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
P33238 UniProt NPD GO	MX_ANAPL	Interferon-induced GTP-binding protein Mx	0.58	-	nuc	0	Cytoplasm. Nucleus				721
P18589 UniProt NPD GO	MX2_RAT	Interferon-induced GTP-binding protein Mx2	0.58	-	nuc	0	Cytoplasm				659
O46612 UniProt NPD GO	IL1A_CANFA	Interleukin-1 alpha precursor (IL-1 alpha)	0.58	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				265
P04822 UniProt NPD GO	IL1A_RABIT	Interleukin-1 alpha precursor (IL-1 alpha)	0.58	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				267
O62674 UniProt NPD GO	IL16_CERAE	Interleukin-16 precursor (IL-16) (Lymphocyte chemoattractant factor) (LCF)	0.58	-	nuc	0	Secreted protein (By similarity)				631
P25140 UniProt NPD GO	IL3_MACMU	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.58	-	exc	0	Secreted protein				143
O45168 UniProt NPD GO	IFC1_CAEEL	Intermediate filament protein ifc-1 (Intermediate filament protein C1) (IF-C1) (Cel IF C1)	0.58	-	nuc	0	Cytoplasm (Probable)				500
Q9Z307 UniProt NPD GO	IRK16_MOUSE	Inward rectifier potassium channel 16 (Potassium channel, inwardly rectifying subfamily J member 16) ...	0.58	+	end	2	Membrane; multi-pass membrane protein				419
Q08180 UniProt NPD GO	ICCR_DROME	Irregular chiasm C-roughest protein precursor (Protein IRREC)	0.58	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]			764
Q05084 UniProt NPD GO	ICA69_HUMAN	Islet cell autoantigen 1 (69 kDa islet cell autoantigen) (ICA69) (p69) (Islet cell autoantigen p69) ...	0.58	-	nuc	0	Cytoplasm; cytosol. Predominantly. Membrane. Also exists as a membrane-bound form which has been fou ...	cytoplasm [TAS] cytosol [ISS] Golgi membrane [IDA] secretory granule membrane [IDA] synaptic vesicle membrane [ISS]	147625		483
Q8WVZ9 UniProt NPD GO	KBTB7_HUMAN	Kelch repeat and BTB domain-containing protein 7	0.58	-	cyt	0					684
Q60653 UniProt NPD GO	KLRA6_MOUSE	Killer cell lectin-like receptor 6 (T-cell surface glycoprotein Ly-49F) (Ly49-F antigen) (Lymphocyte ...	0.58	-	nuc	1 *	Membrane; single-pass type II membrane protein	plasma membrane [TAS]			266
P46824 UniProt NPD GO	KLC_DROME	Kinesin light chain (KLC)	0.58	-	nuc	0					508
Q25132 UniProt NPD GO	LIM_HALRO	LIM/homeobox protein LIM (HRLIM)	0.58	+	nuc	0	Nucleus (Potential)				514
Q90421 UniProt NPD GO	LHX3_BRARE	LIM/homeobox protein Lhx3 (Homeobox protein LIM-3)	0.58	+	nuc	0	Nucleus (By similarity)				398
Q9BYE3 UniProt NPD GO	LCE3D_HUMAN	Late cornified envelope protein 3D (Late envelope protein 16) (Small proline-rich-like epidermal dif ...	0.58	-	nuc	0					92
P16888 UniProt NPD GO	H2BL1_STRPU	Late histone H2B.L1	0.58	+	nuc	0	Nucleus				122
P09802 UniProt NPD GO	LEGA_GOSHI	Legumin A precursor (Beta-globulin) (LEGA-C94) [Contains: Legumin A acidic chain; Legumin A basic ch ...	0.58	-	exc	0					509
P02857 UniProt NPD GO	LEGA_PEA	Legumin A precursor [Contains: Legumin A alpha chain (Legumin A acidic chain); Legumin A beta chain ...	0.58	-	exc	0					517
P08111 UniProt NPD GO	L2GL_DROME	Lethal(2) giant larvae protein	0.58	-	nuc	0	Or: Cell membrane. Or: Secreted protein; extracellular space; extracellular matrix. Intercellular ma ...	apicolateral plasma membrane [IDA] basolateral plasma membrane [TAS] cell cortex [IDA] cytoplasm [IDA] cytoskeleton [NAS] cytosol [TAS] extracellular matrix (sensu Metazoa) [IDA] plasma membrane [IDA] septate junction [TAS] synaptic vesicle [NAS]			1161
Q96JM7 UniProt NPD GO	LMBL3_HUMAN	Lethal(3)malignant brain tumor-like 3 protein (L(3)mbt-like 3 protein) (H-l(3)mbt-like protein)	0.58	-	nuc	0	Nucleus (Potential)	nucleus [NAS]		1WJS	780
Q9ERV7 UniProt NPD GO	PIDD_MOUSE	Leucine-rich repeat and death domain-containing protein	0.58	-	cyt	0	Cytoplasm. Nucleus (By similarity)				915
Q8R5M3 UniProt NPD GO	LRC15_RAT	Leucine-rich repeat-containing protein 15 precursor (rLib)	0.58	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	intracellular [IDA]			578
