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
O46579 UniProt NPD GO	COX41_PONPY	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.13	-	nuc	1	Mitochondrion; mitochondrial inner membrane				144
P10715 UniProt NPD GO	CYC2_RAT	Cytochrome c, testis-specific	0.13	-	cyt	0	Mitochondrion; mitochondrial matrix				104
Q5ZID6 UniProt NPD GO	5NT3_CHICK	Cytosolic 5'-nucleotidase III (EC 3.1.3.5) (cN-III) (Pyrimidine 5'-nucleotidase 1) (P5'N-1) (P5N-1) ...	0.13	-	cyt	0	Cytoplasm (Potential)	cytoplasm [ISS] endoplasmic reticulum [ISS]			285
P24778 UniProt NPD GO	CXH_HEMHA	Cytotoxin homolog (Toxin 9B/9BB)	0.13	-	nuc	0	Secreted protein				63
P14920 UniProt NPD GO	OXDA_HUMAN	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.13	-	mit	0	Peroxisome	peroxisome [NAS]	124050	2GNZ	347
Q80XN0 UniProt NPD GO	BDH_MOUSE	D-beta-hydroxybutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.30) (BDH) (3-hydroxybutyrate ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			343
Q74Z51 UniProt NPD GO	DAD4_ASHGO	DASH complex subunit DAD4 (Outer kinetochore protein DAD4)	0.13	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				72
P69851 UniProt NPD GO	DAD4_YEAST	DASH complex subunit DAD4 (Outer kinetochore protein DAD4) (DUO1 and DAM1-interacting protein 4) (He ...	0.13	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] kinetochore [IDA] spindle [IDA]			72
P08797 UniProt NPD GO	DIF_DICDI	DIF-inducible protein precursor	0.13	-	exc	0	Secreted protein (Potential)				157
Q8CFD5 UniProt NPD GO	ERCC8_MOUSE	DNA excision repair protein ERCC-8 (Cockayne syndrome WD repeat protein CSA homolog)	0.13	-	nuc	0	Nucleus (By similarity)				397
Q21625 UniProt NPD GO	DPOA2_CAEEL	DNA polymerase subunit alpha B (Division delayed protein 1)	0.13	-	cyt	0	Nucleus				581
O75771 UniProt NPD GO	RA51D_HUMAN	DNA repair protein RAD51 homolog 4 (R51H3) (TRAD)	0.13	-	nuc	0	Nucleus (Probable)	nucleus [TAS]	602954		328
P23196 UniProt NPD GO	APEX1_BOVIN	DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (AP endonuclease 1) (APEX nuclease) (APEN)	0.13	-	nuc	0	Nucleus	endoplasmic reticulum [ISS] nucleus [ISS] perinuclear region [ISS] ribosome [ISS]		1LYR	317
P27347 UniProt NPD GO	MNB1B_MAIZE	DNA-binding protein MNB1B (HMG1-like protein)	0.13	-	nuc	0	Nucleus (Probable)				157
Q921X6 UniProt NPD GO	RPO3F_MOUSE	DNA-directed RNA polymerase III subunit F (EC 2.7.7.6) (DNA-directed RNA polymerase III 39 kDa polyp ...	0.13	-	nuc	0	Nucleus (Potential)	DNA-directed RNA polymerase III complex [ISS]			316
Q12362 UniProt NPD GO	RIB2_YEAST	DRAP deaminase	0.13	-	cyt	0		cytoplasm [IDA]			591
Q5R1V9 UniProt NPD GO	PGS2_PANTR	Decorin precursor (Bone proteoglycan II) (PG-S2)	0.13	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				359
P07585 UniProt NPD GO	PGS2_HUMAN	Decorin precursor (Bone proteoglycan II) (PG-S2) (PG40)	0.13	-	exc	0	Secreted protein; extracellular space; extracellular matrix		610048		359
P28654 UniProt NPD GO	PGS2_MOUSE	Decorin precursor (Bone proteoglycan II) (PG-S2) (PG40)	0.13	-	exc	0	Secreted protein; extracellular space; extracellular matrix				354
Q750Y3 UniProt NPD GO	DCN1_ASHGO	Defective in cullin neddylation protein 1	0.13	-	mit	0					256
Q86QI5 UniProt NPD GO	DEF1_DERVA	Defensin precursor (Varisin A1)	0.13	-	exc	1 *	Secreted protein	extracellular region [IDA]			74
Q64263 UniProt NPD GO	DFR10_MOUSE	Defensin-related cryptdin, related sequence 10 precursor (Cryptdin-related protein 4C-4) (CRS4C)	0.13	-	exc	0	Secreted protein				91
P13494 UniProt NPD GO	TXDT1_HADVE	Delta-atracotoxin-Hv1a (Delta-AcTx-Hv1a) (Versutoxin)	0.13	-	nuc	0	Secreted protein			1VTX	42
P19855 UniProt NPD GO	SIX2_LEIQU	Depressant insect toxin 2 precursor (Insect toxin LqqIT2)	0.13	-	vac	0	Secreted protein				82
P45846 UniProt NPD GO	DERM_PIG	Dermatopontin (Tyrosine-rich acidic matrix protein) (TRAMP) (22 kDa extracellular matrix protein) (D ...	0.13	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				44
P48845 UniProt NPD GO	DEXT_PENMI	Dextranase precursor (EC 3.2.1.11) (Alpha-1,6-glucan-6-glucanohydrolase)	0.13	-	exc	0	Secreted protein			1OGO	608
