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
P20175 UniProt NPD GO	PSBJ_HORVU	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q5SD40 UniProt NPD GO	PSBJ_HUPLU	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q9BBR7 UniProt NPD GO	PSBJ_LOTJA	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
O03076 UniProt NPD GO	PSBJ_MAGTR	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P19444 UniProt NPD GO	PSBJ_MAIZE	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P12188 UniProt NPD GO	PSBJ_MARPO	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q9MUQ3 UniProt NPD GO	PSBJ_MESVI	Photosystem II reaction center J protein	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q9TKY4 UniProt NPD GO	PSBJ_NEPOL	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q6EW39 UniProt NPD GO	PSBJ_NYMAL	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q9MTK7 UniProt NPD GO	PSBJ_OENHO	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q6ENF9 UniProt NPD GO	PSBJ_ORYNI	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P12189 UniProt NPD GO	PSBJ_ORYSA	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q68RZ2 UniProt NPD GO	PSBJ_PANGI	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P13555 UniProt NPD GO	PSBJ_PEA	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q6YXL6 UniProt NPD GO	PSBJ_PHYPA	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q85X30 UniProt NPD GO	PSBJ_PINKO	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P41618 UniProt NPD GO	PSBJ_PINTH	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P92417 UniProt NPD GO	PSBJ_POPDE	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P51388 UniProt NPD GO	PSBJ_PORPU	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q8WI06 UniProt NPD GO	PSBJ_PSINU	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q6L386 UniProt NPD GO	PSBJ_SACHY	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q6ENV0 UniProt NPD GO	PSBJ_SACOF	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P19053 UniProt NPD GO	PSBJ_SECCE	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q9M3L2 UniProt NPD GO	PSBJ_SPIOL	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P69692 UniProt NPD GO	PSBJ_TOBAC	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q95H59 UniProt NPD GO	PSBJ_WHEAT	Photosystem II reaction center J protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q85FK7 UniProt NPD GO	PSBL_ADICA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q85A78 UniProt NPD GO	PSBL_ANTFO	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60130 UniProt NPD GO	PSBL_ANTMA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60129 UniProt NPD GO	PSBL_ARATH	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60131 UniProt NPD GO	PSBL_ATRBE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7HKX8 UniProt NPD GO	PSBL_CALFE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60132 UniProt NPD GO	PSBL_CALFL	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60133 UniProt NPD GO	PSBL_CERDE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P46306 UniProt NPD GO	PSBL_CHLEU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P32974 UniProt NPD GO	PSBL_CHLRE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				38
P56339 UniProt NPD GO	PSBL_CHLVU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q8LV29 UniProt NPD GO	PSBL_CUSGR	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	nuc	1 *	Plastid; plastid membrane; single-pass membrane protein (Potential)				39
Q8MAW2 UniProt NPD GO	PSBL_CUSPE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	nuc	1 *	Plastid; plastid membrane; single-pass membrane protein (Potential)				39
Q9TM22 UniProt NPD GO	PSBL_CYACA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q85FQ4 UniProt NPD GO	PSBL_CYAME	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q8HRZ5 UniProt NPD GO	PSBL_EPHSI	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q9GFC2 UniProt NPD GO	PSBL_GNEGN	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6B8K6 UniProt NPD GO	PSBL_GRATL	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
O78464 UniProt NPD GO	PSBL_GUITH	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				38
P60134 UniProt NPD GO	PSBL_GUNCH	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60135 UniProt NPD GO	PSBL_LOTJA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60151 UniProt NPD GO	PSBL_MARPO	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q9MUQ2 UniProt NPD GO	PSBL_MESVI	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P49514 UniProt NPD GO	PSBL_ODOSI	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38

You are viewing entries 96601 to 96650 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.