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
P46435 UniProt NPD GO	MAK16_SCHMA	MAK16 protein homolog (SmMAK16)	0.64	+	nuc	0	Nucleus; nucleolus				259
O22437 UniProt NPD GO	CHLD_PEA	Magnesium-chelatase subunit chlD, chloroplast precursor (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase ...	0.64	-	mit	0	Plastid; chloroplast; chloroplast stroma				754
Q14680 UniProt NPD GO	MELK_HUMAN	Maternal embryonic leucine zipper kinase (EC 2.7.11.1) (hMELK) (Protein kinase PK38) (hPK38)	0.64	-	nuc	0	Cytoplasm (Potential)		607025		651
Q9NPA2 UniProt NPD GO	MMP25_HUMAN	Matrix metalloproteinase-25 precursor (EC 3.4.24.-) (MMP-25) (Membrane-type matrix metalloproteinase ...	0.64	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	cell surface [IEP] extracellular matrix (sensu Metazoa) [NAS] membrane [NAS]			562
Q7YJH1 UniProt NPD GO	MATK_ASPLU	Maturase K (Intron maturase)	0.64	-	cyt	0	Plastid; chloroplast				523
Q95EA5 UniProt NPD GO	MATK_BROHE	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				507
Q71ML1 UniProt NPD GO	MATK_CHIUM	Maturase K (Intron maturase)	0.64	-	cyt	0	Plastid; chloroplast				504
Q6EIJ2 UniProt NPD GO	MATK_OCHPY	Maturase K (Intron maturase)	0.64	-	cyt	0	Plastid; chloroplast				504
Q5YJY5 UniProt NPD GO	MATK_PARAU	Maturase K (Intron maturase)	0.64	-	cyt	0	Plastid; chloroplast				499
Q9TKS4 UniProt NPD GO	MATK_PHACN	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				514
Q8WHM8 UniProt NPD GO	MATK_PISST	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				511
O62984 UniProt NPD GO	MATK_RHOFR	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				506
Q646M7 UniProt NPD GO	MATK_SAPSA	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				522
Q6DT84 UniProt NPD GO	MATK_SOLAP	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				512
Q9TKS6 UniProt NPD GO	MATK_SOYBN	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				505
Q6EIG9 UniProt NPD GO	MATK_THECC	Maturase K (Intron maturase)	0.64	-	cyt	0	Plastid; chloroplast				502
Q8MCM3 UniProt NPD GO	MATK_TRISM	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				509
Q8MCM1 UniProt NPD GO	MATK_TRISR	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				506
Q8MCL9 UniProt NPD GO	MATK_TRITL	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				506
Q9MV49 UniProt NPD GO	MATK_TSUCA	Maturase K (Intron maturase)	0.64	-	nuc	0	Plastid; chloroplast				514
P31916 UniProt NPD GO	MAT2_EUGGR	Maturase-like protein 2	0.64	-	cyt	1	Plastid; chloroplast				758
Q99583 UniProt NPD GO	MNT_HUMAN	Max-binding protein MNT (Protein ROX) (Myc antagonist MNT)	0.64	-	nuc	0	Nucleus		603039		582
O08789 UniProt NPD GO	MNT_MOUSE	Max-binding protein MNT (Protein ROX) (Myc antagonist MNT)	0.64	-	nuc	0	Nucleus	nucleus [IC]			591
P32581 UniProt NPD GO	IME2_YEAST	Meiosis induction protein kinase IME2/SME1 (EC 2.7.11.1)	0.64	-	nuc	0		nucleus [IDA]			645
Q9QYH6 UniProt NPD GO	MAGD1_MOUSE	Melanoma-associated antigen D1 (MAGE-D1 antigen) (Neurotrophin receptor-interacting MAGE homolog) (D ...	0.64	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Expression shifts from the cytoplasm to the p ...				775
Q9ES73 UniProt NPD GO	MAGD1_RAT	Melanoma-associated antigen D1 (MAGE-D1 antigen) (Neurotrophin receptor-interacting MAGE homolog) (S ...	0.64	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Expression shifts from the cytoplasm to the p ...				775
Q9SJL6 UniProt NPD GO	MEM11_ARATH	Membrin 11 (AtMEMB11) (Golgi SNAP receptor complex member 2-1) (27 kDa Golgi SNARE protein)	0.64	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (Potential)				225
O95983 UniProt NPD GO	MBD3_HUMAN	Methyl-CpG-binding domain protein 3 (Methyl-CpG-binding protein MBD3)	0.64	-	nuc	0	Nucleus. Nuclear, in discrete foci		603573		291
