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
P10803 UniProt NPD GO	PSBD_SECCE	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P06005 UniProt NPD GO	PSBD_SPIOL	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein			1DOP	352
P69686 UniProt NPD GO	PSBD_TOBAC	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q36814 UniProt NPD GO	PSBD_WHEAT	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
O19893 UniProt NPD GO	PSBY_CYACA	Photosystem II protein Y	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
P48272 UniProt NPD GO	PSBY_CYAPA	Photosystem II protein Y	0.00	-	nuc	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				38
P51206 UniProt NPD GO	PSBY_PORPU	Photosystem II protein Y	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q85FJ4 UniProt NPD GO	PSBH_ADICA	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				73
Q85CN0 UniProt NPD GO	PSBH_ANTFO	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				73
P56780 UniProt NPD GO	PSBH_ARATH	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				72
P22666 UniProt NPD GO	PSBH_CHLRE	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				87
P56323 UniProt NPD GO	PSBH_CHLVU	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				79
Q85FZ2 UniProt NPD GO	PSBH_CYAME	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				64
P48105 UniProt NPD GO	PSBH_CYAPA	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				67
Q6B8Y7 UniProt NPD GO	PSBH_GRATL	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				67
O78514 UniProt NPD GO	PSBH_GUITH	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				67
P12160 UniProt NPD GO	PSBH_MARPO	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				73
Q9MUV4 UniProt NPD GO	PSBH_MESVI	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				73
Q9TKW7 UniProt NPD GO	PSBH_NEPOL	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				81
P49475 UniProt NPD GO	PSBH_ODOSI	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				67
Q85X08 UniProt NPD GO	PSBH_PINKO	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				74
P51325 UniProt NPD GO	PSBH_PORPU	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				67
Q8WHZ4 UniProt NPD GO	PSBH_PSINU	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				73
Q71KP6 UniProt NPD GO	PSBH_SPIMX	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.00	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				77
Q85FN6 UniProt NPD GO	PSBI_ADICA	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q8M9Z9 UniProt NPD GO	PSBI_CHAGL	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
P59763 UniProt NPD GO	PSBI_CHLRE	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
P30395 UniProt NPD GO	PSBI_EUGGR	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	exc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				53
Q9TKW3 UniProt NPD GO	PSBI_NEPOL	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
O78676 UniProt NPD GO	PSBI_OROMI	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	mit	1 *	Plastid; plastid membrane				36
Q85X70 UniProt NPD GO	PSBI_PINKO	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P41599 UniProt NPD GO	PSBI_PINTH	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				36
P69558 UniProt NPD GO	PSBI_PSEJA	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P69559 UniProt NPD GO	PSBI_PSEMZ	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P60247 UniProt NPD GO	PSBJ_AMBTC	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q85CD4 UniProt NPD GO	PSBJ_ANTFO	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P56781 UniProt NPD GO	PSBJ_ARATH	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P69690 UniProt NPD GO	PSBJ_ATRBE	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P69691 UniProt NPD GO	PSBJ_BETVU	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q7YJV9 UniProt NPD GO	PSBJ_CALFE	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q8M9X0 UniProt NPD GO	PSBJ_CHAGL	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
O19930 UniProt NPD GO	PSBJ_CHLRE	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q9TM23 UniProt NPD GO	PSBJ_CYACA	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q85FQ5 UniProt NPD GO	PSBJ_CYAME	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P19155 UniProt NPD GO	PSBJ_CYAPA	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				40
Q9THZ1 UniProt NPD GO	PSBJ_GINBI	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q6B8K7 UniProt NPD GO	PSBJ_GRATL	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
O78463 UniProt NPD GO	PSBJ_GUITH	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6W6R2 UniProt NPD GO	PSBJ_HORJU	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q6W6Q8 UniProt NPD GO	PSBJ_HORSP	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40

You are viewing entries 96551 to 96600 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.