Table 1 |
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Proteins with false-positive detected RING domains that were eliminated from the dataset |
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Protein ID |
Reason |
Remarks |
|
|
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|
At1g02860 |
Wrong ligand spacing |
Spacer between metal ligands 2 and 3 too long |
|
At1g05890 |
Wrong ligand spacing |
Protein contains one RING-variant domain |
|
At1g09060 |
Incomplete |
|
|
At1g10170 |
PHD domain |
|
|
At1g55530 |
Incomplete |
Protein contains one RING-H2 domain |
|
At1g60360 |
Incomplete |
Protein contains one RING-H2 domain |
|
At1g62310 |
Incomplete |
|
|
At1g74870 |
Incomplete |
|
|
At2g28530 |
Incomplete |
|
|
At2g31770 |
Wrong ligand spacing |
Either wrong spacing or incomplete |
|
Protein contains one RING-variant domain |
||
|
At2g31780 |
Wrong ligand spacing |
Either wrong spacing or incomplete |
|
Protein contains one RING-variant domain |
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|
At2g39720 |
Incomplete |
Protein contains one RING-H2 domain |
|
At2g42170 |
Wrong ligand spacing |
Pseudogene |
|
At2g44330 |
Incomplete |
Two false-positive motifs |
|
Protein contains one RING-H2 domain |
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|
At3g05870 |
Incomplete |
Protein contains one RING-H2 domain |
|
At3g06330 |
Wrong ligand spacing |
|
|
At3g07610 |
Incomplete |
|
|
At3g08020 |
PHD domain |
|
|
At3g18290 |
Incomplete |
Protein contains one RING-H2 domain |
|
At3g19910 |
Incomplete |
|
|
At3g19950 |
Incomplete |
Protein contains one RING-H2 domain |
|
At3g23060 |
Incomplete |
Two false-positive motifs |
|
At3g42830 |
Incomplete |
Rbx1-like |
|
Protein contains one RING-variant domain |
||
|
At3g45470 |
Wrong ligand spacing |
Protein contains one RING-variant domain |
|
At3g45540 |
Incomplete |
Protein contains one RING-variant domain |
|
At3g45630 |
Incomplete |
|
|
At3g48070 |
Wrong ligand spacing |
|
|
At3g52100 |
PHD domain |
|
|
At3g60080 |
Incomplete |
Protein contains one RING-H2 domain |
|
At3g62970 |
Incomplete |
Protein contains one RING-H2 domain |
|
At4g00070 |
Incomplete |
|
|
At4g01020 |
Incomplete |
Protein contains one RING-HC and |
|
One RING-variant domain |
||
|
At4g10940 |
Incomplete |
|
|
At4g12150 |
Incomplete |
Protein contains one RING-variant domain, |
|
Which is part of a RING-H2 cluster |
||
|
At4g26400 |
Incomplete |
Protein contains one RING-H2 domain |
|
At4g37880 |
Incomplete |
|
|
At4g39350 |
Wrong ligand spacing |
Cellulose synthase |
|
At5g05170 |
Wrong ligand spacing |
Cellulose synthase |
|
At5g09870 |
Wrong ligand spacing |
Cellulose synthase |
|
At5g10370 |
Incomplete |
Protein contains one RING variant domain |
|
At5g15790 |
Incomplete |
Protein contains one RING-H2 domain |
|
At5g17420 |
Wrong ligand spacing |
Cellulose synthase |
|
At5g23110 |
Incomplete |
Protein contains one RING-HC domain |
|
At5g25560 |
Incomplete |
Protein contains one RING-H2 domain |
|
At5g28340 |
Incomplete |
|
|
At5g38070 |
Wrong ligand spacing |
|
|
At5g45290 |
Incomplete |
|
|
At5g47430 |
Incomplete |
|
|
At5g52140 |
Incomplete |
|
|
At5g52150 |
Incomplete |
|
|
At5g56340 |
Incomplete |
Protein contains one RING-H2 domain |
|
At5g58410 |
Wrong ligand spacing |
|
|
At5g62910 |
Wrong ligand spacing |
|
|
At5g63740 |
Incomplete |
|
|
At5g63750 |
Incomplete |
Drosophila Ariadne-like |
|
Protein contains one RING-variant domain |
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|
At5g63970 |
Incomplete |
|
|
At5g64740 |
Wrong ligand spacing |
Cellulose synthase |
|
|
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|
To eliminate false-positive RING domains detected through computational analysis, the complete dataset was curated and false positives were eliminated. The first column shows proteins in which false-positive RING domains were detected. The principal reason for their elimination from the dataset is given in the second column. 'Incomplete', at least two metal ligands are missing; 'wrong ligand spacing', the spacing between the prospective metal ligands is not conserved; 'PHD domain', the domain has a PHD rather than a RING structure. See text for additional criteria for RING domains. Alternative gene names and other remarks are given in the third column. For instance, many of the proteins contain an independent, verified RING domain and are thus also listed in Table 3. |
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Kosarev et al. Genome Biology 2002 3:research0016.1 doi:10.1186/gb-2002-3-4-research0016 |
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