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
P60150 UniProt NPD GO	PSBL_SPIOL	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)				37
Q71L51 UniProt NPD GO	PSBL_STAER	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
Q6EYP1 UniProt NPD GO	PSBL_STEPS	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
Q6EYN0 UniProt NPD GO	PSBL_TAXBR	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
Q6EYM6 UniProt NPD GO	PSBL_THUPL	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
P60139 UniProt NPD GO	PSBL_TOBAC	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
Q7J1A1 UniProt NPD GO	PSBL_TROAR	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
P60140 UniProt NPD GO	PSBL_WHEAT	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)				37
Q67H84 UniProt NPD GO	PSBL_YUCGL	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
Q7IW42 UniProt NPD GO	PSBL_ZAMFU	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
Q85FM6 UniProt NPD GO	PSBM_ADICA	Photosystem II reaction center M protein (PSII-M)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P56325 UniProt NPD GO	PSBM_CHLVU	Photosystem II reaction center M protein (PSII-M)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P48107 UniProt NPD GO	PSBM_CYAPA	Photosystem II reaction center M protein (PSII-M)	0.01	-	cyt	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				38
Q85FJ5 UniProt NPD GO	PSBN_ADICA	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				45
Q6EYL8 UniProt NPD GO	PSBN_AGARO	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71LB9 UniProt NPD GO	PSBN_BOWSE	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q8M9Z2 UniProt NPD GO	PSBN_CHAGL	Photosystem II reaction center N protein	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71KQ8 UniProt NPD GO	PSBN_COLOB	Photosystem II reaction center N protein	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P48108 UniProt NPD GO	PSBN_CYAPA	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				43
Q71LA6 UniProt NPD GO	PSBN_CYCRE	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9TKW6 UniProt NPD GO	PSBN_NEPOL	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				44
Q6YLT7 UniProt NPD GO	PSBN_SCIVE	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71L86 UniProt NPD GO	PSBN_STAER	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYC3 UniProt NPD GO	PSBN_TAXBR	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9MSR1 UniProt NPD GO	PSBN_ZAMFU	Photosystem II reaction center N protein	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7YNH4 UniProt NPD GO	PSBT_ALLOC	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q6EYL5 UniProt NPD GO	PSBT_ARIMA	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q7YNG3 UniProt NPD GO	PSBT_BASHY	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q7YNI1 UniProt NPD GO	PSBT_BORAR	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P48109 UniProt NPD GO	PSBT_CYAPA	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				31
P49516 UniProt NPD GO	PSBT_ODOSI	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				32
P69672 UniProt NPD GO	PSBT_OENAR	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P69673 UniProt NPD GO	PSBT_OENHO	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q8HS25 UniProt NPD GO	PSBT_PEA	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q7GZA2 UniProt NPD GO	PSBT_SALEU	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q7YNT6 UniProt NPD GO	PSBT_SUAMA	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q7YNH0 UniProt NPD GO	PSBT_TECAU	Photosystem II reaction center T protein (PSII-T)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P51197 UniProt NPD GO	PSBX_PORPU	Photosystem II reaction center X protein	0.01	-	nuc	1 *	Plastid; chloroplast				39
P32095 UniProt NPD GO	PSBZ_EUGGR	Photosystem II reaction center Z protein	0.01	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				65
Q85X72 UniProt NPD GO	PSBK_PINKO	Photosystem II reaction center protein K precursor (PSII-K)	0.01	-	nuc	1 *	Plastid; chloroplast				59
P41598 UniProt NPD GO	PSBK_PINTH	Photosystem II reaction center protein K precursor (PSII-K)	0.01	-	nuc	1 *	Plastid; chloroplast				56
Q8WI34 UniProt NPD GO	PSBK_PSINU	Photosystem II reaction center protein K precursor (PSII-K)	0.01	-	nuc	1 *	Plastid; chloroplast				58
P07753 UniProt NPD GO	PSBA_CHLRE	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.01	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P12719 UniProt NPD GO	PSBA_CYAPA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.01	-	end	6 *	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				360
P24726 UniProt NPD GO	PSBA_ECTSI	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.01	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
P06631 UniProt NPD GO	PSBA_EUGGR	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.01	-	mit	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				345
O98733 UniProt NPD GO	PSBA_PALPL	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
P51212 UniProt NPD GO	PSBA_PORPU	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
Q01366 UniProt NPD GO	PSBA_PHAVU	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) (Fragment)	0.01	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				147
P23815 UniProt NPD GO	PH61_CHRSP	Phycocyanin-645 alpha-1 chain (PC-645)	0.01	-	cyt	0					70

You are viewing entries 90551 to 90600 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.