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
Q7HKY2 UniProt NPD GO	PSBI_CALFE	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P56324 UniProt NPD GO	PSBI_CHLVU	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P48106 UniProt NPD GO	PSBI_CYAPA	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	mit	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				38
P25876 UniProt NPD GO	PSBI_HORVU	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				36
Q5SCX0 UniProt NPD GO	PSBI_HUPLU	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q56P16 UniProt NPD GO	PSBI_LACSA	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P09969 UniProt NPD GO	PSBI_MARPO	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				36
Q6EW64 UniProt NPD GO	PSBI_NYMAL	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6ENJ3 UniProt NPD GO	PSBI_ORYNI	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P12161 UniProt NPD GO	PSBI_ORYSA	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				36
Q68S22 UniProt NPD GO	PSBI_PANGI	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6YXN3 UniProt NPD GO	PSBI_PHYPA	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q8WI33 UniProt NPD GO	PSBI_PSINU	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6L3B2 UniProt NPD GO	PSBI_SACHY	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6ENY3 UniProt NPD GO	PSBI_SACOF	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q589B2 UniProt NPD GO	PSBI_SILLA	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P62100 UniProt NPD GO	PSBI_ARATH	Photosystem II reaction center I protein (PSII 4.8 kDa protein) (PSII I-protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P62105 UniProt NPD GO	PSBI_LOTJA	Photosystem II reaction center I protein (PSII 4.8 kDa protein) (PSII I-protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P62101 UniProt NPD GO	PSBI_MAIZE	Photosystem II reaction center I protein (PSII 4.8 kDa protein) (PSII I-protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P62106 UniProt NPD GO	PSBI_OENHO	Photosystem II reaction center I protein (PSII 4.8 kDa protein) (PSII I-protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P62107 UniProt NPD GO	PSBI_SECCE	Photosystem II reaction center I protein (PSII 4.8 kDa protein) (PSII I-protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P62108 UniProt NPD GO	PSBI_SINAL	Photosystem II reaction center I protein (PSII 4.8 kDa protein) (PSII I-protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P62103 UniProt NPD GO	PSBI_SPIOL	Photosystem II reaction center I protein (PSII 4.8 kDa protein) (PSII I-protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				36
P62102 UniProt NPD GO	PSBI_TOBAC	Photosystem II reaction center I protein (PSII 4.8 kDa protein) (PSII I-protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P62104 UniProt NPD GO	PSBI_WHEAT	Photosystem II reaction center I protein (PSII 4.8 kDa protein) (PSII I-protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q85FK8 UniProt NPD GO	PSBJ_ADICA	Photosystem II reaction center J protein	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P56338 UniProt NPD GO	PSBJ_CHLVU	Photosystem II reaction center J protein	0.01	-	exc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P12229 UniProt NPD GO	PSBJ_EUGGR	Photosystem II reaction center J protein	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P49512 UniProt NPD GO	PSBJ_ODOSI	Photosystem II reaction center J protein	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1C4 UniProt NPD GO	PSBL_ACOCL	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
Q6EYW2 UniProt NPD GO	PSBL_AGARO	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
Q67HC0 UniProt NPD GO	PSBL_ALLTE	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
Q9GE29 UniProt NPD GO	PSBL_AMBTC	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
Q67HN6 UniProt NPD GO	PSBL_ANACO	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
Q6EYV8 UniProt NPD GO	PSBL_ARIMA	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
Q7J1C3 UniProt NPD GO	PSBL_ASACA	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
Q67HB2 UniProt NPD GO	PSBL_ASPOF	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
P60141 UniProt NPD GO	PSBL_BETVU	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
Q71L82 UniProt NPD GO	PSBL_BOWSE	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
Q67HR8 UniProt NPD GO	PSBL_BUTUM	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
Q7J1C0 UniProt NPD GO	PSBL_CABCA	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
Q7H8E6 UniProt NPD GO	PSBL_CALSE	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
P60142 UniProt NPD GO	PSBL_CAPAN	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
Q71L78 UniProt NPD GO	PSBL_CEDDE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q7J1B6 UniProt NPD GO	PSBL_CERJA	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
Q8M9W9 UniProt NPD GO	PSBL_CHAGL	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
Q67HH2 UniProt NPD GO	PSBL_COECR	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
Q7H8E4 UniProt NPD GO	PSBL_CONAR	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
Q6EYU3 UniProt NPD GO	PSBL_CORMA	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
Q6EYT9 UniProt NPD GO	PSBL_CUNLA	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 90451 to 90500 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.