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
P97411 UniProt NPD GO	ICA69_MOUSE	Islet cell autoantigen 1 (69 kDa islet cell autoantigen) (ICA69) (p69) (Islet cell autoantigen p69) ...	0.52	-	nuc	0	Cytoplasm; cytosol. Predominantly. Membrane. Also exists as a membrane-bound form which has been fou ...	cytosol [IDA] Golgi membrane [ISS] secretory granule membrane [ISS] synaptic vesicle membrane [IDA]			478
Q8TBB5 UniProt NPD GO	KLDC4_HUMAN	Kelch domain-containing protein 4	0.52	+	nuc	0					520
P97861 UniProt NPD GO	KRHB6_MOUSE	Keratin, type II cuticular Hb6 (Hair keratin, type II Hb6)	0.52	-	mit	0					486
Q6IG01 UniProt NPD GO	K2C1B_RAT	Keratin, type II cytoskeletal 1b (Type II keratin Kb39)	0.52	+	mit	0					519
P35908 UniProt NPD GO	K22E_HUMAN	Keratin, type II cytoskeletal 2 epidermal (Cytokeratin-2e) (K2e) (CK 2e)	0.52	+	cyt	0		intermediate filament [TAS]	600194		645
P19013 UniProt NPD GO	K2C4_HUMAN	Keratin, type II cytoskeletal 4 (Cytokeratin-4) (CK-4) (Keratin-4) (K4)	0.52	-	cyt	1		keratin filament [ISS]	193900		534
P05787 UniProt NPD GO	K2C8_HUMAN	Keratin, type II cytoskeletal 8 (Cytokeratin-8) (CK-8) (Keratin-8) (K8)	0.52	-	mit	0		intermediate filament [NAS]	215600		482
Q9NZS2 UniProt NPD GO	KLRF1_HUMAN	Killer cell lectin-like receptor subfamily F member 1 (Lectin-like receptor F1) (Activating corecept ...	0.52	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)	integral to plasma membrane [TAS] membrane [TAS]	605029		231
P46014 UniProt NPD GO	KAPP_ARATH	Kinase-associated protein phosphatase (EC 3.1.3.16)	0.52	-	mit	1 *	Membrane; single-pass type I membrane protein			1MZK	581
Q91W40 UniProt NPD GO	KLC3_MOUSE	Kinesin light chain 3	0.52	-	nuc	0	Elongating spermatid tail midpiece. Localized in outer dense fibers (ODFs) and associates with mitoc ...	ciliary rootlet [IDA] cytoplasm [IDA] flagellum (sensu Eukaryota) [IDA] neuron projection [IDA]			508
Q68G30 UniProt NPD GO	KLC3_RAT	Kinesin light chain 3 (Kinesin light chain KLCt)	0.52	-	nuc	0	Elongating spermatid tail midpiece, localized in outer dense fibers (ODFs) and associates with mitoc ...				505
P46864 UniProt NPD GO	ATK2_ARATH	Kinesin-2 (Kinesin-like protein B)	0.52	-	nuc	0					745
P83060 UniProt NPD GO	KNL1_BOMOR	Kininogen-1 precursor (BOK-1) [Contains: Bradykinin]	0.52	-	exc	0	Secreted protein				167
O35739 UniProt NPD GO	KLF9_MOUSE	Krueppel-like factor 9 (Transcription factor BTEB1) (Basic transcription element-binding protein 1) ...	0.52	-	nuc	0	Nucleus	nucleus [IDA]			244
Q01713 UniProt NPD GO	KLF9_RAT	Krueppel-like factor 9 (Transcription factor BTEB1) (Basic transcription element-binding protein 1) ...	0.52	-	nuc	0	Nucleus				244
O42936 UniProt NPD GO	LAS1L_SCHPO	LAS1-like protein	0.52	-	cyt	0					470
Q16363 UniProt NPD GO	LAMA4_HUMAN	Laminin alpha-4 chain precursor	0.52	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basal lamina [TAS]	600133		1823
Q5TCM9 UniProt NPD GO	LCE5A_HUMAN	Late cornified envelope protein 5A (Late envelope protein 18) (Small proline-rich-like epidermal dif ...	0.52	-	nuc	0					118
Q7SAP7 UniProt NPD GO	LCMT1_NEUCR	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.52	-	nuc	0					431
Q5ZLN0 UniProt NPD GO	LRC40_CHICK	Leucine-rich repeat-containing protein 40	0.52	-	nuc	0					603
O22340 UniProt NPD GO	TPSDA_ABIGR	Limonene synthase, chloroplast precursor (EC 4.2.3.16) ((-)-(4S)-limonene synthase) (Agg-lim1)	0.52	-	mit	0	Plastid; chloroplast				637
Q99KG5 UniProt NPD GO	LSR_MOUSE	Lipolysis-stimulated lipoprotein receptor precursor (Liver-specific bHLH-Zip transcription factor) ( ...	0.52	-	exc	1 *	Cell membrane; single-pass type I membrane protein (Potential)	plasma membrane [IDA]			594
Q5F464 UniProt NPD GO	LPP_CHICK	Lipoma-preferred partner homolog	0.52	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Cell membrane; cell-cell junction (By similarity ...				604
