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
P13298 UniProt NPD GO	PYRE_YEAST	Orotate phosphoribosyltransferase 1 (EC 2.4.2.10) (OPRT 1) (OPRTase 1)	0.05	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			226
P30402 UniProt NPD GO	PYRX_YEAST	Orotate phosphoribosyltransferase 2 (EC 2.4.2.10) (OPRT 2) (OPRTase 2)	0.05	-	cyt	0		cytoplasm [IDA]			227
Q9C150 UniProt NPD GO	PYRF_CANDU	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.05	-	cyt	0					270
Q6IUR4 UniProt NPD GO	PYRF_CANGY	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.05	-	cyt	0					262
Q12595 UniProt NPD GO	PYRF_CANPA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.05	-	cyt	0					268
Q9HFV8 UniProt NPD GO	PYRF_CLAFU	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.05	-	mit	0					278
P78724 UniProt NPD GO	PYRF_HANAN	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.05	-	cyt	0					267
P79075 UniProt NPD GO	PYRF_HANFA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.05	-	cyt	0					265
Q9C1J2 UniProt NPD GO	PYRF_PICPA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.05	-	mit	0					263
P25777 UniProt NPD GO	ORYB_ORYSA	Oryzain beta chain precursor (EC 3.4.22.-)	0.05	-	end	1 *				1FWO	466
Q8R448 UniProt NPD GO	OTOSP_MOUSE	Otospiralin precursor (Organ of Corti 10 kDa protein)	0.05	-	cyt	0	Secreted protein (Probable)				89
P46274 UniProt NPD GO	VDAC1_WHEAT	Outer mitochondrial membrane protein porin (Voltage-dependent anion-selective channel protein) (VDAC ...	0.05	-	nuc	0	Mitochondrion; mitochondrial outer membrane				275
P01012 UniProt NPD GO	OVAL_CHICK	Ovalbumin (Plakalbumin) (Allergen Gal d 2) (Gal d II)	0.05	-	nuc	0	Secreted protein			1VAC	385
Q90YI1 UniProt NPD GO	OCX32_CHICK	Ovocalyxin-32 precursor (OCX-32) (32 kDa eggshell matrix protein)	0.05	-	exc	0	Secreted protein				275
Q42029 UniProt NPD GO	PSBP1_ARATH	Oxygen-evolving enhancer protein 2-1, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolvin ...	0.05	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				263
P29530 UniProt NPD GO	OLEO1_SOYBN	P24 oleosin isoform A (P89)	0.05	-	end	2	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				226
P51577 UniProt NPD GO	P2RX4_RAT	P2X purinoceptor 4 (ATP receptor) (P2X4) (Purinergic receptor)	0.05	-	end	2 *	Membrane; multi-pass membrane protein			2BP5	388
O15547 UniProt NPD GO	P2RX6_HUMAN	P2X purinoceptor 6 (ATP receptor) (P2X6) (Purinergic receptor) (P2XM) (Purinergic receptor P2X-like ...	0.05	-	end	1 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	608077		431
Q8BMC0 UniProt NPD GO	P2RY5_MOUSE	P2Y purinoceptor 5 (P2Y5) (Purinergic receptor 5)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				344
P09131 UniProt NPD GO	P3_HUMAN	P3 protein (Solute carrier family 10 member 3)	0.05	-	end	7	Membrane; multi-pass membrane protein (Probable)	integral to membrane [NAS]	312090		477
Q865P3 UniProt NPD GO	PDZD1_RABIT	PDZ domain-containing protein 1 (CFTR-associated protein of 70 kDa) (Na(+)/H(+) exchanger regulatory ...	0.05	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with pe ...				518
Q9JIL4 UniProt NPD GO	PDZD1_MOUSE	PDZ domain-containing protein 1 (CFTR-associated protein of 70 kDa) (Na/Pi cotransporter C-terminal- ...	0.05	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with peripheral membranes. Localizes to ...				519
Q498D9 UniProt NPD GO	GIPC2_RAT	PDZ domain-containing protein GIPC2	0.05	-	cyt	0	Cytoplasm (Probable)				314
Q9YGI6 UniProt NPD GO	VSP2_AGKHP	Pallabin-2 precursor (EC 3.4.21.-)	0.05	-	exc	0	Secreted protein				260
Q949X0 UniProt NPD GO	ADS3_ARATH	Palmitoyl-monogalactosyldiacylglycerol delta-7 desaturase, chloroplast precursor (EC 1.14.19.-) (Mon ...	0.05	-	end	2	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				371
