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
P48624 UniProt NPD GO	FAD3E_BRANA	Omega-3 fatty acid desaturase, endoplasmic reticulum (EC 1.14.19.-)	0.01	-	mit	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				383
Q9XYZ0 UniProt NPD GO	CXO1A_CONPL	Omega-conotoxin PuIA precursor	0.01	-	exc	1 *	Secreted protein (By similarity)				80
Q9XZK9 UniProt NPD GO	CXO2_CONTE	Omega-type conotoxin TxO2 precursor	0.01	-	exc	1 *	Secreted protein (By similarity)				76
Q9XZL0 UniProt NPD GO	CXO3_CONTE	Omega-type conotoxin TxO3 precursor	0.01	-	exc	1 *	Secreted protein (By similarity)				76
Q9XZL2 UniProt NPD GO	CXO5_CONTE	Omega-type conotoxin TxO5 precursor	0.01	-	vac	1 *	Secreted protein (By similarity)				76
Q14982 UniProt NPD GO	OPCM_HUMAN	Opioid-binding protein/cell adhesion molecule precursor (OBCAM) (Opioid-binding cell adhesion molecu ...	0.01	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	integral to plasma membrane [TAS] plasma membrane [TAS]	600632		345
Q5IS61 UniProt NPD GO	OPCM_PANTR	Opioid-binding protein/cell adhesion molecule precursor (OBCAM) (Opioid-binding cell adhesion molecu ...	0.01	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				345
P22269 UniProt NPD GO	OPS1_CALVI	Opsin Rh1 (Outer R1-R6 photoreceptor cells opsin)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				371
P06002 UniProt NPD GO	OPS1_DROME	Opsin Rh1 (Outer R1-R6 photoreceptor cells opsin) (Neither inactivation nor afterpotential E protein ...	0.01	-	nuc	7	Membrane; multi-pass membrane protein	cytoplasmic membrane-bound vesicle [IDA] inaD signaling complex [IPI] multivesicular body [IDA] rough endoplasmic reticulum [IDA] secondary lysosome [IDA] subrhabdomeral cisterna [IDA]			373
P90680 UniProt NPD GO	OPSB_APIME	Opsin, blue-sensitive (AMBLOP)	0.01	-	end	7	Membrane; multi-pass membrane protein				377
Q8CH62 UniProt NPD GO	ORAV1_MOUSE	Oral cancer overexpressed protein 1 homolog	0.01	-	nuc	0					137
P37086 UniProt NPD GO	ORCK_ORCLI	Orcokinin	0.01	-		0	Secreted protein				13
P82455 UniProt NPD GO	ORMY_ORCLI	Orcomyotropin (OMT)	0.01	-		0	Secreted protein				8
O62809 UniProt NPD GO	OX2R_PIG	Orexin receptor type 2 (Ox2r) (Hypocretin receptor type 2) (Fragment)	0.01	-	mit	0	Membrane; multi-pass membrane protein				77
Q78KK3 UniProt NPD GO	ORCT2_MOUSE	Organic cation transporter-like protein 2 (Imprinted multi-membrane spanning polyspecific transporte ...	0.01	-	end	8 *	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Localized at the a ...				406
P07991 UniProt NPD GO	OAT_YEAST	Ornithine aminotransferase (EC 2.6.1.13) (Ornithine--oxo-acid aminotransferase)	0.01	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			424
Q9VW26 UniProt NPD GO	OAT_DROME	Ornithine aminotransferase, mitochondrial precursor (EC 2.6.1.13) (Ornithine--oxo-acid aminotransfer ...	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial matrix [NAS] mitochondrion [IDA]			431
Q43814 UniProt NPD GO	OTC_PEA	Ornithine carbamoyltransferase, chloroplast precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbamyl ...	0.01	-	mit	0	Plastid; chloroplast				375
Q92445 UniProt NPD GO	DCOR_PARBR	Ornithine decarboxylase (EC 4.1.1.17) (ODC) (Fragment)	0.01	-	cyt	0					79
P40807 UniProt NPD GO	DCOR1_DROME	Ornithine decarboxylase 1 (EC 4.1.1.17) (ODC)	0.01	-	cyt	0					394
Q9NHZ6 UniProt NPD GO	OAZ_CAEEL	Ornithine decarboxylase antizyme (ODC-Az)	0.01	-	mit	0					159
Q9NHZ5 UniProt NPD GO	OAZ_ONCVO	Ornithine decarboxylase antizyme (ODC-Az)	0.01	-	cyt	0					145
