Table 1

Characterization of our high ranking Arabidopsis candidate G-protein coupled receptors

Locus

ID

QFC

GPCRHMM

TMHMM

HMMTOP

Phobius

Pcut-T

Pcut-H


Upper bin

At1g48270.1

GCR1

*

*

7 (out)

7 (out)

7 (out)

At3g26090.1

RGS1

*

*

7 (out)

7 (out)

7 (out)

At1g57680.1

Cand1

*

*

7 (out)

7 (out)

7 (out)

At3g05010.1

Cand2

*

*

7 (in)

7 (out)

7 (out)

At3g59090.1

Cand3

*

*

7 (out)

7 (out)

7 (out)

At3g59090.2

Cand4

*

*

7 (out)

7 (out)

7 (out)

At3g59090.3

Cand5

*

*

7 (out)

7 (out)

7 (out)

At4g21790.1

TOM1

*

*

7 (out)

7 (out)

8 (in)

At5g02630.1

Cand6

*

*

6 (out)

8 (out)

7 (out)

7 (in)

7 (in)

At5g18520.1

Cand7

*

*

8 (in)

8 (in)

7 (out)

7 (out)

7 (out)

At5g27210.1

Cand8

*

*

7 (in)

7 (out)

7 (out)

Lower bin

At2g02180.1

TOM3

*

-0.47

6 (in)

7 (out)

7 (out)

At4g30850.1

HHP2

*

-4.83

7 (in)

7 (in)

8 (out)

At5g26740.1

Cand9

*

-7.95

7 (out)

7 (out)

7 (out)

At1g14530.1

THH1

*

-8.95

6 (in)

7 (out)

7 (out)

At3g05940.1

Cand10

*

-9.89

7 (out)

7 (out)

7 (out)


Protein sequences predicted to be GPCRs by QFC and GPCRHMM are indicated by an asterisk and the GPCRHMM global score is provided for sequences we identify as GPCRs using a relaxed cutoff threshold score of -10. The predicted number of transmembrane domains and the intracellular (in) or extracellular (out) localization of the amino terminus are shown. Pcut-T and Pcut-H describe topology predictions of the mature proteins by TMHMM and HMMTOP, respectively, after in silico cleavage at the signal peptide cleavage site predicted by Phobius. Candidates shown to interact with GPA1 in vivo using the split-ubiquitin system are identified in bold while the sole negative result from that assay is shown in italics. GCR1 interaction with GPA1 in the split-ubiquitin system was previously described by Pandey and Assmann [60]. RGS1 interaction with GPA1 in the split-ubiquitin system was previously described by Chen et al. [20]; the RGS1 sequence was truncated at the upstream border of the RGS box prior to analysis by GPCRHMM.

Gookin et al. Genome Biology 2008 9:R120   doi:10.1186/gb-2008-9-7-r120

Open Data