Genome phylogeny and taxonomy from the Genome Taxonomy Database (GTDB) release R214. The reference tree (bac120_r214.tree) comprises 80,789 bacterial genomes placed on a 120-marker concatenated protein phylogeny. The subtree shown here was extracted as the most recent common ancestor (MRCA) of all genomes assigned to Pseudomonas sensu lato in GTDB, encompassing Pseudomonas, Pseudomonas_B, Pseudomonas_E, Pseudomonas_F, Pseudomonas_H, Pseudomonas_K, Pseudomonas_M, Stutzerimonas, and Azotobacter (782 genomes after quality filtering). Nitrogen cycle gene annotations (narG, napA, nirS, nirK, norB, nosZ) were obtained from AnnoTree, which assigns gene presence/absence using hidden Markov model (HMM) searches against KEGG Orthology profiles.
Only genomes classified as Complete/High Quality (≥95% completeness, ≤5% contamination) or Near Complete (90–95% completeness, ≤5% contamination) are included. No nosZ clade II or nrfA were identified among the pseudomonads.
AnnoTree reports a single norB annotation. Sequences were classified as cytochrome c-oxidizing (cNor) or quinol-oxidizing (qNor) based on protein length. qNor is a fusion of NorB and NorC into a single polypeptide (~765 aa), whereas cNor NorB alone is ~455 aa. A histogram of all 11,399 norB sequence lengths revealed a bimodal distribution with a clear valley at ~635 aa, which was used as the classification cutoff. Only 83 sequences (0.7%) fell within ±30 aa of the cutoff.
NosZ sequences were classified as Clade I (typical) or Clade II (atypical) by scoring all 7,062 sequences against two profile HMMs using HMMER v3.4: the FunGene nosZ profile (Clade I, 638 positions) and the FunGene nosZ_a2 profile (Clade II, 656 positions). Each sequence was assigned to whichever HMM yielded the higher full-sequence bit score. Only 8 sequences (0.1%) had a score difference below 50 bits. All nosZ in pseudomonads was Clade I.
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Data processed by Aayushi Shah and Karna Gowda (2026).