GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Pseudomonas fluorescens FW300-N2E2

Found 35 low-confidence and 9 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
D-serine cycA: D-serine:H+ symporter CycA Pf6N2E2_5459 Pf6N2E2_5633
D-serine dsdA: D-serine ammonia-lyase Pf6N2E2_3918 Pf6N2E2_3938
deoxyinosine deoB: phosphopentomutase Pf6N2E2_3357
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Pf6N2E2_1375 Pf6N2E2_1663
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter Pf6N2E2_1105 Pf6N2E2_2115
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme Pf6N2E2_4692
deoxyribose deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Pf6N2E2_1375 Pf6N2E2_1663
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter Pf6N2E2_1105 Pf6N2E2_2115
deoxyribose ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme Pf6N2E2_4692
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 Pf6N2E2_163 Pf6N2E2_524
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter Pf6N2E2_4466
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) Pf6N2E2_2809
maltose susB: alpha-glucosidase (maltase) Pf6N2E2_2118
mannose manP: mannose PTS system, EII-CBA components Pf6N2E2_3337
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) Pf6N2E2_4217
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
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 Pf6N2E2_5315
phenylacetate paaK: phenylacetate-CoA ligase Pf6N2E2_2873 Pf6N2E2_2872
phenylacetate paaZ1: oxepin-CoA hydrolase Pf6N2E2_1834 Pf6N2E2_1147
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa Pf6N2E2_5849
propionate putP: propionate transporter; proline:Na+ symporter Pf6N2E2_3684
rhamnose LRA1: L-rhamnofuranose dehydrogenase Pf6N2E2_1323 Pf6N2E2_5209
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase Pf6N2E2_1314 Pf6N2E2_1103
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
thymidine deoB: phosphopentomutase Pf6N2E2_3357
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB Pf6N2E2_326
tryptophan tnaA: tryptophanase
xylitol PLT5: xylitol:H+ symporter PLT5 Pf6N2E2_883
xylitol xdhA: xylitol dehydrogenase Pf6N2E2_5889 Pf6N2E2_1375

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, the preprint 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