUMAN	Killer cell immunoglobulin-like receptor 2DS1 precursor (MHC class I NK cell receptor Eb6 ActI) (CD1 ...	0.19	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	604952		304
P01044 UniProt NPD GO	KNG1_BOVIN	Kininogen-1 precursor (Kininogen I) (Thiol proteinase inhibitor) [Contains: Kininogen-1 heavy chain; ...	0.19	-	exc	0	Secreted protein; extracellular space				621
Q9CXF0 UniProt NPD GO	KYNU_MOUSE	Kynureninase (EC 3.7.1.3) (L-kynurenine hydrolase)	0.19	-	cyt	0	Cytoplasm (By similarity)				465
Q05431 UniProt NPD GO	APX1_ARATH	L-ascorbate peroxidase, cytosolic (EC 1.11.1.11) (AP)	0.19	-	cyt	0	Cytoplasm				249
Q24372 UniProt NPD GO	LACH_DROME	Lachesin precursor	0.19	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor; extracellular side. Located at the extracellular face of th ...	septate junction [IDA]			359
Q9NPC4 UniProt NPD GO	A4GAT_HUMAN	Lactosylceramide 4-alpha-galactosyltransferase (EC 2.4.1.228) (Alpha-1,4-galactosyltransferase) (UDP ...	0.19	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to Golgi membrane [NAS] membrane fraction [IDA]	607922		353
Q29477 UniProt NPD GO	TRFL_CAPHI	Lactotransferrin precursor (EC 3.4.21.-) (Lactoferrin)	0.19	-	exc	0	Secreted protein			1JW1	708
Q42376 UniProt NPD GO	LEA3_MAIZE	Late embryogenesis abundant protein, group 3 (LEA)	0.19	-	nuc	0					221
Q03968 UniProt NPD GO	LEA3_WHEAT	Late embryogenesis abundant protein, group 3 (LEA) (PMA2005)	0.19	-	nuc	0					224
Q42876 UniProt NPD GO	AMPL2_LYCES	Leucine aminopeptidase 2, chloroplast precursor (EC 3.4.11.1) (LAP 2) (Leucyl aminopeptidase 2) (Pro ...	0.19	-	mit	0	Plastid; chloroplast				569
P31427 UniProt NPD GO	AMPL_SOLTU	Leucine aminopeptidase, chloroplast precursor (EC 3.4.11.1) (LAP) (Leucyl aminopeptidase) (Proline a ...	0.19	-	mit	0	Plastid; chloroplast (By similarity)				573
Q3T181 UniProt NPD GO	LT4R1_BOVIN	Leukotriene B4 receptor 1 (LTB4-R 1)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				349
P17454 UniProt NPD GO	LBP_RABIT	Lipopolysaccharide-binding protein precursor (LBP)	0.19	-	exc	1 *	Secreted protein				482
Q9NDC9 UniProt NPD GO	LIS1_CAEEL	Lissencephaly-1 homolog (Pronuclear migration abnormal protein 1)	0.19	-	cyt	0	Localizes to the plus end of microtubules (By similarity). Cytoplasm. Concentrates in the vicinity o ...				404
P23132 UniProt NPD GO	LITH_BOVIN	Lithostathine precursor (Pancreatic stone protein) (PSP) (Pancreatic thread protein) (PTP) (Islet of ...	0.19	-	exc	0					175
O64948 UniProt NPD GO	LONH1_ARATH	Lon protease homolog 1, mitochondrial precursor (EC 3.4.21.-)	0.19	-	nuc	0	Mitochondrion; mitochondrial matrix (Potential)				888
P93655 UniProt NPD GO	LONH2_ARATH	Lon protease homolog 2, mitochondrial precursor (EC 3.4.21.-)	0.19	-	mit	0	Mitochondrion; mitochondrial matrix				940
Q9QUJ7 UniProt NPD GO	ACSL4_MOUSE	Long-chain-fatty-acid--CoA ligase 4 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 4) (LACS 4) (mACS4) ...	0.19	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...				711
Q9D358 UniProt NPD GO	PPAC_MOUSE	Low molecular weight phosphotyrosine protein phosphatase (EC 3.1.3.48) (LMW-PTP) (Low molecular weig ...	0.19	-	nuc	0	Cytoplasm (By similarity)				157
P11064 UniProt NPD GO	PPAC_BOVIN	Low molecular weight phosphotyrosine protein phosphatase (EC 3.1.3.48) (Low molecular weight cytosol ...	0.19	-	cyt	0	Cytoplasm			1Z13	157
Q03685 UniProt NPD GO	BIP5_TOBAC	Luminal-binding protein 5 precursor (BiP 5) (78 kDa glucose-regulated protein homolog 5) (GRP 78-5)	0.19	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				668
Q8BLC3 UniProt NPD GO	LYPD1_MOUSE	Ly6/PLAUR domain-containing protein 1 precursor	0.19	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				141
Q8BVP6 UniProt NPD GO	LYPD4_MOUSE	Ly6/PLAUR domain-containing protein 4 precursor	0.19	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				246
Q9XT48 UniProt NPD GO	TNFB_MACEU	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.19	-	exc	0	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				201
P10154 UniProt NPD GO	TNFB_RABIT	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.19	-	end	0	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				197
P00707 UniProt NPD GO	LYSC_ORTVE	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.19	-	nuc	0					129
P08905 UniProt NPD GO	LYSCM_MOUSE	Lysozyme C type M precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.19	-	exc	0		mitochondrion [IDA]		1IVM	148
P00719 UniProt NPD GO	LYG_STRCA	Lysozyme g (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase) (Goose-type lysozyme)	0.19	-	nuc	0	Secreted protein				185
Q9Z175 UniProt NPD GO	LOXL3_MOUSE	Lysyl oxidase homolog 3 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 3) (Lysyl oxidase-related ...	0.19	-	exc	0	Secreted protein; extracellular space (Potential)				754
Q61542 UniProt NPD GO	MLN64_MOUSE	MLN 64 protein (StAR-related lipid transfer protein 3) (StARD3) (START domain-containing protein 3) ...	0.19	-	end	3	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity)	late endosome [TAS]			446

You are viewing entries 52001 to 52050 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.