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
Q13651 UniProt NPD GO	I10R1_HUMAN	Interleukin-10 receptor alpha chain precursor (IL-10R-A) (IL-10R1) (CDw210a antigen)	0.49	-	exc	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	146933	1Y6K	578
Q13261 UniProt NPD GO	I15RA_HUMAN	Interleukin-15 receptor alpha chain precursor (IL-15R-alpha) (IL-15RA)	0.49	-	exc	0	Membrane; single-pass type I membrane protein. Secreted protein. Mainly found associated with the nu ...		601070	2ERS	267
O54824 UniProt NPD GO	IL16_MOUSE	Interleukin-16 precursor (IL-16) (Lymphocyte chemoattractant factor) (LCF)	0.49	-	nuc	0	Secreted protein (By similarity)	intracellular [IDA]			624
Q5MNY4 UniProt NPD GO	IL2RA_MACMU	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (CD25 ...	0.49	+	cyt	1	Membrane; single-pass type I membrane protein				272
P16297 UniProt NPD GO	IL2RB_MOUSE	Interleukin-2 receptor beta chain precursor (IL-2 receptor) (P70-75) (High affinity IL-2 receptor su ...	0.49	-	exc	2 *	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			539
Q9UHF4 UniProt NPD GO	I20RA_HUMAN	Interleukin-20 receptor alpha chain precursor (IL-20R-alpha) (IL-20R1) (Cytokine receptor family 2 m ...	0.49	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)		605620		553
P16871 UniProt NPD GO	IL7RA_HUMAN	Interleukin-7 receptor alpha chain precursor (IL-7R-alpha) (CD127 antigen) (CDw127)	0.49	-	end	1	Isoform H20, isoform H1: Cell membrane; single-pass type I membrane protein. Isoform H6: Secreted pr ...		146661		459
P81068 UniProt NPD GO	IRX1_MOUSE	Iroquois-class homeodomain protein IRX-1 (Iroquois homeobox protein 1) (Homeodomain protein IRXA1)	0.49	-	nuc	0	Nucleus (Probable)				480
P81066 UniProt NPD GO	IRX2_MOUSE	Iroquois-class homeodomain protein IRX-2 (Iroquois homeobox protein 2) (Homeodomain protein IRXA2)	0.49	-	nuc	0	Nucleus (Probable)				474
O61585 UniProt NPD GO	KTNB1_STRPU	Katanin p80 WD40-containing subunit B1 (Katanin p80 subunit B1) (p80 katanin)	0.49	-	nuc	0	Centrosome. Spindle. Localized to the interphase centrosome and mitotic spindle poles				690
Q86V97 UniProt NPD GO	KBTB6_HUMAN	Kelch repeat and BTB domain-containing protein 6	0.49	-	cyt	0					674
Q5K2P2 UniProt NPD GO	K1C15_PROAT	Keratin, type I cytoskeletal 15 (Cytokeratin-15) (CK-15) (Keratin-15) (K15) (Fragment)	0.49	-	exc	0					441
Q9BYQ8 UniProt NPD GO	KRA49_HUMAN	Keratin-associated protein 4-9 (Keratin-associated protein 4.9) (Ultrahigh sulfur keratin-associated ...	0.49	-	nuc	0					191
Q60651 UniProt NPD GO	KLRA4_MOUSE	Killer cell lectin-like receptor 4 (T-cell surface glycoprotein Ly-49D) (Ly49-D antigen) (Lymphocyte ...	0.49	-	nuc	1 *	Membrane; single-pass type II membrane protein	plasma membrane [TAS]			263
Q60652 UniProt NPD GO	KLRA5_MOUSE	Killer cell lectin-like receptor 5 (T-cell surface glycoprotein Ly-49E) (Ly49-E antigen) (Lymphocyte ...	0.49	+	nuc	1 *	Membrane; single-pass type II membrane protein				266
