1. Identity of homolog for similarity-based annotations. In cases where evidence is inferred from sequence similarity, the "with" field is used to identify homolog on which the annotation is based. For example, if an effector was characterized in P. syringae maculicola ES4326, GO annotations for the homologous effector from P. syringae tomato DC3000 will specify the identify of the homolog from Pma ES4326 in the "with" field
2. Identity of other genes mutagenized. In cases where an annotation is based on mutation of multiple gene products, identities of the additionally mutagenized genes are shown in the "with" field. For example, if the annotation is based on a double mutation, one of which is the gene being annotated, the identifier for the second mutated gene would be placed in the "with" field.
3. Identity of interacting gene products. For terms reflecting binding, this field specifies the identity of the bound gene product. NOTE: For the purposes of the Pto DC3000-Plant Interaction model, interacting gene products derived from the host are placed in the "host interaction" field