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
P57770 UniProt NPD GO	AKA10_PIG	A kinase anchor protein 10, mitochondrial precursor (Protein kinase A-anchoring protein 10) (PRKA10) ...	0.57	-	nuc	0	Mitochondrion (By similarity). Membrane (By similarity). Cytoplasm (By similarity). Predominantly mi ...				650
P04627 UniProt NPD GO	ARAF_MOUSE	A-Raf proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1)	0.57	-	cyt	0		mitochondrion [IDA]			604
Q8W4A5 UniProt NPD GO	APO2_ARATH	APO protein 2, chloroplast precursor (Accumulation of photosystem I protein 2)	0.57	-	mit	0	Plastid; chloroplast (Potential)				440
Q8N5M1 UniProt NPD GO	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2, mitochondrial precursor (ATP12 homolog)	0.57	-	mit	0	Mitochondrion (Probable)		608918		289
Q6FS54 UniProt NPD GO	DBP3_CANGA	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-)	0.57	+	nuc	0	Nucleus; nucleolus (By similarity)				540
P53734 UniProt NPD GO	DBP6_YEAST	ATP-dependent RNA helicase DBP6 (EC 3.6.1.-) (DEAD box protein 6)	0.57	-	nuc	0	Nucleus; nucleolus	nucleolar preribosome, large subunit precursor [IDA] nucleolus [IDA]			629
Q62095 UniProt NPD GO	DDX3Y_MOUSE	ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-) (DEAD box protein 3, Y-chromosomal) (DEAD-box RNA heli ...	0.57	-	nuc	0	Cytoplasm. Nucleus. Shuttles between the nucleus and the cytoplasm in an XPO1-dependent manner				658
Q5AK59 UniProt NPD GO	HAS1_CANAL	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-)	0.57	-	nuc	0	Nucleus; nucleolus (By similarity)				565
Q6BH93 UniProt NPD GO	HAS1_DEBHA	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-)	0.57	+	nuc	0	Nucleus; nucleolus (By similarity)				568
P25808 UniProt NPD GO	SPB4_YEAST	ATP-dependent rRNA helicase SPB4 (EC 3.6.1.-) (Suppressor of PAB1 protein 4)	0.57	-	cyt	0	Nucleus; nucleolus	nucleolus [TAS]			606
P10084 UniProt NPD GO	AST4_DROME	Achaete-scute complex protein T4 (Scute protein)	0.57	-	nuc	0					345
Q60485 UniProt NPD GO	ACRBP_CAVPO	Acrosin-binding protein precursor (Proacrosin-binding protein sp32)	0.57	-	exc	0	Secreted protein (By similarity). Acrosome (By similarity). Colocalizes with proacrosin in the acros ...				543
Q9JMB5 UniProt NPD GO	ADRM1_RAT	Adhesion-regulating molecule 1 precursor (110 kDa cell membrane glycoprotein) (Gp110)	0.57	-	nuc	0					407
O04067 UniProt NPD GO	AGL9_SINAL	Agamous-like MADS-box protein AGL9 homolog (MADS D)	0.57	-	nuc	0	Nucleus (By similarity)				254
Q9VVF7 UniProt NPD GO	MIP_DROME	Allatostatins MIP precursor (Myoinhibitory-like protein) (B-type Allostatin preprohormone) [Contains ...	0.57	-	exc	1 *	Secreted protein				211
P23565 UniProt NPD GO	AINX_RAT	Alpha-internexin (Alpha-Inx)	0.57	-	nuc	0					505
P39195 UniProt NPD GO	ALU8_HUMAN	Alu subfamily SX sequence contamination warning entry	0.57	-	nuc	0					591
Q06335 UniProt NPD GO	APLP2_MOUSE	Amyloid-like protein 2 precursor (CDEI box-binding protein) (CDEBP)	0.57	-	end	2 *	Cell membrane; single-pass type I membrane protein (Potential). Nucleus (Potential)				695
O35460 UniProt NPD GO	ANGP1_RAT	Angiopoietin-1 precursor (ANG-1)	0.57	-	nuc	0	Secreted protein				497
Q6NY19 UniProt NPD GO	ANR47_HUMAN	Ankyrin repeat domain-containing protein 47	0.57	-	nuc	0					840
Q28502 UniProt NPD GO	APOE_MACMU	Apolipoprotein E (Apo-E) (Fragment)	0.57	-	nuc	0	Secreted protein				107
Q3ZBE1 UniProt NPD GO	ARMC1_BOVIN	Armadillo repeat-containing protein 1	0.57	-	nuc	0					282
Q805D8 UniProt NPD GO	ANF_FUGRU	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.57	-	nuc	0	Secreted protein				139
Q758N2 UniProt NPD GO	ATG13_ASHGO	Autophagy-related protein 13	0.57	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				659
Q6CS21 UniProt NPD GO	ATG18_KLULA	Autophagy-related protein 18	0.57	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				500
Q75A48 UniProt NPD GO	ATG9_ASHGO	Autophagy-related protein 9	0.57	-	vac	7	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				897
Q6AXU1 UniProt NPD GO	BTBDG_RAT	BTB/POZ domain-containing protein 16	0.57	-	mit	0					506
