GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Burkholderia vietnamiensis G4

Found 21 low-confidence and 26 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 WP_011883162.1 WP_011880942.1
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component WP_011876052.1 WP_011884020.1
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 WP_011884019.1 WP_011885685.1
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 WP_011885684.1 WP_011884017.1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component WP_034192590.1 WP_011880970.1
citrulline arcC: carbamate kinase
citrulline aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) WP_011884025.1 WP_011884024.1
D-serine cycA: D-serine:H+ symporter CycA WP_011881650.1 WP_011882166.1
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase WP_011884992.1 WP_011885879.1
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter WP_011885696.1 WP_011881175.1
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme WP_011880746.1
deoxyribose deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase WP_011884992.1 WP_011885879.1
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter WP_011885696.1 WP_011881175.1
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit WP_011882594.1 WP_011882246.1
deoxyribose ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme WP_011880746.1
fucose HSERO_RS05250: ABC transporter for L-fucose, ATPase component WP_011884460.1 WP_011883236.1
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) WP_011886083.1
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctM: D-glucuronate TRAP transporter, large permease component WP_011880621.1
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component WP_011880622.1
lactose lacP: lactose permease LacP
lysine davD: glutarate semialdehyde dehydrogenase WP_011880938.1 WP_011880486.1
lysine patA: cadaverine aminotransferase WP_011881939.1 WP_011879744.1
lysine patD: 5-aminopentanal dehydrogenase WP_011880783.1 WP_011879745.1
maltose susB: alpha-glucosidase (maltase) WP_011879950.1
mannitol mt2d: mannitol 2-dehydrogenase WP_011885869.1 WP_043292259.1
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE WP_011885876.1
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) WP_011885875.1 WP_011881167.1
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) WP_011885874.1 WP_011881166.1
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG WP_011885872.1 WP_011881170.1
rhamnose LRA1: L-rhamnofuranose dehydrogenase WP_011885879.1 WP_034194084.1
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase WP_011880908.1 WP_011885941.1
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase WP_011882092.1 WP_011886350.1
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
sucrose ams: sucrose hydrolase (invertase) WP_011882121.1 WP_043292210.1
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) WP_011880722.1 WP_011885758.1
thymidine deoA: thymidine phosphorylase DeoA WP_011882353.1
thymidine deoB: phosphopentomutase
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase WP_043292259.1 WP_011881129.1

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