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
Q9FG72 UniProt NPD GO	OPT1_ARATH	Oligopeptide transporter 1 (AtOPT1)	0.02	-	end	12	Membrane; multi-pass membrane protein (Probable)				755
P48618 UniProt NPD GO	FAD3C_BRANA	Omega-3 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-) (Fragment)	0.02	-	nuc	3	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Probable)				404
P48626 UniProt NPD GO	FAD3E_TOBAC	Omega-3 fatty acid desaturase, endoplasmic reticulum (EC 1.14.19.-)	0.02	-	mit	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				379
P48630 UniProt NPD GO	FD6E1_SOYBN	Omega-6 fatty acid desaturase, endoplasmic reticulum isozyme 1 (EC 1.14.19.-)	0.02	-	mit	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				387
P15969 UniProt NPD GO	TOG1A_AGEAP	Omega-agatoxin-1A precursor (Omega-agatoxin IA) (Omega-Aga-IA) [Contains: Omega-agatoxin-1A major ch ...	0.02	-	exc	0	Secreted protein				112
P37045 UniProt NPD GO	TOG4B_AGEAP	Omega-agatoxin-4B precursor (Omega-agatoxin IVB) (Omega-Aga-IVB) (Omega-agatoxin tsukuba) (Omega-Aga ...	0.02	-	gol	0	Secreted protein			1OMB	83
P82852 UniProt NPD GO	TOT2A_HADVE	Omega-atracotoxin-Hv2a (Omega-AcTx-Hv2a) (AcTx-Hv2)	0.02	-	nuc	0	Secreted protein			1HP3	45
P31420 UniProt NPD GO	OMBP_MANSE	Ommochrome-binding protein precursor (OBP) (YCP)	0.02	-	mit	0					274
P84814 UniProt NPD GO	OPIP1_AMBTS	Opioid peptide	0.02	-		0					9
P08099 UniProt NPD GO	OPS2_DROME	Opsin Rh2 (Ocellar opsin)	0.02	-	end	7	Membrane; multi-pass membrane protein				381
P28679 UniProt NPD GO	OPS2_DROPS	Opsin Rh2 (Ocellar opsin)	0.02	-	end	7	Membrane; multi-pass membrane protein				381
P04950 UniProt NPD GO	OPS3_DROME	Opsin Rh3 (Inner R7 photoreceptor cells opsin)	0.02	-	end	7	Membrane; multi-pass membrane protein				383
P17646 UniProt NPD GO	OPS4_DROVI	Opsin Rh4 (Inner R7 photoreceptor cells opsin)	0.02	-	end	7	Membrane; multi-pass membrane protein				383
P34989 UniProt NPD GO	OPSL_CALJA	Opsin, longwave 563 nm (Fragment)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				350
P17771 UniProt NPD GO	OSP4_PEA	Organ-specific protein P4	0.02	-	cyt	0					130
O75751 UniProt NPD GO	S22A3_HUMAN	Organic cation transporter 3 (Extraneuronal monoamine transporter) (EMT) (Solute carrier family 22 m ...	0.02	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604842		556
Q6A4L0 UniProt NPD GO	ORCT3_MOUSE	Organic cation transporter-like 3 (Solute carrier family 22 member 13)	0.02	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				551
P29758 UniProt NPD GO	OAT_MOUSE	Ornithine aminotransferase, mitochondrial precursor (EC 2.6.1.13) (Ornithine--oxo-acid aminotransfer ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			439
P04182 UniProt NPD GO	OAT_RAT	Ornithine aminotransferase, mitochondrial precursor (EC 2.6.1.13) (Ornithine--oxo-acid aminotransfer ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				439
P27117 UniProt NPD GO	DCOR_BOVIN	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.02	-	cyt	0					461
P11926 UniProt NPD GO	DCOR_HUMAN	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.02	-	cyt	0			165640	1D7K	461
P27118 UniProt NPD GO	DCOR_CHICK	Ornithine decarboxylase (EC 4.1.1.17) (ODC) (Fragment)	0.02	-	cyt	0					450
P27120 UniProt NPD GO	DCOR1_XENLA	Ornithine decarboxylase 1 (EC 4.1.1.17) (ODC 1) (xODC1)	0.02	-	cyt	0					460
O94331 UniProt NPD GO	PYRE_SCHPO	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.02	-	mit	0					215
Q757S1 UniProt NPD GO	PYRF_ASHGO	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.02	-	cyt	0					267
O13410 UniProt NPD GO	PYRF_ASPFU	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.02	-	cyt	0					278
P32430 UniProt NPD GO	PYRF_CANMA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.02	-	mit	0					266
P07922 UniProt NPD GO	PYRF_KLULA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.02	-	cyt	0					267
O93864 UniProt NPD GO	PYRF_PACTA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.02	-	cyt	0					268
Q12724 UniProt NPD GO	PYRF_YARLI	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.02	-	cyt	0					286
P84349 UniProt NPD GO	OSTC_GORGO	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.02	-	cyt	0	Secreted protein				49
P28317 UniProt NPD GO	OSTC_LEPMA	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.02	-	cyt	0	Secreted protein				45
P81869 UniProt NPD GO	OC90_CAVPO	Otoconin 90 (Oc90) (Fragment)	0.02	-	cyt	0	Secreted protein				51
P83518 UniProt NPD GO	ODAIF_SARBU	Ovary-derived ACE interactive factor (Neb-ODAIF) [Contains: Neb-ODAIF(1-9); Neb-ODAIF(1-7)]	0.02	-		0					11
P05584 UniProt NPD GO	IOVO_ABUPI	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P68436 UniProt NPD GO	IOVO_AGROC	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P68144 UniProt NPD GO	IOVO_AIXGA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68145 UniProt NPD GO	IOVO_AIXSP	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68146 UniProt NPD GO	IOVO_ALECH	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68147 UniProt NPD GO	IOVO_ALERU	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68148 UniProt NPD GO	IOVO_ALOAE	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68149 UniProt NPD GO	IOVO_ANACA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68150 UniProt NPD GO	IOVO_ANAPL	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05567 UniProt NPD GO	IOVO_ANSSE	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68381 UniProt NPD GO	IOVO_ANTVI	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68391 UniProt NPD GO	IOVO_AYTAM	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P52239 UniProt NPD GO	IOVO_BALPA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05575 UniProt NPD GO	IOVO_CERNO	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P67887 UniProt NPD GO	IOVO_CHACH	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P67888 UniProt NPD GO	IOVO_CHATO	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54

You are viewing entries 84751 to 84800 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.