Q9ZNU6 UniProt NPD GO	DET1_LYCES	Light-mediated development protein DET1 (Deetiolated1 homolog) (tDET1) (High pigmentation protein 2) ...	0.58	-	mit	0	Nucleus (By similarity)				523
O60449 UniProt NPD GO	LY75_HUMAN	Lymphocyte antigen 75 precursor (DEC-205) (gp200-MR6) (CD205 antigen)	0.58	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	604524		1722
Q13094 UniProt NPD GO	LCP2_HUMAN	Lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76 kDa) (SLP-76 tyrosine ...	0.58	-	nuc	0	Cytoplasm (Probable)		601603	1YWO	533
Q9UQQ2 UniProt NPD GO	LNK_HUMAN	Lymphocyte-specific adapter protein Lnk (Signal transduction protein Lnk) (Lymphocyte adapter protei ...	0.58	-	nuc	0			605093		575
P19973 UniProt NPD GO	LSP1_MOUSE	Lymphocyte-specific protein 1 (Protein pp52) (52 kDa phosphoprotein) (Lymphocyte-specific antigen WP ...	0.58	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side				330
Q6ZQ88 UniProt NPD GO	LSD1_MOUSE	Lysine-specific histone demethylase 1 (EC 1.-.-.-) (Flavin-containing amine oxidase domain-containin ...	0.58	-	cyt	0	Nucleus (By similarity)				853
Q6H711 UniProt NPD GO	MAD29_ORYSA	MADS-box transcription factor 29 (OsMADS29)	0.58	-	nuc	0	Nucleus (Probable)				260
Q14168 UniProt NPD GO	MPP2_HUMAN	MAGUK p55 subfamily member 2 (Protein MPP2) (Discs large homolog 2)	0.58	-	cyt	0		cell surface [IEP] integral to plasma membrane [TAS] membrane [ISS] membrane fraction [TAS]	600723		576
Q13368 UniProt NPD GO	MPP3_HUMAN	MAGUK p55 subfamily member 3 (Protein MPP3) (Discs large homolog 3)	0.58	-	cyt	0		cell surface [IEP] integral to plasma membrane [TAS]	601114		585
P32490 UniProt NPD GO	MKK1_YEAST	MAP kinase kinase MKK1/SSP32 (EC 2.7.12.2)	0.58	-	nuc	0		bud tip [IDA]			508
Q16644 UniProt NPD GO	MAPK3_HUMAN	MAP kinase-activated protein kinase 3 (EC 2.7.11.1) (MAPK-activated protein kinase 3) (MAPKAP kinase ...	0.58	-	nuc	0	Nucleus. Cytoplasm. Predominantly located in the nucleus, when activated it translocates to the cyto ...	nucleus [TAS]	602130		382
P40745 UniProt NPD GO	B915_XENLA	Maternal B9.15 protein (P30 B9.15)	0.58	-	nuc	0					233
P12866 UniProt NPD GO	STE6_YEAST	Mating factor A secretion protein STE6 (Multiple drug resistance protein homolog) (P-glycoprotein)	0.58	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] mating projection tip [IDA]			1290
P78966 UniProt NPD GO	MAM1_SCHPO	Mating factor M secretion protein mam1 (Multiple drug resistance protein homolog) (P-glycoprotein)	0.58	-	end	9	Membrane; multi-pass membrane protein				1336
P10840 UniProt NPD GO	MATMC_SCHPO	Mating-type M-specific polypeptide Mc (mat-Mc)	0.58	-	nuc	0	Nucleus (Potential)				181
Q9Y8D3 UniProt NPD GO	MAT1_COCKU	Mating-type protein MAT-1	0.58	-	nuc	0	Nucleus (Potential)				379
Q90YC2 UniProt NPD GO	MMP21_CYNPY	Matrix metalloproteinase-21 precursor (EC 3.4.24.-) (MMP-21)	0.58	+	mit	0	Secreted protein (Potential)				616
Q70Y16 UniProt NPD GO	MATK_AMBTC	Maturase K (Intron maturase)	0.58	-	cyt	0	Plastid; chloroplast				501
Q8MEH7 UniProt NPD GO	MATK_AMOBY	Maturase K (Intron maturase)	0.58	-	cyt	0	Plastid; chloroplast				512
Q9MSV4 UniProt NPD GO	MATK_CHAOB	Maturase K (Intron maturase)	0.58	-	cyt	0	Plastid; chloroplast				509
Q8HUG7 UniProt NPD GO	MATK_CORVR	Maturase K (Intron maturase)	0.58	-	mit	0	Plastid; chloroplast				508
Q8WKE7 UniProt NPD GO	MATK_FAGJA	Maturase K (Intron maturase)	0.58	-	cyt	0	Plastid; chloroplast				504
Q8MCV5 UniProt NPD GO	MATK_GOSTU	Maturase K (Intron maturase)	0.58	-	cyt	0	Plastid; chloroplast				504
Q8WHM4 UniProt NPD GO	MATK_LEMMN	Maturase K (Intron maturase)	0.58	-	nuc	0	Plastid; chloroplast				512
Q9GHR6 UniProt NPD GO	MATK_PERAE	Maturase K (Intron maturase)	0.58	-	cyt	0	Plastid; chloroplast				507
Q75VB3 UniProt NPD GO	MATK_QUEGA	Maturase K (Intron maturase)	0.58	-	cyt	0	Plastid; chloroplast				504
Q9GFN8 UniProt NPD GO	MATK_RHISY	Maturase K (Intron maturase)	0.58	-	nuc	0	Plastid; chloroplast				505

You are viewing entries 20251 to 20300 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.