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
Q8M9W6 UniProt NPD GO	PSBZ_CHAGL	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P92276 UniProt NPD GO	PSBZ_CHLRE	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P56313 UniProt NPD GO	PSBZ_CHLVU	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q5IHA3 UniProt NPD GO	PSBZ_CRYJA	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q85FY1 UniProt NPD GO	PSBZ_CYAME	Photosystem II reaction center Z protein	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P17159 UniProt NPD GO	PSBZ_CYAPA	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein. Associated with the pho ...				65
Q6B8V1 UniProt NPD GO	PSBZ_GRATL	Photosystem II reaction center Z protein	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				65
O78503 UniProt NPD GO	PSBZ_GUITH	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P69696 UniProt NPD GO	PSBZ_HORVU	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q5SD09 UniProt NPD GO	PSBZ_HUPLU	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q5IHA9 UniProt NPD GO	PSBZ_LIRTU	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q9BBT2 UniProt NPD GO	PSBZ_LOTJA	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q5IHB0 UniProt NPD GO	PSBZ_MAGAC	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q5IHA8 UniProt NPD GO	PSBZ_MAGTR	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q33300 UniProt NPD GO	PSBZ_MAIZE	Photosystem II reaction center Z protein	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P09973 UniProt NPD GO	PSBZ_MARPO	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q9MUP9 UniProt NPD GO	PSBZ_MESVI	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q9TKX2 UniProt NPD GO	PSBZ_NEPOL	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q6EW51 UniProt NPD GO	PSBZ_NYMAL	Photosystem II reaction center Z protein	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P49528 UniProt NPD GO	PSBZ_ODOSI	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				61
Q9MTN5 UniProt NPD GO	PSBZ_OENHO	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q6ENI9 UniProt NPD GO	PSBZ_ORYNI	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				62
P12194 UniProt NPD GO	PSBZ_ORYSA	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q68S09 UniProt NPD GO	PSBZ_PANGI	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q32902 UniProt NPD GO	PSBZ_PEA	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P41642 UniProt NPD GO	PSBZ_PINTH	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P51316 UniProt NPD GO	PSBZ_PORPU	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q8WI21 UniProt NPD GO	PSBZ_PSINU	Photosystem II reaction center Z protein	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q6L3B0 UniProt NPD GO	PSBZ_SACHY	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q6ENX9 UniProt NPD GO	PSBZ_SACOF	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
O96798 UniProt NPD GO	PSBZ_SKECO	Photosystem II reaction center Z protein	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				61
Q9M3M6 UniProt NPD GO	PSBZ_SPIOL	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P09974 UniProt NPD GO	PSBZ_TOBAC	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P69695 UniProt NPD GO	PSBZ_WHEAT	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q8SL95 UniProt NPD GO	PSBZ_EUGAN	Photosystem II reaction center Z protein (Fragment)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				32
Q8SL93 UniProt NPD GO	PSBZ_EUGGA	Photosystem II reaction center Z protein (Fragment)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				32
Q8SL91 UniProt NPD GO	PSBZ_EUGMY	Photosystem II reaction center Z protein (Fragment)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				32
Q8SL89 UniProt NPD GO	PSBZ_EUGST	Photosystem II reaction center Z protein (Fragment)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				32
Q8SL87 UniProt NPD GO	PSBZ_EUGVI	Photosystem II reaction center Z protein (Fragment)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				32
Q85FN7 UniProt NPD GO	PSBK_ADICA	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				58
Q70Y14 UniProt NPD GO	PSBK_AMBTC	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
Q85BB6 UniProt NPD GO	PSBK_ANTFO	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				55
P56782 UniProt NPD GO	PSBK_ARATH	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
Q7YJY5 UniProt NPD GO	PSBK_CALFE	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				59
Q8MA00 UniProt NPD GO	PSBK_CHAGL	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				58
P18263 UniProt NPD GO	PSBK_CHLRE	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				46
P56348 UniProt NPD GO	PSBK_CHLVU	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				42
Q9TLR0 UniProt NPD GO	PSBK_CYACA	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				41
Q85FY2 UniProt NPD GO	PSBK_CYAME	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				43
P14237 UniProt NPD GO	PSBK_CYAPA	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; cyanelle				45

You are viewing entries 96901 to 96950 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.