Q9NHZ4 UniProt NPD GO	OAZ_PRIPA	Ornithine decarboxylase antizyme (ODC-Az)	0.01	-	vac	0					142
O13474 UniProt NPD GO	PYRE_KLULA	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.01	-	cyt	0					226
P41923 UniProt NPD GO	PYRE_YARLI	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.01	-	mit	0					219
P33283 UniProt NPD GO	PYRF_CANGA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.01	-	cyt	0					265
P41769 UniProt NPD GO	PYRF_KLUMA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.01	-	mit	0					267
Q8J0E6 UniProt NPD GO	PYRF_TORDE	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.01	-	cyt	0					264
P03962 UniProt NPD GO	PYRF_YEAST	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.01	-	cyt	0				1DQX	267
Q9HFX0 UniProt NPD GO	PYRF_ZYGBA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.01	-	cyt	0					265
P25778 UniProt NPD GO	ORYC_ORYSA	Oryzain gamma chain precursor (EC 3.4.22.-)	0.01	-	end	1 *					362
P83005 UniProt NPD GO	OSTC_HORSE	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone GLA-protein) (BGP)	0.01	-	cyt	0	Secreted protein	extracellular region [ISS]			49
P84348 UniProt NPD GO	OSTC_PANTR	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.01	-	cyt	0	Secreted protein				49
P02823 UniProt NPD GO	OSTC_XIPGL	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.01	-	cyt	0	Secreted protein				47
P83238 UniProt NPD GO	OSTC_BRARE	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP) (Fragment)	0.01	-	cyt	0	Secreted protein	extracellular matrix [TAS]			45
Q9NRC9 UniProt NPD GO	OTOR_HUMAN	Otoraplin precursor (Fibrocyte-derived protein) (Melanoma inhibitory activity-like protein)	0.01	-	end	1 *	Secreted protein (Potential)		606067		128
Q9JIE3 UniProt NPD GO	OTOR_MOUSE	Otoraplin precursor (Melanoma inhibitory activity-like protein)	0.01	-	end	1 *	Secreted protein (Potential)				128
Q8NHW6 UniProt NPD GO	OTOSP_HUMAN	Otospiralin precursor	0.01	-	exc	0	Secreted protein (Probable)		607877		89
P04840 UniProt NPD GO	VDAC1_YEAST	Outer mitochondrial membrane protein porin 1 (Voltage-dependent anion-selective channel protein 1) ( ...	0.01	-	nuc	0	Mitochondrion; mitochondrial outer membrane	integral to mitochondrial outer membrane [IDA] mitochondrial outer membrane [IDA]			282
P42054 UniProt NPD GO	VDAC_PEA	Outer plastidial membrane protein porin (Voltage-dependent anion-selective channel protein) (VDAC)	0.01	-	nuc	0	Plastid; plastid outer membrane. Found in non-photosynthetic root plastids only				275
P01014 UniProt NPD GO	OVALY_CHICK	Ovalbumin-related protein Y (Gene Y protein)	0.01	-	nuc	1 *					388
P01003 UniProt NPD GO	IOVO_COTJA	Ovomucoid	0.01	-	nuc	0	Secreted protein			3OVO	186
P68390 UniProt NPD GO	IOVO_MELGA	Ovomucoid	0.01	-	nuc	0	Secreted protein			3SGQ	185
P52241 UniProt NPD GO	IOVO_AEPAR	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P68389 UniProt NPD GO	IOVO_ANSAN	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P68394 UniProt NPD GO	IOVO_ANSCA	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P68437 UniProt NPD GO	IOVO_ANSIN	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P68376 UniProt NPD GO	IOVO_AQUAU	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P05608 UniProt NPD GO	IOVO_ARGAR	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54
P68393 UniProt NPD GO	IOVO_BRACA	Ovomucoid (Fragment)	0.01	-	nuc	0	Secreted protein				54

You are viewing entries 90051 to 90100 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.