P46874 UniProt NPD GO	KLP2_BOMMO	Kinesin-like protein KLP2 (Fragment)	0.49	-	nuc	0					378
Q9UST6 UniProt NPD GO	SPC24_SCHPO	Kinetochore protein spc24	0.49	-	nuc	0	Nucleus. Associated with kinetochores	Ndc80 complex [TAS]			198
Q8WP17 UniProt NPD GO	KLOT_MACFA	Klotho precursor (EC 3.2.1.31) [Contains: Klotho peptide]	0.49	-	gol	1	Isoform 1: Cell membrane; single-pass type I membrane protein (By similarity). Its shedding leads to ...				1014
P46099 UniProt NPD GO	KLF1_MOUSE	Krueppel-like factor 1 (Erythroid krueppel-like transcription factor) (EKLF) (Erythroid transcriptio ...	0.49	-	nuc	0	Nucleus				358
Q5E9N4 UniProt NPD GO	AADAT_BOVIN	Kynurenine/alpha-aminoadipate aminotransferase mitochondrial precursor (KAT/AadAT) (Kynurenine--oxog ...	0.49	-	mit	0	Mitochondrion (Potential)				425
Q61792 UniProt NPD GO	LASP1_MOUSE	LIM and SH3 domain protein 1 (LASP-1) (MLN 50)	0.49	-	nuc	0	Cytoplasm (By similarity). Associated with the F-actin rich cortical cytoskeleton (By similarity)	cortical actin cytoskeleton [ISS] cytoplasm [IDA] focal adhesion [IDA]			263
Q8VEE1 UniProt NPD GO	LMCD1_MOUSE	LIM and cysteine-rich domains protein 1	0.49	-	nuc	0		nucleus [IDA]			365
Q8IRC7 UniProt NPD GO	AWH_DROME	LIM/homeobox protein Awh (Protein arrowhead)	0.49	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			275
O81323 UniProt NPD GO	LBD30_ARATH	LOB domain-containing protein 30	0.49	-	nuc	0					228
Q8BLN5 UniProt NPD GO	ERG7_MOUSE	Lanosterol synthase (EC 5.4.99.7) (Oxidosqualene--lanosterol cyclase) (2,3-epoxysqualene--lanosterol ...	0.49	-	cyt	0					733
O95490 UniProt NPD GO	LPHN2_HUMAN	Latrophilin-2 precursor (Calcium-independent alpha-latrotoxin receptor 2) (Latrophilin homolog 1) (L ...	0.49	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [NAS]	607018		1459
Q588F8 UniProt NPD GO	LEP_TETNG	Leptin precursor	0.49	-	nuc	0	Secreted protein (Probable)				160
Q8K377 UniProt NPD GO	LRTM1_MOUSE	Leucine-rich repeat transmembrane neuronal protein 1 precursor	0.49	-	end	1	Membrane; single-pass type I membrane protein (Potential)				522
Q9BYS8 UniProt NPD GO	LRRC2_HUMAN	Leucine-rich repeat-containing protein 2	0.49	-	nuc	0			607180		371
Q96E66 UniProt NPD GO	LRC51_HUMAN	Leucine-rich repeat-containing protein 51	0.49	-	nuc	0					192
Q9D1G5 UniProt NPD GO	LRC57_MOUSE	Leucine-rich repeat-containing protein 57	0.49	-	nuc	0					239
Q9M7C9 UniProt NPD GO	TPSDB_ABIGR	Limonene/alpha-pinene synthase, chloroplast precursor ((-)-(4S)-limonene synthase) (EC 4.2.3.-) ((-) ...	0.49	-	mit	0	Plastid; chloroplast (By similarity)				637
P16582 UniProt NPD GO	LSHR_PIG	Lutropin-choriogonadotropic hormone receptor precursor (LH/CG-R) (LSH-R) (Luteinizing hormone recept ...	0.49	-	end	7	Membrane; multi-pass membrane protein				696