Q8R242 UniProt NPD GO	DIAC_MOUSE	Di-N-acetylchitobiase precursor (EC 3.2.1.-)	0.13	-	cyt	0	Lysosome (By similarity)				366
Q9FVC8 UniProt NPD GO	DAPA2_ARATH	Dihydrodipicolinate synthase 2, chloroplast precursor (EC 4.2.1.52) (DHDPS 2)	0.13	-	cyt	0	Plastid; chloroplast				365
P17719 UniProt NPD GO	DYR_DROME	Dihydrofolate reductase (EC 1.5.1.3)	0.13	-	cyt	0					182
Q5R6X6 UniProt NPD GO	PYRD_PONPY	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.13	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				395
P32747 UniProt NPD GO	PYRD_SCHPO	Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdeha ...	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			443
Q62952 UniProt NPD GO	DPYL3_RAT	Dihydropyrimidinase-related protein 3 (DRP-3) (Collapsin response mediator protein 4) (CRMP-4) (TUC- ...	0.13	-	cyt	0	Cytoplasm. Colocalizes with synaptic vesicle protein 2 in the central region of the growth cone	growth cone [IDA] vesicle [IDA]			570
Q62188 UniProt NPD GO	DPYL3_MOUSE	Dihydropyrimidinase-related protein 3 (DRP-3) (Unc-33-like phosphoprotein) (ULIP protein)	0.13	-	cyt	0	Cytoplasm (By similarity). Colocalizes with synaptic vesicle protein 2 in the central region of the ...				570
Q14195 UniProt NPD GO	DPYL3_HUMAN	Dihydropyrimidinase-related protein 3 (DRP-3) (Unc-33-like phosphoprotein) (ULIP protein) (Collapsin ...	0.13	-	cyt	0	Cytoplasm (By similarity). Colocalizes with synaptic vesicle protein 2 in the central region of the ...		601168		570
O55096 UniProt NPD GO	DPP3_RAT	Dipeptidyl-peptidase 3 (EC 3.4.14.4) (Dipeptidyl-peptidase III) (DPP III) (Dipeptidyl aminopeptidase ...	0.13	-	nuc	0	Cytoplasm				738
Q62371 UniProt NPD GO	DDR2_MOUSE	Discoidin domain-containing receptor 2 precursor (EC 2.7.10.1) (Discoidin domain receptor 2) (Recept ...	0.13	-	end	2 *	Membrane; single-pass type I membrane protein				854
Q805F7 UniProt NPD GO	DISA_AGKCO	Disintegrin acostatin alpha precursor	0.13	-	nuc	0	Secreted protein				111
P62384 UniProt NPD GO	DISG_TRIAB	Disintegrin albolabrin (Platelet aggregation activation inhibitor)	0.13	-	nuc	0	Secreted protein				73
P22828 UniProt NPD GO	DISI_SISCT	Disintegrin tergeminin (Platelet aggregation activation inhibitor)	0.13	-	nuc	0	Secreted protein				73
P62383 UniProt NPD GO	DISG_TRIGA	Disintegrin trigramin-gamma (Platelet aggregation activation inhibitor)	0.13	-	nuc	0	Secreted protein				73
P83376 UniProt NPD GO	DBB2_DOLAU	Dolabellanin-B2	0.13	-	nuc	0	Secreted protein				33
Q9P838 UniProt NPD GO	OST4_CANAL	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 4 kDa subunit (EC 2.4.1.119) (Oligosa ...	0.13	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				60
P33775 UniProt NPD GO	PMT1_YEAST	Dolichyl-phosphate-mannose--protein mannosyltransferase 1 (EC 2.4.1.109)	0.13	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [TAS]			817
P42934 UniProt NPD GO	PMT6_YEAST	Dolichyl-phosphate-mannose--protein mannosyltransferase 6 (EC 2.4.1.109)	0.13	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [TAS]			759
P15101 UniProt NPD GO	DOPO_BOVIN	Dopamine beta-hydroxylase precursor (EC 1.14.17.1) (Dopamine beta-monooxygenase)	0.13	-	end	1 *	Exists both in a soluble form (in chromaffin granules) and as membrane bound (the membrane bound for ...				610
Q8VE01 UniProt NPD GO	DUS18_MOUSE	Dual specificity protein phosphatase 18 (EC 3.1.3.48) (EC 3.1.3.16)	0.13	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				188
Q99N11 UniProt NPD GO	DUS22_MOUSE	Dual specificity protein phosphatase 22 (EC 3.1.3.48) (EC 3.1.3.16) (LMW-DSP2)	0.13	-	cyt	0	Cytoplasm. Nucleus				184
Q58D68 UniProt NPD GO	ENPP6_BOVIN	Ectonucleotide pyrophosphatase/phosphodiesterase 6 precursor (EC 3.1.-.-) (E-NPP6) (NPP-6) [Contains ...	0.13	-	exc	0	Cell membrane; single-pass type I membrane protein. A minor secreted form also exists (By similarity ...				440
Q27140 UniProt NPD GO	EF12_EUPCR	Elongation factor 1-alpha 2 (EF-1-alpha-2)	0.13	-	mit	0	Cytoplasm				439
Q9QYU2 UniProt NPD GO	EFTS_RAT	Elongation factor Ts, mitochondrial precursor (EF-Ts) (EF-TsMt) (2A3-2)	0.13	-	mit	0	Mitochondrion (By similarity)				324

You are viewing entries 59601 to 59650 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.