Q9Z2D8 UniProt NPD GO	MBD3_MOUSE	Methyl-CpG-binding domain protein 3 (Methyl-CpG-binding protein MBD3)	0.64	-	nuc	0	Nucleus. Nuclear, in discrete foci	chromatin [IDA] nucleus [IDA]			285
Q9NP92 UniProt NPD GO	RT30_HUMAN	Mitochondrial 28S ribosomal protein S30 (S30mt) (MRP-S30) (Programmed cell death protein 9)	0.64	-	mit	0	Mitochondrion				439
Q06324 UniProt NPD GO	MMR1_YEAST	Mitochondrial MYO2 receptor-related protein 1	0.64	-	nuc	0	Bud tip. Bud neck. Mitochondrion; mitochondrial outer membrane; peripheral membrane protein	bud neck [IDA] incipient bud site [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			491
Q12171 UniProt NPD GO	MDM32_YEAST	Mitochondrial distribution and morphology protein 32, mitochondrial precursor	0.64	-	nuc	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA] mitochondrion [IDA]			653
P26863 UniProt NPD GO	RT01_MARPO	Mitochondrial ribosomal protein S1	0.64	-	mit	0	Mitochondrion				270
Q84M93 UniProt NPD GO	MPK17_ARATH	Mitogen-activated protein kinase 17 (EC 2.7.11.24) (MAP kinase 17) (AtMPK17)	0.64	-	cyt	0					486
Q9LV37 UniProt NPD GO	MPK9_ARATH	Mitogen-activated protein kinase 9 (EC 2.7.11.24) (MAP kinase 9) (AtMPK9)	0.64	-	nuc	0					510
Q12852 UniProt NPD GO	M3K12_HUMAN	Mitogen-activated protein kinase kinase kinase 12 (EC 2.7.11.25) (Mixed lineage kinase) (Leucine-zip ...	0.64	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytoplasm [TAS] cytosol [ISS] membrane fraction [ISS] plasma membrane [ISS]	600447		859
Q07174 UniProt NPD GO	M3K8_MOUSE	Mitogen-activated protein kinase kinase kinase 8 (EC 2.7.11.25) (COT proto-oncogene serine/threonine ...	0.64	-	cyt	0	Cytoplasm				467
Q63562 UniProt NPD GO	M3K8_RAT	Mitogen-activated protein kinase kinase kinase 8 (EC 2.7.11.25) (Tumor progression locus 2) (TPL-2)	0.64	-	cyt	0	Cytoplasm				467
Q9QUM7 UniProt NPD GO	MSH5_MOUSE	MutS protein homolog 5	0.64	-	mit	0					833
Q6MG62 UniProt NPD GO	MSH5_RAT	MutS protein homolog 5	0.64	-	mit	0					831
Q5R4T3 UniProt NPD GO	MLF1_PONPY	Myeloid leukemia factor 1 (Myelodysplasia-myeloid leukemia factor 1)	0.64	-	nuc	0	Cytoplasm. Nucleus (By similarity)				268
Q23979 UniProt NPD GO	MY61F_DROME	Myosin IB (MIB) (Brush border myosin IB) (BBMIB)	0.64	-	nuc	0	Cytoplasm. Protein shifts from the basolateral to apical domain in enterocytes and follicle cells				1035
O15527 UniProt NPD GO	OGG1_HUMAN	N-glycosylase/DNA lyase [Includes: 8-oxoguanine DNA glycosylase (EC 3.2.2.-); DNA-(apurinic or apyri ...	0.64	-	mit	0	Isoform 1A: Nucleus. Isoform 2A: Mitochondrion	nucleoplasm [TAS]	144700	1YQR	345
Q9R1M5 UniProt NPD GO	NALP5_MOUSE	NACHT, LRR and PYD-containing protein 5 (Maternal antigen that embryos require) (Mater protein) (Oop ...	0.64	-	nuc	0	Cytoplasm	cytosol [IDA]			1111
Q8WX94 UniProt NPD GO	NALP7_HUMAN	NACHT, LRR and PYD-containing protein 7 (PYRIN-containing APAF1-like protein 3)	0.64	-	cyt	0			609661		980
P70670 UniProt NPD GO	NACAM_MOUSE	Nascent polypeptide-associated complex subunit alpha, muscle-specific form (Alpha-NAC, muscle-specif ...	0.64	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			2187
Q95JB9 UniProt NPD GO	NCTR1_MACFA	Natural cytotoxicity triggering receptor 1 precursor (Natural killer cell p46-related protein) (NKp4 ...	0.64	-	end	1	Membrane; single-pass type I membrane protein (Potential)				306
Q90922 UniProt NPD GO	NET1_CHICK	Netrin-1 precursor	0.64	-	nuc	0	Secreted protein; extracellular space				606
O42414 UniProt NPD GO	NFASC_CHICK	Neurofascin precursor	0.64	-	exc	1	Membrane; single-pass type I membrane protein				1369
P79765 UniProt NPD GO	NDF1_CHICK	Neurogenic differentiation factor 1 (NeuroD1) (NeuroD)	0.64	-	nuc	0	Nucleus (Potential)				357

You are viewing entries 16951 to 17000 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.