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 (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