P39010 UniProt NPD GO	AKR1_YEAST	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.05	-	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...	membrane [IDA]			764
Q5KLN1 UniProt NPD GO	PFA4_CRYNE	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.05	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				456
Q04629 UniProt NPD GO	SWF1_YEAST	Palmitoyltransferase SWF1 (EC 2.3.1.-) (Spore wall formation protein 1)	0.05	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	nuclear envelope-endoplasmic reticulum network [IDA]			336
Q9NXF8 UniProt NPD GO	ZDHC7_HUMAN	Palmitoyltransferase ZDHHC7 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 7) (DHHC-7) (Zi ...	0.05	+	end	4 *	Membrane; multi-pass membrane protein (Potential)				308
Q5BKQ4 UniProt NPD GO	LIPR1_MOUSE	Pancreatic lipase-related protein 1 precursor (EC 3.1.1.3)	0.05	-	exc	0	Secreted protein. Secreted in acinar cells				473
P54318 UniProt NPD GO	LIPR2_RAT	Pancreatic lipase-related protein 2 precursor (EC 3.1.1.3) (Secretory glycoprotein GP-3)	0.05	-	vac	0	Or: Secreted protein. Or: Membrane			1BU8	468
Q58CQ9 UniProt NPD GO	VNN1_BOVIN	Pantetheinase precursor (EC 3.5.1.92) (Pantetheine hydrolase) (Vascular non-inflammatory molecule 1) ...	0.05	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				510
O80765 UniProt NPD GO	PANK1_ARATH	Pantothenate kinase 1 (EC 2.7.1.33) (Pantothenic acid kinase 1) (AtCoaA)	0.05	-	cyt	0					383
Q8I7J4 UniProt NPD GO	COQ2_CAEEL	Para-hydroxybenzoate--polyprenyltransferase, mitochondrial precursor (EC 2.5.1.-) (PHB:polyprenyltra ...	0.05	-	end	3	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				356
O46167 UniProt NPD GO	TXI2_TEGAG	Paralytic insecticidal toxin 2 precursor (TaITX-2)	0.05	-	exc	0	Secreted protein				68
P30251 UniProt NPD GO	PAP1_HELVI	Paralytic peptide 1 (Paralytic peptide I) (PP I)	0.05	-	nuc	0					23
P02626 UniProt NPD GO	PRVA_AMPME	Parvalbumin alpha	0.05	-	cyt	0					109
P05940 UniProt NPD GO	PRVB_XENLA	Parvalbumin beta	0.05	-	cyt	0					108
P08299 UniProt NPD GO	PR1A_TOBAC	Pathogenesis-related protein 1A precursor (PR-1A)	0.05	-	vac	1 *	Vacuole. Accumulates in within the vacuoles of specialized cells known as crystal idioblasts				168
P81056 UniProt NPD GO	PEN1_PENVA	Penaeidin-1 (Pen-1) (P1)	0.05	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				50
Q95NT0 UniProt NPD GO	PEN4A_PENVA	Penaeidin-4a precursor (Pen-4a)	0.05	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				67
Q963C3 UniProt NPD GO	PEN4C_PENVA	Penaeidin-4c precursor (Pen-4c)	0.05	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				67
Q962A7 UniProt NPD GO	PEN4D_LITSE	Penaeidin-4d precursor (Pen-4d)	0.05	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...			1XV3	67
P20140 UniProt NPD GO	PEP2_THUTO	Pepsin-2 precursor (EC 3.4.23.-) (Fragment)	0.05	-	nuc	0					72
Q9GQW4 UniProt NPD GO	KN1_MESMA	Peptide BmKn1 precursor (Biologically active peptide 4)	0.05	-	exc	1 *	Secreted protein				70
Q9I8P2 UniProt NPD GO	PYY_BRARE	Peptide YY precursor	0.05	-	vac	1 *	Secreted protein				97
Q9EPS2 UniProt NPD GO	PYY_MOUSE	Peptide YY precursor (PYY) (Peptide tyrosine tyrosine)	0.05	-	exc	1 *	Secreted protein				98
P10631 UniProt NPD GO	PYY_RAT	Peptide YY precursor (PYY) (Peptide tyrosine tyrosine)	0.05	-	exc	1 *	Secreted protein				98
P81028 UniProt NPD GO	PYY_ORENI	Peptide YY-like (PYY)	0.05	-	nuc	0	Secreted protein				36
P46032 UniProt NPD GO	PTR2_ARATH	Peptide transporter PTR2 (Histidine-transporting protein)	0.05	-	end	10	Membrane; multi-pass membrane protein				585

You are viewing entries 75101 to 75150 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.