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
Q5TA81 UniProt NPD GO	LCE2C_HUMAN	Late cornified envelope protein 2C (Late envelope protein 11)	0.54	-	mit	0					110
Q5TA82 UniProt NPD GO	LCE2D_HUMAN	Late cornified envelope protein 2D (Late envelope protein 12) (Small proline-rich-like epidermal dif ...	0.54	-	mit	0					110
Q5TA77 UniProt NPD GO	LCE3B_HUMAN	Late cornified envelope protein 3B (Late envelope protein 14)	0.54	-	mit	0					95
O08999 UniProt NPD GO	LTBP2_MOUSE	Latent-transforming growth factor beta-binding protein 2 precursor (LTBP-2)	0.54	-	mit	0	Secreted protein (By similarity). Localized in nuchal ligament and aorta to the fibrillin-containing ...				1813
O35806 UniProt NPD GO	LTBP2_RAT	Latent-transforming growth factor beta-binding protein 2 precursor (LTBP-2)	0.54	-	mit	0	Secreted protein (By similarity). Localized in nuchal ligament and aorta to the fibrillin-containing ...				1764
Q61810 UniProt NPD GO	LTBP3_MOUSE	Latent-transforming growth factor beta-binding protein 3 precursor (LTBP-3)	0.54	+	exc	0	Secreted protein. Secretion occurs after coexpression with TGFB1 and requires complexing with Cys-33 ...	extracellular region [IDA]			1268
Q14766 UniProt NPD GO	LTB1L_HUMAN	Latent-transforming growth factor beta-binding protein, isoform 1L precursor (LTBP-1) (Transforming ...	0.54	-	nuc	0	Secreted protein	extracellular matrix (sensu Metazoa) [NAS]	150390		1595
Q9Z2I0 UniProt NPD GO	LETM1_MOUSE	Leucine zipper-EF-hand-containing transmembrane protein 1, mitochondrial precursor	0.54	-	nuc	1	Mitochondrion; mitochondrial membrane (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			738
Q9JIA1 UniProt NPD GO	LGI1_MOUSE	Leucine-rich glioma-inactivated protein 1 precursor	0.54	-	mit	0	Secreted protein (Potential)				557
Q86UE6 UniProt NPD GO	LRTM1_HUMAN	Leucine-rich repeat transmembrane neuronal protein 1 precursor	0.54	-	end	1	Membrane; single-pass type I membrane protein (Potential)				522
Q5R6B1 UniProt NPD GO	LRTM1_PONPY	Leucine-rich repeat transmembrane neuronal protein 1 precursor	0.54	-	end	1	Membrane; single-pass type I membrane protein (Potential)				522
O43300 UniProt NPD GO	LRTM2_HUMAN	Leucine-rich repeat transmembrane neuronal protein 2 precursor (Leucine-rich repeat neuronal 2 prote ...	0.54	-	nuc	1 *	Membrane; single-pass type I membrane protein (Potential)				516
Q61809 UniProt NPD GO	LRRN1_MOUSE	Leucine-rich repeats neuronal protein 1 precursor (Neuronal leucine-rich repeat protein 1) (NLRR-1)	0.54	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				716
P93184 UniProt NPD GO	LOX21_HORVU	Lipoxygenase 2.1, chloroplast precursor (EC 1.13.11.12) (LOX-100) (LOX2:Hv:1)	0.54	-	mit	0	Plastid; chloroplast				936
Q28832 UniProt NPD GO	LDLR_PIG	Low-density lipoprotein receptor (LDL receptor) (Fragment)	0.54	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS] plasma membrane [ISS]			811
O75197 UniProt NPD GO	LRP5_HUMAN	Low-density lipoprotein receptor-related protein 5 precursor	0.54	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [TAS]	607636		1615
Q29451 UniProt NPD GO	MA2B1_BOVIN	Lysosomal alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase, alpha B) (Lysosomal acid alpha-man ...	0.54	-	end	0	Lysosome			1O7D	999
P49006 UniProt NPD GO	MRP_HUMAN	MARCKS-related protein (MARCKS-like protein 1) (Macrophage myristoylated alanine-rich C kinase subst ...	0.54	+	nuc	0			602940		194
P28667 UniProt NPD GO	MRP_MOUSE	MARCKS-related protein (MARCKS-like protein 1) (Macrophage myristoylated alanine-rich C kinase subst ...	0.54	+	nuc	0					199
P10841 UniProt NPD GO	MATPC_SCHPO	Mating-type P-specific polypeptide Pc	0.54	-	nuc	0	Nucleus (Potential)				118
Q8MEC8 UniProt NPD GO	MATK_ARITO	Maturase K (Intron maturase)	0.54	-	nuc	0	Plastid; chloroplast				512
Q9MV56 UniProt NPD GO	MATK_CEDAT	Maturase K (Intron maturase)	0.54	-	nuc	0	Plastid; chloroplast				515
