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
Q90341 UniProt NPD GO	MYC1_CYPCA	MYC I protein (C-MYC I)	0.93	+	nuc	0	Nucleus				394
P43553 UniProt NPD GO	ALR2_YEAST	Magnesium transporter ALR2 (Aluminum resistance protein 2)	0.93	-	nuc	2	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IMP]			858
P37937 UniProt NPD GO	MAAZ3_SCHCO	Mating-type protein A-alpha Z3	0.93	+	nuc	0	Nucleus				891
Q9UW23 UniProt NPD GO	MATA1_CANAL	Mating-type-like protein A1 (MTLa1 protein)	0.93	+	nuc	0	Nucleus (By similarity)				210
P43244 UniProt NPD GO	MATR3_RAT	Matrin-3 (Nuclear scaffold protein P130/MAT3)	0.93	-	nuc	0	Nucleus; nucleoplasm; nuclear matrix				845
P36626 UniProt NPD GO	REC8_SCHPO	Meiotic recombination protein rec8 (Cohesin rec8)	0.93	+	nuc	0	Nucleus	inner kinetochore of condensed chromosome [IDA] meiotic cohesin complex [IDA]			561
Q86UL8 UniProt NPD GO	MAGI2_HUMAN	Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (Membrane-associated gu ...	0.93	+	nuc	0	Synaptosome; peripheral membrane protein (By similarity). Membrane-associated in synaptosomes (By si ...		606382	1WFV	1455
Q9NI63 UniProt NPD GO	PMYT1_DROME	Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (EC 2.7.11.1) (Myt1 kina ...	0.93	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein (Probable)	Golgi apparatus [IDA]			533
Q9Z2E2 UniProt NPD GO	MBD1_MOUSE	Methyl-CpG-binding domain protein 1 (Methyl-CpG-binding protein MBD1)	0.93	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nuclear, in a punctate pattern. Associated with euchromatic r ...	heterochromatin [IDA] nucleus [IDA]			636
Q9UIS9 UniProt NPD GO	MBD1_HUMAN	Methyl-CpG-binding domain protein 1 (Methyl-CpG-binding protein MBD1) (Protein containing methyl-CpG ...	0.93	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nuclear, in a punctate pattern. Associated with euchromatic r ...	nucleus [NAS]	156535	1IG4	605
Q9NU22 UniProt NPD GO	MDN1_HUMAN	Midasin (MIDAS-containing protein)	0.93	+	end	0	Nucleus (By similarity)	nucleus [NAS]			5596
Q03834 UniProt NPD GO	MSH6_YEAST	MutS protein homolog 6	0.93	-	nuc	0	Nucleus (Probable)	nucleus [IPI]			1242
P06646 UniProt NPD GO	MYC_ONCMY	Myc protein (c-myc) (Fragment)	0.93	+	nuc	0	Nucleus				414
P49032 UniProt NPD GO	MYC_CALJA	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.93	+	nuc	0	Nucleus				438
Q28350 UniProt NPD GO	MYC_CANFA	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.93	+	nuc	0	Nucleus				439
Q9MZU0 UniProt NPD GO	MYC_CYNVA	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.93	+	nuc	0	Nucleus				439
P68271 UniProt NPD GO	MYC_FELCA	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.93	+	nuc	0	Nucleus (By similarity)				439
P01106 UniProt NPD GO	MYC_HUMAN	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.93	+	nuc	0	Nucleus	nucleus [IDA]	190080	2A93	439
P22555 UniProt NPD GO	MYC_MARMO	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.93	+	nuc	0	Nucleus				439
P23583 UniProt NPD GO	MYC_PANTR	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.93	+	nuc	0	Nucleus				439
Q9MZT6 UniProt NPD GO	MYC_SYLFL	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.93	+	nuc	0	Nucleus				438
P13539 UniProt NPD GO	MYH6_MESAU	Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha)	0.93	+	nuc	0	Thick filaments of the myofibrils				1939
Q02566 UniProt NPD GO	MYH6_MOUSE	Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha)	0.93	+	nuc	0	Thick filaments of the myofibrils				1938
P12883 UniProt NPD GO	MYH7_HUMAN	Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta)	0.93	+	nuc	0	Thick filaments of the myofibrils	muscle myosin [TAS]	115200	1IK2	1935
O14157 UniProt NPD GO	MYO3_SCHPO	Myosin type-2 heavy chain 2 (Myosin type II heavy chain 2)	0.93	+	nuc	0		myosin II [TAS]			2104
P35580 UniProt NPD GO	MYH10_HUMAN	Myosin-10 (Myosin heavy chain, nonmuscle IIb) (Nonmuscle myosin heavy chain IIb) (NMMHC II-b) (NMMHC ...	0.93	+	nuc	0		myosin [NAS]	160776		1976
O08638 UniProt NPD GO	MYH11_MOUSE	Myosin-11 (Myosin heavy chain, smooth muscle isoform) (SMMHC)	0.93	+	nuc	0	Thick filaments of the myofibrils	muscle myosin [IDA]			1972
