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
Q9MS76 UniProt NPD GO	PSBK_EUGAN	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				53
Q9MS70 UniProt NPD GO	PSBK_EUGDE	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				54
P31481 UniProt NPD GO	PSBK_EUGGR	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				54
Q9MS67 UniProt NPD GO	PSBK_EUGMU	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				54
Q9MS64 UniProt NPD GO	PSBK_EUGMY	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				50
Q9MS61 UniProt NPD GO	PSBK_EUGSA	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				48
Q9MS58 UniProt NPD GO	PSBK_EUGST	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				54
Q9MS55 UniProt NPD GO	PSBK_EUGVI	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				45
Q6B8V0 UniProt NPD GO	PSBK_GRATL	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				45
O78504 UniProt NPD GO	PSBK_GUITH	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				45
P69693 UniProt NPD GO	PSBK_HORVU	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
Q5SCX1 UniProt NPD GO	PSBK_HUPLU	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				53
Q56P17 UniProt NPD GO	PSBK_LACSA	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				59
Q9MS73 UniProt NPD GO	PSBK_LEPBU	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				48
Q9BBS2 UniProt NPD GO	PSBK_LOTJA	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
P48188 UniProt NPD GO	PSBK_MAIZE	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
P10348 UniProt NPD GO	PSBK_MARPO	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				55
Q9MUS0 UniProt NPD GO	PSBK_MESVI	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				47
Q9TKY7 UniProt NPD GO	PSBK_NEPOL	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				46
Q6EW65 UniProt NPD GO	PSBK_NYMAL	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
P49513 UniProt NPD GO	PSBK_ODOSI	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				44
Q9MTL6 UniProt NPD GO	PSBK_OENHO	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				59
Q6ENJ4 UniProt NPD GO	PSBK_ORYNI	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
P12162 UniProt NPD GO	PSBK_ORYSA	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
Q68S23 UniProt NPD GO	PSBK_PANGI	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
Q9MS79 UniProt NPD GO	PSBK_PHAAC	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				49
Q6YXN4 UniProt NPD GO	PSBK_PHYPA	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				58
P51317 UniProt NPD GO	PSBK_PORPU	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				45
Q6L3B3 UniProt NPD GO	PSBK_SACHY	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
Q6ENY5 UniProt NPD GO	PSBK_SACOF	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
P69694 UniProt NPD GO	PSBK_SECCE	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
Q589B1 UniProt NPD GO	PSBK_SILLA	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				59
P10347 UniProt NPD GO	PSBK_SINAL	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
O96812 UniProt NPD GO	PSBK_SKECO	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	1 *	Plastid; chloroplast				44
P12163 UniProt NPD GO	PSBK_SPIOL	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				59
P12164 UniProt NPD GO	PSBK_TOBAC	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
P58273 UniProt NPD GO	PSBK_WHEAT	Photosystem II reaction center protein K precursor (PSII-K)	0.00	-	nuc	2 *	Plastid; chloroplast				61
P28642 UniProt NPD GO	PSBK_PEA	Photosystem II reaction center protein K precursor (PSII-K) (Fragment)	0.00	-	mit	1 *	Plastid; chloroplast				46
P02956 UniProt NPD GO	PSBA_AMAHY	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P24625 UniProt NPD GO	PSBA_ANTSP	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
P48265 UniProt NPD GO	PSBA_BUMFI	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
P69565 UniProt NPD GO	PSBA_CHERU	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P35860 UniProt NPD GO	PSBA_CHLEL	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P09752 UniProt NPD GO	PSBA_CHLMO	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P56318 UniProt NPD GO	PSBA_CHLVU	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q9T351 UniProt NPD GO	PSBA_CONCI	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q9TNF8 UniProt NPD GO	PSBA_CONSU	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P32036 UniProt NPD GO	PSBA_CUSRE	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; plastid thylakoid membrane; multi-pass membrane protein				353
O19895 UniProt NPD GO	PSBA_CYACA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
Q9TNF7 UniProt NPD GO	PSBA_DUMHI	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353

You are viewing entries 96951 to 97000 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.