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
Q9MUY0 UniProt NPD GO	MATK_MOLCA	Maturase K (Intron maturase)	0.83	+	cyt	0	Plastid; chloroplast				513
P68753 UniProt NPD GO	MATK_PAECA	Maturase K (Intron maturase)	0.83	-	nuc	0	Plastid; chloroplast				496
O46996 UniProt NPD GO	MATK_PAELC	Maturase K (Intron maturase)	0.83	-	nuc	0	Plastid; chloroplast				496
Q7J5Z9 UniProt NPD GO	MATK_PAEOF	Maturase K (Intron maturase)	0.83	-	nuc	0	Plastid; chloroplast				496
Q7J5Z8 UniProt NPD GO	MATK_PAEPE	Maturase K (Intron maturase)	0.83	-	nuc	0	Plastid; chloroplast				496
P68754 UniProt NPD GO	MATK_PAERU	Maturase K (Intron maturase)	0.83	-	nuc	0	Plastid; chloroplast				496
Q7J602 UniProt NPD GO	MATK_PAETE	Maturase K (Intron maturase)	0.83	-	nuc	0	Plastid; chloroplast				496
Q8M930 UniProt NPD GO	MATK_PAUTO	Maturase K (Intron maturase)	0.83	-	pox	0	Plastid; chloroplast				511
P13828 UniProt NPD GO	MSP1_PLAYO	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA) (230 kDa) (PY230)	0.83	+	mit	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				1772
P41772 UniProt NPD GO	AMT1_CANGA	Metal-activated transcriptional activator protein AMT1	0.83	-	nuc	0	Nucleus			1CO4	265
Q8C0P0 UniProt NPD GO	MASTL_MOUSE	Microtubule-associated serine/threonine-protein kinase-like (EC 2.7.11.1)	0.83	-	nuc	0					865
P53349 UniProt NPD GO	M3K1_MOUSE	Mitogen-activated protein kinase kinase kinase 1 (EC 2.7.11.25) (MAPK/ERK kinase kinase 1) (MEK kina ...	0.83	-	nuc	0					1493
Q16584 UniProt NPD GO	M3K11_HUMAN	Mitogen-activated protein kinase kinase kinase 11 (EC 2.7.11.25) (Mixed lineage kinase 3) (Src-homol ...	0.83	-	nuc	0	Centrosome. Location is cell cycle dependent	centrosome [IDA] microtubule [IDA]	600050		847
Q9FZ36 UniProt NPD GO	M3K2_ARATH	Mitogen-activated protein kinase kinase kinase 2 (EC 2.7.11.25) (Arabidopsis NPK1-related protein ki ...	0.83	+	nuc	0					651
O13620 UniProt NPD GO	MRD1_SCHPO	Multiple RNA-binding domain-containing protein 1	0.83	-	nuc	0	Nucleus				833
Q9N2A4 UniProt NPD GO	ACM3_PANTR	Muscarinic acetylcholine receptor M3	0.83	+	vac	7	Membrane; multi-pass membrane protein				590
P10085 UniProt NPD GO	MYOD1_MOUSE	Myoblast determination protein 1	0.83	+	nuc	0	Nucleus	nucleus [IDA]		1MDY	318
Q91206 UniProt NPD GO	MYOD2_ONCMY	Myoblast determination protein 1 homolog 2 (Myogenic factor 1-2)	0.83	+	nuc	0	Nucleus				275
P17667 UniProt NPD GO	MYF5_BOVIN	Myogenic factor 5 (Myf-5)	0.83	+	nuc	0	Nucleus				255
Q08856 UniProt NPD GO	MYF5_CHICK	Myogenic factor 5 (Myf-5)	0.83	+	nuc	0	Nucleus				258
P34060 UniProt NPD GO	MYOG_COTJA	Myogenin (Myogenic factor 2)	0.83	+	nuc	0	Nucleus				226
Q12965 UniProt NPD GO	MYO1E_HUMAN	Myosin Ie (Myosin Ic)	0.83	+	cyt	0		actin cytoskeleton [TAS]	601479		1109
Q9C000 UniProt NPD GO	NALP1_HUMAN	NACHT, LRR and PYD-containing protein 1 (Death effector filament-forming ced-4-like apoptosis protei ...	0.83	-	cyt	0	Cytoplasm	intracellular [IC]	606636	1PN5	1473
Q8BZZ3 UniProt NPD GO	WWP1_MOUSE	NEDD4-like E3 ubiquitin-protein ligase WWP1 (EC 6.3.2.-) (WW domain-containing protein 1)	0.83	+	nuc	0		ubiquitin ligase complex [ISS]			918
P54729 UniProt NPD GO	NUB1_MOUSE	NEDD8 ultimate buster 1 (Protein BS4)	0.83	+	nuc	0	Nucleus (By similarity). Predominantly (By similarity)			1VEG	614
P20929 UniProt NPD GO	NEBU_HUMAN	Nebulin	0.83	-	nuc	0		actin cytoskeleton [TAS] Z disc [IDA]	161650	1NEB	6669
P32831 UniProt NPD GO	NGR1_YEAST	Negative growth regulatory protein NGR1 (RNA-binding protein RBP1)	0.83	-	nuc	0		cytoplasm [IDA] perinuclear region [IDA]			672
Q9QY53 UniProt NPD GO	NPHP1_MOUSE	Nephrocystin-1	0.83	+	mit	0	Cell membrane; cell-cell junction; adherens junction. Localizes at or near the cell-cell adherens ju ...				687
