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 Sep 17 2021. 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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