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
P04181 UniProt NPD GO	OAT_HUMAN	Ornithine aminotransferase, mitochondrial precursor (EC 2.6.1.13) (Ornithine--oxo-acid aminotransfer ...	0.00	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS] mitochondrion [TAS]	258870	2OAT	439
P07805 UniProt NPD GO	DCOR_TRYBB	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.00	-	cyt	0				2TOD	423
P40808 UniProt NPD GO	DCOR2_DROME	Ornithine decarboxylase 2 (EC 4.1.1.17) (ODC) (dODC2)	0.00	-	cyt	0					393
O93849 UniProt NPD GO	PYRE_COCIM	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.00	-	mit	0					238
Q9H1V8 UniProt NPD GO	S6A17_HUMAN	Orphan sodium- and chloride-dependent neurotransmitter transporter NTT4 (Solute carrier family 6 mem ...	0.00	-	end	12	Membrane; multi-pass membrane protein				727
Q8BJI1 UniProt NPD GO	S6A17_MOUSE	Orphan sodium- and chloride-dependent neurotransmitter transporter NTT4 (Solute carrier family 6 mem ...	0.00	-	end	12	Membrane; multi-pass membrane protein				727
P31662 UniProt NPD GO	S6A17_RAT	Orphan sodium- and chloride-dependent neurotransmitter transporter NTT4 (Solute carrier family 6 mem ...	0.00	-	end	12	Membrane; multi-pass membrane protein				727
Q28001 UniProt NPD GO	S6A17_BOVIN	Orphan sodium- and chloride-dependent neurotransmitter transporter NTT4 (Solute carrier family 6 mem ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				225
Q7LZI4 UniProt NPD GO	OSTC_CYPCA	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.00	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				48
P15504 UniProt NPD GO	OSTC_DRONO	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.00	-	cyt	0	Secreted protein				48
P84351 UniProt NPD GO	OSTC_HOMNE	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP) (Fragment)	0.00	-	cyt	0	Secreted protein				24
P83467 UniProt NPD GO	OSTL_PLEOS	Ostreolysin (Fragment)	0.00	-	cyt	0					50
Q9I8P6 UniProt NPD GO	OTOR_CHICK	Otoraplin precursor	0.00	-	mit	1 *	Secreted protein (Potential)				132
Q9I8P5 UniProt NPD GO	OTOR_RANCA	Otoraplin precursor	0.00	-	nuc	1 *	Secreted protein (Potential)				133
P07144 UniProt NPD GO	VDAC_NEUCR	Outer mitochondrial membrane protein porin	0.00	-	cyt	0	Mitochondrion; mitochondrial outer membrane				283
Q9SMX3 UniProt NPD GO	VDAC2_ARATH	Outer mitochondrial membrane protein porin 2 (Voltage-dependent anion-selective channel protein 2) ( ...	0.00	-	cyt	0	Mitochondrion; mitochondrial outer membrane				273
P42985 UniProt NPD GO	OVM_LEPDE	Oviductal motility-stimulating peptide (LeD-OVM)	0.00	-		0					6
P80155 UniProt NPD GO	HEMTO_THETS	Ovohemerythrin (YP14) (Fragment)	0.00	-		0	Secreted protein				18
P52259 UniProt NPD GO	IOVO_BAMTH	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				56
P62336 UniProt NPD GO	IOVO_CASBE	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				54
P62337 UniProt NPD GO	IOVO_CASCA	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				54
P05579 UniProt NPD GO	IOVO_CIRAE	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				54
P05592 UniProt NPD GO	IOVO_CYRMO	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				56
P05560 UniProt NPD GO	IOVO_DRONO	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				54
P68378 UniProt NPD GO	IOVO_FULAT	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				54
