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
P78552 UniProt NPD GO	I13R1_HUMAN	Interleukin-13 receptor alpha-1 chain precursor (IL-13R-alpha-1) (IL-13RA-1) (CD213a1 antigen)	0.33	-	end	2 *	Membrane; single-pass type I membrane protein	interleukin-13 receptor complex [TAS] plasma membrane [TAS]	300119		427
Q865Y1 UniProt NPD GO	IL2_PAPAN	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.33	-	exc	0	Secreted protein	extracellular space [ISS]			154
P26898 UniProt NPD GO	IL2RA_SHEEP	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (CD25 ...	0.33	-	nuc	1	Membrane; single-pass type I membrane protein				275
Q80XF5 UniProt NPD GO	I22RA_MOUSE	Interleukin-22 receptor alpha-2 chain precursor (IL-22R-alpha-2) (Interleukin 22-binding protein) (I ...	0.33	-	exc	0	Secreted protein	cytosol [IDA]			230
Q8IZI9 UniProt NPD GO	IL28B_HUMAN	Interleukin-28B precursor (IL-28B) (IL-28C) (Interferon lambda-3) (IFN-lambda-3) (Interferon lambda- ...	0.33	-	nuc	1 *	Secreted protein		607402		200
Q28334 UniProt NPD GO	IL3_CALJA	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.33	-	exc	0	Secreted protein				142
P51445 UniProt NPD GO	IL3_SAGOE	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.33	-	exc	0	Secreted protein				142
Q8MKH0 UniProt NPD GO	IL6_SAISC	Interleukin-6 precursor (IL-6)	0.33	-	exc	0	Secreted protein	extracellular region [ISS] extracellular space [ISS]			212
P15247 UniProt NPD GO	IL9_MOUSE	Interleukin-9 precursor (IL-9) (T-cell growth factor P40) (P40 cytokine)	0.33	-	exc	0	Secreted protein				144
O94030 UniProt NPD GO	MIA40_CANAL	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.33	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				252
P52190 UniProt NPD GO	IRK4_RAT	Inward rectifier potassium channel 4 (Potassium channel, inwardly rectifying subfamily J member 4) ( ...	0.33	-	mit	3	Membrane; multi-pass membrane protein				446
Q9U6V7 UniProt NPD GO	JDP_BOMMO	J domain-containing protein	0.33	-	nuc	0					170
Q9W422 UniProt NPD GO	JOSL_DROME	Josephin-like protein	0.33	-	nuc	1					221
P14691 UniProt NPD GO	KAF2_SORBI	Kafirin PSKR2 precursor	0.33	-	exc	1 *					267
O94819 UniProt NPD GO	KBTBB_HUMAN	Kelch repeat and BTB domain-containing protein 11 (Kelch domain-containing protein 7B)	0.33	-	nuc	0					623
Q9JI74 UniProt NPD GO	KLHL1_MOUSE	Kelch-like protein 1	0.33	-	nuc	0	Cytoplasm	cytoplasm [ISS]			751
P02439 UniProt NPD GO	KRB2B_SHEEP	Keratin, high-sulfur matrix protein, B2B	0.33	-	nuc	0					156
P08777 UniProt NPD GO	K1C1_XENLA	Keratin, type I cytoskeletal 47 kDa	0.33	-	nuc	0					429
Q4W7H1 UniProt NPD GO	KR134_HYLAG	Keratin-associated protein 13-4	0.33	-	mit	0					160
Q4W7H0 UniProt NPD GO	KR134_HYLLA	Keratin-associated protein 13-4	0.33	-	mit	0					160
O60938 UniProt NPD GO	KERA_HUMAN	Keratocan precursor (KTN) (Keratan sulfate proteoglycan keratocan)	0.33	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [NAS]	603288		352
Q6X936 UniProt NPD GO	KIRR1_RAT	Kin of IRRE-like protein 1 precursor (Kin of irregular chiasm-like protein 1) (Nephrin-like protein ...	0.33	-	end	2 *	Membrane; single-pass type I membrane protein (Potential). Predominantly located at podocyte slit di ...				789
Q36736 UniProt NPD GO	KM11_LEIDO	Kinetoplastid membrane protein 11 (KMP-11) (Lipophosphoglycan-associated protein) (LPGAP)	0.33	-	nuc	0	Cytoplasm. Associated with microtubules	microtubule cytoskeleton [ISS]			92
Q64602 UniProt NPD GO	AADAT_RAT	Kynurenine/alpha-aminoadipate aminotransferase mitochondrial precursor (KAT/AadAT) (Kynurenine--oxog ...	0.33	-	mit	0	Mitochondrion (Potential)				425
Q95119 UniProt NPD GO	TYRP2_BOVIN	L-dopachrome tautomerase precursor (EC 5.3.3.12) (DT) (DCT) (L-dopachrome delta-isomerase) (Tyrosina ...	0.33	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (By similarity)				517
