GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Burkholderia phytofirmans PsJN

Found 12 low-confidence and 24 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase BPHYT_RS29385 BPHYT_RS17345
alanine cycA: L-alanine symporter CycA BPHYT_RS15500 BPHYT_RS07280
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BPHYT_RS05495 BPHYT_RS07685
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BPHYT_RS07680 BPHYT_RS05500
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BPHYT_RS05505 BPHYT_RS07675
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component BPHYT_RS29525 BPHYT_RS07735
citrulline aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) BPHYT_RS07705 BPHYT_RS07700
D-serine cycA: D-serine:H+ symporter CycA BPHYT_RS15500 BPHYT_RS21680
D-serine dsdA: D-serine ammonia-lyase BPHYT_RS15425 BPHYT_RS09280
deoxyinosine deoB: phosphopentomutase BPHYT_RS14155
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyribose drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit BPHYT_RS24630 BPHYT_RS32800
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit BPHYT_RS24635 BPHYT_RS32805
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) BPHYT_RS02745
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
lactose lacP: lactose permease LacP
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) BPHYT_RS05500 BPHYT_RS07680
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) BPHYT_RS05505 BPHYT_RS07675
lysine patA: cadaverine aminotransferase BPHYT_RS27170 BPHYT_RS07695
lysine patD: 5-aminopentanal dehydrogenase BPHYT_RS09900 BPHYT_RS25160
maltose susB: alpha-glucosidase (maltase) BPHYT_RS33775
mannitol mt2d: mannitol 2-dehydrogenase BPHYT_RS28510 BPHYT_RS23425
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE BPHYT_RS16115
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) BPHYT_RS16110 BPHYT_RS35665
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) BPHYT_RS16105 BPHYT_RS27970
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG BPHYT_RS16095 BPHYT_RS22760
rhamnose LRA2: L-rhamnono-gamma-lactonase
sucrose ams: sucrose hydrolase (invertase) BPHYT_RS33775
threonine snatA: L-threonine transporter snatA BPHYT_RS17695
thymidine deoA: thymidine phosphorylase DeoA BPHYT_RS33245
thymidine deoB: phosphopentomutase BPHYT_RS14155
tryptophan hpaH: anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) BPHYT_RS15605 BPHYT_RS31740
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BPHYT_RS01885 BPHYT_RS31715
xylitol PS417_12055: xylitol ABC transporter, substrate-binding component
xylitol PS417_12065: xylitol ABC transporter, ATPase component BPHYT_RS27185 BPHYT_RS28215

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory