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 (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