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 (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