Q13075 UniProt NPD GO	BIRC1_HUMAN	Baculoviral IAP repeat-containing protein 1 (Neuronal apoptosis inhibitory protein)	0.57	-	nuc	0			600355		1403
Q9R016 UniProt NPD GO	BIR1E_MOUSE	Baculoviral IAP repeat-containing protein 1e (Neuronal apoptosis inhibitory protein 5)	0.57	-	nuc	0					1403
P02851 UniProt NPD GO	BAR2_CHITE	Balbiani ring protein 2 (Giant secretory protein I-B) (GSP-IB) (Fragment)	0.57	-	nuc	0	Secreted protein				210
Q9W1I2 UniProt NPD GO	BGCN_DROME	Benign gonial cell neoplasm protein	0.57	-	end	0					1215
Q9UBV7 UniProt NPD GO	B4GT7_HUMAN	Beta-1,4-galactosyltransferase 7 (EC 2.4.1.-) (Beta-1,4-GalTase 7) (Beta4Gal-T7) (b4Gal-T7) (UDP-gal ...	0.57	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Cis cister ...		604327		327
Q99MK8 UniProt NPD GO	ARBK1_MOUSE	Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) (Beta-ARK-1) (G-protein-coupled receptor kinase 2)	0.57	-	cyt	0		membrane [IDA]			689
P33336 UniProt NPD GO	SKN1_YEAST	Beta-glucan synthesis-associated protein SKN1	0.57	-	nuc	1	Membrane; single-pass type II membrane protein	integral to membrane [IDA]			771
O95972 UniProt NPD GO	BMP15_HUMAN	Bone morphogenetic protein 15 precursor (BMP-15) (Growth/differentiation factor 9B) (GDF-9B)	0.57	-	nuc	0	Secreted protein		300510		392
Q9UQF2 UniProt NPD GO	JIP1_HUMAN	C-jun-amino-terminal kinase-interacting protein 1 (JNK-interacting protein 1) (JIP-1) (JNK MAP kinas ...	0.57	-	nuc	0	Cytoplasm (By similarity). Accumulates in cell surface projections. Cytoplasm; perinuclear region (B ...	cytoplasm [IEP]	604641		711
O77728 UniProt NPD GO	CEBPE_SHEEP	CCAAT/enhancer-binding protein epsilon (C/EBP epsilon)	0.57	+	nuc	0	Nucleus (By similarity)				281
Q9JLQ0 UniProt NPD GO	CD2AP_MOUSE	CD2-associated protein (Mesenchyme-to-epithelium transition protein with SH3 domains 1) (METS-1)	0.57	+	nuc	0	Cytoplasm. Located at podocyte slit diaphragm between podocyte foot processes	cytoplasm [IDA]			637
Q28284 UniProt NPD GO	CD44_CANFA	CD44 antigen precursor (Phagocytic glycoprotein I) (PGP-1) (HUTCH-I) (Extracellular matrix receptor- ...	0.57	-	nuc	1	Membrane; single-pass type I membrane protein				351
Q8BTW8 UniProt NPD GO	CK5P1_MOUSE	CDK5 regulatory subunit-associated protein 1 (CDK5 activator-binding protein C42)	0.57	-	mit	0					588
Q6CU48 UniProt NPD GO	CSN11_KLULA	COP9 signalosome complex subunit 11	0.57	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)				389
Q7SD63 UniProt NPD GO	CSN12_NEUCR	COP9 signalosome complex subunit 12	0.57	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				461
O01422 UniProt NPD GO	CSN2_CAEEL	COP9 signalosome complex subunit 2 (Signalosome subunit 2)	0.57	-	nuc	0	Cytoplasm. Nucleus				495
Q91ZI0 UniProt NPD GO	CELR3_MOUSE	Cadherin EGF LAG seven-pass G-type receptor 3 precursor	0.57	-	end	7 *	Membrane; multi-pass membrane protein				3301
P36054 UniProt NPD GO	RCN1_YEAST	Calcipressin-like protein (Regulator of calcineurin) (Down syndrome candidate region 1-like protein) ...	0.57	-	nuc	0					211
P49101 UniProt NPD GO	CDPK2_MAIZE	Calcium-dependent protein kinase 2 (EC 2.7.11.1) (CDPK 2)	0.57	-	mit	0					513
Q99LL3 UniProt NPD GO	CHSTC_MOUSE	Carbohydrate sulfotransferase 12 (EC 2.8.2.5) (Chondroitin 4-O-sulfotransferase 2) (Chondroitin 4-su ...	0.57	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to Golgi membrane [ISS]			419
Q5XHM7 UniProt NPD GO	CHSTC_XENLA	Carbohydrate sulfotransferase 12 (EC 2.8.2.5) (Chondroitin 4-O-sulfotransferase 2) (Chondroitin 4-su ...	0.57	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				420
Q6XQG8 UniProt NPD GO	CHST7_RAT	Carbohydrate sulfotransferase 7 (EC 2.8.2.17) (EC 2.8.2.-) (Chondroitin 6-sulfotransferase 2) (C6ST- ...	0.57	+	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				485
Q63704 UniProt NPD GO	CPT1B_RAT	Carnitine O-palmitoyltransferase I, muscle isoform (EC 2.3.1.21) (CPT I) (CPTI-M) (Carnitine palmito ...	0.57	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				772

You are viewing entries 20601 to 20650 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.