GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms.

InterPro-based electronic annotation correctly identifies a bacterial response regulator with transcription-related domains.

file:PSEPK/gacA/gacA-notes.md

Curator notes for gacA in Pseudomonas putida KT2440

KT2440 literature best supports GacA as a phosphorelay response regulator that promotes biofilm-associated adhesin expression and other lifestyle outputs.
Direct KT2440 evidence is strongest for biofilm regulation and K1-T6SS regulation, while other outputs are more strain-specific.
GO:0003677 is too general; phosphorelay response regulator activity is a better core molecular-function summary.

file:PSEPK/gacA/gacA-deep-research-codex.md

Deep research report for gacA in Pseudomonas putida KT2440

The strongest direct KT2440 evidence links GacA to adhesin regulation, biofilm development, c-di-GMP-associated surface phenotypes, and positive regulation of the K1-T6SS.
The broader Gac/Rsm model supports interpreting GacA as a phosphorelay-activated transcription regulator, but direct KT2440 promoter targets remain incompletely mapped.

file:PSEPK/gacA/gacA-deep-research-falcon.md

Falcon (Edison Scientific) deep research report for gacA in Pseudomonas putida KT2440

GacA is the response regulator of the GacS/GacA two-component system; the sensor kinase GacS phosphorylates GacA to activate it.

"GacA is the **response regulator** of the **GacS/GacA two-component system (TCS)**."
Activated GacA acts largely indirectly, functioning as a master transcriptional activator of Rsm-family small regulatory RNAs that then impose broad post-transcriptional control.

"activated GacA is best understood as a **master transcriptional activator of small regulatory RNAs (sRNAs)** in the **Gac–Rsm pathway**, which then exerts broad post-transcriptional control through RNA-binding proteins."
The GacA-induced sRNAs (RsmX/Y/Z) act as protein sponges that sequester RsmA/CsrA-family RNA-binding proteins, relieving translational repression of target mRNAs.

"GacA-dependent sRNAs (commonly **RsmX/RsmY/RsmZ** in pseudomonads) function as **protein sponges**: they contain repeated **GGA** motifs that bind and sequester **RsmA/CsrA-family RNA-binding proteins**, relieving translational repression on target mRNAs."
GacA has an N-terminal receiver (REC) domain with a conserved phospho-accepting Asp-54 and a C-terminal helix-turn-helix DNA-binding domain.

"**N-terminal receiver (REC) domain** with a conserved phospho-accepting Asp (reported as **Asp-54** in one Pseudomonas GacA model) and"
The strongest KT2440-specific output of the Gac system is control of the large adhesins LapA and LapF, both of which are under GacS/GacA control.

"A well-defined *KT2440-specific* regulatory output of the Gac system is control of the large adhesins **LapA** and **LapF**, which function sequentially in biofilm development (LapA early adhesion; LapF later maturation). Both **lapA and lapF are under GacS/GacA control**."
GacA is a cytosolic response regulator that, upon phosphorylation, acts as a DNA-binding transcription factor activating transcription of sRNA genes; its primary action occurs inside the cell.

"**GacA** as a **cytosolic response regulator** that, upon phosphorylation, acts as a DNA-binding transcription factor to activate transcription of sRNA genes."
In KT2440, rpoS expression is abolished in a gacS mutant, providing an indirect route by which the Gac system controls lapF via RpoS.

"**rpoS expression is abolished in a gacS mutant**, supporting an indirect route for Gac → lapF via RpoS."

file:PSEPK/gacA/gacA-uniprot.txt

UniProt entry Q88FJ6

UniProt names the protein Response regulator GacA, records the gene name as uvrY, and assigns locus tag PP_4099.
The protein contains a response-regulator receiver domain, a LuxR-type HTH domain, and a predicted 4-aspartylphosphate residue at position 54.