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:

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