Q6AZT7 UniProt NPD GO	NPHP3_XENLA	Nephrocystin-3	0.83	-	cyt	0					1300
Q01705 UniProt NPD GO	NOTC1_MOUSE	Neurogenic locus notch homolog protein 1 precursor (Notch 1) (Motch A) (mT14) (p300) [Contains: Notc ...	0.83	+	exc	0	Cell membrane; single-pass type I membrane protein. NICD: Nucleus. Following proteolytical processin ...	integral to plasma membrane [IC] nucleus [IDA]			2531
Q22555 UniProt NPD GO	NHR44_CAEEL	Nuclear hormone receptor family member nhr-44	0.83	-	mit	0	Nucleus (Potential)				428
P35658 UniProt NPD GO	NU214_HUMAN	Nuclear pore complex protein Nup214 (Nucleoporin Nup214) (214 kDa nucleoporin) (CAN protein)	0.83	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex. Cytoplasmic filaments	nuclear pore [TAS]	114350		2090
Q91W39 UniProt NPD GO	NCOA5_MOUSE	Nuclear receptor coactivator 5 (NCoA-5) (Coactivator independent of AF-2) (CIA)	0.83	-	nuc	0	Nucleus (By similarity)				579
O15381 UniProt NPD GO	NVL_HUMAN	Nuclear valosin-containing protein-like (Nuclear VCP-like protein) (NVLp)	0.83	+	nuc	0	Nucleus; nucleolus	nucleus [TAS]	602426		856
P60954 UniProt NPD GO	NOL4_MOUSE	Nucleolar protein 4	0.83	-	nuc	0	Nucleus; nucleolus (By similarity)				523
O00567 UniProt NPD GO	NOP56_HUMAN	Nucleolar protein Nop56 (Nucleolar protein 5A)	0.83	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]			594
Q95K50 UniProt NPD GO	NOP56_MACFA	Nucleolar protein Nop56 (Nucleolar protein 5A)	0.83	+	nuc	0	Nucleus; nucleolus (By similarity)				594
Q5RA29 UniProt NPD GO	NOP56_PONPY	Nucleolar protein Nop56 (Nucleolar protein 5A)	0.83	+	nuc	0	Nucleus; nucleolus (By similarity)				594
Q2TA45 UniProt NPD GO	NUPL_BOVIN	Nucleoporin-like protein RIP (HIV-1 Rev-binding protein homolog)	0.83	-	nuc	0	Nucleus (By similarity). Cytoplasmic vesicle (By similarity)				562
P50874 UniProt NPD GO	ORC5_YEAST	Origin recognition complex subunit 5 (Origin recognition complex 53 kDa subunit)	0.83	+	cyt	0	Nucleus	nuclear origin of replication recognition c... [TAS] pre-replicative complex [TAS]			479
Q9Y5N6 UniProt NPD GO	ORC6_HUMAN	Origin recognition complex subunit 6	0.83	+	nuc	0	Nucleus		607213		252
O00482 UniProt NPD GO	NR5A2_HUMAN	Orphan nuclear receptor NR5A2 (Alpha-1-fetoprotein transcription factor) (Hepatocytic transcription ...	0.83	+	nuc	0	Nucleus (Probable)	nucleus [TAS]	604453	2A66	541
Q86WC4 UniProt NPD GO	OSTM1_HUMAN	Osteopetrosis-associated transmembrane protein 1 precursor	0.83	+	exc	2 *	Membrane; single-pass type I membrane protein (By similarity)		607649		334
Q92613 UniProt NPD GO	PHF16_HUMAN	PHD finger protein 16	0.83	-	nuc	0					823
Q05437 UniProt NPD GO	PRRX1_CHICK	Paired mesoderm homeobox protein 1 (Homeobox protein MHOX) (GMHOX) (Homeobox protein PRX-1)	0.83	+	nuc	0	Nucleus				245
Q90963 UniProt NPD GO	PRRX2_CHICK	Paired mesoderm homeobox protein 2 (PRX-2) (Fragment)	0.83	+	nuc	0	Nucleus (By similarity)				165
Q09928 UniProt NPD GO	PPIL2_SCHPO	Peptidyl-prolyl cis-trans isomerase cyp8 (EC 5.2.1.8) (PPIase cyp8) (Rotamase cyp8)	0.83	-	nuc	0	Nucleus				516
Q4IE79 UniProt NPD GO	PPIL4_GIBZE	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase)	0.83	+	nuc	0	Nucleus (By similarity)				605
P0C1I6 UniProt NPD GO	PPIL4_RHIOR	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase)	0.83	+	nuc	0	Nucleus (By similarity)				446
O14002 UniProt NPD GO	MAK2_SCHPO	Peroxide stress-activated histidine kinase mak2 (EC 2.7.13.3) (Mcs4-associated kinase 2) (His-Asp ph ...	0.83	-	end	0	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			2310

You are viewing entries 7451 to 7500 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.