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
P68151 UniProt NPD GO	IOVO_CHLPI	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05571 UniProt NPD GO	IOVO_COSCO	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05600 UniProt NPD GO	IOVO_COTDE	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				52
P52245 UniProt NPD GO	IOVO_CROCS	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P68152 UniProt NPD GO	IOVO_CYACY	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68129 UniProt NPD GO	IOVO_CYGAT	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68130 UniProt NPD GO	IOVO_CYGOL	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05617 UniProt NPD GO	IOVO_DACNO	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				55
P05570 UniProt NPD GO	IOVO_DENVD	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05562 UniProt NPD GO	IOVO_EUDEL	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				51
P05594 UniProt NPD GO	IOVO_FRAAF	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				53
P05596 UniProt NPD GO	IOVO_FRAER	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P52266 UniProt NPD GO	IOVO_GALAS	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68383 UniProt NPD GO	IOVO_GRUCA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68380 UniProt NPD GO	IOVO_GRUJA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68382 UniProt NPD GO	IOVO_GRUVI	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05581 UniProt NPD GO	IOVO_LEIOC	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P52261 UniProt NPD GO	IOVO_LOPBU	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P68387 UniProt NPD GO	IOVO_LOPCA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P68388 UniProt NPD GO	IOVO_LOPGA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P68153 UniProt NPD GO	IOVO_LOPSP	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05580 UniProt NPD GO	IOVO_MEGFR	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68154 UniProt NPD GO	IOVO_MERCU	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68155 UniProt NPD GO	IOVO_NEOJU	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68392 UniProt NPD GO	IOVO_NETRU	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P52248 UniProt NPD GO	IOVO_NOTPE	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				51
P52249 UniProt NPD GO	IOVO_OPIHO	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05587 UniProt NPD GO	IOVO_OREPI	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P05582 UniProt NPD GO	IOVO_ORTVE	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P68131 UniProt NPD GO	IOVO_OXYJA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68132 UniProt NPD GO	IOVO_OXYVI	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05609 UniProt NPD GO	IOVO_PAVCR	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P52263 UniProt NPD GO	IOVO_PAVMU	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P67895 UniProt NPD GO	IOVO_PENJC	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P67896 UniProt NPD GO	IOVO_PENSU	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				56
P52251 UniProt NPD GO	IOVO_RHYFU	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				51
P68156 UniProt NPD GO	IOVO_SARME	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P05557 UniProt NPD GO	IOVO_STRCA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P68157 UniProt NPD GO	IOVO_TADRA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
P52254 UniProt NPD GO	IOVO_TINMA	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				51
P52256 UniProt NPD GO	IOVO_TURME	Ovomucoid (Fragment)	0.02	-	nuc	0	Secreted protein				54
Q6C443 UniProt NPD GO	OXR1_YARLI	Oxidation resistance protein 1	0.02	-	cyt	0	Mitochondrion (By similarity)				229
Q9BUP3 UniProt NPD GO	TIP30_HUMAN	Oxidoreductase HTATIP2 (EC 1.1.1.-) (HIV-1 TAT-interactive protein 2) (30 kDa HIV-1 TAT-interacting ...	0.02	-	cyt	0	Cytoplasm. Nucleus; nuclear envelope	cytoplasm [IDA] nuclear envelope [IDA]	605628	2BKA	242
P12359 UniProt NPD GO	PSBO_SPIOL	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolving ...	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				332
P12302 UniProt NPD GO	PSBP_SPIOL	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				267
Q96334 UniProt NPD GO	PSBP_BRAJU	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				217
Q9ES40 UniProt NPD GO	PRAF3_RAT	PRA1 family protein 3 (ARL-6-interacting protein 5) (ADP-ribosylation-like factor 6-interacting prot ...	0.02	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Cytoplasm. Also ...				188
Q8R5J9 UniProt NPD GO	PRAF3_MOUSE	PRA1 family protein 3 (ARL-6-interacting protein 5) (ADP-ribosylation-like factor 6-interacting prot ...	0.02	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Cytoplasm. Also ...				188
O88531 UniProt NPD GO	PPT1_MOUSE	Palmitoyl-protein thioesterase 1 precursor (EC 3.1.2.22) (PPT-1) (Palmitoyl-protein hydrolase 1)	0.02	-	exc	0	Lysosome				306
P45479 UniProt NPD GO	PPT1_RAT	Palmitoyl-protein thioesterase 1 precursor (EC 3.1.2.22) (PPT-1) (Palmitoyl-protein hydrolase 1)	0.02	-	exc	0	Lysosome				306

You are viewing entries 84801 to 84850 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.