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
Q8HYY9 UniProt NPD GO	OSTC_PIG	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.03	-	cyt	0	Secreted protein			1Q8H	49
P40147 UniProt NPD GO	OSTC_XENLA	Osteocalcin precursor (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP) (xBGP ...	0.03	-	vac	0	Secreted protein				101
Q6K548 UniProt NPD GO	VDAC1_ORYSA	Outer mitochondrial membrane protein porin (Voltage-dependent anion-selective channel protein) (VDAC ...	0.03	-	nuc	0	Mitochondrion; mitochondrial outer membrane				273
P68469 UniProt NPD GO	IOVO_ACRVU	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				54
P52258 UniProt NPD GO	IOVO_AFRCO	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P05565 UniProt NPD GO	IOVO_ANHNO	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				54
P05601 UniProt NPD GO	IOVO_ARBTO	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				53
P05585 UniProt NPD GO	IOVO_BONUM	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67957 UniProt NPD GO	IOVO_CATWA	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67945 UniProt NPD GO	IOVO_CENUR	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P68128 UniProt NPD GO	IOVO_CHRAM	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P68127 UniProt NPD GO	IOVO_CHRPC	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67951 UniProt NPD GO	IOVO_CROAU	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67952 UniProt NPD GO	IOVO_CROMA	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P52260 UniProt NPD GO	IOVO_GUTPU	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				54
P67961 UniProt NPD GO	IOVO_LAGLU	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67893 UniProt NPD GO	IOVO_LOPDI	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67953 UniProt NPD GO	IOVO_LOPED	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67894 UniProt NPD GO	IOVO_LOPIG	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67950 UniProt NPD GO	IOVO_LOPIM	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67954 UniProt NPD GO	IOVO_LOPNY	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein			4OVO	56
P67955 UniProt NPD GO	IOVO_LOPSW	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P68468 UniProt NPD GO	IOVO_NUMME	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				54
P05599 UniProt NPD GO	IOVO_PERPE	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P68470 UniProt NPD GO	IOVO_PHACO	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P68471 UniProt NPD GO	IOVO_PHAVE	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67956 UniProt NPD GO	IOVO_PUCMA	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P52252 UniProt NPD GO	IOVO_ROLRO	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P05563 UniProt NPD GO	IOVO_SPHHU	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				54
P67958 UniProt NPD GO	IOVO_SYREL	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67959 UniProt NPD GO	IOVO_SYRHU	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P52269 UniProt NPD GO	IOVO_SYRMI	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				54
P05605 UniProt NPD GO	IOVO_SYRRE	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67960 UniProt NPD GO	IOVO_SYRSO	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67946 UniProt NPD GO	IOVO_TRABL	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67947 UniProt NPD GO	IOVO_TRACA	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67948 UniProt NPD GO	IOVO_TRASA	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67949 UniProt NPD GO	IOVO_TRATE	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P67944 UniProt NPD GO	IOVO_TYMCU	Ovomucoid (Fragment)	0.03	-	nuc	0	Secreted protein				56
P20739 UniProt NPD GO	OVOS_ANAPL	Ovostatin (Ovomacroglobulin) (Fragment)	0.03	-	cyt	0	Secreted protein				32
O14284 UniProt NPD GO	OXR1_SCHPO	Oxidation resistance protein 1	0.03	-	nuc	0	Mitochondrion (By similarity)				188
Q9Z2G9 UniProt NPD GO	TIP30_MOUSE	Oxidoreductase HTATIP2 (EC 1.1.1.-)	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus; nuclear envelope (By similarity)	cytoplasm [ISS] nuclear envelope [ISS]		2FMU	242
P11471 UniProt NPD GO	PSBP_CHLRE	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2)	0.03	-	exc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				245
P29795 UniProt NPD GO	PSBP_LYCES	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.03	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				258
P11594 UniProt NPD GO	PSBP_SINAL	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.03	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				260
P18212 UniProt NPD GO	PSBP2_TOBAC	Oxygen-evolving enhancer protein 2-2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolvin ...	0.03	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex			1V2B	265
P51576 UniProt NPD GO	P2RX1_MOUSE	P2X purinoceptor 1 (ATP receptor) (P2X1) (Purinergic receptor)	0.03	-	end	2 *	Membrane; multi-pass membrane protein				399
P47824 UniProt NPD GO	P2RX1_RAT	P2X purinoceptor 1 (ATP receptor) (P2X1) (Purinergic receptor) (RP-2 protein)	0.03	-	end	2 *	Membrane; multi-pass membrane protein				399
P49654 UniProt NPD GO	P2RX3_RAT	P2X purinoceptor 3 (ATP receptor) (P2X3) (Purinergic receptor)	0.03	-	nuc	2 *	Membrane; multi-pass membrane protein				397
Q99571 UniProt NPD GO	P2RX4_HUMAN	P2X purinoceptor 4 (ATP receptor) (P2X4) (Purinergic receptor)	0.03	-	end	2 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600846		388

You are viewing entries 80901 to 80950 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.