GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Pseudomonas fluorescens FW300-N2C3

Found 31 low-confidence and 9 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
D-serine dsdA: D-serine ammonia-lyase AO356_10230 AO356_10330
deoxyinosine deoB: phosphopentomutase AO356_07445
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase AO356_27985 AO356_28740
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter AO356_26160 AO356_01235
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme AO356_13850
deoxyribose deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase AO356_27985 AO356_28740
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter AO356_26160 AO356_01235
deoxyribose ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme AO356_13850
fucose fdh: L-fucose 1-dehydrogenase AO356_29900 AO356_23595
fucose fucD: L-fuconate dehydratase AO356_27460 AO356_24195
fucose fuconolactonase: L-fucono-1,5-lactonase
fucose fucU: L-fucose mutarotase FucU
fucose HSERO_RS05255: ABC transporter for L-fucose, permease component AO356_00960 AO356_23210
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter AO356_12955
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) AO356_04805
maltose susB: alpha-glucosidase (maltase) AO356_01250
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E AO356_16950
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase AO356_26360 AO356_30355
phenylacetate paaK: phenylacetate-CoA ligase AO356_05105 AO356_05100
phenylacetate paaZ1: oxepin-CoA hydrolase AO356_26360 AO356_30355
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa AO356_19665
propionate putP: propionate transporter; proline:Na+ symporter AO356_09010
rhamnose LRA1: L-rhamnofuranose dehydrogenase AO356_25515 AO356_21080
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase AO356_25560 AO356_26150
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
thymidine deoB: phosphopentomutase AO356_07445
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB AO356_22300
tryptophan tnaA: tryptophanase
xylitol PLT5: xylitol:H+ symporter PLT5 AO356_27270
xylitol xdhA: xylitol dehydrogenase AO356_28545 AO356_19860

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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