| Claim/Aspect | Evidence summary | Organism/Context | Source (with year) | URL/DOI |
|---|---|---|---|---|
| Identity | Target matches **glnK / PP_5234 / UniProt Q88CE7** in *Pseudomonas putida* KT2440; described as the strain’s **single PII-like protein** and nitrogen-regulated gene, avoiding confusion with glnK homologs from other species. (pqac-00000000, pqac-00000016) | *P. putida* KT2440 | Hervás et al. 2009; Hervás et al. 2008 | https://doi.org/10.1128/jb.00744-09 ; https://doi.org/10.1128/jb.01230-07 |
| Family/domains | The protein belongs to the **PII/GlnK family**, whose canonical properties include a homotrimeric architecture, flexible **T-loops**, and sensing of **ATP, ADP, and 2-oxoglutarate**; these features are consistent with the UniProt domain assignment to the PII family. (pqac-00000004, pqac-00000006) | Conserved bacterial/archaeal PII proteins; used to interpret KT2440 GlnK | Ormeno 2024; Ensinck et al. 2024 | https://doi.org/10.6094/unifr/255197 ; https://doi.org/10.3389/fmicb.2024.1366111 |
| Regulation by NtrC | In *P. putida* KT2440, **glnK transcription is directly activated by NtrC**. Footprinting identified **two contiguous NtrC-binding sites** upstream of the glnK promoter, and promoter opening additionally required **IHF**. This places glnK in an NtrC-controlled nitrogen-starvation response. (pqac-00000000) | Nitrogen-regulated transcription in KT2440 | Hervás et al. 2009 | https://doi.org/10.1128/jb.00744-09 |
| Operon / neighboring transporter context | The adjacent ammonium transporter gene **amtB (PP_5233)** is reported as being in the same functional context and is presumed to form an operon with upstream **glnK**, linking GlnK to ammonium uptake control. (pqac-00000013) | *P. putida* KT2440 nitrogen assimilation locus | Hervás et al. 2008 | https://doi.org/10.1128/jb.01230-07 |
| Pathway role | KT2440 GlnK is placed in the canonical **GlnD → GlnK → NtrB → NtrC** signaling cascade controlling nitrogen assimilation genes: **GlnD modulates GlnK**, **GlnK activates NtrB**, and NtrB changes **NtrC phosphorylation state**. (pqac-00000001, pqac-00000015, pqac-00000017) | Nitrogen-starvation signaling in KT2440 | Schmidt et al. 2022; Incha 2023 | https://doi.org/10.1128/aem.02430-21 ; source URL not available in retrieved metadata |
| Functional class / primary role | GlnK is **not an enzyme or transporter**; it is a **signal-transduction/adaptor protein** that couples intracellular nitrogen/energy status to regulation of NtrB/NtrC and likely ammonium transport-related functions, matching the UniProt description “activator of NRII (GlnL/NtrB) phosphatase” at the family level. (pqac-00000000, pqac-00000002, pqac-00000006) | Interpreted from KT2440 data plus conserved PII mechanism | Hervás et al. 2009; Atkinson et al. 2002; Ormeno 2024 | https://doi.org/10.1128/jb.00744-09 ; https://doi.org/10.1128/jb.184.19.5364-5375.2002 ; https://doi.org/10.6094/unifr/255197 |
| PTM | Direct PTM evidence for **KT2440 GlnK** was not found in the retrieved organism-specific literature, but the KT2440 pathway explicitly includes **GlnD**, and conserved PII biology indicates reversible **uridylylation/deuridylylation** as the expected nitrogen-responsive modification controlling NtrB/NtrC signaling. This should be treated as strong family-based inference rather than direct strain-specific biochemical proof. (pqac-00000015, pqac-00000017, pqac-00000006) | KT2440 inference from pathway membership plus conserved PII mechanism | Schmidt et al. 2022; Incha 2023; Ormeno 2024 | https://doi.org/10.1128/aem.02430-21 ; source URL not available in retrieved metadata ; https://doi.org/10.6094/unifr/255197 |
| Localization | No direct localization experiment for KT2440 GlnK was identified. Given PII-family biology, the default localization is **cytosolic**, with possible condition-dependent association with membrane transport systems such as AmtB inferred from homologous systems, but not directly demonstrated here for KT2440. (pqac-00000007, pqac-00000011) | Inference from conserved GlnK/Amt systems | Ensinck et al. 2024 | https://doi.org/10.3389/fmicb.2024.1366111 |
| Quantitative expression | **Hervás et al. 2008 Table 1** reports glnK expression ratios **9.2, 3.2, 5.7, 4.9, 1.2, 2.6**, from RT-PCR/microarray comparisons across nitrogen and NtrC conditions, supporting strong induction under nitrogen limitation and NtrC responsiveness. (pqac-00000013, pqac-00000018) | *P. putida* KT2440 transcriptomics / validation table | Hervás et al. 2008 | https://doi.org/10.1128/jb.01230-07 |
| Additional transcriptomic context | In a later KT2440 study, **glnK was described as upregulated** under the tested nitrogen/stationary-phase-related conditions, while **NtrC** showed strong activation (**8.8-fold**), reinforcing that glnK participates in nitrogen stress signaling. A specific numeric fold-change for glnK was not given in the excerpt. (pqac-00000014) | KT2440 transcriptome under stationary phase / nitrogen-linked response | Możejko-Ciesielska et al. 2017 | https://doi.org/10.1186/s13568-017-0396-z |
| Fitness data | In the KT2440 **RB-TnSeq** resource, the transposon library had **no insertions in glnK**, so **no direct fitness value/phenotype** could be assigned to PP_5234 from that dataset. This is an important limitation for current functional-genetics evidence. (pqac-00000015, pqac-00000017) | *P. putida* KT2440 pooled mutant fitness assays | Schmidt et al. 2022; Incha 2023 | https://doi.org/10.1128/aem.02430-21 ; source URL not available in retrieved metadata |
| Recent developments relevant to annotation | Recent 2024 PII research reinforces the modern view of GlnK/PII proteins as **allosteric metabolite sensors** whose partner binding is remodeled by ATP/ADP/2-OG and can regulate transport complexes; this supports annotation of KT2440 GlnK as a dynamic nitrogen-sensing regulator rather than a static structural protein. (pqac-00000008, pqac-00000012) | General PII field update, relevant by homology | Li et al. 2024; Rozbeh & Forchhammer 2024 | https://doi.org/10.1073/pnas.2318320121 ; https://doi.org/10.3390/ijms25063409 |


*Table: This table summarizes the evidence base for functional annotation of *Pseudomonas putida* KT2440 GlnK (PP_5234; UniProt Q88CE7). It highlights identity verification, pathway placement, quantitative transcript data, and the current limits of direct experimental evidence such as fitness and localization.*