Q99547 UniProt NPD GO	MPH6_HUMAN	M-phase phosphoprotein 6	0.49	-	mit	0	Nucleus; nucleolus. Cytoplasm. Cytoplasmic in M phase		605500		160
O43708 UniProt NPD GO	MAAI_HUMAN	Maleylacetoacetate isomerase (EC 5.2.1.2) (MAAI) (Glutathione S-transferase zeta 1) (EC 2.5.1.18) (G ...	0.49	-	mit	0	Cytoplasm (By similarity)	mitochondrion [ISS]	603758	1FW1	216
Q5PXH1 UniProt NPD GO	KISS1_MACMU	Malignant melanoma metastasis-suppressor KiSS-1 (Kisspeptin-1) [Contains: Metastin; Kisspeptin-10] ( ...	0.49	-	nuc	0	Secreted protein				88
Q9NR34 UniProt NPD GO	MA1C1_HUMAN	Mannosyl-oligosaccharide 1,2-alpha-mannosidase IC (EC 3.2.1.113) (Processing alpha-1,2-mannosidase I ...	0.49	+	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to Golgi membrane [TAS]			630
P25822 UniProt NPD GO	PUM_DROME	Maternal protein pumilio	0.49	-	nuc	0	Cytoplasm. It is concentrated in the cortical region of the embryo beneath the nuclei				1533
P51511 UniProt NPD GO	MMP15_HUMAN	Matrix metalloproteinase-15 precursor (EC 3.4.24.-) (MMP-15) (Membrane-type matrix metalloproteinase ...	0.49	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	602261		669
Q33142 UniProt NPD GO	MATK_SAXPU	Maturase K (Intron maturase) (Fragment)	0.49	-	cyt	0	Plastid; chloroplast				353
P40384 UniProt NPD GO	REC12_SCHPO	Meiotic recombination protein rec12	0.49	-	cyt	0					345
Q96M61 UniProt NPD GO	MAGBI_HUMAN	Melanoma-associated antigen B18 (MAGE-B18 antigen)	0.49	-	nuc	0					343
Q5AI97 UniProt NPD GO	MG101_CANAL	Mitochondrial genome maintenance protein MGM101, mitochondrial precursor	0.49	+	mit	0	Mitochondrion. Associated with the mitochondrial nucleoid structure (By similarity)				275
P37932 UniProt NPD GO	PMIP_SCHCO	Mitochondrial intermediate peptidase, mitochondrial precursor (EC 3.4.24.59) (MIP)	0.49	-	mit	0	Mitochondrion; mitochondrial matrix				775
Q01902 UniProt NPD GO	RT07_WHEAT	Mitochondrial ribosomal protein S7	0.49	-	cyt	0	Mitochondrion				148
Q6P5G0 UniProt NPD GO	MK04_MOUSE	Mitogen-activated protein kinase 4 (EC 2.7.11.24) (Extracellular signal-regulated kinase 4) (ERK-4)	0.49	-	nuc	0					583
Q750A9 UniProt NPD GO	HOG1_ASHGO	Mitogen-activated protein kinase HOG1 (EC 2.7.11.24) (MAP kinase HOG1)	0.49	-	cyt	0					447
Q39008 UniProt NPD GO	M3K1_ARATH	Mitogen-activated protein kinase kinase kinase 1 (EC 2.7.11.25) (MAP kinase kinase kinase 1) (AtMEKK ...	0.49	-	nuc	0					608
P91797 UniProt NPD GO	MPI7_LYMST	Molluscan insulin-related peptide 7 precursor (MIP VII) [Contains: Molluscan insulin-related peptide ...	0.49	-	nuc	1 *	Secretory granules				180
Q9QYP0 UniProt NPD GO	MEGF8_RAT	Multiple epidermal growth factor-like domains 8 (EGF-like domain-containing protein 4) (Multiple EGF ...	0.49	-	nuc	1	Membrane; single-pass type III membrane protein (Potential)				874

You are viewing entries 25701 to 25750 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.