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
Q67HV0 UniProt NPD GO	PSBN_ASPOF	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P62115 UniProt NPD GO	PSBN_ATRBE	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7GZ99 UniProt NPD GO	PSBN_BASHY	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6Y8A2 UniProt NPD GO	PSBN_BEREX	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7YNI0 UniProt NPD GO	PSBN_BORAR	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67IA0 UniProt NPD GO	PSBN_BUTUM	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7J198 UniProt NPD GO	PSBN_CABCA	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7HKX5 UniProt NPD GO	PSBN_CALFE	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9GFA1 UniProt NPD GO	PSBN_CALFL	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYK6 UniProt NPD GO	PSBN_CANWI	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71LB5 UniProt NPD GO	PSBN_CEDDE	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7J196 UniProt NPD GO	PSBN_CERDE	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7J194 UniProt NPD GO	PSBN_CERJA	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67I10 UniProt NPD GO	PSBN_COECR	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYJ8 UniProt NPD GO	PSBN_CORMA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q5IHC2 UniProt NPD GO	PSBN_CRYJA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q4VZJ0 UniProt NPD GO	PSBN_CUCSA	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYJ4 UniProt NPD GO	PSBN_CUNLA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q85FZ3 UniProt NPD GO	PSBN_CYAME	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9GF93 UniProt NPD GO	PSBN_DIOBU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7J192 UniProt NPD GO	PSBN_DRIWI	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q4G3C3 UniProt NPD GO	PSBN_EMIHU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q8HS39 UniProt NPD GO	PSBN_EPHSI	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q49KX0 UniProt NPD GO	PSBN_EUCGG	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYJ0 UniProt NPD GO	PSBN_EUOAL	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9GF82 UniProt NPD GO	PSBN_GNEGN	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q2L935 UniProt NPD GO	PSBN_GOSHI	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
O78513 UniProt NPD GO	PSBN_GUITH	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7HIW6 UniProt NPD GO	PSBN_GUNCH	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7YN52 UniProt NPD GO	PSBN_HOOLU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYH8 UniProt NPD GO	PSBN_HOUCO	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q5SD31 UniProt NPD GO	PSBN_HUPLU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7HIW4 UniProt NPD GO	PSBN_HYDCA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71NS7 UniProt NPD GO	PSBN_HYLSP	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71P68 UniProt NPD GO	PSBN_HYPCP	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7J190 UniProt NPD GO	PSBN_ILLPA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71KN5 UniProt NPD GO	PSBN_KLEBI	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9GF77 UniProt NPD GO	PSBN_LACFR	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q332U9 UniProt NPD GO	PSBN_LACSA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71NV7 UniProt NPD GO	PSBN_LEUSC	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7HIW2 UniProt NPD GO	PSBN_LILSU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7J187 UniProt NPD GO	PSBN_LIRTU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7YN54 UniProt NPD GO	PSBN_LOPCO	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q2MI73 UniProt NPD GO	PSBN_LYCES	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q8HS28 UniProt NPD GO	PSBN_MAGST	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67HT8 UniProt NPD GO	PSBN_MAIRA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P12170 UniProt NPD GO	PSBN_MARPO	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71L94 UniProt NPD GO	PSBN_METGY	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67HT0 UniProt NPD GO	PSBN_MUSCM	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7YMA2 UniProt NPD GO	PSBN_NECCR	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43

You are viewing entries 96701 to 96750 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.