Q9QZZ4 UniProt NPD GO	MYO15_MOUSE	Myosin-15 (Myosin XV) (Unconventional myosin-15)	0.93	+	nuc	0	Cytoplasm (By similarity)				3511
Q5SPR8 UniProt NPD GO	ESCO1_BRARE	N-acetyltransferase ESCO1 (EC 2.3.1.-) (Establishment of cohesion 1 homolog 1) (ECO1 homolog 1)	0.93	-	nuc	0	Nucleus (By similarity)				609
Q91WE2 UniProt NPD GO	NIP30_MOUSE	NEFA-interacting nuclear protein NIP30	0.93	+	nuc	0	Nucleus (Potential)				254
P56182 UniProt NPD GO	NNP1_HUMAN	NNP-1 protein (Novel nuclear protein 1) (Nucleolar protein Nop52) (D21S2056E)	0.93	+	nuc	0	Nucleus; nucleolus	nucleus [TAS]			461
Q07763 UniProt NPD GO	CD244_MOUSE	Natural killer cell receptor 2B4 precursor (NKR2B4) (NK cell type I receptor protein 2B4) (CD244 ant ...	0.93	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA]			397
P14598 UniProt NPD GO	NCF1_HUMAN	Neutrophil cytosol factor 1 (NCF-1) (Neutrophil NADPH oxidase factor 1) (47 kDa neutrophil oxidase f ...	0.93	-	nuc	0	Cytoplasm	cytosol [TAS] soluble fraction [TAS]	233700	1WLP	390
P28349 UniProt NPD GO	NIT4_NEUCR	Nitrogen assimilation transcription factor nit-4	0.93	+	nuc	0	Nucleus				1090
P17429 UniProt NPD GO	AREA_EMENI	Nitrogen regulatory protein areA	0.93	-	nuc	0	Nucleus			7GAT	876
O13508 UniProt NPD GO	AREA_PENRO	Nitrogen regulatory protein areA (Nitrogen regulator nmc)	0.93	-	nuc	0	Nucleus				860
P52591 UniProt NPD GO	PO121_RAT	Nuclear envelope pore membrane protein POM 121 (Pore membrane protein of 121 kDa) (P145)	0.93	+	nuc	1 *	Nucleus; nuclear envelope; nuclear pore complex; single-pass type II membrane protein. Endoplasmic r ...	nuclear pore [IDA]			1199
P17923 UniProt NPD GO	NFIA_CHICK	Nuclear factor 1 A-type (Nuclear factor 1/A) (NF1-A) (NFI-A) (NF-I/A) (CCAAT-box-binding transcripti ...	0.93	-	nuc	0	Nucleus				522
Q12857 UniProt NPD GO	NFIA_HUMAN	Nuclear factor 1 A-type (Nuclear factor 1/A) (NF1-A) (NFI-A) (NF-I/A) (CCAAT-box-binding transcripti ...	0.93	-	nuc	0	Nucleus	nucleus [NAS]	600727		509
P09414 UniProt NPD GO	NFIA_RAT	Nuclear factor 1 A-type (Nuclear factor 1/A) (NF1-A) (NFI-A) (NF-I/A) (CCAAT-box-binding transcripti ...	0.93	-	nuc	0	Nucleus				509
P17926 UniProt NPD GO	NFIC_CHICK	Nuclear factor 1 C-type (Nuclear factor 1/C) (NF1-C) (NFI-C) (NF-I/C) (CCAAT-box-binding transcripti ...	0.93	-	nuc	0	Nucleus				439
Q61985 UniProt NPD GO	NF2L1_MOUSE	Nuclear factor erythroid 2-related factor 1 (NF-E2-related factor 1) (NFE2-related factor 1) (Nuclea ...	0.93	+	nuc	0	Nucleus (By similarity)				741
Q14494 UniProt NPD GO	NF2L1_HUMAN	Nuclear factor erythroid 2-related factor 1 (NF-E2-related factor 1) (NFE2-related factor 1) (Nuclea ...	0.93	+	nuc	0	Nucleus (By similarity)		163260		772
Q9WV30 UniProt NPD GO	NFAT5_MOUSE	Nuclear factor of activated T-cells 5 (T cell transcription factor NFAT5) (NF-AT5) (Rel domain-conta ...	0.93	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			1225
Q15596 UniProt NPD GO	NCOA2_HUMAN	Nuclear receptor coactivator 2 (NCoA-2) (Transcriptional intermediary factor 2)	0.93	-	nuc	0	Nucleus	nucleus [NAS]	601993	2AO6	1464
Q61026 UniProt NPD GO	NCOA2_MOUSE	Nuclear receptor coactivator 2 (NCoA-2) (Transcriptional intermediary factor 2) (Glucocorticoid rece ...	0.93	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]		1WM0	1462
Q6DFV7 UniProt NPD GO	NCOA7_MOUSE	Nuclear receptor coactivator 7	0.93	+	nuc	0	Nucleus (By similarity)				943
Q8WNV1 UniProt NPD GO	STP2_MACFA	Nuclear transition protein 2 (TP-2) (TP2)	0.93	+	mit	0	Nucleus (By similarity)				141
Q14978 UniProt NPD GO	NOLC1_HUMAN	Nucleolar phosphoprotein p130 (Nucleolar 130 kDa protein) (140 kDa nucleolar phosphoprotein) (Nopp14 ...	0.93	+	nuc	0	Nucleus; nucleolus. Cytoplasm. Shuttles between the nucleolus and the cytoplasm. At telophase it beg ...	cytoplasm [TAS] nucleolus [TAS]	602394		699
Q6GM06 UniProt NPD GO	OTU6B_XENLA	OTU domain-containing protein 6B	0.93	+	nuc	0					294

You are viewing entries 2851 to 2900 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.