Table 1

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

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.

Kosarev et al. Genome Biology 2002 3:research0016.1-research0016.12   doi:10.1186/gb-2002-3-4-research0016

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