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
Q12285 UniProt NPD GO	MDY2_YEAST	Ubiquitin-like protein MDY2 (Mating-deficient protein 2) (Translation machinery-associated protein 2 ...	0.18	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			212
Q12306 UniProt NPD GO	SMT3_YEAST	Ubiquitin-like protein SMT3 precursor	0.18	-	nuc	0		nucleus [IDA] septin ring [IDA]		1L2N	101
P53082 UniProt NPD GO	YGX0_YEAST	Uncharacterized bolA-like protein YGL220W	0.18	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			120
Q9SMZ9 UniProt NPD GO	Y4331_ARATH	Uncharacterized protein At4g33100	0.18	-	nuc	0					92
Q8N9R9 UniProt NPD GO	CN065_HUMAN	Uncharacterized protein C14orf65	0.18	-	nuc	0					162
Q66JT5 UniProt NPD GO	CR010_MOUSE	Uncharacterized protein C18orf10 homolog	0.18	-	nuc	0					237
Q5RF08 UniProt NPD GO	CA043_PONPY	Uncharacterized protein C1orf43 homolog	0.18	-	nuc	1 *					189
Q08919 UniProt NPD GO	TRE1_YEAST	Uncharacterized protein TRE1 (Transferrin receptor-like protein 1)	0.18	-	mit	1	Cell membrane; single-pass type II membrane protein (Potential)	plasma membrane [IDA]			783
P25577 UniProt NPD GO	YCE9_YEAST	Uncharacterized protein YCL049C precursor	0.18	-	exc	0		membrane fraction [IDA]			312
P53110 UniProt NPD GO	YGP9_YEAST	Uncharacterized protein YGL159W	0.18	-	nuc	0					370
Q3E828 UniProt NPD GO	YJ127_YEAST	Uncharacterized protein YJL127C-B	0.18	-	mit	0	Membrane; single-pass membrane protein (Potential)				52
Q12144 UniProt NPD GO	YL064_YEAST	Uncharacterized protein YLR064W	0.18	-	mit	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			273
Q05497 UniProt NPD GO	YD338_YEAST	Uncharacterized transporter YDR338C	0.18	-	end	10	Membrane; multi-pass membrane protein (Potential)				695
Q5KCQ6 UniProt NPD GO	UREA_CRYNE	Urease (EC 3.5.1.5) (Urea amidohydrolase)	0.18	-	cyt	0					833
Q8CGR7 UniProt NPD GO	UPP2_MOUSE	Uridine phosphorylase 2 (EC 2.4.2.3) (UrdPase 2) (UPase 2) (Liver-specific uridine phosphorylase) (L ...	0.18	-	nuc	0		cytosol [ISS] type III intermediate filament [ISS]			320
Q8HYC3 UniProt NPD GO	UR2R_MACMU	Urotensin II receptor (UR-II-R)	0.18	-	end	7	Membrane; multi-pass membrane protein				389
Q9UKP6 UniProt NPD GO	UR2R_HUMAN	Urotensin II receptor (UR-II-R) (G-protein coupled receptor 14)	0.18	-	end	7	Membrane; multi-pass membrane protein	membrane [TAS]	600896		389
P16140 UniProt NPD GO	VATB_YEAST	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit) ...	0.18	-	cyt	0		cytoplasm [IDA] hydrogen-transporting ATPase V1 domain [TAS]			517
P10977 UniProt NPD GO	CARPV_CANAL	Vacuolar aspartic protease precursor (EC 3.4.23.-) (Aspartate protease) (ACP)	0.18	-	vac	0	Vacuole. Lysosome-like vacuoles (Potential)				419
Q12255 UniProt NPD GO	NYV1_YEAST	Vacuolar v-SNARE NYV1 (R-SNARE NYV1) (Synaptobrevin NYV1) (New v-SNARE 1)	0.18	-	nuc	1	Vacuole; vacuolar membrane; single-pass type IV membrane protein	vacuolar membrane [TAS]		2FZ0	251
P26332 UniProt NPD GO	VSM2_TRYBB	Variant surface glycoprotein MITAT 1.2 precursor (VSG 221)	0.18	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...			1XU6	476
P97751 UniProt NPD GO	VIPR1_MOUSE	Vasoactive intestinal polypeptide receptor 1 precursor (VIP-R-1) (VPAC1) (Pituitary adenylate cyclas ...	0.18	-	end	7	Membrane; multi-pass membrane protein				459
P48043 UniProt NPD GO	V1AR_SHEEP	Vasopressin V1a receptor (V1aR) (Vascular/hepatic-type arginine vasopressin receptor) (Antidiuretic ...	0.18	-	end	7	Membrane; multi-pass membrane protein				418
P10769 UniProt NPD GO	NEU2_CAVPO	Vasopressin-neurophysin 2-copeptin precursor (AVP-NPII) [Contains: Arg-vasopressin; Neurophysin 2 (N ...	0.18	-	nuc	0	Secreted protein				144
P16229 UniProt NPD GO	NEU4_CATCO	Vasotocin-neurophysin VT 2 precursor [Contains: Vasotocin (VT); Neurophysin VT 2]	0.18	-	nuc	1 *	Secreted protein				155
