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
Q7H826 UniProt NPD GO	PSBL_CUSEU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; plastid membrane; single-pass membrane protein (Potential)				38
P19154 UniProt NPD GO	PSBL_CYAPA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				38
Q71L70 UniProt NPD GO	PSBL_CYCRE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7J1B4 UniProt NPD GO	PSBL_DIOBU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7J1B2 UniProt NPD GO	PSBL_DRIWI	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P12228 UniProt NPD GO	PSBL_EUGGR	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				38
Q9THZ2 UniProt NPD GO	PSBL_GINBI	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6W6R3 UniProt NPD GO	PSBL_HORJU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6W6Q9 UniProt NPD GO	PSBL_HORSP	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60143 UniProt NPD GO	PSBL_HORVU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q5SD41 UniProt NPD GO	PSBL_HUPLU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7HIU9 UniProt NPD GO	PSBL_HYDCA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7J1A8 UniProt NPD GO	PSBL_ILLPA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7H8J7 UniProt NPD GO	PSBL_IPOAL	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7H8K8 UniProt NPD GO	PSBL_IPOAQ	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7H8J9 UniProt NPD GO	PSBL_IPOBA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7H8L5 UniProt NPD GO	PSBL_IPOCC	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7H8I7 UniProt NPD GO	PSBL_IPOOB	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7H8L2 UniProt NPD GO	PSBL_IPOQU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7H8K6 UniProt NPD GO	PSBL_IPOSE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7H8L0 UniProt NPD GO	PSBL_IPOWR	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7J1A6 UniProt NPD GO	PSBL_LACFR	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7HIU7 UniProt NPD GO	PSBL_LILSU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7J1A4 UniProt NPD GO	PSBL_LIRTU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7HIU5 UniProt NPD GO	PSBL_MAGST	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q67HA0 UniProt NPD GO	PSBL_MAIRA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60138 UniProt NPD GO	PSBL_MAIZE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60144 UniProt NPD GO	PSBL_MESCR	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q71L58 UniProt NPD GO	PSBL_METGY	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7H827 UniProt NPD GO	PSBL_MONCA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q67H92 UniProt NPD GO	PSBL_MUSCM	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q9TKY3 UniProt NPD GO	PSBL_NEPOL	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60145 UniProt NPD GO	PSBL_NICSY	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60146 UniProt NPD GO	PSBL_NICTO	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6EW38 UniProt NPD GO	PSBL_NYMAL	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7IW39 UniProt NPD GO	PSBL_NYMOD	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6ENF8 UniProt NPD GO	PSBL_ORYNI	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60137 UniProt NPD GO	PSBL_ORYSA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q68RZ1 UniProt NPD GO	PSBL_PANGI	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60147 UniProt NPD GO	PSBL_PEA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q67HD6 UniProt NPD GO	PSBL_PHOTN	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q85X31 UniProt NPD GO	PSBL_PINKO	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				41
P60148 UniProt NPD GO	PSBL_POPDE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6L385 UniProt NPD GO	PSBL_SACHY	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6ENU9 UniProt NPD GO	PSBL_SACOF	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7HIU0 UniProt NPD GO	PSBL_SAGLA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7HIT8 UniProt NPD GO	PSBL_SCHCH	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7HIT6 UniProt NPD GO	PSBL_SCIVE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60149 UniProt NPD GO	PSBL_SECCE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7HIT4 UniProt NPD GO	PSBL_SPAWA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38

You are viewing entries 90501 to 90550 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.