Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome

Kosarev, Peter; Mayer, Klaus FX; Hardtke, Christian S

doi:10.1186/gb-2002-3-4-research0016

Table 1 Proteins with false-positive detected RING domains that were eliminated from the dataset

From: Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome

Protein ID	Reason	Remarks
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
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
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
At5g63970	Incomplete
At5g64740	Wrong ligand spacing	Cellulose synthase

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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ISSN: 1474-760X

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