GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Pseudomonas simiae WCS417

Found 24 low-confidence and 12 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
D-serine dsdA: D-serine ammonia-lyase PS417_12925 PS417_01110
deoxyinosine deoB: phosphopentomutase PS417_24005
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
fucose aldA: lactaldehyde dehydrogenase PS417_17430 PS417_24810
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 PS417_13640 PS417_12060
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter PS417_27345
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) PS417_06840
maltose susB: alpha-glucosidase (maltase) PS417_23045 PS417_12800
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 PS417_23400
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase PS417_13845 PS417_10680
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PS417_10680 PS417_13845
phenylacetate paaK: phenylacetate-CoA ligase PS417_15170 PS417_22070
phenylacetate paaZ1: oxepin-CoA hydrolase PS417_13845 PS417_10680
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa PS417_08865
propionate putP: propionate transporter; proline:Na+ symporter PS417_02180
rhamnose aldA: lactaldehyde dehydrogenase PS417_17430 PS417_24810
rhamnose LRA1: L-rhamnofuranose dehydrogenase PS417_17895 PS417_11520
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase PS417_04210 PS417_00165
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase PS417_17865
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
sucrose ams: sucrose hydrolase (invertase) PS417_23045 PS417_12800
thymidine deoB: phosphopentomutase PS417_24005
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB

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