Q8GSM3 UniProt NPD GO	LOX22_HORVU	Lipoxygenase 2.2, chloroplast precursor (EC 1.13.11.12) (LOX2:Hv:2)	0.52	-	mit	0	Plastid; chloroplast				932
Q28110 UniProt NPD GO	FCGR2_BOVIN	Low affinity immunoglobulin gamma Fc region receptor II precursor (Fc-gamma RII) (FcRII) (IgG Fc rec ...	0.52	-	end	1	Membrane; single-pass type I membrane protein				296
Q40703 UniProt NPD GO	MADS4_ORYSA	MADS-box transcription factor 4 (OsMADS4)	0.52	-	nuc	0	Nucleus (Probable)				215
Q94KB7 UniProt NPD GO	MLO6_ARATH	MLO-like protein 6 (AtMlo6)	0.52	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				583
Q9D071 UniProt NPD GO	MMS19_MOUSE	MMS19-like protein (MET18 homolog)	0.52	-	cyt	0	Nucleus (By similarity)				1031
O54732 UniProt NPD GO	MMP15_MOUSE	Matrix metalloproteinase-15 precursor (EC 3.4.24.-) (MMP-15) (Membrane-type matrix metalloproteinase ...	0.52	-	end	1	Membrane; single-pass type I membrane protein (Potential)				657
Q95BY0 UniProt NPD GO	MATK_CANSA	Maturase K (Intron maturase)	0.52	-	cyt	0	Plastid; chloroplast				507
Q85WL2 UniProt NPD GO	MATK_ERYGA	Maturase K (Intron maturase)	0.52	-	cyt	0	Plastid; chloroplast				514
Q85WL0 UniProt NPD GO	MATK_ERYRE	Maturase K (Intron maturase)	0.52	-	cyt	0	Plastid; chloroplast				514
Q9B1U9 UniProt NPD GO	MATK_LILLO	Maturase K (Intron maturase)	0.52	-	cyt	0	Plastid; chloroplast				512
Q8WKM2 UniProt NPD GO	MATK_LINPE	Maturase K (Intron maturase)	0.52	-	cyt	0	Plastid; chloroplast				520
Q8WKM1 UniProt NPD GO	MATK_MORAL	Maturase K (Intron maturase)	0.52	-	cyt	0	Plastid; chloroplast				505
Q9GHB2 UniProt NPD GO	MATK_PHODC	Maturase K (Intron maturase)	0.52	-	nuc	0	Plastid; chloroplast				514
Q7IS11 UniProt NPD GO	MATK_TAXCU	Maturase K (Intron maturase)	0.52	-	cyt	0	Plastid; chloroplast				510
P21190 UniProt NPD GO	IME1_YEAST	Meiosis-inducing protein 1	0.52	-	nuc	0	Nucleus	nucleus [IDA]			360
P36625 UniProt NPD GO	REC7_SCHPO	Meiotic recombination protein rec7	0.52	-	nuc	0		nucleus [IDA]			339
Q5PPP4 UniProt NPD GO	MAGH1_RAT	Melanoma-associated antigen H1 (MAGE-H1 antigen)	0.52	-	nuc	1					218
O35954 UniProt NPD GO	PITM1_MOUSE	Membrane-associated phosphatidylinositol transfer protein 1 (Phosphatidylinositol transfer protein, ...	0.52	-	nuc	0	Cytoplasm. Peripheral membrane protein associated with Golgi stacks in interphase cells. A minor pro ...				1243
Q5U2N3 UniProt NPD GO	PITM1_RAT	Membrane-associated phosphatidylinositol transfer protein 1 (Phosphatidylinositol transfer protein, ...	0.52	-	nuc	0	Cytoplasm. Peripheral membrane protein associated with Golgi stacks in interphase cells. A minor pro ...				1242
Q9FV49 UniProt NPD GO	AMP2A_ARATH	Methionine aminopeptidase 2A (EC 3.4.11.18) (MetAP 2A) (MAP 2A) (Peptidase M 2A)	0.52	+	nuc	0	Cytoplasm				441
Q86BS6 UniProt NPD GO	METL_DROME	Methyltransferase-like protein (EC 2.1.1.-)	0.52	-	cyt	0					325
Q9IAC6 UniProt NPD GO	MCR_ONCMY	Mineralocorticoid receptor (MR) (Fragment)	0.52	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic and nuclear in the absence of ligand ...				359
Q9D2R8 UniProt NPD GO	RT33_MOUSE	Mitochondrial 28S ribosomal protein S33 (S33mt) (MRP-S33) (Ganglioside-induced differentiation-assoc ...	0.52	-	nuc	0	Mitochondrion				106
P82908 UniProt NPD GO	RT36_BOVIN	Mitochondrial 28S ribosomal protein S36 (S36mt) (MRP-S36)	0.52	-	mit	0	Mitochondrion				103
O14354 UniProt NPD GO	MG101_SCHPO	Mitochondrial genome maintenance protein mgm101, mitochondrial precursor	0.52	+	nuc	0	Mitochondrion. Associated with the mitochondrial nucleoid structure (By similarity)				267
P46759 UniProt NPD GO	RT12_ACACA	Mitochondrial ribosomal protein S12	0.52	-	nuc	0	Mitochondrion				127
P48943 UniProt NPD GO	RT12_CHLS6	Mitochondrial ribosomal protein S12	0.52	-	mit	0	Mitochondrion				126

You are viewing entries 23801 to 23850 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.