P38188 UniProt NPD GO	YBG5_YEAST	Very hypothetical protein YBL065W	0.18	-	nuc	1 *					114
P63024 UniProt NPD GO	VAMP3_MOUSE	Vesicle-associated membrane protein 3 (VAMP-3) (Synaptobrevin-3) (Cellubrevin) (CEB)	0.18	-	nuc	1	Membrane; single-pass type IV membrane protein (Probable)				103
P63025 UniProt NPD GO	VAMP3_RAT	Vesicle-associated membrane protein 3 (VAMP-3) (Synaptobrevin-3) (Cellubrevin) (CEB)	0.18	-	nuc	1	Membrane; single-pass type IV membrane protein (Probable)				103
Q6Q595 UniProt NPD GO	SCS22_YEAST	Vesicle-associated membrane protein-associated protein SCS22 (VAMP-associated protein SCS22) (VAP ho ...	0.18	-	cyt	1	Membrane; single-pass type IV membrane protein (Potential)				175
P34579 UniProt NPD GO	UNC47_CAEEL	Vesicular GABA transporter (Uncoordinated protein 47) (Protein unc-47)	0.18	-	end	9	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein				486
Q75D68 UniProt NPD GO	SEC17_ASHGO	Vesicular-fusion protein SEC17	0.18	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				291
P13238 UniProt NPD GO	VTU2_DROME	Vitelline membrane protein Vm26Ab precursor (Protein TU-4) (Protein SV23)	0.18	-	exc	0					168
Q9JJV3 UniProt NPD GO	CCGL_MOUSE	Voltage-dependent calcium channel gamma-like subunit (Neuronal voltage-gated calcium channel gamma-l ...	0.18	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				211
Q4PJK1 UniProt NPD GO	KCAB1_BOVIN	Voltage-gated potassium channel subunit beta-1 (K(+) channel subunit beta-1) (Kv-beta-1)	0.18	-	cyt	0	Cytoplasm (Potential)				401
P63143 UniProt NPD GO	KCAB1_MOUSE	Voltage-gated potassium channel subunit beta-1 (K(+) channel subunit beta-1) (Kv-beta-1)	0.18	-	cyt	0	Cytoplasm (Potential)				401
P63144 UniProt NPD GO	KCAB1_RAT	Voltage-gated potassium channel subunit beta-1 (K(+) channel subunit beta-1) (Kv-beta-1)	0.18	-	cyt	0	Cytoplasm (Potential)				401
Q9CYU6 UniProt NPD GO	WDR85_MOUSE	WD repeat protein 85	0.18	-	nuc	0					477
Q09373 UniProt NPD GO	FZY1_CAEEL	WD repeat-containing protein fzy-1 (Fizzy protein 1)	0.18	-	mit	0					507
O46655 UniProt NPD GO	WAP_PIG	Whey acidic protein precursor (WAP)	0.18	-	exc	0	Secreted protein			1CJH	132
P09412 UniProt NPD GO	WAP_RABIT	Whey acidic protein precursor (WAP)	0.18	-	exc	0	Secreted protein				127
Q6IN38 UniProt NPD GO	WIF1_RAT	Wnt inhibitory factor 1 precursor (WIF-1)	0.18	-	mit	0	Secreted protein				379
Q5GH60 UniProt NPD GO	XKR2_RAT	XK-related protein 2 (X Kell blood group-related, X-linked)	0.18	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				448
Q6PP77 UniProt NPD GO	XKR2_HUMAN	XK-related protein 2 (X Kell blood group-related, X-linked) (Membrane protein XPLAC)	0.18	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				449
Q23229 UniProt NPD GO	XOL1_CAEEL	XO lethal protein 1	0.18	-	mit	0	Nucleus			1MG7	417
Q99546 UniProt NPD GO	ZWIA_HUMAN	ZW10 interactor, antisense (M-phase phosphoprotein 5) (Fragment)	0.18	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]	605499		124
Q8SW34 UniProt NPD GO	Z394_ENCCU	Zinc finger C2H2 protein ECU03_0940	0.18	-	nuc	0					196
Q8N782 UniProt NPD GO	ZN525_HUMAN	Zinc finger protein 525	0.18	-	nuc	0	Nucleus (Potential)				365
Q31125 UniProt NPD GO	KE4_MOUSE	Zinc transporter SLC39A7 (Solute carrier family 39 member 7) (Histidine-rich membrane protein Ke4)	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				476
P25311 UniProt NPD GO	ZA2G_HUMAN	Zinc-alpha-2-glycoprotein precursor (Zn-alpha-2-glycoprotein) (Zn-alpha-2-GP)	0.18	-	mit	0	Secreted protein	extracellular region [NAS]	194460	1ZAG	295
O54937 UniProt NPD GO	PDK4_RAT	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.18	-	mit	0	Mitochondrion; mitochondrial matrix				412

You are viewing entries 53851 to 53900 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.