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Plant Growth Promoting Rhizobacteria (PGPR) influence plants’ physiological characteristics, metabolites, pathways and proteins via alteration of corresponding gene expression. In the current study, a total of 42 upregulated uncharacterized sorghum bicolor root proteins influenced by PGPR were subjected to different analyses: phylogenetic tree, protein functional network, sequences similarity network (SSN), Genome Neighborhood Network (GNN) and motif analysis. The screen for homologous bacterial proteins to uncover associated protein families and similar proteins in non-PGPRs was identified. The sorghum roots’ uncharacterized protein sequences analysis indicated the existence of two protein categories, the first being related to phytobeneficial protein family associated with DNA regulation such as Sulfatase, FGGY_C, Phosphodiesterase or stress tolerance such as HSP70. The second is associated with bacterial transcriptional regulators such as FtsZ, MreB_Mbl and DNA-binding transcriptional regulators, as well as the AcrR family, which existed in PGPR and non PGPR. Therefore, Plant Growth-Promoting Rhizobacteria (PGPR) regulated phytobeneficial traits through reciprocal protein stimulation via microbe plant interactions, both during and post colonization.