GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Pseudomonas fluorescens GW456-L13

Found 35 low-confidence and 15 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
deoxyinosine deoB: phosphopentomutase PfGW456L13_5092
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase PfGW456L13_3458 PfGW456L13_2058
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter PfGW456L13_3929 PfGW456L13_2481
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme PfGW456L13_1095
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucU: L-fucose mutarotase FucU
fucose HSERO_RS05255: ABC transporter for L-fucose, permease component PfGW456L13_3910 PfGW456L13_2122
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
galacturonate udh: D-galacturonate dehydrogenase PfGW456L13_1301
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) PfGW456L13_2118
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) PfGW456L13_4833
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter PfGW456L13_887
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuB: D-mannonate dehydrogenase PfGW456L13_3038
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
maltose susB: alpha-glucosidase (maltase) PfGW456L13_3254
mannose manP: mannose PTS system, EII-CBA components PfGW456L13_5073
myoinositol iolG: myo-inositol 2-dehydrogenase PfGW456L13_2810 PfGW456L13_1420
myoinositol iolM: 2-inosose 4-dehydrogenase PfGW456L13_1122
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase PfGW456L13_3038
propionate putP: propionate transporter; proline:Na+ symporter PfGW456L13_221
rhamnose LRA1: L-rhamnofuranose dehydrogenase PfGW456L13_3499 PfGW456L13_4129
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase PfGW456L13_3931
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
sorbitol sdh: sorbitol dehydrogenase PfGW456L13_3038 PfGW456L13_3657
sucrose ams: sucrose hydrolase (invertase) PfGW456L13_3254
thymidine deoB: phosphopentomutase PfGW456L13_5092
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase PfGW456L13_3254
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase PfGW456L13_3657 PfGW456L13_2058
xylose gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA PfGW456L13_1894
xylose gtsB: xylose ABC transporter, permease component 1 GtsB PfGW456L13_1895
xylose gtsC: xylose ABC transporter, permease component 2 GtsC PfGW456L13_1896
xylose gtsD: xylose ABC transporter, ATPase component GtsD PfGW456L13_1897 PfGW456L13_3039
xylose xylA: xylose isomerase

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