P68379 UniProt NPD GO	IOVO_GALCH	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				54
P52246 UniProt NPD GO	IOVO_GUIGU	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				54
P05566 UniProt NPD GO	IOVO_NYCNY	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				54
P05607 UniProt NPD GO	IOVO_POLBI	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				53
P52253 UniProt NPD GO	IOVO_SCYNO	Ovomucoid (Fragment)	0.00	-	nuc	0	Secreted protein				52
P45850 UniProt NPD GO	OXO1_HORVU	Oxalate oxidase 1 (EC 1.2.3.4) (Germin)	0.00	-	cyt	0	Cell wall (By similarity)			2ETE	201
P45851 UniProt NPD GO	OXO2_HORVU	Oxalate oxidase 2 precursor (EC 1.2.3.4) (Germin)	0.00	-	exc	1 *	Cell wall (By similarity)				224
P15290 UniProt NPD GO	GER2_WHEAT	Oxalate oxidase GF-2.8 precursor (EC 1.2.3.4) (Germin GF-2.8)	0.00	-	exc	1 *	Secreted protein; extracellular space; apoplast. Cytoplasm. Found in the apoplast and the cytoplasm ...				224
P26759 UniProt NPD GO	GER3_WHEAT	Oxalate oxidase GF-3.8 precursor (EC 1.2.3.4) (Germin GF-3.8)	0.00	-	exc	0	Secreted protein; extracellular space; apoplast. Cytoplasm. Found in the apoplast and the cytoplasm ...				224
P81665 UniProt NPD GO	PSBO_PINPS	Oxygen-evolving enhancer protein 1 (OEE1) (33 kDa subunit of oxygen evolving system of photosystem I ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				26
P12853 UniProt NPD GO	PSBO_CHLRE	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				291
Q9SBN6 UniProt NPD GO	PSBO_VOLCA	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				293
P80660 UniProt NPD GO	PSBP1_PHYPA	Oxygen-evolving enhancer protein 2 (OEE2) (20 kDa subunit of oxygen evolving system of photosystem I ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				43
P80661 UniProt NPD GO	PSBP2_PHYPA	Oxygen-evolving enhancer protein 2 (OEE2) (22 kDa subunit of oxygen evolving system of photosystem I ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				22
P69056 UniProt NPD GO	NEU1_BALPH	Oxytocin (Ocytocin)	0.00	-		0	Secreted protein			1XY2	9
P69044 UniProt NPD GO	NEU1_HIPAM	Oxytocin (Ocytocin)	0.00	-		0	Secreted protein			1XY2	9
P69043 UniProt NPD GO	NEU1_RABIT	Oxytocin (Ocytocin)	0.00	-		0	Secreted protein			1XY2	9
P69057 UniProt NPD GO	NEU1_TACAC	Oxytocin (Ocytocin)	0.00	-		0	Secreted protein			1XY2	9
P69058 UniProt NPD GO	OXYT_HYDCO	Oxytocin (Ocytocin)	0.00	-		0	Secreted protein				9
O80446 UniProt NPD GO	PDXL4_ARATH	PDX1-like protein 4	0.00	-	cyt	0					79
Q2KIP5 UniProt NPD GO	PDZ1I_BOVIN	PDZK1-interacting protein 1	0.00	-	end	1 *	Membrane; single-pass membrane protein (By similarity)				114
Q6ITQ4 UniProt NPD GO	PDZ1I_PIG	PDZK1-interacting protein 1 (17 kDa membrane-associated protein)	0.00	-	end	1 *	Membrane; single-pass membrane protein (By similarity)				114
Q5RA41 UniProt NPD GO	PDZ1I_PONPY	PDZK1-interacting protein 1 (17 kDa membrane-associated protein)	0.00	-	end	1 *	Membrane; single-pass membrane protein (By similarity)				114
Q13113 UniProt NPD GO	PDZ1I_HUMAN	PDZK1-interacting protein 1 (17 kDa membrane-associated protein) (Protein DD96)	0.00	-	end	1 *	Membrane; single-pass membrane protein		607178		114
Q6CG20 UniProt NPD GO	SWF1_YARLI	Palmitoyltransferase SWF1 (EC 2.3.1.-)	0.00	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				381

You are viewing entries 96201 to 96250 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.