Q9MSA7 UniProt NPD GO	MATK_CEPFR	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				502
Q9TMC8 UniProt NPD GO	MATK_GAGLU	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				516
Q6DT83 UniProt NPD GO	MATK_HOTPA	Maturase K (Intron maturase)	0.54	-	nuc	0	Plastid; chloroplast				509
Q8WHL6 UniProt NPD GO	MATK_LEMGI	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				512
Q9TNA1 UniProt NPD GO	MATK_LIRPL	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				520
Q717X1 UniProt NPD GO	MATK_NYPFR	Maturase K (Intron maturase)	0.54	-	nuc	0	Plastid; chloroplast				470
Q9MSS0 UniProt NPD GO	MATK_THUDO	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				509
Q4H178 UniProt NPD GO	MATK_TIGPA	Maturase K (Intron maturase)	0.54	-	nuc	0	Plastid; chloroplast				522
Q7JEW6 UniProt NPD GO	MATK_TRICE	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				521
Q7JEW0 UniProt NPD GO	MATK_TRIEE	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				521
Q7JEV9 UniProt NPD GO	MATK_TRIFE	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				521
Q7JEV7 UniProt NPD GO	MATK_TRIGN	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				517
Q9XPP1 UniProt NPD GO	MATK_TRIMC	Maturase K (Intron maturase)	0.54	-	cyt	0	Plastid; chloroplast				517
P09088 UniProt NPD GO	MEC3_CAEEL	Mechanosensory protein 3	0.54	+	nuc	0	Nucleus				321
Q9Y3C7 UniProt NPD GO	MED31_HUMAN	Mediator of RNA polymerase II transcription subunit 31 (Mediator complex subunit SOH1) (hSOH1)	0.54	-	cyt	0	Nucleus (Potential)				131
O13730 UniProt NPD GO	MDE6_SCHPO	Mei4-dependent protein 6	0.54	-	cyt	0					716
P50082 UniProt NPD GO	AMA1_YEAST	Meiosis-specific APC/C activator protein AMA1 (Activator of meiotic APC/C protein 1) (Sporulation-sp ...	0.54	-	nuc	0		anaphase-promoting complex [IPI]			593
Q6ITT4 UniProt NPD GO	MAGD1_PIG	Melanoma-associated antigen D1 (MAGE-D1 antigen)	0.54	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Expression shifts from the cytoplasm to the p ...				784
P70669 UniProt NPD GO	PHEX_MOUSE	Metalloendopeptidase homolog PEX (EC 3.4.24.-) (Phosphate regulating neutral endopeptidase) (X-linke ...	0.54	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				749
Q9UBK8 UniProt NPD GO	MTRR_HUMAN	Methionine synthase reductase, mitochondrial precursor (EC 1.16.1.8) (MSR)	0.54	-	mit	0	Isoform B, isoform C: Cytoplasm. Isoform A: Mitochondrion (Probable)	cytosol [TAS]	602568		725
Q10113 UniProt NPD GO	MAL3_SCHPO	Microtubule integrity protein mal3	0.54	-	nuc	0	Cytoplasm. Associated with microtubules	cell cortex of cell tip [IDA] cytoplasm [TAS] kinetochore microtubule [IDA] microtubule cytoskeleton [IDA]			308
P92532 UniProt NPD GO	RT12_ARATH	Mitochondrial ribosomal protein S12	0.54	-	nuc	0	Mitochondrion				125
P28520 UniProt NPD GO	RT12_ORYSA	Mitochondrial ribosomal protein S12	0.54	-	nuc	0	Mitochondrion				125
Q9Z1B7 UniProt NPD GO	MK13_MOUSE	Mitogen-activated protein kinase 13 (EC 2.7.11.24) (Stress-activated protein kinase 4) (Mitogen-acti ...	0.54	-	cyt	0					366
P31152 UniProt NPD GO	MK04_HUMAN	Mitogen-activated protein kinase 4 (EC 2.7.11.24) (Extracellular signal-regulated kinase 4) (ERK-4) ...	0.54	-	nuc	0			176949		557
Q16659 UniProt NPD GO	MK06_HUMAN	Mitogen-activated protein kinase 6 (EC 2.7.11.24) (Extracellular signal-regulated kinase 3) (ERK-3) ...	0.54	-	nuc	0			602904		721
Q99683 UniProt NPD GO	M3K5_HUMAN	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25) (MAPK/ERK kinase kinase 5) (MEK kina ...	0.54	-	cyt	0			602448	2CLQ	1374
P97588 UniProt NPD GO	SMAD1_RAT	Mothers against decapentaplegic homolog 1 (SMAD 1) (Mothers against DPP homolog 1)	0.54	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	integral to membrane [ISS] intracellular [ISS] nucleus [ISS]			468

You are viewing entries 22601 to 22650 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.