Q8N5B7 UniProt NPD GO	LASS5_HUMAN	LAG1 longevity assurance homolog 5	0.33	-	end	5 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum; endoplasm ...				392
P80195 UniProt NPD GO	LCTN_BOVIN	Lactophorin precursor (28 kDa milk glycoprotein PP3) (Proteose-peptone component 3) (Glycosylation-d ...	0.33	-	exc	0	Membrane; peripheral membrane protein				153
P46517 UniProt NPD GO	EMB5_MAIZE	Late embryogenesis abundant protein EMB564	0.33	-	nuc	0					91
Q257X2 UniProt NPD GO	LEP_CAPHI	Leptin precursor (Obesity factor)	0.33	-	exc	0	Secreted protein (Probable)				167
O42164 UniProt NPD GO	LEP_CHICK	Leptin precursor (Obesity factor)	0.33	-	mit	0	Secreted protein (Probable)				163
Q706D0 UniProt NPD GO	LEP_HALGR	Leptin precursor (Obesity factor)	0.33	-	exc	0	Secreted protein (Probable)				167
Q29406 UniProt NPD GO	LEP_PIG	Leptin precursor (Obesity factor)	0.33	-	exc	0	Secreted protein (Probable)				167
P02750 UniProt NPD GO	A2GL_HUMAN	Leucine-rich alpha-2-glycoprotein precursor (LRG)	0.33	-	nuc	0	Secreted protein	extracellular region [NAS] membrane [NAS]			347
Q8K406 UniProt NPD GO	LGI3_MOUSE	Leucine-rich repeat LGI family member 3 precursor (Leucine-rich glioma-inactivated protein 3) (Leubr ...	0.33	-	mit	0	Secreted protein (Potential)				548
Q7L1W4 UniProt NPD GO	LRC8D_HUMAN	Leucine-rich repeat-containing protein 8D	0.33	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				858
Q8BGR2 UniProt NPD GO	LRC8D_MOUSE	Leucine-rich repeat-containing protein 8D	0.33	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				859
Q6NU09 UniProt NPD GO	LRC8E_XENLA	Leucine-rich repeat-containing protein 8E	0.33	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				806
Q9H3W5 UniProt NPD GO	LRRN3_HUMAN	Leucine-rich repeats neuronal protein 3 precursor (Neuronal leucine-rich repeat protein 3) (NLRR-3)	0.33	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				708
P26637 UniProt NPD GO	SYLC_YEAST	Leucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS)	0.33	-	cyt	0	Cytoplasm	cytoplasm [IDA]			1090
Q64281 UniProt NPD GO	LIRB4_MOUSE	Leukocyte immunoglobulin-like receptor subfamily B member 4 precursor (Mast cell surface glycoprotei ...	0.33	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Ligand binding leads to internal ...				335
O60711 UniProt NPD GO	LPXN_HUMAN	Leupaxin	0.33	-	nuc	0	Cytoplasm		605390	1X3H	386
P38418 UniProt NPD GO	LOXC_ARATH	Lipoxygenase, chloroplast precursor (EC 1.13.11.12)	0.33	+	mit	0	Plastid; chloroplast (Potential)				896
P38703 UniProt NPD GO	LAG1_YEAST	Longevity-assurance protein 1 (Longevity assurance factor 1)	0.33	+	end	7	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			411
O00906 UniProt NPD GO	AGLU_TETPY	Lysosomal acid alpha-glucosidase precursor (EC 3.2.1.20) (Acid maltase)	0.33	-	cyt	1 *	Lysosome. Secreted protein				923
Q8N1E2 UniProt NPD GO	LYG1_HUMAN	Lysozyme g-like protein 1 precursor	0.33	-	exc	0	Secreted protein (Probable)				194
Q9DCX1 UniProt NPD GO	MD2BP_MOUSE	MAD2L1-binding protein	0.33	-	cyt	0	Nucleus (By similarity). During early mitosis, unevenly distributed throughout the nucleoplasm. From ...				276
P30554 UniProt NPD GO	MAS_MOUSE	MAS proto-oncogene	0.33	-	end	7 *	Membrane; multi-pass membrane protein				324
Q94KB2 UniProt NPD GO	MLO13_ARATH	MLO-like protein 13 (AtMlo13) (AtMlo20)	0.33	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				478
Q94KB4 UniProt NPD GO	MLO9_ARATH	MLO-like protein 9 (AtMlo9)	0.33	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				460
Q90405 UniProt NPD GO	MVP_DISOM	Major vault protein (MVP100) (P100)	0.33	-	cyt	0	Cytoplasm (By similarity)				852

You are viewing entries 37701 to 37750 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.