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
Q02768 UniProt NPD GO	CYB_PLAFA	Cytochrome b	0.04	-	end	8 *					376
Q9B2C4 UniProt NPD GO	CYB_PUNCO	Cytochrome b	0.04	-	end	9 *					380
O79228 UniProt NPD GO	CYB_PYGPA	Cytochrome b	0.04	-	end	8 *					380
O48109 UniProt NPD GO	CYB_PYTRG	Cytochrome b	0.04	-	end	10 *					371
Q9XNW4 UniProt NPD GO	CYB_RHIWE	Cytochrome b	0.04	-	end	9 *					380
Q36548 UniProt NPD GO	CYB_SCOSC	Cytochrome b	0.04	-	end	9 *					380
Q8SFK5 UniProt NPD GO	CYB_SORTE	Cytochrome b	0.04	-	end	9 *					379
P34876 UniProt NPD GO	CYB_SPHTT	Cytochrome b	0.04	-	end	9 *					381
P34875 UniProt NPD GO	CYB_SPHTV	Cytochrome b	0.04	-	end	9 *					381
Q8SJK9 UniProt NPD GO	CYB_TERCA	Cytochrome b	0.04	-	end	9 *					379
Q9XNW9 UniProt NPD GO	CYB_THOIS	Cytochrome b	0.04	-	end	9 *					380
Q8M0E7 UniProt NPD GO	CYB_TRASA	Cytochrome b	0.04	-	end	9 *					380
P00164 UniProt NPD GO	CYB_TRYBB	Cytochrome b	0.04	-	end	10 *					363
Q9MI97 UniProt NPD GO	CYB_TYPNA	Cytochrome b	0.04	-	end	9 *					380
Q9MLJ0 UniProt NPD GO	CYB_WALAE	Cytochrome b	0.04	-	end	8 *					372
O78761 UniProt NPD GO	CYB_PITSU	Cytochrome b (Fragment)	0.04	-	end	3 *					134
O21414 UniProt NPD GO	CYB_SORHO	Cytochrome b (Fragment)	0.04	-	end	3 *					134
O21424 UniProt NPD GO	CYB_SORRO	Cytochrome b (Fragment)	0.04	-	end	3 *					134
O43169 UniProt NPD GO	CYB5B_HUMAN	Cytochrome b5 type B precursor (Cytochrome b5 outer mitochondrial membrane isoform)	0.04	-	cyt	1	Mitochondrion; mitochondrial outer membrane (By similarity)				146
Q70XY9 UniProt NPD GO	PSBE_AMBTC	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P59702 UniProt NPD GO	PSBE_ATRBE	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P69382 UniProt NPD GO	PSBE_BETVU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q4VZH5 UniProt NPD GO	PSBE_CUCSA	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q9TM20 UniProt NPD GO	PSBE_CYACA	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				84
P05333 UniProt NPD GO	PSBE_EUGGR	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				80
Q2L925 UniProt NPD GO	PSBE_GOSHI	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
O78466 UniProt NPD GO	PSBE_GUITH	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
P69390 UniProt NPD GO	PSBE_HORVU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P69388 UniProt NPD GO	PSBE_MAIZE	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q9MUQ0 UniProt NPD GO	PSBE_MESVI	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				80
Q9TKY1 UniProt NPD GO	PSBE_NEPOL	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P05170 UniProt NPD GO	PSBE_OENBE	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q6ENF6 UniProt NPD GO	PSBE_ORYNI	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P69389 UniProt NPD GO	PSBE_ORYSA	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q6L383 UniProt NPD GO	PSBE_SACHY	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q6ENU7 UniProt NPD GO	PSBE_SACOF	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P69387 UniProt NPD GO	PSBE_SECCE	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P69383 UniProt NPD GO	PSBE_SPIOL	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P69386 UniProt NPD GO	PSBE_WHEAT	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q9TM21 UniProt NPD GO	PSBF_CYACA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				43
Q3ZJ21 UniProt NPD GO	PSBF_PSEAK	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q5E965 UniProt NPD GO	C56D2_BOVIN	Cytochrome b561 domain-containing protein 2	0.04	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				222
Q5CC92 UniProt NPD GO	UCRIB_CYAPA	Cytochrome b6-f complex iron-sulfur subunit 2, cyanelle precursor (EC 1.10.99.1) (Rieske iron-sulfur ...	0.04	-	mit	1	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity). The tr ...				241
O49078 UniProt NPD GO	UCRIA_FRIAG	Cytochrome b6-f complex iron-sulfur subunit, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sulfu ...	0.04	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...				230
Q9TLQ9 UniProt NPD GO	PETG_CYACA	Cytochrome b6-f complex subunit 5 (Cytochrome b6-f complex subunit V) (Cytochrome b6-f complex subun ...	0.04	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q9SBM5 UniProt NPD GO	PETO_VOLCA	Cytochrome b6-f complex subunit petO, chloroplast precursor (Cytochrome b6-f-associated phosphoprote ...	0.04	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				203
P00043 UniProt NPD GO	CYC_DEBHA	Cytochrome c	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				109
P00035 UniProt NPD GO	CYC_HAEIR	Cytochrome c	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix				107
P00025 UniProt NPD GO	CYC_KATPE	Cytochrome c	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix			1CYC	103
P32556 UniProt NPD GO	CYC_KLULA	Cytochrome c	0.04	-	nuc	0	Mitochondrion; mitochondrial matrix				110

You are viewing entries 76701 to 76750 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.