Updated annotations for Bifidobacterium breve UCC2003

7 genes with updated (or confirmed) annotations:

BBR_RS12915 : glycine synthesis protein GlyXS
Original description: ACT domain-containing protein
SEED: ACT domain protein
KEGG: ACT domain-containing protein
Rationale: # Important when glycine is not available. A homolog from Methanococcus has similar phenotypes, so this appears to be part of a novel route to glycine, along with GlyXS (BBR_RS12920). Also has milder phenotypes on Irgasan and Clotrimazole which are not explained.

BBR_RS12920 : glycine synthesis protein GlyXL
Original description: PFL family protein
SEED: FIG00672359: hypothetical protein
KEGG: hypothetical protein
Rationale: # Specifically important in nutrient dropout no Glycine. A homolog from Methanococcus has similar phenotypes, so this appears to be part of a novel route to glycine, along with GlyXS (BBR_RS12915). Also has milder phenotypes on Irgasan and Clotrimazole which are not explained.

BBR_RS14070 : threonine synthase (EC 4.2.3.1)
Original description: threonine synthase
SEED: Threonine synthase (EC 4.2.3.1)
KEGG: threonine synthase
Rationale: # Important for fitness in minimal media and cofit with homoserine kinase BBR_RS19535, which performs the preceding step in threonine synthesis.

BBR_RS15475 : Histidinol-phosphatase (EC 3.1.3.15)
Original description: HAD family phosphatase
SEED: possible alpha beta hydrolase
KEGG: no annotation
Rationale: # Specifically important in nutrient dropout media with no histidine. This function was confirmed by heterologous complementation, see doi: 10.1101/2023.08.29.555234

BBR_RS16680 : prephenate dehydratase (EC 4.2.1.51)
Original description: chorismate mutase
SEED: Prephenate dehydratase (EC 4.2.1.51)
KEGG: prephenate dehydratase
Rationale: # Specifically important for fitness in defined media without phenylalanine. Prephenate dehydratases are often fused to chorismate mutase, but this is not, which raises the possibility that it could be arogenate dehydratase instead. It is 33% identical to G4V39_RS01170, which is fused to chorismate mutase (implying channeling of prephenate), so we expect that BBR_RS16680 is a prephenate dehydratase. Sometimes misannotated as chorismate mutase, but BBR_RS16680 has the PDH domain only.

BBR_RS19535 : homoserine kinase (EC 2.7.1.39)
Original description: homoserine kinase
SEED: Homoserine kinase (EC 2.7.1.39)
KEGG: homoserine kinase
Rationale: # Important for fitness in minimal media and cofit with the threonine synthase (BBR_RS14070), the succeeding step in threonine synthesis. Another potential candidate for this enzyme is BBR_RS19535, but that protein is fused to AroB and must be shikimate kinase

BBR_RS19555 : diaminopimelate decarboxylase (EC 4.1.1.20)
Original description: diaminopimelate decarboxylase
SEED: Diaminopimelate decarboxylase (EC 4.1.1.20)
KEGG: no annotation
Rationale: # Important for fitness in most minimal media, and has a virtually identical with diaminopimelate epimerase BBR_RS13700, the preceding step in the lysine synthesis pathway. 34% identical to the DAP decarboxylase from Mycobacterium.

Or download reannotations for Bifidobacterium breve UCC2003 or for all organisms as tab-delimited tables