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
P19152 UniProt NPD GO	PSBE_CYAPA	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.01	-	mit	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				73
P06851 UniProt NPD GO	PSBE_MARPO	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P59703 UniProt NPD GO	PSBE_PINKO	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P41615 UniProt NPD GO	PSBE_PINTH	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q7J1C5 UniProt NPD GO	PSBF_ACOCL	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q85FK6 UniProt NPD GO	PSBF_ADICA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EYW3 UniProt NPD GO	PSBF_AGARO	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67HC1 UniProt NPD GO	PSBF_ALLTE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P60248 UniProt NPD GO	PSBF_AMBTC	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67HN7 UniProt NPD GO	PSBF_ANACO	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P60249 UniProt NPD GO	PSBF_ANTFO	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P62095 UniProt NPD GO	PSBF_ARATH	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EYV9 UniProt NPD GO	PSBF_ARIMA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1C2 UniProt NPD GO	PSBF_ASACA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67HB3 UniProt NPD GO	PSBF_ASPOF	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P60250 UniProt NPD GO	PSBF_ATRBE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P46613 UniProt NPD GO	PSBF_BETVU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q71L83 UniProt NPD GO	PSBF_BOWSE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67HR9 UniProt NPD GO	PSBF_BUTUM	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1C1 UniProt NPD GO	PSBF_CABCA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7HKX7 UniProt NPD GO	PSBF_CALFE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1B9 UniProt NPD GO	PSBF_CALFL	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8E7 UniProt NPD GO	PSBF_CALSE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EYV1 UniProt NPD GO	PSBF_CANWI	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1B8 UniProt NPD GO	PSBF_CERDE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1B7 UniProt NPD GO	PSBF_CERJA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P60251 UniProt NPD GO	PSBF_CHAGL	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67HH3 UniProt NPD GO	PSBF_COECR	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8E5 UniProt NPD GO	PSBF_CONAR	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EYU4 UniProt NPD GO	PSBF_CORMA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8A5 UniProt NPD GO	PSBF_CRETR	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q4VZH6 UniProt NPD GO	PSBF_CUCSA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EYU0 UniProt NPD GO	PSBF_CUNLA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q8MAW5 UniProt NPD GO	PSBF_CUSEU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; plastid membrane; single-pass membrane protein (Potential)				39
Q7H823 UniProt NPD GO	PSBF_CUSGR	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; plastid membrane; single-pass membrane protein (Potential)				39
Q7H834 UniProt NPD GO	PSBF_CUSJA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; plastid membrane; single-pass membrane protein (Potential)				39
Q7H825 UniProt NPD GO	PSBF_CUSPE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; plastid membrane; single-pass membrane protein (Potential)				39
Q71L71 UniProt NPD GO	PSBF_CYCRE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1B5 UniProt NPD GO	PSBF_DIOBU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1B3 UniProt NPD GO	PSBF_DRIWI	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67HM5 UniProt NPD GO	PSBF_ENSVE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q8HRZ6 UniProt NPD GO	PSBF_EPHSI	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q49KY3 UniProt NPD GO	PSBF_EUCGG	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EYT6 UniProt NPD GO	PSBF_EUOAL	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1B1 UniProt NPD GO	PSBF_GINBI	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q9GFC3 UniProt NPD GO	PSBF_GNEGN	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q2L918 UniProt NPD GO	PSBF_GOSHI	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7HIV1 UniProt NPD GO	PSBF_GUNCH	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P60126 UniProt NPD GO	PSBF_HORVU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6EYS6 UniProt NPD GO	PSBF_HOUCO	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39

You are viewing entries 87651 to 87700 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.