Is KT2440 PP_0375 (UniProt Q88QV9) a close sequence homolog of the
experimentally implicated Pseudomonas fluorescens B16 PqqG/PqqM protein
(GenPept AAX10035.1)?
The script downloads PP_0375 and two comparison proteins from UniProt and NCBI
and compares them with MMseqs2 easy-search. The recorded run used MMseqs2
18-8cc5c; the script writes the installed build to results/MMSEQS_VERSION.txt:
./compare_pqqg_ortholog.sh results
Q88QV9 aligned to AAX10035.1 at 66.0% amino-acid identity across 606 residues,
covering 98.9% of Q88QV9 and 99.8% of AAX10035.1. The alignment had an E-value
of 5.125e-294 and a bit score of 817.
Q88QV9 aligned to the Pseudomonas aeruginosa PA1990/PqqH protein Q9I2B9 at
52.2% amino-acid identity across 597 residues, covering 97.1% of Q88QV9 and
98.2% of Q9I2B9. The alignment had an E-value of 2.409e-197 and a bit score of
569.
The nearly full-length, high-identity match supports treating PP_0375 as a
PqqG/PqqM pathway candidate for follow-up. It does not establish the native
PP_0375 substrate, prove that this S9 peptidase directly processes PqqA, or
justify a PQQ-biosynthetic-process annotation by itself. Those mechanistic
questions remain open.
The NCBI protein record names AAX10035.1 as the Pseudomonas fluorescens B16
pqqG gene product, a dipeptidyl aminopeptidase/acylaminoacyl-peptidase. The
B16 full text names pqqM among 11 ORFs and states that "the Tn3-gusA
insertions in each ORF abolished PQQ production" [PMID:18055583;
PMCID:PMC2245851]. The measured material was culture filtrate, so this result
does not distinguish failed PQQ formation from failed export and does not
identify the PqqM substrate or biochemical reaction. The KT2440 operon study
independently names PP_0375 as putative pqqG based on conserved locus and
sequence PMID:27287323.
The PA1990 study reports that disruption of this S9-family ortholog eliminated
PQQ excretion into the culture supernatant, whereas a separate pqqF mutant
could not produce PQQ PMID:19902179. Thus, close homologs support a conserved
association with PQQ-related biology but do not establish whether PP_0375 acts
in precursor maturation, PQQ export, or both.